From 3bfb473562c3660e609bad34f80290a152953042 Mon Sep 17 00:00:00 2001
From: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Date: Fri, 12 May 2023 08:43:14 +0000
Subject: [PATCH] Built site for AMR: 2.0.0.9015@5f9769a

---
 404.html                                  |   2 +-
 LICENSE-text.html                         |   2 +-
 articles/AMR.html                         |  14 +--
 articles/EUCAST.html                      |   2 +-
 articles/MDR.html                         |  56 ++++++------
 articles/PCA.html                         |   2 +-
 articles/SPSS.html                        |   4 +-
 articles/WHONET.html                      |   2 +-
 articles/datasets.html                    |  76 +++++++++++-----
 articles/index.html                       |   2 +-
 articles/resistance_predict.html          |   2 +-
 articles/welcome_to_AMR.html              |   2 +-
 authors.html                              |   2 +-
 index.html                                |   4 +-
 news/index.html                           |  15 ++-
 pkgdown.yml                               |   2 +-
 reference/AMR-deprecated.html             |   2 +-
 reference/AMR-options.html                |   2 +-
 reference/AMR.html                        |   2 +-
 reference/Rplot005.png                    | Bin 13212 -> 13189 bytes
 reference/Rplot006.png                    | Bin 13227 -> 13198 bytes
 reference/Rplot007.png                    | Bin 15552 -> 13156 bytes
 reference/Rplot008.png                    | Bin 18962 -> 18978 bytes
 reference/Rplot009.png                    | Bin 8644 -> 8407 bytes
 reference/WHOCC.html                      |   2 +-
 reference/WHONET.html                     |   2 +-
 reference/ab_from_text.html               |   2 +-
 reference/ab_property.html                |   2 +-
 reference/add_custom_antimicrobials.html  |   2 +-
 reference/add_custom_microorganisms.html  |  15 ++-
 reference/age.html                        |  22 ++---
 reference/age_groups.html                 |   2 +-
 reference/antibiogram.html                |   4 +-
 reference/antibiotic_class_selectors.html |  10 +-
 reference/antibiotics.html                |   2 +-
 reference/as.ab.html                      |   2 +-
 reference/as.av.html                      |   2 +-
 reference/as.disk.html                    |   2 +-
 reference/as.mic.html                     |   2 +-
 reference/as.mo.html                      |   9 +-
 reference/as.sir.html                     |  22 ++---
 reference/atc_online.html                 |   2 +-
 reference/av_from_text.html               |   2 +-
 reference/av_property.html                |   2 +-
 reference/availability.html               |   2 +-
 reference/bug_drug_combinations.html      |   2 +-
 reference/clinical_breakpoints.html       |   2 +-
 reference/count.html                      |   2 +-
 reference/custom_eucast_rules.html        |   4 +-
 reference/dosage.html                     |   2 +-
 reference/eucast_rules.html               |   2 +-
 reference/example_isolates.html           |   2 +-
 reference/example_isolates_unclean.html   |   2 +-
 reference/first_isolate.html              |   2 +-
 reference/g.test.html                     |   2 +-
 reference/get_episode.html                | 106 +++++++++++-----------
 reference/ggplot_pca.html                 |   2 +-
 reference/ggplot_sir.html                 |   2 +-
 reference/guess_ab_col.html               |   2 +-
 reference/index.html                      |   4 +-
 reference/intrinsic_resistant.html        |   2 +-
 reference/italicise_taxonomy.html         |   2 +-
 reference/join.html                       |  66 +++++++-------
 reference/key_antimicrobials.html         |   2 +-
 reference/kurtosis.html                   |   6 +-
 reference/like.html                       |   2 +-
 reference/mdro.html                       |   2 +-
 reference/mean_amr_distance.html          |  72 +++++++--------
 reference/microorganisms.codes.html       |   2 +-
 reference/microorganisms.html             |  28 +++---
 reference/mo_matching_score.html          |   3 +-
 reference/mo_property.html                |  35 ++++++-
 reference/mo_source.html                  |   2 +-
 reference/pca.html                        |   2 +-
 reference/plot-1.png                      | Bin 26433 -> 26597 bytes
 reference/plot-2.png                      | Bin 26515 -> 26510 bytes
 reference/plot-3.png                      | Bin 28204 -> 28211 bytes
 reference/plot-4.png                      | Bin 39431 -> 39755 bytes
 reference/plot-5.png                      | Bin 39071 -> 39065 bytes
 reference/plot-6.png                      | Bin 38223 -> 38220 bytes
 reference/plot-7.png                      | Bin 40465 -> 37056 bytes
 reference/plot-8.png                      | Bin 56446 -> 56401 bytes
 reference/plot-9.png                      | Bin 26350 -> 26152 bytes
 reference/plot.html                       |   2 +-
 reference/proportion.html                 |   2 +-
 reference/random.html                     |  34 +++----
 reference/resistance_predict.html         |   2 +-
 reference/skewness.html                   |   4 +-
 reference/translate.html                  |   2 +-
 search.json                               |   2 +-
 90 files changed, 394 insertions(+), 325 deletions(-)

diff --git a/404.html b/404.html
index 53cc6b0a..bfb4abfe 100644
--- a/404.html
+++ b/404.html
@@ -36,7 +36,7 @@
     
     <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index 16dd7277..93a06b30 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/AMR.html b/articles/AMR.html
index 6f6c5de6..fc7e4994 100644
--- a/articles/AMR.html
+++ b/articles/AMR.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -187,7 +187,7 @@
 website update since they are based on randomly created values and the
 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
 Markdown</a>. However, the methodology remains unchanged. This page was
-generated on 08 May 2023.</p>
+generated on 12 May 2023.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -243,21 +243,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2023-05-08</td>
+<td align="center">2023-05-12</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2023-05-08</td>
+<td align="center">2023-05-12</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2023-05-08</td>
+<td align="center">2023-05-12</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -371,7 +371,6 @@ taxonomic codes. Let’s check this:</p>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
 <span><span class="co">#&gt; "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
-<span><span class="co">#&gt;              Based on input "E coli"</span></span>
 <span><span class="co">#&gt; Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span></span>
 <span><span class="co">#&gt;               (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span></span>
 <span><span class="co">#&gt;               (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span></span>
@@ -380,7 +379,6 @@ taxonomic codes. Let’s check this:</p>
 <span><span class="co">#&gt;               dissolvens (0.565)</span></span>
 <span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
 <span><span class="co">#&gt; "K. pneumoniae" -&gt; Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
-<span><span class="co">#&gt;                    Based on input "K pneumoniae"</span></span>
 <span><span class="co">#&gt; Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
 <span><span class="co">#&gt;               pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis</span></span>
 <span><span class="co">#&gt;               (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500),</span></span>
@@ -389,7 +387,6 @@ taxonomic codes. Let’s check this:</p>
 <span><span class="co">#&gt;               (0.333)</span></span>
 <span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
 <span><span class="co">#&gt; "S. aureus" -&gt; Staphylococcus aureus (B_STPHY_AURS, 0.690)</span></span>
-<span><span class="co">#&gt;                Based on input "S aureus"</span></span>
 <span><span class="co">#&gt; Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus</span></span>
 <span><span class="co">#&gt;               argenteus (0.625), Staphylococcus aureus anaerobius (0.625),</span></span>
 <span><span class="co">#&gt;               Streptomyces argenteolus (0.483), Streptomyces aureus (0.474),</span></span>
@@ -398,7 +395,6 @@ taxonomic codes. Let’s check this:</p>
 <span><span class="co">#&gt;               Streptomyces aureocirculatus (0.429)</span></span>
 <span><span class="co">#&gt; --------------------------------------------------------------------------------</span></span>
 <span><span class="co">#&gt; "S. pneumoniae" -&gt; Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)</span></span>
-<span><span class="co">#&gt;                    Based on input "S pneumoniae"</span></span>
 <span><span class="co">#&gt; Also matched: Streptococcus pseudopneumoniae (0.700), Serratia</span></span>
 <span><span class="co">#&gt;               proteamaculans quinovora (0.545), Streptococcus pseudoporcinus (0.536),</span></span>
 <span><span class="co">#&gt;               Staphylococcus pseudintermedius (0.532), Serratia proteamaculans</span></span>
diff --git a/articles/EUCAST.html b/articles/EUCAST.html
index 518ea109..78daeee0 100644
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/MDR.html b/articles/MDR.html
index bf123bd7..72a44ee3 100644
--- a/articles/MDR.html
+++ b/articles/MDR.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -385,18 +385,18 @@ names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
 <span><span class="co">#&gt;   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
-<span><span class="co">#&gt; 1          S         R            R          S            R            R</span></span>
-<span><span class="co">#&gt; 2          S         R            S          I            S            R</span></span>
-<span><span class="co">#&gt; 3          S         R            I          I            I            S</span></span>
-<span><span class="co">#&gt; 4          S         I            R          I            R            R</span></span>
-<span><span class="co">#&gt; 5          R         S            R          R            R            I</span></span>
-<span><span class="co">#&gt; 6          S         S            S          R            I            R</span></span>
+<span><span class="co">#&gt; 1          S         I            I          I            S            S</span></span>
+<span><span class="co">#&gt; 2          R         R            I          I            S            R</span></span>
+<span><span class="co">#&gt; 3          R         I            S          S            R            R</span></span>
+<span><span class="co">#&gt; 4          I         S            R          I            I            S</span></span>
+<span><span class="co">#&gt; 5          S         R            R          I            R            R</span></span>
+<span><span class="co">#&gt; 6          S         R            S          I            I            I</span></span>
 <span><span class="co">#&gt;   kanamycin</span></span>
-<span><span class="co">#&gt; 1         I</span></span>
+<span><span class="co">#&gt; 1         S</span></span>
 <span><span class="co">#&gt; 2         R</span></span>
-<span><span class="co">#&gt; 3         I</span></span>
+<span><span class="co">#&gt; 3         S</span></span>
 <span><span class="co">#&gt; 4         S</span></span>
-<span><span class="co">#&gt; 5         R</span></span>
+<span><span class="co">#&gt; 5         I</span></span>
 <span><span class="co">#&gt; 6         R</span></span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can
 use:</p>
@@ -438,40 +438,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3189</td>
-<td align="right">63.78%</td>
-<td align="right">3189</td>
-<td align="right">63.78%</td>
+<td align="right">3190</td>
+<td align="right">63.80%</td>
+<td align="right">3190</td>
+<td align="right">63.80%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">996</td>
-<td align="right">19.92%</td>
-<td align="right">4185</td>
-<td align="right">83.70%</td>
+<td align="right">1008</td>
+<td align="right">20.16%</td>
+<td align="right">4198</td>
+<td align="right">83.96%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">465</td>
-<td align="right">9.30%</td>
-<td align="right">4650</td>
-<td align="right">93.00%</td>
+<td align="right">477</td>
+<td align="right">9.54%</td>
+<td align="right">4675</td>
+<td align="right">93.50%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">239</td>
-<td align="right">4.78%</td>
-<td align="right">4889</td>
-<td align="right">97.78%</td>
+<td align="right">224</td>
+<td align="right">4.48%</td>
+<td align="right">4899</td>
+<td align="right">97.98%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">111</td>
-<td align="right">2.22%</td>
+<td align="right">101</td>
+<td align="right">2.02%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
diff --git a/articles/PCA.html b/articles/PCA.html
index f8da2f52..2cae86f8 100644
--- a/articles/PCA.html
+++ b/articles/PCA.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/SPSS.html b/articles/SPSS.html
index 62efe04b..e4f54990 100644
--- a/articles/SPSS.html
+++ b/articles/SPSS.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -178,7 +178,7 @@
                         <h4 data-toc-skip class="author">Dr. Matthijs
 Berends</h4>
             
-            <h4 data-toc-skip class="date">08 May 2023</h4>
+            <h4 data-toc-skip class="date">12 May 2023</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
       <div class="d-none name"><code>SPSS.Rmd</code></div>
diff --git a/articles/WHONET.html b/articles/WHONET.html
index 4deddaef..aa2d39e9 100644
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/datasets.html b/articles/datasets.html
index 2cd07699..260d7439 100644
--- a/articles/datasets.html
+++ b/articles/datasets.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -176,7 +176,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">08 May 2023</h4>
+            <h4 data-toc-skip class="date">12 May 2023</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="d-none name"><code>datasets.Rmd</code></div>
@@ -197,47 +197,52 @@ of the data sets look like.</p>
 <h2 id="microorganisms-full-microbial-taxonomy">
 <code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
 </h2>
-<p>A data set with 52 151 rows and 22 columns, containing the following
+<p>A data set with 52 151 rows and 23 columns, containing the following
 column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
 <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
 <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
-<em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>,
-<em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>,
-<em>gbif_renamed_to</em>, <em>prevalence</em>, and <em>snomed</em>.</p>
+<em>ref</em>, <em>oxygen_tolerance</em>, <em>source</em>, <em>lpsn</em>,
+<em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>,
+<em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em>, and
+<em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 20 April 2023 13:20:41 UTC. Find more info
-about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<p>It was last updated on 11 May 2023 19:56:27 UTC. Find more info about
+the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original
 R Data Structure (RDS) file</a> (1.2 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">tab-separated
-text file</a> (11.3 MB)<br>
+text file</a> (11.7 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Microsoft
-Excel workbook</a> (5 MB)<br>
+Excel workbook</a> (5.2 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.feather" class="external-link">Apache
-Feather file</a> (5.4 MB)<br>
+Feather file</a> (5.5 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.parquet" class="external-link">Apache
 Parquet file</a> (2.6 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS
-data file</a> (50.9 MB)<br>
+data (SAS) file</a> (50.9 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xpt" class="external-link">SAS
+transport (XPT) file</a> (48.4 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
-SPSS Statistics data file</a> (16.9 MB)<br>
+SPSS Statistics data file</a> (17.7 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
-DTA file</a> (47.1 MB)</li>
+DTA file</a> (48.5 MB)</li>
 </ul>
 <p><strong>NOTE: The exported files for SAS, SPSS and Stata contain only
 the first 50 SNOMED codes per record, as their file size would otherwise
-exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R
-instead.</p>
+exceed 100 MB; the file size limit of GitHub.</strong> Their file
+structures and compression techniques are very inefficient. Advice? Use
+R instead. It’s free and much better in many ways.</p>
 <p>The tab-separated text file and Microsoft Excel workbook both contain
 all SNOMED codes as comma separated values.</p>
 <div class="section level3">
@@ -296,7 +301,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 </tbody>
 </table>
 <p>Example rows when filtering on genus <em>Escherichia</em>:</p>
-<table style="width:100%;" class="table">
+<table class="table">
 <colgroup>
 <col width="3%">
 <col width="7%">
@@ -304,12 +309,13 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 <col width="2%">
 <col width="4%">
 <col width="5%">
-<col width="5%">
+<col width="4%">
 <col width="5%">
 <col width="3%">
 <col width="4%">
 <col width="3%">
 <col width="2%">
+<col width="6%">
 <col width="7%">
 <col width="2%">
 <col width="2%">
@@ -319,7 +325,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 <col width="3%">
 <col width="4%">
 <col width="3%">
-<col width="12%">
+<col width="11%">
 </colgroup>
 <thead><tr class="header">
 <th align="center">mo</th>
@@ -335,6 +341,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 <th align="center">subspecies</th>
 <th align="center">rank</th>
 <th align="center">ref</th>
+<th align="center">oxygen_tolerance</th>
 <th align="center">source</th>
 <th align="center">lpsn</th>
 <th align="center">lpsn_parent</th>
@@ -360,6 +367,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 <td align="center"></td>
 <td align="center">genus</td>
 <td align="center">Castellani et al., 1919</td>
+<td align="center">facultative anaerobe</td>
 <td align="center">LPSN</td>
 <td align="center">515602</td>
 <td align="center">482</td>
@@ -384,6 +392,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 <td align="center"></td>
 <td align="center">species</td>
 <td align="center">Leclerc, 1962</td>
+<td align="center">aerobe</td>
 <td align="center">LPSN</td>
 <td align="center">776052</td>
 <td align="center">515602</td>
@@ -408,6 +417,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 <td align="center"></td>
 <td align="center">species</td>
 <td align="center">Huys et al., 2003</td>
+<td align="center">aerobe</td>
 <td align="center">LPSN</td>
 <td align="center">776053</td>
 <td align="center">515602</td>
@@ -432,6 +442,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 <td align="center"></td>
 <td align="center">species</td>
 <td align="center">Burgess et al., 1973</td>
+<td align="center">likely facultative anaerobe</td>
 <td align="center">LPSN</td>
 <td align="center">776056</td>
 <td align="center">515602</td>
@@ -456,6 +467,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 <td align="center"></td>
 <td align="center">species</td>
 <td align="center">Castellani et al., 1919</td>
+<td align="center">facultative anaerobe</td>
 <td align="center">LPSN</td>
 <td align="center">776057</td>
 <td align="center">515602</td>
@@ -480,6 +492,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 <td align="center"></td>
 <td align="center">species</td>
 <td align="center"></td>
+<td align="center">likely facultative anaerobe</td>
 <td align="center">GBIF</td>
 <td align="center"></td>
 <td align="center"></td>
@@ -525,7 +538,10 @@ Feather file</a> (0.1 MB)<br>
 Parquet file</a> (97 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS
-data file</a> (1.9 MB)<br>
+data (SAS) file</a> (1.9 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xpt" class="external-link">SAS
+transport (XPT) file</a> (1.4 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">IBM
 SPSS Statistics data file</a> (0.3 MB)<br>
@@ -725,7 +741,10 @@ Feather file</a> (15 kB)<br>
 Parquet file</a> (13 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS
-data file</a> (84 kB)<br>
+data (SAS) file</a> (84 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xpt" class="external-link">SAS
+transport (XPT) file</a> (68 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">IBM
 SPSS Statistics data file</a> (30 kB)<br>
@@ -903,7 +922,10 @@ Feather file</a> (0.7 MB)<br>
 Parquet file</a> (88 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sas" class="external-link">SAS
-data file</a> (3.6 MB)<br>
+data (SAS) file</a> (3.6 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xpt" class="external-link">SAS
+transport (XPT) file</a> (3.4 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.sav" class="external-link">IBM
 SPSS Statistics data file</a> (2.3 MB)<br>
@@ -1076,7 +1098,10 @@ Feather file</a> (1.2 MB)<br>
 Parquet file</a> (0.2 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS
-data file</a> (9.8 MB)<br>
+data (SAS) file</a> (9.8 MB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xpt" class="external-link">SAS
+transport (XPT) file</a> (9.5 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM
 SPSS Statistics data file</a> (7.4 MB)<br>
@@ -1364,7 +1389,10 @@ Feather file</a> (16 kB)<br>
 Parquet file</a> (8 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS
-data file</a> (92 kB)<br>
+data (SAS) file</a> (92 kB)<br>
+</li>
+<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xpt" class="external-link">SAS
+transport (XPT) file</a> (79 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">IBM
 SPSS Statistics data file</a> (43 kB)<br>
diff --git a/articles/index.html b/articles/index.html
index 9f4ea399..411a4ef3 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/resistance_predict.html b/articles/resistance_predict.html
index c3b1d8ff..0e6d8357 100644
--- a/articles/resistance_predict.html
+++ b/articles/resistance_predict.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/welcome_to_AMR.html b/articles/welcome_to_AMR.html
index 49d486ea..78299f1e 100644
--- a/articles/welcome_to_AMR.html
+++ b/articles/welcome_to_AMR.html
@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/authors.html b/authors.html
index c1d42745..a508bf87 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/index.html b/index.html
index 7a60ccf7..831ee504 100644
--- a/index.html
+++ b/index.html
@@ -42,7 +42,7 @@
     
     <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -762,7 +762,7 @@
 <p>Manually, using:</p>
 <div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
-<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
 </li>
 <li>
 <p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
diff --git a/news/index.html b/news/index.html
index b269a2f7..43711561 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -142,10 +142,16 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.0.0.9014" id="amr-2009014">AMR 2.0.0.9014<a class="anchor" aria-label="anchor" href="#amr-2009014"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.0.0.9015" id="amr-2009015">AMR 2.0.0.9015<a class="anchor" aria-label="anchor" href="#amr-2009015"></a></h2>
 <div class="section level3">
-<h3 id="changed-2-0-0-9014">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9014"></a></h3>
-<ul><li>formatting fix for <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code>
+<h3 id="changed-2-0-0-9015">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9015"></a></h3>
+<ul><li>Added oxygen tolerance to over 25,000 bacteria in the <code>microorganisms</code> data set
+<ul><li>Added <code><a href="../reference/mo_property.html">mo_oxygen_tolerance()</a></code> to retrieve the values</li>
+<li>Added <code><a href="../reference/mo_property.html">mo_is_anaerobic()</a></code> to determine which species are obligate anaerobic bacteria</li>
+</ul></li>
+<li>Added LPSN and GBIF identifiers, and oxygen tolerance to <code><a href="../reference/mo_property.html">mo_info()</a></code>
+</li>
+<li>formatting fix for <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code>
 </li>
 <li>Fixed some WHONET codes for microorganisms and consequently a couple of entries in <code>clinical_breakpoints</code>
 </li>
@@ -153,6 +159,7 @@
 <li>
 <code><a href="../reference/mo_property.html">mo_rank()</a></code> now returns <code>NA</code> for ‘unknown’ microorganisms (<code>B_ANAER</code>, <code>B_ANAER-NEG</code>, <code>B_ANAER-POS</code>, <code>B_GRAMN</code>, <code>B_GRAMP</code>, <code>F_FUNGUS</code>, <code>F_YEAST</code>, and <code>UNKNOWN</code>)</li>
 <li>Fixed a bug for <code><a href="../reference/as.mo.html">as.mo()</a></code> that led to coercion of <code>NA</code> values when using custom microorganism codes</li>
+<li>Added SAS Transport files (file extension <code>.xpt</code>) to <a href="https://msberends.github.io/AMR/articles/datasets.html">our download page</a> to use in SAS software</li>
 </ul></div>
 </div>
     <div class="section level2">
diff --git a/pkgdown.yml b/pkgdown.yml
index 14e4851f..a98c6945 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2023-05-08T11:07Z
+last_built: 2023-05-12T08:39Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles
diff --git a/reference/AMR-deprecated.html b/reference/AMR-deprecated.html
index 3f50e63d..654b143e 100644
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/AMR-options.html b/reference/AMR-options.html
index 77f7a6b0..57578fbc 100644
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/AMR.html b/reference/AMR.html
index 76e2181d..3c31ce03 100644
--- a/reference/AMR.html
+++ b/reference/AMR.html
@@ -24,7 +24,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/Rplot005.png b/reference/Rplot005.png
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diff --git a/reference/WHOCC.html b/reference/WHOCC.html
index b03d83d6..9495926d 100644
--- a/reference/WHOCC.html
+++ b/reference/WHOCC.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/WHONET.html b/reference/WHONET.html
index 9363347a..b89c7d8b 100644
--- a/reference/WHONET.html
+++ b/reference/WHONET.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/ab_from_text.html b/reference/ab_from_text.html
index d45bf4e7..03a07557 100644
--- a/reference/ab_from_text.html
+++ b/reference/ab_from_text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/ab_property.html b/reference/ab_property.html
index fd88aea4..f889ef7d 100644
--- a/reference/ab_property.html
+++ b/reference/ab_property.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_custom_antimicrobials.html b/reference/add_custom_antimicrobials.html
index 3a24490b..ae8ca2dd 100644
--- a/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_custom_microorganisms.html b/reference/add_custom_microorganisms.html
index 26fa3d04..34de2fac 100644
--- a/reference/add_custom_microorganisms.html
+++ b/reference/add_custom_microorganisms.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -209,7 +209,7 @@
 <span class="r-in"><span><span class="co"># its code:</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] CUSTOM1_ENTRBC_A_C</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] CUSTOM1_ENTRB_ASB/</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># all internal algorithms will work as well:</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Ent asburia cloacae"</span><span class="op">)</span></span></span>
@@ -223,7 +223,7 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_info</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $mo</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "CUSTOM1_ENTRBC_A_C"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "CUSTOM1_ENTRB_ASB/"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $kingdom</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
@@ -258,6 +258,9 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> $gramstain</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $oxygen_tolerance</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $url</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] ""</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -267,6 +270,12 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> $snomed</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $lpsn</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $gbif</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># the function tries to be forgiving:</span></span></span>
diff --git a/reference/age.html b/reference/age.html
index 8cc62d5d..56aa3060 100644
--- a/reference/age.html
+++ b/reference/age.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -205,16 +205,16 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    birth_date age age_exact age_at_y2k</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1981-06-07  41  41.91781         18</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1959-05-16  63  63.97808         40</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1944-01-22  79  79.29041         55</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1931-09-03  91  91.67671         68</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1976-01-01  47  47.34795         24</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1975-04-23  48  48.04110         24</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1935-01-20  88  88.29589         64</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1968-07-18  54  54.80548         31</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1970-12-26  52  52.36438         29</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1994-02-26  29  29.19452          5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1935-04-26  88  88.04384         64</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1939-12-20  83  83.39178         60</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1940-09-26  82  82.62466         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1981-04-16  42  42.07123         18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1946-10-07  76  76.59452         53</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1974-10-27  48  48.53973         25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1938-08-21  84  84.72329         61</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1941-05-13  81  81.99726         58</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1933-07-19  89  89.81370         66</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1977-01-31  46  46.27671         22</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/age_groups.html b/reference/age_groups.html
index cd5c38b3..f7e4486c 100644
--- a/reference/age_groups.html
+++ b/reference/age_groups.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/antibiogram.html b/reference/antibiogram.html
index d508279b..83d591a4 100644
--- a/reference/antibiogram.html
+++ b/reference/antibiogram.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -198,7 +198,7 @@
 
 
 <dt>mo_transform</dt>
-<dd><p>a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be <code>NULL</code> to not transform the input.</p></dd>
+<dd><p>a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed". Can also be <code>NULL</code> to not transform the input.</p></dd>
 
 
 <dt>ab_transform</dt>
diff --git a/reference/antibiotic_class_selectors.html b/reference/antibiotic_class_selectors.html
index 309a5460..be83351d 100644
--- a/reference/antibiotic_class_selectors.html
+++ b/reference/antibiotic_class_selectors.html
@@ -12,7 +12,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -609,11 +609,11 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 1</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   kefzol</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> S     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> I     </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> R     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> S     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> S     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> I     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> R     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> I     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> R     </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># get AMR for all aminoglycosides e.g., per ward:</span></span></span>
diff --git a/reference/antibiotics.html b/reference/antibiotics.html
index c947db78..e1b7aba4 100644
--- a/reference/antibiotics.html
+++ b/reference/antibiotics.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/as.ab.html b/reference/as.ab.html
index ff5977d5..3ec4a048 100644
--- a/reference/as.ab.html
+++ b/reference/as.ab.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/as.av.html b/reference/as.av.html
index 02a71306..acd8afe0 100644
--- a/reference/as.av.html
+++ b/reference/as.av.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/as.disk.html b/reference/as.disk.html
index 009f9ec3..8bf9e1e2 100644
--- a/reference/as.disk.html
+++ b/reference/as.disk.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/as.mic.html b/reference/as.mic.html
index 451c9547..667d0c06 100644
--- a/reference/as.mic.html
+++ b/reference/as.mic.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/as.mo.html b/reference/as.mo.html
index b5263839..60c324f6 100644
--- a/reference/as.mo.html
+++ b/reference/as.mo.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -278,15 +278,16 @@
 <ol><li><p>Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a></p></li>
 <li><p>Becker K <em>et al.</em> (2014). <strong>Coagulase-Negative Staphylococci.</strong> <em>Clin Microbiol Rev.</em> 27(4): 870-926; <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">doi:10.1128/CMR.00109-13</a></p></li>
 <li><p>Becker K <em>et al.</em> (2019). <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> <em>Clin Microbiol Infect</em>; <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">doi:10.1016/j.cmi.2019.02.028</a></p></li>
-<li><p>Becker K <em>et al.</em> (2020). <strong>Emergence of coagulase-negative staphylococci</strong> <em>Expert Rev Anti Infect Ther.</em> 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
-<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
-<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019</strong> <em>Microorganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
+<li><p>Becker K <em>et al.</em> (2020). <strong>Emergence of coagulase-negative staphylococci.</strong> <em>Expert Rev Anti Infect Ther.</em> 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
+<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci.</strong> <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
+<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/</strong> <em>Micro.rganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
 <li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
 . Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 11 December, 2022.</p></li>
 <li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
 . Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 11 December, 2022.</p></li>
 <li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
 <li><p>Bartlett A <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
+<li><p>Reimer <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong>  <em>Nucleic Acids Res.</em> 2022 Jan 7;50(D1):D741-D746; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a></p></li>
 </ol></div>
     <div class="section level2">
     <h2 id="matching-score-for-microorganisms">Matching Score for Microorganisms<a class="anchor" aria-label="anchor" href="#matching-score-for-microorganisms"></a></h2>
diff --git a/reference/as.sir.html b/reference/as.sir.html
index de489868..1f053c6b 100644
--- a/reference/as.sir.html
+++ b/reference/as.sir.html
@@ -12,7 +12,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -534,16 +534,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_input ab_guideline mo_input     mo_guideline    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-05-08 <span style="color: #949494;">11:08:51</span>     1 TOB      TOB          Escherichia… B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-05-08 <span style="color: #949494;">11:08:51</span>     1 GEN      GEN          Escherichia… B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-05-08 <span style="color: #949494;">11:08:50</span>     1 CIP      CIP          Escherichia… B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-05-08 <span style="color: #949494;">11:08:50</span>     1 AMP      AMP          Escherichia… B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-05-08 <span style="color: #949494;">11:08:45</span>     1 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-05-08 <span style="color: #949494;">11:08:45</span>     2 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-05-08 <span style="color: #949494;">11:08:45</span>     3 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-05-08 <span style="color: #949494;">11:08:45</span>     4 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-05-08 <span style="color: #949494;">11:08:45</span>     5 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-05-08 <span style="color: #949494;">11:08:45</span>     6 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-05-12 <span style="color: #949494;">08:40:42</span>     1 TOB      TOB          Escherichia… B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-05-12 <span style="color: #949494;">08:40:42</span>     1 GEN      GEN          Escherichia… B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-05-12 <span style="color: #949494;">08:40:42</span>     1 CIP      CIP          Escherichia… B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-05-12 <span style="color: #949494;">08:40:41</span>     1 AMP      AMP          Escherichia… B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-05-12 <span style="color: #949494;">08:40:37</span>     1 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-05-12 <span style="color: #949494;">08:40:37</span>     2 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-05-12 <span style="color: #949494;">08:40:37</span>     3 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-05-12 <span style="color: #949494;">08:40:37</span>     4 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-05-12 <span style="color: #949494;">08:40:37</span>     5 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-05-12 <span style="color: #949494;">08:40:37</span>     6 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 40 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: guideline &lt;chr&gt;, ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;</span></span>
diff --git a/reference/atc_online.html b/reference/atc_online.html
index 45538d37..5f918d56 100644
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/av_from_text.html b/reference/av_from_text.html
index 86765eb2..9d35fa74 100644
--- a/reference/av_from_text.html
+++ b/reference/av_from_text.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/av_property.html b/reference/av_property.html
index 7ed0cfa7..28f93cf1 100644
--- a/reference/av_property.html
+++ b/reference/av_property.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/availability.html b/reference/availability.html
index a21c9f9b..b2dadb69 100644
--- a/reference/availability.html
+++ b/reference/availability.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/bug_drug_combinations.html b/reference/bug_drug_combinations.html
index 1467ecf8..ebabe115 100644
--- a/reference/bug_drug_combinations.html
+++ b/reference/bug_drug_combinations.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/clinical_breakpoints.html b/reference/clinical_breakpoints.html
index 79b96de4..e4ab9a65 100644
--- a/reference/clinical_breakpoints.html
+++ b/reference/clinical_breakpoints.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/count.html b/reference/count.html
index f94bd395..d732b501 100644
--- a/reference/count.html
+++ b/reference/count.html
@@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/custom_eucast_rules.html b/reference/custom_eucast_rules.html
index 49121999..cc1c042a 100644
--- a/reference/custom_eucast_rules.html
+++ b/reference/custom_eucast_rules.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -207,7 +207,7 @@
 <h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3>
 
 
-<p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
+<p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
 <p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
 <span>                         <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
 <span></span>
diff --git a/reference/dosage.html b/reference/dosage.html
index 3700700f..bc1fa264 100644
--- a/reference/dosage.html
+++ b/reference/dosage.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/eucast_rules.html b/reference/eucast_rules.html
index 09a8c43e..900bcab5 100644
--- a/reference/eucast_rules.html
+++ b/reference/eucast_rules.html
@@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/example_isolates.html b/reference/example_isolates.html
index 49ea8da6..6ad502e7 100644
--- a/reference/example_isolates.html
+++ b/reference/example_isolates.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/example_isolates_unclean.html b/reference/example_isolates_unclean.html
index 0d82160c..c86b1ecd 100644
--- a/reference/example_isolates_unclean.html
+++ b/reference/example_isolates_unclean.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/first_isolate.html b/reference/first_isolate.html
index 7634fbf4..5fbe150a 100644
--- a/reference/first_isolate.html
+++ b/reference/first_isolate.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/g.test.html b/reference/g.test.html
index b1c04705..2d0d6e0d 100644
--- a/reference/g.test.html
+++ b/reference/g.test.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_episode.html b/reference/get_episode.html
index fde568fa..07dbe722 100644
--- a/reference/get_episode.html
+++ b/reference/get_episode.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -246,27 +246,27 @@
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  6 20 15 33 38  6 16 28 13  7 46 37  2  3 47 40 10  8 40  6 22 48 37 28 31</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 32 22 42  9 40 37 41 21 14 23 43  6 35 46  1 24 45 20 43 41  9  4  6 32 39</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 46 48 13 19  2 38 44 12 45 41 38  5 33 27 24  5 26 29 11 19 41 27 30 37 45</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 23  5  2  9 24  1  7 34 23  5  4 13 46 48 19 47 45 36  7 38 25 15 18 17 37</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 45 13 42 35 36 17 26 23 21 32 27 48 22 10 19  4 37  5 18 11  7 15  3 38 28</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 47 51 35  6 41 16 25 24 26  4 38 24 35  2 26 10 44 43  1 46 19 12 15 49 41</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 29  5 31 11 33 18  9 48 12 20 25 47 36 46 16 52  8 30 34 51  7 27 50 40 47</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 39 34 35 15 32 27 10 26 36 26 11 34 44 37 50 48 14 22  2 45  5 26 30 51  5</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49]  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE FALSE</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
 <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 46</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward  mo           PEN   OXA   FLC   AMX  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-30 218912     76 F      ICU   B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;,</span></span>
@@ -300,19 +300,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">condition</span>, <span class="va">date</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, condition [96]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, condition [99]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient date       condition new_episode</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 001213  2009-08-03 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 006827  2009-07-24 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 032343  2003-06-09 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 083080  2010-02-25 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 088256  2003-01-25 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 097186  2015-10-28 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 0C0688  2014-09-05 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 0DBB93  2003-10-02 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 113236  2006-11-20 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 125492  2016-05-13 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 023456  2009-11-02 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 036063  2010-01-28 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 0DBB93  2003-10-02 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 0DBF93  2015-10-12 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0E2483  2007-06-21 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 114570  2003-04-08 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 14D826  2006-09-14 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 156730  2012-04-12 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1710B8  2008-01-22 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 180928  2008-06-13 A         TRUE       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -326,19 +326,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">patient</span>, <span class="va">ward</span>, <span class="va">date</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 5</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [92]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [94]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    ward     date       patient new_index new_logical</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-08-03 001213          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2009-07-24 006827          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2003-06-09 032343          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2010-02-25 083080          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU      2003-01-25 088256          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2015-10-28 097186          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2014-09-05 0C0688          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU      2003-10-02 0DBB93          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2006-11-20 113236          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU      2016-05-13 125492          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2009-11-02 023456          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2010-01-28 036063          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU      2003-10-02 0DBB93          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2015-10-12 0DBF93          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU      2007-06-21 0E2483          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2003-04-08 114570          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2006-09-14 14D826          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2012-04-12 156730          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2008-01-22 1710B8          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2008-06-14 180928          1 FALSE      </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -354,9 +354,9 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical           61             14            39            46</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                25              8            20            24</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          6              5             6             6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical           64             14            40            49</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                23              9            20            21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          7              5             6             7</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
 <span class="r-in"><span><span class="co"># results as first_isolate() when using 'episode-based':</span></span></span>
@@ -385,19 +385,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 100 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [95]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [98]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo           ward     flag_episode</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> F35553  B_ENTRC      ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 195736  B_STPHY_AURS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 113236  B_ESCHR_COLI Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 545388  B_ESCHR_COLI Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 534091  B_ESCHR_COLI Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0DBB93  B_ESCHR_COLI ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> C67282  B_STPHY_CONS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E58140  B_STPHY_CONS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 54890C  B_ESCHR_COLI Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 570937  B_KLBSL_PNMN Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> A76045  B_ENTRC_FACM ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 452212  B_ENTRC_FACM ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 419568  B_STRPT_PNMN Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> BC9909  B_ESCHR_COLI Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 443847  B_KLBSL_PNMN Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F32657  B_STPHY_EPDR ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 180928  B_STRPT_AGLC Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B82692  B_STPHY_CONS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 89F578  B_STPHY_CONS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 597301  B_ESCHR_COLI ICU      TRUE        </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 90 more rows</span></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
diff --git a/reference/ggplot_pca.html b/reference/ggplot_pca.html
index 65c4f6e4..d51b4b45 100644
--- a/reference/ggplot_pca.html
+++ b/reference/ggplot_pca.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/ggplot_sir.html b/reference/ggplot_sir.html
index dc375cd2..9bd3c981 100644
--- a/reference/ggplot_sir.html
+++ b/reference/ggplot_sir.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/guess_ab_col.html b/reference/guess_ab_col.html
index 5b95b5e5..7232508c 100644
--- a/reference/guess_ab_col.html
+++ b/reference/guess_ab_col.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index d19da064..8052fcb2 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -158,7 +158,7 @@
         <dd>Transform Arbitrary Input to Valid Microbial Taxonomy</dd>
       </dl><dl><dt>
           
-          <code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_status()</a></code> <code><a href="mo_property.html">mo_pathogenicity()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_lpsn()</a></code> <code><a href="mo_property.html">mo_gbif()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_current()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> 
+          <code><a href="mo_property.html">mo_name()</a></code> <code><a href="mo_property.html">mo_fullname()</a></code> <code><a href="mo_property.html">mo_shortname()</a></code> <code><a href="mo_property.html">mo_subspecies()</a></code> <code><a href="mo_property.html">mo_species()</a></code> <code><a href="mo_property.html">mo_genus()</a></code> <code><a href="mo_property.html">mo_family()</a></code> <code><a href="mo_property.html">mo_order()</a></code> <code><a href="mo_property.html">mo_class()</a></code> <code><a href="mo_property.html">mo_phylum()</a></code> <code><a href="mo_property.html">mo_kingdom()</a></code> <code><a href="mo_property.html">mo_domain()</a></code> <code><a href="mo_property.html">mo_type()</a></code> <code><a href="mo_property.html">mo_status()</a></code> <code><a href="mo_property.html">mo_pathogenicity()</a></code> <code><a href="mo_property.html">mo_gramstain()</a></code> <code><a href="mo_property.html">mo_is_gram_negative()</a></code> <code><a href="mo_property.html">mo_is_gram_positive()</a></code> <code><a href="mo_property.html">mo_is_yeast()</a></code> <code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code> <code><a href="mo_property.html">mo_oxygen_tolerance()</a></code> <code><a href="mo_property.html">mo_is_anaerobic()</a></code> <code><a href="mo_property.html">mo_snomed()</a></code> <code><a href="mo_property.html">mo_ref()</a></code> <code><a href="mo_property.html">mo_authors()</a></code> <code><a href="mo_property.html">mo_year()</a></code> <code><a href="mo_property.html">mo_lpsn()</a></code> <code><a href="mo_property.html">mo_gbif()</a></code> <code><a href="mo_property.html">mo_rank()</a></code> <code><a href="mo_property.html">mo_taxonomy()</a></code> <code><a href="mo_property.html">mo_synonyms()</a></code> <code><a href="mo_property.html">mo_current()</a></code> <code><a href="mo_property.html">mo_info()</a></code> <code><a href="mo_property.html">mo_url()</a></code> <code><a href="mo_property.html">mo_property()</a></code> 
         </dt>
         <dd>Get Properties of a Microorganism</dd>
       </dl><dl><dt>
diff --git a/reference/intrinsic_resistant.html b/reference/intrinsic_resistant.html
index e64f98a5..5502cbf2 100644
--- a/reference/intrinsic_resistant.html
+++ b/reference/intrinsic_resistant.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/italicise_taxonomy.html b/reference/italicise_taxonomy.html
index 7445e8e9..ace3d969 100644
--- a/reference/italicise_taxonomy.html
+++ b/reference/italicise_taxonomy.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/join.html b/reference/join.html
index 7e8633e6..60ee3e24 100644
--- a/reference/join.html
+++ b/reference/join.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -196,21 +196,23 @@
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 22</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 23</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   mo           fullname   status kingdom phylum class order family genus species</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 12 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;, source &lt;chr&gt;,</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;,</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   gbif_parent &lt;chr&gt;, gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 13 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   oxygen_tolerance &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   lpsn_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
 <span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="st">"B_KLBSL_PNMN"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 22</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 23</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   mo           fullname   status kingdom phylum class order family genus species</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 12 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;, source &lt;chr&gt;,</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;,</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   gbif_parent &lt;chr&gt;, gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 13 more variables: subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   oxygen_tolerance &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   lpsn_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span></span></span>
@@ -229,12 +231,12 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df_joined</span> <span class="op">&lt;-</span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">df</span>, <span class="st">"bacteria"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df_joined</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "date"            "bacteria"        "fullname"        "status"         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "kingdom"         "phylum"          "class"           "order"          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "family"          "genus"           "species"         "subspecies"     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "rank"            "ref"             "source"          "lpsn"           </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "lpsn_parent"     "lpsn_renamed_to" "gbif"            "gbif_parent"    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "gbif_renamed_to" "prevalence"      "snomed"         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "date"             "bacteria"         "fullname"         "status"          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "kingdom"          "phylum"           "class"            "order"           </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "family"           "genus"            "species"          "subspecies"      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "rank"             "ref"              "oxygen_tolerance" "source"          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "lpsn"             "lpsn_parent"      "lpsn_renamed_to"  "gbif"            </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "gbif_parent"      "gbif_renamed_to"  "prevalence"       "snomed"          </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
@@ -243,23 +245,23 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Joining, by = "mo"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "date"            "patient"         "age"             "gender"         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "ward"            "mo"              "PEN"             "OXA"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "FLC"             "AMX"             "AMC"             "AMP"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "TZP"             "CZO"             "FEP"             "CXM"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "FOX"             "CTX"             "CAZ"             "CRO"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "GEN"             "TOB"             "AMK"             "KAN"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "TMP"             "SXT"             "NIT"             "FOS"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [29] "LNZ"             "CIP"             "MFX"             "VAN"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [33] "TEC"             "TCY"             "TGC"             "DOX"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "ERY"             "CLI"             "AZM"             "IPM"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [41] "MEM"             "MTR"             "CHL"             "COL"            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [45] "MUP"             "RIF"             "fullname"        "status"         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "kingdom"         "phylum"          "class"           "order"          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [53] "family"          "genus"           "species"         "subspecies"     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [57] "rank"            "ref"             "source"          "lpsn"           </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "lpsn_parent"     "lpsn_renamed_to" "gbif"            "gbif_parent"    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [65] "gbif_renamed_to" "prevalence"      "snomed"         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] "date"             "patient"          "age"              "gender"          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5] "ward"             "mo"               "PEN"              "OXA"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] "FLC"              "AMX"              "AMC"              "AMP"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [13] "TZP"              "CZO"              "FEP"              "CXM"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [17] "FOX"              "CTX"              "CAZ"              "CRO"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "GEN"              "TOB"              "AMK"              "KAN"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [25] "TMP"              "SXT"              "NIT"              "FOS"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [29] "LNZ"              "CIP"              "MFX"              "VAN"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [33] "TEC"              "TCY"              "TGC"              "DOX"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [37] "ERY"              "CLI"              "AZM"              "IPM"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [41] "MEM"              "MTR"              "CHL"              "COL"             </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [45] "MUP"              "RIF"              "fullname"         "status"          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [49] "kingdom"          "phylum"           "class"            "order"           </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [53] "family"           "genus"            "species"          "subspecies"      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [57] "rank"             "ref"              "oxygen_tolerance" "source"          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "lpsn"             "lpsn_parent"      "lpsn_renamed_to"  "gbif"            </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [65] "gbif_parent"      "gbif_renamed_to"  "prevalence"       "snomed"          </span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/key_antimicrobials.html b/reference/key_antimicrobials.html
index f888f01a..24f50a9e 100644
--- a/reference/key_antimicrobials.html
+++ b/reference/key_antimicrobials.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/kurtosis.html b/reference/kurtosis.html
index f285c52f..5c1f95b2 100644
--- a/reference/kurtosis.html
+++ b/reference/kurtosis.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -182,9 +182,9 @@
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.983132</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.027601</span>
 <span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04668891</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.04687044</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/like.html b/reference/like.html
index feeef757..e0238bd6 100644
--- a/reference/like.html
+++ b/reference/like.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/mdro.html b/reference/mdro.html
index 4677446f..6726cdac 100644
--- a/reference/mdro.html
+++ b/reference/mdro.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/mean_amr_distance.html b/reference/mean_amr_distance.html
index dd2c4d16..547ad707 100644
--- a/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -201,30 +201,30 @@
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">sir</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] I I R I I I R S S R</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] R R R I S R S I S R</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.621059 -0.621059  1.449138 -0.621059 -0.621059 -0.621059  1.449138</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] -0.621059 -0.621059  1.449138</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.9486833  0.9486833  0.9486833 -0.9486833 -0.9486833  0.9486833</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.9486833 -0.9486833 -0.9486833  0.9486833</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">mic</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.01  8     0.025 2     0.125 0.005 128   0.01  2     1    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 4     128   0.5   0.025 0.002 32    128   16    0.5   128  </span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.0080431  0.9684558 -0.7371152  0.5585577 -0.2612383 -1.2129921</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  1.7882519 -1.0080431  0.5585577  0.3536087</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.07714511  0.97675198 -0.46261901 -1.24022626 -1.89583387  0.61690923</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.97675198  0.43698786 -0.46261901  0.97675198</span>
 <span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
 <span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.0080431  0.9684558 -0.7371152  0.5585577 -0.2612383 -1.2129921</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  1.7882519 -1.0080431  0.5585577  0.3536087</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.07714511  0.97675198 -0.46261901 -1.24022626 -1.89583387  0.61690923</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.97675198  0.43698786 -0.46261901  0.97675198</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">disk</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 10 50 31 17 26 49 37 45 28 13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  9 46 37 23 13 47 10 23  6 38</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.41392483  1.33156027  0.02745485 -0.93346493 -0.31573079  1.26292315</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.43927762  0.98837464 -0.17845653 -1.20801344</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.0287932  1.3209197  0.7493679 -0.1397127 -0.7747702  1.3844254</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.9652875 -0.1397127 -1.2193105  0.8128737</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -234,22 +234,22 @@
 <span class="r-in"><span>  tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">y</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr gent tobr</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    S   19 &gt;=16  &lt;=1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    R   20    8  &lt;=1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    I   20    2    4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    S   19  &lt;=1    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    I   23    4    4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    I   31  &lt;=1    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    R   18    2    4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    I   22    2  &lt;=1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    I   22  &lt;=1  &lt;=1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    I   25 &gt;=16    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr  gent tobr</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    I   18     4    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    I   23    16 0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    R   20     2    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    I   20     8    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   25 &lt;=0.5    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    R   22     1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    I   26     1 0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    R   22     2    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    I   31     2 0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   19     8 0.25</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   and "tobr"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.1865874  0.3129310 -0.1974612 -0.2212515  0.1561783  0.5594410</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.2653504 -0.4668135 -0.6252799  0.4034927</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.14918777 -0.03570087  0.13005928  0.13771386 -0.17506383  0.10002806</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.47691376  0.43333913  0.00264067  0.03308522</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
@@ -265,17 +265,17 @@
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   and "tobr"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr gent tobr amr_distance check_id_C</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    I   20    2    4   -0.1974612 0.00000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   A    S   19 &gt;=16  &lt;=1   -0.1865874 0.01087383</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   D    S   19  &lt;=1    8   -0.2212515 0.02379027</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   H    I   22    2  &lt;=1   -0.4668135 0.26935231</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    I   23    4    4    0.1561783 0.35363955</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   I    I   22  &lt;=1  &lt;=1   -0.6252799 0.42781873</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    R   18    2    4    0.2653504 0.46281164</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   B    R   20    8  &lt;=1    0.3129310 0.51039218</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   J    I   25 &gt;=16    2    0.4034927 0.60095395</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  F    I   31  &lt;=1    8    0.5594410 0.75690225</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr  gent tobr amr_distance  check_id_C</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    R   20     2    1   0.13005928 0.000000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   D    I   20     8    2   0.13771386 0.007654579</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   F    R   22     1    1   0.10002806 0.030031221</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   J    R   19     8 0.25   0.03308522 0.096974059</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   I    I   31     2 0.25   0.00264067 0.127418609</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   B    I   23    16 0.25  -0.03570087 0.165760150</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   A    I   18     4    2  -0.14918777 0.279247046</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    R   22     2    2   0.43333913 0.303279854</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   E    S   25 &lt;=0.5    2  -0.17506383 0.305123107</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  G    I   26     1 0.25  -0.47691376 0.606973037</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># support for groups</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
diff --git a/reference/microorganisms.codes.html b/reference/microorganisms.codes.html
index 38b34779..fc8ded3a 100644
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/microorganisms.html b/reference/microorganisms.html
index 153b664e..caad9e5b 100644
--- a/reference/microorganisms.html
+++ b/reference/microorganisms.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -153,13 +153,14 @@
 
     <div class="section level2">
     <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 52 151 observations and 22 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 52 151 observations and 23 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
 <li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code>. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.</p></li>
 <li><p><code>status</code> <br> Status of the taxon, either "accepted" or "synonym"</p></li>
 <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism</p></li>
 <li><p><code>rank</code><br> Text of the taxonomic rank of the microorganism, such as <code>"species"</code> or <code>"genus"</code></p></li>
 <li><p><code>ref</code><br> Author(s) and year of related scientific publication. This contains only the <em>first surname</em> and year of the <em>latest</em> authors, e.g. "Wallis <em>et al.</em> 2006 <em>emend.</em> Smith and Jones 2018" becomes "Smith <em>et al.</em>, 2018". This field is directly retrieved from the source specified in the column <code>source</code>. Moreover, accents were removed to comply with CRAN that only allows ASCII characters, e.g. "Váňová" becomes "Vanova".</p></li>
 <li><p><code>lpsn</code><br> Identifier ('Record number') of the List of Prokaryotic names with Standing in Nomenclature (LPSN). This will be the first/highest LPSN identifier to keep one identifier per row. For example, <em>Acetobacter ascendens</em> has LPSN Record number 7864 and 11011. Only the first is available in the <code>microorganisms</code> data set.</p></li>
+<li><p><code>oxygen_tolerance</code> <br> Oxygen tolerance, either "aerobe", "anaerobe", "anaerobe/microaerophile", "facultative anaerobe", "likely facultative anaerobe", or "microaerophile". These data were retrieved from BacDive (see <em>Source</em>). Items that contain "likely" are missing from BacDive and were extrapolated from other species within the same genus to guess the oxygen tolerance. Currently 73.4% of all ~36 000 bacteria in the data set contain an oxygen tolerance.</p></li>
 <li><p><code>lpsn_parent</code><br> LPSN identifier of the parent taxon</p></li>
 <li><p><code>lpsn_renamed_to</code><br> LPSN identifier of the currently valid taxon</p></li>
 <li><p><code>gbif</code><br> Identifier ('taxonID') of the Global Biodiversity Information Facility (GBIF)</p></li>
@@ -180,6 +181,7 @@
 <li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
 <li><p>Grimont <em>et al.</em> (2007). Antigenic Formulae of the Salmonella Serovars, 9th Edition. WHO Collaborating Centre for Reference and Research on <em>Salmonella</em> (WHOCC-SALM).</p></li>
 <li><p>Bartlett <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
+<li><p>Reimer <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong>  <em>Nucleic Acids Res.</em> 2022 Jan 7;50(D1):D741-D746; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a></p></li>
 </ul></div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -236,24 +238,24 @@
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">microorganisms</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 52,151 × 22</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 52,151 × 23</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    mo               fullname      status kingdom phylum class order family genus</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>             <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ANAER          (unknown ana… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_ANAER-NEG      (unknown ana… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_ANAER-POS      (unknown ana… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F_FUNGUS         (unknown fun… accep… Fungi   (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_GRAMN          (unknown Gra… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_GRAMP          (unknown Gra… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_GRAMN          (unknown Gra… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_GRAMP          (unknown Gra… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_ANAER-NEG      (unknown ana… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_ANAER-POS      (unknown ana… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_ANAER          (unknown ana… accep… Bacter… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F_FUNGUS         (unknown fun… accep… Fungi   (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span>   UNKNOWN        (unknown nam… accep… (unkno… (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> F_YEAST          (unknown yea… accep… Fungi   (unkn… (unk… (unk… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span>   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… Abdi… <span style="color: #949494;">""</span>     <span style="color: #949494;">""</span>   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 52,141 more rows</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 13 more variables: species &lt;chr&gt;, subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   source &lt;chr&gt;, lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;,</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;, gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;,</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   snomed &lt;list&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 14 more variables: species &lt;chr&gt;, subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   oxygen_tolerance &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;, lpsn_parent &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   lpsn_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/mo_matching_score.html b/reference/mo_matching_score.html
index 334bfb15..17efb87b 100644
--- a/reference/mo_matching_score.html
+++ b/reference/mo_matching_score.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -216,7 +216,6 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> --------------------------------------------------------------------------------</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>              Based on input "E coli"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span>
diff --git a/reference/mo_property.html b/reference/mo_property.html
index 735f8f31..96e585f4 100644
--- a/reference/mo_property.html
+++ b/reference/mo_property.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -289,6 +289,20 @@
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>
+<span><span class="fu">mo_oxygen_tolerance</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="fu">mo_is_anaerobic</span><span class="op">(</span></span>
+<span>  <span class="va">x</span>,</span>
+<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  keep_synonyms <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_keep_synonyms"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
+<span>  <span class="va">...</span></span>
+<span><span class="op">)</span></span>
+<span></span>
 <span><span class="fu">mo_snomed</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
@@ -405,7 +419,7 @@
 
 
 <dt>property</dt>
-<dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be <code>"shortname"</code></p></dd>
+<dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "oxygen_tolerance", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence", or "snomed", or must be <code>"shortname"</code></p></dd>
 
 </dl></div>
     <div class="section level2">
@@ -431,6 +445,7 @@
 <p>Determination of the Gram stain (<code>mo_gramstain()</code>) will be based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
 <p>Determination of yeasts (<code>mo_is_yeast()</code>) will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
 <p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) will be based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/expert_rules_and_expected_phenotypes/" class="external-link">'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3</a> (2021). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antibiotics).</p>
+<p>Determination of bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) will be based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicting an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
 <p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
 <p>SNOMED codes (<code>mo_snomed()</code>) are from the version of 1 July, 2021. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
 <p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code> (which will have the scientific reference as <a href="https://rdrr.io/r/base/names.html" class="external-link">name</a>), the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>
@@ -449,15 +464,16 @@
 <ol><li><p>Berends MS <em>et al.</em> (2022). <strong>AMR: An R Package for Working with Antimicrobial Resistance Data</strong>. <em>Journal of Statistical Software</em>, 104(3), 1-31; <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">doi:10.18637/jss.v104.i03</a></p></li>
 <li><p>Becker K <em>et al.</em> (2014). <strong>Coagulase-Negative Staphylococci.</strong> <em>Clin Microbiol Rev.</em> 27(4): 870-926; <a href="https://doi.org/10.1128/CMR.00109-13" class="external-link">doi:10.1128/CMR.00109-13</a></p></li>
 <li><p>Becker K <em>et al.</em> (2019). <strong>Implications of identifying the recently defined members of the <em>S. aureus</em> complex, <em>S. argenteus</em> and <em>S. schweitzeri</em>: A position paper of members of the ESCMID Study Group for staphylococci and Staphylococcal Diseases (ESGS).</strong> <em>Clin Microbiol Infect</em>; <a href="https://doi.org/10.1016/j.cmi.2019.02.028" class="external-link">doi:10.1016/j.cmi.2019.02.028</a></p></li>
-<li><p>Becker K <em>et al.</em> (2020). <strong>Emergence of coagulase-negative staphylococci</strong> <em>Expert Rev Anti Infect Ther.</em> 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
-<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
-<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019</strong> <em>Microorganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
+<li><p>Becker K <em>et al.</em> (2020). <strong>Emergence of coagulase-negative staphylococci.</strong> <em>Expert Rev Anti Infect Ther.</em> 18(4):349-366; <a href="https://doi.org/10.1080/14787210.2020.1730813" class="external-link">doi:10.1080/14787210.2020.1730813</a></p></li>
+<li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci.</strong> <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
+<li><p>Berends MS <em>et al.</em> (2022). <strong>Trends in Occurrence and Phenotypic Resistance of Coagulase-Negative Staphylococci (CoNS) Found in Human Blood in the Northern Netherlands between 2013 and 2019/</strong> <em>Micro.rganisms</em> 10(9), 1801; <a href="https://doi.org/10.3390/microorganisms10091801" class="external-link">doi:10.3390/microorganisms10091801</a></p></li>
 <li><p>Parte, AC <em>et al.</em> (2020). <strong>List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.</strong> International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; <a href="https://doi.org/10.1099/ijsem.0.004332" class="external-link">doi:10.1099/ijsem.0.004332</a>
 . Accessed from <a href="https://lpsn.dsmz.de" class="external-link">https://lpsn.dsmz.de</a> on 11 December, 2022.</p></li>
 <li><p>GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset <a href="https://doi.org/10.15468/39omei" class="external-link">doi:10.15468/39omei</a>
 . Accessed from <a href="https://www.gbif.org" class="external-link">https://www.gbif.org</a> on 11 December, 2022.</p></li>
 <li><p>Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href="https://phinvads.cdc.gov" class="external-link">https://phinvads.cdc.gov</a></p></li>
 <li><p>Bartlett A <em>et al.</em> (2022). <strong>A comprehensive list of bacterial pathogens infecting humans</strong> <em>Microbiology</em> 168:001269; <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a></p></li>
+<li><p>Reimer <em>et al.</em> (2022). <strong><em>BacDive</em> in 2022: the knowledge base for standardized bacterial and archaeal data.</strong>  <em>Nucleic Acids Res.</em> 2022 Jan 7;50(D1):D741-D746; <a href="https://doi.org/10.1093/nar/gkab961" class="external-link">doi:10.1093/nar/gkab961</a></p></li>
 </ol></div>
     <div class="section level2">
     <h2 id="reference-data-publicly-available">Reference Data Publicly Available<a class="anchor" aria-label="anchor" href="#reference-data-publicly-available"></a></h2>
@@ -750,6 +766,9 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> $gramstain</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $oxygen_tolerance</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "aerobe"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $url</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "https://lpsn.dsmz.de/species/klebsiella-pneumoniae"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
@@ -760,6 +779,12 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1098101000112102" "446870005"        "1098201000112108" "409801009"       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [5] "56415008"         "714315002"        "713926009"       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $lpsn</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "777151"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> $gbif</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "3221874"</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/mo_source.html b/reference/mo_source.html
index d2c8f13f..2baaba48 100644
--- a/reference/mo_source.html
+++ b/reference/mo_source.html
@@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/pca.html b/reference/pca.html
index f64c88be..1bad63b1 100644
--- a/reference/pca.html
+++ b/reference/pca.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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diff --git a/reference/plot.html b/reference/plot.html
index 7289ab48..bdb9f7ea 100644
--- a/reference/plot.html
+++ b/reference/plot.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/proportion.html b/reference/proportion.html
index 73c20bfb..5af3656f 100644
--- a/reference/proportion.html
+++ b/reference/proportion.html
@@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/random.html b/reference/random.html
index 5e13653c..2d80e865 100644
--- a/reference/random.html
+++ b/reference/random.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -193,42 +193,42 @@
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 8       &gt;=256   &gt;=256   0.5     0.25    8       0.002   0.005   4      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 4       0.125   32      0.002   0.25    0.005   0.025   128     &lt;=0.001</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.01    8       128     16      0.002   1       0.025  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 4     4     128   4     4     2     0.25  0.002 2     128   1     0.25 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 128   0.5   0.005 0.025 4     256   64    16    16    0.01  0.25  0.001</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.002</span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 34 27 17  6 44 17 49 39 32 27 49 45 15 40 29 29 26 10 26 50 23 10 32 33  6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 42  9 27 42 18  9 46 39 38 20 26 48  6 47 40 23 13 29 22  6  8 16 40 20 16</span>
 <span class="r-in"><span><span class="fu">random_sir</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] I R S S I I S S S I R S R R R R I S R R S S I R S</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] S S I I S S S I R R I R I I S R R R R I I S R I I</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.005   128     0.01    &lt;=0.001 128     16      16      0.5     0.25   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 8       2       &lt;=0.001 16      128     &lt;=0.001 64      0.0625  0.25   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 16      128     4       &lt;=0.001 0.125   0.01    16     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 32    0.125 0.025 0.001 0.01  64    0.125 0.01  2     2     64    1    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.025 0.25  0.125 16    8     0.125 0.002 4     0.025 128   256   0.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 16   </span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 2   16  8   4   &lt;=1 8   8   4   4   2   2   &lt;=1 16  4   2   8   2   2   8  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [20] 2   8   8   16  2   &lt;=1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16 32 1  16 2  4  32 32 32 2  4  2  16 1  16 16 2  16 2  8  8  1  8  32 2 </span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] &lt;=0.125 2       0.5     2       &gt;=4     2       &gt;=4     2       &lt;=0.125</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.125 0.25    &gt;=4     &lt;=0.125 0.5     &gt;=4     1       1       1      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [19] &lt;=0.125 &lt;=0.125 2       1       2       &lt;=0.125 1      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] &lt;=0.0625 0.25     4        0.5      0.5      2        16       1       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9] 0.5      &lt;=0.0625 &lt;=0.0625 0.25     0.125    8        1        0.125   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [17] 0.25     0.25     0.5      4        &lt;=0.0625 0.5      2        0.5     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [25] &lt;=0.0625</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 35 25 44 48 10 20 33 12 47 28 19 41 45 26 36 38 31 37 50  8 39 46 43 14 41</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 15 40 46 17 10 19 38 43 35 33 44  9 22 30 24 49 11 48  8 18  8 12 21 24 33</span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 14 11 14 13 15 16 14 12 14 13 11 11 14 13 17 17 11 12 17 14 16 16 15 12 16</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 12 13 15 12 15 17 11 14 17 15 15 13 13 13 13 13 11 17 16 13 12 13 13 12 17</span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 24 20 26 16 17 20 22 26 15 18 25 27 27 24 26 18 19 24 23 26 19 20 17 20 27</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 21 23 23 18 25 24 16 19 20 22 15 22 23 24 21 24 23 17 22 17 23 27 23 26 19</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>
diff --git a/reference/resistance_predict.html b/reference/resistance_predict.html
index d6528cac..e77abffa 100644
--- a/reference/resistance_predict.html
+++ b/reference/resistance_predict.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/skewness.html b/reference/skewness.html
index 57e22568..aa211d18 100644
--- a/reference/skewness.html
+++ b/reference/skewness.html
@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -181,7 +181,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.01851817</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.02857046</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
diff --git a/reference/translate.html b/reference/translate.html
index f132c1f9..d9cbb15c 100644
--- a/reference/translate.html
+++ b/reference/translate.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9015</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 71a04dda..85ec150f 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #>    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN   #>    <chr>      <chr>    <date>     <chr>         <chr> <chr> <chr> <chr> #>  1 J3         A        2012-11-21 E. coli       R     I     S     S     #>  2 R7         A        2018-04-03 K. pneumoniae R     I     S     S     #>  3 P3         A        2014-09-19 E. coli       R     S     S     S     #>  4 P10        A        2015-12-10 E. coli       S     I     S     S     #>  5 B7         A        2015-03-02 E. coli       S     S     S     S     #>  6 W3         A        2018-03-31 S. aureus     R     S     R     S     #>  7 J8         A        2016-06-14 E. coli       R     S     S     S     #>  8 M3         A        2015-10-25 E. coli       R     S     S     S     #>  9 J3         A        2019-06-19 E. coli       S     S     S     S     #> 10 G6         A        2015-04-27 S. aureus     S     S     S     S     #> # ℹ 2,990 more rows  # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 11 Dec 2022. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLPN\") #> Class 'mo' #> [1] B_KLBSL_PNMN mo_family(\"K. pneumoniae\") #> [1] \"Enterobacteriaceae\" mo_genus(\"K. pneumoniae\") #> [1] \"Klebsiella\" mo_species(\"K. pneumoniae\") #> [1] \"pneumoniae\"  mo_gramstain(\"Klebsiella pneumoniae\") #> [1] \"Gram-negative\"  mo_ref(\"K. pneumoniae\") #> [1] \"Trevisan, 1887\"  mo_snomed(\"K. pneumoniae\") #> [[1]] #> [1] \"1098101000112102\" \"446870005\"        \"1098201000112108\" \"409801009\"        #> [5] \"56415008\"         \"714315002\"        \"713926009\" our_data$bacteria <- as.mo(our_data$bacteria, info = TRUE) #> ℹ Microorganism translation was uncertain for four microorganisms. Run #>   mo_uncertainties() to review these uncertainties, or use #>   add_custom_microorganisms() to add custom entries. mo_uncertainties() #> Matching scores are based on the resemblance between the input and the full #> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score. #>  #> -------------------------------------------------------------------------------- #> \"E. coli\" -> Escherichia coli (B_ESCHR_COLI, 0.688) #>              Based on input \"E coli\" #> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii #>               (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi #>               (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides #>               (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae #>               cloacae (0.571), Ehrlichia canis (0.567), and Enterobacter cloacae #>               dissolvens (0.565) #> -------------------------------------------------------------------------------- #> \"K. pneumoniae\" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786) #>                    Based on input \"K pneumoniae\" #> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella #>               pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis #>               (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500), #>               Kingella potus (0.400), Kosakonia pseudosacchari (0.361), Kaistella #>               palustris (0.333), Kocuria palustris (0.333), and Kocuria pelophila #>               (0.333) #> -------------------------------------------------------------------------------- #> \"S. aureus\" -> Staphylococcus aureus (B_STPHY_AURS, 0.690) #>                Based on input \"S aureus\" #> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus #>               argenteus (0.625), Staphylococcus aureus anaerobius (0.625), #>               Streptomyces argenteolus (0.483), Streptomyces aureus (0.474), #>               Streptomyces azureus (0.467), Streptomyces aureorectus (0.444), #>               Streptomyces auratus (0.433), Streptomyces aurantiogriseus (0.429), and #>               Streptomyces aureocirculatus (0.429) #> -------------------------------------------------------------------------------- #> \"S. pneumoniae\" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750) #>                    Based on input \"S pneumoniae\" #> Also matched: Streptococcus pseudopneumoniae (0.700), Serratia #>               proteamaculans quinovora (0.545), Streptococcus pseudoporcinus (0.536), #>               Staphylococcus pseudintermedius (0.532), Serratia proteamaculans #>               proteamaculans (0.526), Salmonella Portanigra (0.524), Sphingomonas #>               paucimobilis (0.520), Streptococcus pluranimalium (0.519), #>               Streptococcus constellatus pharyngis (0.514), and Salmonella Pakistan #>               (0.500) #>  #> Only the first 10 other matches of each record are shown. Run #> print(mo_uncertainties(), n = ...) to view more entries, or save #> mo_uncertainties() to an object."},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"antibiotic-results","dir":"Articles","previous_headings":"Preparation","what":"Antibiotic results","title":"How to conduct AMR data analysis","text":"column antibiotic test results must also cleaned. AMR package comes three new data types work test results: mic minimal inhibitory concentrations (MIC), disk disk diffusion diameters, sir SIR data interpreted already. package can also determine SIR values based MIC disk diffusion values, read .sir() page. now, just clean SIR columns data using dplyr: basically cleaning, time start data inclusion.","code":"# method 1, be explicit about the columns: our_data <- our_data %>%   mutate_at(vars(AMX:GEN), as.sir)  # method 2, let the AMR package determine the eligible columns our_data <- our_data %>%   mutate_if(is_sir_eligible, as.sir)  # result: our_data #> # A tibble: 3,000 × 8 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> #>  1 J3         A        2012-11-21 B_ESCHR_COLI R     I     S     S     #>  2 R7         A        2018-04-03 B_KLBSL_PNMN R     I     S     S     #>  3 P3         A        2014-09-19 B_ESCHR_COLI R     S     S     S     #>  4 P10        A        2015-12-10 B_ESCHR_COLI S     I     S     S     #>  5 B7         A        2015-03-02 B_ESCHR_COLI S     S     S     S     #>  6 W3         A        2018-03-31 B_STPHY_AURS R     S     R     S     #>  7 J8         A        2016-06-14 B_ESCHR_COLI R     S     S     S     #>  8 M3         A        2015-10-25 B_ESCHR_COLI R     S     S     S     #>  9 J3         A        2019-06-19 B_ESCHR_COLI S     S     S     S     #> 10 G6         A        2015-04-27 B_STPHY_AURS S     S     S     S     #> # ℹ 2,990 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"first-isolates","dir":"Articles","previous_headings":"Preparation","what":"First isolates","title":"How to conduct AMR data analysis","text":"need know isolates can actually use analysis without repetition bias. conduct analysis antimicrobial resistance, must include first isolate every patient per episode (Hindler et al., Clin Infect Dis. 2007). , easily get overestimate underestimate resistance antibiotic. Imagine patient admitted MRSA found 5 different blood cultures following weeks (yes, countries like Netherlands blood drawing policies). resistance percentage oxacillin isolates overestimated, included MRSA . clearly selection bias. Clinical Laboratory Standards Institute (CLSI) appoints follows: (…) preparing cumulative antibiogram guide clinical decisions empirical antimicrobial therapy initial infections, first isolate given species per patient, per analysis period (eg, one year) included, irrespective body site, antimicrobial susceptibility profile, phenotypical characteristics (eg, biotype). first isolate easily identified, cumulative antimicrobial susceptibility test data prepared using first isolate generally comparable cumulative antimicrobial susceptibility test data calculated methods, providing duplicate isolates excluded. M39-A4 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 4th Edition. CLSI, 2014. Chapter 6.4 AMR package includes methodology first_isolate() function able apply four different methods defined Hindler et al. 2007: phenotype-based, episode-based, patient-based, isolate-based. right method depends goals analysis, default phenotype-based method case method properly correct duplicate isolates. Read methods first_isolate() page. outcome function can easily added data: 88% suitable resistance analysis! can now filter filter() function, also dplyr package: future use, two syntaxes can shortened: end 2 626 isolates analysis. Now data looks like: Time analysis.","code":"our_data <- our_data %>%   mutate(first = first_isolate(info = TRUE)) #> Determining first isolates using an episode length of 365 days #> ℹ Using column 'bacteria' as input for col_mo. #> ℹ Using column 'date' as input for col_date. #> ℹ Using column 'patient_id' as input for col_patient_id. #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #> => Found 2,626 'phenotype-based' first isolates (87.6% within scope and #>    87.5% of total where a microbial ID was available) our_data_1st <- our_data %>%   filter(first == TRUE) our_data_1st <- our_data %>%   filter_first_isolate() our_data_1st #> # A tibble: 2,626 × 9 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl> #>  1 J3         A        2012-11-21 B_ESCHR_COLI R     I     S     S     TRUE  #>  2 R7         A        2018-04-03 B_KLBSL_PNMN R     I     S     S     TRUE  #>  3 P10        A        2015-12-10 B_ESCHR_COLI S     I     S     S     TRUE  #>  4 B7         A        2015-03-02 B_ESCHR_COLI S     S     S     S     TRUE  #>  5 W3         A        2018-03-31 B_STPHY_AURS R     S     R     S     TRUE  #>  6 J8         A        2016-06-14 B_ESCHR_COLI R     S     S     S     TRUE  #>  7 M3         A        2015-10-25 B_ESCHR_COLI R     S     S     S     TRUE  #>  8 J3         A        2019-06-19 B_ESCHR_COLI S     S     S     S     TRUE  #>  9 G6         A        2015-04-27 B_STPHY_AURS S     S     S     S     TRUE  #> 10 P4         A        2011-06-21 B_ESCHR_COLI S     S     S     S     TRUE  #> # ℹ 2,616 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"analysing-the-data","dir":"Articles","previous_headings":"","what":"Analysing the data","title":"How to conduct AMR data analysis","text":"base R summary() function gives good first impression, comes support new mo sir classes now data set:","code":"summary(our_data_1st) #>   patient_id          hospital              date            #>  Length:2626        Length:2626        Min.   :2011-01-01   #>  Class :character   Class :character   1st Qu.:2013-04-14   #>  Mode  :character   Mode  :character   Median :2015-06-05   #>                                        Mean   :2015-06-15   #>                                        3rd Qu.:2017-08-23   #>                                        Max.   :2020-01-01   #>    bacteria               AMX                    AMC                 #>  Class :mo             Class:sir              Class:sir              #>  <NA>  :0              %R   :43.2% (n=1134)   %R   :36.1% (n=947)    #>  Unique:4              %SI  :56.8% (n=1492)   %SI  :63.9% (n=1679)   #>  #1    :B_ESCHR_COLI   - %S :41.1% (n=1080)   - %S :52.7% (n=1383)   #>  #2    :B_STPHY_AURS   - %I :15.7% (n=412)    - %I :11.3% (n=296)    #>  #3    :B_STRPT_PNMN                                                 #>     CIP                    GEN                  first         #>  Class:sir              Class:sir              Mode:logical   #>  %R   :42.0% (n=1102)   %R   :37.0% (n=971)    TRUE:2626      #>  %SI  :58.0% (n=1524)   %SI  :63.0% (n=1655)                  #>  - %S :51.9% (n=1362)   - %S :59.9% (n=1574)                  #>  - %I : 6.2% (n=162)    - %I : 3.1% (n=81)                    #>   glimpse(our_data_1st) #> Rows: 2,626 #> Columns: 9 #> $ patient_id <chr> \"J3\", \"R7\", \"P10\", \"B7\", \"W3\", \"J8\", \"M3\", \"J3\", \"G6\", \"P4\"… #> $ hospital   <chr> \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\",… #> $ date       <date> 2012-11-21, 2018-04-03, 2015-12-10, 2015-03-02, 2018-03-31… #> $ bacteria   <mo> \"B_ESCHR_COLI\", \"B_KLBSL_PNMN\", \"B_ESCHR_COLI\", \"B_ESCHR_COL… #> $ AMX        <sir> R, R, S, S, R, R, R, S, S, S, S, R, S, S, R, R, R, R, I, S,… #> $ AMC        <sir> I, I, I, S, S, S, S, S, S, S, S, S, S, S, S, S, S, R, S, R,… #> $ CIP        <sir> S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S, S,… #> $ GEN        <sir> S, S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S,… #> $ first      <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…  # number of unique values per column: sapply(our_data_1st, n_distinct) #> patient_id   hospital       date   bacteria        AMX        AMC        CIP  #>        260          3       1808          4          3          3          3  #>        GEN      first  #>          3          1"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"availability-of-species","dir":"Articles","previous_headings":"Analysing the data","what":"Availability of species","title":"How to conduct AMR data analysis","text":"just get idea species distributed, create frequency table count() based name microorganisms:","code":"our_data %>%   count(mo_name(bacteria), sort = TRUE) #> # A tibble: 4 × 2 #>   `mo_name(bacteria)`          n #>   <chr>                    <int> #> 1 Escherichia coli          1518 #> 2 Staphylococcus aureus      730 #> 3 Streptococcus pneumoniae   426 #> 4 Klebsiella pneumoniae      326  our_data_1st %>%   count(mo_name(bacteria), sort = TRUE) #> # A tibble: 4 × 2 #>   `mo_name(bacteria)`          n #>   <chr>                    <int> #> 1 Escherichia coli          1250 #> 2 Staphylococcus aureus      661 #> 3 Streptococcus pneumoniae   399 #> 4 Klebsiella pneumoniae      316"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"select-and-filter-with-antibiotic-selectors","dir":"Articles","previous_headings":"Analysing the data","what":"Select and filter with antibiotic selectors","title":"How to conduct AMR data analysis","text":"Using -called antibiotic class selectors, can select filter columns based antibiotic class antibiotic results :","code":"our_data_1st %>%   select(date, aminoglycosides()) #> ℹ For aminoglycosides() using column 'GEN' (gentamicin) #> # A tibble: 2,626 × 2 #>    date       GEN   #>    <date>     <sir> #>  1 2012-11-21 S     #>  2 2018-04-03 S     #>  3 2015-12-10 S     #>  4 2015-03-02 S     #>  5 2018-03-31 S     #>  6 2016-06-14 S     #>  7 2015-10-25 S     #>  8 2019-06-19 S     #>  9 2015-04-27 S     #> 10 2011-06-21 S     #> # ℹ 2,616 more rows  our_data_1st %>%   select(bacteria, betalactams()) #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #>   (amoxicillin/clavulanic acid) #> # A tibble: 2,626 × 3 #>    bacteria     AMX   AMC   #>    <mo>         <sir> <sir> #>  1 B_ESCHR_COLI R     I     #>  2 B_KLBSL_PNMN R     I     #>  3 B_ESCHR_COLI S     I     #>  4 B_ESCHR_COLI S     S     #>  5 B_STPHY_AURS R     S     #>  6 B_ESCHR_COLI R     S     #>  7 B_ESCHR_COLI R     S     #>  8 B_ESCHR_COLI S     S     #>  9 B_STPHY_AURS S     S     #> 10 B_ESCHR_COLI S     S     #> # ℹ 2,616 more rows  our_data_1st %>%   select(bacteria, where(is.sir)) #> # A tibble: 2,626 × 5 #>    bacteria     AMX   AMC   CIP   GEN   #>    <mo>         <sir> <sir> <sir> <sir> #>  1 B_ESCHR_COLI R     I     S     S     #>  2 B_KLBSL_PNMN R     I     S     S     #>  3 B_ESCHR_COLI S     I     S     S     #>  4 B_ESCHR_COLI S     S     S     S     #>  5 B_STPHY_AURS R     S     R     S     #>  6 B_ESCHR_COLI R     S     S     S     #>  7 B_ESCHR_COLI R     S     S     S     #>  8 B_ESCHR_COLI S     S     S     S     #>  9 B_STPHY_AURS S     S     S     S     #> 10 B_ESCHR_COLI S     S     S     S     #> # ℹ 2,616 more rows  # filtering using AB selectors is also possible: our_data_1st %>%   filter(any(aminoglycosides() == \"R\")) #> ℹ For aminoglycosides() using column 'GEN' (gentamicin) #> # A tibble: 971 × 9 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl> #>  1 J5         A        2017-12-25 B_STRPT_PNMN R     S     S     R     TRUE  #>  2 X1         A        2017-07-04 B_STPHY_AURS R     S     S     R     TRUE  #>  3 B3         A        2016-07-24 B_ESCHR_COLI S     S     S     R     TRUE  #>  4 V7         A        2012-04-03 B_ESCHR_COLI S     S     S     R     TRUE  #>  5 C9         A        2017-03-23 B_ESCHR_COLI S     S     S     R     TRUE  #>  6 R1         A        2018-06-10 B_STPHY_AURS S     S     S     R     TRUE  #>  7 S2         A        2013-07-19 B_STRPT_PNMN S     S     S     R     TRUE  #>  8 P5         A        2019-03-09 B_STPHY_AURS S     S     S     R     TRUE  #>  9 Q8         A        2019-08-10 B_STPHY_AURS S     S     S     R     TRUE  #> 10 K5         A        2013-03-15 B_STRPT_PNMN S     S     S     R     TRUE  #> # ℹ 961 more rows  our_data_1st %>%   filter(all(betalactams() == \"R\")) #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #>   (amoxicillin/clavulanic acid) #> # A tibble: 471 × 9 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl> #>  1 M7         A        2013-07-22 B_STRPT_PNMN R     R     S     S     TRUE  #>  2 R10        A        2013-12-20 B_STPHY_AURS R     R     S     S     TRUE  #>  3 R7         A        2015-10-25 B_STPHY_AURS R     R     S     S     TRUE  #>  4 R8         A        2019-10-25 B_STPHY_AURS R     R     S     S     TRUE  #>  5 I7         A        2015-08-19 B_ESCHR_COLI R     R     S     S     TRUE  #>  6 N3         A        2014-12-29 B_STRPT_PNMN R     R     R     S     TRUE  #>  7 Q2         A        2019-09-22 B_ESCHR_COLI R     R     S     S     TRUE  #>  8 X7         A        2011-03-20 B_ESCHR_COLI R     R     S     R     TRUE  #>  9 C5         A        2015-08-30 B_KLBSL_PNMN R     R     S     R     TRUE  #> 10 W9         A        2013-10-02 B_ESCHR_COLI R     R     S     S     TRUE  #> # ℹ 461 more rows  # even works in base R (since R 3.0): our_data_1st[all(betalactams() == \"R\"), ] #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #>   (amoxicillin/clavulanic acid) #> # A tibble: 471 × 9 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl> #>  1 M7         A        2013-07-22 B_STRPT_PNMN R     R     S     S     TRUE  #>  2 R10        A        2013-12-20 B_STPHY_AURS R     R     S     S     TRUE  #>  3 R7         A        2015-10-25 B_STPHY_AURS R     R     S     S     TRUE  #>  4 R8         A        2019-10-25 B_STPHY_AURS R     R     S     S     TRUE  #>  5 I7         A        2015-08-19 B_ESCHR_COLI R     R     S     S     TRUE  #>  6 N3         A        2014-12-29 B_STRPT_PNMN R     R     R     S     TRUE  #>  7 Q2         A        2019-09-22 B_ESCHR_COLI R     R     S     S     TRUE  #>  8 X7         A        2011-03-20 B_ESCHR_COLI R     R     S     R     TRUE  #>  9 C5         A        2015-08-30 B_KLBSL_PNMN R     R     S     R     TRUE  #> 10 W9         A        2013-10-02 B_ESCHR_COLI R     R     S     S     TRUE  #> # ℹ 461 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"generate-antibiograms","dir":"Articles","previous_headings":"Analysing the data","what":"Generate antibiograms","title":"How to conduct AMR data analysis","text":"Since AMR v2.0 (March 2023), easy create different types antibiograms, support 20 different languages. four antibiogram types, proposed Klinker et al. (2021, DOI 10.1177/20499361211011373), supported new antibiogram() function: Traditional Antibiogram (TA) e.g, susceptibility Pseudomonas aeruginosa piperacillin/tazobactam (TZP) Combination Antibiogram (CA) e.g, sdditional susceptibility Pseudomonas aeruginosa TZP + tobramycin versus TZP alone Syndromic Antibiogram (SA) e.g, susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) Weighted-Incidence Syndromic Combination Antibiogram (WISCA) e.g, susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) male patients age >=65 years heart failure section, show use antibiogram() function create antibiogram types. starters, included example_isolates data set looks like:","code":"example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"traditional-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Traditional Antibiogram","title":"How to conduct AMR data analysis","text":"create traditional antibiogram, simply state antibiotics used. antibiotics argument antibiogram() function supports (combination) previously mentioned antibiotic class selectors: Notice antibiogram() function automatically prints right format using Quarto R Markdown (page), even applies italics taxonomic names (using italicise_taxonomy() internally). also uses language OS either English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, Ukrainian. next example, force language Spanish using language argument:","code":"antibiogram(example_isolates,             antibiotics = c(aminoglycosides(), carbapenems())) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) antibiogram(example_isolates,             mo_transform = \"gramstain\",             antibiotics = aminoglycosides(),             ab_transform = \"name\",             language = \"es\") #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"combined-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Combined Antibiogram","title":"How to conduct AMR data analysis","text":"create combined antibiogram, use antibiotic codes names plus + character like :","code":"antibiogram(example_isolates,             antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"syndromic-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Syndromic Antibiogram","title":"How to conduct AMR data analysis","text":"create syndromic antibiogram, syndromic_group argument must used. can column data, e.g. ifelse() calculations based certain columns:","code":"antibiogram(example_isolates,             antibiotics = c(aminoglycosides(), carbapenems()),             syndromic_group = \"ward\") #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"weighted-incidence-syndromic-combination-antibiogram-wisca","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Weighted-Incidence Syndromic Combination Antibiogram (WISCA)","title":"How to conduct AMR data analysis","text":"create WISCA, must state combination therapy antibiotics argument (similar Combination Antibiogram), define syndromic group syndromic_group argument (similar Syndromic Antibiogram) cases predefined based clinical demographic characteristics (e.g., endocarditis 75+ females). next example simplification without clinical characteristics, just gives idea WISCA can created:","code":"wisca <- antibiogram(example_isolates,                      antibiotics = c(\"AMC\", \"AMC+CIP\", \"TZP\", \"TZP+TOB\"),                      mo_transform = \"gramstain\",                      minimum = 10, # this should be >= 30, but now just as example                      syndromic_group = ifelse(example_isolates$age >= 65 &                                                 example_isolates$gender == \"M\",                                               \"WISCA Group 1\", \"WISCA Group 2\")) wisca"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"plotting-antibiograms","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Plotting antibiograms","title":"How to conduct AMR data analysis","text":"Antibiograms can plotted using autoplot() ggplot2 packages, since AMR package provides extension function:  calculate antimicrobial resistance sensible way, also correcting results, use resistance() susceptibility() functions.","code":"autoplot(wisca)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"resistance-percentages","dir":"Articles","previous_headings":"Analysing the data","what":"Resistance percentages","title":"How to conduct AMR data analysis","text":"functions resistance() susceptibility() can used calculate antimicrobial resistance susceptibility. specific analyses, functions proportion_S(), proportion_SI(), proportion_I(), proportion_IR() proportion_R() can used determine proportion specific antimicrobial outcome. functions contain minimum argument, denoting minimum required number test results returning value. functions otherwise return NA. default minimum = 30, following CLSI M39-A4 guideline applying microbial epidemiology. per EUCAST guideline 2019, calculate resistance proportion R (proportion_R(), equal resistance()) susceptibility proportion S (proportion_SI(), equal susceptibility()). functions can used : can used conjunction group_by() summarise(), dplyr package: Author: Dr. Matthijs Berends, 26th Feb 2023","code":"our_data_1st %>% resistance(AMX) #> [1] 0.4318355 our_data_1st %>%   group_by(hospital) %>%   summarise(amoxicillin = resistance(AMX)) #> # A tibble: 3 × 2 #>   hospital amoxicillin #>   <chr>          <dbl> #> 1 A              0.343 #> 2 B              0.569 #> 3 C              0.375"},{"path":"https://msberends.github.io/AMR/articles/EUCAST.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to apply EUCAST rules","text":"EUCAST rules? European Committee Antimicrobial Susceptibility Testing (EUCAST) states website: EUCAST expert rules tabulated collection expert knowledge intrinsic resistances, exceptional resistance phenotypes interpretive rules may applied antimicrobial susceptibility testing order reduce errors make appropriate recommendations reporting particular resistances. Europe, lot medical microbiological laboratories already apply rules (Brown et al., 2015). package features latest insights intrinsic resistance unusual phenotypes (v3.3, 2021). Moreover, eucast_rules() function use purpose can also apply additional rules, like forcing ampicillin = R isolates amoxicillin/clavulanic acid = R.","code":""},{"path":"https://msberends.github.io/AMR/articles/EUCAST.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"How to apply EUCAST rules","text":"rules can used discard impossible bug-drug combinations data. example, Klebsiella produces beta-lactamase prevents ampicillin (amoxicillin) working . words, practically every strain Klebsiella resistant ampicillin. Sometimes, laboratory data can still contain strains ampicillin susceptible ampicillin. antibiogram available identification available, antibiogram re-interpreted based identification (namely, Klebsiella). EUCAST expert rules solve , can applied using eucast_rules(): convenient function mo_is_intrinsic_resistant() uses guideline, allows check one specific microorganisms antibiotics: EUCAST rules can used correction, can also used filling known resistance susceptibility based results antimicrobials drugs. process called interpretive reading, basically form imputation, part eucast_rules() function well:","code":"oops <- data.frame(   mo = c(     \"Klebsiella\",     \"Escherichia\"   ),   ampicillin = \"S\" ) oops #>            mo ampicillin #> 1  Klebsiella          S #> 2 Escherichia          S  eucast_rules(oops, info = FALSE) #>            mo ampicillin #> 1  Klebsiella          R #> 2 Escherichia          S mo_is_intrinsic_resistant(   c(\"Klebsiella\", \"Escherichia\"),   \"ampicillin\" ) #> [1]  TRUE FALSE  mo_is_intrinsic_resistant(   \"Klebsiella\",   c(\"ampicillin\", \"kanamycin\") ) #> [1]  TRUE FALSE data <- data.frame(   mo = c(     \"Staphylococcus aureus\",     \"Enterococcus faecalis\",     \"Escherichia coli\",     \"Klebsiella pneumoniae\",     \"Pseudomonas aeruginosa\"   ),   VAN = \"-\", # Vancomycin   AMX = \"-\", # Amoxicillin   COL = \"-\", # Colistin   CAZ = \"-\", # Ceftazidime   CXM = \"-\", # Cefuroxime   PEN = \"S\", # Benzylenicillin   FOX = \"S\", # Cefoxitin   stringsAsFactors = FALSE ) data eucast_rules(data)"},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"type-of-input","dir":"Articles","previous_headings":"","what":"Type of input","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function takes data set input, regular data.frame. tries automatically determine right columns info isolates, name species columns results antimicrobial agents. See help page info set right settings data command ?mdro. WHONET data (data), settings automatically set correctly.","code":""},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"guidelines","dir":"Articles","previous_headings":"","what":"Guidelines","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function support multiple guidelines. can select guideline guideline parameter. Currently supported guidelines (case-insensitive): guideline = \"CMI2012\" (default) Magiorakos AP, Srinivasan et al. “Multidrug-resistant, extensively drug-resistant pandrug-resistant bacteria: international expert proposal interim standard definitions acquired resistance.” Clinical Microbiology Infection (2012) (link) guideline = \"EUCAST3.2\" (simply guideline = \"EUCAST\") European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance Unusual Phenotypes” (link) guideline = \"EUCAST3.1\" European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance Exceptional Phenotypes Tables” (link) guideline = \"TB\" international guideline multi-drug resistant tuberculosis - World Health Organization “Companion handbook guidelines programmatic management drug-resistant tuberculosis” (link) guideline = \"MRGN\" German national guideline - Mueller et al. (2015) Antimicrobial Resistance Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6 guideline = \"BRMO\" Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (link) Please suggest (country-specific) guidelines letting us know: https://github.com/msberends/AMR/issues/new.","code":""},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"custom-guidelines","dir":"Articles","previous_headings":"Guidelines","what":"Custom Guidelines","title":"How to determine multi-drug resistance (MDR)","text":"can also use custom guideline. Custom guidelines can set custom_mdro_guideline() function. great importance custom rules determine MDROs hospital, e.g., rules dependent ward, state contact isolation variables data. familiar case_when() dplyr package, recognise input method set rules. Rules must set using R considers ‘formula notation’: row/isolate matches first rule, value first ~ (case ‘Elderly Type ’) set MDRO value. Otherwise, second rule tried . maximum number rules unlimited. can print rules set console overview. Colours help reading console supports colours. outcome function can used guideline argument mdro() function: rules set (custom object case) exported shared file location using saveRDS() collaborate multiple users. custom rules set imported using readRDS().","code":"custom <- custom_mdro_guideline(   CIP == \"R\" & age > 60 ~ \"Elderly Type A\",   ERY == \"R\" & age > 60 ~ \"Elderly Type B\" ) custom #> A set of custom MDRO rules: #>   1. If CIP is \"R\" and age is higher than 60 then: Elderly Type A #>   2. If ERY is \"R\" and age is higher than 60 then: Elderly Type B #>   3. Otherwise: Negative #>  #> Unmatched rows will return NA. #> Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B x <- mdro(example_isolates, guideline = custom) table(x) #> x #>       Negative Elderly Type A Elderly Type B  #>           1070            198            732"},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function always returns ordered factor predefined guidelines. example, output default guideline Magiorakos et al. returns factor levels ‘Negative’, ‘MDR’, ‘XDR’ ‘PDR’ order. next example uses example_isolates data set. data set included package contains full antibiograms 2,000 microbial isolates. reflects reality can used practise AMR data analysis. test MDR/XDR/PDR guideline data set, get: (16 isolates test results) Frequency table Class: factor > ordered (numeric) Length: 2,000 Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant … Available: 1,729 (86.45%, NA: 271 = 13.55%) Unique: 2 another example, create data set determine multi-drug resistant TB: column names automatically verified valid drug names codes, worked exactly way: data set now looks like : can now add interpretation MDR-TB data set. can use: shortcut mdr_tb(): Create frequency table results: Frequency table Class: factor > ordered (numeric) Length: 5,000 Levels: 5: Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant <… Available: 5,000 (100%, NA: 0 = 0%) Unique: 5","code":"library(dplyr) # to support pipes: %>% library(cleaner) # to create frequency tables example_isolates %>%   mdro() %>%   freq() # show frequency table of the result #> Warning: in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) # random_sir() is a helper function to generate # a random vector with values S, I and R my_TB_data <- data.frame(   rifampicin = random_sir(5000),   isoniazid = random_sir(5000),   gatifloxacin = random_sir(5000),   ethambutol = random_sir(5000),   pyrazinamide = random_sir(5000),   moxifloxacin = random_sir(5000),   kanamycin = random_sir(5000) ) my_TB_data <- data.frame(   RIF = random_sir(5000),   INH = random_sir(5000),   GAT = random_sir(5000),   ETH = random_sir(5000),   PZA = random_sir(5000),   MFX = random_sir(5000),   KAN = random_sir(5000) ) head(my_TB_data) #>   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin #> 1          S         R            R          S            R            R #> 2          S         R            S          I            S            R #> 3          S         R            I          I            I            S #> 4          S         I            R          I            R            R #> 5          R         S            R          R            R            I #> 6          S         S            S          R            I            R #>   kanamycin #> 1         I #> 2         R #> 3         I #> 4         S #> 5         R #> 6         R mdro(my_TB_data, guideline = \"TB\") my_TB_data$mdr <- mdr_tb(my_TB_data) #> ℹ No column found as input for col_mo, assuming all rows contain #>   Mycobacterium tuberculosis. freq(my_TB_data$mdr)"},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"transforming","dir":"Articles","previous_headings":"","what":"Transforming","title":"How to conduct principal component analysis (PCA) for AMR","text":"PCA, need transform AMR data first. example_isolates data set package looks like: Now transform data set resistance percentages per taxonomic order genus:","code":"library(AMR) library(dplyr) glimpse(example_isolates) #> Rows: 2,000 #> Columns: 46 #> $ date    <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-01-13, 2… #> $ patient <chr> \"A77334\", \"A77334\", \"067927\", \"067927\", \"067927\", \"067927\", \"4… #> $ age     <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71, 75, 50… #> $ gender  <chr> \"F\", \"F\", \"F\", \"F\", \"F\", \"F\", \"M\", \"M\", \"F\", \"F\", \"M\", \"M\", \"M… #> $ ward    <chr> \"Clinical\", \"Clinical\", \"ICU\", \"ICU\", \"ICU\", \"ICU\", \"Clinical\"… #> $ mo      <mo> \"B_ESCHR_COLI\", \"B_ESCHR_COLI\", \"B_STPHY_EPDR\", \"B_STPHY_EPDR\",… #> $ PEN     <sir> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,… #> $ OXA     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ FLC     <sir> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R… #> $ AMX     <sir> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N… #> $ AMC     <sir> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N… #> $ AMP     <sir> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N… #> $ TZP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CZO     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,… #> $ FEP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CXM     <sir> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S… #> $ FOX     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,… #> $ CTX     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ CAZ     <sir> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, … #> $ CRO     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ GEN     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ TOB     <sir> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA… #> $ AMK     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ KAN     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ TMP     <sir> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, … #> $ SXT     <sir> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N… #> $ NIT     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,… #> $ FOS     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ LNZ     <sir> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… #> $ CIP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S… #> $ MFX     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ VAN     <sir> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, … #> $ TEC     <sir> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… #> $ TCY     <sir> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, … #> $ TGC     <sir> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA… #> $ DOX     <sir> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA… #> $ ERY     <sir> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,… #> $ CLI     <sir> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA… #> $ AZM     <sir> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,… #> $ IPM     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ MEM     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ MTR     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CHL     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ COL     <sir> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, … #> $ MUP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ RIF     <sir> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… resistance_data <- example_isolates %>%   group_by(     order = mo_order(mo), # group on anything, like order     genus = mo_genus(mo)   ) %>% #  and genus as we do here   summarise_if(is.sir, resistance) %>% # then get resistance of all drugs   select(     order, genus, AMC, CXM, CTX,     CAZ, GEN, TOB, TMP, SXT   ) # and select only relevant columns  head(resistance_data) #> # A tibble: 6 × 10 #> # Groups:   order [5] #>   order             genus          AMC   CXM   CTX   CAZ   GEN   TOB   TMP   SXT #>   <chr>             <chr>        <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 (unknown order)   (unknown ge…    NA    NA    NA    NA    NA    NA    NA    NA #> 2 Actinomycetales   Schaalia        NA    NA    NA    NA    NA    NA    NA    NA #> 3 Bacteroidales     Bacteroides     NA    NA    NA    NA    NA    NA    NA    NA #> 4 Campylobacterales Campylobact…    NA    NA    NA    NA    NA    NA    NA    NA #> 5 Caryophanales     Gemella         NA    NA    NA    NA    NA    NA    NA    NA #> 6 Caryophanales     Listeria        NA    NA    NA    NA    NA    NA    NA    NA"},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"perform-principal-component-analysis","dir":"Articles","previous_headings":"","what":"Perform principal component analysis","title":"How to conduct principal component analysis (PCA) for AMR","text":"new pca() function automatically filter rows contain numeric values selected variables, now need : result can reviewed good old summary() function: Good news. first two components explain total 93.3% variance (see PC1 PC2 values Proportion Variance. can create -called biplot base R biplot() function, see antimicrobial resistance per drug explain difference per microorganism.","code":"pca_result <- pca(resistance_data) #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", #>   \"TMP\", and \"TOB\". Total observations available: 7. summary(pca_result) #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\" #> Importance of components: #>                           PC1    PC2    PC3     PC4     PC5     PC6       PC7 #> Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00 #> Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00 #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\""},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"plotting-the-results","dir":"Articles","previous_headings":"","what":"Plotting the results","title":"How to conduct principal component analysis (PCA) for AMR","text":"can’t see explanation points. Perhaps works better new ggplot_pca() function, automatically adds right labels even groups:  can also print ellipse per group, edit appearance:","code":"biplot(pca_result) ggplot_pca(pca_result) ggplot_pca(pca_result, ellipse = TRUE) +   ggplot2::labs(title = \"An AMR/PCA biplot!\")"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"spss-sas-stata","dir":"Articles","previous_headings":"","what":"SPSS / SAS / Stata","title":"How to import data from SPSS / SAS / Stata","text":"SPSS (Statistical Package Social Sciences) probably well-known software package statistical analysis. SPSS easier learn R, SPSS click menu run parts analysis. user-friendliness, taught universities particularly useful students new statistics. experience, guess pretty much (bio)medical students know time graduate. SAS Stata comparable statistical packages popular big industries.","code":""},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"compared-to-r","dir":"Articles","previous_headings":"","what":"Compared to R","title":"How to import data from SPSS / SAS / Stata","text":"said, SPSS easier learn R. SPSS, SAS Stata come major downsides comparing R: R highly modular. official R network (CRAN) features 16,000 packages time writing, AMR package one . packages peer-reviewed publication. Aside official channel, also developers choose submit CRAN, rather keep public repository, like GitHub. may even lot 14,000 packages . Bottom line , can really extend ask somebody . Take example AMR package. Among things, adds reliable reference data R help data cleaning analysis. SPSS, SAS Stata never know valid MIC value Gram stain E. coli . species Klebiella resistant amoxicillin Floxapen® trade name flucloxacillin. facts properties often needed clean existing data, inconvenient software package without reliable reference data. See demonstration. R extremely flexible. write syntax , can anything want. flexibility transforming, arranging, grouping summarising data, drawing plots, endless - SPSS, SAS Stata bound algorithms format styles. may bit flexible, can probably never create specific publication-ready plot without using (paid) software. sometimes write syntaxes SPSS run complete analysis ‘automate’ work, lot less time R. notice writing syntaxes R lot nifty clever SPSS. Still, working statistical package, knowledge (statistically) willing accomplish. R can easily automated. last years, R Markdown really made interesting development. R Markdown, can easily produce reports, whether format Word, PowerPoint, website, PDF document just raw data Excel. even allows use reference file containing layout style (e.g. fonts colours) organisation. use lot generate weekly monthly reports automatically. Just write code enjoy automatically updated reports interval like. even professional environment, create Shiny apps: live manipulation data using custom made website. webdesign knowledge needed (JavaScript, CSS, HTML) almost zero. R huge community. Many R users just ask questions websites like StackOverflow.com, largest online community programmers. time writing, 489 114 R-related questions already asked platform (covers questions answers programming language). experience, questions answered within couple minutes. R understands data type, including SPSS/SAS/Stata. ’s vice versa ’m afraid. can import data source R. example SPSS, SAS Stata (link), Minitab, Epi Info EpiData (link), Excel (link), flat files like CSV, TXT TSV (link), directly databases datawarehouses anywhere world (link). can even scrape websites download tables live internet (link) get results API call transform data one command (link). best part - can export R data formats well. can import SPSS file, analysis neatly R export resulting tables Excel files sharing. R completely free open-source. strings attached. created maintained volunteers believe (data) science open publicly available everybody. SPSS, SAS Stata quite expensive. IBM SPSS Staticstics comes subscriptions nowadays, varying USD 1,300 USD 8,500 per user per year. SAS Analytics Pro costs around USD 10,000 per computer. Stata also business model subscription fees, varying USD 600 USD 2,800 per computer per year, lower prices come limitation number variables can work . still offer benefits R. working midsized small company, can save tens thousands dollars using R instead e.g. SPSS - gaining even functions flexibility. R enthousiasts can much PR want (like ), nobody officially associated affiliated R. really free. R (nowadays) preferred analysis software academic papers. present, R among world powerful statistical languages, generally popular science (Bollmann et al., 2017). reasons, number references R analysis method academic papers rising continuously even surpassed SPSS academic use (Muenchen, 2014). believe thing SPSS , always great user interface easy learn use. Back developed , little competition, let alone R. R didn’t even professional user interface last decade (called RStudio, see ). people used R nineties 2010 almost completely incomparable R used now. language restyled completely volunteers dedicated professionals field data science. SPSS great nothing else compete. now 2023, don’t see reason SPSS better use R. demonstrate first point:","code":"# not all values are valid MIC values: as.mic(0.125) #> Class 'mic' #> [1] 0.125 as.mic(\"testvalue\") #> Class 'mic' #> [1] <NA>  # the Gram stain is available for all bacteria: mo_gramstain(\"E. coli\") #> [1] \"Gram-negative\"  # Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST: klebsiella_test <- data.frame(   mo = \"klebsiella\",   amox = \"S\",   stringsAsFactors = FALSE ) klebsiella_test # (our original data) #>           mo amox #> 1 klebsiella    S eucast_rules(klebsiella_test, info = FALSE) # (the edited data by EUCAST rules) #>           mo amox #> 1 klebsiella    R  # hundreds of trade names can be translated to a name, trade name or an ATC code: ab_name(\"floxapen\") #> [1] \"Flucloxacillin\" ab_tradenames(\"floxapen\") #>  [1] \"culpen\"               \"floxacillin\"          \"floxacillin sodium\"   #>  [4] \"floxapen\"             \"floxapen sodium salt\" \"fluclox\"              #>  [7] \"flucloxacilina\"       \"flucloxacillin\"       \"flucloxacilline\"      #> [10] \"flucloxacillinum\"     \"fluorochloroxacillin\" \"staphylex\" ab_atc(\"floxapen\") #> [1] \"J01CF05\""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"rstudio","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata","what":"RStudio","title":"How to import data from SPSS / SAS / Stata","text":"work R, probably best option use RStudio. open-source free desktop environment allows run R code, also supports project management, version management, package management convenient import menus work data sources. can also install RStudio Server private corporate server, brings nothing less complete RStudio software website (home work). import data file, just click Import Dataset Environment tab:  additional packages needed, RStudio ask installed beforehand. window opens, can define options (parameters) used import ’re ready go:  want named variables imported factors resembles SPSS , use as_factor(). difference :","code":"SPSS_data # # A tibble: 4,203 x 4 #     v001 sex       status    statusage #    <dbl> <dbl+lbl> <dbl+lbl>     <dbl> #  1 10002 1         1              76.6 #  2 10004 0         1              59.1 #  3 10005 1         1              54.5 #  4 10006 1         1              54.1 #  5 10007 1         1              57.7 #  6 10008 1         1              62.8 #  7 10010 0         1              63.7 #  8 10011 1         1              73.1 #  9 10017 1         1              56.7 # 10 10018 0         1              66.6 # # ... with 4,193 more rows  as_factor(SPSS_data) # # A tibble: 4,203 x 4 #     v001 sex    status statusage #    <dbl> <fct>  <fct>      <dbl> #  1 10002 Male   alive       76.6 #  2 10004 Female alive       59.1 #  3 10005 Male   alive       54.5 #  4 10006 Male   alive       54.1 #  5 10007 Male   alive       57.7 #  6 10008 Male   alive       62.8 #  7 10010 Female alive       63.7 #  8 10011 Male   alive       73.1 #  9 10017 Male   alive       56.7 # 10 10018 Female alive       66.6 # # ... with 4,193 more rows"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"base-r","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata","what":"Base R","title":"How to import data from SPSS / SAS / Stata","text":"import data SPSS, SAS Stata, can use great haven package : can now import files follows:","code":"# download and install the latest version: install.packages(\"haven\") # load the package you just installed: library(haven)"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"spss","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata > Base R","what":"SPSS","title":"How to import data from SPSS / SAS / Stata","text":"read files SPSS R: forget as_factor(), mentioned . export R objects SPSS file format:","code":"# read any SPSS file based on file extension (best way): read_spss(file = \"path/to/file\")  # read .sav or .zsav file: read_sav(file = \"path/to/file\")  # read .por file: read_por(file = \"path/to/file\") # save as .sav file: write_sav(data = yourdata, path = \"path/to/file\")  # save as compressed .zsav file: write_sav(data = yourdata, path = \"path/to/file\", compress = TRUE)"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"sas","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata > Base R","what":"SAS","title":"How to import data from SPSS / SAS / Stata","text":"read files SAS R: export R objects SAS file format:","code":"# read .sas7bdat + .sas7bcat files: read_sas(data_file = \"path/to/file\", catalog_file = NULL)  # read SAS transport files (version 5 and version 8): read_xpt(file = \"path/to/file\") # save as regular SAS file: write_sas(data = yourdata, path = \"path/to/file\")  # the SAS transport format is an open format # (required for submission of the data to the FDA) write_xpt(data = yourdata, path = \"path/to/file\", version = 8)"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"stata","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata > Base R","what":"Stata","title":"How to import data from SPSS / SAS / Stata","text":"read files Stata R: export R objects Stata file format:","code":"# read .dta file: read_stata(file = \"/path/to/file\")  # works exactly the same: read_dta(file = \"/path/to/file\") # save as .dta file, Stata version 14: # (supports Stata v8 until v15 at the time of writing) write_dta(data = yourdata, path = \"/path/to/file\", version = 14)"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"import-of-data","dir":"Articles","previous_headings":"","what":"Import of data","title":"How to work with WHONET data","text":"tutorial assumes already imported WHONET data e.g. readxl package. RStudio, can done using menu button ‘Import Dataset’ tab ‘Environment’. Choose option ‘Excel’ select exported file. Make sure date fields imported correctly. example syntax look like : package comes example data set WHONET. use analysis.","code":"library(readxl) data <- read_excel(path = \"path/to/your/file.xlsx\")"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to work with WHONET data","text":"First, load relevant packages yet . use tidyverse analyses. . don’t know yet, suggest read website: https://www.tidyverse.org/. transform variables simplify automate analysis: Microorganisms transformed microorganism codes (called mo) using Catalogue Life reference data set, contains ~70,000 microorganisms taxonomic kingdoms Bacteria, Fungi Protozoa. tranformation .mo(). function also recognises almost WHONET abbreviations microorganisms. Antimicrobial results interpretations clean valid. words, contain values \"S\", \"\" \"R\". exactly .sir() function . errors warnings, values transformed succesfully. also created package dedicated data cleaning checking, called cleaner package. freq() function can used create frequency tables. let’s check data, couple frequency tables: Frequency table Class: character Length: 500 Available: 500 (100%, NA: 0 = 0%) Unique: 38 Shortest: 11 Longest: 40 (omitted 28 entries, n = 57 [11.4%]) Frequency table Class: factor > ordered > sir (numeric) Length: 500 Levels: 3: S < < R Available: 481 (96.2%, NA: 19 = 3.8%) Unique: 3 Drug: Amoxicillin/clavulanic acid (AMC, J01CR02) Drug group: Beta-lactams/penicillins %SI: 78.59%","code":"library(dplyr) # part of tidyverse library(ggplot2) # part of tidyverse library(AMR) # this package library(cleaner) # to create frequency tables # transform variables data <- WHONET %>%   # get microbial ID based on given organism   mutate(mo = as.mo(Organism)) %>%   # transform everything from \"AMP_ND10\" to \"CIP_EE\" to the new `sir` class   mutate_at(vars(AMP_ND10:CIP_EE), as.sir) # our newly created `mo` variable, put in the mo_name() function data %>% freq(mo_name(mo), nmax = 10) # our transformed antibiotic columns # amoxicillin/clavulanic acid (J01CR02) as an example data %>% freq(AMC_ND2)"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"a-first-glimpse-at-results","dir":"Articles","previous_headings":"","what":"A first glimpse at results","title":"How to work with WHONET data","text":"easy ggplot already give lot information, using included ggplot_sir() function:","code":"data %>%   group_by(Country) %>%   select(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) %>%   ggplot_sir(translate_ab = \"ab\", facet = \"Country\", datalabels = FALSE)"},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"microorganisms-full-microbial-taxonomy","dir":"Articles","previous_headings":"","what":"microorganisms: Full Microbial Taxonomy","title":"Data sets for download / own use","text":"data set 52 151 rows 22 columns, containing following column names:mo, fullname, status, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, source, lpsn, lpsn_parent, lpsn_renamed_to, gbif, gbif_parent, gbif_renamed_to, prevalence, snomed. data set R available microorganisms, load AMR package. last updated 20 April 2023 13:20:41 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (1.2 MB) Download tab-separated text file (11.3 MB) Download Microsoft Excel workbook (5 MB) Download Apache Feather file (5.4 MB) Download Apache Parquet file (2.6 MB) Download SAS data file (50.9 MB) Download IBM SPSS Statistics data file (16.9 MB) Download Stata DTA file (47.1 MB) NOTE: exported files SAS, SPSS Stata contain first 50 SNOMED codes per record, file size otherwise exceed 100 MB; file size limit GitHub. Advice? Use R instead. tab-separated text file Microsoft Excel workbook contain SNOMED codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source","dir":"Articles","previous_headings":"microorganisms: Full Microbial Taxonomy","what":"Source","title":"Data sets for download / own use","text":"data set contains full microbial taxonomy five kingdoms List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF): Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example-content","dir":"Articles","previous_headings":"microorganisms: Full Microbial Taxonomy","what":"Example content","title":"Data sets for download / own use","text":"Included (sub)species per taxonomic kingdom: Example rows filtering genus Escherichia:","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"antibiotics-antibiotic-antifungal-drugs","dir":"Articles","previous_headings":"","what":"antibiotics: Antibiotic (+Antifungal) Drugs","title":"Data sets for download / own use","text":"data set 483 rows 14 columns, containing following column names:ab, cid, name, group, atc, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc. data set R available antibiotics, load AMR package. last updated 22 February 2023 13:38:57 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (39 kB) Download tab-separated text file (0.1 MB) Download Microsoft Excel workbook (66 kB) Download Apache Feather file (0.1 MB) Download Apache Parquet file (97 kB) Download SAS data file (1.9 MB) Download IBM SPSS Statistics data file (0.3 MB) Download Stata DTA file (0.4 MB) tab-separated text file Microsoft Excel workbook, SAS, SPSS Stata files contain ATC codes, common abbreviations, trade names LOINC codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-1","dir":"Articles","previous_headings":"antibiotics: Antibiotic (+Antifungal) Drugs","what":"Source","title":"Data sets for download / own use","text":"data set contains EARS-Net ATC codes gathered WHONET, compound IDs PubChem. also contains brand names (synonyms) found PubChem Defined Daily Doses (DDDs) oral parenteral administration. ATC/DDD index Collaborating Centre Drug Statistics Methodology (note: may used commercial purposes, freely available CC website personal use) PubChem US National Library Medicine WHONET software 2019 LOINC (Logical Observation Identifiers Names Codes)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"antivirals-antiviral-drugs","dir":"Articles","previous_headings":"","what":"antivirals: Antiviral Drugs","title":"Data sets for download / own use","text":"data set 120 rows 11 columns, containing following column names:av, name, atc, cid, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc. data set R available antivirals, load AMR package. last updated 13 November 2022 07:46:10 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (5 kB) Download tab-separated text file (16 kB) Download Microsoft Excel workbook (16 kB) Download Apache Feather file (15 kB) Download Apache Parquet file (13 kB) Download SAS data file (84 kB) Download IBM SPSS Statistics data file (30 kB) Download Stata DTA file (73 kB) tab-separated text file Microsoft Excel workbook, SAS, SPSS Stata files contain trade names LOINC codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-2","dir":"Articles","previous_headings":"antivirals: Antiviral Drugs","what":"Source","title":"Data sets for download / own use","text":"data set contains ATC codes gathered compound IDs PubChem. also contains brand names (synonyms) found PubChem Defined Daily Doses (DDDs) oral parenteral administration. ATC/DDD index Collaborating Centre Drug Statistics Methodology (note: may used commercial purposes, freely available CC website personal use) PubChem US National Library Medicine LOINC (Logical Observation Identifiers Names Codes)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir","dir":"Articles","previous_headings":"","what":"clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR","title":"Data sets for download / own use","text":"data set 18 271 rows 11 columns, containing following column names:guideline, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti. data set R available clinical_breakpoints, load AMR package. last updated 20 April 2023 13:20:41 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (43 kB) Download tab-separated text file (1.9 MB) Download Microsoft Excel workbook (0.8 MB) Download Apache Feather file (0.7 MB) Download Apache Parquet file (88 kB) Download SAS data file (3.6 MB) Download IBM SPSS Statistics data file (2.3 MB) Download Stata DTA file (3.3 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-3","dir":"Articles","previous_headings":"clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR","what":"Source","title":"Data sets for download / own use","text":"data set contains interpretation rules MIC values disk diffusion diameters. Included guidelines CLSI (2013-2022) EUCAST (2013-2022).","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"intrinsic_resistant-intrinsic-bacterial-resistance","dir":"Articles","previous_headings":"","what":"intrinsic_resistant: Intrinsic Bacterial Resistance","title":"Data sets for download / own use","text":"data set 134 634 rows 2 columns, containing following column names:mo ab. data set R available intrinsic_resistant, load AMR package. last updated 16 December 2022 15:10:43 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (78 kB) Download tab-separated text file (5.1 MB) Download Microsoft Excel workbook (1.3 MB) Download Apache Feather file (1.2 MB) Download Apache Parquet file (0.2 MB) Download SAS data file (9.8 MB) Download IBM SPSS Statistics data file (7.4 MB) Download Stata DTA file (9.5 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-4","dir":"Articles","previous_headings":"intrinsic_resistant: Intrinsic Bacterial Resistance","what":"Source","title":"Data sets for download / own use","text":"data set contains defined intrinsic resistance EUCAST bug-drug combinations, based ‘EUCAST Expert Rules’ ‘EUCAST Intrinsic Resistance Unusual Phenotypes’ v3.3 (2021).","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example-content-4","dir":"Articles","previous_headings":"intrinsic_resistant: Intrinsic Bacterial Resistance","what":"Example content","title":"Data sets for download / own use","text":"Example rows filtering Enterobacter cloacae:","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"dosage-dosage-guidelines-from-eucast","dir":"Articles","previous_headings":"","what":"dosage: Dosage Guidelines from EUCAST","title":"Data sets for download / own use","text":"data set 336 rows 9 columns, containing following column names:ab, name, type, dose, dose_times, administration, notes, original_txt, eucast_version. data set R available dosage, load AMR package. last updated 14 November 2022 14:20:39 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (3 kB) Download tab-separated text file (29 kB) Download Microsoft Excel workbook (19 kB) Download Apache Feather file (16 kB) Download Apache Parquet file (8 kB) Download SAS data file (92 kB) Download IBM SPSS Statistics data file (43 kB) Download Stata DTA file (82 kB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-5","dir":"Articles","previous_headings":"dosage: Dosage Guidelines from EUCAST","what":"Source","title":"Data sets for download / own use","text":"EUCAST breakpoints used package based dosages data set. Currently included dosages data set meant : ‘EUCAST Clinical Breakpoint Tables’ v11.0 (2021) ‘EUCAST Clinical Breakpoint Tables’ v12.0 (2022).","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example_isolates-example-data-for-practice","dir":"Articles","previous_headings":"","what":"example_isolates: Example Data for Practice","title":"Data sets for download / own use","text":"data set 2 000 rows 46 columns, containing following column names:date, patient, age, gender, ward, mo, PEN, OXA, FLC, AMX, AMC, AMP, TZP, CZO, FEP, CXM, FOX, CTX, CAZ, CRO, GEN, TOB, AMK, KAN, TMP, SXT, NIT, FOS, LNZ, CIP, MFX, VAN, TEC, TCY, TGC, DOX, ERY, CLI, AZM, IPM, MEM, MTR, CHL, COL, MUP, RIF. data set R available example_isolates, load AMR package. last updated 21 January 2023 22:47:20 UTC. Find info structure data set .","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-6","dir":"Articles","previous_headings":"example_isolates: Example Data for Practice","what":"Source","title":"Data sets for download / own use","text":"data set contains randomised fictitious data, reflects reality can used practise AMR data analysis.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example_isolates_unclean-example-data-for-practice","dir":"Articles","previous_headings":"","what":"example_isolates_unclean: Example Data for Practice","title":"Data sets for download / own use","text":"data set 3 000 rows 8 columns, containing following column names:patient_id, hospital, date, bacteria, AMX, AMC, CIP, GEN. data set R available example_isolates_unclean, load AMR package. last updated 27 August 2022 18:49:37 UTC. Find info structure data set .","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-7","dir":"Articles","previous_headings":"example_isolates_unclean: Example Data for Practice","what":"Source","title":"Data sets for download / own use","text":"data set contains randomised fictitious data, reflects reality can used practise AMR data analysis.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"needed-r-packages","dir":"Articles","previous_headings":"","what":"Needed R packages","title":"How to predict antimicrobial resistance","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. AMR package depends packages even extends use functions.","code":"library(dplyr) library(ggplot2) library(AMR)  # (if not yet installed, install with:) # install.packages(c(\"tidyverse\", \"AMR\"))"},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"prediction-analysis","dir":"Articles","previous_headings":"","what":"Prediction analysis","title":"How to predict antimicrobial resistance","text":"package contains function resistance_predict(), takes input functions AMR data analysis. Based date column, calculates cases per year uses regression model predict antimicrobial resistance. basically easy : function look date column col_date set. running commands, summary regression model printed unless using resistance_predict(..., info = FALSE). text printed summary - actual result (output) function data.frame containing year: number observations, actual observed resistance, estimated resistance standard error estimation: function plot available base R, can extended packages depend output based type input. extended function cope resistance predictions:  fastest way plot result. automatically adds right axes, error bars, titles, number available observations type model. also support ggplot2 package custom function ggplot_sir_predict() create appealing plots:","code":"# resistance prediction of piperacillin/tazobactam (TZP): resistance_predict(tbl = example_isolates, col_date = \"date\", col_ab = \"TZP\", model = \"binomial\")  # or: example_isolates %>%   resistance_predict(     col_ab = \"TZP\",     model = \"binomial\"   )  # to bind it to object 'predict_TZP' for example: predict_TZP <- example_isolates %>%   resistance_predict(     col_ab = \"TZP\",     model = \"binomial\"   ) predict_TZP #> # A tibble: 32 × 7 #>     year  value se_min se_max observations observed estimated #>  * <dbl>  <dbl>  <dbl>  <dbl>        <int>    <dbl>     <dbl> #>  1  2002 0.2        NA     NA           15   0.2       0.0562 #>  2  2003 0.0625     NA     NA           32   0.0625    0.0616 #>  3  2004 0.0854     NA     NA           82   0.0854    0.0676 #>  4  2005 0.05       NA     NA           60   0.05      0.0741 #>  5  2006 0.0508     NA     NA           59   0.0508    0.0812 #>  6  2007 0.121      NA     NA           66   0.121     0.0889 #>  7  2008 0.0417     NA     NA           72   0.0417    0.0972 #>  8  2009 0.0164     NA     NA           61   0.0164    0.106  #>  9  2010 0.0566     NA     NA           53   0.0566    0.116  #> 10  2011 0.183      NA     NA           93   0.183     0.127  #> # ℹ 22 more rows plot(predict_TZP) ggplot_sir_predict(predict_TZP) # choose for error bars instead of a ribbon ggplot_sir_predict(predict_TZP, ribbon = FALSE)"},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"choosing-the-right-model","dir":"Articles","previous_headings":"Prediction analysis","what":"Choosing the right model","title":"How to predict antimicrobial resistance","text":"Resistance easily predicted; look vancomycin resistance Gram-positive bacteria, spread (.e. standard error) enormous:  Vancomycin resistance 100% ten years, might remain low. can define model model parameter. model chosen generalised linear regression model using binomial distribution, assuming period zero resistance followed period increasing resistance leading slowly resistance. Valid values : vancomycin resistance Gram-positive bacteria, linear model might appropriate:  model also available object, attribute:","code":"example_isolates %>%   filter(mo_gramstain(mo, language = NULL) == \"Gram-positive\") %>%   resistance_predict(col_ab = \"VAN\", year_min = 2010, info = FALSE, model = \"binomial\") %>%   ggplot_sir_predict() example_isolates %>%   filter(mo_gramstain(mo, language = NULL) == \"Gram-positive\") %>%   resistance_predict(col_ab = \"VAN\", year_min = 2010, info = FALSE, model = \"linear\") %>%   ggplot_sir_predict() model <- attributes(predict_TZP)$model  summary(model)$family #>  #> Family: binomial  #> Link function: logit  summary(model)$coefficients #>                  Estimate  Std. Error   z value     Pr(>|z|) #> (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05 #> year           0.09883005  0.02295317  4.305725 1.664395e-05"},{"path":"https://msberends.github.io/AMR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Matthijs S. Berends. Author, maintainer. Christian F. Luz. Author, contributor. Dennis Souverein. Author, contributor. Erwin E. . Hassing. Author, contributor. Casper J. Albers. Thesis advisor. Peter Dutey-Magni. Contributor. Judith M. Fonville. Contributor. Alex W. Friedrich. Thesis advisor. Corinna Glasner. Thesis advisor. Eric H. L. C. M. Hazenberg. Contributor. Gwen Knight. Contributor. Annick Lenglet. Contributor. Bart C. Meijer. Contributor. Dmytro Mykhailenko. Contributor. Anton Mymrikov. Contributor. Andrew P. Norgan. Contributor. Sofia Ny. Contributor. Jonas Salm. Contributor. Rogier P. Schade. Contributor. Bhanu N. M. Sinha. Thesis advisor. Anthony Underwood. Contributor. Anita Williams. Contributor.","code":""},{"path":"https://msberends.github.io/AMR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). “AMR: R Package Working Antimicrobial Resistance Data.” Journal Statistical Software, 104(3), 1–31. doi:10.18637/jss.v104.i03.","code":"@Article{,   title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},   author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},   journal = {Journal of Statistical Software},   year = {2022},   volume = {104},   number = {3},   pages = {1--31},   doi = {10.18637/jss.v104.i03}, }"},{"path":"https://msberends.github.io/AMR/index.html","id":"the-amr-package-for-r-","dir":"","previous_headings":"","what":"Antimicrobial Resistance Data Analysis","title":"Antimicrobial Resistance Data Analysis","text":"Generates antibiograms - traditional, combined, syndromic, even WISCA Provides full microbiological taxonomy data antimicrobial drugs Applies recent CLSI EUCAST clinical breakpoints MICs disk zones Corrects duplicate isolates, calculates predicts AMR per antibiotic class Integrates WHONET, ATC, EARS-Net, PubChem, LOINC SNOMED CT Works Windows, macOS Linux versions R since R-3.0 completely dependency-free, highly suitable places limited resources https://msberends.github.io/AMR https://doi.org/10.18637/jss.v104.i03","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Antimicrobial Resistance Data Analysis","text":"AMR package free open-source R package zero dependencies simplify analysis prediction Antimicrobial Resistance (AMR) work microbial antimicrobial data properties, using evidence-based methods. aim provide standard clean reproducible AMR data analysis, can therefore empower epidemiological analyses continuously enable surveillance treatment evaluation setting. Many different researchers around globe continually helping us make successful durable project! work published Journal Statistical Software (Volume 104(3); DOI 10.18637/jss.v104.i03) formed basis two PhD theses (DOI 10.33612/diss.177417131 DOI 10.33612/diss.192486375). installing package, R knows ~52,000 distinct microbial species (updated December 2022) ~600 antibiotic, antimycotic antiviral drugs name code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC SNOMED CT), knows valid SIR MIC values. integral breakpoint guidelines CLSI EUCAST included last 10 years. supports can read data format, including WHONET data. package works Windows, macOS Linux versions R since R-3.0 (April 2013). designed work setting, including limited resources. created routine data analysis academic research Faculty Medical Sciences University Groningen, collaboration non-profit organisations Certe Medical Diagnostics Advice Foundation University Medical Center Groningen.","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"used-in-over-175-countries-translated-into-20-languages","dir":"","previous_headings":"Introduction","what":"Used in over 175 countries, translated into 20 languages","title":"Antimicrobial Resistance Data Analysis","text":"Since first public release early 2018, R package used almost countries world. Click map enlarge see country names. help contributors corners world, AMR package available  English,  Czech,  Chinese,  Danish,  Dutch,  Finnish,  French,  German,  Greek,  Italian,  Japanese,  Norwegian,  Polish,  Portuguese,  Romanian,  Russian,  Spanish,  Swedish,  Turkish,  Ukrainian. Antimicrobial drug (group) names colloquial microorganism names provided languages.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/index.html","id":"filtering-and-selecting-data","dir":"","previous_headings":"Practical examples","what":"Filtering and selecting data","title":"Antimicrobial Resistance Data Analysis","text":"One powerful functions package, aside calculating plotting AMR, selecting filtering based antibiotic columns. can done using -called antibiotic class selectors work base R, dplyr data.table: defined row filter Gram-negative bacteria intrinsic resistance cefotaxime (mo_is_gram_negative() mo_is_intrinsic_resistant()) column selection two antibiotic groups (aminoglycosides() carbapenems()), reference data microorganisms antibiotics AMR package make sure get meant: base R equivalent : base R code work version R since April 2013 (R-3.0). Moreover, code works identically data.table package, starting :","code":"# AMR works great with dplyr, but it's not required or neccesary library(AMR) library(dplyr)  example_isolates %>%   mutate(bacteria = mo_fullname()) %>%   # filtering functions for microorganisms:   filter(mo_is_gram_negative(),          mo_is_intrinsic_resistant(ab = \"cefotax\")) %>%   # antibiotic selectors:   select(bacteria,          aminoglycosides(),          carbapenems()) library(AMR) example_isolates$bacteria <- mo_fullname(example_isolates$mo) example_isolates[which(mo_is_gram_negative() &                          mo_is_intrinsic_resistant(ab = \"cefotax\")),                  c(\"bacteria\", aminoglycosides(), carbapenems())] example_isolates <- data.table::as.data.table(example_isolates)"},{"path":"https://msberends.github.io/AMR/index.html","id":"generating-antibiograms","dir":"","previous_headings":"Practical examples","what":"Generating antibiograms","title":"Antimicrobial Resistance Data Analysis","text":"AMR package supports generating traditional, combined, syndromic, even weighted-incidence syndromic combination antibiograms (WISCA). used inside R Markdown Quarto, table printed right output format automatically (markdown, LaTeX, HTML, etc.). combination antibiograms, clear combined antibiotics yield higher empiric coverage: Like many functions package, antibiogram() comes support 20 languages often detected automatically based system language:","code":"antibiogram(example_isolates,             antibiotics = c(aminoglycosides(), carbapenems())) antibiogram(example_isolates,             antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"),             mo_transform = \"gramstain\") antibiogram(example_isolates,             antibiotics = c(\"cipro\", \"tobra\", \"genta\"), # any arbitrary name or code will work             mo_transform = \"gramstain\",             ab_transform = \"name\",             language = \"uk\") # Ukrainian"},{"path":"https://msberends.github.io/AMR/index.html","id":"calculating-resistance-per-group","dir":"","previous_headings":"Practical examples","what":"Calculating resistance per group","title":"Antimicrobial Resistance Data Analysis","text":"manual approach, can use resistance susceptibility() function: use antibiotic class selectors select series antibiotic columns:","code":"example_isolates %>%   # group by ward:   group_by(ward) %>%   # calculate AMR using resistance() for gentamicin and tobramycin   # and get their 95% confidence intervals using sir_confidence_interval():   summarise(across(c(GEN, TOB),                    list(total_R = resistance,                         conf_int = function(x) sir_confidence_interval(x, collapse = \"-\")))) library(AMR) library(dplyr)  out <- example_isolates %>%   # group by ward:   group_by(ward) %>%   # calculate AMR using resistance(), over all aminoglycosides and polymyxins:   summarise(across(c(aminoglycosides(), polymyxins()),             resistance)) out # transform the antibiotic columns to names: out %>% set_ab_names() # transform the antibiotic column to ATC codes: out %>% set_ab_names(property = \"atc\")"},{"path":"https://msberends.github.io/AMR/index.html","id":"what-else-can-you-do-with-this-package","dir":"","previous_headings":"","what":"What else can you do with this package?","title":"Antimicrobial Resistance Data Analysis","text":"package intended comprehensive toolbox integrated AMR data analysis. package can used : Reference taxonomy microorganisms, since package contains microbial (sub)species List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF) (manual) Interpreting raw MIC disk diffusion values, based CLSI EUCAST guideline last 10 years (manual) Retrieving antimicrobial drug names, doses forms administration clinical health care records (manual) Determining first isolates used AMR data analysis (manual) Calculating antimicrobial resistance (tutorial) Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (tutorial) Calculating (empirical) susceptibility mono therapy combination therapies (tutorial) Predicting future antimicrobial resistance using regression models (tutorial) Getting properties microorganism (like Gram stain, species, genus family) (manual) Getting properties antibiotic (like name, code EARS-Net/ATC/LOINC/PubChem, defined daily dose trade name) (manual) Plotting antimicrobial resistance (tutorial) Applying EUCAST expert rules (manual) Getting SNOMED codes microorganism, getting properties microorganism based SNOMED code (manual) Getting LOINC codes antibiotic, getting properties antibiotic based LOINC code (manual) Machine reading EUCAST CLSI guidelines 2011-2021 translate MIC values disk diffusion diameters SIR (link) Principal component analysis AMR (tutorial)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/index.html","id":"latest-official-version","dir":"","previous_headings":"Get this package","what":"Latest official version","title":"Antimicrobial Resistance Data Analysis","text":"package available official R network (CRAN). Install package R CRAN using command: downloaded installed automatically. RStudio, click menu Tools > Install Packages… type “AMR” press Install. Note: functions website may available latest release. use functions data sets mentioned website, install latest development version.","code":"install.packages(\"AMR\")"},{"path":"https://msberends.github.io/AMR/index.html","id":"latest-development-version","dir":"","previous_headings":"Get this package","what":"Latest development version","title":"Antimicrobial Resistance Data Analysis","text":"Please read Developer Guideline . latest unpublished development version can installed GitHub two ways: Manually, using: Automatically, using rOpenSci R-universe platform, adding R-universe address list repositories (‘repos’): , can install update AMR package like official release (e.g., using install.packages(\"AMR\") RStudio via Tools > Check Package Updates…).","code":"install.packages(\"remotes\") # if you haven't already remotes::install_github(\"msberends/AMR\") options(repos = c(getOption(\"repos\"),                   msberends = \"https://msberends.r-universe.dev\"))"},{"path":"https://msberends.github.io/AMR/index.html","id":"get-started","dir":"","previous_headings":"","what":"Get started","title":"Antimicrobial Resistance Data Analysis","text":"find conduct AMR data analysis, please continue reading get started click link ‘’ menu.","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"partners","dir":"","previous_headings":"","what":"Partners","title":"Antimicrobial Resistance Data Analysis","text":"development package part , related , made possible following non-profit organisations initiatives:","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"copyright","dir":"","previous_headings":"","what":"Copyright","title":"Antimicrobial Resistance Data Analysis","text":"R package free, open-source software licensed GNU General Public License v2.0 (GPL-2). nutshell, means package: May used commercial purposes May used private purposes May used patent purposes May modified, although: Modifications must released license distributing package Changes made code must documented May distributed, although: Source code must made available package distributed copy license copyright notice must included package. Comes LIMITATION liability Comes warranty","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-deprecated.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated Functions — AMR-deprecated","title":"Deprecated Functions — AMR-deprecated","text":"functions -called 'Deprecated'. removed future release. Using functions give warning name function replaced (one).","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-deprecated.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated Functions — AMR-deprecated","text":"","code":"NA_rsi_  as.rsi(x, ...)  facet_rsi(...)  geom_rsi(...)  ggplot_rsi(...)  ggplot_rsi_predict(...)  is.rsi(...)  is.rsi.eligible(...)  labels_rsi_count(...)  n_rsi(...)  random_rsi(...)  rsi_df(...)  rsi_predict(...)  scale_rsi_colours(...)  theme_rsi(...)"},{"path":"https://msberends.github.io/AMR/reference/AMR-deprecated.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deprecated Functions — AMR-deprecated","text":"object class rsi (inherits ordered, factor) length 1.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":null,"dir":"Reference","previous_headings":"","what":"Options for the AMR package — AMR-options","title":"Options for the AMR package — AMR-options","text":"overview package-specific options() can set AMR package.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"options","dir":"Reference","previous_headings":"","what":"Options","title":"Options for the AMR package — AMR-options","text":"AMR_custom_ab  Allows use custom antimicrobial drugs package. explained add_custom_antimicrobials(). AMR_custom_mo  Allows use custom microorganisms package. explained add_custom_microorganisms(). AMR_eucastrules  Used setting default types rules eucast_rules() function, must one : \"breakpoints\", \"expert\", \"\", \"custom\", \"\", defaults c(\"breakpoints\", \"expert\"). AMR_guideline  Used setting default guideline interpreting MIC values disk diffusion diameters .sir(). Can guideline name (e.g., \"CLSI\") name year (e.g. \"CLSI 2019\"). default latest implemented EUCAST guideline, currently \"EUCAST 2022\". Supported guideline currently EUCAST (2013-2022) CLSI (2013-2022). AMR_ignore_pattern  regular expression ignore (.e., make NA) match given .mo() mo_* functions. AMR_include_PKPD  logical use .sir(), indicate PK/PD clinical breakpoints must applied last resort - default TRUE. AMR_include_screening  logical use .sir(), indicate clinical breakpoints screening allowed - default FALSE. AMR_keep_synonyms  logical use .mo() mo_* functions, indicate old, previously valid taxonomic names must preserved corrected currently accepted names. default FALSE. AMR_cleaning_regex  regular expression (case-insensitive) use .mo() mo_* functions, clean user input. default outcome mo_cleaning_regex(), removes texts brackets texts \"species\" \"serovar\". AMR_locale  language use AMR package, can one supported language names ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), Ukrainian (uk). default current system language (supported). AMR_mo_source  file location manual code list used .mo() mo_* functions. explained set_mo_source().","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"saving-settings-between-sessions","dir":"Reference","previous_headings":"","what":"Saving Settings Between Sessions","title":"Options for the AMR package — AMR-options","text":"Settings R saved globally thus lost R exited. can save options .Rprofile file, user-specific file. can edit using:   file, can set options :   add Portuguese language support antibiotics, allow PK/PD rules interpreting MIC values .sir().","code":"utils::file.edit(\"~/.Rprofile\") options(AMR_locale = \"pt\")  options(AMR_include_PKPD = TRUE)"},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"share-options-within-team","dir":"Reference","previous_headings":"","what":"Share Options Within Team","title":"Options for the AMR package — AMR-options","text":"global approach, e.g. within data team, save options file remote file location, shared network drive. work way: Save plain text file e.g. \"X:/team_folder/R_options.R\" fill preferred settings. user, open .Rprofile file using utils::file.edit(\"~/.Rprofile\") put :   Reload R/RStudio check settings getOption(), e.g. getOption(\"AMR_locale\") set value. Now team settings configured one place, can maintained .","code":"source(\"X:/team_folder/R_options.R\")"},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":null,"dir":"Reference","previous_headings":"","what":"The AMR Package — AMR","title":"The AMR Package — AMR","text":"Welcome AMR package. AMR package free open-source R package zero dependencies simplify analysis prediction Antimicrobial Resistance (AMR) work microbial antimicrobial data properties, using evidence-based methods. aim provide standard clean reproducible AMR data analysis, can therefore empower epidemiological analyses continuously enable surveillance treatment evaluation setting. Many different researchers around globe continually helping us make successful durable project! work published Journal Statistical Software (Volume 104(3); doi:jss.v104.i03 ) formed basis two PhD theses (doi:10.33612/diss.177417131  doi:10.33612/diss.192486375 ). installing package, R knows ~52 000 microorganisms (updated December 2022) ~600 antibiotic, antimycotic antiviral drugs name code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC SNOMED CT), knows valid SIR MIC values. integral breakpoint guidelines CLSI EUCAST included last 10 years. supports can read data format, including WHONET data. package works Windows, macOS Linux versions R since R-3.0 (April 2013). designed work setting, including limited resources. created routine data analysis academic research Faculty Medical Sciences University Groningen, collaboration non-profit organisations Certe Medical Diagnostics Advice Foundation University Medical Center Groningen. AMR package available English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, Ukrainian. Antimicrobial drug (group) names colloquial microorganism names provided languages.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"The AMR Package — AMR","text":"cite AMR publications use: Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). \"AMR: R Package Working Antimicrobial Resistance Data.\" Journal Statistical Software, 104(3), 1-31. doi:10.18637/jss.v104.i03 . BibTeX entry LaTeX users :","code":"@Article{,   title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},   author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},   journal = {Journal of Statistical Software},   year = {2022},   volume = {104},   number = {3},   pages = {1--31},   doi = {10.18637/jss.v104.i03}, }"},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"The AMR Package — AMR","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The AMR Package — AMR","text":"Maintainer: Matthijs S. Berends m.berends@certe.nl (ORCID) Authors: Christian F. Luz (ORCID) [contributor] Dennis Souverein (ORCID) [contributor] Erwin E. . Hassing [contributor] contributors: Casper J. Albers (ORCID) [thesis advisor] Peter Dutey-Magni (ORCID) [contributor] Judith M. Fonville [contributor] Alex W. Friedrich (ORCID) [thesis advisor] Corinna Glasner (ORCID) [thesis advisor] Eric H. L. C. M. Hazenberg [contributor] Gwen Knight (ORCID) [contributor] Annick Lenglet (ORCID) [contributor] Bart C. Meijer [contributor] Dmytro Mykhailenko [contributor] Anton Mymrikov [contributor] Andrew P. Norgan (ORCID) [contributor] Sofia Ny (ORCID) [contributor] Jonas Salm [contributor] Rogier P. Schade [contributor] Bhanu N. M. Sinha (ORCID) [thesis advisor] Anthony Underwood (ORCID) [contributor] Anita Williams (ORCID) [contributor]","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":null,"dir":"Reference","previous_headings":"","what":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"antimicrobial drugs official names, ATC codes, ATC groups defined daily dose (DDD) included package, using Collaborating Centre Drug Statistics Methodology.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"","code":"as.ab(\"meropenem\") #> Class 'ab' #> [1] MEM ab_name(\"J01DH02\") #> [1] \"Meropenem\"  ab_tradenames(\"flucloxacillin\") #>  [1] \"culpen\"               \"floxacillin\"          \"floxacillin sodium\"   #>  [4] \"floxapen\"             \"floxapen sodium salt\" \"fluclox\"              #>  [7] \"flucloxacilina\"       \"flucloxacillin\"       \"flucloxacilline\"      #> [10] \"flucloxacillinum\"     \"fluorochloroxacillin\" \"staphylex\""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 500 Isolates - WHONET Example — WHONET","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"example data set exact structure export file WHONET. files can used package, example data set shows. antibiotic results example_isolates data set. patient names created using online surname generators place practice purposes.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"","code":"WHONET"},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"tibble 500 observations 53 variables: Identification number ID sample Specimen number ID specimen Organism Name microorganism. analysis, transform valid microbial class, using .mo(). Country Country origin Laboratory Name laboratory Last name Fictitious last name patient First name Fictitious initial patient Sex Fictitious gender patient Age Fictitious age patient Age category Age group, can also looked using age_groups() Date admissionDate hospital admission Specimen dateDate specimen received laboratory Specimen type Specimen type group Specimen type (Numeric) Translation \"Specimen type\" Reason Reason request Differential Diagnosis Isolate number ID isolate Organism type Type microorganism, can also looked using mo_type() Serotype Serotype microorganism Beta-lactamase Microorganism produces beta-lactamase? ESBL Microorganism produces extended spectrum beta-lactamase? Carbapenemase Microorganism produces carbapenemase? MRSA screening test Microorganism possible MRSA? Inducible clindamycin resistance Clindamycin can induced? Comment comments Date data entryDate data entered WHONET AMP_ND10:CIP_EE 28 different antibiotics. can lookup abbreviations antibiotics data set, use e.g. ab_name(\"AMP\") get official name immediately. analysis, transform valid antibiotic class, using .sir().","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"","code":"WHONET #> # A tibble: 500 × 53 #>    `Identification number` `Specimen number` Organism Country         Laboratory #>    <chr>                               <int> <chr>    <chr>           <chr>      #>  1 fe41d7bafa                           1748 SPN      Belgium         National … #>  2 91f175ec37                           1767 eco      The Netherlands National … #>  3 cc4015056e                           1343 eco      The Netherlands National … #>  4 e864b692f5                           1894 MAP      Denmark         National … #>  5 3d051fe345                           1739 PVU      Belgium         National … #>  6 c80762a08d                           1846 103      The Netherlands National … #>  7 8022d3727c                           1628 103      Denmark         National … #>  8 f3dc5f553d                           1493 eco      The Netherlands National … #>  9 15add38f6c                           1847 eco      France          National … #> 10 fd41248def                           1458 eco      Germany         National … #> # ℹ 490 more rows #> # ℹ 48 more variables: `Last name` <chr>, `First name` <chr>, Sex <chr>, #> #   Age <dbl>, `Age category` <chr>, `Date of admission` <date>, #> #   `Specimen date` <date>, `Specimen type` <chr>, #> #   `Specimen type (Numeric)` <dbl>, Reason <chr>, `Isolate number` <int>, #> #   `Organism type` <chr>, Serotype <chr>, `Beta-lactamase` <lgl>, ESBL <lgl>, #> #   Carbapenemase <lgl>, `MRSA screening test` <lgl>, …"},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"Use function e.g. clinical texts health care records. returns list antimicrobial drugs, doses forms administration found texts.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"","code":"ab_from_text(   text,   type = c(\"drug\", \"dose\", \"administration\"),   collapse = NULL,   translate_ab = FALSE,   thorough_search = NULL,   info = interactive(),   ... )"},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"text text analyse type type property search , either \"drug\", \"dose\" \"administration\", see Examples collapse character pass paste(, collapse = ...) return one character per element text, see Examples translate_ab type = \"drug\": column name antibiotics data set translate antibiotic abbreviations , using ab_property(). default FALSE. Using TRUE equal using \"name\". thorough_search logical indicate whether input must extensively searched misspelling faulty input values. Setting TRUE take considerably time using FALSE. default, turn TRUE input elements contain maximum three words. info logical indicate whether progress bar printed - default TRUE interactive mode ... arguments passed .ab()","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"list,  character collapse NULL","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"function also internally used .ab(), although searches first drug name throw note drug names returned. Note: .ab() function may use long regular expression match brand names antimicrobial drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"argument-type","dir":"Reference","previous_headings":"","what":"Argument type","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"default, function search antimicrobial drug names. text elements searched official names, ATC codes brand names. uses .ab() internally, correct misspelling. type = \"dose\" (similar, like \"dosing\", \"doses\"), text elements searched numeric values higher 100 resemble years. output numeric. supports unit (g, mg, IE, etc.) multiple values one clinical text, see Examples. type = \"administration\" (abbreviations, like \"admin\", \"adm\"), text elements searched form drug administration. supports following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal vaginal. Abbreviations oral ('po', 'per os') become \"oral\", values intravenous ('iv', 'intraven') become \"iv\". supports multiple values one clinical text, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"argument-collapse","dir":"Reference","previous_headings":"","what":"Argument collapse","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"Without using collapse, function return list. can convenient use e.g. inside mutate()):df %>% mutate(abx = ab_from_text(clinical_text)) returned AB codes can transformed official names, groups, etc. ab_* functions ab_name() ab_group(), using translate_ab argument. using collapse, function return character:df %>% mutate(abx = ab_from_text(clinical_text, collapse = \"|\"))","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"","code":"# mind the bad spelling of amoxicillin in this line, # straight from a true health care record: ab_from_text(\"28/03/2020 regular amoxicilliin 500mg po tid\") #> [[1]] #> Class 'ab' #> [1] AMX #>   ab_from_text(\"500 mg amoxi po and 400mg cipro iv\") #> [[1]] #> Class 'ab' #> [1] AMX CIP #>  ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", type = \"dose\") #> [[1]] #> [1] 500 400 #>  ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", type = \"admin\") #> [[1]] #> [1] \"oral\" \"iv\"   #>   ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", collapse = \", \") #> [1] \"AMX, CIP\" # \\donttest{ # if you want to know which antibiotic groups were administered, do e.g.: abx <- ab_from_text(\"500 mg amoxi po and 400mg cipro iv\") ab_group(abx[[1]]) #> [1] \"Beta-lactams/penicillins\" \"Quinolones\"                if (require(\"dplyr\")) {   tibble(clinical_text = c(     \"given 400mg cipro and 500 mg amox\",     \"started on doxy iv today\"   )) %>%     mutate(       abx_codes = ab_from_text(clinical_text),       abx_doses = ab_from_text(clinical_text, type = \"doses\"),       abx_admin = ab_from_text(clinical_text, type = \"admin\"),       abx_coll = ab_from_text(clinical_text, collapse = \"|\"),       abx_coll_names = ab_from_text(clinical_text,         collapse = \"|\",         translate_ab = \"name\"       ),       abx_coll_doses = ab_from_text(clinical_text,         type = \"doses\",         collapse = \"|\"       ),       abx_coll_admin = ab_from_text(clinical_text,         type = \"admin\",         collapse = \"|\"       )     ) } #> Loading required package: dplyr #>  #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union #> # A tibble: 2 × 8 #>   clinical_text            abx_codes abx_doses abx_admin abx_coll abx_coll_names #>   <chr>                    <list>    <list>    <list>    <chr>    <chr>          #> 1 given 400mg cipro and 5… <ab [2]>  <dbl [2]> <chr [1]> CIP|AMX  Ciprofloxacin… #> 2 started on doxy iv today <ab [1]>  <dbl [1]> <chr [1]> DOX      Doxycycline    #> # ℹ 2 more variables: abx_coll_doses <chr>, abx_coll_admin <chr> # }"},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Properties of an Antibiotic — ab_property","title":"Get Properties of an Antibiotic — ab_property","text":"Use functions return specific property antibiotic antibiotics data set. input values evaluated internally .ab().","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Properties of an Antibiotic — ab_property","text":"","code":"ab_name(x, language = get_AMR_locale(), tolower = FALSE, ...)  ab_cid(x, ...)  ab_synonyms(x, ...)  ab_tradenames(x, ...)  ab_group(x, language = get_AMR_locale(), ...)  ab_atc(x, only_first = FALSE, ...)  ab_atc_group1(x, language = get_AMR_locale(), ...)  ab_atc_group2(x, language = get_AMR_locale(), ...)  ab_loinc(x, ...)  ab_ddd(x, administration = \"oral\", ...)  ab_ddd_units(x, administration = \"oral\", ...)  ab_info(x, language = get_AMR_locale(), ...)  ab_url(x, open = FALSE, ...)  ab_property(x, property = \"name\", language = get_AMR_locale(), ...)  set_ab_names(   data,   ...,   property = \"name\",   language = get_AMR_locale(),   snake_case = NULL )"},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Properties of an Antibiotic — ab_property","text":"x (vector ) text can coerced valid antibiotic drug code .ab() language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. tolower logical indicate whether first character every output transformed lower case character. lead e.g. \"polymyxin B\" \"polymyxin b\". ... case set_ab_names() data data.frame: columns select (supports tidy selection column1:column4), otherwise arguments passed .ab() only_first logical indicate whether first ATC code must returned, giving preference J0-codes (.e., antimicrobial drug group) administration way administration, either \"oral\" \"iv\" open browse URL using utils::browseURL() property one column names one antibiotics data set: vector_or(colnames(antibiotics), sort = FALSE). data data.frame columns need renamed, character vector column names snake_case logical indicate whether names -called snake case: lower case spaces/slashes replaced underscore (_)","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Properties of an Antibiotic — ab_property","text":"integer case ab_cid() named list case ab_info() multiple ab_atc()/ab_synonyms()/ab_tradenames() double case ab_ddd() data.frame case set_ab_names() character cases","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Properties of an Antibiotic — ab_property","text":"output translated possible. function ab_url() return direct URL official website. warning returned required ATC code available. function set_ab_names() special column renaming function data.frames. renames columns names resemble antimicrobial drugs. always makes sure new column names unique. property = \"atc\" set, preference given ATC codes J-group.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Properties of an Antibiotic — ab_property","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Get Properties of an Antibiotic — ab_property","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Properties of an Antibiotic — ab_property","text":"","code":"# all properties: ab_name(\"AMX\") #> [1] \"Amoxicillin\" ab_atc(\"AMX\") #> [1] \"J01CA04\" ab_cid(\"AMX\") #> [1] 33613 ab_synonyms(\"AMX\") #>  [1] \"actimoxi\"            \"amoclen\"             \"amolin\"              #>  [4] \"amopen\"              \"amopenixin\"          \"amoxibiotic\"         #>  [7] \"amoxicaps\"           \"amoxicilina\"         \"amoxicillin\"         #> [10] \"amoxicillin hydrate\" \"amoxicilline\"        \"amoxicillinum\"       #> [13] \"amoxiden\"            \"amoxil\"              \"amoxivet\"            #> [16] \"amoxy\"               \"amoxycillin\"         \"amoxyke\"             #> [19] \"anemolin\"            \"aspenil\"             \"atoksilin\"           #> [22] \"biomox\"              \"bristamox\"           \"cemoxin\"             #> [25] \"clamoxyl\"            \"damoxy\"              \"delacillin\"          #> [28] \"demoksil\"            \"dispermox\"           \"efpenix\"             #> [31] \"flemoxin\"            \"hiconcil\"            \"histocillin\"         #> [34] \"hydroxyampicillin\"   \"ibiamox\"             \"imacillin\"           #> [37] \"lamoxy\"              \"largopen\"            \"metafarma capsules\"  #> [40] \"metifarma capsules\"  \"moksilin\"            \"moxacin\"             #> [43] \"moxatag\"             \"ospamox\"             \"pamoxicillin\"        #> [46] \"piramox\"             \"promoxil\"            \"remoxil\"             #> [49] \"robamox\"             \"sawamox pm\"          \"tolodina\"            #> [52] \"topramoxin\"          \"unicillin\"           \"utimox\"              #> [55] \"vetramox\"            ab_tradenames(\"AMX\") #>  [1] \"actimoxi\"            \"amoclen\"             \"amolin\"              #>  [4] \"amopen\"              \"amopenixin\"          \"amoxibiotic\"         #>  [7] \"amoxicaps\"           \"amoxicilina\"         \"amoxicillin\"         #> [10] \"amoxicillin hydrate\" \"amoxicilline\"        \"amoxicillinum\"       #> [13] \"amoxiden\"            \"amoxil\"              \"amoxivet\"            #> [16] \"amoxy\"               \"amoxycillin\"         \"amoxyke\"             #> [19] \"anemolin\"            \"aspenil\"             \"atoksilin\"           #> [22] \"biomox\"              \"bristamox\"           \"cemoxin\"             #> [25] \"clamoxyl\"            \"damoxy\"              \"delacillin\"          #> [28] \"demoksil\"            \"dispermox\"           \"efpenix\"             #> [31] \"flemoxin\"            \"hiconcil\"            \"histocillin\"         #> [34] \"hydroxyampicillin\"   \"ibiamox\"             \"imacillin\"           #> [37] \"lamoxy\"              \"largopen\"            \"metafarma capsules\"  #> [40] \"metifarma capsules\"  \"moksilin\"            \"moxacin\"             #> [43] \"moxatag\"             \"ospamox\"             \"pamoxicillin\"        #> [46] \"piramox\"             \"promoxil\"            \"remoxil\"             #> [49] \"robamox\"             \"sawamox pm\"          \"tolodina\"            #> [52] \"topramoxin\"          \"unicillin\"           \"utimox\"              #> [55] \"vetramox\"            ab_group(\"AMX\") #> [1] \"Beta-lactams/penicillins\" ab_atc_group1(\"AMX\") #> [1] \"Beta-lactam antibacterials, penicillins\" ab_atc_group2(\"AMX\") #> [1] \"Penicillins with extended spectrum\" ab_url(\"AMX\") #>                                                           Amoxicillin  #> \"https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no\"   # smart lowercase tranformation ab_name(x = c(\"AMC\", \"PLB\")) #> [1] \"Amoxicillin/clavulanic acid\" \"Polymyxin B\"                 ab_name(x = c(\"AMC\", \"PLB\"), tolower = TRUE) #> [1] \"amoxicillin/clavulanic acid\" \"polymyxin B\"                  # defined daily doses (DDD) ab_ddd(\"AMX\", \"oral\") #> [1] 1.5 ab_ddd_units(\"AMX\", \"oral\") #> [1] \"g\" ab_ddd(\"AMX\", \"iv\") #> [1] 3 ab_ddd_units(\"AMX\", \"iv\") #> [1] \"g\"  ab_info(\"AMX\") # all properties as a list #> $ab #> [1] \"AMX\" #>  #> $cid #> [1] 33613 #>  #> $name #> [1] \"Amoxicillin\" #>  #> $group #> [1] \"Beta-lactams/penicillins\" #>  #> $atc #> [1] \"J01CA04\" #>  #> $atc_group1 #> [1] \"Beta-lactam antibacterials, penicillins\" #>  #> $atc_group2 #> [1] \"Penicillins with extended spectrum\" #>  #> $tradenames #>  [1] \"actimoxi\"            \"amoclen\"             \"amolin\"              #>  [4] \"amopen\"              \"amopenixin\"          \"amoxibiotic\"         #>  [7] \"amoxicaps\"           \"amoxicilina\"         \"amoxicillin\"         #> [10] \"amoxicillin hydrate\" \"amoxicilline\"        \"amoxicillinum\"       #> [13] \"amoxiden\"            \"amoxil\"              \"amoxivet\"            #> [16] \"amoxy\"               \"amoxycillin\"         \"amoxyke\"             #> [19] \"anemolin\"            \"aspenil\"             \"atoksilin\"           #> [22] \"biomox\"              \"bristamox\"           \"cemoxin\"             #> [25] \"clamoxyl\"            \"damoxy\"              \"delacillin\"          #> [28] \"demoksil\"            \"dispermox\"           \"efpenix\"             #> [31] \"flemoxin\"            \"hiconcil\"            \"histocillin\"         #> [34] \"hydroxyampicillin\"   \"ibiamox\"             \"imacillin\"           #> [37] \"lamoxy\"              \"largopen\"            \"metafarma capsules\"  #> [40] \"metifarma capsules\"  \"moksilin\"            \"moxacin\"             #> [43] \"moxatag\"             \"ospamox\"             \"pamoxicillin\"        #> [46] \"piramox\"             \"promoxil\"            \"remoxil\"             #> [49] \"robamox\"             \"sawamox pm\"          \"tolodina\"            #> [52] \"topramoxin\"          \"unicillin\"           \"utimox\"              #> [55] \"vetramox\"            #>  #> $loinc #> [1] \"16365-9\" \"25274-2\" \"3344-9\"  \"80133-2\" #>  #> $ddd #> $ddd$oral #> $ddd$oral$amount #> [1] 1.5 #>  #> $ddd$oral$units #> [1] \"g\" #>  #>  #> $ddd$iv #> $ddd$iv$amount #> [1] 3 #>  #> $ddd$iv$units #> [1] \"g\" #>  #>  #>   # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any': ab_atc(\"AMP\") #> [1] \"J01CA01\" \"S01AA19\" ab_group(\"J01CA01\") #> [1] \"Beta-lactams/penicillins\" ab_loinc(\"ampicillin\") #> [1] \"21066-6\" \"3355-5\"  \"33562-0\" \"33919-2\" \"43883-8\" \"43884-6\" \"87604-5\" ab_name(\"21066-6\") #> [1] \"Ampicillin\" ab_name(6249) #> [1] \"Ampicillin\" ab_name(\"J01CA01\") #> [1] \"Ampicillin\"  # spelling from different languages and dyslexia are no problem ab_atc(\"ceftriaxon\") #> [1] \"J01DD04\" ab_atc(\"cephtriaxone\") #> [1] \"J01DD04\" ab_atc(\"cephthriaxone\") #> [1] \"J01DD04\" ab_atc(\"seephthriaaksone\") #> [1] \"J01DD04\"  # use set_ab_names() for renaming columns colnames(example_isolates) #>  [1] \"date\"    \"patient\" \"age\"     \"gender\"  \"ward\"    \"mo\"      \"PEN\"     #>  [8] \"OXA\"     \"FLC\"     \"AMX\"     \"AMC\"     \"AMP\"     \"TZP\"     \"CZO\"     #> [15] \"FEP\"     \"CXM\"     \"FOX\"     \"CTX\"     \"CAZ\"     \"CRO\"     \"GEN\"     #> [22] \"TOB\"     \"AMK\"     \"KAN\"     \"TMP\"     \"SXT\"     \"NIT\"     \"FOS\"     #> [29] \"LNZ\"     \"CIP\"     \"MFX\"     \"VAN\"     \"TEC\"     \"TCY\"     \"TGC\"     #> [36] \"DOX\"     \"ERY\"     \"CLI\"     \"AZM\"     \"IPM\"     \"MEM\"     \"MTR\"     #> [43] \"CHL\"     \"COL\"     \"MUP\"     \"RIF\"     colnames(set_ab_names(example_isolates)) #>  [1] \"date\"                          \"patient\"                       #>  [3] \"age\"                           \"gender\"                        #>  [5] \"ward\"                          \"mo\"                            #>  [7] \"benzylpenicillin\"              \"oxacillin\"                     #>  [9] \"flucloxacillin\"                \"amoxicillin\"                   #> [11] \"amoxicillin_clavulanic_acid\"   \"ampicillin\"                    #> [13] \"piperacillin_tazobactam\"       \"cefazolin\"                     #> [15] \"cefepime\"                      \"cefuroxime\"                    #> [17] \"cefoxitin\"                     \"cefotaxime\"                    #> [19] \"ceftazidime\"                   \"ceftriaxone\"                   #> [21] \"gentamicin\"                    \"tobramycin\"                    #> [23] \"amikacin\"                      \"kanamycin\"                     #> [25] \"trimethoprim\"                  \"trimethoprim_sulfamethoxazole\" #> [27] \"nitrofurantoin\"                \"fosfomycin\"                    #> [29] \"linezolid\"                     \"ciprofloxacin\"                 #> [31] \"moxifloxacin\"                  \"vancomycin\"                    #> [33] \"teicoplanin\"                   \"tetracycline\"                  #> [35] \"tigecycline\"                   \"doxycycline\"                   #> [37] \"erythromycin\"                  \"clindamycin\"                   #> [39] \"azithromycin\"                  \"imipenem\"                      #> [41] \"meropenem\"                     \"metronidazole\"                 #> [43] \"chloramphenicol\"               \"colistin\"                      #> [45] \"mupirocin\"                     \"rifampicin\"                    colnames(set_ab_names(example_isolates, NIT:VAN)) #>  [1] \"date\"           \"patient\"        \"age\"            \"gender\"         #>  [5] \"ward\"           \"mo\"             \"PEN\"            \"OXA\"            #>  [9] \"FLC\"            \"AMX\"            \"AMC\"            \"AMP\"            #> [13] \"TZP\"            \"CZO\"            \"FEP\"            \"CXM\"            #> [17] \"FOX\"            \"CTX\"            \"CAZ\"            \"CRO\"            #> [21] \"GEN\"            \"TOB\"            \"AMK\"            \"KAN\"            #> [25] \"TMP\"            \"SXT\"            \"nitrofurantoin\" \"fosfomycin\"     #> [29] \"linezolid\"      \"ciprofloxacin\"  \"moxifloxacin\"   \"vancomycin\"     #> [33] \"TEC\"            \"TCY\"            \"TGC\"            \"DOX\"            #> [37] \"ERY\"            \"CLI\"            \"AZM\"            \"IPM\"            #> [41] \"MEM\"            \"MTR\"            \"CHL\"            \"COL\"            #> [45] \"MUP\"            \"RIF\"            # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     set_ab_names()    # this does the same:   example_isolates %>%     rename_with(set_ab_names)    # set_ab_names() works with any AB property:   example_isolates %>%     set_ab_names(property = \"atc\")    example_isolates %>%     set_ab_names(where(is.sir)) %>%     colnames()    example_isolates %>%     set_ab_names(NIT:VAN) %>%     colnames() } #>  [1] \"date\"           \"patient\"        \"age\"            \"gender\"         #>  [5] \"ward\"           \"mo\"             \"PEN\"            \"OXA\"            #>  [9] \"FLC\"            \"AMX\"            \"AMC\"            \"AMP\"            #> [13] \"TZP\"            \"CZO\"            \"FEP\"            \"CXM\"            #> [17] \"FOX\"            \"CTX\"            \"CAZ\"            \"CRO\"            #> [21] \"GEN\"            \"TOB\"            \"AMK\"            \"KAN\"            #> [25] \"TMP\"            \"SXT\"            \"nitrofurantoin\" \"fosfomycin\"     #> [29] \"linezolid\"      \"ciprofloxacin\"  \"moxifloxacin\"   \"vancomycin\"     #> [33] \"TEC\"            \"TCY\"            \"TGC\"            \"DOX\"            #> [37] \"ERY\"            \"CLI\"            \"AZM\"            \"IPM\"            #> [41] \"MEM\"            \"MTR\"            \"CHL\"            \"COL\"            #> [45] \"MUP\"            \"RIF\"            # }"},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Custom Antimicrobials — add_custom_antimicrobials","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"add_custom_antimicrobials() can add custom antimicrobial drug names codes.","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"","code":"add_custom_antimicrobials(x)  clear_custom_antimicrobials()"},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"x data.frame resembling antibiotics data set, least containing columns \"ab\" \"name\"","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"Important: Due R works, add_custom_antimicrobials() function run every R session - added antimicrobials stored sessions thus lost R exited. two ways circumvent automate process adding antimicrobials: Method 1: Using package option AMR_custom_ab, preferred method. use method: Create data set structure antibiotics data set (containing least columns \"ab\" \"name\") save saveRDS() location choice, e.g. \"~/my_custom_ab.rds\", remote location. Set file location package option AMR_custom_ab: options(AMR_custom_ab = \"~/my_custom_ab.rds\"). can even remote file location, https URL. Since options saved R sessions, best save option .Rprofile file loaded start-R. , open .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"), add text save file:   Upon package load, file loaded run add_custom_antimicrobials() function. Method 2: Loading antimicrobial additions directly .Rprofile file. Note definitions stored user-specific R file, suboptimal workflow. use method: Edit .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"). Add text like save file:   Use clear_custom_antimicrobials() clear previously added antimicrobials.","code":"# Add custom antimicrobial codes: options(AMR_custom_ab = \"~/my_custom_ab.rds\") # Add custom antibiotic drug codes:  AMR::add_custom_antimicrobials(    data.frame(ab = \"TESTAB\",               name = \"Test Antibiotic\",               group = \"Test Group\")  )"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"","code":"# \\donttest{  # returns NA and throws a warning (which is suppressed here): suppressWarnings(   as.ab(\"testab\") ) #> Class 'ab' #> [1] <NA>  # now add a custom entry - it will be considered by as.ab() and # all ab_*() functions add_custom_antimicrobials(   data.frame(     ab = \"TESTAB\",     name = \"Test Antibiotic\",     # you can add any property present in the     # 'antibiotics' data set, such as 'group':     group = \"Test Group\"   ) ) #> ℹ Added one record to the internal antibiotics data set.  # \"testab\" is now a new antibiotic: as.ab(\"testab\") #> Class 'ab' #> [1] TESTAB ab_name(\"testab\") #> [1] \"Test Antibiotic\" ab_group(\"testab\") #> [1] \"Test Group\"  ab_info(\"testab\") #> $ab #> [1] \"TESTAB\" #>  #> $cid #> [1] NA #>  #> $name #> [1] \"Test Antibiotic\" #>  #> $group #> [1] \"Test Group\" #>  #> $atc #> [1] NA #>  #> $atc_group1 #> [1] NA #>  #> $atc_group2 #> [1] NA #>  #> $tradenames #> [1] NA #>  #> $loinc #> [1] NA #>  #> $ddd #> $ddd$oral #> $ddd$oral$amount #> [1] NA #>  #> $ddd$oral$units #> [1] NA #>  #>  #> $ddd$iv #> $ddd$iv$amount #> [1] NA #>  #> $ddd$iv$units #> [1] NA #>  #>  #>    # Add Co-fluampicil, which is one of the many J01CR50 codes, see # https://www.whocc.no/ddd/list_of_ddds_combined_products/ add_custom_antimicrobials(   data.frame(     ab = \"COFLU\",     name = \"Co-fluampicil\",     atc = \"J01CR50\",     group = \"Beta-lactams/penicillins\"   ) ) #> ℹ Added one record to the internal antibiotics data set. ab_atc(\"Co-fluampicil\") #> [1] \"J01CR50\" ab_name(\"J01CR50\") #> [1] \"Co-fluampicil\"  # even antibiotic selectors work x <- data.frame(   random_column = \"some value\",   coflu = as.sir(\"S\"),   ampicillin = as.sir(\"R\") ) x #>   random_column coflu ampicillin #> 1    some value     S          R x[, betalactams()] #> ℹ For betalactams() using columns 'coflu' (co-fluampicil) and #>   'ampicillin' #>   coflu ampicillin #> 1     S          R # }"},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Custom Microorganisms — add_custom_microorganisms","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"add_custom_microorganisms() can add custom microorganisms, non-taxonomic outcome laboratory analysis.","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"","code":"add_custom_microorganisms(x)  clear_custom_microorganisms()"},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"x data.frame resembling microorganisms data set, least containing column \"genus\" (case-insensitive)","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"function fill missing taxonomy , specific taxonomic columns missing, see Examples. Important: Due R works, add_custom_microorganisms() function run every R session - added microorganisms stored sessions thus lost R exited. two ways circumvent automate process adding microorganisms: Method 1: Using package option AMR_custom_mo, preferred method. use method: Create data set structure microorganisms data set (containing least column \"genus\") save saveRDS() location choice, e.g. \"~/my_custom_mo.rds\", remote location. Set file location package option AMR_custom_mo: options(AMR_custom_mo = \"~/my_custom_mo.rds\"). can even remote file location, https URL. Since options saved R sessions, best save option .Rprofile file loaded start-R. , open .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"), add text save file:   Upon package load, file loaded run add_custom_microorganisms() function. Method 2: Loading microorganism directly .Rprofile file. Note definitions stored user-specific R file, suboptimal workflow. use method: Edit .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"). Add text like save file:   Use clear_custom_microorganisms() clear previously added microorganisms.","code":"# Add custom microorganism codes: options(AMR_custom_mo = \"~/my_custom_mo.rds\") # Add custom antibiotic drug codes:  AMR::add_custom_microorganisms(    data.frame(genus = \"Enterobacter\",               species = \"asburiae/cloacae\")  )"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"","code":"# \\donttest{ # a combination of species is not formal taxonomy, so # this will result in only \"Enterobacter asburiae\": mo_name(\"Enterobacter asburiae/cloacae\") #> [1] \"Enterobacter asburiae\"  # now add a custom entry - it will be considered by as.mo() and # all mo_*() functions add_custom_microorganisms(   data.frame(     genus = \"Enterobacter\",     species = \"asburiae/cloacae\"   ) ) #> ℹ Added Enterobacter asburiae/cloacae to the internal microorganisms data #>   set.  # E. asburiae/cloacae is now a new microorganism: mo_name(\"Enterobacter asburiae/cloacae\") #> [1] \"Enterobacter asburiae/cloacae\"  # its code: as.mo(\"Enterobacter asburiae/cloacae\") #> Class 'mo' #> [1] CUSTOM1_ENTRBC_A_C  # all internal algorithms will work as well: mo_name(\"Ent asburia cloacae\") #> [1] \"Enterobacter asburiae/cloacae\"  # and even the taxonomy was added based on the genus! mo_family(\"E. asburiae/cloacae\") #> [1] \"Enterobacteriaceae\" mo_gramstain(\"Enterobacter asburiae/cloacae\") #> [1] \"Gram-negative\"  mo_info(\"Enterobacter asburiae/cloacae\") #> $mo #> [1] \"CUSTOM1_ENTRBC_A_C\" #>  #> $kingdom #> [1] \"Bacteria\" #>  #> $phylum #> [1] \"Pseudomonadota\" #>  #> $class #> [1] \"Gammaproteobacteria\" #>  #> $order #> [1] \"Enterobacterales\" #>  #> $family #> [1] \"Enterobacteriaceae\" #>  #> $genus #> [1] \"Enterobacter\" #>  #> $species #> [1] \"asburiae/cloacae\" #>  #> $subspecies #> [1] \"\" #>  #> $status #> [1] \"accepted\" #>  #> $synonyms #> NULL #>  #> $gramstain #> [1] \"Gram-negative\" #>  #> $url #> [1] \"\" #>  #> $ref #> [1] \"Self-added, 2023\" #>  #> $snomed #> [1] NA #>    # the function tries to be forgiving: add_custom_microorganisms(   data.frame(     GENUS = \"BACTEROIDES / PARABACTEROIDES SLASHLINE\",     SPECIES = \"SPECIES\"   ) ) #> ℹ Added Bacteroides/Parabacteroides to the internal microorganisms data #>   set. mo_name(\"BACTEROIDES / PARABACTEROIDES\") #> [1] \"Bacteroides/Parabacteroides\" mo_rank(\"BACTEROIDES / PARABACTEROIDES\") #> [1] \"genus\"  # taxonomy still works, although a slashline genus was given as input: mo_family(\"Bacteroides/Parabacteroides\") #> [1] \"Bacteroidaceae\"   # for groups and complexes, set them as species or subspecies: add_custom_microorganisms(   data.frame(     genus = \"Citrobacter\",     species = c(\"freundii\", \"braakii complex\"),     subspecies = c(\"complex\", \"\")   ) ) #> ℹ Added Citrobacter braakii complex and Citrobacter freundii complex to the #>   internal microorganisms data set. mo_name(c(\"C. freundii complex\", \"C. braakii complex\")) #> [1] \"Citrobacter freundii complex\" \"Citrobacter braakii complex\"  mo_species(c(\"C. freundii complex\", \"C. braakii complex\")) #> [1] \"freundii complex\" \"braakii complex\"  mo_gramstain(c(\"C. freundii complex\", \"C. braakii complex\")) #> [1] \"Gram-negative\" \"Gram-negative\" # }"},{"path":"https://msberends.github.io/AMR/reference/age.html","id":null,"dir":"Reference","previous_headings":"","what":"Age in Years of Individuals — age","title":"Age in Years of Individuals — age","text":"Calculates age years based reference date, system date default.","code":""},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Age in Years of Individuals — age","text":"","code":"age(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...)"},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Age in Years of Individuals — age","text":"x date(s), character (vectors) coerced .POSIXlt() reference reference date(s) (default today), character (vectors) coerced .POSIXlt() exact logical indicate whether age calculation exact, .e. decimals. divides number days year--date (YTD) x number days year reference (either 365 366). na.rm logical indicate whether missing values removed ... arguments passed .POSIXlt(), origin","code":""},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Age in Years of Individuals — age","text":"integer (decimals) exact = FALSE, double (decimals) otherwise","code":""},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Age in Years of Individuals — age","text":"Ages 0 returned NA warning. Ages 120 give warning. function vectorises x reference, meaning either can length 1 argument larger length.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Age in Years of Individuals — age","text":"","code":"# 10 random pre-Y2K birth dates df <- data.frame(birth_date = as.Date(\"2000-01-01\") - runif(10) * 25000)  # add ages df$age <- age(df$birth_date)  # add exact ages df$age_exact <- age(df$birth_date, exact = TRUE)  # add age at millenium switch df$age_at_y2k <- age(df$birth_date, \"2000-01-01\")  df #>    birth_date age age_exact age_at_y2k #> 1  1981-06-07  41  41.91781         18 #> 2  1959-05-16  63  63.97808         40 #> 3  1944-01-22  79  79.29041         55 #> 4  1931-09-03  91  91.67671         68 #> 5  1976-01-01  47  47.34795         24 #> 6  1975-04-23  48  48.04110         24 #> 7  1935-01-20  88  88.29589         64 #> 8  1968-07-18  54  54.80548         31 #> 9  1970-12-26  52  52.36438         29 #> 10 1994-02-26  29  29.19452          5"},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Split Ages into Age Groups — age_groups","title":"Split Ages into Age Groups — age_groups","text":"Split ages age groups defined split argument. allows easier demographic (antimicrobial resistance) analysis.","code":""},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split Ages into Age Groups — age_groups","text":"","code":"age_groups(x, split_at = c(12, 25, 55, 75), na.rm = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split Ages into Age Groups — age_groups","text":"x age, e.g. calculated age() split_at values split x - default age groups 0-11, 12-24, 25-54, 55-74 75+. See Details. na.rm logical indicate whether missing values removed","code":""},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split Ages into Age Groups — age_groups","text":"Ordered factor","code":""},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split Ages into Age Groups — age_groups","text":"split ages, input split_at argument can : numeric vector. value e.g. c(10, 20) split x 0-9, 10-19 20+. value 50 split x 0-49 50+. default split young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) elderly (75+). character: \"children\" \"kids\", equivalent : c(0, 1, 2, 4, 6, 13, 18). split 0, 1, 2-3, 4-5, 6-12, 13-17 18+. \"elderly\" \"seniors\", equivalent : c(65, 75, 85). split 0-64, 65-74, 75-84, 85+. \"fives\", equivalent : 1:20 * 5. split 0-4, 5-9, ..., 95-99, 100+. \"tens\", equivalent : 1:10 * 10. split 0-9, 10-19, ..., 90-99, 100+.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split Ages into Age Groups — age_groups","text":"","code":"ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)  # split into 0-49 and 50+ age_groups(ages, 50) #> [1] 0-49 0-49 0-49 50+  0-49 50+  50+  0-49 0-49 #> Levels: 0-49 < 50+  # split into 0-19, 20-49 and 50+ age_groups(ages, c(20, 50)) #> [1] 0-19  0-19  0-19  50+   20-49 50+   50+   20-49 20-49 #> Levels: 0-19 < 20-49 < 50+  # split into groups of ten years age_groups(ages, 1:10 * 10) #> [1] 0-9   0-9   10-19 50-59 30-39 70-79 100+  40-49 20-29 #> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+ age_groups(ages, split_at = \"tens\") #> [1] 0-9   0-9   10-19 50-59 30-39 70-79 100+  40-49 20-29 #> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+  # split into groups of five years age_groups(ages, 1:20 * 5) #> [1] 0-4   5-9   15-19 50-54 30-34 75-79 100+  40-44 20-24 #> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+ age_groups(ages, split_at = \"fives\") #> [1] 0-4   5-9   15-19 50-54 30-34 75-79 100+  40-44 20-24 #> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+  # split specifically for children age_groups(ages, c(1, 2, 4, 6, 13, 18)) #> [1] 2-3   6-12  13-17 18+   18+   18+   18+   18+   18+   #> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-17 < 18+ age_groups(ages, \"children\") #> [1] 2-3   6-12  13-17 18+   18+   18+   18+   18+   18+   #> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-17 < 18+  # \\donttest{ # resistance of ciprofloxacin per age group if (require(\"dplyr\") && require(\"ggplot2\")) {   example_isolates %>%     filter_first_isolate() %>%     filter(mo == as.mo(\"Escherichia coli\")) %>%     group_by(age_group = age_groups(age)) %>%     select(age_group, CIP) %>%     ggplot_sir(       x = \"age_group\",       minimum = 0,       x.title = \"Age Group\",       title = \"Ciprofloxacin resistance per age group\"     ) } #> Loading required package: ggplot2  # }"},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"Generate antibiogram, communicate results plots tables. functions follow logic Klinker et al. Barbieri et al. (see Source), allow reporting e.g. R Markdown Quarto well.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"","code":"antibiogram(   x,   antibiotics = where(is.sir),   mo_transform = \"shortname\",   ab_transform = NULL,   syndromic_group = NULL,   add_total_n = TRUE,   only_all_tested = FALSE,   digits = 0,   col_mo = NULL,   language = get_AMR_locale(),   minimum = 30,   combine_SI = TRUE,   sep = \" + \",   info = interactive() )  # S3 method for antibiogram plot(x, ...)  # S3 method for antibiogram autoplot(object, ...)  # S3 method for antibiogram knit_print(   x,   italicise = TRUE,   na = getOption(\"knitr.kable.NA\", default = \"\"),   ... )"},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"Klinker KP et al. (2021). Antimicrobial stewardship antibiograms: importance moving beyond traditional antibiograms. Therapeutic Advances Infectious Disease, May 5;8:20499361211011373; doi:10.1177/20499361211011373 Barbieri E et al. (2021). Development Weighted-Incidence Syndromic Combination Antibiogram (WISCA) guide choice empiric antibiotic treatment urinary tract infection paediatric patients: Bayesian approach Antimicrobial Resistance & Infection Control May 1;10(1):74; doi:10.1186/s13756-021-00939-2 M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 5th Edition, 2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"x data.frame containing least column microorganisms columns antibiotic results (class 'sir', see .sir()) antibiotics vector antibiotic name code (evaluated .ab(), column name x, (combinations ) antibiotic selectors aminoglycosides() carbapenems(). combination antibiograms, can also set values separated \"+\", \"TZP+TOB\" \"cipro + genta\", given columns resembling antibiotics exist x. See Examples. mo_transform character transform microorganism input - must \"name\", \"shortname\", \"gramstain\", one column names microorganisms data set: \"mo\", \"fullname\", \"status\", \"kingdom\", \"phylum\", \"class\", \"order\", \"family\", \"genus\", \"species\", \"subspecies\", \"rank\", \"ref\", \"source\", \"lpsn\", \"lpsn_parent\", \"lpsn_renamed_to\", \"gbif\", \"gbif_parent\", \"gbif_renamed_to\", \"prevalence\", \"snomed\". Can also NULL transform input. ab_transform character transform antibiotic input - must one column names antibiotics data set: \"ab\", \"cid\", \"name\", \"group\", \"atc\", \"atc_group1\", \"atc_group2\", \"abbreviations\", \"synonyms\", \"oral_ddd\", \"oral_units\", \"iv_ddd\", \"iv_units\", \"loinc\". Can also NULL transform input. syndromic_group column name x, values calculated split rows x, e.g. using ifelse() case_when(). See Examples. add_total_n logical indicate whether total available numbers per pathogen added table (default TRUE). add lowest highest number available isolate per antibiotic (e.g, E. coli 200 isolates available ciprofloxacin 150 amoxicillin, returned number \"150-200\"). only_all_tested (combination antibiograms): logical indicate isolates must tested antibiotics, see Details digits number digits use rounding col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). language language translate text, defaults system language (see get_AMR_locale()) minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. combine_SI logical indicate whether susceptibility determined results either S , instead S (default TRUE) sep separating character antibiotic columns combination antibiograms info logical indicate info printed - default TRUE interactive mode ... used R Markdown Quarto: arguments passed knitr::kable() (otherwise, use) object antibiogram() object italicise logical indicate whether microorganism names knitr table made italic, using italicise_taxonomy(). na character use showing NA values","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"function returns table values 0 100 susceptibility, resistance. Remember filter data let contain first isolates! needed exclude duplicates reduce selection bias. Use first_isolate() determine data set one four available algorithms. types antibiograms listed can plotted (using ggplot2::autoplot() base R plot()/barplot()). antibiogram object can also used directly R Markdown / Quarto (.e., knitr) reports. case, knitr::kable() applied automatically microorganism names even printed italics default (see argument italicise). can also use functions specific 'table reporting' packages transform output antibiogram() needs, e.g. flextable::as_flextable() gt::gt().","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"antibiogram-types","dir":"Reference","previous_headings":"","what":"Antibiogram Types","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"four antibiogram types, proposed Klinker et al. (2021, doi:10.1177/20499361211011373 ), supported antibiogram(): Traditional Antibiogram Case example: Susceptibility Pseudomonas aeruginosa piperacillin/tazobactam (TZP) Code example:   Combination Antibiogram Case example: Additional susceptibility Pseudomonas aeruginosa TZP + tobramycin versus TZP alone Code example:   Syndromic Antibiogram Case example: Susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) Code example:   Weighted-Incidence Syndromic Combination Antibiogram (WISCA) Case example: Susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) male patients age >=65 years heart failure Code example:   Note combination antibiograms, important realise susceptibility can calculated two ways, can set only_all_tested argument (default FALSE). See example two antibiotics, Drug Drug B, antibiogram() works calculate %SI:","code":"antibiogram(your_data,             antibiotics = \"TZP\") antibiogram(your_data,             antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\")) antibiogram(your_data,             antibiotics = penicillins(),             syndromic_group = \"ward\") library(dplyr) your_data %>%   filter(ward == \"ICU\" & specimen_type == \"Respiratory\") %>%   antibiogram(antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"),               syndromic_group = ifelse(.$age >= 65 &                                          .$gender == \"Male\" &                                          .$condition == \"Heart Disease\",                                        \"Study Group\", \"Control Group\")) --------------------------------------------------------------------                     only_all_tested = FALSE  only_all_tested = TRUE                     -----------------------  -----------------------  Drug A    Drug B   include as  include as   include as  include as                     numerator   denominator  numerator   denominator --------  --------  ----------  -----------  ----------  -----------  S or I    S or I       X            X            X            X    R       S or I       X            X            X            X   <NA>     S or I       X            X            -            -  S or I      R          X            X            X            X    R         R          -            X            -            X   <NA>       R          -            -            -            -  S or I     <NA>        X            X            -            -    R        <NA>        -            -            -            -   <NA>      <NA>        -            -            -            - --------------------------------------------------------------------"},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # \\donttest{ # Traditional antibiogram ----------------------------------------------  antibiogram(example_isolates,   antibiotics = c(aminoglycosides(), carbapenems()) ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 10 × 7 #>    `Pathogen (N min-max)`   AMK   GEN   IPM   KAN   MEM   TOB #>  * <chr>                  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1 CoNS (43-309)              0    86    52     0    52    22 #>  2 E. coli (0-462)          100    98   100    NA   100    97 #>  3 E. faecalis (0-39)         0     0   100     0    NA     0 #>  4 K. pneumoniae (0-58)      NA    90   100    NA   100    90 #>  5 P. aeruginosa (17-30)     NA   100    NA     0    NA   100 #>  6 P. mirabilis (0-34)       NA    94    94    NA    NA    94 #>  7 S. aureus (2-233)         NA    99    NA    NA    NA    98 #>  8 S. epidermidis (8-163)     0    79    NA     0    NA    51 #>  9 S. hominis (3-80)         NA    92    NA    NA    NA    85 #> 10 S. pneumoniae (11-117)     0     0    NA     0    NA     0  antibiogram(example_isolates,   antibiotics = aminoglycosides(),   ab_transform = \"atc\",   mo_transform = \"gramstain\" ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 2 × 5 #>   `Pathogen (N min-max)`   J01GB01 J01GB03 J01GB04 J01GB06 #> * <chr>                      <dbl>   <dbl>   <dbl>   <dbl> #> 1 Gram-negative (35-686)        96      96       0      98 #> 2 Gram-positive (436-1170)      34      63       0       0  antibiogram(example_isolates,   antibiotics = carbapenems(),   ab_transform = \"name\",   mo_transform = \"name\" ) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 5 × 3 #>   `Pathogen (N min-max)`                           Imipenem Meropenem #> * <chr>                                               <dbl>     <dbl> #> 1 Coagulase-negative Staphylococcus (CoNS) (48-48)       52        52 #> 2 Enterococcus faecalis (0-38)                          100        NA #> 3 Escherichia coli (418-422)                            100       100 #> 4 Klebsiella pneumoniae (51-53)                         100       100 #> 5 Proteus mirabilis (27-32)                              94        NA   # Combined antibiogram -------------------------------------------------  # combined antibiotics yield higher empiric coverage antibiogram(example_isolates,   antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"),   mo_transform = \"gramstain\" ) #> # A tibble: 2 × 4 #>   `Pathogen (N min-max)`     TZP `TZP + GEN` `TZP + TOB` #> * <chr>                    <dbl>       <dbl>       <dbl> #> 1 Gram-negative (641-693)     88          99          98 #> 2 Gram-positive (345-1044)    86          98          95  # names of antibiotics do not need to resemble columns exactly: antibiogram(example_isolates,   antibiotics = c(\"Cipro\", \"cipro + genta\"),   mo_transform = \"gramstain\",   ab_transform = \"name\",   sep = \" & \" ) #> # A tibble: 2 × 3 #>   `Pathogen (N min-max)`  Ciprofloxacin `Ciprofloxacin & Gentamicin` #> * <chr>                           <dbl>                        <dbl> #> 1 Gram-negative (684-694)            91                           99 #> 2 Gram-positive (724-847)            77                           93   # Syndromic antibiogram ------------------------------------------------  # the data set could contain a filter for e.g. respiratory specimens antibiogram(example_isolates,   antibiotics = c(aminoglycosides(), carbapenems()),   syndromic_group = \"ward\" ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 14 × 8 #>    `Syndromic Group` `Pathogen (N min-max)`   AMK   GEN   IPM   KAN   MEM   TOB #>  * <chr>             <chr>                  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1 Clinical          CoNS (23-205)             NA    89    57    NA    57    26 #>  2 ICU               CoNS (10-73)              NA    79    NA    NA    NA    NA #>  3 Outpatient        CoNS (3-31)               NA    84    NA    NA    NA    NA #>  4 Clinical          E. coli (0-299)          100    98   100    NA   100    98 #>  5 ICU               E. coli (0-137)          100    99   100    NA   100    96 #>  6 Clinical          K. pneumoniae (0-51)      NA    92   100    NA   100    92 #>  7 Clinical          P. mirabilis (0-30)       NA   100    NA    NA    NA   100 #>  8 Clinical          S. aureus (2-150)         NA    99    NA    NA    NA    97 #>  9 ICU               S. aureus (0-66)          NA   100    NA    NA    NA    NA #> 10 Clinical          S. epidermidis (4-79)     NA    82    NA    NA    NA    55 #> 11 ICU               S. epidermidis (4-75)     NA    72    NA    NA    NA    41 #> 12 Clinical          S. hominis (1-45)         NA    96    NA    NA    NA    94 #> 13 Clinical          S. pneumoniae (5-78)       0     0    NA     0    NA     0 #> 14 ICU               S. pneumoniae (5-30)       0     0    NA     0    NA     0  # now define a data set with only E. coli ex1 <- example_isolates[which(mo_genus() == \"Escherichia\"), ] #> ℹ Using column 'mo' as input for mo_genus()  # with a custom language, though this will be determined automatically # (i.e., this table will be in Spanish on Spanish systems) antibiogram(ex1,   antibiotics = aminoglycosides(),   ab_transform = \"name\",   syndromic_group = ifelse(ex1$ward == \"ICU\",     \"UCI\", \"No UCI\"   ),   language = \"es\" ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 2 × 5 #>   `Grupo sindrómico` `Patógeno (N min-max)` Amikacina Gentamicina Tobramicina #> * <chr>              <chr>                      <dbl>       <dbl>       <dbl> #> 1 No UCI             E. coli (0-325)              100          98          98 #> 2 UCI                E. coli (0-137)              100          99          96   # Weighted-incidence syndromic combination antibiogram (WISCA) ---------  # the data set could contain a filter for e.g. respiratory specimens/ICU antibiogram(example_isolates,   antibiotics = c(\"AMC\", \"AMC+CIP\", \"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\",   minimum = 10, # this should be >=30, but now just as example   syndromic_group = ifelse(example_isolates$age >= 65 &     example_isolates$gender == \"M\",   \"WISCA Group 1\", \"WISCA Group 2\"   ) ) #> # A tibble: 4 × 6 #>   `Syndromic Group` `Pathogen (N min-max)`    AMC `AMC + CIP`   TZP `TZP + TOB` #> * <chr>             <chr>                   <dbl>       <dbl> <dbl>       <dbl> #> 1 WISCA Group 1     Gram-negative (261-285)    76          95    89          99 #> 2 WISCA Group 2     Gram-negative (380-442)    76          98    88          98 #> 3 WISCA Group 1     Gram-positive (123-406)    76          89    81          95 #> 4 WISCA Group 2     Gram-positive (222-732)    76          89    88          95   # Print the output for R Markdown / Quarto -----------------------------  ureido <- antibiogram(example_isolates,   antibiotics = ureidopenicillins(),   ab_transform = \"name\" ) #> ℹ For ureidopenicillins() using column 'TZP' (piperacillin/tazobactam)  # in an Rmd file, you would just need to return `ureido` in a chunk, # but to be explicit here: if (requireNamespace(\"knitr\")) {   cat(knitr::knit_print(ureido)) } #>  #>  #> |Pathogen (N)          | Piperacillin/tazobactam| #> |:---------------------|-----------------------:| #> |CoNS (33)             |                      30| #> |*E. coli* (416)       |                      94| #> |*K. pneumoniae* (53)  |                      89| #> |*S. pneumoniae* (112) |                     100|   # Generate plots with ggplot2 or base R --------------------------------  ab1 <- antibiogram(example_isolates,   antibiotics = c(\"AMC\", \"CIP\", \"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\" ) ab2 <- antibiogram(example_isolates,   antibiotics = c(\"AMC\", \"CIP\", \"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\",   syndromic_group = \"ward\" )  if (requireNamespace(\"ggplot2\")) {   ggplot2::autoplot(ab1) }  if (requireNamespace(\"ggplot2\")) {   ggplot2::autoplot(ab2) }   plot(ab1)  plot(ab2)  # }"},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":null,"dir":"Reference","previous_headings":"","what":"Antibiotic Selectors — antibiotic_class_selectors","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"functions allow filtering rows selecting columns based antibiotic test results specific antibiotic class group (according antibiotics data set), without need define columns antibiotic abbreviations. short, column name resembles antimicrobial drug, picked functions matches pharmaceutical class: \"cefazolin\", \"kefzol\", \"CZO\" \"J01DB04\" picked cephalosporins().","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"","code":"ab_class(ab_class, only_sir_columns = FALSE, only_treatable = TRUE, ...)  ab_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE, ...)  aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE, ...)  aminopenicillins(only_sir_columns = FALSE, ...)  antifungals(only_sir_columns = FALSE, ...)  antimycobacterials(only_sir_columns = FALSE, ...)  betalactams(only_sir_columns = FALSE, only_treatable = TRUE, ...)  carbapenems(only_sir_columns = FALSE, only_treatable = TRUE, ...)  cephalosporins(only_sir_columns = FALSE, ...)  cephalosporins_1st(only_sir_columns = FALSE, ...)  cephalosporins_2nd(only_sir_columns = FALSE, ...)  cephalosporins_3rd(only_sir_columns = FALSE, ...)  cephalosporins_4th(only_sir_columns = FALSE, ...)  cephalosporins_5th(only_sir_columns = FALSE, ...)  fluoroquinolones(only_sir_columns = FALSE, ...)  glycopeptides(only_sir_columns = FALSE, ...)  lincosamides(only_sir_columns = FALSE, ...)  lipoglycopeptides(only_sir_columns = FALSE, ...)  macrolides(only_sir_columns = FALSE, ...)  oxazolidinones(only_sir_columns = FALSE, ...)  penicillins(only_sir_columns = FALSE, ...)  polymyxins(only_sir_columns = FALSE, only_treatable = TRUE, ...)  streptogramins(only_sir_columns = FALSE, ...)  quinolones(only_sir_columns = FALSE, ...)  tetracyclines(only_sir_columns = FALSE, ...)  trimethoprims(only_sir_columns = FALSE, ...)  ureidopenicillins(only_sir_columns = FALSE, ...)  administrable_per_os(only_sir_columns = FALSE, ...)  administrable_iv(only_sir_columns = FALSE, ...)  not_intrinsic_resistant(   only_sir_columns = FALSE,   col_mo = NULL,   version_expertrules = 3.3,   ... )"},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"ab_class antimicrobial class part , \"carba\" \"carbapenems\". columns group, atc_group1 atc_group2 antibiotics data set searched (case-insensitive) value. only_sir_columns logical indicate whether columns class sir must selected (default FALSE), see .sir() only_treatable logical indicate whether antimicrobial drugs excluded laboratory tests (default TRUE), gentamicin-high (GEH) imipenem/EDTA (IPE) ... ignored, place allow future extensions filter expression evaluated antibiotics data set, name %like% \"trim\" col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). version_expertrules version number use EUCAST Expert Rules Intrinsic Resistance guideline. Can either \"3.3\", \"3.2\", \"3.1\".","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"(internally) character vector column names, additional class \"ab_selector\"","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"functions can used data set calls selecting columns filtering rows. work base R, Tidyverse, data.table. heavily inspired Tidyverse selection helpers everything(), limited dplyr verbs. Nonetheless, convenient use dplyr functions select(), filter() summarise(), see Examples. columns data functions called searched known antibiotic names, abbreviations, brand names, codes (ATC, EARS-Net, , etc.) according antibiotics data set. means selector aminoglycosides() pick column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. ab_class() function can used filter/select manually defined antibiotic class. searches results antibiotics data set within columns group, atc_group1 atc_group2. ab_selector() function can used internally filter antibiotics data set results, see Examples. allows filtering (part ) certain name, /group name even minimum DDDs oral treatment. function yields highest flexibility, also least user-friendly, since requires hard-coded filter set. administrable_per_os() administrable_iv() functions also rely antibiotics data set - antibiotic columns matched DDD (defined daily dose) resp. oral IV treatment available antibiotics data set. not_intrinsic_resistant() function can used select antibiotic columns pose intrinsic resistance microorganisms data set. example, data set contains microorganism codes names E. coli K. pneumoniae contains column \"vancomycin\", column removed (rather, unselected) using function. currently applies 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021) determine intrinsic resistance, using eucast_rules() function internally. determination, function quite slow terms performance.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"full-list-of-supported-antibiotic-classes","dir":"Reference","previous_headings":"","what":"Full list of supported (antibiotic) classes","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"aminoglycosides() can select:  amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), tobramycin-high (TOH) aminopenicillins() can select:  amoxicillin (AMX) ampicillin (AMP) antifungals() can select:  amphotericin B (AMB), anidulafungin (ANI), butoconazole (), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), voriconazole (VOR) antimycobacterials() can select:  4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), viomycin (VIO) betalactams() can select:  amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC) carbapenems() can select:  biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), tebipenem (TBP) cephalosporins() can select:  cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), loracarbef (LOR) cephalosporins_1st() can select:  cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephradine (CED) cephalosporins_2nd() can select:  cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), loracarbef (LOR) cephalosporins_3rd() can select:  cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), latamoxef (LTM) cephalosporins_4th() can select:  cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), cefquinome (CEQ) cephalosporins_5th() can select:  ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT) fluoroquinolones() can select:  besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), trovafloxacin (TVA) glycopeptides() can select:  avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM) lincosamides() can select:  acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL), tylvalosin (TYL1) lipoglycopeptides() can select:  dalbavancin (DAL), oritavancin (ORI), telavancin (TLV) macrolides() can select:  acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), tylvalosin (TYL1) oxazolidinones() can select:  cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), thiacetazone (THA) penicillins() can select:  amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC) polymyxins() can select:  colistin (COL), polymyxin B (PLB), polymyxin B/polysorbate 80 (POP) quinolones() can select:  besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), trovafloxacin (TVA) streptogramins() can select:  pristinamycin (PRI) quinupristin/dalfopristin (QDA) tetracyclines() can select:  cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tigecycline (TGC) trimethoprims() can select:  brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), trimethoprim/sulfamethoxazole (SXT) ureidopenicillins() can select:  azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …   # Examples sections below are split into 'base R', 'dplyr', and 'data.table':   # base R ------------------------------------------------------------------  # select columns 'IPM' (imipenem) and 'MEM' (meropenem) example_isolates[, carbapenems()] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 2,000 × 2 #>    IPM   MEM   #>    <sir> <sir> #>  1 NA    NA    #>  2 NA    NA    #>  3 NA    NA    #>  4 NA    NA    #>  5 NA    NA    #>  6 NA    NA    #>  7 NA    NA    #>  8 NA    NA    #>  9 NA    NA    #> 10 NA    NA    #> # ℹ 1,990 more rows  # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB' example_isolates[, c(\"mo\", aminoglycosides())] #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 2,000 × 5 #>    mo           GEN   TOB   AMK   KAN   #>    <mo>         <sir> <sir> <sir> <sir> #>  1 B_ESCHR_COLI NA    NA    NA    NA    #>  2 B_ESCHR_COLI NA    NA    NA    NA    #>  3 B_STPHY_EPDR NA    NA    NA    NA    #>  4 B_STPHY_EPDR NA    NA    NA    NA    #>  5 B_STPHY_EPDR NA    NA    NA    NA    #>  6 B_STPHY_EPDR NA    NA    NA    NA    #>  7 B_STPHY_AURS NA    S     NA    NA    #>  8 B_STPHY_AURS NA    S     NA    NA    #>  9 B_STPHY_EPDR NA    NA    NA    NA    #> 10 B_STPHY_EPDR NA    NA    NA    NA    #> # ℹ 1,990 more rows  # select only antibiotic columns with DDDs for oral treatment example_isolates[, administrable_per_os()] #> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC' #>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF' #>   (rifampicin) #> # A tibble: 2,000 × 23 #>    OXA   FLC   AMX   AMC   AMP   CXM   KAN   TMP   NIT   FOS   LNZ   CIP   MFX   #>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    I     NA    R     NA    NA    R     NA    NA    #>  2 NA    NA    NA    I     NA    I     NA    R     NA    NA    R     NA    NA    #>  3 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    NA    NA    #>  4 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    NA    NA    #>  5 NA    R     NA    NA    NA    R     NA    R     NA    NA    NA    NA    NA    #>  6 NA    R     NA    NA    NA    R     NA    R     NA    NA    NA    NA    NA    #>  7 NA    S     R     S     R     S     NA    R     NA    NA    NA    NA    NA    #>  8 NA    S     R     S     R     S     NA    R     NA    NA    NA    NA    NA    #>  9 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    S     NA    #> 10 NA    S     NA    NA    NA    S     NA    S     NA    NA    NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 10 more variables: VAN <sir>, TCY <sir>, DOX <sir>, ERY <sir>, CLI <sir>, #> #   AZM <sir>, MTR <sir>, CHL <sir>, COL <sir>, RIF <sir>  # filter using any() or all() example_isolates[any(carbapenems() == \"R\"), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 55 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  2 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  3 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R     #>  4 2005-04-21 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  5 2005-04-22 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  6 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  7 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  8 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  9 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> 10 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> # ℹ 45 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … subset(example_isolates, any(carbapenems() == \"R\")) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 55 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  2 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  3 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R     #>  4 2005-04-21 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  5 2005-04-22 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  6 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  7 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  8 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  9 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> 10 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> # ℹ 45 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # filter on any or all results in the carbapenem columns (i.e., IPM, MEM): example_isolates[any(carbapenems()), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value \"S\", \"I\" or \"R\" #> # A tibble: 962 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  4 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  5 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  6 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  7 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  8 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R     #>  9 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R     #> 10 2002-03-08 4FC193     69 M      Clinical B_ESCHR_COLI R     NA    NA    R     #> # ℹ 952 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … example_isolates[all(carbapenems()), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value \"S\", \"I\" or \"R\" #> # A tibble: 756 × 46 #>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir> #>  1 2002-04-14 F30196     73 M      Outpat… B_STRPT_GRPB  S     NA    S     S     #>  2 2003-04-08 114570     74 M      ICU     B_STRPT_PYGN  S     NA    S     S     #>  3 2003-04-08 114570     74 M      ICU     B_STRPT_GRPA  S     NA    S     S     #>  4 2003-04-08 114570     74 M      ICU     B_STRPT_GRPA  S     NA    S     S     #>  5 2003-08-14 F71508      0 F      Clinic… B_STRPT_GRPB  S     NA    S     S     #>  6 2003-10-16 650870     63 F      ICU     B_ESCHR_COLI  R     NA    NA    R     #>  7 2003-10-20 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  8 2003-10-20 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  9 2003-11-04 2FC253     87 F      ICU     B_ESCHR_COLI  R     NA    NA    NA    #> 10 2003-11-04 2FC253     87 F      ICU     B_ESCHR_COLI  R     NA    NA    NA    #> # ℹ 746 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # filter with multiple antibiotic selectors using c() example_isolates[all(c(carbapenems(), aminoglycosides()) == \"R\"), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 26 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R     #>  2 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  3 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  4 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  5 2008-12-06 501361     43 F      Clinical B_STNTR_MLTP R     NA    NA    R     #>  6 2011-05-09 207325     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  7 2012-03-12 582258     80 M      ICU      B_STPHY_CONS R     R     R     R     #>  8 2012-05-19 C25552     89 F      Outpati… B_STPHY_CONS R     R     R     R     #>  9 2012-07-17 F05015     83 M      ICU      B_STPHY_CONS R     R     R     R     #> 10 2012-07-20 404299     66 F      Clinical B_STPHY_CONS R     R     R     R     #> # ℹ 16 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # filter + select in one go: get penicillins in carbapenem-resistant strains example_isolates[any(carbapenems() == \"R\"), penicillins()] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP' #>   (piperacillin/tazobactam) #> # A tibble: 55 × 7 #>    PEN   OXA   FLC   AMX   AMC   AMP   TZP   #>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    NA    NA    NA    NA    #>  2 NA    NA    NA    NA    NA    NA    NA    #>  3 R     NA    NA    R     R     R     R     #>  4 NA    NA    NA    NA    NA    NA    R     #>  5 NA    NA    NA    NA    NA    NA    R     #>  6 NA    NA    NA    NA    NA    NA    R     #>  7 NA    NA    NA    NA    NA    NA    R     #>  8 NA    NA    NA    NA    NA    NA    R     #>  9 R     NA    NA    NA    S     NA    S     #> 10 R     NA    NA    NA    S     NA    S     #> # ℹ 45 more rows  # You can combine selectors with '&' to be more specific. For example, # penicillins() would select benzylpenicillin ('peni G') and # administrable_per_os() would select erythromycin. Yet, when combined these # drugs are both omitted since benzylpenicillin is not administrable per os # and erythromycin is not a penicillin: example_isolates[, penicillins() & administrable_per_os()] #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP' #>   (piperacillin/tazobactam) #> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC' #>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF' #>   (rifampicin) #> # A tibble: 2,000 × 5 #>    OXA   FLC   AMX   AMC   AMP   #>    <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    #>  2 NA    NA    NA    I     NA    #>  3 NA    R     NA    NA    NA    #>  4 NA    R     NA    NA    NA    #>  5 NA    R     NA    NA    NA    #>  6 NA    R     NA    NA    NA    #>  7 NA    S     R     S     R     #>  8 NA    S     R     S     R     #>  9 NA    R     NA    NA    NA    #> 10 NA    S     NA    NA    NA    #> # ℹ 1,990 more rows  # ab_selector() applies a filter in the `antibiotics` data set and is thus # very flexible. For instance, to select antibiotic columns with an oral DDD # of at least 1 gram: example_isolates[, ab_selector(oral_ddd > 1 & oral_units == \"g\")] #> ℹ For ab_selector(oral_ddd > 1 & oral_units == \"g\") using columns 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'KAN' (kanamycin), 'FOS' #>   (fosfomycin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'ERY' (erythromycin), #>   'CLI' (clindamycin), 'MTR' (metronidazole), and 'CHL' (chloramphenicol) #> # A tibble: 2,000 × 13 #>    OXA   FLC   AMX   AMC   AMP   KAN   FOS   LNZ   VAN   ERY   CLI   MTR   CHL   #>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    NA    NA    R     R     R     R     NA    NA    #>  2 NA    NA    NA    I     NA    NA    NA    R     R     R     R     NA    NA    #>  3 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #>  4 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #>  5 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #>  6 NA    R     NA    NA    NA    NA    NA    NA    S     R     R     NA    NA    #>  7 NA    S     R     S     R     NA    NA    NA    S     S     NA    NA    NA    #>  8 NA    S     R     S     R     NA    NA    NA    S     S     NA    NA    NA    #>  9 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #> 10 NA    S     NA    NA    NA    NA    NA    NA    S     S     NA    NA    NA    #> # ℹ 1,990 more rows  # \\donttest{ # dplyr -------------------------------------------------------------------  if (require(\"dplyr\")) {   tibble(kefzol = random_sir(5)) %>%     select(cephalosporins()) } #> ℹ For cephalosporins() using column 'kefzol' (cefazolin) #> # A tibble: 5 × 1 #>   kefzol #>   <sir>  #> 1 S      #> 2 R      #> 3 S      #> 4 S      #> 5 I       if (require(\"dplyr\")) {   # get AMR for all aminoglycosides e.g., per ward:   example_isolates %>%     group_by(ward) %>%     summarise(across(aminoglycosides(), resistance)) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> Warning: There was 1 warning in `summarise()`. #> ℹ In argument: `across(aminoglycosides(), resistance)`. #> ℹ In group 3: `ward = \"Outpatient\"`. #> Caused by warning: #> ! Introducing NA: only 23 results available for KAN in group: ward = #> \"Outpatient\" (minimum = 30). #> # A tibble: 3 × 5 #>   ward         GEN   TOB   AMK   KAN #>   <chr>      <dbl> <dbl> <dbl> <dbl> #> 1 Clinical   0.229 0.315 0.626     1 #> 2 ICU        0.290 0.400 0.662     1 #> 3 Outpatient 0.2   0.368 0.605    NA if (require(\"dplyr\")) {   # You can combine selectors with '&' to be more specific:   example_isolates %>%     select(penicillins() & administrable_per_os()) } #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP' #>   (piperacillin/tazobactam) #> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC' #>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF' #>   (rifampicin) #> # A tibble: 2,000 × 5 #>    OXA   FLC   AMX   AMC   AMP   #>    <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    #>  2 NA    NA    NA    I     NA    #>  3 NA    R     NA    NA    NA    #>  4 NA    R     NA    NA    NA    #>  5 NA    R     NA    NA    NA    #>  6 NA    R     NA    NA    NA    #>  7 NA    S     R     S     R     #>  8 NA    S     R     S     R     #>  9 NA    R     NA    NA    NA    #> 10 NA    S     NA    NA    NA    #> # ℹ 1,990 more rows if (require(\"dplyr\")) {   # get AMR for only drugs that matter - no intrinsic resistance:   example_isolates %>%     filter(mo_genus() %in% c(\"Escherichia\", \"Klebsiella\")) %>%     group_by(ward) %>%     summarise(across(not_intrinsic_resistant(), resistance)) } #> ℹ Using column 'mo' as input for mo_genus() #> ℹ For not_intrinsic_resistant() removing columns 'PEN' #>   (benzylpenicillin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'TEC' #>   (teicoplanin), 'ERY' (erythromycin), 'CLI' (clindamycin), 'AZM' #>   (azithromycin), and 'RIF' (rifampicin) #> Warning: There were 52 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `across(not_intrinsic_resistant(), resistance)`. #> ℹ In group 1: `ward = \"Clinical\"`. #> Caused by warning: #> ! Introducing NA: no results available for OXA in group: ward = \"Clinical\" #> (minimum = 30). #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 51 remaining warnings. #> # A tibble: 3 × 33 #>   ward    OXA   FLC    AMX    AMC    AMP     TZP     CZO     FEP     CXM     FOX #>   <chr> <dbl> <dbl>  <dbl>  <dbl>  <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl> #> 1 Clin…    NA    NA  0.606  0.121  0.606  0.0504  0.0656  0.0159  0.0622  0.0648 #> 2 ICU      NA    NA  0.535  0.172  0.535  0.119  NA       0.0722  0.0828  0.0992 #> 3 Outp…    NA    NA NA     NA     NA     NA      NA      NA      NA      NA      #> # ℹ 22 more variables: CTX <dbl>, CAZ <dbl>, CRO <dbl>, GEN <dbl>, TOB <dbl>, #> #   AMK <dbl>, KAN <dbl>, TMP <dbl>, SXT <dbl>, NIT <dbl>, FOS <dbl>, #> #   CIP <dbl>, MFX <dbl>, TCY <dbl>, TGC <dbl>, DOX <dbl>, IPM <dbl>, #> #   MEM <dbl>, MTR <dbl>, CHL <dbl>, COL <dbl>, MUP <dbl> if (require(\"dplyr\")) {   # get susceptibility for antibiotics whose name contains \"trim\":   example_isolates %>%     filter(first_isolate()) %>%     group_by(ward) %>%     summarise(across(ab_selector(name %like% \"trim\"), susceptibility)) } #> ℹ For ab_selector(name %like% \"trim\") using columns 'TMP' (trimethoprim) #>   and 'SXT' (trimethoprim/sulfamethoxazole) #> # A tibble: 3 × 3 #>   ward         TMP   SXT #>   <chr>      <dbl> <dbl> #> 1 Clinical   0.627 0.808 #> 2 ICU        0.549 0.778 #> 3 Outpatient 0.667 0.821 if (require(\"dplyr\")) {   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):   example_isolates %>%     select(carbapenems()) } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 2,000 × 2 #>    IPM   MEM   #>    <sir> <sir> #>  1 NA    NA    #>  2 NA    NA    #>  3 NA    NA    #>  4 NA    NA    #>  5 NA    NA    #>  6 NA    NA    #>  7 NA    NA    #>  8 NA    NA    #>  9 NA    NA    #> 10 NA    NA    #> # ℹ 1,990 more rows if (require(\"dplyr\")) {   # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':   example_isolates %>%     select(mo, aminoglycosides()) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 2,000 × 5 #>    mo           GEN   TOB   AMK   KAN   #>    <mo>         <sir> <sir> <sir> <sir> #>  1 B_ESCHR_COLI NA    NA    NA    NA    #>  2 B_ESCHR_COLI NA    NA    NA    NA    #>  3 B_STPHY_EPDR NA    NA    NA    NA    #>  4 B_STPHY_EPDR NA    NA    NA    NA    #>  5 B_STPHY_EPDR NA    NA    NA    NA    #>  6 B_STPHY_EPDR NA    NA    NA    NA    #>  7 B_STPHY_AURS NA    S     NA    NA    #>  8 B_STPHY_AURS NA    S     NA    NA    #>  9 B_STPHY_EPDR NA    NA    NA    NA    #> 10 B_STPHY_EPDR NA    NA    NA    NA    #> # ℹ 1,990 more rows if (require(\"dplyr\")) {   # any() and all() work in dplyr's filter() too:   example_isolates %>%     filter(       any(aminoglycosides() == \"R\"),       all(cephalosporins_2nd() == \"R\")     ) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For cephalosporins_2nd() using columns 'CXM' (cefuroxime) and 'FOX' #>   (cefoxitin) #> # A tibble: 112 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  2 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R     #>  3 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  4 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA    #>  5 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA    #>  6 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R     #>  7 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R     #>  8 2003-08-13 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  9 2003-09-05 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #> 10 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #> # ℹ 102 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # also works with c():   example_isolates %>%     filter(any(c(carbapenems(), aminoglycosides()) == \"R\")) } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 531 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  2 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R     #>  3 2002-03-17 B30560     78 M      Clinical B_STPHY_CONS R     NA    R     R     #>  4 2002-04-04 E61143     67 M      Clinical B_STRPT_SNGN S     NA    NA    S     #>  5 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  6 2002-04-14 F30196     73 M      Outpati… B_STRPT_GRPB S     NA    S     S     #>  7 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  8 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  9 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #> 10 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #> # ℹ 521 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # not setting any/all will automatically apply all():   example_isolates %>%     filter(aminoglycosides() == \"R\") } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ Assuming a filter on all 4 aminoglycosides. Wrap around all() or #>   any() to prevent this note. #> # A tibble: 427 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  2 2002-03-17 B30560     78 M      Clinical B_STPHY_CONS R     NA    R     R     #>  3 2002-04-04 E61143     67 M      Clinical B_STRPT_SNGN S     NA    NA    S     #>  4 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  5 2002-04-14 F30196     73 M      Outpati… B_STRPT_GRPB S     NA    S     S     #>  6 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  7 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  8 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #>  9 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #> 10 2002-05-16 D25302     65 F      ICU      B_STRPT_ANGN S     NA    NA    S     #> # ℹ 417 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):   example_isolates %>%     select(mo, ab_class(\"mycobact\")) } #> ℹ For ab_class(\"mycobact\") using column 'RIF' (rifampicin) #> # A tibble: 2,000 × 2 #>    mo           RIF   #>    <mo>         <sir> #>  1 B_ESCHR_COLI R     #>  2 B_ESCHR_COLI R     #>  3 B_STPHY_EPDR NA    #>  4 B_STPHY_EPDR NA    #>  5 B_STPHY_EPDR NA    #>  6 B_STPHY_EPDR NA    #>  7 B_STPHY_AURS NA    #>  8 B_STPHY_AURS NA    #>  9 B_STPHY_EPDR NA    #> 10 B_STPHY_EPDR NA    #> # ℹ 1,990 more rows if (require(\"dplyr\")) {   # get bug/drug combinations for only glycopeptides in Gram-positives:   example_isolates %>%     filter(mo_is_gram_positive()) %>%     select(mo, glycopeptides()) %>%     bug_drug_combinations() %>%     format() } #> ℹ Using column 'mo' as input for mo_is_gram_positive() #> ℹ For glycopeptides() using columns 'VAN' (vancomycin) and 'TEC' #>   (teicoplanin) #> # A tibble: 2 × 8 #>   Group      Drug  CoNS  `E. faecalis` `S. aureus` `S. epidermidis` `S. hominis` #>   <chr>      <chr> <chr> <chr>         <chr>       <chr>            <chr>        #> 1 \"Glycopep… Teic… \"\"    \"\"            \" 0.0% (0/… \"64.1% (25/39)\"  \" 6.8% (4/5… #> 2 \"\"         Vanc… \" 0.… \" 0.0% (0/39… \" 0.0% (0/… \" 0.0% (0/171)\"  \" 0.0% (0/8… #> # ℹ 1 more variable: `S. pneumoniae` <chr> if (require(\"dplyr\")) {   data.frame(     some_column = \"some_value\",     J01CA01 = \"S\"   ) %>% # ATC code of ampicillin     select(penicillins()) # only the 'J01CA01' column will be selected } #> ℹ For penicillins() using column 'J01CA01' (ampicillin) #>   J01CA01 #> 1       S if (require(\"dplyr\")) {   # with recent versions of dplyr, this is all equal:   x <- example_isolates[carbapenems() == \"R\", ]   y <- example_isolates %>% filter(carbapenems() == \"R\")   z <- example_isolates %>% filter(if_all(carbapenems(), ~ .x == \"R\"))   identical(x, y) && identical(y, z) } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Assuming a filter on all 2 carbapenems. Wrap around all() or any() to #>   prevent this note. #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Assuming a filter on all 2 carbapenems. Wrap around all() or any() to #>   prevent this note. #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> [1] TRUE   # data.table --------------------------------------------------------------  # data.table is supported as well, just use it in the same way as with # base R, but add `with = FALSE` if using a single AB selector.  if (require(\"data.table\")) {   dt <- as.data.table(example_isolates)    # this does not work, it returns column *names*   dt[, carbapenems()] } #> Loading required package: data.table #>  #> Attaching package: ‘data.table’ #> The following objects are masked from ‘package:dplyr’: #>  #>     between, first, last #> The following objects are masked from ‘package:AMR’: #>  #>     %like%, like #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> [1] \"IPM\" \"MEM\" #> attr(,\"class\") #> [1] \"ab_selector\" \"character\"   if (require(\"data.table\")) {   # so `with = FALSE` is required   dt[, carbapenems(), with = FALSE] } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #>        IPM  MEM #>    1: <NA> <NA> #>    2: <NA> <NA> #>    3: <NA> <NA> #>    4: <NA> <NA> #>    5: <NA> <NA> #>   ---           #> 1996: <NA> <NA> #> 1997:    S    S #> 1998:    S    S #> 1999:    S    S #> 2000:    S    S  # for multiple selections or AB selectors, `with = FALSE` is not needed: if (require(\"data.table\")) {   dt[, c(\"mo\", aminoglycosides())] } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #>                 mo  GEN  TOB  AMK  KAN #>    1: B_ESCHR_COLI <NA> <NA> <NA> <NA> #>    2: B_ESCHR_COLI <NA> <NA> <NA> <NA> #>    3: B_STPHY_EPDR <NA> <NA> <NA> <NA> #>    4: B_STPHY_EPDR <NA> <NA> <NA> <NA> #>    5: B_STPHY_EPDR <NA> <NA> <NA> <NA> #>   ---                                  #> 1996: B_STRPT_PNMN    R    R    R    R #> 1997: B_ESCHR_COLI    S    S    S <NA> #> 1998: B_STPHY_CONS    S <NA> <NA> <NA> #> 1999: B_ESCHR_COLI    S    S <NA> <NA> #> 2000: B_KLBSL_PNMN    S    S <NA> <NA> if (require(\"data.table\")) {   dt[, c(carbapenems(), aminoglycosides())] } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #>        IPM  MEM  GEN  TOB  AMK  KAN #>    1: <NA> <NA> <NA> <NA> <NA> <NA> #>    2: <NA> <NA> <NA> <NA> <NA> <NA> #>    3: <NA> <NA> <NA> <NA> <NA> <NA> #>    4: <NA> <NA> <NA> <NA> <NA> <NA> #>    5: <NA> <NA> <NA> <NA> <NA> <NA> #>   ---                               #> 1996: <NA> <NA>    R    R    R    R #> 1997:    S    S    S    S    S <NA> #> 1998:    S    S    S <NA> <NA> <NA> #> 1999:    S    S    S    S <NA> <NA> #> 2000:    S    S    S    S <NA> <NA>  # row filters are also supported: if (require(\"data.table\")) {   dt[any(carbapenems() == \"S\"), ] } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #>            date patient age gender       ward           mo PEN  OXA  FLC  AMX #>   1: 2002-01-19  738003  71      M   Clinical B_ESCHR_COLI   R <NA> <NA> <NA> #>   2: 2002-01-19  738003  71      M   Clinical B_ESCHR_COLI   R <NA> <NA> <NA> #>   3: 2002-01-22  F35553  50      M        ICU B_PROTS_MRBL   R <NA> <NA> <NA> #>   4: 2002-01-22  F35553  50      M        ICU B_PROTS_MRBL   R <NA> <NA> <NA> #>   5: 2002-02-05  067927  45      F        ICU B_SERRT_MRCS   R <NA> <NA>    R #>  ---                                                                          #> 905: 2005-04-12  D71461  70      M        ICU B_ESCHR_COLI   R <NA> <NA>    S #> 906: 2009-11-12  650870  69      F Outpatient B_ESCHR_COLI   R <NA> <NA>    S #> 907: 2012-06-14  8CBCF2  41      F   Clinical B_STPHY_CONS   R    S    S <NA> #> 908: 2012-10-11  175532  78      M   Clinical B_ESCHR_COLI   R <NA> <NA>    R #> 909: 2013-11-23  A97263  77      M   Clinical B_KLBSL_PNMN   R <NA> <NA>    R #>      AMC  AMP  TZP  CZO  FEP CXM  FOX  CTX  CAZ  CRO  GEN  TOB  AMK  KAN  TMP #>   1:   I <NA> <NA> <NA> <NA>   S <NA>    S <NA>    S <NA>    S <NA> <NA>    S #>   2:   I <NA> <NA> <NA> <NA>   S <NA>    S <NA>    S <NA>    S <NA> <NA>    S #>   3:   I <NA> <NA> <NA> <NA>   S <NA>    S    S    S <NA> <NA> <NA> <NA>    S #>   4:   I <NA> <NA> <NA> <NA>   S <NA>    S    S    S <NA> <NA> <NA> <NA>    S #>   5:   R    R <NA>    R <NA>   R    R <NA> <NA> <NA> <NA> <NA> <NA> <NA>    S #>  ---                                                                          #> 905:   S    S    S <NA>    S   S    S    S    S    S    S    S    S <NA> <NA> #> 906:   S    S    S    S    S   S    S    S    S    S    S    S    S <NA>    S #> 907:   S <NA> <NA>    S    S   S    S    S    R    S    S <NA> <NA> <NA>    S #> 908:   S    R    S <NA>    S   R    R    S    S    S    S    S <NA> <NA>    R #> 909:   S    R    S <NA>    S   S    S    S    S    S    S    S <NA> <NA>    S #>      SXT  NIT  FOS  LNZ  CIP  MFX VAN  TEC  TCY  TGC  DOX ERY CLI AZM IPM  MEM #>   1:   S <NA> <NA>    R <NA> <NA>   R    R <NA> <NA> <NA>   R   R   R   S <NA> #>   2:   S <NA> <NA>    R <NA> <NA>   R    R <NA> <NA> <NA>   R   R   R   S <NA> #>   3:   S    R <NA>    R    S <NA>   R    R    R    R    R   R   R   R   S <NA> #>   4:   S    R <NA>    R    S <NA>   R    R    R    R    R   R   R   R   S <NA> #>   5:   S    R <NA>    R    S <NA>   R    R    R    R    R   R   R   R   S <NA> #>  ---                                                                           #> 905:   S    S <NA>    R    S <NA>   R    R <NA> <NA> <NA>   R   R   R   S    S #> 906:   S    S <NA>    R    S <NA>   R    R <NA> <NA> <NA>   R   R   R   S    S #> 907:   S <NA> <NA> <NA>    S <NA>   S <NA> <NA> <NA> <NA>   S   S   S   S    S #> 908:   R    R <NA>    R    R    R   R    R <NA> <NA> <NA>   R   R   R   S    S #> 909:   S    S <NA>    R    S <NA>   R    R <NA> <NA> <NA>   R   R   R   S    S #>       MTR  CHL  COL  MUP  RIF #>   1: <NA> <NA> <NA> <NA>    R #>   2: <NA> <NA> <NA> <NA>    R #>   3: <NA> <NA>    R <NA>    R #>   4: <NA> <NA>    R <NA>    R #>   5: <NA> <NA>    R <NA>    R #>  ---                          #> 905: <NA> <NA> <NA> <NA>    R #> 906: <NA> <NA> <NA> <NA>    R #> 907: <NA> <NA>    R <NA> <NA> #> 908: <NA> <NA>    S <NA>    R #> 909: <NA> <NA>    S <NA>    R if (require(\"data.table\")) {   dt[any(carbapenems() == \"S\"), penicillins(), with = FALSE] } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP' #>   (piperacillin/tazobactam) #>      PEN  OXA  FLC  AMX AMC  AMP  TZP #>   1:   R <NA> <NA> <NA>   I <NA> <NA> #>   2:   R <NA> <NA> <NA>   I <NA> <NA> #>   3:   R <NA> <NA> <NA>   I <NA> <NA> #>   4:   R <NA> <NA> <NA>   I <NA> <NA> #>   5:   R <NA> <NA>    R   R    R <NA> #>  ---                                  #> 905:   R <NA> <NA>    S   S    S    S #> 906:   R <NA> <NA>    S   S    S    S #> 907:   R    S    S <NA>   S <NA> <NA> #> 908:   R <NA> <NA>    R   S    R    S #> 909:   R <NA> <NA>    R   S    R    S # }"},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Sets with 603 Antimicrobial Drugs — antibiotics","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"Two data sets containing antibiotics/antimycotics antivirals. Use .ab() one ab_* functions retrieve values antibiotics data set. Three identifiers included data set: antibiotic ID (ab, primarily used package) defined WHONET/EARS-Net, ATC code (atc) defined , Compound ID (cid) found PubChem. properties data set derived one codes. Note drugs multiple ATC codes.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"","code":"antibiotics  antivirals"},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"object class tbl_df (inherits tbl, data.frame) 120 rows 11 columns.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"for-the-antibiotics-data-set-a-tibble-with-observations-and-variables-","dir":"Reference","previous_headings":"","what":"For the antibiotics data set: a tibble with 483 observations and 14 variables:","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"ab Antibiotic ID used package (AMC), using official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes available cid Compound ID found PubChem name Official name used WHONET/EARS-Net group short concise group name, based WHONET WHOCC definitions atc ATC codes (Anatomical Therapeutic Chemical) defined WHOCC, like J01CR02 atc_group1 Official pharmacological subgroup (3rd level ATC code) defined WHOCC, like \"Macrolides, lincosamides streptogramins\" atc_group2 Official chemical subgroup (4th level ATC code) defined WHOCC, like \"Macrolides\" abbr List abbreviations used many countries, also antibiotic susceptibility testing (AST) synonyms Synonyms (often trade names) drug, found PubChem based compound ID oral_ddd Defined Daily Dose (DDD), oral treatment, currently available 174 drugs oral_units Units oral_ddd iv_ddd Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available 146 drugs iv_units Units iv_ddd loinc LOINC codes (Logical Observation Identifiers Names Codes) associated name antimicrobial drug. Use ab_loinc() retrieve quickly, see ab_property().","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"for-the-antivirals-data-set-a-tibble-with-observations-and-variables-","dir":"Reference","previous_headings":"","what":"For the antivirals data set: a tibble with 120 observations and 11 variables:","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"av Antibiotic ID used package (AMC), using official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes available name Official name used WHONET/EARS-Net atc ATC codes (Anatomical Therapeutic Chemical) defined WHOCC cid Compound ID found PubChem atc_group Official pharmacological subgroup (3rd level ATC code) defined WHOCC synonyms Synonyms (often trade names) drug, found PubChem based compound ID oral_ddd Defined Daily Dose (DDD), oral treatment oral_units Units oral_ddd iv_ddd Defined Daily Dose (DDD), parenteral treatment iv_units Units iv_ddd loinc LOINC codes (Logical Observation Identifiers Names Codes) associated name antimicrobial drug.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology (WHOCC): https://www.whocc./atc_ddd_index/ Logical Observation Identifiers Names Codes (LOINC), Version 2.73 (8 August, 2022). Accessed https://loinc.org 30 October, 2022. European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"Properties based ATC code available ATC available. properties : atc_group1, atc_group2, oral_ddd, oral_units, iv_ddd iv_units. Synonyms (.e. trade names) derived PubChem Compound ID (column cid) consequently available CID available.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"Like data sets package, data sets publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"","code":"antibiotics #> # A tibble: 483 × 14 #>    ab        cid name   group atc   atc_group1 atc_group2 abbreviations synonyms #>    <ab>    <dbl> <chr>  <chr> <lis> <chr>      <chr>      <list>        <named > #>  1 AMA      4649 4-ami… Anti… <chr> Drugs for… Aminosali… <chr [1]>     <chr>    #>  2 ACM   6450012 Acety… Macr… <chr> NA         NA         <chr [1]>     <chr>    #>  3 ASP  49787020 Acety… Macr… <chr> NA         NA         <chr [1]>     <chr>    #>  4 ALS      8954 Aldes… Othe… <chr> Drugs for… Drugs for… <chr [1]>     <chr>    #>  5 AMK     37768 Amika… Amin… <chr> Aminoglyc… Other ami… <chr [5]>     <chr>    #>  6 AKF        NA Amika… Amin… <chr> NA         NA         <chr [1]>     <chr>    #>  7 AMX     33613 Amoxi… Beta… <chr> Beta-lact… Penicilli… <chr [3]>     <chr>    #>  8 AMC  23665637 Amoxi… Beta… <chr> Beta-lact… Combinati… <chr [5]>     <chr>    #>  9 AXS    465441 Amoxi… Beta… <chr> NA         NA         <chr [1]>     <chr>    #> 10 AMB   5280965 Ampho… Anti… <chr> Antimycot… Antibioti… <chr [3]>     <chr>    #> # ℹ 473 more rows #> # ℹ 5 more variables: oral_ddd <dbl>, oral_units <chr>, iv_ddd <dbl>, #> #   iv_units <chr>, loinc <list> antivirals #> # A tibble: 120 × 11 #>    av       name      atc      cid atc_group synonyms oral_ddd oral_units iv_ddd #>    <av>     <chr>     <chr>  <dbl> <chr>     <list>      <dbl> <chr>       <dbl> #>  1 ABA      Abacavir  J05A… 4.41e5 Nucleosi… <chr>         0.6 g              NA #>  2 ACI      Aciclovir J05A… 1.35e8 Nucleosi… <chr>         4   g               4 #>  3 ADD      Adefovir… J05A… 6.09e4 Nucleosi… <chr>        10   mg             NA #>  4 AME      Amenamev… J05A… 1.14e7 Other an… <chr>         0.4 g              NA #>  5 AMP      Amprenav… J05A… 6.50e4 Protease… <chr>         1.2 g              NA #>  6 ASU      Asunapre… J05A… 1.61e7 Antivira… <chr>         0.2 g              NA #>  7 ATA      Atazanav… J05A… 1.48e5 Protease… <chr>         0.3 g              NA #>  8 ATA+COBI Atazanav… J05A… 8.66e7 Antivira… <chr>        NA   NA             NA #>  9 ATA+RIT  Atazanav… J05A… 2.51e7 Antivira… <chr>         0.3 g              NA #> 10 BAM      Baloxavi… J05A… 1.24e8 Other an… <chr>        40   mg             NA #> # ℹ 110 more rows #> # ℹ 2 more variables: iv_units <chr>, loinc <list>"},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to an Antibiotic ID — as.ab","title":"Transform Input to an Antibiotic ID — as.ab","text":"Use function determine antibiotic drug code one antibiotics. data set antibiotics searched abbreviations, official names synonyms (brand names).","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to an Antibiotic ID — as.ab","text":"","code":"as.ab(x, flag_multiple_results = TRUE, info = interactive(), ...)  is.ab(x)"},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to an Antibiotic ID — as.ab","text":"x character vector determine antibiotic ID flag_multiple_results logical indicate whether note printed console probably one antibiotic drug code name can retrieved single input value. info logical indicate whether progress bar printed - default TRUE interactive mode ... arguments passed internal functions","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to an Antibiotic ID — as.ab","text":"character  vector additional class ab","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to an Antibiotic ID — as.ab","text":"entries antibiotics data set three different identifiers: human readable EARS-Net code (column ab, used ECDC WHONET), ATC code (column atc, used ), CID code (column cid, Compound ID, used PubChem). data set contains 5,000 official brand names many different countries, found PubChem. drugs contain multiple ATC codes. properties searched user input. .ab() can correct different forms misspelling: Wrong spelling drug names (\"tobramicin\" \"gentamycin\"), corrects audible similarities f/ph, x/ks, c/z/s, t/th, etc. many vowels consonants Switching two characters (\"mreopenem\", often case clinical data, doctors typed fast) Digitalised paper records, leaving artefacts like 0/o/O (zero O's), B/8, n/r, etc. Use ab_* functions get properties based returned antibiotic ID, see Examples. Note: .ab() ab_* functions may use long regular expression match brand names antimicrobial drugs. may fail systems. can add manual codes considered .ab() ab_* functions, see add_custom_antimicrobials().","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Transform Input to an Antibiotic ID — as.ab","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"Transform Input to an Antibiotic ID — as.ab","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Transform Input to an Antibiotic ID — as.ab","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to an Antibiotic ID — as.ab","text":"","code":"# these examples all return \"ERY\", the ID of erythromycin: as.ab(\"J01FA01\") #> Class 'ab' #> [1] ERY as.ab(\"J 01 FA 01\") #> Class 'ab' #> [1] ERY as.ab(\"Erythromycin\") #> Class 'ab' #> [1] ERY as.ab(\"eryt\") #> Class 'ab' #> [1] ERY as.ab(\"   eryt 123\") #> Class 'ab' #> [1] ERY as.ab(\"ERYT\") #> Class 'ab' #> [1] ERY as.ab(\"ERY\") #> Class 'ab' #> [1] ERY as.ab(\"eritromicine\") # spelled wrong, yet works #> Class 'ab' #> [1] ERY as.ab(\"Erythrocin\") # trade name #> Class 'ab' #> [1] ERY as.ab(\"Romycin\") # trade name #> Class 'ab' #> [1] ERY  # spelling from different languages and dyslexia are no problem ab_atc(\"ceftriaxon\") #> [1] \"J01DD04\" ab_atc(\"cephtriaxone\") # small spelling error #> [1] \"J01DD04\" ab_atc(\"cephthriaxone\") # or a bit more severe #> [1] \"J01DD04\" ab_atc(\"seephthriaaksone\") # and even this works #> [1] \"J01DD04\"  # use ab_* functions to get a specific properties (see ?ab_property); # they use as.ab() internally: ab_name(\"J01FA01\") #> [1] \"Erythromycin\" ab_name(\"eryt\") #> [1] \"Erythromycin\"  # \\donttest{ if (require(\"dplyr\")) {   # you can quickly rename 'sir' columns using set_ab_names() with dplyr:   example_isolates %>%     set_ab_names(where(is.sir), property = \"atc\") } #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           J01CE01 J01CF04 J01CF05 #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir>   <sir>   <sir>   #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R       NA      NA      #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R       NA      NA      #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R       NA      S       #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R       NA      S       #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R       NA      S       #> # ℹ 1,990 more rows #> # ℹ 37 more variables: J01CA04 <sir>, J01CR02 <sir>, J01CA01 <sir>, #> #   J01CR05 <sir>, J01DB04 <sir>, J01DE01 <sir>, J01DC02 <sir>, J01DC01 <sir>, #> #   J01DD01 <sir>, J01DD02 <sir>, J01DD04 <sir>, J01GB03 <sir>, J01GB01 <sir>, #> #   J01GB06 <sir>, J01GB04 <sir>, J01EA01 <sir>, J01EE01 <sir>, J01XE01 <sir>, #> #   J01XX01 <sir>, J01XX08 <sir>, J01MA02 <sir>, J01MA14 <sir>, J01XA01 <sir>, #> #   J01XA02 <sir>, J01AA07 <sir>, J01AA12 <sir>, J01AA02 <sir>, … # }"},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to an Antiviral Drug ID — as.av","title":"Transform Input to an Antiviral Drug ID — as.av","text":"Use function determine antiviral drug code one antiviral drugs. data set antivirals searched abbreviations, official names synonyms (brand names).","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to an Antiviral Drug ID — as.av","text":"","code":"as.av(x, flag_multiple_results = TRUE, info = interactive(), ...)  is.av(x)"},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to an Antiviral Drug ID — as.av","text":"x character vector determine antiviral drug ID flag_multiple_results logical indicate whether note printed console probably one antiviral drug code name can retrieved single input value. info logical indicate whether progress bar printed - default TRUE interactive mode ... arguments passed internal functions","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to an Antiviral Drug ID — as.av","text":"character  vector additional class ab","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to an Antiviral Drug ID — as.av","text":"entries antivirals data set three different identifiers: human readable EARS-Net code (column ab, used ECDC WHONET), ATC code (column atc, used ), CID code (column cid, Compound ID, used PubChem). data set contains 5,000 official brand names many different countries, found PubChem. drugs contain multiple ATC codes. properties searched user input. .av() can correct different forms misspelling: Wrong spelling drug names (\"acyclovir\"), corrects audible similarities f/ph, x/ks, c/z/s, t/th, etc. many vowels consonants Switching two characters (\"aycclovir\", often case clinical data, doctors typed fast) Digitalised paper records, leaving artefacts like 0/o/O (zero O's), B/8, n/r, etc. Use av_* functions get properties based returned antiviral drug ID, see Examples. Note: .av() av_* functions may use long regular expression match brand names antimicrobial drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Transform Input to an Antiviral Drug ID — as.av","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"Transform Input to an Antiviral Drug ID — as.av","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Transform Input to an Antiviral Drug ID — as.av","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to an Antiviral Drug ID — as.av","text":"","code":"# these examples all return \"ACI\", the ID of aciclovir: as.av(\"J05AB01\") #> Class 'av' #> [1] ACI as.av(\"J 05 AB 01\") #> Class 'av' #> [1] ACI as.av(\"Aciclovir\") #> Class 'av' #> [1] ACI as.av(\"aciclo\") #> Class 'av' #> [1] ACI as.av(\"   aciclo 123\") #> Class 'av' #> [1] ACI as.av(\"ACICL\") #> Class 'av' #> [1] ACI as.av(\"ACI\") #> Class 'av' #> [1] ACI as.av(\"Virorax\") # trade name #> Class 'av' #> [1] ACI as.av(\"Zovirax\") # trade name #> Class 'av' #> [1] ACI  as.av(\"acyklofir\") # severe spelling error, yet works #> Class 'av' #> [1] ACI  # use av_* functions to get a specific properties (see ?av_property); # they use as.av() internally: av_name(\"J05AB01\") #> [1] \"Aciclovir\" av_name(\"acicl\") #> [1] \"Aciclovir\""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to Disk Diffusion Diameters — as.disk","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"transforms vector new class disk, disk diffusion growth zone size (around antibiotic disk) millimetres 6 50.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"","code":"as.disk(x, na.rm = FALSE)  NA_disk_  is.disk(x)"},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"object class disk (inherits integer) length 1.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"x vector na.rm logical indicating whether missing values removed","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"integer additional class disk","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"Interpret disk values SIR values .sir(). supports guidelines EUCAST CLSI. Disk diffusion growth zone sizes must 6 50 millimetres. Values higher 50 lower 100 maximised 50. others input values outside 6-50 range return NA. NA_disk_ missing value new disk class.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"","code":"# transform existing disk zones to the `disk` class (using base R) df <- data.frame(   microorganism = \"Escherichia coli\",   AMP = 20,   CIP = 14,   GEN = 18,   TOB = 16 ) df[, 2:5] <- lapply(df[, 2:5], as.disk) str(df) #> 'data.frame':\t1 obs. of  5 variables: #>  $ microorganism: chr \"Escherichia coli\" #>  $ AMP          : 'disk' int 20 #>  $ CIP          : 'disk' int 14 #>  $ GEN          : 'disk' int 18 #>  $ TOB          : 'disk' int 16  # \\donttest{ # transforming is easier with dplyr: if (require(\"dplyr\")) {   df %>% mutate(across(AMP:TOB, as.disk)) } #>      microorganism AMP CIP GEN TOB #> 1 Escherichia coli  20  14  18  16 # }  # interpret disk values, see ?as.sir as.sir(   x = as.disk(18),   mo = \"Strep pneu\", # `mo` will be coerced with as.mo()   ab = \"ampicillin\", # and `ab` with as.ab()   guideline = \"EUCAST\" ) #> => Interpreting disk diffusion zones of 'ampicillin' (AMP) according to #>    EUCAST 2022... #>  OK. #> Class 'sir' #> [1] R  # interpret whole data set, pretend to be all from urinary tract infections: as.sir(df, uti = TRUE) #> => Interpreting disk diffusion zones of column 'AMP' (ampicillin) according #>    to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'CIP' (ciprofloxacin) #>    according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'GEN' (gentamicin) according #>    to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according #>    to EUCAST 2022... #>  OK. #>      microorganism AMP CIP GEN TOB #> 1 Escherichia coli   S   R   S   S"},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"transforms vectors new class mic, treats input decimal numbers, maintaining operators (\">=\") allowing valid MIC values known field (medical) microbiology.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"","code":"as.mic(x, na.rm = FALSE)  NA_mic_  is.mic(x)  # S3 method for mic droplevels(x, as.mic = FALSE, ...)"},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"x character numeric vector na.rm logical indicating whether missing values removed .mic logical indicate whether mic class kept - default FALSE ... arguments passed methods","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"Ordered factor additional class mic, mathematical operations acts decimal numbers. Bare mind outcome mathematical operation MICs return numeric value.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"interpret MIC values SIR values, use .sir() MIC values. supports guidelines EUCAST (2013-2022) CLSI (2013-2022). class MIC values quite special data type: formally ordered factor valid MIC values factor levels (make sure valid MIC values retained), mathematical operation acts decimal numbers:   makes possible maintain operators often come MIC values, \">=\" \"<=\", even filtering using numeric values data analysis, e.g.:   following generic functions implemented MIC class: !, !=, %%, %/%, &, *, +, -, /, <, <=, ==, >, >=, ^, |, abs(), acos(), acosh(), (), (), asin(), asinh(), atan(), atanh(), ceiling(), cos(), cosh(), cospi(), cummax(), cummin(), cumprod(), cumsum(), digamma(), exp(), expm1(), floor(), gamma(), lgamma(), log(), log1p(), log2(), log10(), max(), mean(), min(), prod(), range(), round(), sign(), signif(), sin(), sinh(), sinpi(), sqrt(), sum(), tan(), tanh(), tanpi(), trigamma() trunc(). functions stats package also implemented: median(), quantile(), mad(), IQR(), fivenum(). Also, boxplot.stats() supported. Since sd() var() non-generic functions, extended. Use mad() alternative, use e.g. sd(.numeric(x)) x vector MIC values. Using .double() .numeric() MIC values remove operators return numeric vector. use .integer() MIC values R convention factors, return index factor levels (often useless regular users). Use droplevels() drop unused levels. default, return plain factor. Use droplevels(..., .mic = TRUE) maintain mic class. NA_mic_ missing value new mic class, analogous e.g. base R's NA_character_.","code":"x <- random_mic(10) x #> Class 'mic' #>  [1] 16     1      8      8      64     >=128  0.0625 32     32     16  is.factor(x) #> [1] TRUE  x[1] * 2 #> [1] 32  median(x) #> [1] 26 x[x > 4] #> Class 'mic' #> [1] 16    8     8     64    >=128 32    32    16  df <- data.frame(x, hospital = \"A\") subset(df, x > 4) # or with dplyr: df %>% filter(x > 4) #>        x hospital #> 1     16        A #> 5     64        A #> 6  >=128        A #> 8     32        A #> 9     32        A #> 10    16        A"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"","code":"mic_data <- as.mic(c(\">=32\", \"1.0\", \"1\", \"1.00\", 8, \"<=0.128\", \"8\", \"16\", \"16\")) mic_data #> Class 'mic' #> [1] >=32    1       1       1       8       <=0.128 8       16      16      is.mic(mic_data) #> [1] TRUE  # this can also coerce combined MIC/SIR values: as.mic(\"<=0.002; S\") #> Class 'mic' #> [1] <=0.002  # mathematical processing treats MICs as numeric values fivenum(mic_data) #> [1]  0.128  1.000  8.000 16.000 32.000 quantile(mic_data) #>     0%    25%    50%    75%   100%  #>  0.128  1.000  8.000 16.000 32.000  all(mic_data < 512) #> [1] TRUE  # interpret MIC values as.sir(   x = as.mic(2),   mo = as.mo(\"Streptococcus pneumoniae\"),   ab = \"AMX\",   guideline = \"EUCAST\" ) #> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST #>    2022... #>  Note: #>    • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus #>      pneumoniae - assuming body site 'Meningitis'. #> Class 'sir' #> [1] R as.sir(   x = as.mic(c(0.01, 2, 4, 8)),   mo = as.mo(\"Streptococcus pneumoniae\"),   ab = \"AMX\",   guideline = \"EUCAST\" ) #> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST #>    2022... #>  Note: #>    • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus #>      pneumoniae - assuming body site 'Meningitis'. #> Class 'sir' #> [1] S R R R  # plot MIC values, see ?plot plot(mic_data)  plot(mic_data, mo = \"E. coli\", ab = \"cipro\")   if (require(\"ggplot2\")) {   autoplot(mic_data, mo = \"E. coli\", ab = \"cipro\") }  if (require(\"ggplot2\")) {   autoplot(mic_data, mo = \"E. coli\", ab = \"cipro\", language = \"nl\") # Dutch }  if (require(\"ggplot2\")) {   autoplot(mic_data, mo = \"E. coli\", ab = \"cipro\", language = \"uk\") # Ukrainian }"},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"Use function get valid microorganism code (mo) based arbitrary user input. Determination done using intelligent rules complete taxonomic tree kingdoms Animalia, Archaea, Bacteria, Protozoa, microbial species kingdom Fungi (see Source). input can almost anything: full name (like \"Staphylococcus aureus\"), abbreviated name (\"S. aureus\"), abbreviation known field (\"MRSA\"), just genus. See Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"","code":"as.mo(   x,   Becker = FALSE,   Lancefield = FALSE,   minimum_matching_score = NULL,   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   reference_df = get_mo_source(),   ignore_pattern = getOption(\"AMR_ignore_pattern\", NULL),   cleaning_regex = getOption(\"AMR_cleaning_regex\", mo_cleaning_regex()),   language = get_AMR_locale(),   info = interactive(),   ... )  is.mo(x)  mo_uncertainties()  mo_renamed()  mo_failures()  mo_reset_session()  mo_cleaning_regex()"},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"x character vector data.frame one two columns Becker logical indicate whether staphylococci categorised coagulase-negative staphylococci (\"CoNS\") coagulase-positive staphylococci (\"CoPS\") instead species, according Karsten Becker et al. (see Source). Please see Details full list staphylococcal species converted. excludes Staphylococcus aureus default, use Becker = \"\" also categorise S. aureus \"CoPS\". Lancefield logical indicate whether beta-haemolytic Streptococcus categorised Lancefield groups instead species, according Rebecca C. Lancefield (see Source). streptococci categorised first group, e.g. Streptococcus dysgalactiae group C, although officially also categorised groups G L. . Please see Details full list streptococcal species converted. excludes enterococci default (group D), use Lancefield = \"\" also categorise enterococci group D. minimum_matching_score numeric value set lower limit MO matching score. left blank, determined automatically based character length x, taxonomic kingdom human pathogenicity. keep_synonyms logical indicate old, previously valid taxonomic names must preserved corrected currently accepted names. default FALSE, return note old taxonomic names processed. default can set package option AMR_keep_synonyms, .e. options(AMR_keep_synonyms = TRUE) options(AMR_keep_synonyms = FALSE). reference_df data.frame used extra reference translating x valid mo. See set_mo_source() get_mo_source() automate usage codes (e.g. used analysis organisation). ignore_pattern Perl-compatible regular expression (case-insensitive) matches x must return NA. can convenient exclude known non-relevant input can also set package option AMR_ignore_pattern, e.g. options(AMR_ignore_pattern = \"(reported|contaminated flora)\"). cleaning_regex Perl-compatible regular expression (case-insensitive) clean input x. Every matched part x removed. default, outcome mo_cleaning_regex(), removes texts brackets texts \"species\" \"serovar\". default can set package option AMR_cleaning_regex. language language translate text like \"growth\", defaults system language (see get_AMR_locale()) info logical indicate progress bar printed 25 items coerced - default TRUE interactive mode ... arguments passed functions","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"character  vector additional class mo","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"microorganism (MO) code package (class: mo) human readable typically looks like examples:   Values coerced considered 'unknown' returned MO code UNKNOWN warning. Use mo_* functions get properties based returned code, see Examples. .mo() function uses novel matching score algorithm (see Matching Score Microorganisms ) match input available microbial taxonomy package. lead effect e.g. \"E. coli\" (microorganism highly prevalent humans) return microbial ID Escherichia coli Entamoeba coli (microorganism less prevalent humans), although latter alphabetically come first. Becker = TRUE, following 85 staphylococci converted coagulase-negative group: S. argensis, S. arlettae, S. auricularis, S. borealis, S. caeli, S. caledonicus, S. canis, S. capitis, S. capitis capitis, S. capitis urealyticus, S. capitis ureolyticus, S. caprae, S. carnosus, S. carnosus carnosus, S. carnosus utilis, S. casei, S. caseolyticus, S. chromogenes, S. cohnii, S. cohnii cohnii, S. cohnii urealyticum, S. cohnii urealyticus, S. condimenti, S. croceilyticus, S. debuckii, S. devriesei, S. durrellii, S. edaphicus, S. epidermidis, S. equorum, S. equorum equorum, S. equorum linens, S. felis, S. fleurettii, S. gallinarum, S. haemolyticus, S. hominis, S. hominis hominis, S. hominis novobiosepticus, S. jettensis, S. kloosii, S. lentus, S. lloydii, S. lugdunensis, S. massiliensis, S. microti, S. muscae, S. nepalensis, S. pasteuri, S. petrasii, S. petrasii croceilyticus, S. petrasii jettensis, S. petrasii petrasii, S. petrasii pragensis, S. pettenkoferi, S. piscifermentans, S. pragensis, S. pseudoxylosus, S. pulvereri, S. ratti, S. rostri, S. saccharolyticus, S. saprophyticus, S. saprophyticus bovis, S. saprophyticus saprophyticus, S. schleiferi, S. schleiferi schleiferi, S. sciuri, S. sciuri carnaticus, S. sciuri lentus, S. sciuri rodentium, S. sciuri sciuri, S. simulans, S. stepanovicii, S. succinus, S. succinus casei, S. succinus succinus, S. taiwanensis, S. urealyticus, S. ureilyticus, S. veratri, S. vitulinus, S. vitulus, S. warneri, S. xylosus. following 16 staphylococci converted coagulase-positive group: S. agnetis, S. argenteus, S. coagulans, S. cornubiensis, S. delphini, S. hyicus, S. hyicus chromogenes, S. hyicus hyicus, S. intermedius, S. lutrae, S. pseudintermedius, S. roterodami, S. schleiferi coagulans, S. schweitzeri, S. simiae, S. singaporensis. Lancefield = TRUE, following streptococci converted corresponding Lancefield group: S. agalactiae (Group B), S. anginosus anginosus (Group F), S. anginosus whileyi (Group F), S. anginosus (Group F), S. canis (Group G), S. dysgalactiae dysgalactiae (Group C), S. dysgalactiae equisimilis (Group C), S. dysgalactiae (Group C), S. equi equi (Group C), S. equi ruminatorum (Group C), S. equi zooepidemicus (Group C), S. equi (Group C), S. pyogenes (Group ), S. salivarius salivarius (Group K), S. salivarius thermophilus (Group K), S. salivarius (Group K), S. sanguinis (Group H).","code":"Code               Full name   ---------------    --------------------------------------   B_KLBSL            Klebsiella   B_KLBSL_PNMN       Klebsiella pneumoniae   B_KLBSL_PNMN_RHNS  Klebsiella pneumoniae rhinoscleromatis   |   |    |    |   |   |    |    |   |   |    |    \\---> subspecies, a 3-5 letter acronym   |   |    \\----> species, a 3-6 letter acronym   |   \\----> genus, a 4-8 letter acronym   \\----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),                             F (Fungi), PL (Plantae), P (Protozoa)"},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"coping-with-uncertain-results","dir":"Reference","previous_headings":"","what":"Coping with Uncertain Results","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"Results non-exact taxonomic input based matching score. lowest allowed score can set minimum_matching_score argument. default determined based character length input, taxonomic kingdom human pathogenicity taxonomic outcome. values matched uncertainty, message shown suggest user evaluate results mo_uncertainties(), returns data.frame specifications. increase quality matching, cleaning_regex argument can used clean input (.e., x). must regular expression matches parts input removed input matched available microbial taxonomy. matched Perl-compatible case-insensitive. default value cleaning_regex outcome helper function mo_cleaning_regex(). three helper functions can run using .mo() function: Use mo_uncertainties() get data.frame prints pretty format taxonomic names guessed. output contains matching score matches (see Matching Score Microorganisms ). Use mo_failures() get character vector values coerced valid value. Use mo_renamed() get data.frame values coerced based old, previously accepted taxonomic names.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"microbial-prevalence-of-pathogens-in-humans","dir":"Reference","previous_headings":"","what":"Microbial Prevalence of Pathogens in Humans","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"coercion rules consider prevalence microorganisms humans, available prevalence column microorganisms data set. grouping human pathogenic prevalence explained section Matching Score Microorganisms .","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"Berends MS et al. (2022). AMR: R Package Working Antimicrobial Resistance Data. Journal Statistical Software, 104(3), 1-31; doi:10.18637/jss.v104.i03 Becker K et al. (2014). Coagulase-Negative Staphylococci. Clin Microbiol Rev. 27(4): 870-926; doi:10.1128/CMR.00109-13 Becker K et al. (2019). Implications identifying recently defined members S. aureus complex, S. argenteus S. schweitzeri: position paper members ESCMID Study Group staphylococci Staphylococcal Diseases (ESGS). Clin Microbiol Infect; doi:10.1016/j.cmi.2019.02.028 Becker K et al. (2020). Emergence coagulase-negative staphylococci Expert Rev Anti Infect Ther. 18(4):349-366; doi:10.1080/14787210.2020.1730813 Lancefield RC (1933). serological differentiation human groups hemolytic streptococci. J Exp Med. 57(4): 571-95; doi:10.1084/jem.57.4.571 Berends MS et al. (2022). Trends Occurrence Phenotypic Resistance Coagulase-Negative Staphylococci (CoNS) Found Human Blood Northern Netherlands 2013 2019 Microorganisms 10(9), 1801; doi:10.3390/microorganisms10091801 Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332 . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov Bartlett et al. (2022). comprehensive list bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"matching-score-for-microorganisms","dir":"Reference","previous_headings":"","what":"Matching Score for Microorganisms","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"ambiguous user input .mo() mo_* functions, returned results chosen based matching score using mo_matching_score(). matching score \\(m\\), calculated :  : \\(x\\) user input; \\(n\\) taxonomic name (genus, species, subspecies); \\(l_n\\) length \\(n\\); \\(lev\\) Levenshtein distance function (counting insertion 1, deletion substitution 2) needed change \\(x\\) \\(n\\); \\(p_n\\) human pathogenic prevalence group \\(n\\), described ; \\(k_n\\) taxonomic kingdom \\(n\\), set Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5. grouping human pathogenic prevalence \\(p\\) based recent work Bartlett et al. (2022, doi:10.1099/mic.0.001269 ) extensively studied medical-scientific literature categorise bacterial species groups: Established, taxonomic species infected least three persons three references. records prevalence = 1.0 microorganisms data set; Putative, taxonomic species fewer three known cases. records prevalence = 1.25 microorganisms data set. Furthermore, genus present established list also prevalence = 1.0 microorganisms data set; genus present putative list prevalence = 1.25 microorganisms data set; species subspecies genus present two aforementioned groups, prevalence = 1.5 microorganisms data set; non-bacterial genus, species subspecies genus present following list, prevalence = 1.5 microorganisms data set: Absidia, Acanthamoeba, Acremonium, Aedes, Alternaria, Amoeba, Ancylostoma, Angiostrongylus, Anisakis, Anopheles, Apophysomyces, Aspergillus, Aureobasidium, Basidiobolus, Beauveria, Blastocystis, Blastomyces, Candida, Capillaria, Chaetomium, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Contracaecum, Cordylobia, Cryptococcus, Curvularia, Demodex, Dermatobia, Dientamoeba, Diphyllobothrium, Dirofilaria, Echinostoma, Entamoeba, Enterobius, Exophiala, Exserohilum, Fasciola, Fonsecaea, Fusarium, Giardia, Haloarcula, Halobacterium, Halococcus, Hendersonula, Heterophyes, Histomonas, Histoplasma, Hymenolepis, Hypomyces, Hysterothylacium, Leishmania, Malassezia, Malbranchea, Metagonimus, Meyerozyma, Microsporidium, Microsporum, Mortierella, Mucor, Mycocentrospora, Necator, Nectria, Ochroconis, Oesophagostomum, Oidiodendron, Opisthorchis, Pediculus, Penicillium, Phlebotomus, Phoma, Pichia, Piedraia, Pithomyces, Pityrosporum, Pneumocystis, Pseudallescheria, Pseudoterranova, Pulex, Rhizomucor, Rhizopus, Rhodotorula, Saccharomyces, Sarcoptes, Scolecobasidium, Scopulariopsis, Scytalidium, Spirometra, Sporobolomyces, Stachybotrys, Strongyloides, Syngamus, Taenia, Talaromyces, Toxocara, Trichinella, Trichobilharzia, Trichoderma, Trichomonas, Trichophyton, Trichosporon, Trichostrongylus, Trichuris, Tritirachium, Trombicula, Trypanosoma, Tunga, Wuchereria; records prevalence = 2.0 microorganisms data set. calculating matching score, characters \\(x\\) \\(n\\) ignored -Z, -z, 0-9, spaces parentheses. matches sorted descending matching score user input values, top match returned. lead effect e.g., \"E. coli\" return microbial ID Escherichia coli (\\(m = 0.688\\), highly prevalent microorganism found humans) Entamoeba coli (\\(m = 0.159\\), less prevalent microorganism humans), although latter alphabetically come first.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"","code":"# \\donttest{ # These examples all return \"B_STPHY_AURS\", the ID of S. aureus: as.mo(c(   \"sau\", # WHONET code   \"stau\",   \"STAU\",   \"staaur\",   \"S. aureus\",   \"S aureus\",   \"Sthafilokkockus aureus\", # handles incorrect spelling   \"Staphylococcus aureus (MRSA)\",   \"MRSA\", # Methicillin Resistant S. aureus   \"VISA\", # Vancomycin Intermediate S. aureus   \"VRSA\", # Vancomycin Resistant S. aureus   115329001 # SNOMED CT code )) #> Class 'mo' #>  [1] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS #>  [6] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS #> [11] B_STPHY_AURS B_STPHY_AURS  # Dyslexia is no problem - these all work: as.mo(c(   \"Ureaplasma urealyticum\",   \"Ureaplasma urealyticus\",   \"Ureaplasmium urealytica\",   \"Ureaplazma urealitycium\" )) #> Class 'mo' #> [1] B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY  as.mo(\"Streptococcus group A\") #> Class 'mo' #> [1] B_STRPT_GRPA  as.mo(\"S. epidermidis\") # will remain species: B_STPHY_EPDR #> Class 'mo' #> [1] B_STPHY_EPDR as.mo(\"S. epidermidis\", Becker = TRUE) # will not remain species: B_STPHY_CONS #> Class 'mo' #> [1] B_STPHY_CONS  as.mo(\"S. pyogenes\") # will remain species: B_STRPT_PYGN #> Class 'mo' #> [1] B_STRPT_PYGN as.mo(\"S. pyogenes\", Lancefield = TRUE) # will not remain species: B_STRPT_GRPA #> Class 'mo' #> [1] B_STRPT_GRPA  # All mo_* functions use as.mo() internally too (see ?mo_property): mo_genus(\"E. coli\") #> [1] \"Escherichia\" mo_gramstain(\"ESCO\") #> [1] \"Gram-negative\" mo_is_intrinsic_resistant(\"ESCCOL\", ab = \"vanco\") #> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and #>   'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021). This note #>   will be shown once per session. #> [1] TRUE # }"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":null,"dir":"Reference","previous_headings":"","what":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"Interpret minimum inhibitory concentration (MIC) values disk diffusion diameters according EUCAST CLSI, clean existing SIR values. transforms input new class sir, ordered factor levels S < < R. breakpoints used interpretation publicly available clinical_breakpoints data set.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"","code":"as.sir(x, ...)  NA_sir_  is.sir(x)  is_sir_eligible(x, threshold = 0.05)  # S3 method for mic as.sir(   x,   mo = NULL,   ab = deparse(substitute(x)),   guideline = getOption(\"AMR_guideline\", \"EUCAST\"),   uti = NULL,   conserve_capped_values = FALSE,   add_intrinsic_resistance = FALSE,   reference_data = AMR::clinical_breakpoints,   include_screening = getOption(\"AMR_include_screening\", FALSE),   include_PKPD = getOption(\"AMR_include_PKPD\", TRUE),   ... )  # S3 method for disk as.sir(   x,   mo = NULL,   ab = deparse(substitute(x)),   guideline = getOption(\"AMR_guideline\", \"EUCAST\"),   uti = NULL,   add_intrinsic_resistance = FALSE,   reference_data = AMR::clinical_breakpoints,   include_screening = getOption(\"AMR_include_screening\", FALSE),   include_PKPD = getOption(\"AMR_include_PKPD\", TRUE),   ... )  # S3 method for data.frame as.sir(   x,   ...,   col_mo = NULL,   guideline = getOption(\"AMR_guideline\", \"EUCAST\"),   uti = NULL,   conserve_capped_values = FALSE,   add_intrinsic_resistance = FALSE,   reference_data = AMR::clinical_breakpoints,   include_screening = getOption(\"AMR_include_screening\", FALSE),   include_PKPD = getOption(\"AMR_include_PKPD\", TRUE) )  sir_interpretation_history(clean = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"object class sir (inherits ordered, factor) length 1.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"interpretations minimum inhibitory concentration (MIC) values disk diffusion diameters: M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 2013-2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/. M100 Performance Standard Antimicrobial Susceptibility Testing, 2013-2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m100/. Breakpoint tables interpretation MICs zone diameters, 2013-2022, European Committee Antimicrobial Susceptibility Testing (EUCAST). https://www.eucast.org/clinical_breakpoints.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"x vector values (class mic: MIC values mg/L, class disk: disk diffusion radius millimetres) ... using data.frame: names columns apply .sir() (supports tidy selection column1:column4). Otherwise: arguments passed methods. threshold maximum fraction invalid antimicrobial interpretations x, see Examples mo (vector ) text can coerced valid microorganism codes .mo(), can left empty determine automatically ab (vector ) text can coerced valid antimicrobial drug code .ab() guideline defaults EUCAST 2022 (latest implemented EUCAST guideline clinical_breakpoints data set), can set package option AMR_guideline. Currently supports EUCAST (2013-2022) CLSI (2013-2022), see Details. uti (Urinary Tract Infection) vector logicals (TRUE FALSE) specify whether UTI specific interpretation guideline chosen. using .sir() data.frame, can also column containing logicals left blank, data set searched column 'specimen', rows within column containing 'urin' ('urine', 'urina') regarded isolates UTI. See Examples. conserve_capped_values logical indicate MIC values starting \">\" (\">=\") must always return \"R\" , MIC values starting \"<\" (\"<=\") must always return \"S\" add_intrinsic_resistance (useful using EUCAST guideline) logical indicate whether intrinsic antibiotic resistance must also considered applicable bug-drug combinations, meaning e.g. ampicillin always return \"R\" Klebsiella species. Determination based intrinsic_resistant data set, based 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021). reference_data data.frame used interpretation, defaults clinical_breakpoints data set. Changing argument allows using interpretation guidelines. argument must contain data set equal structure clinical_breakpoints data set (column names column types). Please note guideline argument ignored reference_data manually set. include_screening logical indicate clinical breakpoints screening allowed - default FALSE. Can also set package option AMR_include_screening. include_PKPD logical indicate PK/PD clinical breakpoints must applied last resort - default TRUE. Can also set package option AMR_include_PKPD. col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). clean logical indicate whether previously stored results forgotten returning 'logbook' results","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"Ordered factor new class sir","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"NA_sir_ missing value new sir class, analogous e.g. base R's NA_character_.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"how-it-works","dir":"Reference","previous_headings":"","what":"How it Works","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":".sir() function works four ways: cleaning raw / untransformed data. data cleaned contain values S, R try best determine intelligence. example, mixed values SIR interpretations MIC values \"<0.25; S\" coerced \"S\". Combined interpretations multiple test methods (seen laboratory records) \"S; S\" coerced \"S\", value like \"S; \" return NA warning input unclear. interpreting minimum inhibitory concentration (MIC) values according EUCAST CLSI. must clean MIC values first using .mic(), also gives columns new data class mic. Also, sure column microorganism names codes. found automatically, can set manually using mo argument. Using dplyr, SIR interpretation can done easily either:   Operators like \"<=\" stripped interpretation. using conserve_capped_values = TRUE, MIC value e.g. \">2\" always return \"R\", even breakpoint according chosen guideline \">=4\". prevent capped values raw laboratory data treated conservatively. default behaviour (conserve_capped_values = FALSE) considers \">2\" lower \">=4\" might case return \"S\" \"\". interpreting disk diffusion diameters according EUCAST CLSI. must clean disk zones first using .disk(), also gives columns new data class disk. Also, sure column microorganism names codes. found automatically, can set manually using mo argument. Using dplyr, SIR interpretation can done easily either:   interpreting complete data set, automatic determination MIC values, disk diffusion diameters, microorganism names codes, antimicrobial test results. done simply running .sir(your_data). points 2, 3 4: Use sir_interpretation_history() retrieve data.frame (tibble tibble package installed) results last .sir() call.","code":"your_data %>% mutate_if(is.mic, as.sir) your_data %>% mutate(across(where(is.mic), as.sir)) your_data %>% mutate_if(is.disk, as.sir) your_data %>% mutate(across(where(is.disk), as.sir))"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"supported-guidelines","dir":"Reference","previous_headings":"","what":"Supported Guidelines","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"interpreting MIC values well disk diffusion diameters, currently implemented guidelines EUCAST (2013-2022) CLSI (2013-2022). Thus, guideline argument must set e.g., \"EUCAST 2022\" \"CLSI 2022\". simply using \"EUCAST\" (default) \"CLSI\" input, latest included version guideline automatically selected. can set data set using reference_data argument. guideline argument ignored. can set default guideline package option AMR_guideline (e.g. .Rprofile file), :","code":"options(AMR_guideline = \"CLSI\")   options(AMR_guideline = \"CLSI 2018\")   options(AMR_guideline = \"EUCAST 2020\")   # or to reset:   options(AMR_guideline = NULL)"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"after-interpretation","dir":"Reference","previous_headings":"","what":"After Interpretation","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"using .sir(), can use eucast_rules() defined EUCAST (1) apply inferred susceptibility resistance based results antimicrobials (2) apply intrinsic resistance based taxonomic properties microorganism.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"machine-readable-clinical-breakpoints","dir":"Reference","previous_headings":"","what":"Machine-Readable Clinical Breakpoints","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"repository package contains machine-readable version guidelines. CSV file consisting 18 271 rows 11 columns. file machine-readable, since contains one row every unique combination test method (MIC disk diffusion), antimicrobial drug microorganism. allows easy implementation rules laboratory information systems (LIS). Note contains interpretation guidelines humans - interpretation guidelines CLSI animals removed.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"other","dir":"Reference","previous_headings":"","what":"Other","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"function .sir() detects input contains class sir. input data.frame, iterates columns returns logical vector. function is_sir_eligible() returns TRUE columns contains 5% invalid antimicrobial interpretations (S //R), FALSE otherwise. threshold 5% can set threshold argument. input data.frame, iterates columns returns logical vector.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"","code":"example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … summary(example_isolates) # see all SIR results at a glance #>       date              patient               age           gender          #>  Min.   :2002-01-02   Length:2000        Min.   : 0.00   Length:2000        #>  1st Qu.:2005-07-31   Class :character   1st Qu.:63.00   Class :character   #>  Median :2009-07-31   Mode  :character   Median :74.00   Mode  :character   #>  Mean   :2009-11-20                      Mean   :70.69                      #>  3rd Qu.:2014-05-30                      3rd Qu.:82.00                      #>  Max.   :2017-12-28                      Max.   :97.00                      #>      ward                mo                  PEN                 #>  Length:2000        Class :mo             Class:sir              #>  Class :character   <NA>  :0              %R   :73.7% (n=1201)   #>  Mode  :character   Unique:90             %SI  :26.3% (n=428)    #>                     #1    :B_ESCHR_COLI   - %S :25.6% (n=417)    #>                     #2    :B_STPHY_CONS   - %I : 0.7% (n=11)     #>                     #3    :B_STPHY_AURS                          #>     OXA                   FLC                   AMX                #>  Class:sir             Class:sir             Class:sir             #>  %R   :31.2% (n=114)   %R   :29.5% (n=278)   %R   :59.6% (n=804)   #>  %SI  :68.8% (n=251)   %SI  :70.5% (n=665)   %SI  :40.4% (n=546)   #>  - %S :68.8% (n=251)   - %S :70.5% (n=665)   - %S :40.2% (n=543)   #>  - %I : 0.0% (n=0)     - %I : 0.0% (n=0)     - %I : 0.2% (n=3)     #>                                                                    #>     AMC                    AMP                   TZP                #>  Class:sir              Class:sir             Class:sir             #>  %R   :23.7% (n=446)    %R   :59.6% (n=804)   %R   :12.6% (n=126)   #>  %SI  :76.3% (n=1433)   %SI  :40.4% (n=546)   %SI  :87.4% (n=875)   #>  - %S :71.4% (n=1342)   - %S :40.2% (n=543)   - %S :86.1% (n=862)   #>  - %I : 4.8% (n=91)     - %I : 0.2% (n=3)     - %I : 1.3% (n=13)    #>                                                                     #>     CZO                   FEP                   CXM                 #>  Class:sir             Class:sir             Class:sir              #>  %R   :44.6% (n=199)   %R   :14.2% (n=103)   %R   :26.3% (n=470)    #>  %SI  :55.4% (n=247)   %SI  :85.8% (n=621)   %SI  :73.7% (n=1319)   #>  - %S :54.9% (n=245)   - %S :85.6% (n=620)   - %S :72.5% (n=1297)   #>  - %I : 0.4% (n=2)     - %I : 0.1% (n=1)     - %I : 1.2% (n=22)     #>                                                                     #>     FOX                   CTX                   CAZ                 #>  Class:sir             Class:sir             Class:sir              #>  %R   :27.4% (n=224)   %R   :15.5% (n=146)   %R   :66.5% (n=1204)   #>  %SI  :72.6% (n=594)   %SI  :84.5% (n=797)   %SI  :33.5% (n=607)    #>  - %S :71.6% (n=586)   - %S :84.4% (n=796)   - %S :33.5% (n=607)    #>  - %I : 1.0% (n=8)     - %I : 0.1% (n=1)     - %I : 0.0% (n=0)      #>                                                                     #>     CRO                   GEN                    TOB                #>  Class:sir             Class:sir              Class:sir             #>  %R   :15.5% (n=146)   %R   :24.6% (n=456)    %R   :34.4% (n=465)   #>  %SI  :84.5% (n=797)   %SI  :75.4% (n=1399)   %SI  :65.6% (n=886)   #>  - %S :84.4% (n=796)   - %S :74.0% (n=1372)   - %S :65.1% (n=879)   #>  - %I : 0.1% (n=1)     - %I : 1.5% (n=27)     - %I : 0.5% (n=7)     #>                                                                     #>     AMK                   KAN                    TMP                #>  Class:sir             Class:sir              Class:sir             #>  %R   :63.7% (n=441)   %R   :100.0% (n=471)   %R   :38.1% (n=571)   #>  %SI  :36.3% (n=251)   %SI  : 0.0% (n=0)      %SI  :61.9% (n=928)   #>  - %S :36.3% (n=251)   - %S : 0.0% (n=0)      - %S :61.2% (n=918)   #>  - %I : 0.0% (n=0)     - %I : 0.0% (n=0)      - %I : 0.7% (n=10)    #>                                                                     #>     SXT                    NIT                   FOS                #>  Class:sir              Class:sir             Class:sir             #>  %R   :20.5% (n=361)    %R   :17.1% (n=127)   %R   :42.2% (n=148)   #>  %SI  :79.5% (n=1398)   %SI  :82.9% (n=616)   %SI  :57.8% (n=203)   #>  - %S :79.1% (n=1392)   - %S :76.0% (n=565)   - %S :57.8% (n=203)   #>  - %I : 0.3% (n=6)      - %I : 6.9% (n=51)    - %I : 0.0% (n=0)     #>                                                                     #>     LNZ                   CIP                    MFX                #>  Class:sir             Class:sir              Class:sir             #>  %R   :69.3% (n=709)   %R   :16.2% (n=228)    %R   :33.6% (n=71)    #>  %SI  :30.7% (n=314)   %SI  :83.8% (n=1181)   %SI  :66.4% (n=140)   #>  - %S :30.7% (n=314)   - %S :78.9% (n=1112)   - %S :64.5% (n=136)   #>  - %I : 0.0% (n=0)     - %I : 4.9% (n=69)     - %I : 1.9% (n=4)     #>                                                                     #>     VAN                    TEC                   TCY                #>  Class:sir              Class:sir             Class:sir             #>  %R   :38.3% (n=712)    %R   :75.7% (n=739)   %R   :29.8% (n=357)   #>  %SI  :61.7% (n=1149)   %SI  :24.3% (n=237)   %SI  :70.3% (n=843)   #>  - %S :61.7% (n=1149)   - %S :24.3% (n=237)   - %S :68.3% (n=820)   #>  - %I : 0.0% (n=0)      - %I : 0.0% (n=0)     - %I : 1.9% (n=23)    #>                                                                     #>     TGC                   DOX                   ERY                 #>  Class:sir             Class:sir             Class:sir              #>  %R   :12.7% (n=101)   %R   :27.7% (n=315)   %R   :57.2% (n=1084)   #>  %SI  :87.3% (n=697)   %SI  :72.3% (n=821)   %SI  :42.8% (n=810)    #>  - %S :87.3% (n=697)   - %S :71.7% (n=814)   - %S :42.3% (n=801)    #>  - %I : 0.0% (n=0)     - %I : 0.6% (n=7)     - %I : 0.5% (n=9)      #>                                                                     #>     CLI                   AZM                    IPM                #>  Class:sir             Class:sir              Class:sir             #>  %R   :61.2% (n=930)   %R   :57.2% (n=1084)   %R   : 6.2% (n=55)    #>  %SI  :38.8% (n=590)   %SI  :42.8% (n=810)    %SI  :93.8% (n=834)   #>  - %S :38.6% (n=586)   - %S :42.3% (n=801)    - %S :92.7% (n=824)   #>  - %I : 0.3% (n=4)     - %I : 0.5% (n=9)      - %I : 1.1% (n=10)    #>                                                                     #>     MEM                   MTR                  CHL                #>  Class:sir             Class:sir            Class:sir             #>  %R   : 5.9% (n=49)    %R   :14.7% (n=5)    %R   :21.4% (n=33)    #>  %SI  :94.1% (n=780)   %SI  :85.3% (n=29)   %SI  :78.6% (n=121)   #>  - %S :94.1% (n=780)   - %S :85.3% (n=29)   - %S :78.6% (n=121)   #>  - %I : 0.0% (n=0)     - %I : 0.0% (n=0)    - %I : 0.0% (n=0)     #>                                                                   #>     COL                    MUP                   RIF                #>  Class:sir              Class:sir             Class:sir             #>  %R   :81.2% (n=1331)   %R   : 5.9% (n=16)    %R   :69.6% (n=698)   #>  %SI  :18.8% (n=309)    %SI  :94.1% (n=254)   %SI  :30.4% (n=305)   #>  - %S :18.8% (n=309)    - %S :93.0% (n=251)   - %S :30.2% (n=303)   #>  - %I : 0.0% (n=0)      - %I : 1.1% (n=3)     - %I : 0.2% (n=2)     #>                                                                      # For INTERPRETING disk diffusion and MIC values -----------------------  # a whole data set, even with combined MIC values and disk zones df <- data.frame(   microorganism = \"Escherichia coli\",   AMP = as.mic(8),   CIP = as.mic(0.256),   GEN = as.disk(18),   TOB = as.disk(16),   ERY = \"R\" ) as.sir(df) #> => Interpreting MIC values of column 'AMP' (ampicillin) according to EUCAST #>    2022... #>  OK. #> => Interpreting MIC values of column 'CIP' (ciprofloxacin) according to #>    EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'GEN' (gentamicin) according #>    to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according #>    to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Assigning class 'sir' to already clean column 'ERY' (erythromycin)... #>  OK. #>      microorganism AMP CIP GEN TOB ERY #> 1 Escherichia coli   S   I   S   S   R  # return a 'logbook' about the results: sir_interpretation_history() #> # A tibble: 50 × 12 #>    datetime            index ab_input ab_guideline mo_input     mo_guideline     #>    <dttm>              <int> <chr>    <ab>         <chr>        <mo>             #>  1 2023-05-08 11:08:51     1 TOB      TOB          Escherichia… B_[ORD]_ENTRBCTR #>  2 2023-05-08 11:08:51     1 GEN      GEN          Escherichia… B_[ORD]_ENTRBCTR #>  3 2023-05-08 11:08:50     1 CIP      CIP          Escherichia… B_[ORD]_ENTRBCTR #>  4 2023-05-08 11:08:50     1 AMP      AMP          Escherichia… B_[ORD]_ENTRBCTR #>  5 2023-05-08 11:08:45     1 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #>  6 2023-05-08 11:08:45     2 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #>  7 2023-05-08 11:08:45     3 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #>  8 2023-05-08 11:08:45     4 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #>  9 2023-05-08 11:08:45     5 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #> 10 2023-05-08 11:08:45     6 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #> # ℹ 40 more rows #> # ℹ 6 more variables: guideline <chr>, ref_table <chr>, method <chr>, #> #   input <dbl>, outcome <sir>, breakpoint_S_R <chr>  # for single values as.sir(   x = as.mic(2),   mo = as.mo(\"S. pneumoniae\"),   ab = \"AMP\",   guideline = \"EUCAST\" ) #> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST #>    2022... #>  Note: #>    • Multiple breakpoints available for ampicillin (AMP) in Streptococcus #>      pneumoniae - assuming body site 'Non-meningitis'. #> Class 'sir' #> [1] R  as.sir(   x = as.disk(18),   mo = \"Strep pneu\", # `mo` will be coerced with as.mo()   ab = \"ampicillin\", # and `ab` with as.ab()   guideline = \"EUCAST\" ) #> => Interpreting disk diffusion zones of 'ampicillin' (AMP) according to #>    EUCAST 2022... #>  OK. #> Class 'sir' #> [1] R  # \\donttest{ # the dplyr way if (require(\"dplyr\")) {   df %>% mutate_if(is.mic, as.sir)   df %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)   df %>% mutate(across(where(is.mic), as.sir))   df %>% mutate_at(vars(AMP:TOB), as.sir)   df %>% mutate(across(AMP:TOB, as.sir))    df %>%     mutate_at(vars(AMP:TOB), as.sir, mo = .$microorganism)    # to include information about urinary tract infections (UTI)   data.frame(     mo = \"E. coli\",     NIT = c(\"<= 2\", 32),     from_the_bladder = c(TRUE, FALSE)   ) %>%     as.sir(uti = \"from_the_bladder\")    data.frame(     mo = \"E. coli\",     NIT = c(\"<= 2\", 32),     specimen = c(\"urine\", \"blood\")   ) %>%     as.sir() # automatically determines urine isolates    df %>%     mutate_at(vars(AMP:TOB), as.sir, mo = \"E. coli\", uti = TRUE) } #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST #>    2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST #>    2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to #>    EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to #>    EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to #>    EUCAST 2022... #> Warning: in as.sir(): interpretation of nitrofurantoin (NIT) is only available for #> (uncomplicated) urinary tract infections (UTI) for some microorganisms, #> thus assuming uti = TRUE. See ?as.sir. #>  * WARNING * #> ℹ Assuming value \"urine\" in column 'specimen' reflects a urinary tract #>   infection. #>   Use as.sir(uti = FALSE) to prevent this. #> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to #>    EUCAST 2022... #> Warning: in as.sir(): interpretation of nitrofurantoin (NIT) is only available for #> (uncomplicated) urinary tract infections (UTI) for some microorganisms, #> thus assuming uti = TRUE. See ?as.sir. #>  * WARNING * #> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST #>    2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST #>    2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to #>    EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to #>    EUCAST 2022... #>  OK. #>      microorganism AMP CIP GEN TOB ERY #> 1 Escherichia coli   S   I   S   S   R  # For CLEANING existing SIR values ------------------------------------  as.sir(c(\"S\", \"I\", \"R\", \"A\", \"B\", \"C\")) #> Warning: in as.sir(): 3 results in column '24' truncated (50%) that were invalid #> antimicrobial interpretations: \"A\", \"B\", and \"C\" #> Class 'sir' #> [1] S    I    R    <NA> <NA> <NA> as.sir(\"<= 0.002; S\") # will return \"S\" #> Class 'sir' #> [1] S sir_data <- as.sir(c(rep(\"S\", 474), rep(\"I\", 36), rep(\"R\", 370))) is.sir(sir_data) #> [1] TRUE plot(sir_data) # for percentages  barplot(sir_data) # for frequencies   # the dplyr way if (require(\"dplyr\")) {   example_isolates %>%     mutate_at(vars(PEN:RIF), as.sir)   # same:   example_isolates %>%     as.sir(PEN:RIF)    # fastest way to transform all columns with already valid AMR results to class `sir`:   example_isolates %>%     mutate_if(is_sir_eligible, as.sir)    # since dplyr 1.0.0, this can also be:   # example_isolates %>%   #   mutate(across(where(is_sir_eligible), as.sir)) } #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … # }"},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":null,"dir":"Reference","previous_headings":"","what":"Get ATC Properties from WHOCC Website — atc_online_property","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"Gets data WHOCC website determine properties Anatomical Therapeutic Chemical (ATC) (e.g. antibiotic), name, defined daily dose (DDD) standard unit.","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"","code":"atc_online_property(   atc_code,   property,   administration = \"O\",   url = \"https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no\",   url_vet = \"https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no\" )  atc_online_groups(atc_code, ...)  atc_online_ddd(atc_code, ...)  atc_online_ddd_units(atc_code, ...)"},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"https://www.whocc./atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"atc_code character (vector) ATC code(s) antibiotics, coerced .ab() ab_atc() internally valid ATC code property property ATC code. Valid values \"ATC\", \"Name\", \"DDD\", \"U\" (\"unit\"), \"Adm.R\", \"Note\" groups. last option, hierarchical groups ATC code returned, see Examples. administration type administration using property = \"Adm.R\", see Details url url website WHOCC. sign %s can used placeholder ATC codes. url_vet url website WHOCC veterinary medicine. sign %s can used placeholder ATC_vet codes (start \"Q\"). ... arguments pass atc_property","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"Options argument administration: \"Implant\" = Implant \"Inhal\" = Inhalation \"Instill\" = Instillation \"N\" = nasal \"O\" = oral \"P\" = parenteral \"R\" = rectal \"SL\" = sublingual/buccal \"TD\" = transdermal \"V\" = vaginal Abbreviations return values using property = \"U\" (unit): \"g\" = gram \"mg\" = milligram \"mcg\" = microgram \"U\" = unit \"TU\" = thousand units \"MU\" = million units \"mmol\" = millimole \"ml\" = millilitre (e.g. eyedrops) N.B. function requires internet connection works following packages installed: curl, rvest, xml2.","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"","code":"# \\donttest{ if (requireNamespace(\"curl\") && requireNamespace(\"rvest\") && requireNamespace(\"xml2\")) {   # oral DDD (Defined Daily Dose) of amoxicillin   atc_online_property(\"J01CA04\", \"DDD\", \"O\")   atc_online_ddd(ab_atc(\"amox\"))    # parenteral DDD (Defined Daily Dose) of amoxicillin   atc_online_property(\"J01CA04\", \"DDD\", \"P\")    atc_online_property(\"J01CA04\", property = \"groups\") # search hierarchical groups of amoxicillin } #> Loading required namespace: rvest #> [1] \"ANTIINFECTIVES FOR SYSTEMIC USE\"         #> [2] \"ANTIBACTERIALS FOR SYSTEMIC USE\"         #> [3] \"BETA-LACTAM ANTIBACTERIALS, PENICILLINS\" #> [4] \"Penicillins with extended spectrum\"      # }"},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"Use function e.g. clinical texts health care records. returns list antiviral drugs, doses forms administration found texts.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"","code":"av_from_text(   text,   type = c(\"drug\", \"dose\", \"administration\"),   collapse = NULL,   translate_av = FALSE,   thorough_search = NULL,   info = interactive(),   ... )"},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"text text analyse type type property search , either \"drug\", \"dose\" \"administration\", see Examples collapse character pass paste(, collapse = ...) return one character per element text, see Examples translate_av type = \"drug\": column name antivirals data set translate antibiotic abbreviations , using av_property(). default FALSE. Using TRUE equal using \"name\". thorough_search logical indicate whether input must extensively searched misspelling faulty input values. Setting TRUE take considerably time using FALSE. default, turn TRUE input elements contain maximum three words. info logical indicate whether progress bar printed - default TRUE interactive mode ... arguments passed .av()","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"list,  character collapse NULL","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"function also internally used .av(), although searches first drug name throw note drug names returned. Note: .av() function may use long regular expression match brand names antiviral drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"argument-type","dir":"Reference","previous_headings":"","what":"Argument type","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"default, function search antiviral drug names. text elements searched official names, ATC codes brand names. uses .av() internally, correct misspelling. type = \"dose\" (similar, like \"dosing\", \"doses\"), text elements searched numeric values higher 100 resemble years. output numeric. supports unit (g, mg, IE, etc.) multiple values one clinical text, see Examples. type = \"administration\" (abbreviations, like \"admin\", \"adm\"), text elements searched form drug administration. supports following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal vaginal. Abbreviations oral ('po', 'per os') become \"oral\", values intravenous ('iv', 'intraven') become \"iv\". supports multiple values one clinical text, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"argument-collapse","dir":"Reference","previous_headings":"","what":"Argument collapse","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"Without using collapse, function return list. can convenient use e.g. inside mutate()):df %>% mutate(avx = av_from_text(clinical_text)) returned AV codes can transformed official names, groups, etc. av_* functions av_name() av_group(), using translate_av argument. using collapse, function return character:df %>% mutate(avx = av_from_text(clinical_text, collapse = \"|\"))","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"","code":"av_from_text(\"28/03/2020 valaciclovir po tid\") #> [[1]] #> Class 'av' #> [1] VALA #>  av_from_text(\"28/03/2020 valaciclovir po tid\", type = \"admin\") #> [[1]] #> [1] \"oral\" #>"},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Properties of an Antiviral Drug — av_property","title":"Get Properties of an Antiviral Drug — av_property","text":"Use functions return specific property antiviral drug antivirals data set. input values evaluated internally .av().","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Properties of an Antiviral Drug — av_property","text":"","code":"av_name(x, language = get_AMR_locale(), tolower = FALSE, ...)  av_cid(x, ...)  av_synonyms(x, ...)  av_tradenames(x, ...)  av_group(x, language = get_AMR_locale(), ...)  av_atc(x, ...)  av_loinc(x, ...)  av_ddd(x, administration = \"oral\", ...)  av_ddd_units(x, administration = \"oral\", ...)  av_info(x, language = get_AMR_locale(), ...)  av_url(x, open = FALSE, ...)  av_property(x, property = \"name\", language = get_AMR_locale(), ...)"},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Properties of an Antiviral Drug — av_property","text":"x (vector ) text can coerced valid antiviral drug code .av() language language returned text - default system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. tolower logical indicate whether first character every output transformed lower case character. ... arguments passed .av() administration way administration, either \"oral\" \"iv\" open browse URL using utils::browseURL() property one column names one antivirals data set: vector_or(colnames(antivirals), sort = FALSE).","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Properties of an Antiviral Drug — av_property","text":"integer case av_cid() named list case av_info() multiple av_atc()/av_synonyms()/av_tradenames() double case av_ddd() character cases","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Properties of an Antiviral Drug — av_property","text":"output translated possible. function av_url() return direct URL official website. warning returned required ATC code available.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Properties of an Antiviral Drug — av_property","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Get Properties of an Antiviral Drug — av_property","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Properties of an Antiviral Drug — av_property","text":"","code":"# all properties: av_name(\"ACI\") #> [1] \"Aciclovir\" av_atc(\"ACI\") #> [1] \"J05AB01\" av_cid(\"ACI\") #> [1] 135398513 av_synonyms(\"ACI\") #>  [1] \"acicloftal\"        \"aciclovier\"        \"aciclovirum\"       #>  [4] \"activir\"           \"acyclofoam\"        \"acycloguanosine\"   #>  [7] \"acyclovir\"         \"acyclovir lauriad\" \"avaclyr\"           #> [10] \"cargosil\"          \"cyclovir\"          \"genvir\"            #> [13] \"gerpevir\"          \"hascovir\"          \"maynar\"            #> [16] \"novirus\"           \"poviral\"           \"sitavig\"           #> [19] \"sitavir\"           \"vipral\"            \"viropump\"          #> [22] \"virorax\"           \"zovirax\"           \"zyclir\"            av_tradenames(\"ACI\") #>  [1] \"acicloftal\"        \"aciclovier\"        \"aciclovirum\"       #>  [4] \"activir\"           \"acyclofoam\"        \"acycloguanosine\"   #>  [7] \"acyclovir\"         \"acyclovir lauriad\" \"avaclyr\"           #> [10] \"cargosil\"          \"cyclovir\"          \"genvir\"            #> [13] \"gerpevir\"          \"hascovir\"          \"maynar\"            #> [16] \"novirus\"           \"poviral\"           \"sitavig\"           #> [19] \"sitavir\"           \"vipral\"            \"viropump\"          #> [22] \"virorax\"           \"zovirax\"           \"zyclir\"            av_group(\"ACI\") #> [1] \"Nucleosides and nucleotides excl. reverse transcriptase inhibitors\" av_url(\"ACI\") #>                                                             Aciclovir  #> \"https://www.whocc.no/atc_ddd_index/?code=J05AB01&showdescription=no\"   # smart lowercase tranformation av_name(x = c(\"ACI\", \"VALA\")) #> [1] \"Aciclovir\"    \"Valaciclovir\" av_name(x = c(\"ACI\", \"VALA\"), tolower = TRUE) #> [1] \"aciclovir\"    \"valaciclovir\"  # defined daily doses (DDD) av_ddd(\"ACI\", \"oral\") #> [1] 4 av_ddd_units(\"ACI\", \"oral\") #> [1] \"g\" av_ddd(\"ACI\", \"iv\") #> [1] 4 av_ddd_units(\"ACI\", \"iv\") #> [1] \"g\"  av_info(\"ACI\") # all properties as a list #> $av #> [1] \"ACI\" #>  #> $cid #> [1] 135398513 #>  #> $name #> [1] \"Aciclovir\" #>  #> $group #> [1] \"Nucleosides and nucleotides excl. reverse transcriptase inhibitors\" #>  #> $atc #> [1] \"J05AB01\" #>  #> $tradenames #>  [1] \"acicloftal\"        \"aciclovier\"        \"aciclovirum\"       #>  [4] \"activir\"           \"acyclofoam\"        \"acycloguanosine\"   #>  [7] \"acyclovir\"         \"acyclovir lauriad\" \"avaclyr\"           #> [10] \"cargosil\"          \"cyclovir\"          \"genvir\"            #> [13] \"gerpevir\"          \"hascovir\"          \"maynar\"            #> [16] \"novirus\"           \"poviral\"           \"sitavig\"           #> [19] \"sitavir\"           \"vipral\"            \"viropump\"          #> [22] \"virorax\"           \"zovirax\"           \"zyclir\"            #>  #> $loinc #> [1] \"\" #>  #> $ddd #> $ddd$oral #> $ddd$oral$amount #> [1] 4 #>  #> $ddd$oral$units #> [1] \"g\" #>  #>  #> $ddd$iv #> $ddd$iv$amount #> [1] 4 #>  #> $ddd$iv$units #> [1] \"g\" #>  #>  #>   # all av_* functions use as.av() internally, so you can go from 'any' to 'any': av_atc(\"ACI\") #> [1] \"J05AB01\" av_group(\"J05AB01\") #> [1] \"Nucleosides and nucleotides excl. reverse transcriptase inhibitors\" av_loinc(\"abacavir\") #> [1] \"29113-8\" \"78772-1\" \"78773-9\" \"79134-3\" \"80118-3\" av_name(\"29113-8\") #> [1] \"Abacavir\" av_name(135398513) #> [1] \"Aciclovir\" av_name(\"J05AB01\") #> [1] \"Aciclovir\""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Availability of Columns — availability","title":"Check Availability of Columns — availability","text":"Easy check data availability columns data set. makes easy get idea antimicrobial combinations can used calculation e.g. susceptibility() resistance().","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Availability of Columns — availability","text":"","code":"availability(tbl, width = NULL)"},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Availability of Columns — availability","text":"tbl data.frame list width number characters present visual availability - default filling width console","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Availability of Columns — availability","text":"data.frame column names tbl row names","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check Availability of Columns — availability","text":"function returns data.frame columns \"resistant\" \"visual_resistance\". values columns calculated resistance().","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Availability of Columns — availability","text":"","code":"availability(example_isolates) #>         count available     visual_availabilty resistant      visual_resistance #> date     2000    100.0% |####################|                                  #> patient  2000    100.0% |####################|                                  #> age      2000    100.0% |####################|                                  #> gender   2000    100.0% |####################|                                  #> ward     2000    100.0% |####################|                                  #> mo       2000    100.0% |####################|                                  #> PEN      1629     81.5% |################----|     73.7% |##############------| #> OXA       365     18.3% |###-----------------|     31.2% |######--------------| #> FLC       943     47.2% |#########-----------|     29.5% |#####---------------| #> AMX      1350     67.5% |#############-------|     59.6% |###########---------| #> AMC      1879     94.0% |##################--|     23.7% |####----------------| #> AMP      1350     67.5% |#############-------|     59.6% |###########---------| #> TZP      1001     50.0% |##########----------|     12.6% |##------------------| #> CZO       446     22.3% |####----------------|     44.6% |########------------| #> FEP       724     36.2% |#######-------------|     14.2% |##------------------| #> CXM      1789     89.5% |#################---|     26.3% |#####---------------| #> FOX       818     40.9% |########------------|     27.4% |#####---------------| #> CTX       943     47.2% |#########-----------|     15.5% |###-----------------| #> CAZ      1811     90.6% |##################--|     66.5% |#############-------| #> CRO       943     47.2% |#########-----------|     15.5% |###-----------------| #> GEN      1855     92.8% |##################--|     24.6% |####----------------| #> TOB      1351     67.6% |#############-------|     34.4% |######--------------| #> AMK       692     34.6% |######--------------|     63.7% |############--------| #> KAN       471     23.6% |####----------------|    100.0% |####################| #> TMP      1499     75.0% |###############-----|     38.1% |#######-------------| #> SXT      1759     88.0% |#################---|     20.5% |####----------------| #> NIT       743     37.2% |#######-------------|     17.1% |###-----------------| #> FOS       351     17.6% |###-----------------|     42.2% |########------------| #> LNZ      1023     51.2% |##########----------|     69.3% |#############-------| #> CIP      1409     70.5% |#############-------|     16.2% |###-----------------| #> MFX       211     10.6% |##------------------|     33.6% |######--------------| #> VAN      1861     93.1% |##################--|     38.3% |#######-------------| #> TEC       976     48.8% |#########-----------|     75.7% |###############-----| #> TCY      1200     60.0% |###########---------|     29.8% |#####---------------| #> TGC       798     39.9% |########------------|     12.7% |##------------------| #> DOX      1136     56.8% |###########---------|     27.7% |#####---------------| #> ERY      1894     94.7% |##################--|     57.2% |###########---------| #> CLI      1520     76.0% |###############-----|     61.2% |############--------| #> AZM      1894     94.7% |##################--|     57.2% |###########---------| #> IPM       889     44.5% |########------------|      6.2% |#-------------------| #> MEM       829     41.5% |########------------|      5.9% |#-------------------| #> MTR        34      1.7% |--------------------|     14.7% |##------------------| #> CHL       154      7.7% |#-------------------|     21.4% |####----------------| #> COL      1640     82.0% |################----|     81.2% |################----| #> MUP       270     13.5% |##------------------|      5.9% |#-------------------| #> RIF      1003     50.2% |##########----------|     69.6% |#############-------| # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     filter(mo == as.mo(\"Escherichia coli\")) %>%     select_if(is.sir) %>%     availability() } #>     count available       visual_availabilty resistant        visual_resistance #> PEN   467    100.0% |######################|    100.0% |######################| #> OXA     0      0.0% |----------------------|                                    #> FLC     0      0.0% |----------------------|                                    #> AMX   392     83.9% |##################----|     50.0% |###########-----------| #> AMC   467    100.0% |######################|     13.1% |##--------------------| #> AMP   392     83.9% |##################----|     50.0% |###########-----------| #> TZP   416     89.1% |###################---|      5.5% |#---------------------| #> CZO    82     17.6% |###-------------------|      2.4% |----------------------| #> FEP   317     67.9% |##############--------|      2.8% |----------------------| #> CXM   465     99.6% |######################|      5.4% |#---------------------| #> FOX   377     80.7% |#################-----|      6.9% |#---------------------| #> CTX   459     98.3% |#####################-|      2.4% |----------------------| #> CAZ   460     98.5% |#####################-|      2.4% |----------------------| #> CRO   459     98.3% |#####################-|      2.4% |----------------------| #> GEN   460     98.5% |#####################-|      2.0% |----------------------| #> TOB   462     98.9% |#####################-|      2.6% |----------------------| #> AMK   171     36.6% |########--------------|      0.0% |----------------------| #> KAN     0      0.0% |----------------------|                                    #> TMP   396     84.8% |##################----|     39.1% |########--------------| #> SXT   465     99.6% |######################|     31.6% |######----------------| #> NIT   458     98.1% |#####################-|      2.8% |----------------------| #> FOS    61     13.1% |##--------------------|      0.0% |----------------------| #> LNZ   467    100.0% |######################|    100.0% |######################| #> CIP   456     97.6% |#####################-|     12.5% |##--------------------| #> MFX    57     12.2% |##--------------------|    100.0% |######################| #> VAN   467    100.0% |######################|    100.0% |######################| #> TEC   467    100.0% |######################|    100.0% |######################| #> TCY     3      0.6% |----------------------|     66.7% |##############--------| #> TGC    68     14.6% |###-------------------|      0.0% |----------------------| #> DOX     0      0.0% |----------------------|                                    #> ERY   467    100.0% |######################|    100.0% |######################| #> CLI   467    100.0% |######################|    100.0% |######################| #> AZM   467    100.0% |######################|    100.0% |######################| #> IPM   422     90.4% |###################---|      0.0% |----------------------| #> MEM   418     89.5% |###################---|      0.0% |----------------------| #> MTR     2      0.4% |----------------------|      0.0% |----------------------| #> CHL     0      0.0% |----------------------|                                    #> COL   240     51.4% |###########-----------|      0.0% |----------------------| #> MUP     0      0.0% |----------------------|                                    #> RIF   467    100.0% |######################|    100.0% |######################| # }"},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Bug-Drug Combinations — bug_drug_combinations","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"Determine antimicrobial resistance (AMR) bug-drug combinations data set least 30 (default) isolates available per species. Use format() result prettify publishable/printable format, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"","code":"bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)  # S3 method for bug_drug_combinations format(   x,   translate_ab = \"name (ab, atc)\",   language = get_AMR_locale(),   minimum = 30,   combine_SI = TRUE,   add_ab_group = TRUE,   remove_intrinsic_resistant = FALSE,   decimal.mark = getOption(\"OutDec\"),   big.mark = ifelse(decimal.mark == \",\", \".\", \",\"),   ... )"},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"x data set antibiotic columns, amox, AMX AMC col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). FUN function call mo column transform microorganism codes - default mo_shortname() ... arguments passed FUN translate_ab character length 1 containing column names antibiotics data set language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. combine_SI logical indicate whether values S summed, resistance based R - default TRUE add_ab_group logical indicate group antimicrobials must included first column remove_intrinsic_resistant logical indicate rows columns 100% resistance tested antimicrobials must removed table decimal.mark character used indicate numeric     decimal point. big.mark character; empty used mark every     big.interval decimals (hence big)     decimal point.","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"function bug_drug_combinations() returns data.frame columns \"mo\", \"ab\", \"S\", \"\", \"R\" \"total\".","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"function format() calculates resistance per bug-drug combination returns table ready reporting/publishing. Use combine_SI = TRUE (default) test R vs. S+combine_SI = FALSE test R+vs. S. table can also directly used R Markdown / Quarto without need e.g. knitr::kable().","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # \\donttest{ x <- bug_drug_combinations(example_isolates) head(x) #> # A tibble: 6 × 6 #>   mo                ab        S     I     R total #>   <chr>             <chr> <int> <int> <int> <int> #> 1 (unknown species) AMC      15     0     0    15 #> 2 (unknown species) AMK       0     0     0     0 #> 3 (unknown species) AMP      15     0     1    16 #> 4 (unknown species) AMX      15     0     1    16 #> 5 (unknown species) AZM       3     0     3     6 #> 6 (unknown species) CAZ       0     0     0     0 #> Use 'format()' on this result to get a publishable/printable format. format(x, translate_ab = \"name (atc)\") #> # A tibble: 39 × 12 #>    Group     Drug  CoNS  `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa` #>    <chr>     <chr> <chr> <chr>     <chr>         <chr>           <chr>           #>  1 \"Aminogl… Amik… \"100… \"  0.0% … \"100.0% (39/… \"\"              \"\"              #>  2 \"\"        Gent… \" 13… \"  2.0% … \"100.0% (39/… \" 10.3% (6/58)\" \"  0.0% (0/30)\" #>  3 \"\"        Kana… \"100… \"\"        \"100.0% (39/… \"\"              \"100.0% (30/30… #>  4 \"\"        Tobr… \" 78… \"  2.6% … \"100.0% (39/… \" 10.3% (6/58)\" \"  0.0% (0/30)\" #>  5 \"Ampheni… Chlo… \"\"    \"\"        \"\"            \"\"              \"100.0% (30/30… #>  6 \"Antimyc… Rifa… \"\"    \"100.0% … \"\"            \"100.0% (58/58… \"100.0% (30/30… #>  7 \"Beta-la… Amox… \" 93… \" 50.0% … \"\"            \"100.0% (58/58… \"100.0% (30/30… #>  8 \"\"        Amox… \" 42… \" 13.1% … \"\"            \" 10.3% (6/58)\" \"100.0% (30/30… #>  9 \"\"        Ampi… \" 93… \" 50.0% … \"\"            \"100.0% (58/58… \"100.0% (30/30… #> 10 \"\"        Benz… \" 77… \"100.0% … \"\"            \"100.0% (58/58… \"100.0% (30/30… #> # ℹ 29 more rows #> # ℹ 5 more variables: `P. mirabilis` <chr>, `S. aureus` <chr>, #> #   `S. epidermidis` <chr>, `S. hominis` <chr>, `S. pneumoniae` <chr>  # Use FUN to change to transformation of microorganism codes bug_drug_combinations(example_isolates,   FUN = mo_gramstain ) #> # A tibble: 80 × 6 #>    mo            ab        S     I     R total #>  * <chr>         <chr> <int> <int> <int> <int> #>  1 Gram-negative AMC     463    89   174   726 #>  2 Gram-negative AMK     251     0     5   256 #>  3 Gram-negative AMP     226     0   405   631 #>  4 Gram-negative AMX     226     0   405   631 #>  5 Gram-negative AZM       1     2   696   699 #>  6 Gram-negative CAZ     607     0    27   634 #>  7 Gram-negative CHL       1     0    30    31 #>  8 Gram-negative CIP     610    11    63   684 #>  9 Gram-negative CLI      18     1   709   728 #> 10 Gram-negative COL     309     0    78   387 #> # ℹ 70 more rows #> Use 'format()' on this result to get a publishable/printable format.  bug_drug_combinations(example_isolates,   FUN = function(x) {     ifelse(x == as.mo(\"Escherichia coli\"),       \"E. coli\",       \"Others\"     )   } ) #> # A tibble: 80 × 6 #>    mo      ab        S     I     R total #>  * <chr>   <chr> <int> <int> <int> <int> #>  1 E. coli AMC     332    74    61   467 #>  2 E. coli AMK     171     0     0   171 #>  3 E. coli AMP     196     0   196   392 #>  4 E. coli AMX     196     0   196   392 #>  5 E. coli AZM       0     0   467   467 #>  6 E. coli CAZ     449     0    11   460 #>  7 E. coli CHL       0     0     0     0 #>  8 E. coli CIP     398     1    57   456 #>  9 E. coli CLI       0     0   467   467 #> 10 E. coli COL     240     0     0   240 #> # ℹ 70 more rows #> Use 'format()' on this result to get a publishable/printable format. # }"},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"Data set containing clinical breakpoints interpret MIC disk diffusion SIR values, according international guidelines. Currently implemented guidelines EUCAST (2013-2022) CLSI (2013-2022). Use .sir() transform MICs disks measurements SIR values.","code":""},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"","code":"clinical_breakpoints"},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"tibble 18 271 observations 11 variables: guideline Name guideline method Either \"DISK\" \"MIC\" site Body site, e.g. \"Oral\" \"Respiratory\" mo Microbial ID, see .mo() rank_index Taxonomic rank index mo 1 (subspecies/infraspecies) 5 (unknown microorganism) ab Antibiotic ID, see .ab() ref_tbl Info guideline rule can found disk_dose Dose used disk diffusion method breakpoint_S Lowest MIC value highest number millimetres leads \"S\" breakpoint_R Highest MIC value lowest number millimetres leads \"R\" uti logical value (TRUE/FALSE) indicate whether rule applies urinary tract infection (UTI)","code":""},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository. allow machine reading EUCAST CLSI guidelines, almost impossible MS Excel PDF files distributed EUCAST CLSI.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"","code":"clinical_breakpoints #> # A tibble: 18,271 × 11 #>    guideline   method site  mo               rank_index ab   ref_tbl   disk_dose #>    <chr>       <chr>  <chr> <mo>                  <dbl> <ab> <chr>     <chr>     #>  1 EUCAST 2022 MIC    NA    F_ASPRG_MGTS              2 AMB  Aspergil… NA        #>  2 EUCAST 2022 MIC    NA    F_ASPRG_NIGR              2 AMB  Aspergil… NA        #>  3 EUCAST 2022 MIC    NA    F_CANDD_ALBC              2 AMB  Candida   NA        #>  4 EUCAST 2022 MIC    NA    F_CANDD_DBLN              2 AMB  Candida   NA        #>  5 EUCAST 2022 MIC    NA    F_CANDD_GLBR              2 AMB  Candida   NA        #>  6 EUCAST 2022 MIC    NA    F_CANDD_KRUS              2 AMB  Candida   NA        #>  7 EUCAST 2022 MIC    NA    F_CANDD_PRPS              2 AMB  Candida   NA        #>  8 EUCAST 2022 MIC    NA    F_CANDD_TRPC              2 AMB  Candida   NA        #>  9 EUCAST 2022 MIC    NA    F_CRYPT_NFRM              2 AMB  Candida   NA        #> 10 EUCAST 2022 DISK   NA    B_[ORD]_ENTRBCTR          5 AMC  Enteroba… 20ug/10ug #> # ℹ 18,261 more rows #> # ℹ 3 more variables: breakpoint_S <dbl>, breakpoint_R <dbl>, uti <lgl>"},{"path":"https://msberends.github.io/AMR/reference/count.html","id":null,"dir":"Reference","previous_headings":"","what":"Count Available Isolates — count","title":"Count Available Isolates — count","text":"functions can used count resistant/susceptible microbial isolates. functions support quasiquotation pipes, can used summarise() dplyr package also support grouped variables, see Examples. count_resistant() used count resistant isolates, count_susceptible() used count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count Available Isolates — count","text":"","code":"count_resistant(..., only_all_tested = FALSE)  count_susceptible(..., only_all_tested = FALSE)  count_R(..., only_all_tested = FALSE)  count_IR(..., only_all_tested = FALSE)  count_I(..., only_all_tested = FALSE)  count_SI(..., only_all_tested = FALSE)  count_S(..., only_all_tested = FALSE)  count_all(..., only_all_tested = FALSE)  n_sir(..., only_all_tested = FALSE)  count_df(   data,   translate_ab = \"name\",   language = get_AMR_locale(),   combine_SI = TRUE )"},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count Available Isolates — count","text":"... one vectors (columns) antibiotic interpretations. transformed internally .sir() needed. only_all_tested (combination therapies, .e. using one variable ...): logical indicate isolates must tested antibiotics, see section Combination Therapy data data.frame containing columns class sir (see .sir()) translate_ab column name antibiotics data set translate antibiotic abbreviations , using ab_property() language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. combine_SI logical indicate whether values S must merged one, output consists S+vs. R (susceptible vs. resistant) - default TRUE","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count Available Isolates — count","text":"integer","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Count Available Isolates — count","text":"functions meant count isolates. Use resistance()/susceptibility() functions calculate microbial resistance/susceptibility. function count_resistant() equal function count_R(). function count_susceptible() equal function count_SI(). function n_sir() alias count_all(). can used count available isolates, .e. input antibiotics available result (S, R). use equal n_distinct(). function equal count_susceptible(...) + count_resistant(...). function count_df() takes variable data sir class (created .sir()) counts number S's, 's R's. also supports grouped variables. function sir_df() works exactly like count_df(), adds percentage S, R.","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Count Available Isolates — count","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"combination-therapy","dir":"Reference","previous_headings":"","what":"Combination Therapy","title":"Count Available Isolates — count","text":"using one variable ... (= combination therapy), use only_all_tested count isolates tested antibiotics/variables test . See example two antibiotics, Drug Drug B, susceptibility() works calculate %SI:   Please note , combination therapies, only_all_tested = TRUE applies :   , combination therapies, only_all_tested = FALSE applies :   Using only_all_tested impact using one antibiotic input.","code":"--------------------------------------------------------------------                     only_all_tested = FALSE  only_all_tested = TRUE                     -----------------------  -----------------------  Drug A    Drug B   include as  include as   include as  include as                     numerator   denominator  numerator   denominator --------  --------  ----------  -----------  ----------  -----------  S or I    S or I       X            X            X            X    R       S or I       X            X            X            X   <NA>     S or I       X            X            -            -  S or I      R          X            X            X            X    R         R          -            X            -            X   <NA>       R          -            -            -            -  S or I     <NA>        X            X            -            -    R        <NA>        -            -            -            -   <NA>      <NA>        -            -            -            - -------------------------------------------------------------------- count_S()    +   count_I()    +   count_R()    = count_all()   proportion_S() + proportion_I() + proportion_R() = 1 count_S()    +   count_I()    +   count_R()    >= count_all()   proportion_S() + proportion_I() + proportion_R() >= 1"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count Available Isolates — count","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info.  # base R ------------------------------------------------------------ count_resistant(example_isolates$AMX) # counts \"R\" #> [1] 804 count_susceptible(example_isolates$AMX) # counts \"S\" and \"I\" #> [1] 546 count_all(example_isolates$AMX) # counts \"S\", \"I\" and \"R\" #> [1] 1350  # be more specific count_S(example_isolates$AMX) #> Using count_S() is discouraged; use count_susceptible() instead to also #> consider \"I\" being susceptible. This note will be shown once for this #> session. #> [1] 543 count_SI(example_isolates$AMX) #> [1] 546 count_I(example_isolates$AMX) #> [1] 3 count_IR(example_isolates$AMX) #> Using count_IR() is discouraged; use count_resistant() instead to not #> consider \"I\" being resistant. This note will be shown once for this #> session. #> [1] 807 count_R(example_isolates$AMX) #> [1] 804  # Count all available isolates count_all(example_isolates$AMX) #> [1] 1350 n_sir(example_isolates$AMX) #> [1] 1350  # n_sir() is an alias of count_all(). # Since it counts all available isolates, you can # calculate back to count e.g. susceptible isolates. # These results are the same: count_susceptible(example_isolates$AMX) #> [1] 546 susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX) #> [1] 546  # dplyr ------------------------------------------------------------- # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       R = count_R(CIP),       I = count_I(CIP),       S = count_S(CIP),       n1 = count_all(CIP), # the actual total; sum of all three       n2 = n_sir(CIP), # same - analogous to n_distinct       total = n()     ) # NOT the number of tested isolates!    # Number of available isolates for a whole antibiotic class   # (i.e., in this data set columns GEN, TOB, AMK, KAN)   example_isolates %>%     group_by(ward) %>%     summarise(across(aminoglycosides(), n_sir))    # Count co-resistance between amoxicillin/clav acid and gentamicin,   # so we can see that combination therapy does a lot more than mono therapy.   # Please mind that `susceptibility()` calculates percentages right away instead.   example_isolates %>% count_susceptible(AMC) # 1433   example_isolates %>% count_all(AMC) # 1879    example_isolates %>% count_susceptible(GEN) # 1399   example_isolates %>% count_all(GEN) # 1855    example_isolates %>% count_susceptible(AMC, GEN) # 1764   example_isolates %>% count_all(AMC, GEN) # 1936    # Get number of S+I vs. R immediately of selected columns   example_isolates %>%     select(AMX, CIP) %>%     count_df(translate = FALSE)    # It also supports grouping variables   example_isolates %>%     select(ward, AMX, CIP) %>%     group_by(ward) %>%     count_df(translate = FALSE) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 12 × 4 #>    ward       antibiotic interpretation value #>  * <chr>      <chr>      <ord>          <int> #>  1 Clinical   AMX        SI               357 #>  2 Clinical   AMX        R                487 #>  3 Clinical   CIP        SI               741 #>  4 Clinical   CIP        R                128 #>  5 ICU        AMX        SI               158 #>  6 ICU        AMX        R                270 #>  7 ICU        CIP        SI               362 #>  8 ICU        CIP        R                 85 #>  9 Outpatient AMX        SI                31 #> 10 Outpatient AMX        R                 47 #> 11 Outpatient CIP        SI                78 #> 12 Outpatient CIP        R                 15 # }"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":null,"dir":"Reference","previous_headings":"","what":"Define Custom EUCAST Rules — custom_eucast_rules","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"Define custom EUCAST rules organisation specific analysis use output function eucast_rules().","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"","code":"custom_eucast_rules(...)"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"... rules formula notation, see Examples","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"list containing custom rules","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"organisations adoption EUCAST rules. function can used define custom EUCAST rules used eucast_rules() function.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"basics","dir":"Reference","previous_headings":"","what":"Basics","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"familiar case_when() function dplyr package, recognise input method set rules. Rules must set using R considers 'formula notation'. rule written tilde (~) consequence rule written tilde:   two custom EUCAST rules: TZP (piperacillin/tazobactam) \"S\", aminopenicillins (ampicillin amoxicillin) must made \"S\", TZP \"R\", aminopenicillins must made \"R\". rules can also printed console, immediately clear work:   rules (part tilde, example TZP == \"S\" TZP == \"R\") must evaluable data set: able run filter data set without errors. means example column TZP must exist. create sample data set test rules set:","code":"x <- custom_eucast_rules(TZP == \"S\" ~ aminopenicillins == \"S\",                          TZP == \"R\" ~ aminopenicillins == \"R\") x #> A set of custom EUCAST rules: #> #>   1. If TZP is \"S\" then set to  S : #>      amoxicillin (AMX), ampicillin (AMP) #> #>   2. If TZP is \"R\" then set to  R : #>      amoxicillin (AMX), ampicillin (AMP) df <- data.frame(mo = c(\"Escherichia coli\", \"Klebsiella pneumoniae\"),                  TZP = as.sir(\"R\"),                  ampi = as.sir(\"S\"),                  cipro = as.sir(\"S\")) df #>                      mo TZP ampi cipro #> 1      Escherichia coli   R    S     S #> 2 Klebsiella pneumoniae   R    S     S  eucast_rules(df, rules = \"custom\", custom_rules = x, info = FALSE) #>                      mo TZP ampi cipro #> 1      Escherichia coli   R    R     S #> 2 Klebsiella pneumoniae   R    R     S"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"using-taxonomic-properties-in-rules","dir":"Reference","previous_headings":"","what":"Using taxonomic properties in rules","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"one exception columns used rules: column names microorganisms data set can also used, exist data set. column names : \"mo\", \"fullname\", \"status\", \"kingdom\", \"phylum\", \"class\", \"order\", \"family\", \"genus\", \"species\", \"subspecies\", \"rank\", \"ref\", \"source\", \"lpsn\", \"lpsn_parent\", \"lpsn_renamed_to\", \"gbif\", \"gbif_parent\", \"gbif_renamed_to\", \"prevalence\", \"snomed\". Thus, next example work well, despite fact df data set contain column genus:","code":"y <- custom_eucast_rules(TZP == \"S\" & genus == \"Klebsiella\" ~ aminopenicillins == \"S\",                          TZP == \"R\" & genus == \"Klebsiella\" ~ aminopenicillins == \"R\")  eucast_rules(df, rules = \"custom\", custom_rules = y, info = FALSE) #>                      mo TZP ampi cipro #> 1      Escherichia coli   R    S     S #> 2 Klebsiella pneumoniae   R    R     S"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"usage-of-antibiotic-group-names","dir":"Reference","previous_headings":"","what":"Usage of antibiotic group names","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"possible define antibiotic groups instead single antibiotics rule consequence, part tilde. examples, antibiotic group aminopenicillins used include ampicillin amoxicillin. following groups allowed (case-insensitive). Within parentheses drugs matched running rule. \"aminoglycosides\"(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, tobramycin-high) \"aminopenicillins\"(amoxicillin ampicillin) \"antifungals\"(amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, voriconazole) \"antimycobacterials\"(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, viomycin) \"betalactams\"(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid) \"carbapenems\"(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, tebipenem) \"cephalosporins\"(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, loracarbef) \"cephalosporins_1st\"(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephradine) \"cephalosporins_2nd\"(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, loracarbef) \"cephalosporins_3rd\"(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, latamoxef) \"cephalosporins_4th\"(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome, cefquinome) \"cephalosporins_5th\"(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam) \"cephalosporins_except_caz\"(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, loracarbef) \"fluoroquinolones\"(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin) \"glycopeptides\"(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod) \"glycopeptides_except_lipo\"(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod) \"lincosamides\"(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, tylvalosin) \"lipoglycopeptides\"(dalbavancin, oritavancin, telavancin) \"macrolides\"(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, tylvalosin) \"oxazolidinones\"(cadazolid, cycloserine, linezolid, tedizolid, thiacetazone) \"penicillins\"(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, ticarcillin/clavulanic acid) \"polymyxins\"(colistin, polymyxin B, polymyxin B/polysorbate 80) \"quinolones\"(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin) \"streptogramins\"(pristinamycin quinupristin/dalfopristin) \"tetracyclines\"(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tigecycline) \"tetracyclines_except_tgc\"(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline) \"trimethoprims\"(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, trimethoprim/sulfamethoxazole) \"ureidopenicillins\"(azlocillin, mezlocillin, piperacillin, piperacillin/tazobactam)","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"","code":"x <- custom_eucast_rules(   AMC == \"R\" & genus == \"Klebsiella\" ~ aminopenicillins == \"R\",   AMC == \"I\" & genus == \"Klebsiella\" ~ aminopenicillins == \"I\" ) x #> A set of custom EUCAST rules: #>  #>   1. If AMC is \"R\" and genus is \"Klebsiella\" then set to  R : #>      amoxicillin (AMX), ampicillin (AMP) #>  #>   2. If AMC is \"I\" and genus is \"Klebsiella\" then set to  I : #>      amoxicillin (AMX), ampicillin (AMP)  # run the custom rule set (verbose = TRUE will return a logbook instead of the data set): eucast_rules(example_isolates,   rules = \"custom\",   custom_rules = x,   info = FALSE,   verbose = TRUE ) #> # A tibble: 8 × 9 #>     row col   mo_fullname     old   new   rule  rule_group rule_name rule_source #>   <int> <chr> <chr>           <ord> <chr> <chr> <chr>      <chr>     <chr>       #> 1    33 AMP   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 2    33 AMX   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 3    34 AMP   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 4    34 AMX   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 5   531 AMP   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 6   531 AMX   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 7  1485 AMP   Klebsiella oxy… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 8  1485 AMX   Klebsiella oxy… R     I     \"rep… Custom EU… Custom E… Object 'x'…  # combine rule sets x2 <- c(   x,   custom_eucast_rules(TZP == \"R\" ~ carbapenems == \"R\") ) x2 #> A set of custom EUCAST rules: #>  #>   1. If AMC is \"R\" and genus is \"Klebsiella\" then set to  R : #>      amoxicillin (AMX), ampicillin (AMP) #>  #>   2. If AMC is \"I\" and genus is \"Klebsiella\" then set to  I : #>      amoxicillin (AMX), ampicillin (AMP) #>  #>   3. If TZP is \"R\" then set to  R : #>      biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), #>      imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), #>      meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), #>      razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), tebipenem (TBP)"},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"EUCAST breakpoints used package based dosages data set. can retrieved eucast_dosage().","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"","code":"dosage"},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"tibble 336 observations 9 variables: ab Antibiotic ID used package (AMC), using official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes available name Official name antimicrobial drug used WHONET/EARS-Net type Type dosage, either \"high_dosage\", \"standard_dosage\", \"uncomplicated_uti\" dose Dose, \"2 g\" \"25 mg/kg\" dose_times Number times dose must administered administration Route administration, either \"im\", \"iv\", \"oral\" notes Additional dosage notes original_txt Original text PDF file EUCAST eucast_version Version number EUCAST Clinical Breakpoints guideline dosages apply","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"data set based 'EUCAST Clinical Breakpoint Tables' v12.0 (2022) 'EUCAST Clinical Breakpoint Tables' v11.0 (2021).","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"","code":"dosage #> # A tibble: 336 × 9 #>    ab   name            type  dose  dose_times administration notes original_txt #>    <ab> <chr>           <chr> <chr>      <int> <chr>          <chr> <chr>        #>  1 AMK  Amikacin        stan… 25-3…          1 iv             \"\"    25-30 mg/kg… #>  2 AMX  Amoxicillin     high… 2 g            6 iv             \"\"    2 g x 6 iv   #>  3 AMX  Amoxicillin     stan… 1 g            3 iv             \"\"    1 g x 3-4 iv #>  4 AMX  Amoxicillin     high… 0.75…          3 oral           \"\"    0.75-1 g x … #>  5 AMX  Amoxicillin     stan… 0.5 g          3 oral           \"\"    0.5 g x 3 o… #>  6 AMX  Amoxicillin     unco… 0.5 g          3 oral           \"\"    0.5 g x 3 o… #>  7 AMC  Amoxicillin/cl… high… 2 g …          3 iv             \"\"    (2 g amoxic… #>  8 AMC  Amoxicillin/cl… stan… 1 g …          3 iv             \"\"    (1 g amoxic… #>  9 AMC  Amoxicillin/cl… high… 0.87…          3 oral           \"\"    (0.875 g am… #> 10 AMC  Amoxicillin/cl… stan… 0.5 …          3 oral           \"\"    (0.5 g amox… #> # ℹ 326 more rows #> # ℹ 1 more variable: eucast_version <dbl>"},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply EUCAST Rules — eucast_rules","title":"Apply EUCAST Rules — eucast_rules","text":"Apply rules clinical breakpoints intrinsic resistance defined European Committee Antimicrobial Susceptibility Testing (EUCAST, https://www.eucast.org), see Source. Use eucast_dosage() get data.frame advised dosages certain bug-drug combination, based dosage data set. improve interpretation antibiogram EUCAST rules applied, non-EUCAST rules can applied default, see Details.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply EUCAST Rules — eucast_rules","text":"","code":"eucast_rules(   x,   col_mo = NULL,   info = interactive(),   rules = getOption(\"AMR_eucastrules\", default = c(\"breakpoints\", \"expert\")),   verbose = FALSE,   version_breakpoints = 12,   version_expertrules = 3.3,   ampc_cephalosporin_resistance = NA,   only_sir_columns = FALSE,   custom_rules = NULL,   ... )  eucast_dosage(ab, administration = \"iv\", version_breakpoints = 12)"},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Apply EUCAST Rules — eucast_rules","text":"EUCAST Expert Rules. Version 2.0, 2012. Leclercq et al. EUCAST expert rules antimicrobial susceptibility testing. Clin Microbiol Infect. 2013;19(2):141-60; doi:10.1111/j.1469-0691.2011.03703.x EUCAST Expert Rules, Intrinsic Resistance Exceptional Phenotypes Tables. Version 3.1, 2016. (link) EUCAST Intrinsic Resistance Unusual Phenotypes. Version 3.2, 2020. (link) EUCAST Intrinsic Resistance Unusual Phenotypes. Version 3.3, 2021. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 9.0, 2019. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 10.0, 2020. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 11.0, 2021. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 12.0, 2022. (link)","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply EUCAST Rules — eucast_rules","text":"x data set antibiotic columns, amox, AMX AMC col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). info logical indicate whether progress printed console - default print interactive sessions rules character vector specifies rules applied. Must one \"breakpoints\", \"expert\", \"\", \"custom\", \"\", defaults c(\"breakpoints\", \"expert\"). default value can set another value using package option AMR_eucastrules: options(AMR_eucastrules = \"\"). using \"custom\", sure fill argument custom_rules . Custom rules can created custom_eucast_rules(). verbose logical turn Verbose mode (default ). Verbose mode, function apply rules data, instead returns data set logbook form extensive info rows columns effected way. Using Verbose mode takes lot time. version_breakpoints version number use EUCAST Clinical Breakpoints guideline. Can either \"12.0\", \"11.0\", \"10.0\". version_expertrules version number use EUCAST Expert Rules Intrinsic Resistance guideline. Can either \"3.3\", \"3.2\", \"3.1\". ampc_cephalosporin_resistance character value applied cefotaxime, ceftriaxone ceftazidime AmpC de-repressed cephalosporin-resistant mutants - default NA. Currently works version_expertrules 3.2 higher; version 'EUCAST Expert Rules Enterobacterales' state results cefotaxime, ceftriaxone ceftazidime reported note, results suppressed (emptied) three drugs. value NA (default) argument remove results three drugs, e.g. value \"R\" make results drugs resistant. Use NULL FALSE alter results three drugs AmpC de-repressed cephalosporin-resistant mutants. Using TRUE equal using \"R\".  EUCAST Expert Rules v3.2, rule applies : Citrobacter braakii, Citrobacter freundii, Citrobacter gillenii, Citrobacter murliniae, Citrobacter rodenticum, Citrobacter sedlakii, Citrobacter werkmanii, Citrobacter youngae, Enterobacter, Hafnia alvei, Klebsiella aerogenes, Morganella morganii, Providencia, Serratia. only_sir_columns logical indicate whether antibiotic columns must detected transformed class sir (see .sir()) beforehand (default FALSE) custom_rules custom rules apply, created custom_eucast_rules() ... column name antibiotic, see section Antibiotics ab (vector ) text can coerced valid antibiotic drug code .ab() administration route administration, either \"im\", \"iv\", \"oral\"","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply EUCAST Rules — eucast_rules","text":"input x, possibly edited values antibiotics. , verbose = TRUE, data.frame original new values affected bug-drug combinations.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Apply EUCAST Rules — eucast_rules","text":"Note: function translate MIC values SIR values. Use .sir() . Note: ampicillin (AMP, J01CA01) available amoxicillin (AMX, J01CA04) , latter used rules dependency ampicillin. drugs interchangeable comes expression antimicrobial resistance. file containing EUCAST rules located : https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv.  Note: Old taxonomic names replaced current taxonomy applicable. example, Ochrobactrum anthropi renamed Brucella anthropi 2020; original EUCAST rules v3.1 v3.2 yet contain new taxonomic name. AMR package contains full microbial taxonomy updated 11 December, 2022, see microorganisms.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"custom-rules","dir":"Reference","previous_headings":"","what":"Custom Rules","title":"Apply EUCAST Rules — eucast_rules","text":"Custom rules can created using custom_eucast_rules(), e.g.:","code":"x <- custom_eucast_rules(AMC == \"R\" & genus == \"Klebsiella\" ~ aminopenicillins == \"R\",                          AMC == \"I\" & genus == \"Klebsiella\" ~ aminopenicillins == \"I\")  eucast_rules(example_isolates, rules = \"custom\", custom_rules = x)"},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"-other-rules","dir":"Reference","previous_headings":"","what":"'Other' Rules","title":"Apply EUCAST Rules — eucast_rules","text":"processing, two non-EUCAST rules drug combinations can applied improve efficacy EUCAST rules, reliability data (analysis). rules : drug enzyme inhibitor set S drug without enzyme inhibitor S drug without enzyme inhibitor set R drug enzyme inhibitor R Important examples include amoxicillin amoxicillin/clavulanic acid, trimethoprim trimethoprim/sulfamethoxazole. Needless say, rules work, drugs must available data set. Since rules officially approved EUCAST, applied default. use rules, include \"\" rules argument, use eucast_rules(..., rules = \"\"). can also set package option AMR_eucastrules, .e. run options(AMR_eucastrules = \"\").","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"antibiotics","dir":"Reference","previous_headings":"","what":"Antibiotics","title":"Apply EUCAST Rules — eucast_rules","text":"define antibiotics column names, leave determine automatically guess_ab_col() input text (case-insensitive), use NULL skip column (e.g. TIC = NULL skip ticarcillin). Manually defined non-existing columns skipped warning. following antibiotics eligible functions eucast_rules() mdro(). shown format 'name (antimicrobial ID, ATC code)', sorted alphabetically: Amikacin (AMK, J01GB06), amoxicillin (AMX, J01CA04), amoxicillin/clavulanic acid (AMC, J01CR02), ampicillin (AMP, J01CA01), ampicillin/sulbactam (SAM, J01CR01), arbekacin (ARB, J01GB12), aspoxicillin (APX, J01CA19), azidocillin (AZD, J01CE04), azithromycin (AZM, J01FA10), azlocillin (AZL, J01CA09), aztreonam (ATM, J01DF01), bacampicillin (BAM, J01CA06), bekanamycin (BEK, J01GB13), benzathine benzylpenicillin (BNB, J01CE08), benzathine phenoxymethylpenicillin (BNP, J01CE10), benzylpenicillin (PEN, J01CE01), besifloxacin (BES, S01AE08), biapenem (BIA, J01DH05), carbenicillin (CRB, J01CA03), carindacillin (CRN, J01CA05), cefacetrile (CAC, J01DB10), cefaclor (CEC, J01DC04), cefadroxil (CFR, J01DB05), cefalexin (LEX, J01DB01), cefaloridine (RID, J01DB02), cefalotin (CEP, J01DB03), cefamandole (MAN, J01DC03), cefapirin (HAP, J01DB08), cefatrizine (CTZ, J01DB07), cefazedone (CZD, J01DB06), cefazolin (CZO, J01DB04), cefcapene (CCP, J01DD17), cefdinir (CDR, J01DD15), cefditoren (DIT, J01DD16), cefepime (FEP, J01DE01), cefetamet (CAT, J01DD10), cefixime (CFM, J01DD08), cefmenoxime (CMX, J01DD05), cefmetazole (CMZ, J01DC09), cefodizime (DIZ, J01DD09), cefonicid (CID, J01DC06), cefoperazone (CFP, J01DD12), cefoperazone/sulbactam (CSL, J01DD62), ceforanide (CND, J01DC11), cefotaxime (CTX, J01DD01), cefotaxime/clavulanic acid (CTC, J01DD51), cefotetan (CTT, J01DC05), cefotiam (CTF, J01DC07), cefoxitin (FOX, J01DC01), cefozopran (ZOP, J01DE03), cefpiramide (CPM, J01DD11), cefpirome (CPO, J01DE02), cefpodoxime (CPD, J01DD13), cefprozil (CPR, J01DC10), cefroxadine (CRD, J01DB11), cefsulodin (CFS, J01DD03), ceftaroline (CPT, J01DI02), ceftazidime (CAZ, J01DD02), ceftazidime/clavulanic acid (CCV, J01DD52), cefteram (CEM, J01DD18), ceftezole (CTL, J01DB12), ceftibuten (CTB, J01DD14), ceftizoxime (CZX, J01DD07), ceftobiprole medocaril (CFM1, J01DI01), ceftolozane/tazobactam (CZT, J01DI54), ceftriaxone (CRO, J01DD04), ceftriaxone/beta-lactamase inhibitor (CEB, J01DD63), cefuroxime (CXM, J01DC02), cephradine (CED, J01DB09), chloramphenicol (CHL, J01BA01), ciprofloxacin (CIP, J01MA02), clarithromycin (CLR, J01FA09), clindamycin (CLI, J01FF01), clometocillin (CLM, J01CE07), cloxacillin (CLO, J01CF02), colistin (COL, J01XB01), cycloserine (CYC, J04AB01), dalbavancin (DAL, J01XA04), daptomycin (DAP, J01XX09), delafloxacin (DFX, J01MA23), dibekacin (DKB, J01GB09), dicloxacillin (DIC, J01CF01), dirithromycin (DIR, J01FA13), doripenem (DOR, J01DH04), doxycycline (DOX, J01AA02), enoxacin (ENX, J01MA04), epicillin (EPC, J01CA07), ertapenem (ETP, J01DH03), erythromycin (ERY, J01FA01), fleroxacin (FLE, J01MA08), flucloxacillin (FLC, J01CF05), flurithromycin (FLR1, J01FA14), fosfomycin (FOS, J01XX01), framycetin (FRM, D09AA01), fusidic acid (FUS, J01XC01), garenoxacin (GRN, J01MA19), gatifloxacin (GAT, J01MA16), gemifloxacin (GEM, J01MA15), gentamicin (GEN, J01GB03), grepafloxacin (GRX, J01MA11), hetacillin (HET, J01CA18), imipenem (IPM, J01DH51), imipenem/relebactam (IMR, J01DH56), isepamicin (ISE, J01GB11), josamycin (JOS, J01FA07), kanamycin (KAN, J01GB04), lascufloxacin (LSC, J01MA25), latamoxef (LTM, J01DD06), levofloxacin (LVX, J01MA12), levonadifloxacin (LND, J01MA24), lincomycin (LIN, J01FF02), linezolid (LNZ, J01XX08), lomefloxacin (LOM, J01MA07), loracarbef (LOR, J01DC08), mecillinam (MEC, J01CA11), meropenem (MEM, J01DH02), meropenem/vaborbactam (MEV, J01DH52), metampicillin (MTM, J01CA14), meticillin (MET, J01CF03), mezlocillin (MEZ, J01CA10), micronomicin (MCR, S01AA22), midecamycin (MID, J01FA03), minocycline (MNO, J01AA08), miocamycin (MCM, J01FA11), moxifloxacin (MFX, J01MA14), nadifloxacin (NAD, D10AF05), nafcillin (NAF, J01CF06), nalidixic acid (NAL, J01MB02), neomycin (NEO, J01GB05), netilmicin (NET, J01GB07), nitrofurantoin (NIT, J01XE01), norfloxacin (, J01MA06), ofloxacin (OFX, J01MA01), oleandomycin (OLE, J01FA05), oritavancin (ORI, J01XA05), oxacillin (OXA, J01CF04), panipenem (PAN, J01DH55), pazufloxacin (PAZ, J01MA18), pefloxacin (PEF, J01MA03), penamecillin (PNM, J01CE06), pheneticillin (PHE, J01CE05), phenoxymethylpenicillin (PHN, J01CE02), piperacillin (PIP, J01CA12), piperacillin/tazobactam (TZP, J01CR05), pivampicillin (PVM, J01CA02), pivmecillinam (PME, J01CA08), plazomicin (PLZ, J01GB14), polymyxin B (PLB, J01XB02), pristinamycin (PRI, J01FG01), procaine benzylpenicillin (PRB, J01CE09), propicillin (PRP, J01CE03), prulifloxacin (PRU, J01MA17), quinupristin/dalfopristin (QDA, J01FG02), ribostamycin (RST, J01GB10), rifampicin (RIF, J04AB02), rokitamycin (ROK, J01FA12), roxithromycin (RXT, J01FA06), rufloxacin (RFL, J01MA10), sisomicin (SIS, J01GB08), sitafloxacin (SIT, J01MA21), solithromycin (SOL, J01FA16), sparfloxacin (SPX, J01MA09), spiramycin (SPI, J01FA02), streptoduocin (STR, J01GA02), streptomycin (STR1, J01GA01), sulbactam (SUL, J01CG01), sulbenicillin (SBC, J01CA16), sulfadiazine (SDI, J01EC02), sulfadiazine/trimethoprim (SLT1, J01EE02), sulfadimethoxine (SUD, J01ED01), sulfadimidine (SDM, J01EB03), sulfadimidine/trimethoprim (SLT2, J01EE05), sulfafurazole (SLF, J01EB05), sulfaisodimidine (SLF1, J01EB01), sulfalene (SLF2, J01ED02), sulfamazone (SZO, J01ED09), sulfamerazine (SLF3, J01ED07), sulfamerazine/trimethoprim (SLT3, J01EE07), sulfamethizole (SLF4, J01EB02), sulfamethoxazole (SMX, J01EC01), sulfamethoxypyridazine (SLF5, J01ED05), sulfametomidine (SLF6, J01ED03), sulfametoxydiazine (SLF7, J01ED04), sulfametrole/trimethoprim (SLT4, J01EE03), sulfamoxole (SLF8, J01EC03), sulfamoxole/trimethoprim (SLT5, J01EE04), sulfanilamide (SLF9, J01EB06), sulfaperin (SLF10, J01ED06), sulfaphenazole (SLF11, J01ED08), sulfapyridine (SLF12, J01EB04), sulfathiazole (SUT, J01EB07), sulfathiourea (SLF13, J01EB08), sultamicillin (SLT6, J01CR04), talampicillin (TAL, J01CA15), tazobactam (TAZ, J01CG02), tebipenem (TBP, J01DH06), tedizolid (TZD, J01XX11), teicoplanin (TEC, J01XA02), telavancin (TLV, J01XA03), telithromycin (TLT, J01FA15), temafloxacin (TMX, J01MA05), temocillin (TEM, J01CA17), tetracycline (TCY, J01AA07), ticarcillin (TIC, J01CA13), ticarcillin/clavulanic acid (TCC, J01CR03), tigecycline (TGC, J01AA12), tilbroquinol (TBQ, P01AA05), tobramycin (TOB, J01GB01), tosufloxacin (TFX, J01MA22), trimethoprim (TMP, J01EA01), trimethoprim/sulfamethoxazole (SXT, J01EE01), troleandomycin (TRL, J01FA08), trovafloxacin (TVA, J01MA13), vancomycin (VAN, J01XA01)","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Apply EUCAST Rules — eucast_rules","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply EUCAST Rules — eucast_rules","text":"","code":"# \\donttest{ a <- data.frame(   mo = c(     \"Staphylococcus aureus\",     \"Enterococcus faecalis\",     \"Escherichia coli\",     \"Klebsiella pneumoniae\",     \"Pseudomonas aeruginosa\"   ),   VAN = \"-\", # Vancomycin   AMX = \"-\", # Amoxicillin   COL = \"-\", # Colistin   CAZ = \"-\", # Ceftazidime   CXM = \"-\", # Cefuroxime   PEN = \"S\", # Benzylpenicillin   FOX = \"S\", # Cefoxitin   stringsAsFactors = FALSE )  head(a) #>                       mo VAN AMX COL CAZ CXM PEN FOX #> 1  Staphylococcus aureus   -   -   -   -   -   S   S #> 2  Enterococcus faecalis   -   -   -   -   -   S   S #> 3       Escherichia coli   -   -   -   -   -   S   S #> 4  Klebsiella pneumoniae   -   -   -   -   -   S   S #> 5 Pseudomonas aeruginosa   -   -   -   -   -   S   S   # apply EUCAST rules: some results wil be changed b <- eucast_rules(a) #> Warning: in eucast_rules(): not all columns with antimicrobial results are of #> class 'sir'. Transform them on beforehand, with e.g.: #>   - a %>% as.sir(CXM:AMX) #>   - a %>% mutate_if(is_sir_eligible, as.sir) #>   - a %>% mutate(across(where(is_sir_eligible), as.sir))  head(b) #>                       mo VAN AMX COL CAZ CXM PEN FOX #> 1  Staphylococcus aureus   -   S   R   S   S   S   S #> 2  Enterococcus faecalis   -   -   R   R   R   S   R #> 3       Escherichia coli   R   -   -   -   -   R   S #> 4  Klebsiella pneumoniae   R   R   -   -   -   R   S #> 5 Pseudomonas aeruginosa   R   R   -   -   R   R   R   # do not apply EUCAST rules, but rather get a data.frame # containing all details about the transformations: c <- eucast_rules(a, verbose = TRUE) #> Warning: in eucast_rules(): not all columns with antimicrobial results are of #> class 'sir'. Transform them on beforehand, with e.g.: #>   - a %>% as.sir(CXM:AMX) #>   - a %>% mutate_if(is_sir_eligible, as.sir) #>   - a %>% mutate(across(where(is_sir_eligible), as.sir)) head(c) #>   row col           mo_fullname old new rule   rule_group #> 1   1 AMX Staphylococcus aureus   -   S       Breakpoints #> 2   1 CXM Staphylococcus aureus   -   S       Breakpoints #> 3   1 CAZ Staphylococcus aureus   R   S      Expert Rules #> 4   1 CAZ Staphylococcus aureus   -   R      Expert Rules #> 5   1 COL Staphylococcus aureus   -   R      Expert Rules #> 6   2 CAZ Enterococcus faecalis   -   R      Expert Rules #>                                                 rule_name #> 1                                          Staphylococcus #> 2                                          Staphylococcus #> 3                          Expert Rules on Staphylococcus #> 4 Table 4: Intrinsic resistance in gram-positive bacteria #> 5 Table 4: Intrinsic resistance in gram-positive bacteria #> 6 Table 4: Intrinsic resistance in gram-positive bacteria #>                                                                                 rule_source #> 1                                           'EUCAST Clinical Breakpoint Tables' v12.0, 2022 #> 2                                           'EUCAST Clinical Breakpoint Tables' v12.0, 2022 #> 3 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 #> 4 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 #> 5 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 #> 6 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 # }  # Dosage guidelines:  eucast_dosage(c(\"tobra\", \"genta\", \"cipro\"), \"iv\") #> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint #>   Tables' v12.0 (2022). This note will be shown once per session. #> # A tibble: 3 × 4 #>   ab   name          standard_dosage  high_dosage  #>   <ab> <chr>         <chr>            <chr>        #> 1 TOB  Tobramycin    6-7 mg/kg x 1 iv NA           #> 2 GEN  Gentamicin    6-7 mg/kg x 1 iv NA           #> 3 CIP  Ciprofloxacin 0.4 g x 2 iv     0.4 g x 3 iv  eucast_dosage(c(\"tobra\", \"genta\", \"cipro\"), \"iv\", version_breakpoints = 10) #> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint #>   Tables' v10.0 (2020). This note will be shown once per session. #> # A tibble: 3 × 4 #>   ab   name          standard_dosage  high_dosage  #>   <ab> <chr>         <chr>            <chr>        #> 1 TOB  Tobramycin    6-7 mg/kg x 1 iv NA           #> 2 GEN  Gentamicin    6-7 mg/kg x 1 iv NA           #> 3 CIP  Ciprofloxacin 0.4 g x 2 iv     0.4 g x 3 iv"},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 2 000 Example Isolates — example_isolates","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"data set containing 2 000 microbial isolates full antibiograms. data set contains randomised fictitious data, reflects reality can used practise AMR data analysis. examples, please read tutorial website.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"","code":"example_isolates"},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"tibble 2 000 observations 46 variables: date Date receipt laboratory patient ID patient age Age patient gender Gender patient, either \"F\" \"M\" ward Ward type patient admitted, either \"Clinical\", \"ICU\", \"Outpatient\" mo ID microorganism created .mo(), see also microorganisms data set PEN:RIF 40 different antibiotics class sir (see .sir()); column names occur antibiotics data set can translated set_ab_names() ab_name()","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"","code":"example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …"},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Unclean Data — example_isolates_unclean","title":"Data Set with Unclean Data — example_isolates_unclean","text":"data set containing 3 000 microbial isolates cleaned consequently ready AMR data analysis. data set can used practice.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Unclean Data — example_isolates_unclean","text":"","code":"example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Unclean Data — example_isolates_unclean","text":"tibble 3 000 observations 8 variables: patient_id ID patient date date receipt laboratory hospital ID hospital, C bacteria info microorganism can transformed .mo(), see also microorganisms AMX:GEN 4 different antibiotics transformed .sir()","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Unclean Data — example_isolates_unclean","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Unclean Data — example_isolates_unclean","text":"","code":"example_isolates_unclean #> # A tibble: 3,000 × 8 #>    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN   #>    <chr>      <chr>    <date>     <chr>         <chr> <chr> <chr> <chr> #>  1 J3         A        2012-11-21 E. coli       R     I     S     S     #>  2 R7         A        2018-04-03 K. pneumoniae R     I     S     S     #>  3 P3         A        2014-09-19 E. coli       R     S     S     S     #>  4 P10        A        2015-12-10 E. coli       S     I     S     S     #>  5 B7         A        2015-03-02 E. coli       S     S     S     S     #>  6 W3         A        2018-03-31 S. aureus     R     S     R     S     #>  7 J8         A        2016-06-14 E. coli       R     S     S     S     #>  8 M3         A        2015-10-25 E. coli       R     S     S     S     #>  9 J3         A        2019-06-19 E. coli       S     S     S     S     #> 10 G6         A        2015-04-27 S. aureus     S     S     S     S     #> # ℹ 2,990 more rows"},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine First Isolates — first_isolate","title":"Determine First Isolates — first_isolate","text":"Determine first isolates microorganisms every patient per episode (needed) per specimen type. functions support four methods summarised Hindler et al. 2007 (doi:10.1086/511864 ). determine patient episodes necessarily based microorganisms, use is_new_episode() also supports grouping dplyr package.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine First Isolates — first_isolate","text":"","code":"first_isolate(   x = NULL,   col_date = NULL,   col_patient_id = NULL,   col_mo = NULL,   col_testcode = NULL,   col_specimen = NULL,   col_icu = NULL,   col_keyantimicrobials = NULL,   episode_days = 365,   testcodes_exclude = NULL,   icu_exclude = FALSE,   specimen_group = NULL,   type = \"points\",   method = c(\"phenotype-based\", \"episode-based\", \"patient-based\", \"isolate-based\"),   ignore_I = TRUE,   points_threshold = 2,   info = interactive(),   include_unknown = FALSE,   include_untested_sir = TRUE,   ... )  filter_first_isolate(   x = NULL,   col_date = NULL,   col_patient_id = NULL,   col_mo = NULL,   episode_days = 365,   method = c(\"phenotype-based\", \"episode-based\", \"patient-based\", \"isolate-based\"),   ... )"},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Determine First Isolates — first_isolate","text":"Methodology function strictly based : M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 5th Edition, 2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/. Hindler JF Stelling J (2007). Analysis Presentation Cumulative Antibiograms: New Consensus Guideline Clinical Laboratory Standards Institute. Clinical Infectious Diseases, 44(6), 867-873. doi:10.1086/511864","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine First Isolates — first_isolate","text":"x data.frame containing isolates. Can left blank automatic determination, see Examples. col_date column name result date (date received lab) - default first column date class col_patient_id column name unique IDs patients - default first column starts 'patient' 'patid' (case insensitive) col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). col_testcode column name test codes. Use col_testcode = NULL exclude certain test codes (test codes screening). case testcodes_exclude ignored. col_specimen column name specimen type group col_icu column name logicals (TRUE/FALSE) whether ward department Intensive Care Unit (ICU). can also logical vector length rows x. col_keyantimicrobials (useful method = \"phenotype-based\") column name key antimicrobials determine first isolates, see key_antimicrobials(). default first column starts 'key' followed 'ab' 'antibiotics' 'antimicrobials' (case insensitive). Use col_keyantimicrobials = FALSE prevent . Can also output key_antimicrobials(). episode_days episode days genus/species combination determined 'first isolate' . default 365 days based guideline CLSI, see Source. testcodes_exclude character vector test codes excluded (case-insensitive) icu_exclude logical indicate whether ICU isolates excluded (rows value TRUE column set col_icu) specimen_group value column set col_specimen filter type type determine weighed isolates; can \"keyantimicrobials\" \"points\", see Details method method apply, either \"phenotype-based\", \"episode-based\", \"patient-based\" \"isolate-based\" (can abbreviated), see Details. default \"phenotype-based\" antimicrobial test results present data, \"episode-based\" otherwise. ignore_I logical indicate whether antibiotic interpretations \"\" ignored type = \"keyantimicrobials\", see Details points_threshold minimum number points require differences antibiogram lead inclusion isolate type = \"points\", see Details info logical indicate info printed - default TRUE interactive mode include_unknown logical indicate whether 'unknown' microorganisms included , .e. microbial code \"UNKNOWN\", defaults FALSE. WHONET users, means records organism code \"con\" (contamination) excluded default. Isolates microbial ID NA always excluded first isolate. include_untested_sir logical indicate whether also rows without antibiotic results still eligible becoming first isolate. Use include_untested_sir = FALSE always return FALSE rows. checks data set columns class sir consequently requires transforming columns antibiotic results using .sir() first. ... arguments passed first_isolate() using filter_first_isolate(), otherwise arguments passed key_antimicrobials() (universal, gram_negative, gram_positive)","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine First Isolates — first_isolate","text":"logical vector","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine First Isolates — first_isolate","text":"conduct epidemiological analyses antimicrobial resistance data, -called first isolates included prevent overestimation underestimation antimicrobial resistance. Different methods can used , see . functions context-aware. means x argument can left blank used inside data.frame call, see Examples. first_isolate() function wrapper around is_new_episode() function, efficient data sets containing microorganism codes names. isolates microbial ID NA excluded first isolate.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"different-methods","dir":"Reference","previous_headings":"","what":"Different methods","title":"Determine First Isolates — first_isolate","text":"According Hindler et al. (2007, doi:10.1086/511864 ), different methods (algorithms) select first isolates increasing reliability: isolate-based, patient-based, episode-based phenotype-based. methods select combination taxonomic genus species (subspecies). mentioned methods covered first_isolate() function:","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"isolate-based","dir":"Reference","previous_headings":"","what":"Isolate-based","title":"Determine First Isolates — first_isolate","text":"method require selection, isolates included. , however, respect arguments set first_isolate() function. example, default setting include_unknown (FALSE) omit selection rows without microbial ID.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"patient-based","dir":"Reference","previous_headings":"","what":"Patient-based","title":"Determine First Isolates — first_isolate","text":"include every genus-species combination per patient , set episode_days Inf. Although often inappropriate, method makes sure duplicate isolates selected patient. large longitudinal data set, mean isolates excluded found years initial isolate.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"episode-based","dir":"Reference","previous_headings":"","what":"Episode-based","title":"Determine First Isolates — first_isolate","text":"include every genus-species combination per patient episode , set episode_days sensible number days. Depending type analysis, 14, 30, 60 365. Short episodes common analysing specific hospital ward data, long episodes common analysing regional national data. common method correct duplicate isolates. Patients categorised episodes based ID dates (e.g., date specimen receipt laboratory result). common method, take account antimicrobial test results. means e.g. methicillin-resistant Staphylococcus aureus (MRSA) isolate differentiated wildtype Staphylococcus aureus isolate.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"phenotype-based","dir":"Reference","previous_headings":"","what":"Phenotype-based","title":"Determine First Isolates — first_isolate","text":"reliable method, since also weighs antibiogram (antimicrobial test results) yielding -called 'first weighted isolates'. two different methods weigh antibiogram: Using type = \"points\" argument points_threshold (default) method weighs antimicrobial drugs available data set. difference S R (vice versa) counts 0.5 points, difference S R (vice versa) counts 1 point. sum points exceeds points_threshold, defaults 2, isolate selected first weighted isolate. antimicrobials internally selected using all_antimicrobials() function. output function need passed first_isolate() function. Using type = \"keyantimicrobials\" argument ignore_I method weighs specific antimicrobial drugs, called key antimicrobials. difference S R (vice versa) key antimicrobials select isolate first weighted isolate. ignore_I = FALSE, also differences S R (vice versa) lead . Key antimicrobials internally selected using key_antimicrobials() function, can also added manually variable data set col_keyantimicrobials argument. Another option pass output key_antimicrobials() function directly col_keyantimicrobials argument. default method phenotype-based (using type = \"points\") episode-based (using episode_days = 365). makes sure every genus-species combination selected per patient per year, taking account antimicrobial test results. antimicrobial test results available data set, episode-based method applied default.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine First Isolates — first_isolate","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  example_isolates[first_isolate(info = TRUE), ] #> Determining first isolates using an episode length of 365 days #> ℹ Using column 'date' as input for col_date. #> ℹ Using column 'patient' as input for col_patient_id. #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a #>    microbial ID was available) #> # A tibble: 1,379 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  3 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  4 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #>  5 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA    #>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  7 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  8 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  9 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA    #> 10 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA    #> # ℹ 1,369 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … # \\donttest{ # get all first Gram-negatives example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ] #> ℹ Using column 'mo' as input for mo_is_gram_negative() #> # A tibble: 437 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  4 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  5 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  6 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R     #>  7 2002-03-08 4FC193     69 M      Clinical B_ESCHR_COLI R     NA    NA    R     #>  8 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R     #>  9 2002-04-01 496896     46 F      ICU      B_ESCHR_COLI R     NA    NA    NA    #> 10 2002-04-23 EE2510     69 F      ICU      B_ESCHR_COLI R     NA    NA    NA    #> # ℹ 427 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  if (require(\"dplyr\")) {   # filter on first isolates using dplyr:   example_isolates %>%     filter(first_isolate(info = TRUE)) } #> Determining first isolates using an episode length of 365 days #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a #>    microbial ID was available) #> # A tibble: 1,379 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  3 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  4 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #>  5 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA    #>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  7 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  8 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  9 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA    #> 10 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA    #> # ℹ 1,369 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # short-hand version:   example_isolates %>%     filter_first_isolate(info = FALSE) } #> # A tibble: 1,379 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  3 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  4 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #>  5 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA    #>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  7 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  8 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  9 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA    #> 10 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA    #> # ℹ 1,369 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # flag the first isolates per group:   example_isolates %>%     group_by(ward) %>%     mutate(first = first_isolate(info = TRUE)) %>%     select(ward, date, patient, mo, first) } #> Determining first isolates using an episode length of 365 days #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #>  #> Group: ward = \"Clinical\" #> ℹ Excluded 9 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 861 'phenotype-based' first isolates (69.8% of total where a #>    microbial ID was available) #> Including isolates from ICU. #>  #> Group: ward = \"ICU\" #> ℹ Excluded 6 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 449 'phenotype-based' first isolates (69.6% within scope and 69.5% #>    of total where a microbial ID was available) #> Including isolates from ICU. #>  #> Group: ward = \"Outpatient\" #> ℹ Excluded 1 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 98 'phenotype-based' first isolates (82.4% within scope and 81.7% #>    of total where a microbial ID was available) #> # A tibble: 2,000 × 5 #> # Groups:   ward [3] #>    ward     date       patient mo           first #>    <chr>    <date>     <chr>   <mo>         <lgl> #>  1 Clinical 2002-01-02 A77334  B_ESCHR_COLI TRUE  #>  2 Clinical 2002-01-03 A77334  B_ESCHR_COLI FALSE #>  3 ICU      2002-01-07 067927  B_STPHY_EPDR TRUE  #>  4 ICU      2002-01-07 067927  B_STPHY_EPDR FALSE #>  5 ICU      2002-01-13 067927  B_STPHY_EPDR FALSE #>  6 ICU      2002-01-13 067927  B_STPHY_EPDR FALSE #>  7 Clinical 2002-01-14 462729  B_STPHY_AURS TRUE  #>  8 Clinical 2002-01-14 462729  B_STPHY_AURS FALSE #>  9 ICU      2002-01-16 067927  B_STPHY_EPDR FALSE #> 10 ICU      2002-01-17 858515  B_STPHY_EPDR TRUE  #> # ℹ 1,990 more rows # }"},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":null,"dir":"Reference","previous_headings":"","what":"G-test for Count Data — g.test","title":"G-test for Count Data — g.test","text":"g.test() performs chi-squared contingency table tests goodness--fit tests, just like chisq.test() reliable (1). G-test can used see whether number observations category fits theoretical expectation (called G-test goodness--fit), see whether proportions one variable different different values variable (called G-test independence).","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"G-test for Count Data — g.test","text":"","code":"g.test(x, y = NULL, p = rep(1/length(x), length(x)), rescale.p = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"G-test for Count Data — g.test","text":"code function identical chisq.test(), except : calculation statistic changed \\(2 * sum(x * log(x / E))\\) Yates' continuity correction removed apply G-test possibility simulate p values simulate.p.value removed","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"G-test for Count Data — g.test","text":"x numeric vector matrix. x y can also     factors. y numeric vector; ignored x matrix.      x factor, y factor length. p vector probabilities length x.     error given entry p negative. rescale.p logical scalar; TRUE p rescaled     (necessary) sum 1.  rescale.p FALSE,     p sum 1, error given.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"G-test for Count Data — g.test","text":"list class \"htest\" containing following   components: statistic value chi-squared test statistic. parameter degrees freedom approximate     chi-squared distribution test statistic, NA     p-value computed Monte Carlo simulation. p.value p-value test. method character string indicating type test     performed, whether Monte Carlo simulation continuity     correction used. data.name character string giving name(s) data. observed observed counts. expected expected counts null hypothesis. residuals Pearson residuals,     (observed - expected) / sqrt(expected). stdres standardized residuals,     (observed - expected) / sqrt(V), V residual cell variance (Agresti, 2007,     section 2.4.5 case x matrix, n * p * (1 - p) otherwise).","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"G-test for Count Data — g.test","text":"x matrix one row column, x vector y given, goodness--fit test performed (x treated one-dimensional contingency table). entries x must non-negative integers. case, hypothesis tested whether population probabilities equal p, equal p given. x matrix least two rows columns, taken two-dimensional contingency table: entries x must non-negative integers.  Otherwise, x y must vectors factors length; cases missing values removed, objects coerced factors, contingency table computed .  Pearson's chi-squared test performed null hypothesis joint distribution cell counts 2-dimensional contingency table product row column marginals. p-value computed asymptotic chi-squared distribution test statistic. contingency table case simulation done random sampling set contingency tables given marginals, works marginals strictly positive. Note usual sampling situation assumed chi-squared test (G-test) rather Fisher's exact test. goodness--fit case simulation done random sampling discrete distribution specified p, sample size n = sum(x). simulation done R may slow.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"g-test-of-goodness-of-fit-likelihood-ratio-test-","dir":"Reference","previous_headings":"","what":"G-test Of Goodness-of-Fit (Likelihood Ratio Test)","title":"G-test for Count Data — g.test","text":"Use G-test goodness--fit one nominal variable two values (male female, red, pink white flowers). compare observed counts numbers observations category expected counts, calculate using kind theoretical expectation (1:1 sex ratio 1:2:1 ratio genetic cross). expected number observations category small, G-test may give inaccurate results, use exact test instead (fisher.test()). G-test goodness--fit alternative chi-square test goodness--fit (chisq.test()); tests advantages disadvantages, results two tests usually similar.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"g-test-of-independence","dir":"Reference","previous_headings":"","what":"G-test of Independence","title":"G-test for Count Data — g.test","text":"Use G-test independence two nominal variables, two possible values. want know whether proportions one variable different among values variable. also possible G-test independence two nominal variables. example, Jackson et al. (2013) also data children 3, analysis old vs. young, thigh vs. arm, reaction vs. reaction, analyzed together. Fisher's exact test (fisher.test()) exact test, G-test still approximation. 2x2 table, Fisher's Exact test may slower still run seconds, even sum observations multiple millions. G-test independence alternative chi-square test independence (chisq.test()), give approximately results.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"how-the-test-works","dir":"Reference","previous_headings":"","what":"How the Test Works","title":"G-test for Count Data — g.test","text":"Unlike exact test goodness--fit (fisher.test()), G-test directly calculate probability obtaining observed results something extreme. Instead, like almost statistical tests, G-test intermediate step; uses data calculate test statistic measures far observed data null expectation. use mathematical relationship, case chi-square distribution, estimate probability obtaining value test statistic. G-test uses log ratio two likelihoods test statistic, also called likelihood ratio test log-likelihood ratio test. formula calculate G-statistic : \\(G = 2 * sum(x * log(x / E))\\) E expected values. Since chi-square distributed, p value can calculated R :   df degrees freedom. two categories want find ones significantly different null expectation, can use method testing category vs. sum categories, Bonferroni correction. use G-tests category, course.","code":"p <- stats::pchisq(G, df, lower.tail = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"G-test for Count Data — g.test","text":"McDonald, J.H. 2014. Handbook Biological Statistics (3rd ed.). Sparky House Publishing, Baltimore, Maryland. http://www.biostathandbook.com/gtestgof.html.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"G-test for Count Data — g.test","text":"","code":"# = EXAMPLE 1 = # Shivrain et al. (2006) crossed clearfield rice (which are resistant # to the herbicide imazethapyr) with red rice (which are susceptible to # imazethapyr). They then crossed the hybrid offspring and examined the # F2 generation, where they found 772 resistant plants, 1611 moderately # resistant plants, and 737 susceptible plants. If resistance is controlled # by a single gene with two co-dominant alleles, you would expect a 1:2:1 # ratio.  x <- c(772, 1611, 737) g.test(x, p = c(1, 2, 1) / 4) #>  #> \tG-test of goodness-of-fit (likelihood ratio test) #>  #> data:  x #> X-squared = 4.1471, p-value = 0.1257 #>   # There is no significant difference from a 1:2:1 ratio. # Meaning: resistance controlled by a single gene with two co-dominant # alleles, is plausible.   # = EXAMPLE 2 = # Red crossbills (Loxia curvirostra) have the tip of the upper bill either # right or left of the lower bill, which helps them extract seeds from pine # cones. Some have hypothesized that frequency-dependent selection would # keep the number of right and left-billed birds at a 1:1 ratio. Groth (1992) # observed 1752 right-billed and 1895 left-billed crossbills.  x <- c(1752, 1895) g.test(x) #>  #> \tG-test of goodness-of-fit (likelihood ratio test) #>  #> data:  x #> X-squared = 5.6085, p-value = 0.01787 #>   # There is a significant difference from a 1:1 ratio. # Meaning: there are significantly more left-billed birds."},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Clinical or Epidemic Episodes — get_episode","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"functions determine items vector can considered (start ) new episode. can used determine clinical episodes epidemiological analysis. get_episode() function returns index number episode per group, is_new_episode() function returns TRUE every new get_episode() index. absolute relative episode determination supported.","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"","code":"get_episode(x, episode_days = NULL, case_free_days = NULL, ...)  is_new_episode(x, episode_days = NULL, case_free_days = NULL, ...)"},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"x vector dates (class Date POSIXt), sorted internally determine episodes episode_days episode length days specify time period new episode begins, can also less day Inf, see Details case_free_days (inter-epidemic) interval length days new episode start, can also less day Inf, see Details ... ignored, place allow future extensions","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"get_episode(): integer vector is_new_episode(): logical vector","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"Episodes can determined two ways: absolute relative. Absolute method uses episode_days define episode length days, new episode start. common use case AMR data analysis microbial epidemiology: episodes S. aureus bacteraemia ICU patients example. episode length 30 days, new S. aureus isolates ICU episode 30 days considered different (new) episode. Thus, method counts since start previous episode. Relative method uses case_free_days quantify duration case-free days (inter-epidemic interval), new episode start. common use case infectious disease epidemiology: episodes norovirus outbreaks hospital example. case-free period 14 days, new norovirus cases time considered different (new) episode. Thus, methods counts since last case previous episode. table: ** marks start new episode, 8 January 2023 7 days since start previous episode (1 January 2023).  *** marks start new episode, 21 January 2023 7 days since last case previous episode (8 January 2023). Either episode_days case_free_days must provided function.","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"difference-between-get-episode-and-is-new-episode-","dir":"Reference","previous_headings":"","what":"Difference between get_episode() and is_new_episode()","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"get_episode() function returns index number episode, cases/patients/isolates first episode number 1, cases/patients/isolates second episode number 2, etc. is_new_episode() function hand, returns TRUE every new get_episode() index. specify, setting episode_days = 365 (using method 1 explained ), two functions differ:","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"other","dir":"Reference","previous_headings":"","what":"Other","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"first_isolate() function wrapper around is_new_episode() function, efficient data sets containing microorganism codes names allows different isolate selection methods. dplyr package required functions work, episode functions support variable grouping work conveniently inside dplyr verbs filter(), mutate() summarise().","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"","code":"# difference between absolute and relative determination of episodes: x <- data.frame(dates = as.Date(c(   \"2021-01-01\",   \"2021-01-02\",   \"2021-01-05\",   \"2021-01-08\",   \"2021-02-21\",   \"2021-02-22\",   \"2021-02-23\",   \"2021-02-24\",   \"2021-03-01\",   \"2021-03-01\" ))) x$absolute <- get_episode(x$dates, episode_days = 7) x$relative <- get_episode(x$dates, case_free_days = 7) x #>         dates absolute relative #> 1  2021-01-01        1        1 #> 2  2021-01-02        1        1 #> 3  2021-01-05        1        1 #> 4  2021-01-08        2        1 #> 5  2021-02-21        3        2 #> 6  2021-02-22        3        2 #> 7  2021-02-23        3        2 #> 8  2021-02-24        3        2 #> 9  2021-03-01        4        2 #> 10 2021-03-01        4        2   # `example_isolates` is a data set available in the AMR package. # See ?example_isolates df <- example_isolates[sample(seq_len(2000), size = 100), ]  get_episode(df$date, episode_days = 60) # indices #>   [1]  6 20 15 33 38  6 16 28 13  7 46 37  2  3 47 40 10  8 40  6 22 48 37 28 31 #>  [26] 32 22 42  9 40 37 41 21 14 23 43  6 35 46  1 24 45 20 43 41  9  4  6 32 39 #>  [51] 46 48 13 19  2 38 44 12 45 41 38  5 33 27 24  5 26 29 11 19 41 27 30 37 45 #>  [76] 23  5  2  9 24  1  7 34 23  5  4 13 46 48 19 47 45 36  7 38 25 15 18 17 37 is_new_episode(df$date, episode_days = 60) # TRUE/FALSE #>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE #>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE #>  [25]  TRUE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE #>  [37] FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE #>  [49] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE #>  [61] FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE #>  [73]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE #>  [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE #>  [97] FALSE  TRUE  TRUE FALSE  # filter on results from the third 60-day episode only, using base R df[which(get_episode(df$date, 60) == 3), ] #> # A tibble: 1 × 46 #>   date       patient   age gender ward  mo           PEN   OXA   FLC   AMX   #>   <date>     <chr>   <dbl> <chr>  <chr> <mo>         <sir> <sir> <sir> <sir> #> 1 2002-07-30 218912     76 F      ICU   B_ESCHR_COLI R     NA    NA    NA    #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, RIF <sir>  # the functions also work for less than a day, e.g. to include one per hour: get_episode(   c(     Sys.time(),     Sys.time() + 60 * 60   ),   episode_days = 1 / 24 ) #> [1] 1 2  # \\donttest{ if (require(\"dplyr\")) {   # is_new_episode() can also be used in dplyr verbs to determine patient   # episodes based on any (combination of) grouping variables:   df %>%     mutate(condition = sample(       x = c(\"A\", \"B\", \"C\"),       size = 100,       replace = TRUE     )) %>%     group_by(patient, condition) %>%     mutate(new_episode = is_new_episode(date, 365)) %>%     select(patient, date, condition, new_episode) %>%     arrange(patient, condition, date) } #> # A tibble: 100 × 4 #> # Groups:   patient, condition [96] #>    patient date       condition new_episode #>    <chr>   <date>     <chr>     <lgl>       #>  1 001213  2009-08-03 A         TRUE        #>  2 006827  2009-07-24 B         TRUE        #>  3 032343  2003-06-09 A         TRUE        #>  4 083080  2010-02-25 C         TRUE        #>  5 088256  2003-01-25 A         TRUE        #>  6 097186  2015-10-28 C         TRUE        #>  7 0C0688  2014-09-05 C         TRUE        #>  8 0DBB93  2003-10-02 A         TRUE        #>  9 113236  2006-11-20 B         TRUE        #> 10 125492  2016-05-13 B         TRUE        #> # ℹ 90 more rows  if (require(\"dplyr\")) {   df %>%     group_by(ward, patient) %>%     transmute(date,       patient,       new_index = get_episode(date, 60),       new_logical = is_new_episode(date, 60)     ) %>%     arrange(patient, ward, date) } #> # A tibble: 100 × 5 #> # Groups:   ward, patient [92] #>    ward     date       patient new_index new_logical #>    <chr>    <date>     <chr>       <int> <lgl>       #>  1 Clinical 2009-08-03 001213          1 TRUE        #>  2 Clinical 2009-07-24 006827          1 TRUE        #>  3 Clinical 2003-06-09 032343          1 TRUE        #>  4 Clinical 2010-02-25 083080          1 TRUE        #>  5 ICU      2003-01-25 088256          1 TRUE        #>  6 Clinical 2015-10-28 097186          1 TRUE        #>  7 Clinical 2014-09-05 0C0688          1 TRUE        #>  8 ICU      2003-10-02 0DBB93          1 TRUE        #>  9 Clinical 2006-11-20 113236          1 TRUE        #> 10 ICU      2016-05-13 125492          1 TRUE        #> # ℹ 90 more rows  if (require(\"dplyr\")) {   df %>%     group_by(ward) %>%     summarise(       n_patients = n_distinct(patient),       n_episodes_365 = sum(is_new_episode(date, episode_days = 365)),       n_episodes_60 = sum(is_new_episode(date, episode_days = 60)),       n_episodes_30 = sum(is_new_episode(date, episode_days = 30))     ) } #> # A tibble: 3 × 5 #>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30 #>   <chr>           <int>          <int>         <int>         <int> #> 1 Clinical           61             14            39            46 #> 2 ICU                25              8            20            24 #> 3 Outpatient          6              5             6             6  # grouping on patients and microorganisms leads to the same # results as first_isolate() when using 'episode-based': if (require(\"dplyr\")) {   x <- df %>%     filter_first_isolate(       include_unknown = TRUE,       method = \"episode-based\"     )    y <- df %>%     group_by(patient, mo) %>%     filter(is_new_episode(date, 365)) %>%     ungroup()    identical(x, y) } #> [1] FALSE  # but is_new_episode() has a lot more flexibility than first_isolate(), # since you can now group on anything that seems relevant: if (require(\"dplyr\")) {   df %>%     group_by(patient, mo, ward) %>%     mutate(flag_episode = is_new_episode(date, 365)) %>%     select(group_vars(.), flag_episode) } #> # A tibble: 100 × 4 #> # Groups:   patient, mo, ward [95] #>    patient mo           ward     flag_episode #>    <chr>   <mo>         <chr>    <lgl>        #>  1 F35553  B_ENTRC      ICU      TRUE         #>  2 195736  B_STPHY_AURS Clinical TRUE         #>  3 113236  B_ESCHR_COLI Clinical TRUE         #>  4 545388  B_ESCHR_COLI Clinical TRUE         #>  5 534091  B_ESCHR_COLI Clinical TRUE         #>  6 0DBB93  B_ESCHR_COLI ICU      TRUE         #>  7 C67282  B_STPHY_CONS Clinical TRUE         #>  8 E58140  B_STPHY_CONS Clinical TRUE         #>  9 54890C  B_ESCHR_COLI Clinical TRUE         #> 10 570937  B_KLBSL_PNMN Clinical TRUE         #> # ℹ 90 more rows # }"},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"PCA Biplot with ggplot2 — ggplot_pca","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"Produces ggplot2 variant -called biplot PCA (principal component analysis), flexible appealing base R biplot() function.","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"","code":"ggplot_pca(   x,   choices = 1:2,   scale = 1,   pc.biplot = TRUE,   labels = NULL,   labels_textsize = 3,   labels_text_placement = 1.5,   groups = NULL,   ellipse = TRUE,   ellipse_prob = 0.68,   ellipse_size = 0.5,   ellipse_alpha = 0.5,   points_size = 2,   points_alpha = 0.25,   arrows = TRUE,   arrows_colour = \"darkblue\",   arrows_size = 0.5,   arrows_textsize = 3,   arrows_textangled = TRUE,   arrows_alpha = 0.75,   base_textsize = 10,   ... )"},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"ggplot_pca() function based ggbiplot() function ggbiplot package Vince Vu, found GitHub: https://github.com/vqv/ggbiplot (retrieved: 2 March 2020, latest commit: 7325e88; 12 February 2015). per GPL-2 licence demands documentation code changes, changes made based source code : Rewritten code remove dependency packages plyr, scales grid Parametrised options, like arrow ellipse settings Hardened input possibilities defining exact type user input every argument Added total amount explained variance caption plot Cleaned syntax based lintr package, fixed grammatical errors added integrity checks Updated documentation","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"x object returned pca(), prcomp() princomp() choices length 2 vector specifying components plot. default     biplot strict sense. scale variables scaled lambda ^ scale     observations scaled lambda ^ (1-scale)     lambda singular values computed     princomp. Normally 0 <= scale <= 1, warning     issued specified scale outside range. pc.biplot true, use Gabriel (1971) refers \"principal component     biplot\", lambda = 1 observations scaled sqrt(n)     variables scaled sqrt(n).  inner products     variables approximate covariances distances observations     approximate Mahalanobis distance. labels optional vector labels observations. set, labels placed respective points. using pca() function input x, determined automatically based attribute non_numeric_cols, see pca(). labels_textsize size text used labels labels_text_placement adjustment factor placement variable names (>=1 means away arrow head) groups optional vector groups labels, length labels. set, points labels coloured according groups. using pca() function input x, determined automatically based attribute non_numeric_cols, see pca(). ellipse logical indicate whether normal data ellipse drawn group (set groups) ellipse_prob statistical size ellipse normal probability ellipse_size size ellipse line ellipse_alpha alpha (transparency) ellipse line points_size size points points_alpha alpha (transparency) points arrows logical indicate whether arrows drawn arrows_colour colour arrow text arrows_size size (thickness) arrow lines arrows_textsize size text end arrows arrows_textangled logical whether text end arrows angled arrows_alpha alpha (transparency) arrows text base_textsize text size plot elements except labels arrows ... arguments passed functions","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"colours labels points can changed adding another scale layer colour, scale_colour_viridis_d() scale_colour_brewer().","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  # \\donttest{ if (require(\"dplyr\")) {   # calculate the resistance per group first   resistance_data <- example_isolates %>%     group_by(       order = mo_order(mo), # group on anything, like order       genus = mo_genus(mo)     ) %>% #   and genus as we do here;     filter(n() >= 30) %>% # filter on only 30 results per group     summarise_if(is.sir, resistance) # then get resistance of all drugs    # now conduct PCA for certain antimicrobial drugs   pca_result <- resistance_data %>%     pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)    summary(pca_result)    # old base R plotting method:   biplot(pca_result)    # new ggplot2 plotting method using this package:   if (require(\"ggplot2\")) {     ggplot_pca(pca_result)      # still extendible with any ggplot2 function     ggplot_pca(pca_result) +       scale_colour_viridis_d() +       labs(title = \"Title here\")   } } #> Warning: There were 73 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE, #>   only_all_tested = FALSE) ...`. #> ℹ In group 5: `order = \"Lactobacillales\"`, `genus = \"Enterococcus\"`. #> Caused by warning: #> ! Introducing NA: only 14 results available for PEN in group: order = #> \"Lactobacillales\", genus = \"Enterococcus\" (minimum = 30). #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings. #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", #>   \"TMP\", and \"TOB\". Total observations available: 7. #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\"  #>    # }"},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":null,"dir":"Reference","previous_headings":"","what":"AMR Plots with ggplot2 — ggplot_sir","title":"AMR Plots with ggplot2 — ggplot_sir","text":"Use functions create bar plots AMR data analysis. functions rely ggplot2 functions.","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"AMR Plots with ggplot2 — ggplot_sir","text":"","code":"ggplot_sir(   data,   position = NULL,   x = \"antibiotic\",   fill = \"interpretation\",   facet = NULL,   breaks = seq(0, 1, 0.1),   limits = NULL,   translate_ab = \"name\",   combine_SI = TRUE,   minimum = 30,   language = get_AMR_locale(),   nrow = NULL,   colours = c(S = \"#3CAEA3\", SI = \"#3CAEA3\", I = \"#F6D55C\", IR = \"#ED553B\", R =     \"#ED553B\"),   datalabels = TRUE,   datalabels.size = 2.5,   datalabels.colour = \"grey15\",   title = NULL,   subtitle = NULL,   caption = NULL,   x.title = \"Antimicrobial\",   y.title = \"Proportion\",   ... )  geom_sir(   position = NULL,   x = c(\"antibiotic\", \"interpretation\"),   fill = \"interpretation\",   translate_ab = \"name\",   minimum = 30,   language = get_AMR_locale(),   combine_SI = TRUE,   ... )  facet_sir(facet = c(\"interpretation\", \"antibiotic\"), nrow = NULL)  scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL)  scale_sir_colours(..., aesthetics = \"fill\")  theme_sir()  labels_sir_count(   position = NULL,   x = \"antibiotic\",   translate_ab = \"name\",   minimum = 30,   language = get_AMR_locale(),   combine_SI = TRUE,   datalabels.size = 3,   datalabels.colour = \"grey15\" )"},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"AMR Plots with ggplot2 — ggplot_sir","text":"data data.frame column(s) class sir (see .sir()) position position adjustment bars, either \"fill\", \"stack\" \"dodge\" x variable show x axis, either \"antibiotic\" (default) \"interpretation\" grouping variable fill variable categorise using plots legend, either \"antibiotic\" (default) \"interpretation\" grouping variable facet variable split plots , either \"interpretation\" (default) \"antibiotic\" grouping variable breaks numeric vector positions limits numeric vector length two providing limits scale, use NA refer existing minimum maximum translate_ab column name antibiotics data set translate antibiotic abbreviations , using ab_property() combine_SI logical indicate whether values S must merged one, output consists S+vs. R (susceptible vs. resistant) - default TRUE minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. nrow (using facet) number rows colours named vactor colour used filling. default colours colour-blind friendly. datalabels show datalabels using labels_sir_count() datalabels.size size datalabels datalabels.colour colour datalabels title text show title plot subtitle text show subtitle plot caption text show caption plot x.title text show x axis description y.title text show y axis description ... arguments passed geom_sir() , case scale_sir_colours(), named values set colours. default colours colour-blind friendly, maintaining convention e.g. 'susceptible' green 'resistant' red. See Examples. aesthetics aesthetics apply colours - default \"fill\" can also (combination ) \"alpha\", \"colour\", \"fill\", \"linetype\", \"shape\" \"size\"","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"AMR Plots with ggplot2 — ggplot_sir","text":"default, names antibiotics shown plots using ab_name(). can set translate_ab argument. See count_df().","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"the-functions","dir":"Reference","previous_headings":"","what":"The Functions","title":"AMR Plots with ggplot2 — ggplot_sir","text":"geom_sir() take variable data sir class (created .sir()) using sir_df() plot bars percentage S, , R. default behaviour bars stacked different antibiotics x axis. facet_sir() creates 2d plots (default based S//R) using ggplot2::facet_wrap(). scale_y_percent() transforms y axis 0 100% range using ggplot2::scale_y_continuous(). scale_sir_colours() sets colours bars (green S, yellow , red R). multilingual support. default colours colour-blind friendly, maintaining convention e.g. 'susceptible' green 'resistant' red. theme_sir() [ggplot2 theme][ggplot2::theme() minimal distraction. labels_sir_count() print datalabels bars percentage amount isolates using ggplot2::geom_text(). ggplot_sir() wrapper around functions uses data first input. makes possible use function pipe (%>%). See Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"AMR Plots with ggplot2 — ggplot_sir","text":"","code":"# \\donttest{ if (require(\"ggplot2\") && require(\"dplyr\")) {   # get antimicrobial results for drugs against a UTI:   ggplot(example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)) +     geom_sir() }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # prettify the plot using some additional functions:   df <- example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)   ggplot(df) +     geom_sir() +     scale_y_percent() +     scale_sir_colours() +     labels_sir_count() +     theme_sir() }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # or better yet, simplify this using the wrapper function - a single command:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir() }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # get only proportions and no counts:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir(datalabels = FALSE) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # add other ggplot2 arguments as you like:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir(       width = 0.5,       colour = \"black\",       size = 1,       linetype = 2,       alpha = 0.25     ) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # you can alter the colours with colour names:   example_isolates %>%     select(AMX) %>%     ggplot_sir(colours = c(SI = \"yellow\")) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # but you can also use the built-in colour-blind friendly colours for   # your plots, where \"S\" is green, \"I\" is yellow and \"R\" is red:   data.frame(     x = c(\"Value1\", \"Value2\", \"Value3\"),     y = c(1, 2, 3),     z = c(\"Value4\", \"Value5\", \"Value6\")   ) %>%     ggplot() +     geom_col(aes(x = x, y = y, fill = z)) +     scale_sir_colours(Value4 = \"S\", Value5 = \"I\", Value6 = \"R\") }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # resistance of ciprofloxacine per age group   example_isolates %>%     mutate(first_isolate = first_isolate()) %>%     filter(       first_isolate == TRUE,       mo == as.mo(\"Escherichia coli\")     ) %>%     # age_groups() is also a function in this AMR package:     group_by(age_group = age_groups(age)) %>%     select(age_group, CIP) %>%     ggplot_sir(x = \"age_group\") } #> Warning: Removed 6 rows containing missing values (`position_stack()`). #> Warning: Removed 6 rows containing missing values (`position_stack()`).  if (require(\"ggplot2\") && require(\"dplyr\")) {   # a shorter version which also adjusts data label colours:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir(colours = FALSE) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # it also supports groups (don't forget to use the group var on `x` or `facet`):   example_isolates %>%     filter(mo_is_gram_negative(), ward != \"Outpatient\") %>%     # select only UTI-specific drugs     select(ward, AMX, NIT, FOS, TMP, CIP) %>%     group_by(ward) %>%     ggplot_sir(       x = \"ward\",       facet = \"antibiotic\",       nrow = 1,       title = \"AMR of Anti-UTI Drugs Per Ward\",       x.title = \"Ward\",       datalabels = FALSE     ) } #> ℹ Using column 'mo' as input for mo_is_gram_negative()  # }"},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Guess Antibiotic Column — guess_ab_col","title":"Guess Antibiotic Column — guess_ab_col","text":"tries find column name data set based information antibiotics data set. Also supports WHONET abbreviations.","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Guess Antibiotic Column — guess_ab_col","text":"","code":"guess_ab_col(   x = NULL,   search_string = NULL,   verbose = FALSE,   only_sir_columns = FALSE )"},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Guess Antibiotic Column — guess_ab_col","text":"x data.frame search_string text search x , checked .ab() value column x verbose logical indicate whether additional info printed only_sir_columns logical indicate whether antibiotic columns must detected transformed class sir (see .sir()) beforehand (default FALSE)","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Guess Antibiotic Column — guess_ab_col","text":"column name x, NULL result found.","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Guess Antibiotic Column — guess_ab_col","text":"can look antibiotic (trade) name abbreviation search x antibiotics data set column containing name code antibiotic.","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Guess Antibiotic Column — guess_ab_col","text":"","code":"df <- data.frame(   amox = \"S\",   tetr = \"R\" )  guess_ab_col(df, \"amoxicillin\") #> [1] \"amox\" guess_ab_col(df, \"J01AA07\") # ATC code of tetracycline #> [1] \"tetr\"  guess_ab_col(df, \"J01AA07\", verbose = TRUE) #> Auto-guessing columns suitable for analysis #> ... #>  OK. #> ℹ Using column 'amox' as input for AMX (amoxicillin). #> ℹ Using column 'tetr' as input for TCY (tetracycline). #> ℹ Using column 'tetr' as input for J01AA07 (tetracycline). #> [1] \"tetr\" # NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).  # WHONET codes df <- data.frame(   AMP_ND10 = \"R\",   AMC_ED20 = \"S\" ) guess_ab_col(df, \"ampicillin\") #> [1] \"AMP_ND10\" guess_ab_col(df, \"J01CR02\") #> [1] \"AMC_ED20\" guess_ab_col(df, as.ab(\"augmentin\")) #> [1] \"AMC_ED20\""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"Data set containing defined intrinsic resistance EUCAST bug-drug combinations.","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"","code":"intrinsic_resistant"},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"tibble 134 634 observations 2 variables: mo Microorganism ID ab Antibiotic ID","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"data set based 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021).","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository. allow machine reading EUCAST CLSI guidelines, almost impossible MS Excel PDF files distributed EUCAST CLSI.","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"","code":"intrinsic_resistant #> # A tibble: 134,634 × 2 #>    mo      ab    #>    <mo>    <chr> #>  1 B_GRAMP ATM   #>  2 B_GRAMP COL   #>  3 B_GRAMP NAL   #>  4 B_GRAMP PLB   #>  5 B_GRAMP TEM   #>  6 B_ABTRP ATM   #>  7 B_ABTRP COL   #>  8 B_ABTRP NAL   #>  9 B_ABTRP PLB   #> 10 B_ABTRP TEM   #> # ℹ 134,624 more rows"},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":null,"dir":"Reference","previous_headings":"","what":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"According binomial nomenclature, lowest four taxonomic levels (family, genus, species, subspecies) printed italics. function finds taxonomic names within strings makes italic.","code":""},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"","code":"italicise_taxonomy(string, type = c(\"markdown\", \"ansi\"))  italicize_taxonomy(string, type = c(\"markdown\", \"ansi\"))"},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"string character (vector) type type conversion taxonomic names, either \"markdown\" \"ansi\", see Details","code":""},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"function finds taxonomic names makes italic based microorganisms data set. taxonomic names can italicised using markdown (default) adding * taxonomic names, using ANSI colours adding \\033[3m \\033[23m taxonomic names. multiple ANSI colours available, conversion occur. function also supports abbreviation genus followed species, \"E. coli\" \"K. pneumoniae ozaenae\".","code":""},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"","code":"italicise_taxonomy(\"An overview of Staphylococcus aureus isolates\") #> [1] \"An overview of *Staphylococcus aureus* isolates\" italicise_taxonomy(\"An overview of S. aureus isolates\") #> [1] \"An overview of *S. aureus* isolates\"  cat(italicise_taxonomy(\"An overview of S. aureus isolates\", type = \"ansi\")) #> An overview of S. aureus isolates"},{"path":"https://msberends.github.io/AMR/reference/join.html","id":null,"dir":"Reference","previous_headings":"","what":"Join microorganisms to a Data Set — join","title":"Join microorganisms to a Data Set — join","text":"Join data set microorganisms easily existing data set character vector.","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Join microorganisms to a Data Set — join","text":"","code":"inner_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  left_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  right_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  full_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  semi_join_microorganisms(x, by = NULL, ...)  anti_join_microorganisms(x, by = NULL, ...)"},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Join microorganisms to a Data Set — join","text":"x existing data set join, character vector. case character vector, resulting data.frame contain column 'x' values. variable join - left empty search column class mo (created .mo()) \"mo\" column name exists x, otherwise column name x values exist microorganisms$mo (= \"bacteria_id\"), another column microorganisms (named, like = c(\"bacteria_id\" = \"fullname\")) suffix non-joined duplicate variables x y, suffixes added output disambiguate . character vector length 2. ... ignored, place allow future extensions","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Join microorganisms to a Data Set — join","text":"data.frame","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Join microorganisms to a Data Set — join","text":"Note: opposed join() functions dplyr, character vectors supported default existing columns get suffix \"2\" newly joined columns get suffix. dplyr package installed, join functions used. Otherwise, much slower merge() interaction() functions base R used.","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Join microorganisms to a Data Set — join","text":"","code":"left_join_microorganisms(as.mo(\"K. pneumoniae\")) #> # A tibble: 1 × 22 #>   mo           fullname   status kingdom phylum class order family genus species #>   <mo>         <chr>      <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>   #> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo… #> # ℹ 12 more variables: subspecies <chr>, rank <chr>, ref <chr>, source <chr>, #> #   lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>, gbif <chr>, #> #   gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>, snomed <list> left_join_microorganisms(\"B_KLBSL_PNMN\") #> # A tibble: 1 × 22 #>   mo           fullname   status kingdom phylum class order family genus species #>   <mo>         <chr>      <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>   #> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo… #> # ℹ 12 more variables: subspecies <chr>, rank <chr>, ref <chr>, source <chr>, #> #   lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>, gbif <chr>, #> #   gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>  df <- data.frame(   date = seq(     from = as.Date(\"2018-01-01\"),     to = as.Date(\"2018-01-07\"),     by = 1   ),   bacteria = as.mo(c(     \"S. aureus\", \"MRSA\", \"MSSA\", \"STAAUR\",     \"E. coli\", \"E. coli\", \"E. coli\"   )),   stringsAsFactors = FALSE ) colnames(df) #> [1] \"date\"     \"bacteria\"  df_joined <- left_join_microorganisms(df, \"bacteria\") colnames(df_joined) #>  [1] \"date\"            \"bacteria\"        \"fullname\"        \"status\"          #>  [5] \"kingdom\"         \"phylum\"          \"class\"           \"order\"           #>  [9] \"family\"          \"genus\"           \"species\"         \"subspecies\"      #> [13] \"rank\"            \"ref\"             \"source\"          \"lpsn\"            #> [17] \"lpsn_parent\"     \"lpsn_renamed_to\" \"gbif\"            \"gbif_parent\"     #> [21] \"gbif_renamed_to\" \"prevalence\"      \"snomed\"           # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     left_join_microorganisms() %>%     colnames() } #> Joining, by = \"mo\" #>  [1] \"date\"            \"patient\"         \"age\"             \"gender\"          #>  [5] \"ward\"            \"mo\"              \"PEN\"             \"OXA\"             #>  [9] \"FLC\"             \"AMX\"             \"AMC\"             \"AMP\"             #> [13] \"TZP\"             \"CZO\"             \"FEP\"             \"CXM\"             #> [17] \"FOX\"             \"CTX\"             \"CAZ\"             \"CRO\"             #> [21] \"GEN\"             \"TOB\"             \"AMK\"             \"KAN\"             #> [25] \"TMP\"             \"SXT\"             \"NIT\"             \"FOS\"             #> [29] \"LNZ\"             \"CIP\"             \"MFX\"             \"VAN\"             #> [33] \"TEC\"             \"TCY\"             \"TGC\"             \"DOX\"             #> [37] \"ERY\"             \"CLI\"             \"AZM\"             \"IPM\"             #> [41] \"MEM\"             \"MTR\"             \"CHL\"             \"COL\"             #> [45] \"MUP\"             \"RIF\"             \"fullname\"        \"status\"          #> [49] \"kingdom\"         \"phylum\"          \"class\"           \"order\"           #> [53] \"family\"          \"genus\"           \"species\"         \"subspecies\"      #> [57] \"rank\"            \"ref\"             \"source\"          \"lpsn\"            #> [61] \"lpsn_parent\"     \"lpsn_renamed_to\" \"gbif\"            \"gbif_parent\"     #> [65] \"gbif_renamed_to\" \"prevalence\"      \"snomed\"          # }"},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":null,"dir":"Reference","previous_headings":"","what":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"functions can used determine first weighted isolates considering phenotype isolate selection (see first_isolate()). Using phenotype-based method determine first isolates reliable methods disregard phenotypes.","code":""},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"","code":"key_antimicrobials(   x = NULL,   col_mo = NULL,   universal = c(\"ampicillin\", \"amoxicillin/clavulanic acid\", \"cefuroxime\",     \"piperacillin/tazobactam\", \"ciprofloxacin\", \"trimethoprim/sulfamethoxazole\"),   gram_negative = c(\"gentamicin\", \"tobramycin\", \"colistin\", \"cefotaxime\", \"ceftazidime\",     \"meropenem\"),   gram_positive = c(\"vancomycin\", \"teicoplanin\", \"tetracycline\", \"erythromycin\",     \"oxacillin\", \"rifampin\"),   antifungal = c(\"anidulafungin\", \"caspofungin\", \"fluconazole\", \"miconazole\", \"nystatin\",     \"voriconazole\"),   only_sir_columns = FALSE,   ... )  all_antimicrobials(x = NULL, only_sir_columns = FALSE, ...)  antimicrobials_equal(   y,   z,   type = c(\"points\", \"keyantimicrobials\"),   ignore_I = TRUE,   points_threshold = 2,   ... )"},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"x data.frame antibiotics columns, like AMX amox. Can left blank determine automatically col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). universal names broad-spectrum antimicrobial drugs, case-insensitive. Set NULL ignore. See Details default antimicrobial drugs gram_negative names antibiotic drugs Gram-positives, case-insensitive. Set NULL ignore. See Details default antibiotic drugs gram_positive names antibiotic drugs Gram-negatives, case-insensitive. Set NULL ignore. See Details default antibiotic drugs antifungal names antifungal drugs fungi, case-insensitive. Set NULL ignore. See Details default antifungal drugs only_sir_columns logical indicate whether columns must included transformed class sir (see .sir()) beforehand (default FALSE) ... ignored, place allow future extensions y, z character vectors compare type type determine weighed isolates; can \"keyantimicrobials\" \"points\", see Details ignore_I logical indicate whether antibiotic interpretations \"\" ignored type = \"keyantimicrobials\", see Details points_threshold minimum number points require differences antibiogram lead inclusion isolate type = \"points\", see Details","code":""},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"key_antimicrobials() all_antimicrobials() functions context-aware. means x argument can left blank used inside data.frame call, see Examples. function key_antimicrobials() returns character vector 12 antimicrobial results every isolate. function all_antimicrobials() returns character vector antimicrobial drug results every isolate. vectors can compared using antimicrobials_equal(), check two isolates generally antibiogram. Missing invalid values replaced dot (\".\") key_antimicrobials() ignored antimicrobials_equal(). Please see first_isolate() function important functions enable 'phenotype-based' method determination first isolates. default antimicrobial drugs used rows (set universal) : Ampicillin Amoxicillin/clavulanic acid Cefuroxime Ciprofloxacin Piperacillin/tazobactam Trimethoprim/sulfamethoxazole default antimicrobial drugs used Gram-negative bacteria (set gram_negative) : Cefotaxime Ceftazidime Colistin Gentamicin Meropenem Tobramycin default antimicrobial drugs used Gram-positive bacteria (set gram_positive) : Erythromycin Oxacillin Rifampin Teicoplanin Tetracycline Vancomycin default antimicrobial drugs used fungi (set antifungal) : Anidulafungin Caspofungin Fluconazole Miconazole Nystatin Voriconazole","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  # output of the `key_antimicrobials()` function could be like this: strainA <- \"SSSRR.S.R..S\" strainB <- \"SSSIRSSSRSSS\"  # those strings can be compared with: antimicrobials_equal(strainA, strainB, type = \"keyantimicrobials\") #> [1] TRUE # TRUE, because I is ignored (as well as missing values)  antimicrobials_equal(strainA, strainB, type = \"keyantimicrobials\", ignore_I = FALSE) #> [1] FALSE # FALSE, because I is not ignored and so the 4th [character] differs  # \\donttest{ if (require(\"dplyr\")) {   # set key antibiotics to a new variable   my_patients <- example_isolates %>%     mutate(keyab = key_antimicrobials(antifungal = NULL)) %>% # no need to define `x`     mutate(       # now calculate first isolates       first_regular = first_isolate(col_keyantimicrobials = FALSE),       # and first WEIGHTED isolates       first_weighted = first_isolate(col_keyantimicrobials = \"keyab\")     )    # Check the difference in this data set, 'weighted' results in more isolates:   sum(my_patients$first_regular, na.rm = TRUE)   sum(my_patients$first_weighted, na.rm = TRUE) } #> [1] 1395 # }"},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":null,"dir":"Reference","previous_headings":"","what":"Kurtosis of the Sample — kurtosis","title":"Kurtosis of the Sample — kurtosis","text":"Kurtosis measure \"tailedness\" probability distribution real-valued random variable. normal distribution kurtosis 3 excess kurtosis 0.","code":""},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kurtosis of the Sample — kurtosis","text":"","code":"kurtosis(x, na.rm = FALSE, excess = FALSE)  # S3 method for default kurtosis(x, na.rm = FALSE, excess = FALSE)  # S3 method for matrix kurtosis(x, na.rm = FALSE, excess = FALSE)  # S3 method for data.frame kurtosis(x, na.rm = FALSE, excess = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Kurtosis of the Sample — kurtosis","text":"x vector values, matrix data.frame na.rm logical indicate whether NA values stripped computation proceeds excess logical indicate whether excess kurtosis returned, defined kurtosis minus 3.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kurtosis of the Sample — kurtosis","text":"","code":"kurtosis(rnorm(10000)) #> [1] 2.983132 kurtosis(rnorm(10000), excess = TRUE) #> [1] -0.04668891"},{"path":"https://msberends.github.io/AMR/reference/like.html","id":null,"dir":"Reference","previous_headings":"","what":"Vectorised Pattern Matching with Keyboard Shortcut — like","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"Convenient wrapper around grepl() match pattern: x %like% pattern. always returns logical vector always case-insensitive (use x %like_case% pattern case-sensitive matching). Also, pattern can long x compare items index vectors, can length iterate cases.","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"","code":"like(x, pattern, ignore.case = TRUE)  x %like% pattern  x %unlike% pattern  x %like_case% pattern  x %unlike_case% pattern"},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"Idea like function data.table package, although altered explained Details.","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"x character vector matches sought, object can coerced .character() character vector. pattern character vector containing regular expressions (character string fixed = TRUE) matched given character vector. Coerced .character() character string possible. ignore.case FALSE, pattern matching case sensitive TRUE, case ignored matching.","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"logical vector","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"like() %like%/%unlike% functions: case-insensitive (use %like_case%/%unlike_case% case-sensitive matching) Support multiple patterns Check pattern valid regular expression sets fixed = TRUE , greatly improve speed (vectorised pattern) Always use compatibility Perl unless fixed = TRUE, greatly improve speed Using RStudio? %like%/%unlike% functions can also directly inserted code Addins menu can keyboard shortcut like Shift+Ctrl+L Shift+Cmd+L (see menu Tools > Modify Keyboard Shortcuts...). keep pressing shortcut, inserted text iterated %like% -> %unlike% -> %like_case% -> %unlike_case%.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"","code":"# data.table has a more limited version of %like%, so unload it: try(detach(\"package:data.table\", unload = TRUE), silent = TRUE)  a <- \"This is a test\" b <- \"TEST\" a %like% b #> [1] TRUE b %like% a #> [1] FALSE  # also supports multiple patterns a <- c(\"Test case\", \"Something different\", \"Yet another thing\") b <- c(\"case\", \"diff\", \"yet\") a %like% b #> [1] TRUE TRUE TRUE a %unlike% b #> [1] FALSE FALSE FALSE  a[1] %like% b #> [1]  TRUE FALSE FALSE a %like% b[1] #> [1]  TRUE FALSE FALSE  # \\donttest{ # get isolates whose name start with 'Entero' (case-insensitive) example_isolates[which(mo_name() %like% \"^entero\"), ] #> ℹ Using column 'mo' as input for mo_name() #> # A tibble: 106 × 46 #>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinic… B_ENTRC_FACM  NA    NA    NA    NA    #>  2 2002-04-08 130252     78 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  3 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  4 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  5 2003-04-20 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  6 2003-04-21 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  7 2003-08-13 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  8 2003-08-13 F35553     52 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  9 2003-09-05 F35553     52 M      ICU     B_ENTRC       NA    NA    NA    NA    #> 10 2003-09-05 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #> # ℹ 96 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  if (require(\"dplyr\")) {   example_isolates %>%     filter(mo_name() %like% \"^ent\") } #> ℹ Using column 'mo' as input for mo_name() #> # A tibble: 106 × 46 #>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinic… B_ENTRC_FACM  NA    NA    NA    NA    #>  2 2002-04-08 130252     78 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  3 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  4 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  5 2003-04-20 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  6 2003-04-21 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  7 2003-08-13 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  8 2003-08-13 F35553     52 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  9 2003-09-05 F35553     52 M      ICU     B_ENTRC       NA    NA    NA    NA    #> 10 2003-09-05 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #> # ℹ 96 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … # }"},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"Determine isolates multidrug-resistant organisms (MDRO) according international, national custom guidelines.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"","code":"mdro(   x = NULL,   guideline = \"CMI2012\",   col_mo = NULL,   info = interactive(),   pct_required_classes = 0.5,   combine_SI = TRUE,   verbose = FALSE,   only_sir_columns = FALSE,   ... )  custom_mdro_guideline(..., as_factor = TRUE)  brmo(x = NULL, only_sir_columns = FALSE, ...)  mrgn(x = NULL, only_sir_columns = FALSE, ...)  mdr_tb(x = NULL, only_sir_columns = FALSE, ...)  mdr_cmi2012(x = NULL, only_sir_columns = FALSE, ...)  eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE, ...)"},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"See supported guidelines list publications used function.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"x data.frame antibiotics columns, like AMX amox. Can left blank automatic determination. guideline specific guideline follow, see sections Supported international / national guidelines Using Custom Guidelines . left empty, publication Magiorakos et al. (see ) followed. col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). info logical indicate whether progress printed console - default print interactive sessions pct_required_classes minimal required percentage antimicrobial classes must available per isolate, rounded . example, default guideline, 17 antimicrobial classes must available S. aureus. Setting pct_required_classes argument 0.5 (default) means every S. aureus isolate least 8 different classes must available. lower number available classes return NA isolate. combine_SI logical indicate whether values S must merged one, resistance considered isolates R, . default behaviour mdro() function, follows redefinition EUCAST interpretation (increased exposure) 2019, see section 'Interpretation S, R' . using combine_SI = FALSE, resistance considered isolates R . verbose logical turn Verbose mode (default ). Verbose mode, function return MDRO results, instead returns data set logbook form extensive info isolates MDRO-positive, . only_sir_columns logical indicate whether antibiotic columns must detected transformed class sir (see .sir()) beforehand (default FALSE) ... case custom_mdro_guideline(): set rules, see section Using Custom Guidelines . Otherwise: column name antibiotic, see section Antibiotics . as_factor logical indicate whether returned value ordered factor (TRUE, default), otherwise character vector","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"CMI 2012 paper - function mdr_cmi2012() mdro(): Ordered factor levels Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant (XDR) < Pandrug-resistant (PDR) TB guideline - function mdr_tb() mdro(..., guideline = \"TB\"): Ordered factor levels Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensively drug-resistant German guideline - function mrgn() mdro(..., guideline = \"MRGN\"): Ordered factor levels Negative < 3MRGN < 4MRGN Everything else, except custom guidelines: Ordered factor levels Negative < Positive, unconfirmed < Positive. value \"Positive, unconfirmed\" means , according guideline, entirely sure isolate multi-drug resistant confirmed additional (e.g. molecular) tests","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"functions context-aware. means x argument can left blank used inside data.frame call, see Examples. pct_required_classes argument, values 1 divided 100. support fractions (0.75 3/4) percentages (75). Note: Every test involves Enterobacteriaceae family, internally performed using newly named order Enterobacterales, since Enterobacteriaceae family taxonomically reclassified Adeolu et al. 2016. , Enterobacteriaceae family Enterobacteriales () order. species old Enterobacteriaceae family still new Enterobacterales (without ) order, divided multiple families. way tests performed now mdro() function makes sure results 2016 2016 identical.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"supported-international-national-guidelines","dir":"Reference","previous_headings":"","what":"Supported International / National Guidelines","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"Currently supported guidelines (case-insensitive): guideline = \"CMI2012\" (default) Magiorakos AP, Srinivasan et al. \"Multidrug-resistant, extensively drug-resistant pandrug-resistant bacteria: international expert proposal interim standard definitions acquired resistance.\" Clinical Microbiology Infection (2012) (link) guideline = \"EUCAST3.3\" (simply guideline = \"EUCAST\") European international guideline - EUCAST Expert Rules Version 3.3 \"Intrinsic Resistance Unusual Phenotypes\" (link) guideline = \"EUCAST3.2\" European international guideline - EUCAST Expert Rules Version 3.2 \"Intrinsic Resistance Unusual Phenotypes\" (link) guideline = \"EUCAST3.1\" European international guideline - EUCAST Expert Rules Version 3.1 \"Intrinsic Resistance Exceptional Phenotypes Tables\" (link) guideline = \"TB\" international guideline multi-drug resistant tuberculosis - World Health Organization \"Companion handbook guidelines programmatic management drug-resistant tuberculosis\" (link) guideline = \"MRGN\" German national guideline - Mueller et al. (2015) Antimicrobial Resistance Infection Control 4:7; doi:10.1186/s13756-015-0047-6 guideline = \"BRMO\" Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu \"WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)\" (link) Please suggest (country-specific) guidelines letting us know: https://github.com/msberends/AMR/issues/new.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"using-custom-guidelines","dir":"Reference","previous_headings":"","what":"Using Custom Guidelines","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"Custom guidelines can set custom_mdro_guideline() function. great importance custom rules determine MDROs hospital, e.g., rules dependent ward, state contact isolation variables data. familiar case_when() function dplyr package, recognise input method set rules. Rules must set using R considers 'formula notation'. rule written tilde (~) consequence rule written tilde:   row/isolate matches first rule, value first ~ (case 'Elderly Type ') set MDRO value. Otherwise, second rule tried . number rules unlimited. can print rules set console overview. Colours help reading console supports colours.   outcome function can used guideline argument mdro() function:   Rules can also combined custom rules using c():   rules set (custom object case) exported shared file location using saveRDS() collaborate multiple users. custom rules set imported using readRDS().","code":"custom <- custom_mdro_guideline(CIP == \"R\" & age > 60 ~ \"Elderly Type A\",                                 ERY == \"R\" & age > 60 ~ \"Elderly Type B\") custom #> A set of custom MDRO rules: #>   1. CIP is \"R\" and age is higher than 60 -> Elderly Type A #>   2. ERY is \"R\" and age is higher than 60 -> Elderly Type B #>   3. Otherwise -> Negative #> #> Unmatched rows will return NA. x <- mdro(example_isolates,           guideline = custom) table(x) #>       Negative Elderly Type A Elderly Type B #>           1070            198            732 x <- mdro(example_isolates,           guideline = c(custom,                         custom_mdro_guideline(ERY == \"R\" & age > 50 ~ \"Elderly Type C\"))) table(x) #>       Negative Elderly Type A Elderly Type B Elderly Type C #>            961            198            732            109"},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"antibiotics","dir":"Reference","previous_headings":"","what":"Antibiotics","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"define antibiotics column names, leave determine automatically guess_ab_col() input text (case-insensitive), use NULL skip column (e.g. TIC = NULL skip ticarcillin). Manually defined non-existing columns skipped warning. following antibiotics eligible functions eucast_rules() mdro(). shown format 'name (antimicrobial ID, ATC code)', sorted alphabetically: Amikacin (AMK, J01GB06), amoxicillin (AMX, J01CA04), amoxicillin/clavulanic acid (AMC, J01CR02), ampicillin (AMP, J01CA01), ampicillin/sulbactam (SAM, J01CR01), arbekacin (ARB, J01GB12), aspoxicillin (APX, J01CA19), azidocillin (AZD, J01CE04), azithromycin (AZM, J01FA10), azlocillin (AZL, J01CA09), aztreonam (ATM, J01DF01), bacampicillin (BAM, J01CA06), bekanamycin (BEK, J01GB13), benzathine benzylpenicillin (BNB, J01CE08), benzathine phenoxymethylpenicillin (BNP, J01CE10), benzylpenicillin (PEN, J01CE01), besifloxacin (BES, S01AE08), biapenem (BIA, J01DH05), carbenicillin (CRB, J01CA03), carindacillin (CRN, J01CA05), cefacetrile (CAC, J01DB10), cefaclor (CEC, J01DC04), cefadroxil (CFR, J01DB05), cefalexin (LEX, J01DB01), cefaloridine (RID, J01DB02), cefalotin (CEP, J01DB03), cefamandole (MAN, J01DC03), cefapirin (HAP, J01DB08), cefatrizine (CTZ, J01DB07), cefazedone (CZD, J01DB06), cefazolin (CZO, J01DB04), cefcapene (CCP, J01DD17), cefdinir (CDR, J01DD15), cefditoren (DIT, J01DD16), cefepime (FEP, J01DE01), cefetamet (CAT, J01DD10), cefixime (CFM, J01DD08), cefmenoxime (CMX, J01DD05), cefmetazole (CMZ, J01DC09), cefodizime (DIZ, J01DD09), cefonicid (CID, J01DC06), cefoperazone (CFP, J01DD12), cefoperazone/sulbactam (CSL, J01DD62), ceforanide (CND, J01DC11), cefotaxime (CTX, J01DD01), cefotaxime/clavulanic acid (CTC, J01DD51), cefotetan (CTT, J01DC05), cefotiam (CTF, J01DC07), cefoxitin (FOX, J01DC01), cefozopran (ZOP, J01DE03), cefpiramide (CPM, J01DD11), cefpirome (CPO, J01DE02), cefpodoxime (CPD, J01DD13), cefprozil (CPR, J01DC10), cefroxadine (CRD, J01DB11), cefsulodin (CFS, J01DD03), ceftaroline (CPT, J01DI02), ceftazidime (CAZ, J01DD02), ceftazidime/clavulanic acid (CCV, J01DD52), cefteram (CEM, J01DD18), ceftezole (CTL, J01DB12), ceftibuten (CTB, J01DD14), ceftizoxime (CZX, J01DD07), ceftobiprole medocaril (CFM1, J01DI01), ceftolozane/tazobactam (CZT, J01DI54), ceftriaxone (CRO, J01DD04), ceftriaxone/beta-lactamase inhibitor (CEB, J01DD63), cefuroxime (CXM, J01DC02), cephradine (CED, J01DB09), chloramphenicol (CHL, J01BA01), ciprofloxacin (CIP, J01MA02), clarithromycin (CLR, J01FA09), clindamycin (CLI, J01FF01), clometocillin (CLM, J01CE07), cloxacillin (CLO, J01CF02), colistin (COL, J01XB01), cycloserine (CYC, J04AB01), dalbavancin (DAL, J01XA04), daptomycin (DAP, J01XX09), delafloxacin (DFX, J01MA23), dibekacin (DKB, J01GB09), dicloxacillin (DIC, J01CF01), dirithromycin (DIR, J01FA13), doripenem (DOR, J01DH04), doxycycline (DOX, J01AA02), enoxacin (ENX, J01MA04), epicillin (EPC, J01CA07), ertapenem (ETP, J01DH03), erythromycin (ERY, J01FA01), fleroxacin (FLE, J01MA08), flucloxacillin (FLC, J01CF05), flurithromycin (FLR1, J01FA14), fosfomycin (FOS, J01XX01), framycetin (FRM, D09AA01), fusidic acid (FUS, J01XC01), garenoxacin (GRN, J01MA19), gatifloxacin (GAT, J01MA16), gemifloxacin (GEM, J01MA15), gentamicin (GEN, J01GB03), grepafloxacin (GRX, J01MA11), hetacillin (HET, J01CA18), imipenem (IPM, J01DH51), imipenem/relebactam (IMR, J01DH56), isepamicin (ISE, J01GB11), josamycin (JOS, J01FA07), kanamycin (KAN, J01GB04), lascufloxacin (LSC, J01MA25), latamoxef (LTM, J01DD06), levofloxacin (LVX, J01MA12), levonadifloxacin (LND, J01MA24), lincomycin (LIN, J01FF02), linezolid (LNZ, J01XX08), lomefloxacin (LOM, J01MA07), loracarbef (LOR, J01DC08), mecillinam (MEC, J01CA11), meropenem (MEM, J01DH02), meropenem/vaborbactam (MEV, J01DH52), metampicillin (MTM, J01CA14), meticillin (MET, J01CF03), mezlocillin (MEZ, J01CA10), micronomicin (MCR, S01AA22), midecamycin (MID, J01FA03), minocycline (MNO, J01AA08), miocamycin (MCM, J01FA11), moxifloxacin (MFX, J01MA14), nadifloxacin (NAD, D10AF05), nafcillin (NAF, J01CF06), nalidixic acid (NAL, J01MB02), neomycin (NEO, J01GB05), netilmicin (NET, J01GB07), nitrofurantoin (NIT, J01XE01), norfloxacin (, J01MA06), ofloxacin (OFX, J01MA01), oleandomycin (OLE, J01FA05), oritavancin (ORI, J01XA05), oxacillin (OXA, J01CF04), panipenem (PAN, J01DH55), pazufloxacin (PAZ, J01MA18), pefloxacin (PEF, J01MA03), penamecillin (PNM, J01CE06), pheneticillin (PHE, J01CE05), phenoxymethylpenicillin (PHN, J01CE02), piperacillin (PIP, J01CA12), piperacillin/tazobactam (TZP, J01CR05), pivampicillin (PVM, J01CA02), pivmecillinam (PME, J01CA08), plazomicin (PLZ, J01GB14), polymyxin B (PLB, J01XB02), pristinamycin (PRI, J01FG01), procaine benzylpenicillin (PRB, J01CE09), propicillin (PRP, J01CE03), prulifloxacin (PRU, J01MA17), quinupristin/dalfopristin (QDA, J01FG02), ribostamycin (RST, J01GB10), rifampicin (RIF, J04AB02), rokitamycin (ROK, J01FA12), roxithromycin (RXT, J01FA06), rufloxacin (RFL, J01MA10), sisomicin (SIS, J01GB08), sitafloxacin (SIT, J01MA21), solithromycin (SOL, J01FA16), sparfloxacin (SPX, J01MA09), spiramycin (SPI, J01FA02), streptoduocin (STR, J01GA02), streptomycin (STR1, J01GA01), sulbactam (SUL, J01CG01), sulbenicillin (SBC, J01CA16), sulfadiazine (SDI, J01EC02), sulfadiazine/trimethoprim (SLT1, J01EE02), sulfadimethoxine (SUD, J01ED01), sulfadimidine (SDM, J01EB03), sulfadimidine/trimethoprim (SLT2, J01EE05), sulfafurazole (SLF, J01EB05), sulfaisodimidine (SLF1, J01EB01), sulfalene (SLF2, J01ED02), sulfamazone (SZO, J01ED09), sulfamerazine (SLF3, J01ED07), sulfamerazine/trimethoprim (SLT3, J01EE07), sulfamethizole (SLF4, J01EB02), sulfamethoxazole (SMX, J01EC01), sulfamethoxypyridazine (SLF5, J01ED05), sulfametomidine (SLF6, J01ED03), sulfametoxydiazine (SLF7, J01ED04), sulfametrole/trimethoprim (SLT4, J01EE03), sulfamoxole (SLF8, J01EC03), sulfamoxole/trimethoprim (SLT5, J01EE04), sulfanilamide (SLF9, J01EB06), sulfaperin (SLF10, J01ED06), sulfaphenazole (SLF11, J01ED08), sulfapyridine (SLF12, J01EB04), sulfathiazole (SUT, J01EB07), sulfathiourea (SLF13, J01EB08), sultamicillin (SLT6, J01CR04), talampicillin (TAL, J01CA15), tazobactam (TAZ, J01CG02), tebipenem (TBP, J01DH06), tedizolid (TZD, J01XX11), teicoplanin (TEC, J01XA02), telavancin (TLV, J01XA03), telithromycin (TLT, J01FA15), temafloxacin (TMX, J01MA05), temocillin (TEM, J01CA17), tetracycline (TCY, J01AA07), ticarcillin (TIC, J01CA13), ticarcillin/clavulanic acid (TCC, J01CR03), tigecycline (TGC, J01AA12), tilbroquinol (TBQ, P01AA05), tobramycin (TOB, J01GB01), tosufloxacin (TFX, J01MA22), trimethoprim (TMP, J01EA01), trimethoprim/sulfamethoxazole (SXT, J01EE01), troleandomycin (TRL, J01FA08), trovafloxacin (TVA, J01MA13), vancomycin (VAN, J01XA01)","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"","code":"out <- mdro(example_isolates, guideline = \"EUCAST\") #>  (16 isolates had no test results) str(out) #>  Ord.factor w/ 3 levels \"Negative\"<\"Positive, unconfirmed\"<..: 1 1 1 1 1 1 1 1 1 1 ... table(out) #> out #>              Negative Positive, unconfirmed              Positive  #>                  1978                     0                     6   out <- mdro(example_isolates,   guideline = custom_mdro_guideline(     AMX == \"R\" ~ \"Custom MDRO 1\",     VAN == \"R\" ~ \"Custom MDRO 2\"   ) ) table(out) #> out #>      Negative Custom MDRO 1 Custom MDRO 2  #>           870           804           326   # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     mdro() %>%     table()    # no need to define `x` when used inside dplyr verbs:   example_isolates %>%     mutate(MDRO = mdro()) %>%     pull(MDRO) %>%     table() } #>  (16 isolates had no test results) #> Warning: in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) #>  (16 isolates had no test results) #> Warning: There was 1 warning in `mutate()`. #> ℹ In argument: `MDRO = mdro()`. #> Caused by warning: #> ! in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) #> . #>                         Negative       Multi-drug-resistant (MDR)  #>                             1601                              128  #> Extensively drug-resistant (XDR)          Pandrug-resistant (PDR)  #>                                0                                0  # }"},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the Mean AMR Distance — mean_amr_distance","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"Calculates normalised mean antimicrobial resistance multiple observations, help identify similar isolates without comparing antibiograms hand.","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"","code":"mean_amr_distance(x, ...)  # S3 method for sir mean_amr_distance(x, ..., combine_SI = TRUE)  # S3 method for data.frame mean_amr_distance(x, ..., combine_SI = TRUE)  amr_distance_from_row(amr_distance, row)"},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"x vector class sir, mic disk, data.frame containing columns classes ... variables select (supports tidyselect language column1:column4 (.mic), can thus also antibiotic selectors combine_SI logical indicate whether values S must merged one, input consists S+vs. R (susceptible vs. resistant) - default TRUE amr_distance outcome mean_amr_distance() row index, row number","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"mean AMR distance effectively Z-score; normalised numeric value compare AMR test results can help identify similar isolates, without comparing antibiograms hand. MIC values (see .mic()) transformed log2() first; distance thus calculated (log2(x) - mean(log2(x))) / sd(log2(x)). SIR values (see .sir()) transformed using \"S\" = 1, \"\" = 2, \"R\" = 3. combine_SI TRUE (default), \"\" considered 1. data sets, mean AMR distance calculated per column, mean per row returned, see Examples. Use amr_distance_from_row() subtract distances distance one row, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"interpretation","dir":"Reference","previous_headings":"","what":"Interpretation","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"Isolates distances less 0.01 difference considered similar. Differences lower 0.025 considered suspicious.","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"","code":"sir <- random_sir(10) sir #> Class 'sir' #>  [1] I I R I I I R S S R mean_amr_distance(sir) #>  [1] -0.621059 -0.621059  1.449138 -0.621059 -0.621059 -0.621059  1.449138 #>  [8] -0.621059 -0.621059  1.449138  mic <- random_mic(10) mic #> Class 'mic' #>  [1] 0.01  8     0.025 2     0.125 0.005 128   0.01  2     1     mean_amr_distance(mic) #>  [1] -1.0080431  0.9684558 -0.7371152  0.5585577 -0.2612383 -1.2129921 #>  [7]  1.7882519 -1.0080431  0.5585577  0.3536087 # equal to the Z-score of their log2: (log2(mic) - mean(log2(mic))) / sd(log2(mic)) #>  [1] -1.0080431  0.9684558 -0.7371152  0.5585577 -0.2612383 -1.2129921 #>  [7]  1.7882519 -1.0080431  0.5585577  0.3536087  disk <- random_disk(10) disk #> Class 'disk' #>  [1] 10 50 31 17 26 49 37 45 28 13 mean_amr_distance(disk) #>  [1] -1.41392483  1.33156027  0.02745485 -0.93346493 -0.31573079  1.26292315 #>  [7]  0.43927762  0.98837464 -0.17845653 -1.20801344  y <- data.frame(   id = LETTERS[1:10],   amox = random_sir(10, ab = \"amox\", mo = \"Escherichia coli\"),   cipr = random_disk(10, ab = \"cipr\", mo = \"Escherichia coli\"),   gent = random_mic(10, ab = \"gent\", mo = \"Escherichia coli\"),   tobr = random_mic(10, ab = \"tobr\", mo = \"Escherichia coli\") ) y #>    id amox cipr gent tobr #> 1   A    S   19 >=16  <=1 #> 2   B    R   20    8  <=1 #> 3   C    I   20    2    4 #> 4   D    S   19  <=1    8 #> 5   E    I   23    4    4 #> 6   F    I   31  <=1    8 #> 7   G    R   18    2    4 #> 8   H    I   22    2  <=1 #> 9   I    I   22  <=1  <=1 #> 10  J    I   25 >=16    2 mean_amr_distance(y) #> ℹ Calculating mean AMR distance based on columns \"amox\", \"cipr\", \"gent\", #>   and \"tobr\" #>  [1] -0.1865874  0.3129310 -0.1974612 -0.2212515  0.1561783  0.5594410 #>  [7]  0.2653504 -0.4668135 -0.6252799  0.4034927 y$amr_distance <- mean_amr_distance(y, where(is.mic)) #> Error in .subset(x, j): invalid subscript type 'list' y[order(y$amr_distance), ] #> Error in order(y$amr_distance): argument 1 is not a vector  if (require(\"dplyr\")) {   y %>%     mutate(       amr_distance = mean_amr_distance(y),       check_id_C = amr_distance_from_row(amr_distance, id == \"C\")     ) %>%     arrange(check_id_C) } #> ℹ Calculating mean AMR distance based on columns \"amox\", \"cipr\", \"gent\", #>   and \"tobr\" #>    id amox cipr gent tobr amr_distance check_id_C #> 1   C    I   20    2    4   -0.1974612 0.00000000 #> 2   A    S   19 >=16  <=1   -0.1865874 0.01087383 #> 3   D    S   19  <=1    8   -0.2212515 0.02379027 #> 4   H    I   22    2  <=1   -0.4668135 0.26935231 #> 5   E    I   23    4    4    0.1561783 0.35363955 #> 6   I    I   22  <=1  <=1   -0.6252799 0.42781873 #> 7   G    R   18    2    4    0.2653504 0.46281164 #> 8   B    R   20    8  <=1    0.3129310 0.51039218 #> 9   J    I   25 >=16    2    0.4034927 0.60095395 #> 10  F    I   31  <=1    8    0.5594410 0.75690225 if (require(\"dplyr\")) {   # support for groups   example_isolates %>%     filter(mo_genus() == \"Enterococcus\" & mo_species() != \"\") %>%     select(mo, TCY, carbapenems()) %>%     group_by(mo) %>%     mutate(dist = mean_amr_distance(.)) %>%     arrange(mo, dist) } #> ℹ Using column 'mo' as input for mo_genus() #> ℹ Using column 'mo' as input for mo_species() #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Calculating mean AMR distance based on columns \"TCY\", \"IPM\", and \"MEM\" #> # A tibble: 63 × 5 #> # Groups:   mo [4] #>    mo           TCY   IPM   MEM     dist #>    <mo>         <sir> <sir> <sir>  <dbl> #>  1 B_ENTRC_AVIM S     S     NA     0     #>  2 B_ENTRC_AVIM S     S     NA     0     #>  3 B_ENTRC_CSSL NA    S     NA    NA     #>  4 B_ENTRC_FACM S     S     NA    -2.66  #>  5 B_ENTRC_FACM S     R     R     -0.423 #>  6 B_ENTRC_FACM S     R     R     -0.423 #>  7 B_ENTRC_FACM NA    R     R      0.224 #>  8 B_ENTRC_FACM NA    R     R      0.224 #>  9 B_ENTRC_FACM NA    R     R      0.224 #> 10 B_ENTRC_FACM NA    R     R      0.224 #> # ℹ 53 more rows"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"data set containing commonly used codes microorganisms, laboratory systems WHONET. Define set_mo_source(). searched using .mo() consequently mo_* functions.","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"","code":"microorganisms.codes"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"tibble 5 754 observations 2 variables: code Commonly used code microorganism mo ID microorganism microorganisms data set","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"","code":"microorganisms.codes #> # A tibble: 5,754 × 2 #>    code    mo        #>    <chr>   <mo>      #>  1 _FAM_A- B_GRAMN   #>  2 _FAM_A+ B_GRAMP   #>  3 _FAM_AC B_GRAMP   #>  4 _FAM_AE B_GRAMN   #>  5 _FAM_AN B_GRAMN   #>  6 _FAM_AO B_GRAMP   #>  7 _FAM_AP   UNKNOWN #>  8 _FAM_AS F_FUNGUS  #>  9 _FAM_AT   UNKNOWN #> 10 _FAM_AV   UNKNOWN #> # ℹ 5,744 more rows"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 52 151 Microorganisms — microorganisms","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"data set containing full microbial taxonomy (last updated: 11 December, 2022) five kingdoms List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF). data set backbone AMR package. MO codes can looked using .mo().","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"","code":"microorganisms"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"tibble 52 151 observations 22 variables: mo ID microorganism used package fullname Full name, like \"Escherichia coli\". taxonomic ranks genus, species subspecies, 'pasted' text genus, species, subspecies. taxonomic ranks higher genus, name taxon. status  Status taxon, either \"accepted\" \"synonym\" kingdom, phylum, class, order, family, genus, species, subspecies Taxonomic rank microorganism rank Text taxonomic rank microorganism, \"species\" \"genus\" ref Author(s) year related scientific publication. contains first surname year latest authors, e.g. \"Wallis et al. 2006 emend. Smith Jones 2018\" becomes \"Smith et al., 2018\". field directly retrieved source specified column source. Moreover, accents removed comply CRAN allows ASCII characters, e.g. \"Váňová\" becomes \"Vanova\". lpsn Identifier ('Record number') List Prokaryotic names Standing Nomenclature (LPSN). first/highest LPSN identifier keep one identifier per row. example, Acetobacter ascendens LPSN Record number 7864 11011. first available microorganisms data set. lpsn_parent LPSN identifier parent taxon lpsn_renamed_to LPSN identifier currently valid taxon gbif Identifier ('taxonID') Global Biodiversity Information Facility (GBIF) gbif_parent GBIF identifier parent taxon gbif_renamed_to GBIF identifier currently valid taxon source Either \"GBIF\", \"LPSN\", \"manually added\" (see Source) prevalence Prevalence microorganism according Bartlett et al. (2022, doi:10.1099/mic.0.001269 ), see mo_matching_score() full explanation snomed Systematized Nomenclature Medicine (SNOMED) code microorganism, version 1 July, 2021 (see Source). Use mo_snomed() retrieve quickly, see mo_property().","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332 . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov Grimont et al. (2007). Antigenic Formulae Salmonella Serovars, 9th Edition. Collaborating Centre Reference Research Salmonella (WHOCC-SALM). Bartlett et al. (2022). comprehensive list bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"Please note entries based List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF) (see ). Since sources incorporate entries based (recent) publications International Journal Systematic Evolutionary Microbiology (IJSEM), can happen year publication sometimes later one might expect. example, Staphylococcus pettenkoferi described first time Diagnostic Microbiology Infectious Disease 2002 (doi:10.1016/s0732-8893(02)00399-1 ), 2007 publication IJSEM followed (doi:10.1099/ijs.0.64381-0 ). Consequently, AMR package returns 2007 mo_year(\"S. pettenkoferi\").","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"included-taxa","dir":"Reference","previous_headings":"","what":"Included Taxa","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"Included taxonomic data : ~36 000 (sub)species kingdoms Archaea Bacteria ~7 900 (sub)species kingdom Fungi. kingdom Fungi large taxon almost 300,000 different (sub)species, microbial (rather macroscopic, like mushrooms). , fungi fit scope package. relevant fungi covered (species Aspergillus, Candida, Cryptococcus, Histoplasma, Pneumocystis, Saccharomyces Trichophyton). ~5 100 (sub)species kingdom Protozoa ~1 400 (sub)species 43 relevant genera kingdom Animalia (Strongyloides Taenia) ~9 800 previously accepted names included (sub)species (taxonomically renamed) complete taxonomic tree included (sub)species: kingdom subspecies identifier parent taxons year first author related scientific publication","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"manual-additions","dir":"Reference","previous_headings":"","what":"Manual additions","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"convenience, entries added manually: ~1 500 entries Salmonella, city-like serovars groups H 15 entries Streptococcus, beta-haemolytic groups K, viridans, milleri 2 entries Staphylococcus (coagulase-negative (CoNS) coagulase-positive (CoPS)) 1 entry Blastocystis (B.  hominis), although officially exist (Noel et al. 2005, PMID 15634993) 1 entry Moraxella (M. catarrhalis), formally named Branhamella catarrhalis (Catlin, 1970) though change never accepted within field clinical microbiology 8 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, unknown anaerobic Gram-pos/Gram-neg bacteria) syntax used transform original data cleansed R format, can found : https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R.","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"about-the-records-from-lpsn-see-source-","dir":"Reference","previous_headings":"","what":"About the Records from LPSN (see Source)","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"LPSN main source bacteriological taxonomy AMR package. List Prokaryotic names Standing Nomenclature (LPSN) provides comprehensive information nomenclature prokaryotes. LPSN free use service founded Jean P. Euzeby 1997 later maintained Aidan C. Parte.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"","code":"microorganisms #> # A tibble: 52,151 × 22 #>    mo               fullname      status kingdom phylum class order family genus #>    <mo>             <chr>         <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> #>  1 B_ANAER          (unknown ana… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  2 B_ANAER-NEG      (unknown ana… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  3 B_ANAER-POS      (unknown ana… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  4 F_FUNGUS         (unknown fun… accep… Fungi   (unkn… (unk… (unk… \"(unk… \"(un… #>  5 B_GRAMN          (unknown Gra… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  6 B_GRAMP          (unknown Gra… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  7   UNKNOWN        (unknown nam… accep… (unkno… (unkn… (unk… (unk… \"(unk… \"(un… #>  8 F_YEAST          (unknown yea… accep… Fungi   (unkn… (unk… (unk… \"(unk… \"(un… #>  9 B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… Abdi… \"Abdi… \"\"    #> 10 B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… Abdi… \"\"     \"\"    #> # ℹ 52,141 more rows #> # ℹ 13 more variables: species <chr>, subspecies <chr>, rank <chr>, ref <chr>, #> #   source <chr>, lpsn <chr>, lpsn_parent <chr>, lpsn_renamed_to <chr>, #> #   gbif <chr>, gbif_parent <chr>, gbif_renamed_to <chr>, prevalence <dbl>, #> #   snomed <list>"},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the Matching Score for Microorganisms — mo_matching_score","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"algorithm used .mo() mo_* functions determine probable match taxonomic records based user input.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"","code":"mo_matching_score(x, n)"},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"x user input value(s) n full taxonomic name, exists microorganisms$fullname","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"algorithm originally described : Berends MS et al. (2022). AMR: R Package Working Antimicrobial Resistance Data. Journal Statistical Software, 104(3), 1-31; doi:10.18637/jss.v104.i03 . Later, work Bartlett et al. bacterial pathogens infecting humans (2022, doi:10.1099/mic.0.001269 ) incorporated.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"matching-score-for-microorganisms","dir":"Reference","previous_headings":"","what":"Matching Score for Microorganisms","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"ambiguous user input .mo() mo_* functions, returned results chosen based matching score using mo_matching_score(). matching score \\(m\\), calculated :  : \\(x\\) user input; \\(n\\) taxonomic name (genus, species, subspecies); \\(l_n\\) length \\(n\\); \\(lev\\) Levenshtein distance function (counting insertion 1, deletion substitution 2) needed change \\(x\\) \\(n\\); \\(p_n\\) human pathogenic prevalence group \\(n\\), described ; \\(k_n\\) taxonomic kingdom \\(n\\), set Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5. grouping human pathogenic prevalence \\(p\\) based recent work Bartlett et al. (2022, doi:10.1099/mic.0.001269 ) extensively studied medical-scientific literature categorise bacterial species groups: Established, taxonomic species infected least three persons three references. records prevalence = 1.0 microorganisms data set; Putative, taxonomic species fewer three known cases. records prevalence = 1.25 microorganisms data set. Furthermore, genus present established list also prevalence = 1.0 microorganisms data set; genus present putative list prevalence = 1.25 microorganisms data set; species subspecies genus present two aforementioned groups, prevalence = 1.5 microorganisms data set; non-bacterial genus, species subspecies genus present following list, prevalence = 1.5 microorganisms data set: Absidia, Acanthamoeba, Acremonium, Aedes, Alternaria, Amoeba, Ancylostoma, Angiostrongylus, Anisakis, Anopheles, Apophysomyces, Aspergillus, Aureobasidium, Basidiobolus, Beauveria, Blastocystis, Blastomyces, Candida, Capillaria, Chaetomium, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Contracaecum, Cordylobia, Cryptococcus, Curvularia, Demodex, Dermatobia, Dientamoeba, Diphyllobothrium, Dirofilaria, Echinostoma, Entamoeba, Enterobius, Exophiala, Exserohilum, Fasciola, Fonsecaea, Fusarium, Giardia, Haloarcula, Halobacterium, Halococcus, Hendersonula, Heterophyes, Histomonas, Histoplasma, Hymenolepis, Hypomyces, Hysterothylacium, Leishmania, Malassezia, Malbranchea, Metagonimus, Meyerozyma, Microsporidium, Microsporum, Mortierella, Mucor, Mycocentrospora, Necator, Nectria, Ochroconis, Oesophagostomum, Oidiodendron, Opisthorchis, Pediculus, Penicillium, Phlebotomus, Phoma, Pichia, Piedraia, Pithomyces, Pityrosporum, Pneumocystis, Pseudallescheria, Pseudoterranova, Pulex, Rhizomucor, Rhizopus, Rhodotorula, Saccharomyces, Sarcoptes, Scolecobasidium, Scopulariopsis, Scytalidium, Spirometra, Sporobolomyces, Stachybotrys, Strongyloides, Syngamus, Taenia, Talaromyces, Toxocara, Trichinella, Trichobilharzia, Trichoderma, Trichomonas, Trichophyton, Trichosporon, Trichostrongylus, Trichuris, Tritirachium, Trombicula, Trypanosoma, Tunga, Wuchereria; records prevalence = 2.0 microorganisms data set. calculating matching score, characters \\(x\\) \\(n\\) ignored -Z, -z, 0-9, spaces parentheses. matches sorted descending matching score user input values, top match returned. lead effect e.g., \"E. coli\" return microbial ID Escherichia coli (\\(m = 0.688\\), highly prevalent microorganism found humans) Entamoeba coli (\\(m = 0.159\\), less prevalent microorganism humans), although latter alphabetically come first.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"Dr. Matthijs Berends, 2018","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"","code":"mo_reset_session() #> ℹ Reset 17 previously matched input values.  as.mo(\"E. coli\") #> Class 'mo' #> [1] B_ESCHR_COLI mo_uncertainties() #> Matching scores are based on the resemblance between the input and the full #> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score. #>  #> -------------------------------------------------------------------------------- #> \"E. coli\" -> Escherichia coli (B_ESCHR_COLI, 0.688) #>              Based on input \"E coli\" #> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii #>               (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi #>               (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides #>               (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae #>               cloacae (0.571), Ehrlichia canis (0.567), and Enterobacter cloacae #>               dissolvens (0.565) #>  #> Only the first 10 other matches of each record are shown. Run #> print(mo_uncertainties(), n = ...) to view more entries, or save #> mo_uncertainties() to an object.  mo_matching_score(   x = \"E. coli\",   n = c(\"Escherichia coli\", \"Entamoeba coli\") ) #> [1] 0.6875000 0.1587302"},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Properties of a Microorganism — mo_property","title":"Get Properties of a Microorganism — mo_property","text":"Use functions return specific property microorganism based latest accepted taxonomy. input values evaluated internally .mo(), makes possible use microbial abbreviations, codes names input. See Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Properties of a Microorganism — mo_property","text":"","code":"mo_name(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_fullname(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_shortname(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_subspecies(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_species(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_genus(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_family(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_order(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_class(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_phylum(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_kingdom(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_domain(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_type(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_status(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_pathogenicity(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_gramstain(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_gram_negative(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_gram_positive(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_yeast(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_intrinsic_resistant(   x,   ab,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_snomed(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_ref(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_authors(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_year(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_lpsn(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_gbif(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_rank(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_taxonomy(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_synonyms(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_current(x, language = get_AMR_locale(), ...)  mo_info(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_url(   x,   open = FALSE,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_property(   x,   property = \"fullname\",   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )"},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Properties of a Microorganism — mo_property","text":"x character (vector) can coerced valid microorganism code .mo(). Can left blank auto-guessing column containing microorganism codes used data set, see Examples. language language translate text like \"growth\", defaults system language (see get_AMR_locale()) keep_synonyms logical indicate old, previously valid taxonomic names must preserved corrected currently accepted names. default FALSE, return note old taxonomic names processed. default can set package option AMR_keep_synonyms, .e. options(AMR_keep_synonyms = TRUE) options(AMR_keep_synonyms = FALSE). ... arguments passed .mo(), 'minimum_matching_score', 'ignore_pattern', 'remove_from_input' ab (vector ) text can coerced valid antibiotic drug code .ab() open browse URL using browseURL() property one column names microorganisms data set: \"mo\", \"fullname\", \"status\", \"kingdom\", \"phylum\", \"class\", \"order\", \"family\", \"genus\", \"species\", \"subspecies\", \"rank\", \"ref\", \"source\", \"lpsn\", \"lpsn_parent\", \"lpsn_renamed_to\", \"gbif\", \"gbif_parent\", \"gbif_renamed_to\", \"prevalence\", \"snomed\", must \"shortname\"","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Properties of a Microorganism — mo_property","text":"integer case mo_year() ordered factor case mo_pathogenicity() list case mo_taxonomy(), mo_synonyms(), mo_snomed() mo_info() named character case mo_url() character cases","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Properties of a Microorganism — mo_property","text":"functions , default, keep old taxonomic properties, synonyms automatically replaced current taxonomy. Take example Enterobacter aerogenes, initially named 1960 renamed Klebsiella aerogenes 2017: mo_genus(\"Enterobacter aerogenes\") return \"Klebsiella\" (note renaming) mo_genus(\"Enterobacter aerogenes\", keep_synonyms = TRUE) return \"Enterobacter\" (-per-session warning name outdated) mo_ref(\"Enterobacter aerogenes\") return \"Tindall et al., 2017\" (note) mo_ref(\"Enterobacter aerogenes\", keep_synonyms = TRUE) return \"Hormaeche et al., 1960\" (warning) short name (mo_shortname()) returns first character genus full species, \"E. coli\", species subspecies. Exceptions abbreviations staphylococci (\"CoNS\", Coagulase-Negative Staphylococci) beta-haemolytic streptococci (\"GBS\", Group B Streptococci). Please bear mind e.g. E. coli mean Escherichia coli (kingdom Bacteria) well Entamoeba coli (kingdom Protozoa). Returning full name done using .mo() internally, giving priority bacteria human pathogens, .e. \"E. coli\" considered Escherichia coli. result, mo_fullname(mo_shortname(\"Entamoeba coli\")) returns \"Escherichia coli\". Since top-level taxonomy sometimes referred 'kingdom' sometimes 'domain', functions mo_kingdom() mo_domain() return exact results. Determination human pathogenicity (mo_pathogenicity()) strongly based Bartlett et al. (2022, doi:10.1099/mic.0.001269 ). function returns factor levels Pathogenic, Potentially pathogenic, Non-pathogenic, Unknown. Determination Gram stain (mo_gramstain()) based taxonomic kingdom phylum. Originally, Cavalier-Smith defined -called subkingdoms Negibacteria Posibacteria (2002, PMID 11837318), considered phyla Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, Tenericutes. phyla later renamed Actinomycetota, Chloroflexota, Bacillota, Mycoplasmatota (2021, PMID 34694987). Bacteria phyla considered Gram-positive AMR package, except members class Negativicutes (within phylum Bacillota) Gram-negative. bacteria considered Gram-negative. Species outside kingdom Bacteria return value NA. Functions mo_is_gram_negative() mo_is_gram_positive() always return TRUE FALSE (NA input NA MO code UNKNOWN), thus always return FALSE species outside taxonomic kingdom Bacteria. Determination yeasts (mo_is_yeast()) based taxonomic kingdom class. Budding yeasts fungi phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). True yeasts aggregated underlying order Saccharomycetales. Thus, microorganisms member taxonomic class Saccharomycetes, function return TRUE. returns FALSE otherwise (NA input NA MO code UNKNOWN). Determination intrinsic resistance (mo_is_intrinsic_resistant()) based intrinsic_resistant data set, based 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021). mo_is_intrinsic_resistant() function can vectorised argument x (input microorganisms) ab (input antibiotics). function mo_url() return direct URL online database entry, also shows scientific reference concerned species. SNOMED codes (mo_snomed()) version 1 July, 2021. See Source microorganisms data set info. Old taxonomic names (-called 'synonyms') can retrieved mo_synonyms() (scientific reference name), current taxonomic name can retrieved mo_current(). functions return full names. output translated possible.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"matching-score-for-microorganisms","dir":"Reference","previous_headings":"","what":"Matching Score for Microorganisms","title":"Get Properties of a Microorganism — mo_property","text":"function uses .mo() internally, uses advanced algorithm translate arbitrary user input valid taxonomy using -called matching score. can read public algorithm MO matching score page.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Properties of a Microorganism — mo_property","text":"Berends MS et al. (2022). AMR: R Package Working Antimicrobial Resistance Data. Journal Statistical Software, 104(3), 1-31; doi:10.18637/jss.v104.i03 Becker K et al. (2014). Coagulase-Negative Staphylococci. Clin Microbiol Rev. 27(4): 870-926; doi:10.1128/CMR.00109-13 Becker K et al. (2019). Implications identifying recently defined members S. aureus complex, S. argenteus S. schweitzeri: position paper members ESCMID Study Group staphylococci Staphylococcal Diseases (ESGS). Clin Microbiol Infect; doi:10.1016/j.cmi.2019.02.028 Becker K et al. (2020). Emergence coagulase-negative staphylococci Expert Rev Anti Infect Ther. 18(4):349-366; doi:10.1080/14787210.2020.1730813 Lancefield RC (1933). serological differentiation human groups hemolytic streptococci. J Exp Med. 57(4): 571-95; doi:10.1084/jem.57.4.571 Berends MS et al. (2022). Trends Occurrence Phenotypic Resistance Coagulase-Negative Staphylococci (CoNS) Found Human Blood Northern Netherlands 2013 2019 Microorganisms 10(9), 1801; doi:10.3390/microorganisms10091801 Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332 . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov Bartlett et al. (2022). comprehensive list bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Get Properties of a Microorganism — mo_property","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Properties of a Microorganism — mo_property","text":"","code":"# taxonomic tree -----------------------------------------------------------  mo_kingdom(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_phylum(\"Klebsiella pneumoniae\") #> [1] \"Pseudomonadota\" mo_class(\"Klebsiella pneumoniae\") #> [1] \"Gammaproteobacteria\" mo_order(\"Klebsiella pneumoniae\") #> [1] \"Enterobacterales\" mo_family(\"Klebsiella pneumoniae\") #> [1] \"Enterobacteriaceae\" mo_genus(\"Klebsiella pneumoniae\") #> [1] \"Klebsiella\" mo_species(\"Klebsiella pneumoniae\") #> [1] \"pneumoniae\" mo_subspecies(\"Klebsiella pneumoniae\") #> [1] \"\"   # full names and short names -----------------------------------------------  mo_name(\"Klebsiella pneumoniae\") #> [1] \"Klebsiella pneumoniae\" mo_fullname(\"Klebsiella pneumoniae\") #> [1] \"Klebsiella pneumoniae\" mo_shortname(\"Klebsiella pneumoniae\") #> [1] \"K. pneumoniae\"   # other properties ---------------------------------------------------------  mo_pathogenicity(\"Klebsiella pneumoniae\") #> [1] Pathogenic #> Levels: Pathogenic < Potentially pathogenic < Non-pathogenic < Unknown mo_gramstain(\"Klebsiella pneumoniae\") #> [1] \"Gram-negative\" mo_snomed(\"Klebsiella pneumoniae\") #> [[1]] #> [1] \"1098101000112102\" \"446870005\"        \"1098201000112108\" \"409801009\"        #> [5] \"56415008\"         \"714315002\"        \"713926009\"        #>  mo_type(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_rank(\"Klebsiella pneumoniae\") #> [1] \"species\" mo_url(\"Klebsiella pneumoniae\") #>                                Klebsiella pneumoniae  #> \"https://lpsn.dsmz.de/species/klebsiella-pneumoniae\"  mo_is_yeast(c(\"Candida\", \"Trichophyton\", \"Klebsiella\")) #> [1]  TRUE FALSE FALSE   # scientific reference -----------------------------------------------------  mo_ref(\"Klebsiella aerogenes\") #> [1] \"Tindall et al., 2017\" mo_authors(\"Klebsiella aerogenes\") #> [1] \"Tindall et al.\" mo_year(\"Klebsiella aerogenes\") #> [1] 2017 mo_lpsn(\"Klebsiella aerogenes\") #> [1] \"777146\" mo_gbif(\"Klebsiella aerogenes\") #> [1] \"9281703\" mo_synonyms(\"Klebsiella aerogenes\") #>   Hormaeche et al., 1960     Bascomb et al., 1971  #> \"Enterobacter aerogenes\"     \"Klebsiella mobilis\"    # abbreviations known in the field -----------------------------------------  mo_genus(\"MRSA\") #> [1] \"Staphylococcus\" mo_species(\"MRSA\") #> [1] \"aureus\" mo_shortname(\"VISA\") #> [1] \"S. aureus\" mo_gramstain(\"VISA\") #> [1] \"Gram-positive\"  mo_genus(\"EHEC\") #> [1] \"Escherichia\" mo_species(\"EIEC\") #> [1] \"coli\" mo_name(\"UPEC\") #> [1] \"Escherichia coli\"   # known subspecies ---------------------------------------------------------  mo_fullname(\"K. pneu rh\") #> [1] \"Klebsiella pneumoniae rhinoscleromatis\" mo_shortname(\"K. pneu rh\") #> [1] \"K. pneumoniae\"  # \\donttest{ # Becker classification, see ?as.mo ----------------------------------------  mo_fullname(\"Staph epidermidis\") #> [1] \"Staphylococcus epidermidis\" mo_fullname(\"Staph epidermidis\", Becker = TRUE) #> [1] \"Coagulase-negative Staphylococcus (CoNS)\" mo_shortname(\"Staph epidermidis\") #> [1] \"S. epidermidis\" mo_shortname(\"Staph epidermidis\", Becker = TRUE) #> [1] \"CoNS\"   # Lancefield classification, see ?as.mo ------------------------------------  mo_fullname(\"Strep agalactiae\") #> [1] \"Streptococcus agalactiae\" mo_fullname(\"Strep agalactiae\", Lancefield = TRUE) #> [1] \"Streptococcus Group B\" mo_shortname(\"Strep agalactiae\") #> [1] \"S. agalactiae\" mo_shortname(\"Strep agalactiae\", Lancefield = TRUE) #> [1] \"GBS\"   # language support  --------------------------------------------------------  mo_gramstain(\"Klebsiella pneumoniae\", language = \"de\") # German #> [1] \"Gramnegativ\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"nl\") # Dutch #> [1] \"Gram-negatief\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"es\") # Spanish #> [1] \"Gram negativo\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"el\") # Greek #> [1] \"Αρνητικό κατά Gram\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"uk\") # Ukrainian #> [1] \"Грамнегативні\"  # mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated mo_kingdom(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_type(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_kingdom(\"Klebsiella pneumoniae\", language = \"zh\") # Chinese, no effect #> [1] \"Bacteria\" mo_type(\"Klebsiella pneumoniae\", language = \"zh\") # Chinese, translated #> [1] \"细菌\"  mo_fullname(\"S. pyogenes\", Lancefield = TRUE, language = \"de\") #> [1] \"Streptococcus Gruppe A\" mo_fullname(\"S. pyogenes\", Lancefield = TRUE, language = \"uk\") #> [1] \"Streptococcus Група A\"   # other --------------------------------------------------------------------  # gram stains and intrinsic resistance can be used as a filter in dplyr verbs if (require(\"dplyr\")) {   example_isolates %>%     filter(mo_is_gram_positive()) %>%     count(mo_genus(), sort = TRUE) } #> ℹ Using column 'mo' as input for mo_is_gram_positive() #> ℹ Using column 'mo' as input for mo_genus() #> # A tibble: 18 × 2 #>    `mo_genus()`        n #>    <chr>           <int> #>  1 Staphylococcus    840 #>  2 Streptococcus     275 #>  3 Enterococcus       83 #>  4 Corynebacterium    17 #>  5 Micrococcus         6 #>  6 Gemella             3 #>  7 Aerococcus          2 #>  8 Cutibacterium       1 #>  9 Dermabacter         1 #> 10 Fusibacter          1 #> 11 Globicatella        1 #> 12 Granulicatella      1 #> 13 Lactobacillus       1 #> 14 Leuconostoc         1 #> 15 Listeria            1 #> 16 Paenibacillus       1 #> 17 Rothia              1 #> 18 Schaalia            1 if (require(\"dplyr\")) {   example_isolates %>%     filter(mo_is_intrinsic_resistant(ab = \"vanco\")) %>%     count(mo_genus(), sort = TRUE) } #> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant() #> ℹ Using column 'mo' as input for mo_genus() #> # A tibble: 20 × 2 #>    `mo_genus()`         n #>    <chr>            <int> #>  1 Escherichia        467 #>  2 Klebsiella          77 #>  3 Proteus             39 #>  4 Pseudomonas         30 #>  5 Serratia            25 #>  6 Enterobacter        23 #>  7 Citrobacter         11 #>  8 Haemophilus          8 #>  9 Acinetobacter        6 #> 10 Morganella           6 #> 11 Pantoea              4 #> 12 Salmonella           3 #> 13 Neisseria            2 #> 14 Stenotrophomonas     2 #> 15 Campylobacter        1 #> 16 Enterococcus         1 #> 17 Hafnia               1 #> 18 Lactobacillus        1 #> 19 Leuconostoc          1 #> 20 Pseudescherichia     1  # get a list with the complete taxonomy (from kingdom to subspecies) mo_taxonomy(\"Klebsiella pneumoniae\") #> $kingdom #> [1] \"Bacteria\" #>  #> $phylum #> [1] \"Pseudomonadota\" #>  #> $class #> [1] \"Gammaproteobacteria\" #>  #> $order #> [1] \"Enterobacterales\" #>  #> $family #> [1] \"Enterobacteriaceae\" #>  #> $genus #> [1] \"Klebsiella\" #>  #> $species #> [1] \"pneumoniae\" #>  #> $subspecies #> [1] \"\" #>   # get a list with the taxonomy, the authors, Gram-stain, # SNOMED codes, and URL to the online database mo_info(\"Klebsiella pneumoniae\") #> $mo #> [1] \"B_KLBSL_PNMN\" #>  #> $kingdom #> [1] \"Bacteria\" #>  #> $phylum #> [1] \"Pseudomonadota\" #>  #> $class #> [1] \"Gammaproteobacteria\" #>  #> $order #> [1] \"Enterobacterales\" #>  #> $family #> [1] \"Enterobacteriaceae\" #>  #> $genus #> [1] \"Klebsiella\" #>  #> $species #> [1] \"pneumoniae\" #>  #> $subspecies #> [1] \"\" #>  #> $status #> [1] \"accepted\" #>  #> $synonyms #> NULL #>  #> $gramstain #> [1] \"Gram-negative\" #>  #> $url #> [1] \"https://lpsn.dsmz.de/species/klebsiella-pneumoniae\" #>  #> $ref #> [1] \"Trevisan, 1887\" #>  #> $snomed #> [1] \"1098101000112102\" \"446870005\"        \"1098201000112108\" \"409801009\"        #> [5] \"56415008\"         \"714315002\"        \"713926009\"        #>  # }"},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":null,"dir":"Reference","previous_headings":"","what":"User-Defined Reference Data Set for Microorganisms — mo_source","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"functions can used predefine reference used .mo() consequently mo_* functions (mo_genus() mo_gramstain()). fastest way organisation (analysis) specific codes picked translated package, since bother setting .","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"","code":"set_mo_source(   path,   destination = getOption(\"AMR_mo_source\", \"~/mo_source.rds\") )  get_mo_source(destination = getOption(\"AMR_mo_source\", \"~/mo_source.rds\"))"},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"path location reference file, can text file (comma-, tab- pipe-separated) Excel file (see Details). Can also \"\", NULL FALSE delete reference file. destination destination compressed data file - default user's home directory.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"reference file can text file separated commas (CSV) tabs pipes, Excel file (either 'xls' 'xlsx' format) R object file (extension '.rds'). use Excel file, need readxl package installed. set_mo_source() check file validity: must data.frame, must column named \"mo\" contains values microorganisms$mo microorganisms$fullname must reference column defined values. tests pass, set_mo_source() read file R ask export \"~/mo_source.rds\". CRAN policy disallows packages write file system, although 'exceptions may allowed interactive sessions package obtains confirmation user'. reason, function works interactive sessions user can specifically confirm allow file created. destination file can set destination argument defaults user's home directory. can also set package option AMR_mo_source, e.g. options(AMR_mo_source = \"/location/file.rds\"). created compressed data file \"mo_source.rds\" used default MO determination (function .mo() consequently mo_* functions like mo_genus() mo_gramstain()). location timestamp original file saved attribute compressed data file. function get_mo_source() return data set reading \"mo_source.rds\" readRDS(). original file changed (checking location timestamp original file), call set_mo_source() update data file automatically used interactive session. Reading Excel file (.xlsx) one row size 8-9 kB. compressed file created set_mo_source() size 0.1 kB can read get_mo_source() couple microseconds (millionths second).","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"how-to-setup","dir":"Reference","previous_headings":"","what":"How to Setup","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"Imagine data sheet Excel file. first column contains organisation specific codes, second column contains valid taxonomic names:   save \"home//ourcodes.xlsx\". Now set source:   now created file \"~/mo_source.rds\" contents Excel file. first column foreign values 'mo' column kept creating RDS file. now can use functions:   edit Excel file , say, adding row 4 like :   ...new usage MO function package update data file:   delete reference data file, just use \"\", NULL FALSE input set_mo_source():   original file (previous case Excel file) moved deleted, mo_source.rds file removed upon next use .mo() mo_* function.","code":"|         A          |            B          | --|--------------------|-----------------------| 1 | Organisation XYZ   | mo                    | 2 | lab_mo_ecoli       | Escherichia coli      | 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae | 4 |                    |                       | set_mo_source(\"home/me/ourcodes.xlsx\") #> NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns #>       \"Organisation XYZ\" and \"mo\" as.mo(\"lab_mo_ecoli\") #> Class 'mo' #> [1] B_ESCHR_COLI  mo_genus(\"lab_mo_kpneumoniae\") #> [1] \"Klebsiella\"  # other input values still work too as.mo(c(\"Escherichia coli\", \"E. coli\", \"lab_mo_ecoli\")) #> NOTE: Translation to one microorganism was guessed with uncertainty. #>       Use mo_uncertainties() to review it. #> Class 'mo' #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI |         A          |            B          | --|--------------------|-----------------------| 1 | Organisation XYZ   | mo                    | 2 | lab_mo_ecoli       | Escherichia coli      | 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae | 4 | lab_Staph_aureus   | Staphylococcus aureus | 5 |                    |                       | as.mo(\"lab_mo_ecoli\") #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns #>        \"Organisation XYZ\" and \"mo\" #> Class 'mo' #> [1] B_ESCHR_COLI  mo_genus(\"lab_Staph_aureus\") #> [1] \"Staphylococcus\" set_mo_source(NULL) #> Removed mo_source file '/Users/me/mo_source.rds'"},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Principal Component Analysis (for AMR) — pca","title":"Principal Component Analysis (for AMR) — pca","text":"Performs principal component analysis (PCA) based data set automatic determination afterwards plotting groups labels, automatic filtering suitable (.e. non-empty numeric) variables.","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Principal Component Analysis (for AMR) — pca","text":"","code":"pca(   x,   ...,   retx = TRUE,   center = TRUE,   scale. = TRUE,   tol = NULL,   rank. = NULL )"},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Principal Component Analysis (for AMR) — pca","text":"x data.frame containing numeric columns ... columns x selected PCA, can unquoted since supports quasiquotation. retx logical value indicating whether rotated variables     returned. center logical value indicating whether variables     shifted zero centered. Alternately, vector     length equal number columns x can supplied.     value passed scale. scale. logical value indicating whether variables     scaled unit variance analysis takes     place.  default FALSE consistency S,     general scaling advisable.  Alternatively, vector length     equal number columns x can supplied.      value passed scale. tol value indicating magnitude components     omitted. (Components omitted     standard deviations less equal tol times     standard deviation first component.)  default null     setting, components omitted (unless rank. specified     less min(dim(x)).).  settings tol     tol = 0 tol = sqrt(.Machine$double.eps),     omit essentially constant components. rank. optionally, number specifying maximal rank, .e.,     maximal number principal components used.  Can set     alternative addition tol, useful notably     desired rank considerably smaller dimensions matrix.","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Principal Component Analysis (for AMR) — pca","text":"object classes pca prcomp","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Principal Component Analysis (for AMR) — pca","text":"pca() function takes data.frame input performs actual PCA R function prcomp(). result pca() function prcomp object, additional attribute non_numeric_cols vector column names columns contain numeric values. probably groups labels, used ggplot_pca().","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Principal Component Analysis (for AMR) — pca","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  # \\donttest{ if (require(\"dplyr\")) {   # calculate the resistance per group first   resistance_data <- example_isolates %>%     group_by(       order = mo_order(mo), # group on anything, like order       genus = mo_genus(mo)     ) %>% #   and genus as we do here;     filter(n() >= 30) %>% # filter on only 30 results per group     summarise_if(is.sir, resistance) # then get resistance of all drugs    # now conduct PCA for certain antimicrobial drugs   pca_result <- resistance_data %>%     pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)    pca_result   summary(pca_result)    # old base R plotting method:   biplot(pca_result)   # new ggplot2 plotting method using this package:   if (require(\"ggplot2\")) {     ggplot_pca(pca_result)      ggplot_pca(pca_result) +       scale_colour_viridis_d() +       labs(title = \"Title here\")   } } #> Warning: There were 73 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE, #>   only_all_tested = FALSE) ...`. #> ℹ In group 5: `order = \"Lactobacillales\"`, `genus = \"Enterococcus\"`. #> Caused by warning: #> ! Introducing NA: only 14 results available for PEN in group: order = #> \"Lactobacillales\", genus = \"Enterococcus\" (minimum = 30). #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings. #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", #>   \"TMP\", and \"TOB\". Total observations available: 7. #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\"  #>    # }"},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plotting for Classes sir, mic and disk — plot","title":"Plotting for Classes sir, mic and disk — plot","text":"Functions plot classes sir, mic disk, support base R ggplot2.","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plotting for Classes sir, mic and disk — plot","text":"","code":"# S3 method for mic plot(   x,   mo = NULL,   ab = NULL,   guideline = \"EUCAST\",   main = deparse(substitute(x)),   ylab = translate_AMR(\"Frequency\", language = language),   xlab = translate_AMR(\"Minimum Inhibitory Concentration (mg/L)\", language = language),   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for mic autoplot(   object,   mo = NULL,   ab = NULL,   guideline = \"EUCAST\",   title = deparse(substitute(object)),   ylab = translate_AMR(\"Frequency\", language = language),   xlab = translate_AMR(\"Minimum Inhibitory Concentration (mg/L)\", language = language),   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for mic fortify(object, ...)  # S3 method for disk plot(   x,   main = deparse(substitute(x)),   ylab = translate_AMR(\"Frequency\", language = language),   xlab = translate_AMR(\"Disk diffusion diameter (mm)\", language = language),   mo = NULL,   ab = NULL,   guideline = \"EUCAST\",   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for disk autoplot(   object,   mo = NULL,   ab = NULL,   title = deparse(substitute(object)),   ylab = translate_AMR(\"Frequency\", language = language),   xlab = translate_AMR(\"Disk diffusion diameter (mm)\", language = language),   guideline = \"EUCAST\",   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for disk fortify(object, ...)  # S3 method for sir plot(   x,   ylab = translate_AMR(\"Percentage\", language = language),   xlab = translate_AMR(\"Antimicrobial Interpretation\", language = language),   main = deparse(substitute(x)),   language = get_AMR_locale(),   ... )  # S3 method for sir autoplot(   object,   title = deparse(substitute(object)),   xlab = translate_AMR(\"Antimicrobial Interpretation\", language = language),   ylab = translate_AMR(\"Frequency\", language = language),   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   ... )  # S3 method for sir fortify(object, ...)"},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plotting for Classes sir, mic and disk — plot","text":"x, object values created .mic(), .disk() .sir() (random_* variants, random_mic()) mo (vector ) text can coerced valid microorganism code .mo() ab (vector ) text can coerced valid antimicrobial drug code .ab() guideline interpretation guideline use - default latest included EUCAST guideline, see Details main, title title plot xlab, ylab axis title colours_SIR colours use filling bars, must vector three values (order S, R). default colours colour-blind friendly. language language used translate 'Susceptible', 'Increased exposure'/'Intermediate' 'Resistant' - default system language (see get_AMR_locale()) can overwritten setting package option AMR_locale, e.g. options(AMR_locale = \"de\"), see translate. Use language = NULL language = \"\" prevent translation. expand logical indicate whether range x axis expanded lowest highest value. MIC values, intermediate values factors 2 starting highest MIC value. disk diameters, whole diameter range filled. ... arguments passed methods","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plotting for Classes sir, mic and disk — plot","text":"autoplot() functions return ggplot model extendible ggplot2 function. fortify() functions return data.frame extension usage ggplot2::ggplot() function.","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plotting for Classes sir, mic and disk — plot","text":"interpretation \"\" named \"Increased exposure\" EUCAST guidelines since 2019, named \"Intermediate\" cases. interpreting MIC values well disk diffusion diameters, supported guidelines used input guideline argument : \"EUCAST 2022\", \"EUCAST 2021\", \"EUCAST 2020\", \"EUCAST 2019\", \"EUCAST 2018\", \"EUCAST 2017\", \"EUCAST 2016\", \"EUCAST 2015\", \"EUCAST 2014\", \"EUCAST 2013\", \"CLSI 2022\", \"CLSI 2021\", \"CLSI 2020\", \"CLSI 2019\", \"CLSI 2018\", \"CLSI 2017\", \"CLSI 2016\", \"CLSI 2015\", \"CLSI 2014\", \"CLSI 2013\". Simply using \"CLSI\" \"EUCAST\" input automatically select latest version guideline.","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plotting for Classes sir, mic and disk — plot","text":"","code":"some_mic_values <- random_mic(size = 100) some_disk_values <- random_disk(size = 100, mo = \"Escherichia coli\", ab = \"cipro\") some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))  plot(some_mic_values)  plot(some_disk_values)  plot(some_sir_values)   # when providing the microorganism and antibiotic, colours will show interpretations: plot(some_mic_values, mo = \"S. aureus\", ab = \"ampicillin\")  plot(some_disk_values, mo = \"Escherichia coli\", ab = \"cipro\")  plot(some_disk_values, mo = \"Escherichia coli\", ab = \"cipro\", language = \"uk\")   # \\donttest{ if (require(\"ggplot2\")) {   autoplot(some_mic_values) }  if (require(\"ggplot2\")) {   autoplot(some_disk_values, mo = \"Escherichia coli\", ab = \"cipro\") }  if (require(\"ggplot2\")) {   autoplot(some_sir_values) }  # }"},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Antimicrobial Resistance — proportion","title":"Calculate Antimicrobial Resistance — proportion","text":"functions can used calculate (co-)resistance susceptibility microbial isolates (.e. percentage S, SI, , IR R). functions support quasiquotation pipes, can used summarise() dplyr package also support grouped variables, see Examples. resistance() used calculate resistance, susceptibility() used calculate susceptibility.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Antimicrobial Resistance — proportion","text":"","code":"resistance(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  susceptibility(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  sir_confidence_interval(   ...,   ab_result = \"R\",   minimum = 30,   as_percent = FALSE,   only_all_tested = FALSE,   confidence_level = 0.95,   side = \"both\",   collapse = FALSE )  proportion_R(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_IR(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_I(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_SI(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_S(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_df(   data,   translate_ab = \"name\",   language = get_AMR_locale(),   minimum = 30,   as_percent = FALSE,   combine_SI = TRUE,   confidence_level = 0.95 )  sir_df(   data,   translate_ab = \"name\",   language = get_AMR_locale(),   minimum = 30,   as_percent = FALSE,   combine_SI = TRUE,   confidence_level = 0.95 )"},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate Antimicrobial Resistance — proportion","text":"M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 5th Edition, 2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Antimicrobial Resistance — proportion","text":"... one vectors (columns) antibiotic interpretations. transformed internally .sir() needed. Use multiple columns calculate (lack ) co-resistance: probability one two drugs resistant susceptible result. See Examples. minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. as_percent logical indicate whether output must returned hundred fold % sign (character). value 0.123456 returned \"12.3%\". only_all_tested (combination therapies, .e. using one variable ...): logical indicate isolates must tested antibiotics, see section Combination Therapy ab_result antibiotic results test , must one values \"S\", \"\", \"R\" confidence_level confidence level returned confidence interval. calculation, number S SI isolates, R isolates compared total number available isolates R, S, using binom.test(), .e., Clopper-Pearson method. side side confidence interval return. default \"\" length 2 vector, can also (abbreviated ) \"min\"/\"left\"/\"lower\"/\"less\" \"max\"/\"right\"/\"higher\"/\"greater\". collapse logical indicate whether output values 'collapsed', .e. merged together one value, character value use collapsing data data.frame containing columns class sir (see .sir()) translate_ab column name antibiotics data set translate antibiotic abbreviations , using ab_property() language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. combine_SI logical indicate whether values S must merged one, output consists S+vs. R (susceptible vs. resistant) - default TRUE","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Antimicrobial Resistance — proportion","text":"double , as_percent = TRUE, character.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Antimicrobial Resistance — proportion","text":"function resistance() equal function proportion_R(). function susceptibility() equal function proportion_SI(). Use sir_confidence_interval() calculate confidence interval, relies binom.test(), .e., Clopper-Pearson method. function returns vector length 2 default antimicrobial resistance. Change side argument \"left\"/\"min\" \"right\"/\"max\" return single value, change ab_result argument e.g. c(\"S\", \"\") test antimicrobial susceptibility, see Examples. Remember filter data let contain first isolates! needed exclude duplicates reduce selection bias. Use first_isolate() determine data set one four available algorithms. functions meant count isolates, calculate proportion resistance/susceptibility. Use count() functions count isolates. function susceptibility() essentially equal count_susceptible() / count_all(). Low counts can influence outcome - proportion functions may camouflage , since return proportion (albeit dependent minimum argument). function proportion_df() takes variable data sir class (created .sir()) calculates proportions S, , R. also supports grouped variables. function sir_df() works exactly like proportion_df(), adds number isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"combination-therapy","dir":"Reference","previous_headings":"","what":"Combination Therapy","title":"Calculate Antimicrobial Resistance — proportion","text":"using one variable ... (= combination therapy), use only_all_tested count isolates tested antibiotics/variables test . See example two antibiotics, Drug Drug B, susceptibility() works calculate %SI:   Please note , combination therapies, only_all_tested = TRUE applies :   , combination therapies, only_all_tested = FALSE applies :   Using only_all_tested impact using one antibiotic input.","code":"--------------------------------------------------------------------                     only_all_tested = FALSE  only_all_tested = TRUE                     -----------------------  -----------------------  Drug A    Drug B   include as  include as   include as  include as                     numerator   denominator  numerator   denominator --------  --------  ----------  -----------  ----------  -----------  S or I    S or I       X            X            X            X    R       S or I       X            X            X            X   <NA>     S or I       X            X            -            -  S or I      R          X            X            X            X    R         R          -            X            -            X   <NA>       R          -            -            -            -  S or I     <NA>        X            X            -            -    R        <NA>        -            -            -            -   <NA>      <NA>        -            -            -            - -------------------------------------------------------------------- count_S()    +   count_I()    +   count_R()    = count_all()   proportion_S() + proportion_I() + proportion_R() = 1 count_S()    +   count_I()    +   count_R()    >= count_all()   proportion_S() + proportion_I() + proportion_R() >= 1"},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Calculate Antimicrobial Resistance — proportion","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Antimicrobial Resistance — proportion","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …   # base R ------------------------------------------------------------ # determines %R resistance(example_isolates$AMX) #> [1] 0.5955556 sir_confidence_interval(example_isolates$AMX) #> [1] 0.5688204 0.6218738 sir_confidence_interval(example_isolates$AMX,   confidence_level = 0.975 ) #> [1] 0.5650148 0.6255670 sir_confidence_interval(example_isolates$AMX,   confidence_level = 0.975,   collapse = \", \" ) #> [1] \"0.565, 0.626\"  # determines %S+I: susceptibility(example_isolates$AMX) #> [1] 0.4044444 sir_confidence_interval(example_isolates$AMX,   ab_result = c(\"S\", \"I\") ) #> [1] 0.3781262 0.4311796  # be more specific proportion_S(example_isolates$AMX) #> [1] 0.4022222 proportion_SI(example_isolates$AMX) #> [1] 0.4044444 proportion_I(example_isolates$AMX) #> [1] 0.002222222 proportion_IR(example_isolates$AMX) #> [1] 0.5977778 proportion_R(example_isolates$AMX) #> [1] 0.5955556  # dplyr ------------------------------------------------------------- # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       r = resistance(CIP),       n = n_sir(CIP)     ) # n_sir works like n_distinct in dplyr, see ?n_sir } #> # A tibble: 3 × 3 #>   ward           r     n #>   <chr>      <dbl> <int> #> 1 Clinical   0.147   869 #> 2 ICU        0.190   447 #> 3 Outpatient 0.161    93 if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       cipro_R = resistance(CIP),       ci_min = sir_confidence_interval(CIP, side = \"min\"),       ci_max = sir_confidence_interval(CIP, side = \"max\"),     ) } #> # A tibble: 3 × 4 #>   ward       cipro_R ci_min ci_max #>   <chr>        <dbl>  <dbl>  <dbl> #> 1 Clinical     0.147 0.124   0.173 #> 2 ICU          0.190 0.155   0.230 #> 3 Outpatient   0.161 0.0932  0.252 if (require(\"dplyr\")) {   # scoped dplyr verbs with antibiotic selectors   # (you could also use across() of course)   example_isolates %>%     group_by(ward) %>%     summarise_at(       c(aminoglycosides(), carbapenems()),       resistance     ) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> Warning: There was 1 warning in `summarise()`. #> ℹ In argument: `KAN = (function (..., minimum = 30, as_percent = FALSE, #>   only_all_tested = FALSE) ...`. #> ℹ In group 3: `ward = \"Outpatient\"`. #> Caused by warning: #> ! Introducing NA: only 23 results available for KAN in group: ward = #> \"Outpatient\" (minimum = 30). #> # A tibble: 3 × 7 #>   ward         GEN   TOB   AMK   KAN    IPM    MEM #>   <chr>      <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl> #> 1 Clinical   0.229 0.315 0.626     1 0.0498 0.0458 #> 2 ICU        0.290 0.400 0.662     1 0.0862 0.0894 #> 3 Outpatient 0.2   0.368 0.605    NA 0.0541 0.0541 if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       R = resistance(CIP, as_percent = TRUE),       SI = susceptibility(CIP, as_percent = TRUE),       n1 = count_all(CIP), # the actual total; sum of all three       n2 = n_sir(CIP), # same - analogous to n_distinct       total = n()     ) # NOT the number of tested isolates!    # Calculate co-resistance between amoxicillin/clav acid and gentamicin,   # so we can see that combination therapy does a lot more than mono therapy:   example_isolates %>% susceptibility(AMC) # %SI = 76.3%   example_isolates %>% count_all(AMC) #   n = 1879    example_isolates %>% susceptibility(GEN) # %SI = 75.4%   example_isolates %>% count_all(GEN) #   n = 1855    example_isolates %>% susceptibility(AMC, GEN) # %SI = 94.1%   example_isolates %>% count_all(AMC, GEN) #   n = 1939     # See Details on how `only_all_tested` works. Example:   example_isolates %>%     summarise(       numerator = count_susceptible(AMC, GEN),       denominator = count_all(AMC, GEN),       proportion = susceptibility(AMC, GEN)     )    example_isolates %>%     summarise(       numerator = count_susceptible(AMC, GEN, only_all_tested = TRUE),       denominator = count_all(AMC, GEN, only_all_tested = TRUE),       proportion = susceptibility(AMC, GEN, only_all_tested = TRUE)     )     example_isolates %>%     group_by(ward) %>%     summarise(       cipro_p = susceptibility(CIP, as_percent = TRUE),       cipro_n = count_all(CIP),       genta_p = susceptibility(GEN, as_percent = TRUE),       genta_n = count_all(GEN),       combination_p = susceptibility(CIP, GEN, as_percent = TRUE),       combination_n = count_all(CIP, GEN)     )    # Get proportions S/I/R immediately of all sir columns   example_isolates %>%     select(AMX, CIP) %>%     proportion_df(translate = FALSE)    # It also supports grouping variables   # (use sir_df to also include the count)   example_isolates %>%     select(ward, AMX, CIP) %>%     group_by(ward) %>%     sir_df(translate = FALSE) } #> # A tibble: 12 × 7 #>    ward       antibiotic interpretation value ci_min ci_max isolates #>  * <chr>      <chr>      <ord>          <dbl>  <dbl>  <dbl>    <int> #>  1 Clinical   AMX        SI             0.423 0.389   0.457      357 #>  2 Clinical   AMX        R              0.577 0.543   0.611      487 #>  3 Clinical   CIP        SI             0.853 0.827   0.876      741 #>  4 Clinical   CIP        R              0.147 0.124   0.173      128 #>  5 ICU        AMX        SI             0.369 0.323   0.417      158 #>  6 ICU        AMX        R              0.631 0.583   0.677      270 #>  7 ICU        CIP        SI             0.810 0.770   0.845      362 #>  8 ICU        CIP        R              0.190 0.155   0.230       85 #>  9 Outpatient AMX        SI             0.397 0.288   0.515       31 #> 10 Outpatient AMX        R              0.603 0.485   0.712       47 #> 11 Outpatient CIP        SI             0.839 0.748   0.907       78 #> 12 Outpatient CIP        R              0.161 0.0932  0.252       15 # }"},{"path":"https://msberends.github.io/AMR/reference/random.html","id":null,"dir":"Reference","previous_headings":"","what":"Random MIC Values/Disk Zones/SIR Generation — random","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"functions can used generating random MIC values disk diffusion diameters, AMR data analysis practice. providing microorganism antimicrobial drug, generated results reflect reality much possible.","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"","code":"random_mic(size = NULL, mo = NULL, ab = NULL, ...)  random_disk(size = NULL, mo = NULL, ab = NULL, ...)  random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)"},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"size desired size returned vector. used data.frame call dplyr verb, get current (group) size left blank. mo character can coerced valid microorganism code .mo() ab character can coerced valid antimicrobial drug code .ab() ... ignored, place allow future extensions prob_SIR vector length 3: probabilities \"S\" (1st value), \"\" (2nd value) \"R\" (3rd value)","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"class mic random_mic() (see .mic()) class disk random_disk() (see .disk())","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"base R function sample() used generating values. Generated values based EUCAST 2022 guideline implemented clinical_breakpoints data set. create specific generated values per bug drug, set mo /ab argument.","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"","code":"random_mic(25) #> Class 'mic' #>  [1] 8       >=256   >=256   0.5     0.25    8       0.002   0.005   4       #> [10] 4       0.125   32      0.002   0.25    0.005   0.025   128     <=0.001 #> [19] 0.01    8       128     16      0.002   1       0.025   random_disk(25) #> Class 'disk' #>  [1] 34 27 17  6 44 17 49 39 32 27 49 45 15 40 29 29 26 10 26 50 23 10 32 33  6 random_sir(25) #> Class 'sir' #>  [1] I R S S I I S S S I R S R R R R I S R R S S I R S  # \\donttest{ # make the random generation more realistic by setting a bug and/or drug: random_mic(25, \"Klebsiella pneumoniae\") # range 0.0625-64 #> Class 'mic' #>  [1] 0.005   128     0.01    <=0.001 128     16      16      0.5     0.25    #> [10] 8       2       <=0.001 16      128     <=0.001 64      0.0625  0.25    #> [19] 16      128     4       <=0.001 0.125   0.01    16      random_mic(25, \"Klebsiella pneumoniae\", \"meropenem\") # range 0.0625-16 #> Class 'mic' #>  [1] 2   16  8   4   <=1 8   8   4   4   2   2   <=1 16  4   2   8   2   2   8   #> [20] 2   8   8   16  2   <=1 random_mic(25, \"Streptococcus pneumoniae\", \"meropenem\") # range 0.0625-4 #> Class 'mic' #>  [1] <=0.125 2       0.5     2       >=4     2       >=4     2       <=0.125 #> [10] <=0.125 0.25    >=4     <=0.125 0.5     >=4     1       1       1       #> [19] <=0.125 <=0.125 2       1       2       <=0.125 1        random_disk(25, \"Klebsiella pneumoniae\") # range 8-50 #> Class 'disk' #>  [1] 35 25 44 48 10 20 33 12 47 28 19 41 45 26 36 38 31 37 50  8 39 46 43 14 41 random_disk(25, \"Klebsiella pneumoniae\", \"ampicillin\") # range 11-17 #> Class 'disk' #>  [1] 14 11 14 13 15 16 14 12 14 13 11 11 14 13 17 17 11 12 17 14 16 16 15 12 16 random_disk(25, \"Streptococcus pneumoniae\", \"ampicillin\") # range 12-27 #> Class 'disk' #>  [1] 24 20 26 16 17 20 22 26 15 18 25 27 27 24 26 18 19 24 23 26 19 20 17 20 27 # }"},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":null,"dir":"Reference","previous_headings":"","what":"Predict Antimicrobial Resistance — resistance_predict","title":"Predict Antimicrobial Resistance — resistance_predict","text":"Create prediction model predict antimicrobial resistance next years statistical solid ground. Standard errors (SE) returned columns se_min se_max. See Examples real live example.","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Predict Antimicrobial Resistance — resistance_predict","text":"","code":"resistance_predict(   x,   col_ab,   col_date = NULL,   year_min = NULL,   year_max = NULL,   year_every = 1,   minimum = 30,   model = NULL,   I_as_S = TRUE,   preserve_measurements = TRUE,   info = interactive(),   ... )  sir_predict(   x,   col_ab,   col_date = NULL,   year_min = NULL,   year_max = NULL,   year_every = 1,   minimum = 30,   model = NULL,   I_as_S = TRUE,   preserve_measurements = TRUE,   info = interactive(),   ... )  # S3 method for resistance_predict plot(x, main = paste(\"Resistance Prediction of\", x_name), ...)  ggplot_sir_predict(   x,   main = paste(\"Resistance Prediction of\", x_name),   ribbon = TRUE,   ... )  # S3 method for resistance_predict autoplot(   object,   main = paste(\"Resistance Prediction of\", x_name),   ribbon = TRUE,   ... )"},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Predict Antimicrobial Resistance — resistance_predict","text":"x data.frame containing isolates. Can left blank automatic determination, see Examples. col_ab column name x containing antimicrobial interpretations (\"R\", \"\" \"S\") col_date column name date, used calculate years column consist years already - default first column date class year_min lowest year use prediction model, dafaults lowest year col_date year_max highest year use prediction model - default 10 years today year_every unit sequence lowest year found data year_max minimum minimal amount available isolates per year include. Years containing less observations estimated model. model statistical model choice. generalised linear regression model binomial distribution (.e. using glm(..., family = binomial), assuming period zero resistance followed period increasing resistance leading slowly resistance. See Details valid options. I_as_S logical indicate whether values \"\" treated \"S\" (otherwise treated \"R\"). default, TRUE, follows redefinition EUCAST interpretation (increased exposure) 2019, see section Interpretation S, R . preserve_measurements logical indicate whether predictions years actually available data overwritten original data. standard errors years NA. info logical indicate whether textual analysis printed name summary() statistical model. ... arguments passed functions main title plot ribbon logical indicate whether ribbon shown (default) error bars object model data plotted","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Predict Antimicrobial Resistance — resistance_predict","text":"data.frame extra class resistance_predict columns: year value, estimated preserve_measurements = FALSE, combination observed estimated otherwise se_min, lower bound standard error minimum 0 (standard error never go 0%) se_max upper bound standard error maximum 1 (standard error never go 100%) observations, total number available observations year, .e. \\(S + + R\\) observed, original observed resistant percentages estimated, estimated resistant percentages, calculated model Furthermore, model available attribute: attributes(x)$model, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Predict Antimicrobial Resistance — resistance_predict","text":"Valid options statistical model (argument model) : \"binomial\" \"binom\" \"logit\": generalised linear regression model binomial distribution \"loglin\" \"poisson\": generalised log-linear regression model poisson distribution \"lin\" \"linear\": linear regression model","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Predict Antimicrobial Resistance — resistance_predict","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Predict Antimicrobial Resistance — resistance_predict","text":"","code":"x <- resistance_predict(example_isolates,   col_ab = \"AMX\",   year_min = 2010,   model = \"binomial\" ) plot(x)  # \\donttest{ if (require(\"ggplot2\")) {   ggplot_sir_predict(x) }   # using dplyr: if (require(\"dplyr\")) {   x <- example_isolates %>%     filter_first_isolate() %>%     filter(mo_genus(mo) == \"Staphylococcus\") %>%     resistance_predict(\"PEN\", model = \"binomial\")   print(plot(x))    # get the model from the object   mymodel <- attributes(x)$model   summary(mymodel) }  #> NULL #>  #> Call: #> glm(formula = df_matrix ~ year, family = binomial) #>  #> Coefficients: #>             Estimate Std. Error z value Pr(>|z|) #> (Intercept) 47.02915   72.98739   0.644    0.519 #> year        -0.02280    0.03637  -0.627    0.531 #>  #> (Dispersion parameter for binomial family taken to be 1) #>  #>     Null deviance: 5.9620  on 11  degrees of freedom #> Residual deviance: 5.5701  on 10  degrees of freedom #> AIC: 50.533 #>  #> Number of Fisher Scoring iterations: 4 #>   # create nice plots with ggplot2 yourself if (require(\"dplyr\") && require(\"ggplot2\")) {   data <- example_isolates %>%     filter(mo == as.mo(\"E. coli\")) %>%     resistance_predict(       col_ab = \"AMX\",       col_date = \"date\",       model = \"binomial\",       info = FALSE,       minimum = 15     )   head(data)   autoplot(data) }  # }"},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":null,"dir":"Reference","previous_headings":"","what":"Skewness of the Sample — skewness","title":"Skewness of the Sample — skewness","text":"Skewness measure asymmetry probability distribution real-valued random variable mean. negative ('left-skewed'): left tail longer; mass distribution concentrated right histogram. positive ('right-skewed'): right tail longer; mass distribution concentrated left histogram. normal distribution skewness 0.","code":""},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Skewness of the Sample — skewness","text":"","code":"skewness(x, na.rm = FALSE)  # S3 method for default skewness(x, na.rm = FALSE)  # S3 method for matrix skewness(x, na.rm = FALSE)  # S3 method for data.frame skewness(x, na.rm = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Skewness of the Sample — skewness","text":"x vector values, matrix data.frame na.rm logical value indicating whether NA values stripped computation proceeds","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Skewness of the Sample — skewness","text":"","code":"skewness(runif(1000)) #> [1] -0.01851817"},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":null,"dir":"Reference","previous_headings":"","what":"Translate Strings from the AMR Package — translate","title":"Translate Strings from the AMR Package — translate","text":"language-dependent output AMR functions, mo_name(), mo_gramstain(), mo_type() ab_name().","code":""},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translate Strings from the AMR Package — translate","text":"","code":"get_AMR_locale()  set_AMR_locale(language)  reset_AMR_locale()  translate_AMR(x, language = get_AMR_locale())"},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translate Strings from the AMR Package — translate","text":"language language choose. Use one supported language names ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), Ukrainian (uk). x text translate","code":""},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Translate Strings from the AMR Package — translate","text":"currently 20 supported languages English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), Ukrainian (uk). languages translations available antimicrobial drugs colloquial microorganism names. permanently silence -per-session language note non-English operating system, can set package option AMR_locale .Rprofile file like :   save file. Please read adding updating language Wiki.","code":"# Open .Rprofile file utils::file.edit(\"~/.Rprofile\")  # Then add e.g. Italian support to that file using: options(AMR_locale = \"Italian\")"},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"changing-the-default-language","dir":"Reference","previous_headings":"","what":"Changing the Default Language","title":"Translate Strings from the AMR Package — translate","text":"system language used default (returned Sys.getenv(\"LANG\") , LANG set, Sys.getlocale(\"LC_COLLATE\")), language supported. language used can overwritten two ways checked order: Setting package option AMR_locale, either using e.g. set_AMR_locale(\"German\") running e.g. options(AMR_locale = \"German\"). Note setting R option works session. Save command options(AMR_locale = \"(language)\") .Rprofile file apply every session. Run utils::file.edit(\"~/.Rprofile\") edit .Rprofile file. Setting system variable LANGUAGE LANG, e.g. adding LANGUAGE=\"de_DE.utf8\" .Renviron file home directory. Thus, package option AMR_locale set, system variables LANGUAGE LANG ignored.","code":""},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Translate Strings from the AMR Package — translate","text":"","code":"# Current settings (based on system language) ab_name(\"Ciprofloxacin\") #> [1] \"Ciprofloxacin\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Coagulase-negative Staphylococcus (CoNS)\"  # setting another language set_AMR_locale(\"Spanish\") #> ℹ Using Spanish (Español) for the AMR package for this session. ab_name(\"Ciprofloxacin\") #> [1] \"Ciprofloxacina\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Staphylococcus coagulasa negativo (SCN)\"  # setting yet another language set_AMR_locale(\"Greek\") #> ℹ Using Greek (Ελληνικά) for the AMR package for this session. ab_name(\"Ciprofloxacin\") #> [1] \"Σιπροφλοξασίνη\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Σταφυλόκοκκος με αρνητική πηκτικότητα (CoNS)\"  # setting yet another language set_AMR_locale(\"Ukrainian\") #> ℹ Using Ukrainian (Українська) for the AMR package for this session. ab_name(\"Ciprofloxacin\") #> [1] \"Ципрофлоксацин\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Коагулазонегативний стафілокок (КНС)\"  # set_AMR_locale() understands endonyms, English exonyms, and ISO-639-1: set_AMR_locale(\"Deutsch\") #> ℹ Using German (Deutsch) for the AMR package for this session. set_AMR_locale(\"German\") #> ℹ Using German (Deutsch) for the AMR package for this session. set_AMR_locale(\"de\") #> ℹ Using German (Deutsch) for the AMR package for this session. ab_name(\"amox/clav\") #> ℹ More than one result was found for item 1: amoxicillin and clavulansäure #> [1] \"Amoxicillin/Clavulansäure\"  # reset to system default reset_AMR_locale() #> ℹ Using the English language (English) for the AMR package for this #>   session. ab_name(\"amox/clav\") #> [1] \"Amoxicillin/clavulanic acid\""},{"path":[]},{"path":"https://msberends.github.io/AMR/news/index.html","id":"changed-2-0-0-9014","dir":"Changelog","previous_headings":"","what":"Changed","title":"AMR 2.0.0.9014","text":"formatting fix sir_interpretation_history() Fixed WHONET codes microorganisms consequently couple entries clinical_breakpoints Added microbial codes Gram-negative/positive anaerobic bacteria mo_rank() now returns NA ‘unknown’ microorganisms (B_ANAER, B_ANAER-NEG, B_ANAER-POS, B_GRAMN, B_GRAMP, F_FUNGUS, F_YEAST, UNKNOWN) Fixed bug .mo() led coercion NA values using custom microorganism codes","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"amr-200","dir":"Changelog","previous_headings":"","what":"AMR 2.0.0","title":"AMR 2.0.0","text":"CRAN release: 2023-03-12 new major release AMR package, great new additions also breaking changes current users. listed . TL;DR functions arguments ‘rsi’ replaced ‘sir’, interpretation MIC values (now .sir() instead .rsi()) - old functions still work now Many new interesting functions, antibiogram() (generating traditional/combined/syndromic/WISCA antibiograms), sir_confidence_interval() mean_amr_distance(), add_custom_microorganisms() add custom microorganisms package Clinical breakpoints added EUCAST 2022 CLSI 2022 Microbiological taxonomy (microorganisms data set) updated 2022 now based LPSN GBIF Much increased algorithms translate user input valid taxonomy, e.g. using recent scientific work per-species human pathogenicity 20 new antibiotics added updated DDDs ATC codes Extended support antiviral agents (antivirals data set), many new functions Now available 20 languages Many small bug fixes","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/news/index.html","id":"sir-vs-rsi-2-0-0","dir":"Changelog","previous_headings":"New","what":"SIR vs. RSI","title":"AMR 2.0.0","text":"milestone version, replaced mentions RSI SIR, comply actually commonly used field clinical microbiology comes tri-form regarding AMR. existing functions .rsi(), rsi_df() ggplot_rsi() still work, replacements .sir(), sir_df(), ggplot_sir() now current functions AMR data analysis. warning thrown session remind users . data set rsi_translation now called clinical_breakpoints better reflect content. ‘RSI functions’ removed future version, late 2023 / early 2024.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"new-antibiogram-function-2-0-0","dir":"Changelog","previous_headings":"New","what":"New antibiogram function","title":"AMR 2.0.0","text":"new antibiogram() function, users can now generate traditional, combined, syndromic, even weighted-incidence syndromic combination antibiograms (WISCA). , follow logic previously described work Klinker et al. (2021, DOI 10.1177/20499361211011373) Barbieri et al. (2021, DOI 10.1186/s13756-021-00939-2). help page antibiogram() extensively elaborates use cases, antibiogram() also supports printing R Markdown Quarto, support 20 languages. Furthermore, different plotting methods implemented allow graphical visualisations well.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"interpretation-of-mic-and-disk-diffusion-values-2-0-0","dir":"Changelog","previous_headings":"New","what":"Interpretation of MIC and disk diffusion values","title":"AMR 2.0.0","text":"clinical breakpoints intrinsic resistance EUCAST 2022 CLSI 2022 added .sir(). EUCAST 2022 (v12.0) now new default guideline MIC disks diffusion interpretations, eucast_rules() apply EUCAST Expert Rules. default guideline (EUCAST) can now changed new AMR_guideline option, : options(AMR_guideline = \"CLSI 2020\"). new arguments include_PKPD (default: TRUE) include_screening (default: FALSE), users can now specify whether breakpoints screening PK/PD table included interpreting MICs disks diffusion values. options can set globally, can read new manual. Interpretation guidelines older 10 years removed, oldest now included guidelines EUCAST CLSI 2013.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"supported-languages-2-0-0","dir":"Changelog","previous_headings":"New","what":"Supported languages","title":"AMR 2.0.0","text":"added support following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish Ukrainian. antibiotic names now available languages, AMR package automatically determine supported language based user’s system language. grateful valuable input colleagues countries. AMR package now available 20 languages total, according download stats used almost countries world!","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"outbreak-management-2-0-0","dir":"Changelog","previous_headings":"New","what":"Outbreak management","title":"AMR 2.0.0","text":"analysis outbreak management, updated get_episode() is_new_episode() functions: now contain argument case_free_days. argument can used quantify duration case-free days (inter-epidemic interval), new episode start. common requirement outbreak management, e.g. determining number norovirus outbreaks hospital. case-free period 14 28 days, new norovirus cases time considered different (new) episode.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"microbiological-taxonomy-2-0-0","dir":"Changelog","previous_headings":"New","what":"Microbiological taxonomy","title":"AMR 2.0.0","text":"microorganisms data set longer relies Catalogue Life, List Prokaryotic names Standing Nomenclature (LPSN) supplemented ‘backbone taxonomy’ Global Biodiversity Information Facility (GBIF). structure data set changed include separate LPSN GBIF identifiers. Almost previous MO codes retained. contains 1,400 taxonomic names 2022. previously relied experience categorise species pathogenic groups, happy encounter recent work Bartlett et al. (2022, DOI 10.1099/mic.0.001269) extensively studied medical-scientific literature categorise bacterial species groups. See mo_matching_score() work incorporated prevalence column microorganisms data set. Using results, .mo() mo_*() functions now much better capable converting user input valid taxonomic records. new function add_custom_microorganisms() allows users add custom microorganisms AMR package. also made following changes regarding included taxonomy microorganisms functions: Updated full microbiological taxonomy according latest daily LPSN data set (December 2022) latest yearly GBIF taxonomy backbone (November 2022) Added function mo_current() get currently valid taxonomic name microorganism Support 1,516 city-like serovars Salmonella, Salmonella Goldcoast. Formally, serovars belonging S. enterica species, reported name genus city. reason, serovars subspecies column microorganisms data set “enterica” species column, full name contain species name (enterica). new argument keep_synonyms allows correct updated taxonomy, favour now deleted argument allow_uncertain increased tremendously speed returns generally consequent results Sequential coercion now extremely fast results stored package environment, although coercion unknown values must run per session. Previous results can reset/removed new mo_reset_session() function. Support microorganism codes ASIan Antimicrobial Resistance Surveillance Network (ASIARS-Net) MO matching score algorithm (mo_matching_score()) now counts deletions substitutions 2 instead 1, impacts outcome .mo() mo_*() function CRAN allows packages around 5 MB maximum, packages exempted package one Chromista relevant comes antimicrobial resistance, thus lacking primary scope package Chromista almost never clinically relevant, thus lacking secondary scope package microorganisms.old data set removed, previously accepted names now included microorganisms data set. new column status contains \"accepted\" currently accepted names \"synonym\" taxonomic synonyms; currently invalid names. previously accepted names now microorganisms ID - available - LPSN, GBIF SNOMED CT identifier.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"antibiotic-agents-and-selectors-2-0-0","dir":"Changelog","previous_headings":"New","what":"Antibiotic agents and selectors","title":"AMR 2.0.0","text":"new function add_custom_antimicrobials() allows users add custom antimicrobial codes names AMR package. antibiotics data set greatly updated: following 20 antibiotics added (also includes new J01RA ATC group): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), thioacetazone (TAT) Added missing ATC codes Updated DDDs PubChem Compound IDs Updated antibiotic name spelling, now used WHOCC (cephalexin -> cefalexin, phenethicillin -> pheneticillin) Antibiotic code “CEI” ceftolozane/tazobactam replaced “CZT” comply EARS-Net WHONET 2022. old code still work cases using .ab() ab_*() functions. Support antimicrobial interpretation anaerobic bacteria, adding ‘placeholder’ code B_ANAER microorganisms data set adding breakpoints anaerobics clinical_breakpoints data set, used .sir() interpretion MIC disk diffusion values Also, added support using antibiotic selectors scoped dplyr verbs (without using vars()), : ... %>% summarise_at(aminoglycosides(), resistance), please see resistance() examples.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"antiviral-agents-2-0-0","dir":"Changelog","previous_headings":"New","what":"Antiviral agents","title":"AMR 2.0.0","text":"now added extensive support antiviral agents! first time, AMR package extensive support antiviral drugs work names, codes data way. antivirals data set extended 18 new drugs (also new J05AJ ATC group) now also contains antiviral identifiers LOINC codes new data type av (antivirals) added, functionally similar ab antibiotics Functions .av(), av_name(), av_atc(), av_synonyms(), av_from_text() added siblings ab_*() equivalents","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"other-new-functions-2-0-0","dir":"Changelog","previous_headings":"New","what":"Other new functions","title":"AMR 2.0.0","text":"Function sir_confidence_interval() add confidence intervals AMR calculation. now also included sir_df() proportion_df(). Function mean_amr_distance() calculate mean AMR distance. mean AMR distance normalised numeric value compare AMR test results can help identify similar isolates, without comparing antibiograms hand. Function sir_interpretation_history() view history previous runs .sir() (previously .rsi()). returns ‘logbook’ selected guideline, reference table specific interpretation row data set .sir() run.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"changes-2-0-0","dir":"Changelog","previous_headings":"","what":"Changes","title":"AMR 2.0.0","text":"Fix working NA values Fix unsorted dates length 2 Now returns class integer instead numeric since always whole numbers Argument combine_IR removed package (affecting functions count_df(), proportion_df(), sir_df() plotting functions), since replaced combine_SI three years ago Using units ab_ddd(..., units = \"...\") deprecated time now supported anymore. Use ab_ddd_units() instead. Support data.frame-enhancing R packages, specifically: data.table::data.table, janitor::tabyl, tibble::tibble, tsibble::tsibble. AMR package functions data set output (sir_df() bug_drug_combinations()), now return data type input. data sets package now tibble, instead base R data.frames. Older R versions still supported, even support tibbles. data sets now also continually exported Apache Feather Apache Parquet formats. can find info article website. Fixed certain EUCAST breakpoints MIC values Allow NA values (e.g. .sir(.disk(NA), ...)) Fix bug-drug combinations multiple breakpoints different body sites Interpretation MIC disk zones now informative availability breakpoints robust Removed .integer() method MIC values, since MIC integer values running table() MIC values consequently failed able retrieve level position (’s normally .integer() factors work) Fixed determination Gram stains (mo_gramstain()), since taxonomic phyla Actinobacteria, Chloroflexi, Firmicutes, Tenericutes renamed respectively Actinomycetota, Chloroflexota, Bacillota, Mycoplasmatota 2021 droplevels() MIC now return common factor default lose mic class. Use droplevels(..., .mic = TRUE) keep mic class. Small fix using ab_from_text() Fixes reading text files using set_mo_source(), now also allows source file contain valid taxonomic names instead valid microorganism ID package Fixed bug mdro() using similar column names Magiorakos guideline Using random_*() function (random_mic()) now possible directly calling package without loading first: AMR::random_mic(10) Extended support vctrs package, used internally tidyverse. allows change values class mic, disk, sir, mo ab tibbles, use antibiotic selectors selecting/filtering, e.g. df[carbapenems() == \"R\", ] Fix using info = FALSE mdro() interpretation guidelines using .sir() amoxicillin, rules ampicillin used amoxicillin rules available Fix using ab_atc() non-existing ATC codes Black white message texts now reversed colour using RStudio dark theme mo_snomed() now returns class character, numeric anymore (make long SNOMED codes readable) Fix using .ab() NA values Updated support WHONET 2022 microorganism codes Antimicrobial interpretation ‘SDD’ (susceptible dose-dependent, coined CLSI) interpreted ‘’ comply EUCAST’s ‘’ .sir() Fix mo_shortname() case higher taxonomic ranks (order, class, phylum) Cleaning columns .sir(), .mic(), .disk() now show column name warning invalid results Fix using g.test() zeroes 2x2 table mo_synonyns() now contains scientific reference names","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"other-2-0-0","dir":"Changelog","previous_headings":"","what":"Other","title":"AMR 2.0.0","text":"Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, Anita Williams contributors, thank valuable input New website make use new Bootstrap 5 pkgdown 2.0. website now contains results examples automatically regenerated every change repository, using GitHub Actions R Rmd files project now styled using styler package Set scalar conditional expressions (&& ||) possible comply upcoming R 4.3 enormous lot code cleaning, fixing small bugs along way changelog contains changes AMR v2.0 later. prior versions, please see archive.","code":""}]
+[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) reliable data thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations SIR values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables. AMR package contains data set example_isolates_unclean, might look data users extracted laboratory systems: AMR data analysis, like microorganism column contain valid, --date taxonomy, antibiotic columns cleaned SIR values well.","code":"library(dplyr) library(ggplot2) library(AMR)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\")) example_isolates_unclean #> # A tibble: 3,000 × 8 #>    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN   #>    <chr>      <chr>    <date>     <chr>         <chr> <chr> <chr> <chr> #>  1 J3         A        2012-11-21 E. coli       R     I     S     S     #>  2 R7         A        2018-04-03 K. pneumoniae R     I     S     S     #>  3 P3         A        2014-09-19 E. coli       R     S     S     S     #>  4 P10        A        2015-12-10 E. coli       S     I     S     S     #>  5 B7         A        2015-03-02 E. coli       S     S     S     S     #>  6 W3         A        2018-03-31 S. aureus     R     S     R     S     #>  7 J8         A        2016-06-14 E. coli       R     S     S     S     #>  8 M3         A        2015-10-25 E. coli       R     S     S     S     #>  9 J3         A        2019-06-19 E. coli       S     S     S     S     #> 10 G6         A        2015-04-27 S. aureus     S     S     S     S     #> # ℹ 2,990 more rows  # we will use 'our_data' as the data set name for this tutorial our_data <- example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"taxonomy-of-microorganisms","dir":"Articles","previous_headings":"Preparation","what":"Taxonomy of microorganisms","title":"How to conduct AMR data analysis","text":".mo(), users can transform arbitrary microorganism names codes current taxonomy. AMR package contains --date taxonomic data. specific, currently included data retrieved 11 Dec 2022. codes AMR packages come .mo() short, still human readable. importantly, .mo() supports kinds input: first character codes denote taxonomic kingdom, Bacteria (B), Fungi (F), Protozoa (P). AMR package also contain functions directly retrieve taxonomic properties, name, genus, species, family, order, even Gram-stain. start mo_ use .mo() internally, still arbitrary user input can used: Now can thus clean data: Apparently, uncertainty translation taxonomic codes. Let’s check : ’s good.","code":"as.mo(\"Klebsiella pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"K. pneumoniae\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLEPNE\") #> Class 'mo' #> [1] B_KLBSL_PNMN as.mo(\"KLPN\") #> Class 'mo' #> [1] B_KLBSL_PNMN mo_family(\"K. pneumoniae\") #> [1] \"Enterobacteriaceae\" mo_genus(\"K. pneumoniae\") #> [1] \"Klebsiella\" mo_species(\"K. pneumoniae\") #> [1] \"pneumoniae\"  mo_gramstain(\"Klebsiella pneumoniae\") #> [1] \"Gram-negative\"  mo_ref(\"K. pneumoniae\") #> [1] \"Trevisan, 1887\"  mo_snomed(\"K. pneumoniae\") #> [[1]] #> [1] \"1098101000112102\" \"446870005\"        \"1098201000112108\" \"409801009\"        #> [5] \"56415008\"         \"714315002\"        \"713926009\" our_data$bacteria <- as.mo(our_data$bacteria, info = TRUE) #> ℹ Microorganism translation was uncertain for four microorganisms. Run #>   mo_uncertainties() to review these uncertainties, or use #>   add_custom_microorganisms() to add custom entries. mo_uncertainties() #> Matching scores are based on the resemblance between the input and the full #> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score. #>  #> -------------------------------------------------------------------------------- #> \"E. coli\" -> Escherichia coli (B_ESCHR_COLI, 0.688) #> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii #>               (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi #>               (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides #>               (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae #>               cloacae (0.571), Ehrlichia canis (0.567), and Enterobacter cloacae #>               dissolvens (0.565) #> -------------------------------------------------------------------------------- #> \"K. pneumoniae\" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786) #> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella #>               pneumoniae pneumoniae (0.688), Klebsiella pneumoniae rhinoscleromatis #>               (0.658), Klebsiella pasteurii (0.500), Klebsiella planticola (0.500), #>               Kingella potus (0.400), Kosakonia pseudosacchari (0.361), Kaistella #>               palustris (0.333), Kocuria palustris (0.333), and Kocuria pelophila #>               (0.333) #> -------------------------------------------------------------------------------- #> \"S. aureus\" -> Staphylococcus aureus (B_STPHY_AURS, 0.690) #> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus #>               argenteus (0.625), Staphylococcus aureus anaerobius (0.625), #>               Streptomyces argenteolus (0.483), Streptomyces aureus (0.474), #>               Streptomyces azureus (0.467), Streptomyces aureorectus (0.444), #>               Streptomyces auratus (0.433), Streptomyces aurantiogriseus (0.429), and #>               Streptomyces aureocirculatus (0.429) #> -------------------------------------------------------------------------------- #> \"S. pneumoniae\" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750) #> Also matched: Streptococcus pseudopneumoniae (0.700), Serratia #>               proteamaculans quinovora (0.545), Streptococcus pseudoporcinus (0.536), #>               Staphylococcus pseudintermedius (0.532), Serratia proteamaculans #>               proteamaculans (0.526), Salmonella Portanigra (0.524), Sphingomonas #>               paucimobilis (0.520), Streptococcus pluranimalium (0.519), #>               Streptococcus constellatus pharyngis (0.514), and Salmonella Pakistan #>               (0.500) #>  #> Only the first 10 other matches of each record are shown. Run #> print(mo_uncertainties(), n = ...) to view more entries, or save #> mo_uncertainties() to an object."},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"antibiotic-results","dir":"Articles","previous_headings":"Preparation","what":"Antibiotic results","title":"How to conduct AMR data analysis","text":"column antibiotic test results must also cleaned. AMR package comes three new data types work test results: mic minimal inhibitory concentrations (MIC), disk disk diffusion diameters, sir SIR data interpreted already. package can also determine SIR values based MIC disk diffusion values, read .sir() page. now, just clean SIR columns data using dplyr: basically cleaning, time start data inclusion.","code":"# method 1, be explicit about the columns: our_data <- our_data %>%   mutate_at(vars(AMX:GEN), as.sir)  # method 2, let the AMR package determine the eligible columns our_data <- our_data %>%   mutate_if(is_sir_eligible, as.sir)  # result: our_data #> # A tibble: 3,000 × 8 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> #>  1 J3         A        2012-11-21 B_ESCHR_COLI R     I     S     S     #>  2 R7         A        2018-04-03 B_KLBSL_PNMN R     I     S     S     #>  3 P3         A        2014-09-19 B_ESCHR_COLI R     S     S     S     #>  4 P10        A        2015-12-10 B_ESCHR_COLI S     I     S     S     #>  5 B7         A        2015-03-02 B_ESCHR_COLI S     S     S     S     #>  6 W3         A        2018-03-31 B_STPHY_AURS R     S     R     S     #>  7 J8         A        2016-06-14 B_ESCHR_COLI R     S     S     S     #>  8 M3         A        2015-10-25 B_ESCHR_COLI R     S     S     S     #>  9 J3         A        2019-06-19 B_ESCHR_COLI S     S     S     S     #> 10 G6         A        2015-04-27 B_STPHY_AURS S     S     S     S     #> # ℹ 2,990 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"first-isolates","dir":"Articles","previous_headings":"Preparation","what":"First isolates","title":"How to conduct AMR data analysis","text":"need know isolates can actually use analysis without repetition bias. conduct analysis antimicrobial resistance, must include first isolate every patient per episode (Hindler et al., Clin Infect Dis. 2007). , easily get overestimate underestimate resistance antibiotic. Imagine patient admitted MRSA found 5 different blood cultures following weeks (yes, countries like Netherlands blood drawing policies). resistance percentage oxacillin isolates overestimated, included MRSA . clearly selection bias. Clinical Laboratory Standards Institute (CLSI) appoints follows: (…) preparing cumulative antibiogram guide clinical decisions empirical antimicrobial therapy initial infections, first isolate given species per patient, per analysis period (eg, one year) included, irrespective body site, antimicrobial susceptibility profile, phenotypical characteristics (eg, biotype). first isolate easily identified, cumulative antimicrobial susceptibility test data prepared using first isolate generally comparable cumulative antimicrobial susceptibility test data calculated methods, providing duplicate isolates excluded. M39-A4 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 4th Edition. CLSI, 2014. Chapter 6.4 AMR package includes methodology first_isolate() function able apply four different methods defined Hindler et al. 2007: phenotype-based, episode-based, patient-based, isolate-based. right method depends goals analysis, default phenotype-based method case method properly correct duplicate isolates. Read methods first_isolate() page. outcome function can easily added data: 88% suitable resistance analysis! can now filter filter() function, also dplyr package: future use, two syntaxes can shortened: end 2 626 isolates analysis. Now data looks like: Time analysis.","code":"our_data <- our_data %>%   mutate(first = first_isolate(info = TRUE)) #> Determining first isolates using an episode length of 365 days #> ℹ Using column 'bacteria' as input for col_mo. #> ℹ Using column 'date' as input for col_date. #> ℹ Using column 'patient_id' as input for col_patient_id. #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #> => Found 2,626 'phenotype-based' first isolates (87.6% within scope and #>    87.5% of total where a microbial ID was available) our_data_1st <- our_data %>%   filter(first == TRUE) our_data_1st <- our_data %>%   filter_first_isolate() our_data_1st #> # A tibble: 2,626 × 9 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl> #>  1 J3         A        2012-11-21 B_ESCHR_COLI R     I     S     S     TRUE  #>  2 R7         A        2018-04-03 B_KLBSL_PNMN R     I     S     S     TRUE  #>  3 P10        A        2015-12-10 B_ESCHR_COLI S     I     S     S     TRUE  #>  4 B7         A        2015-03-02 B_ESCHR_COLI S     S     S     S     TRUE  #>  5 W3         A        2018-03-31 B_STPHY_AURS R     S     R     S     TRUE  #>  6 J8         A        2016-06-14 B_ESCHR_COLI R     S     S     S     TRUE  #>  7 M3         A        2015-10-25 B_ESCHR_COLI R     S     S     S     TRUE  #>  8 J3         A        2019-06-19 B_ESCHR_COLI S     S     S     S     TRUE  #>  9 G6         A        2015-04-27 B_STPHY_AURS S     S     S     S     TRUE  #> 10 P4         A        2011-06-21 B_ESCHR_COLI S     S     S     S     TRUE  #> # ℹ 2,616 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"analysing-the-data","dir":"Articles","previous_headings":"","what":"Analysing the data","title":"How to conduct AMR data analysis","text":"base R summary() function gives good first impression, comes support new mo sir classes now data set:","code":"summary(our_data_1st) #>   patient_id          hospital              date            #>  Length:2626        Length:2626        Min.   :2011-01-01   #>  Class :character   Class :character   1st Qu.:2013-04-14   #>  Mode  :character   Mode  :character   Median :2015-06-05   #>                                        Mean   :2015-06-15   #>                                        3rd Qu.:2017-08-23   #>                                        Max.   :2020-01-01   #>    bacteria               AMX                    AMC                 #>  Class :mo             Class:sir              Class:sir              #>  <NA>  :0              %R   :43.2% (n=1134)   %R   :36.1% (n=947)    #>  Unique:4              %SI  :56.8% (n=1492)   %SI  :63.9% (n=1679)   #>  #1    :B_ESCHR_COLI   - %S :41.1% (n=1080)   - %S :52.7% (n=1383)   #>  #2    :B_STPHY_AURS   - %I :15.7% (n=412)    - %I :11.3% (n=296)    #>  #3    :B_STRPT_PNMN                                                 #>     CIP                    GEN                  first         #>  Class:sir              Class:sir              Mode:logical   #>  %R   :42.0% (n=1102)   %R   :37.0% (n=971)    TRUE:2626      #>  %SI  :58.0% (n=1524)   %SI  :63.0% (n=1655)                  #>  - %S :51.9% (n=1362)   - %S :59.9% (n=1574)                  #>  - %I : 6.2% (n=162)    - %I : 3.1% (n=81)                    #>   glimpse(our_data_1st) #> Rows: 2,626 #> Columns: 9 #> $ patient_id <chr> \"J3\", \"R7\", \"P10\", \"B7\", \"W3\", \"J8\", \"M3\", \"J3\", \"G6\", \"P4\"… #> $ hospital   <chr> \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\", \"A\",… #> $ date       <date> 2012-11-21, 2018-04-03, 2015-12-10, 2015-03-02, 2018-03-31… #> $ bacteria   <mo> \"B_ESCHR_COLI\", \"B_KLBSL_PNMN\", \"B_ESCHR_COLI\", \"B_ESCHR_COL… #> $ AMX        <sir> R, R, S, S, R, R, R, S, S, S, S, R, S, S, R, R, R, R, I, S,… #> $ AMC        <sir> I, I, I, S, S, S, S, S, S, S, S, S, S, S, S, S, S, R, S, R,… #> $ CIP        <sir> S, S, S, S, R, S, S, S, S, S, S, S, S, S, S, S, S, S, S, S,… #> $ GEN        <sir> S, S, S, S, S, S, S, S, S, S, S, R, S, S, S, S, S, S, S, S,… #> $ first      <lgl> TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE, TRUE,…  # number of unique values per column: sapply(our_data_1st, n_distinct) #> patient_id   hospital       date   bacteria        AMX        AMC        CIP  #>        260          3       1808          4          3          3          3  #>        GEN      first  #>          3          1"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"availability-of-species","dir":"Articles","previous_headings":"Analysing the data","what":"Availability of species","title":"How to conduct AMR data analysis","text":"just get idea species distributed, create frequency table count() based name microorganisms:","code":"our_data %>%   count(mo_name(bacteria), sort = TRUE) #> # A tibble: 4 × 2 #>   `mo_name(bacteria)`          n #>   <chr>                    <int> #> 1 Escherichia coli          1518 #> 2 Staphylococcus aureus      730 #> 3 Streptococcus pneumoniae   426 #> 4 Klebsiella pneumoniae      326  our_data_1st %>%   count(mo_name(bacteria), sort = TRUE) #> # A tibble: 4 × 2 #>   `mo_name(bacteria)`          n #>   <chr>                    <int> #> 1 Escherichia coli          1250 #> 2 Staphylococcus aureus      661 #> 3 Streptococcus pneumoniae   399 #> 4 Klebsiella pneumoniae      316"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"select-and-filter-with-antibiotic-selectors","dir":"Articles","previous_headings":"Analysing the data","what":"Select and filter with antibiotic selectors","title":"How to conduct AMR data analysis","text":"Using -called antibiotic class selectors, can select filter columns based antibiotic class antibiotic results :","code":"our_data_1st %>%   select(date, aminoglycosides()) #> ℹ For aminoglycosides() using column 'GEN' (gentamicin) #> # A tibble: 2,626 × 2 #>    date       GEN   #>    <date>     <sir> #>  1 2012-11-21 S     #>  2 2018-04-03 S     #>  3 2015-12-10 S     #>  4 2015-03-02 S     #>  5 2018-03-31 S     #>  6 2016-06-14 S     #>  7 2015-10-25 S     #>  8 2019-06-19 S     #>  9 2015-04-27 S     #> 10 2011-06-21 S     #> # ℹ 2,616 more rows  our_data_1st %>%   select(bacteria, betalactams()) #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #>   (amoxicillin/clavulanic acid) #> # A tibble: 2,626 × 3 #>    bacteria     AMX   AMC   #>    <mo>         <sir> <sir> #>  1 B_ESCHR_COLI R     I     #>  2 B_KLBSL_PNMN R     I     #>  3 B_ESCHR_COLI S     I     #>  4 B_ESCHR_COLI S     S     #>  5 B_STPHY_AURS R     S     #>  6 B_ESCHR_COLI R     S     #>  7 B_ESCHR_COLI R     S     #>  8 B_ESCHR_COLI S     S     #>  9 B_STPHY_AURS S     S     #> 10 B_ESCHR_COLI S     S     #> # ℹ 2,616 more rows  our_data_1st %>%   select(bacteria, where(is.sir)) #> # A tibble: 2,626 × 5 #>    bacteria     AMX   AMC   CIP   GEN   #>    <mo>         <sir> <sir> <sir> <sir> #>  1 B_ESCHR_COLI R     I     S     S     #>  2 B_KLBSL_PNMN R     I     S     S     #>  3 B_ESCHR_COLI S     I     S     S     #>  4 B_ESCHR_COLI S     S     S     S     #>  5 B_STPHY_AURS R     S     R     S     #>  6 B_ESCHR_COLI R     S     S     S     #>  7 B_ESCHR_COLI R     S     S     S     #>  8 B_ESCHR_COLI S     S     S     S     #>  9 B_STPHY_AURS S     S     S     S     #> 10 B_ESCHR_COLI S     S     S     S     #> # ℹ 2,616 more rows  # filtering using AB selectors is also possible: our_data_1st %>%   filter(any(aminoglycosides() == \"R\")) #> ℹ For aminoglycosides() using column 'GEN' (gentamicin) #> # A tibble: 971 × 9 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl> #>  1 J5         A        2017-12-25 B_STRPT_PNMN R     S     S     R     TRUE  #>  2 X1         A        2017-07-04 B_STPHY_AURS R     S     S     R     TRUE  #>  3 B3         A        2016-07-24 B_ESCHR_COLI S     S     S     R     TRUE  #>  4 V7         A        2012-04-03 B_ESCHR_COLI S     S     S     R     TRUE  #>  5 C9         A        2017-03-23 B_ESCHR_COLI S     S     S     R     TRUE  #>  6 R1         A        2018-06-10 B_STPHY_AURS S     S     S     R     TRUE  #>  7 S2         A        2013-07-19 B_STRPT_PNMN S     S     S     R     TRUE  #>  8 P5         A        2019-03-09 B_STPHY_AURS S     S     S     R     TRUE  #>  9 Q8         A        2019-08-10 B_STPHY_AURS S     S     S     R     TRUE  #> 10 K5         A        2013-03-15 B_STRPT_PNMN S     S     S     R     TRUE  #> # ℹ 961 more rows  our_data_1st %>%   filter(all(betalactams() == \"R\")) #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #>   (amoxicillin/clavulanic acid) #> # A tibble: 471 × 9 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl> #>  1 M7         A        2013-07-22 B_STRPT_PNMN R     R     S     S     TRUE  #>  2 R10        A        2013-12-20 B_STPHY_AURS R     R     S     S     TRUE  #>  3 R7         A        2015-10-25 B_STPHY_AURS R     R     S     S     TRUE  #>  4 R8         A        2019-10-25 B_STPHY_AURS R     R     S     S     TRUE  #>  5 I7         A        2015-08-19 B_ESCHR_COLI R     R     S     S     TRUE  #>  6 N3         A        2014-12-29 B_STRPT_PNMN R     R     R     S     TRUE  #>  7 Q2         A        2019-09-22 B_ESCHR_COLI R     R     S     S     TRUE  #>  8 X7         A        2011-03-20 B_ESCHR_COLI R     R     S     R     TRUE  #>  9 C5         A        2015-08-30 B_KLBSL_PNMN R     R     S     R     TRUE  #> 10 W9         A        2013-10-02 B_ESCHR_COLI R     R     S     S     TRUE  #> # ℹ 461 more rows  # even works in base R (since R 3.0): our_data_1st[all(betalactams() == \"R\"), ] #> ℹ For betalactams() using columns 'AMX' (amoxicillin) and 'AMC' #>   (amoxicillin/clavulanic acid) #> # A tibble: 471 × 9 #>    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first #>    <chr>      <chr>    <date>     <mo>         <sir> <sir> <sir> <sir> <lgl> #>  1 M7         A        2013-07-22 B_STRPT_PNMN R     R     S     S     TRUE  #>  2 R10        A        2013-12-20 B_STPHY_AURS R     R     S     S     TRUE  #>  3 R7         A        2015-10-25 B_STPHY_AURS R     R     S     S     TRUE  #>  4 R8         A        2019-10-25 B_STPHY_AURS R     R     S     S     TRUE  #>  5 I7         A        2015-08-19 B_ESCHR_COLI R     R     S     S     TRUE  #>  6 N3         A        2014-12-29 B_STRPT_PNMN R     R     R     S     TRUE  #>  7 Q2         A        2019-09-22 B_ESCHR_COLI R     R     S     S     TRUE  #>  8 X7         A        2011-03-20 B_ESCHR_COLI R     R     S     R     TRUE  #>  9 C5         A        2015-08-30 B_KLBSL_PNMN R     R     S     R     TRUE  #> 10 W9         A        2013-10-02 B_ESCHR_COLI R     R     S     S     TRUE  #> # ℹ 461 more rows"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"generate-antibiograms","dir":"Articles","previous_headings":"Analysing the data","what":"Generate antibiograms","title":"How to conduct AMR data analysis","text":"Since AMR v2.0 (March 2023), easy create different types antibiograms, support 20 different languages. four antibiogram types, proposed Klinker et al. (2021, DOI 10.1177/20499361211011373), supported new antibiogram() function: Traditional Antibiogram (TA) e.g, susceptibility Pseudomonas aeruginosa piperacillin/tazobactam (TZP) Combination Antibiogram (CA) e.g, sdditional susceptibility Pseudomonas aeruginosa TZP + tobramycin versus TZP alone Syndromic Antibiogram (SA) e.g, susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) Weighted-Incidence Syndromic Combination Antibiogram (WISCA) e.g, susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) male patients age >=65 years heart failure section, show use antibiogram() function create antibiogram types. starters, included example_isolates data set looks like:","code":"example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"traditional-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Traditional Antibiogram","title":"How to conduct AMR data analysis","text":"create traditional antibiogram, simply state antibiotics used. antibiotics argument antibiogram() function supports (combination) previously mentioned antibiotic class selectors: Notice antibiogram() function automatically prints right format using Quarto R Markdown (page), even applies italics taxonomic names (using italicise_taxonomy() internally). also uses language OS either English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, Ukrainian. next example, force language Spanish using language argument:","code":"antibiogram(example_isolates,             antibiotics = c(aminoglycosides(), carbapenems())) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) antibiogram(example_isolates,             mo_transform = \"gramstain\",             antibiotics = aminoglycosides(),             ab_transform = \"name\",             language = \"es\") #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"combined-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Combined Antibiogram","title":"How to conduct AMR data analysis","text":"create combined antibiogram, use antibiotic codes names plus + character like :","code":"antibiogram(example_isolates,             antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"syndromic-antibiogram","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Syndromic Antibiogram","title":"How to conduct AMR data analysis","text":"create syndromic antibiogram, syndromic_group argument must used. can column data, e.g. ifelse() calculations based certain columns:","code":"antibiogram(example_isolates,             antibiotics = c(aminoglycosides(), carbapenems()),             syndromic_group = \"ward\") #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"weighted-incidence-syndromic-combination-antibiogram-wisca","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Weighted-Incidence Syndromic Combination Antibiogram (WISCA)","title":"How to conduct AMR data analysis","text":"create WISCA, must state combination therapy antibiotics argument (similar Combination Antibiogram), define syndromic group syndromic_group argument (similar Syndromic Antibiogram) cases predefined based clinical demographic characteristics (e.g., endocarditis 75+ females). next example simplification without clinical characteristics, just gives idea WISCA can created:","code":"wisca <- antibiogram(example_isolates,                      antibiotics = c(\"AMC\", \"AMC+CIP\", \"TZP\", \"TZP+TOB\"),                      mo_transform = \"gramstain\",                      minimum = 10, # this should be >= 30, but now just as example                      syndromic_group = ifelse(example_isolates$age >= 65 &                                                 example_isolates$gender == \"M\",                                               \"WISCA Group 1\", \"WISCA Group 2\")) wisca"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"plotting-antibiograms","dir":"Articles","previous_headings":"Analysing the data > Generate antibiograms","what":"Plotting antibiograms","title":"How to conduct AMR data analysis","text":"Antibiograms can plotted using autoplot() ggplot2 packages, since AMR package provides extension function:  calculate antimicrobial resistance sensible way, also correcting results, use resistance() susceptibility() functions.","code":"autoplot(wisca)"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"resistance-percentages","dir":"Articles","previous_headings":"Analysing the data","what":"Resistance percentages","title":"How to conduct AMR data analysis","text":"functions resistance() susceptibility() can used calculate antimicrobial resistance susceptibility. specific analyses, functions proportion_S(), proportion_SI(), proportion_I(), proportion_IR() proportion_R() can used determine proportion specific antimicrobial outcome. functions contain minimum argument, denoting minimum required number test results returning value. functions otherwise return NA. default minimum = 30, following CLSI M39-A4 guideline applying microbial epidemiology. per EUCAST guideline 2019, calculate resistance proportion R (proportion_R(), equal resistance()) susceptibility proportion S (proportion_SI(), equal susceptibility()). functions can used : can used conjunction group_by() summarise(), dplyr package: Author: Dr. Matthijs Berends, 26th Feb 2023","code":"our_data_1st %>% resistance(AMX) #> [1] 0.4318355 our_data_1st %>%   group_by(hospital) %>%   summarise(amoxicillin = resistance(AMX)) #> # A tibble: 3 × 2 #>   hospital amoxicillin #>   <chr>          <dbl> #> 1 A              0.343 #> 2 B              0.569 #> 3 C              0.375"},{"path":"https://msberends.github.io/AMR/articles/EUCAST.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to apply EUCAST rules","text":"EUCAST rules? European Committee Antimicrobial Susceptibility Testing (EUCAST) states website: EUCAST expert rules tabulated collection expert knowledge intrinsic resistances, exceptional resistance phenotypes interpretive rules may applied antimicrobial susceptibility testing order reduce errors make appropriate recommendations reporting particular resistances. Europe, lot medical microbiological laboratories already apply rules (Brown et al., 2015). package features latest insights intrinsic resistance unusual phenotypes (v3.3, 2021). Moreover, eucast_rules() function use purpose can also apply additional rules, like forcing ampicillin = R isolates amoxicillin/clavulanic acid = R.","code":""},{"path":"https://msberends.github.io/AMR/articles/EUCAST.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"How to apply EUCAST rules","text":"rules can used discard impossible bug-drug combinations data. example, Klebsiella produces beta-lactamase prevents ampicillin (amoxicillin) working . words, practically every strain Klebsiella resistant ampicillin. Sometimes, laboratory data can still contain strains ampicillin susceptible ampicillin. antibiogram available identification available, antibiogram re-interpreted based identification (namely, Klebsiella). EUCAST expert rules solve , can applied using eucast_rules(): convenient function mo_is_intrinsic_resistant() uses guideline, allows check one specific microorganisms antibiotics: EUCAST rules can used correction, can also used filling known resistance susceptibility based results antimicrobials drugs. process called interpretive reading, basically form imputation, part eucast_rules() function well:","code":"oops <- data.frame(   mo = c(     \"Klebsiella\",     \"Escherichia\"   ),   ampicillin = \"S\" ) oops #>            mo ampicillin #> 1  Klebsiella          S #> 2 Escherichia          S  eucast_rules(oops, info = FALSE) #>            mo ampicillin #> 1  Klebsiella          R #> 2 Escherichia          S mo_is_intrinsic_resistant(   c(\"Klebsiella\", \"Escherichia\"),   \"ampicillin\" ) #> [1]  TRUE FALSE  mo_is_intrinsic_resistant(   \"Klebsiella\",   c(\"ampicillin\", \"kanamycin\") ) #> [1]  TRUE FALSE data <- data.frame(   mo = c(     \"Staphylococcus aureus\",     \"Enterococcus faecalis\",     \"Escherichia coli\",     \"Klebsiella pneumoniae\",     \"Pseudomonas aeruginosa\"   ),   VAN = \"-\", # Vancomycin   AMX = \"-\", # Amoxicillin   COL = \"-\", # Colistin   CAZ = \"-\", # Ceftazidime   CXM = \"-\", # Cefuroxime   PEN = \"S\", # Benzylenicillin   FOX = \"S\", # Cefoxitin   stringsAsFactors = FALSE ) data eucast_rules(data)"},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"type-of-input","dir":"Articles","previous_headings":"","what":"Type of input","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function takes data set input, regular data.frame. tries automatically determine right columns info isolates, name species columns results antimicrobial agents. See help page info set right settings data command ?mdro. WHONET data (data), settings automatically set correctly.","code":""},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"guidelines","dir":"Articles","previous_headings":"","what":"Guidelines","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function support multiple guidelines. can select guideline guideline parameter. Currently supported guidelines (case-insensitive): guideline = \"CMI2012\" (default) Magiorakos AP, Srinivasan et al. “Multidrug-resistant, extensively drug-resistant pandrug-resistant bacteria: international expert proposal interim standard definitions acquired resistance.” Clinical Microbiology Infection (2012) (link) guideline = \"EUCAST3.2\" (simply guideline = \"EUCAST\") European international guideline - EUCAST Expert Rules Version 3.2 “Intrinsic Resistance Unusual Phenotypes” (link) guideline = \"EUCAST3.1\" European international guideline - EUCAST Expert Rules Version 3.1 “Intrinsic Resistance Exceptional Phenotypes Tables” (link) guideline = \"TB\" international guideline multi-drug resistant tuberculosis - World Health Organization “Companion handbook guidelines programmatic management drug-resistant tuberculosis” (link) guideline = \"MRGN\" German national guideline - Mueller et al. (2015) Antimicrobial Resistance Infection Control 4:7. DOI: 10.1186/s13756-015-0047-6 guideline = \"BRMO\" Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu “WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)” (link) Please suggest (country-specific) guidelines letting us know: https://github.com/msberends/AMR/issues/new.","code":""},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"custom-guidelines","dir":"Articles","previous_headings":"Guidelines","what":"Custom Guidelines","title":"How to determine multi-drug resistance (MDR)","text":"can also use custom guideline. Custom guidelines can set custom_mdro_guideline() function. great importance custom rules determine MDROs hospital, e.g., rules dependent ward, state contact isolation variables data. familiar case_when() dplyr package, recognise input method set rules. Rules must set using R considers ‘formula notation’: row/isolate matches first rule, value first ~ (case ‘Elderly Type ’) set MDRO value. Otherwise, second rule tried . maximum number rules unlimited. can print rules set console overview. Colours help reading console supports colours. outcome function can used guideline argument mdro() function: rules set (custom object case) exported shared file location using saveRDS() collaborate multiple users. custom rules set imported using readRDS().","code":"custom <- custom_mdro_guideline(   CIP == \"R\" & age > 60 ~ \"Elderly Type A\",   ERY == \"R\" & age > 60 ~ \"Elderly Type B\" ) custom #> A set of custom MDRO rules: #>   1. If CIP is \"R\" and age is higher than 60 then: Elderly Type A #>   2. If ERY is \"R\" and age is higher than 60 then: Elderly Type B #>   3. Otherwise: Negative #>  #> Unmatched rows will return NA. #> Results will be of class 'factor', with ordered levels: Negative < Elderly Type A < Elderly Type B x <- mdro(example_isolates, guideline = custom) table(x) #> x #>       Negative Elderly Type A Elderly Type B  #>           1070            198            732"},{"path":"https://msberends.github.io/AMR/articles/MDR.html","id":"examples","dir":"Articles","previous_headings":"","what":"Examples","title":"How to determine multi-drug resistance (MDR)","text":"mdro() function always returns ordered factor predefined guidelines. example, output default guideline Magiorakos et al. returns factor levels ‘Negative’, ‘MDR’, ‘XDR’ ‘PDR’ order. next example uses example_isolates data set. data set included package contains full antibiograms 2,000 microbial isolates. reflects reality can used practise AMR data analysis. test MDR/XDR/PDR guideline data set, get: (16 isolates test results) Frequency table Class: factor > ordered (numeric) Length: 2,000 Levels: 4: Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant … Available: 1,729 (86.45%, NA: 271 = 13.55%) Unique: 2 another example, create data set determine multi-drug resistant TB: column names automatically verified valid drug names codes, worked exactly way: data set now looks like : can now add interpretation MDR-TB data set. can use: shortcut mdr_tb(): Create frequency table results: Frequency table Class: factor > ordered (numeric) Length: 5,000 Levels: 5: Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant <… Available: 5,000 (100%, NA: 0 = 0%) Unique: 5","code":"library(dplyr) # to support pipes: %>% library(cleaner) # to create frequency tables example_isolates %>%   mdro() %>%   freq() # show frequency table of the result #> Warning: in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) # random_sir() is a helper function to generate # a random vector with values S, I and R my_TB_data <- data.frame(   rifampicin = random_sir(5000),   isoniazid = random_sir(5000),   gatifloxacin = random_sir(5000),   ethambutol = random_sir(5000),   pyrazinamide = random_sir(5000),   moxifloxacin = random_sir(5000),   kanamycin = random_sir(5000) ) my_TB_data <- data.frame(   RIF = random_sir(5000),   INH = random_sir(5000),   GAT = random_sir(5000),   ETH = random_sir(5000),   PZA = random_sir(5000),   MFX = random_sir(5000),   KAN = random_sir(5000) ) head(my_TB_data) #>   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin #> 1          S         I            I          I            S            S #> 2          R         R            I          I            S            R #> 3          R         I            S          S            R            R #> 4          I         S            R          I            I            S #> 5          S         R            R          I            R            R #> 6          S         R            S          I            I            I #>   kanamycin #> 1         S #> 2         R #> 3         S #> 4         S #> 5         I #> 6         R mdro(my_TB_data, guideline = \"TB\") my_TB_data$mdr <- mdr_tb(my_TB_data) #> ℹ No column found as input for col_mo, assuming all rows contain #>   Mycobacterium tuberculosis. freq(my_TB_data$mdr)"},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"transforming","dir":"Articles","previous_headings":"","what":"Transforming","title":"How to conduct principal component analysis (PCA) for AMR","text":"PCA, need transform AMR data first. example_isolates data set package looks like: Now transform data set resistance percentages per taxonomic order genus:","code":"library(AMR) library(dplyr) glimpse(example_isolates) #> Rows: 2,000 #> Columns: 46 #> $ date    <date> 2002-01-02, 2002-01-03, 2002-01-07, 2002-01-07, 2002-01-13, 2… #> $ patient <chr> \"A77334\", \"A77334\", \"067927\", \"067927\", \"067927\", \"067927\", \"4… #> $ age     <dbl> 65, 65, 45, 45, 45, 45, 78, 78, 45, 79, 67, 67, 71, 71, 75, 50… #> $ gender  <chr> \"F\", \"F\", \"F\", \"F\", \"F\", \"F\", \"M\", \"M\", \"F\", \"F\", \"M\", \"M\", \"M… #> $ ward    <chr> \"Clinical\", \"Clinical\", \"ICU\", \"ICU\", \"ICU\", \"ICU\", \"Clinical\"… #> $ mo      <mo> \"B_ESCHR_COLI\", \"B_ESCHR_COLI\", \"B_STPHY_EPDR\", \"B_STPHY_EPDR\",… #> $ PEN     <sir> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,… #> $ OXA     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ FLC     <sir> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R… #> $ AMX     <sir> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N… #> $ AMC     <sir> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N… #> $ AMP     <sir> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N… #> $ TZP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CZO     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,… #> $ FEP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CXM     <sir> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S… #> $ FOX     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,… #> $ CTX     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ CAZ     <sir> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, … #> $ CRO     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ GEN     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ TOB     <sir> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA… #> $ AMK     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ KAN     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ TMP     <sir> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, … #> $ SXT     <sir> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N… #> $ NIT     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,… #> $ FOS     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ LNZ     <sir> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… #> $ CIP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S… #> $ MFX     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ VAN     <sir> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, … #> $ TEC     <sir> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… #> $ TCY     <sir> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, … #> $ TGC     <sir> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA… #> $ DOX     <sir> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA… #> $ ERY     <sir> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,… #> $ CLI     <sir> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA… #> $ AZM     <sir> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,… #> $ IPM     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S… #> $ MEM     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ MTR     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ CHL     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ COL     <sir> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, … #> $ MUP     <sir> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA… #> $ RIF     <sir> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N… resistance_data <- example_isolates %>%   group_by(     order = mo_order(mo), # group on anything, like order     genus = mo_genus(mo)   ) %>% #  and genus as we do here   summarise_if(is.sir, resistance) %>% # then get resistance of all drugs   select(     order, genus, AMC, CXM, CTX,     CAZ, GEN, TOB, TMP, SXT   ) # and select only relevant columns  head(resistance_data) #> # A tibble: 6 × 10 #> # Groups:   order [5] #>   order             genus          AMC   CXM   CTX   CAZ   GEN   TOB   TMP   SXT #>   <chr>             <chr>        <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #> 1 (unknown order)   (unknown ge…    NA    NA    NA    NA    NA    NA    NA    NA #> 2 Actinomycetales   Schaalia        NA    NA    NA    NA    NA    NA    NA    NA #> 3 Bacteroidales     Bacteroides     NA    NA    NA    NA    NA    NA    NA    NA #> 4 Campylobacterales Campylobact…    NA    NA    NA    NA    NA    NA    NA    NA #> 5 Caryophanales     Gemella         NA    NA    NA    NA    NA    NA    NA    NA #> 6 Caryophanales     Listeria        NA    NA    NA    NA    NA    NA    NA    NA"},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"perform-principal-component-analysis","dir":"Articles","previous_headings":"","what":"Perform principal component analysis","title":"How to conduct principal component analysis (PCA) for AMR","text":"new pca() function automatically filter rows contain numeric values selected variables, now need : result can reviewed good old summary() function: Good news. first two components explain total 93.3% variance (see PC1 PC2 values Proportion Variance. can create -called biplot base R biplot() function, see antimicrobial resistance per drug explain difference per microorganism.","code":"pca_result <- pca(resistance_data) #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", #>   \"TMP\", and \"TOB\". Total observations available: 7. summary(pca_result) #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\" #> Importance of components: #>                           PC1    PC2    PC3     PC4     PC5     PC6       PC7 #> Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17 #> Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00 #> Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00 #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\""},{"path":"https://msberends.github.io/AMR/articles/PCA.html","id":"plotting-the-results","dir":"Articles","previous_headings":"","what":"Plotting the results","title":"How to conduct principal component analysis (PCA) for AMR","text":"can’t see explanation points. Perhaps works better new ggplot_pca() function, automatically adds right labels even groups:  can also print ellipse per group, edit appearance:","code":"biplot(pca_result) ggplot_pca(pca_result) ggplot_pca(pca_result, ellipse = TRUE) +   ggplot2::labs(title = \"An AMR/PCA biplot!\")"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"spss-sas-stata","dir":"Articles","previous_headings":"","what":"SPSS / SAS / Stata","title":"How to import data from SPSS / SAS / Stata","text":"SPSS (Statistical Package Social Sciences) probably well-known software package statistical analysis. SPSS easier learn R, SPSS click menu run parts analysis. user-friendliness, taught universities particularly useful students new statistics. experience, guess pretty much (bio)medical students know time graduate. SAS Stata comparable statistical packages popular big industries.","code":""},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"compared-to-r","dir":"Articles","previous_headings":"","what":"Compared to R","title":"How to import data from SPSS / SAS / Stata","text":"said, SPSS easier learn R. SPSS, SAS Stata come major downsides comparing R: R highly modular. official R network (CRAN) features 16,000 packages time writing, AMR package one . packages peer-reviewed publication. Aside official channel, also developers choose submit CRAN, rather keep public repository, like GitHub. may even lot 14,000 packages . Bottom line , can really extend ask somebody . Take example AMR package. Among things, adds reliable reference data R help data cleaning analysis. SPSS, SAS Stata never know valid MIC value Gram stain E. coli . species Klebiella resistant amoxicillin Floxapen® trade name flucloxacillin. facts properties often needed clean existing data, inconvenient software package without reliable reference data. See demonstration. R extremely flexible. write syntax , can anything want. flexibility transforming, arranging, grouping summarising data, drawing plots, endless - SPSS, SAS Stata bound algorithms format styles. may bit flexible, can probably never create specific publication-ready plot without using (paid) software. sometimes write syntaxes SPSS run complete analysis ‘automate’ work, lot less time R. notice writing syntaxes R lot nifty clever SPSS. Still, working statistical package, knowledge (statistically) willing accomplish. R can easily automated. last years, R Markdown really made interesting development. R Markdown, can easily produce reports, whether format Word, PowerPoint, website, PDF document just raw data Excel. even allows use reference file containing layout style (e.g. fonts colours) organisation. use lot generate weekly monthly reports automatically. Just write code enjoy automatically updated reports interval like. even professional environment, create Shiny apps: live manipulation data using custom made website. webdesign knowledge needed (JavaScript, CSS, HTML) almost zero. R huge community. Many R users just ask questions websites like StackOverflow.com, largest online community programmers. time writing, 489 114 R-related questions already asked platform (covers questions answers programming language). experience, questions answered within couple minutes. R understands data type, including SPSS/SAS/Stata. ’s vice versa ’m afraid. can import data source R. example SPSS, SAS Stata (link), Minitab, Epi Info EpiData (link), Excel (link), flat files like CSV, TXT TSV (link), directly databases datawarehouses anywhere world (link). can even scrape websites download tables live internet (link) get results API call transform data one command (link). best part - can export R data formats well. can import SPSS file, analysis neatly R export resulting tables Excel files sharing. R completely free open-source. strings attached. created maintained volunteers believe (data) science open publicly available everybody. SPSS, SAS Stata quite expensive. IBM SPSS Staticstics comes subscriptions nowadays, varying USD 1,300 USD 8,500 per user per year. SAS Analytics Pro costs around USD 10,000 per computer. Stata also business model subscription fees, varying USD 600 USD 2,800 per computer per year, lower prices come limitation number variables can work . still offer benefits R. working midsized small company, can save tens thousands dollars using R instead e.g. SPSS - gaining even functions flexibility. R enthousiasts can much PR want (like ), nobody officially associated affiliated R. really free. R (nowadays) preferred analysis software academic papers. present, R among world powerful statistical languages, generally popular science (Bollmann et al., 2017). reasons, number references R analysis method academic papers rising continuously even surpassed SPSS academic use (Muenchen, 2014). believe thing SPSS , always great user interface easy learn use. Back developed , little competition, let alone R. R didn’t even professional user interface last decade (called RStudio, see ). people used R nineties 2010 almost completely incomparable R used now. language restyled completely volunteers dedicated professionals field data science. SPSS great nothing else compete. now 2023, don’t see reason SPSS better use R. demonstrate first point:","code":"# not all values are valid MIC values: as.mic(0.125) #> Class 'mic' #> [1] 0.125 as.mic(\"testvalue\") #> Class 'mic' #> [1] <NA>  # the Gram stain is available for all bacteria: mo_gramstain(\"E. coli\") #> [1] \"Gram-negative\"  # Klebsiella is intrinsic resistant to amoxicillin, according to EUCAST: klebsiella_test <- data.frame(   mo = \"klebsiella\",   amox = \"S\",   stringsAsFactors = FALSE ) klebsiella_test # (our original data) #>           mo amox #> 1 klebsiella    S eucast_rules(klebsiella_test, info = FALSE) # (the edited data by EUCAST rules) #>           mo amox #> 1 klebsiella    R  # hundreds of trade names can be translated to a name, trade name or an ATC code: ab_name(\"floxapen\") #> [1] \"Flucloxacillin\" ab_tradenames(\"floxapen\") #>  [1] \"culpen\"               \"floxacillin\"          \"floxacillin sodium\"   #>  [4] \"floxapen\"             \"floxapen sodium salt\" \"fluclox\"              #>  [7] \"flucloxacilina\"       \"flucloxacillin\"       \"flucloxacilline\"      #> [10] \"flucloxacillinum\"     \"fluorochloroxacillin\" \"staphylex\" ab_atc(\"floxapen\") #> [1] \"J01CF05\""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"rstudio","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata","what":"RStudio","title":"How to import data from SPSS / SAS / Stata","text":"work R, probably best option use RStudio. open-source free desktop environment allows run R code, also supports project management, version management, package management convenient import menus work data sources. can also install RStudio Server private corporate server, brings nothing less complete RStudio software website (home work). import data file, just click Import Dataset Environment tab:  additional packages needed, RStudio ask installed beforehand. window opens, can define options (parameters) used import ’re ready go:  want named variables imported factors resembles SPSS , use as_factor(). difference :","code":"SPSS_data # # A tibble: 4,203 x 4 #     v001 sex       status    statusage #    <dbl> <dbl+lbl> <dbl+lbl>     <dbl> #  1 10002 1         1              76.6 #  2 10004 0         1              59.1 #  3 10005 1         1              54.5 #  4 10006 1         1              54.1 #  5 10007 1         1              57.7 #  6 10008 1         1              62.8 #  7 10010 0         1              63.7 #  8 10011 1         1              73.1 #  9 10017 1         1              56.7 # 10 10018 0         1              66.6 # # ... with 4,193 more rows  as_factor(SPSS_data) # # A tibble: 4,203 x 4 #     v001 sex    status statusage #    <dbl> <fct>  <fct>      <dbl> #  1 10002 Male   alive       76.6 #  2 10004 Female alive       59.1 #  3 10005 Male   alive       54.5 #  4 10006 Male   alive       54.1 #  5 10007 Male   alive       57.7 #  6 10008 Male   alive       62.8 #  7 10010 Female alive       63.7 #  8 10011 Male   alive       73.1 #  9 10017 Male   alive       56.7 # 10 10018 Female alive       66.6 # # ... with 4,193 more rows"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"base-r","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata","what":"Base R","title":"How to import data from SPSS / SAS / Stata","text":"import data SPSS, SAS Stata, can use great haven package : can now import files follows:","code":"# download and install the latest version: install.packages(\"haven\") # load the package you just installed: library(haven)"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"spss","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata > Base R","what":"SPSS","title":"How to import data from SPSS / SAS / Stata","text":"read files SPSS R: forget as_factor(), mentioned . export R objects SPSS file format:","code":"# read any SPSS file based on file extension (best way): read_spss(file = \"path/to/file\")  # read .sav or .zsav file: read_sav(file = \"path/to/file\")  # read .por file: read_por(file = \"path/to/file\") # save as .sav file: write_sav(data = yourdata, path = \"path/to/file\")  # save as compressed .zsav file: write_sav(data = yourdata, path = \"path/to/file\", compress = TRUE)"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"sas","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata > Base R","what":"SAS","title":"How to import data from SPSS / SAS / Stata","text":"read files SAS R: export R objects SAS file format:","code":"# read .sas7bdat + .sas7bcat files: read_sas(data_file = \"path/to/file\", catalog_file = NULL)  # read SAS transport files (version 5 and version 8): read_xpt(file = \"path/to/file\") # save as regular SAS file: write_sas(data = yourdata, path = \"path/to/file\")  # the SAS transport format is an open format # (required for submission of the data to the FDA) write_xpt(data = yourdata, path = \"path/to/file\", version = 8)"},{"path":"https://msberends.github.io/AMR/articles/SPSS.html","id":"stata","dir":"Articles","previous_headings":"Import data from SPSS/SAS/Stata > Base R","what":"Stata","title":"How to import data from SPSS / SAS / Stata","text":"read files Stata R: export R objects Stata file format:","code":"# read .dta file: read_stata(file = \"/path/to/file\")  # works exactly the same: read_dta(file = \"/path/to/file\") # save as .dta file, Stata version 14: # (supports Stata v8 until v15 at the time of writing) write_dta(data = yourdata, path = \"/path/to/file\", version = 14)"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"import-of-data","dir":"Articles","previous_headings":"","what":"Import of data","title":"How to work with WHONET data","text":"tutorial assumes already imported WHONET data e.g. readxl package. RStudio, can done using menu button ‘Import Dataset’ tab ‘Environment’. Choose option ‘Excel’ select exported file. Make sure date fields imported correctly. example syntax look like : package comes example data set WHONET. use analysis.","code":"library(readxl) data <- read_excel(path = \"path/to/your/file.xlsx\")"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to work with WHONET data","text":"First, load relevant packages yet . use tidyverse analyses. . don’t know yet, suggest read website: https://www.tidyverse.org/. transform variables simplify automate analysis: Microorganisms transformed microorganism codes (called mo) using Catalogue Life reference data set, contains ~70,000 microorganisms taxonomic kingdoms Bacteria, Fungi Protozoa. tranformation .mo(). function also recognises almost WHONET abbreviations microorganisms. Antimicrobial results interpretations clean valid. words, contain values \"S\", \"\" \"R\". exactly .sir() function . errors warnings, values transformed succesfully. also created package dedicated data cleaning checking, called cleaner package. freq() function can used create frequency tables. let’s check data, couple frequency tables: Frequency table Class: character Length: 500 Available: 500 (100%, NA: 0 = 0%) Unique: 38 Shortest: 11 Longest: 40 (omitted 28 entries, n = 57 [11.4%]) Frequency table Class: factor > ordered > sir (numeric) Length: 500 Levels: 3: S < < R Available: 481 (96.2%, NA: 19 = 3.8%) Unique: 3 Drug: Amoxicillin/clavulanic acid (AMC, J01CR02) Drug group: Beta-lactams/penicillins %SI: 78.59%","code":"library(dplyr) # part of tidyverse library(ggplot2) # part of tidyverse library(AMR) # this package library(cleaner) # to create frequency tables # transform variables data <- WHONET %>%   # get microbial ID based on given organism   mutate(mo = as.mo(Organism)) %>%   # transform everything from \"AMP_ND10\" to \"CIP_EE\" to the new `sir` class   mutate_at(vars(AMP_ND10:CIP_EE), as.sir) # our newly created `mo` variable, put in the mo_name() function data %>% freq(mo_name(mo), nmax = 10) # our transformed antibiotic columns # amoxicillin/clavulanic acid (J01CR02) as an example data %>% freq(AMC_ND2)"},{"path":"https://msberends.github.io/AMR/articles/WHONET.html","id":"a-first-glimpse-at-results","dir":"Articles","previous_headings":"","what":"A first glimpse at results","title":"How to work with WHONET data","text":"easy ggplot already give lot information, using included ggplot_sir() function:","code":"data %>%   group_by(Country) %>%   select(Country, AMP_ND2, AMC_ED20, CAZ_ED10, CIP_ED5) %>%   ggplot_sir(translate_ab = \"ab\", facet = \"Country\", datalabels = FALSE)"},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"microorganisms-full-microbial-taxonomy","dir":"Articles","previous_headings":"","what":"microorganisms: Full Microbial Taxonomy","title":"Data sets for download / own use","text":"data set 52 151 rows 23 columns, containing following column names:mo, fullname, status, kingdom, phylum, class, order, family, genus, species, subspecies, rank, ref, oxygen_tolerance, source, lpsn, lpsn_parent, lpsn_renamed_to, gbif, gbif_parent, gbif_renamed_to, prevalence, snomed. data set R available microorganisms, load AMR package. last updated 11 May 2023 19:56:27 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (1.2 MB) Download tab-separated text file (11.7 MB) Download Microsoft Excel workbook (5.2 MB) Download Apache Feather file (5.5 MB) Download Apache Parquet file (2.6 MB) Download SAS data (SAS) file (50.9 MB) Download SAS transport (XPT) file (48.4 MB) Download IBM SPSS Statistics data file (17.7 MB) Download Stata DTA file (48.5 MB) NOTE: exported files SAS, SPSS Stata contain first 50 SNOMED codes per record, file size otherwise exceed 100 MB; file size limit GitHub. file structures compression techniques inefficient. Advice? Use R instead. ’s free much better many ways. tab-separated text file Microsoft Excel workbook contain SNOMED codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source","dir":"Articles","previous_headings":"microorganisms: Full Microbial Taxonomy","what":"Source","title":"Data sets for download / own use","text":"data set contains full microbial taxonomy five kingdoms List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF): Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example-content","dir":"Articles","previous_headings":"microorganisms: Full Microbial Taxonomy","what":"Example content","title":"Data sets for download / own use","text":"Included (sub)species per taxonomic kingdom: Example rows filtering genus Escherichia:","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"antibiotics-antibiotic-antifungal-drugs","dir":"Articles","previous_headings":"","what":"antibiotics: Antibiotic (+Antifungal) Drugs","title":"Data sets for download / own use","text":"data set 483 rows 14 columns, containing following column names:ab, cid, name, group, atc, atc_group1, atc_group2, abbreviations, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc. data set R available antibiotics, load AMR package. last updated 22 February 2023 13:38:57 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (39 kB) Download tab-separated text file (0.1 MB) Download Microsoft Excel workbook (66 kB) Download Apache Feather file (0.1 MB) Download Apache Parquet file (97 kB) Download SAS data (SAS) file (1.9 MB) Download SAS transport (XPT) file (1.4 MB) Download IBM SPSS Statistics data file (0.3 MB) Download Stata DTA file (0.4 MB) tab-separated text file Microsoft Excel workbook, SAS, SPSS Stata files contain ATC codes, common abbreviations, trade names LOINC codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-1","dir":"Articles","previous_headings":"antibiotics: Antibiotic (+Antifungal) Drugs","what":"Source","title":"Data sets for download / own use","text":"data set contains EARS-Net ATC codes gathered WHONET, compound IDs PubChem. also contains brand names (synonyms) found PubChem Defined Daily Doses (DDDs) oral parenteral administration. ATC/DDD index Collaborating Centre Drug Statistics Methodology (note: may used commercial purposes, freely available CC website personal use) PubChem US National Library Medicine WHONET software 2019 LOINC (Logical Observation Identifiers Names Codes)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"antivirals-antiviral-drugs","dir":"Articles","previous_headings":"","what":"antivirals: Antiviral Drugs","title":"Data sets for download / own use","text":"data set 120 rows 11 columns, containing following column names:av, name, atc, cid, atc_group, synonyms, oral_ddd, oral_units, iv_ddd, iv_units, loinc. data set R available antivirals, load AMR package. last updated 13 November 2022 07:46:10 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (5 kB) Download tab-separated text file (16 kB) Download Microsoft Excel workbook (16 kB) Download Apache Feather file (15 kB) Download Apache Parquet file (13 kB) Download SAS data (SAS) file (84 kB) Download SAS transport (XPT) file (68 kB) Download IBM SPSS Statistics data file (30 kB) Download Stata DTA file (73 kB) tab-separated text file Microsoft Excel workbook, SAS, SPSS Stata files contain trade names LOINC codes comma separated values.","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-2","dir":"Articles","previous_headings":"antivirals: Antiviral Drugs","what":"Source","title":"Data sets for download / own use","text":"data set contains ATC codes gathered compound IDs PubChem. also contains brand names (synonyms) found PubChem Defined Daily Doses (DDDs) oral parenteral administration. ATC/DDD index Collaborating Centre Drug Statistics Methodology (note: may used commercial purposes, freely available CC website personal use) PubChem US National Library Medicine LOINC (Logical Observation Identifiers Names Codes)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir","dir":"Articles","previous_headings":"","what":"clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR","title":"Data sets for download / own use","text":"data set 18 271 rows 11 columns, containing following column names:guideline, method, site, mo, rank_index, ab, ref_tbl, disk_dose, breakpoint_S, breakpoint_R, uti. data set R available clinical_breakpoints, load AMR package. last updated 20 April 2023 13:20:41 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (43 kB) Download tab-separated text file (1.9 MB) Download Microsoft Excel workbook (0.8 MB) Download Apache Feather file (0.7 MB) Download Apache Parquet file (88 kB) Download SAS data (SAS) file (3.6 MB) Download SAS transport (XPT) file (3.4 MB) Download IBM SPSS Statistics data file (2.3 MB) Download Stata DTA file (3.3 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-3","dir":"Articles","previous_headings":"clinical_breakpoints: Interpretation from MIC values & disk diameters to SIR","what":"Source","title":"Data sets for download / own use","text":"data set contains interpretation rules MIC values disk diffusion diameters. Included guidelines CLSI (2013-2022) EUCAST (2013-2022).","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"intrinsic_resistant-intrinsic-bacterial-resistance","dir":"Articles","previous_headings":"","what":"intrinsic_resistant: Intrinsic Bacterial Resistance","title":"Data sets for download / own use","text":"data set 134 634 rows 2 columns, containing following column names:mo ab. data set R available intrinsic_resistant, load AMR package. last updated 16 December 2022 15:10:43 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (78 kB) Download tab-separated text file (5.1 MB) Download Microsoft Excel workbook (1.3 MB) Download Apache Feather file (1.2 MB) Download Apache Parquet file (0.2 MB) Download SAS data (SAS) file (9.8 MB) Download SAS transport (XPT) file (9.5 MB) Download IBM SPSS Statistics data file (7.4 MB) Download Stata DTA file (9.5 MB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-4","dir":"Articles","previous_headings":"intrinsic_resistant: Intrinsic Bacterial Resistance","what":"Source","title":"Data sets for download / own use","text":"data set contains defined intrinsic resistance EUCAST bug-drug combinations, based ‘EUCAST Expert Rules’ ‘EUCAST Intrinsic Resistance Unusual Phenotypes’ v3.3 (2021).","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example-content-4","dir":"Articles","previous_headings":"intrinsic_resistant: Intrinsic Bacterial Resistance","what":"Example content","title":"Data sets for download / own use","text":"Example rows filtering Enterobacter cloacae:","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"dosage-dosage-guidelines-from-eucast","dir":"Articles","previous_headings":"","what":"dosage: Dosage Guidelines from EUCAST","title":"Data sets for download / own use","text":"data set 336 rows 9 columns, containing following column names:ab, name, type, dose, dose_times, administration, notes, original_txt, eucast_version. data set R available dosage, load AMR package. last updated 14 November 2022 14:20:39 UTC. Find info structure data set . Direct download links: Download original R Data Structure (RDS) file (3 kB) Download tab-separated text file (29 kB) Download Microsoft Excel workbook (19 kB) Download Apache Feather file (16 kB) Download Apache Parquet file (8 kB) Download SAS data (SAS) file (92 kB) Download SAS transport (XPT) file (79 kB) Download IBM SPSS Statistics data file (43 kB) Download Stata DTA file (82 kB)","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-5","dir":"Articles","previous_headings":"dosage: Dosage Guidelines from EUCAST","what":"Source","title":"Data sets for download / own use","text":"EUCAST breakpoints used package based dosages data set. Currently included dosages data set meant : ‘EUCAST Clinical Breakpoint Tables’ v11.0 (2021) ‘EUCAST Clinical Breakpoint Tables’ v12.0 (2022).","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example_isolates-example-data-for-practice","dir":"Articles","previous_headings":"","what":"example_isolates: Example Data for Practice","title":"Data sets for download / own use","text":"data set 2 000 rows 46 columns, containing following column names:date, patient, age, gender, ward, mo, PEN, OXA, FLC, AMX, AMC, AMP, TZP, CZO, FEP, CXM, FOX, CTX, CAZ, CRO, GEN, TOB, AMK, KAN, TMP, SXT, NIT, FOS, LNZ, CIP, MFX, VAN, TEC, TCY, TGC, DOX, ERY, CLI, AZM, IPM, MEM, MTR, CHL, COL, MUP, RIF. data set R available example_isolates, load AMR package. last updated 21 January 2023 22:47:20 UTC. Find info structure data set .","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-6","dir":"Articles","previous_headings":"example_isolates: Example Data for Practice","what":"Source","title":"Data sets for download / own use","text":"data set contains randomised fictitious data, reflects reality can used practise AMR data analysis.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"example_isolates_unclean-example-data-for-practice","dir":"Articles","previous_headings":"","what":"example_isolates_unclean: Example Data for Practice","title":"Data sets for download / own use","text":"data set 3 000 rows 8 columns, containing following column names:patient_id, hospital, date, bacteria, AMX, AMC, CIP, GEN. data set R available example_isolates_unclean, load AMR package. last updated 27 August 2022 18:49:37 UTC. Find info structure data set .","code":""},{"path":"https://msberends.github.io/AMR/articles/datasets.html","id":"source-7","dir":"Articles","previous_headings":"example_isolates_unclean: Example Data for Practice","what":"Source","title":"Data sets for download / own use","text":"data set contains randomised fictitious data, reflects reality can used practise AMR data analysis.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"needed-r-packages","dir":"Articles","previous_headings":"","what":"Needed R packages","title":"How to predict antimicrobial resistance","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. AMR package depends packages even extends use functions.","code":"library(dplyr) library(ggplot2) library(AMR)  # (if not yet installed, install with:) # install.packages(c(\"tidyverse\", \"AMR\"))"},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"prediction-analysis","dir":"Articles","previous_headings":"","what":"Prediction analysis","title":"How to predict antimicrobial resistance","text":"package contains function resistance_predict(), takes input functions AMR data analysis. Based date column, calculates cases per year uses regression model predict antimicrobial resistance. basically easy : function look date column col_date set. running commands, summary regression model printed unless using resistance_predict(..., info = FALSE). text printed summary - actual result (output) function data.frame containing year: number observations, actual observed resistance, estimated resistance standard error estimation: function plot available base R, can extended packages depend output based type input. extended function cope resistance predictions:  fastest way plot result. automatically adds right axes, error bars, titles, number available observations type model. also support ggplot2 package custom function ggplot_sir_predict() create appealing plots:","code":"# resistance prediction of piperacillin/tazobactam (TZP): resistance_predict(tbl = example_isolates, col_date = \"date\", col_ab = \"TZP\", model = \"binomial\")  # or: example_isolates %>%   resistance_predict(     col_ab = \"TZP\",     model = \"binomial\"   )  # to bind it to object 'predict_TZP' for example: predict_TZP <- example_isolates %>%   resistance_predict(     col_ab = \"TZP\",     model = \"binomial\"   ) predict_TZP #> # A tibble: 32 × 7 #>     year  value se_min se_max observations observed estimated #>  * <dbl>  <dbl>  <dbl>  <dbl>        <int>    <dbl>     <dbl> #>  1  2002 0.2        NA     NA           15   0.2       0.0562 #>  2  2003 0.0625     NA     NA           32   0.0625    0.0616 #>  3  2004 0.0854     NA     NA           82   0.0854    0.0676 #>  4  2005 0.05       NA     NA           60   0.05      0.0741 #>  5  2006 0.0508     NA     NA           59   0.0508    0.0812 #>  6  2007 0.121      NA     NA           66   0.121     0.0889 #>  7  2008 0.0417     NA     NA           72   0.0417    0.0972 #>  8  2009 0.0164     NA     NA           61   0.0164    0.106  #>  9  2010 0.0566     NA     NA           53   0.0566    0.116  #> 10  2011 0.183      NA     NA           93   0.183     0.127  #> # ℹ 22 more rows plot(predict_TZP) ggplot_sir_predict(predict_TZP) # choose for error bars instead of a ribbon ggplot_sir_predict(predict_TZP, ribbon = FALSE)"},{"path":"https://msberends.github.io/AMR/articles/resistance_predict.html","id":"choosing-the-right-model","dir":"Articles","previous_headings":"Prediction analysis","what":"Choosing the right model","title":"How to predict antimicrobial resistance","text":"Resistance easily predicted; look vancomycin resistance Gram-positive bacteria, spread (.e. standard error) enormous:  Vancomycin resistance 100% ten years, might remain low. can define model model parameter. model chosen generalised linear regression model using binomial distribution, assuming period zero resistance followed period increasing resistance leading slowly resistance. Valid values : vancomycin resistance Gram-positive bacteria, linear model might appropriate:  model also available object, attribute:","code":"example_isolates %>%   filter(mo_gramstain(mo, language = NULL) == \"Gram-positive\") %>%   resistance_predict(col_ab = \"VAN\", year_min = 2010, info = FALSE, model = \"binomial\") %>%   ggplot_sir_predict() example_isolates %>%   filter(mo_gramstain(mo, language = NULL) == \"Gram-positive\") %>%   resistance_predict(col_ab = \"VAN\", year_min = 2010, info = FALSE, model = \"linear\") %>%   ggplot_sir_predict() model <- attributes(predict_TZP)$model  summary(model)$family #>  #> Family: binomial  #> Link function: logit  summary(model)$coefficients #>                  Estimate  Std. Error   z value     Pr(>|z|) #> (Intercept) -200.67944891 46.17315349 -4.346237 1.384932e-05 #> year           0.09883005  0.02295317  4.305725 1.664395e-05"},{"path":"https://msberends.github.io/AMR/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Matthijs S. Berends. Author, maintainer. Christian F. Luz. Author, contributor. Dennis Souverein. Author, contributor. Erwin E. . Hassing. Author, contributor. Casper J. Albers. Thesis advisor. Peter Dutey-Magni. Contributor. Judith M. Fonville. Contributor. Alex W. Friedrich. Thesis advisor. Corinna Glasner. Thesis advisor. Eric H. L. C. M. Hazenberg. Contributor. Gwen Knight. Contributor. Annick Lenglet. Contributor. Bart C. Meijer. Contributor. Dmytro Mykhailenko. Contributor. Anton Mymrikov. Contributor. Andrew P. Norgan. Contributor. Sofia Ny. Contributor. Jonas Salm. Contributor. Rogier P. Schade. Contributor. Bhanu N. M. Sinha. Thesis advisor. Anthony Underwood. Contributor. Anita Williams. Contributor.","code":""},{"path":"https://msberends.github.io/AMR/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). “AMR: R Package Working Antimicrobial Resistance Data.” Journal Statistical Software, 104(3), 1–31. doi:10.18637/jss.v104.i03.","code":"@Article{,   title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},   author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},   journal = {Journal of Statistical Software},   year = {2022},   volume = {104},   number = {3},   pages = {1--31},   doi = {10.18637/jss.v104.i03}, }"},{"path":"https://msberends.github.io/AMR/index.html","id":"the-amr-package-for-r-","dir":"","previous_headings":"","what":"Antimicrobial Resistance Data Analysis","title":"Antimicrobial Resistance Data Analysis","text":"Generates antibiograms - traditional, combined, syndromic, even WISCA Provides full microbiological taxonomy data antimicrobial drugs Applies recent CLSI EUCAST clinical breakpoints MICs disk zones Corrects duplicate isolates, calculates predicts AMR per antibiotic class Integrates WHONET, ATC, EARS-Net, PubChem, LOINC SNOMED CT Works Windows, macOS Linux versions R since R-3.0 completely dependency-free, highly suitable places limited resources https://msberends.github.io/AMR https://doi.org/10.18637/jss.v104.i03","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"introduction","dir":"","previous_headings":"","what":"Introduction","title":"Antimicrobial Resistance Data Analysis","text":"AMR package free open-source R package zero dependencies simplify analysis prediction Antimicrobial Resistance (AMR) work microbial antimicrobial data properties, using evidence-based methods. aim provide standard clean reproducible AMR data analysis, can therefore empower epidemiological analyses continuously enable surveillance treatment evaluation setting. Many different researchers around globe continually helping us make successful durable project! work published Journal Statistical Software (Volume 104(3); DOI 10.18637/jss.v104.i03) formed basis two PhD theses (DOI 10.33612/diss.177417131 DOI 10.33612/diss.192486375). installing package, R knows ~52,000 distinct microbial species (updated December 2022) ~600 antibiotic, antimycotic antiviral drugs name code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC SNOMED CT), knows valid SIR MIC values. integral breakpoint guidelines CLSI EUCAST included last 10 years. supports can read data format, including WHONET data. package works Windows, macOS Linux versions R since R-3.0 (April 2013). designed work setting, including limited resources. created routine data analysis academic research Faculty Medical Sciences University Groningen, collaboration non-profit organisations Certe Medical Diagnostics Advice Foundation University Medical Center Groningen.","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"used-in-over-175-countries-translated-into-20-languages","dir":"","previous_headings":"Introduction","what":"Used in over 175 countries, translated into 20 languages","title":"Antimicrobial Resistance Data Analysis","text":"Since first public release early 2018, R package used almost countries world. Click map enlarge see country names. help contributors corners world, AMR package available  English,  Czech,  Chinese,  Danish,  Dutch,  Finnish,  French,  German,  Greek,  Italian,  Japanese,  Norwegian,  Polish,  Portuguese,  Romanian,  Russian,  Spanish,  Swedish,  Turkish,  Ukrainian. Antimicrobial drug (group) names colloquial microorganism names provided languages.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/index.html","id":"filtering-and-selecting-data","dir":"","previous_headings":"Practical examples","what":"Filtering and selecting data","title":"Antimicrobial Resistance Data Analysis","text":"One powerful functions package, aside calculating plotting AMR, selecting filtering based antibiotic columns. can done using -called antibiotic class selectors work base R, dplyr data.table: defined row filter Gram-negative bacteria intrinsic resistance cefotaxime (mo_is_gram_negative() mo_is_intrinsic_resistant()) column selection two antibiotic groups (aminoglycosides() carbapenems()), reference data microorganisms antibiotics AMR package make sure get meant: base R equivalent : base R code work version R since April 2013 (R-3.0). Moreover, code works identically data.table package, starting :","code":"# AMR works great with dplyr, but it's not required or neccesary library(AMR) library(dplyr)  example_isolates %>%   mutate(bacteria = mo_fullname()) %>%   # filtering functions for microorganisms:   filter(mo_is_gram_negative(),          mo_is_intrinsic_resistant(ab = \"cefotax\")) %>%   # antibiotic selectors:   select(bacteria,          aminoglycosides(),          carbapenems()) library(AMR) example_isolates$bacteria <- mo_fullname(example_isolates$mo) example_isolates[which(mo_is_gram_negative() &                          mo_is_intrinsic_resistant(ab = \"cefotax\")),                  c(\"bacteria\", aminoglycosides(), carbapenems())] example_isolates <- data.table::as.data.table(example_isolates)"},{"path":"https://msberends.github.io/AMR/index.html","id":"generating-antibiograms","dir":"","previous_headings":"Practical examples","what":"Generating antibiograms","title":"Antimicrobial Resistance Data Analysis","text":"AMR package supports generating traditional, combined, syndromic, even weighted-incidence syndromic combination antibiograms (WISCA). used inside R Markdown Quarto, table printed right output format automatically (markdown, LaTeX, HTML, etc.). combination antibiograms, clear combined antibiotics yield higher empiric coverage: Like many functions package, antibiogram() comes support 20 languages often detected automatically based system language:","code":"antibiogram(example_isolates,             antibiotics = c(aminoglycosides(), carbapenems())) antibiogram(example_isolates,             antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"),             mo_transform = \"gramstain\") antibiogram(example_isolates,             antibiotics = c(\"cipro\", \"tobra\", \"genta\"), # any arbitrary name or code will work             mo_transform = \"gramstain\",             ab_transform = \"name\",             language = \"uk\") # Ukrainian"},{"path":"https://msberends.github.io/AMR/index.html","id":"calculating-resistance-per-group","dir":"","previous_headings":"Practical examples","what":"Calculating resistance per group","title":"Antimicrobial Resistance Data Analysis","text":"manual approach, can use resistance susceptibility() function: use antibiotic class selectors select series antibiotic columns:","code":"example_isolates %>%   # group by ward:   group_by(ward) %>%   # calculate AMR using resistance() for gentamicin and tobramycin   # and get their 95% confidence intervals using sir_confidence_interval():   summarise(across(c(GEN, TOB),                    list(total_R = resistance,                         conf_int = function(x) sir_confidence_interval(x, collapse = \"-\")))) library(AMR) library(dplyr)  out <- example_isolates %>%   # group by ward:   group_by(ward) %>%   # calculate AMR using resistance(), over all aminoglycosides and polymyxins:   summarise(across(c(aminoglycosides(), polymyxins()),             resistance)) out # transform the antibiotic columns to names: out %>% set_ab_names() # transform the antibiotic column to ATC codes: out %>% set_ab_names(property = \"atc\")"},{"path":"https://msberends.github.io/AMR/index.html","id":"what-else-can-you-do-with-this-package","dir":"","previous_headings":"","what":"What else can you do with this package?","title":"Antimicrobial Resistance Data Analysis","text":"package intended comprehensive toolbox integrated AMR data analysis. package can used : Reference taxonomy microorganisms, since package contains microbial (sub)species List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF) (manual) Interpreting raw MIC disk diffusion values, based CLSI EUCAST guideline last 10 years (manual) Retrieving antimicrobial drug names, doses forms administration clinical health care records (manual) Determining first isolates used AMR data analysis (manual) Calculating antimicrobial resistance (tutorial) Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (tutorial) Calculating (empirical) susceptibility mono therapy combination therapies (tutorial) Predicting future antimicrobial resistance using regression models (tutorial) Getting properties microorganism (like Gram stain, species, genus family) (manual) Getting properties antibiotic (like name, code EARS-Net/ATC/LOINC/PubChem, defined daily dose trade name) (manual) Plotting antimicrobial resistance (tutorial) Applying EUCAST expert rules (manual) Getting SNOMED codes microorganism, getting properties microorganism based SNOMED code (manual) Getting LOINC codes antibiotic, getting properties antibiotic based LOINC code (manual) Machine reading EUCAST CLSI guidelines 2011-2021 translate MIC values disk diffusion diameters SIR (link) Principal component analysis AMR (tutorial)","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/index.html","id":"latest-official-version","dir":"","previous_headings":"Get this package","what":"Latest official version","title":"Antimicrobial Resistance Data Analysis","text":"package available official R network (CRAN). Install package R CRAN using command: downloaded installed automatically. RStudio, click menu Tools > Install Packages… type “AMR” press Install. Note: functions website may available latest release. use functions data sets mentioned website, install latest development version.","code":"install.packages(\"AMR\")"},{"path":"https://msberends.github.io/AMR/index.html","id":"latest-development-version","dir":"","previous_headings":"Get this package","what":"Latest development version","title":"Antimicrobial Resistance Data Analysis","text":"Please read Developer Guideline . latest unpublished development version can installed GitHub two ways: Manually, using: Automatically, using rOpenSci R-universe platform, adding R-universe address list repositories (‘repos’): , can install update AMR package like official release (e.g., using install.packages(\"AMR\") RStudio via Tools > Check Package Updates…).","code":"install.packages(\"remotes\") # if you haven't already remotes::install_github(\"msberends/AMR\") options(repos = c(getOption(\"repos\"),                   msberends = \"https://msberends.r-universe.dev\"))"},{"path":"https://msberends.github.io/AMR/index.html","id":"get-started","dir":"","previous_headings":"","what":"Get started","title":"Antimicrobial Resistance Data Analysis","text":"find conduct AMR data analysis, please continue reading get started click link ‘’ menu.","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"partners","dir":"","previous_headings":"","what":"Partners","title":"Antimicrobial Resistance Data Analysis","text":"development package part , related , made possible following non-profit organisations initiatives:","code":""},{"path":"https://msberends.github.io/AMR/index.html","id":"copyright","dir":"","previous_headings":"","what":"Copyright","title":"Antimicrobial Resistance Data Analysis","text":"R package free, open-source software licensed GNU General Public License v2.0 (GPL-2). nutshell, means package: May used commercial purposes May used private purposes May used patent purposes May modified, although: Modifications must released license distributing package Changes made code must documented May distributed, although: Source code must made available package distributed copy license copyright notice must included package. Comes LIMITATION liability Comes warranty","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-deprecated.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated Functions — AMR-deprecated","title":"Deprecated Functions — AMR-deprecated","text":"functions -called 'Deprecated'. removed future release. Using functions give warning name function replaced (one).","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-deprecated.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated Functions — AMR-deprecated","text":"","code":"NA_rsi_  as.rsi(x, ...)  facet_rsi(...)  geom_rsi(...)  ggplot_rsi(...)  ggplot_rsi_predict(...)  is.rsi(...)  is.rsi.eligible(...)  labels_rsi_count(...)  n_rsi(...)  random_rsi(...)  rsi_df(...)  rsi_predict(...)  scale_rsi_colours(...)  theme_rsi(...)"},{"path":"https://msberends.github.io/AMR/reference/AMR-deprecated.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Deprecated Functions — AMR-deprecated","text":"object class rsi (inherits ordered, factor) length 1.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":null,"dir":"Reference","previous_headings":"","what":"Options for the AMR package — AMR-options","title":"Options for the AMR package — AMR-options","text":"overview package-specific options() can set AMR package.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"options","dir":"Reference","previous_headings":"","what":"Options","title":"Options for the AMR package — AMR-options","text":"AMR_custom_ab  Allows use custom antimicrobial drugs package. explained add_custom_antimicrobials(). AMR_custom_mo  Allows use custom microorganisms package. explained add_custom_microorganisms(). AMR_eucastrules  Used setting default types rules eucast_rules() function, must one : \"breakpoints\", \"expert\", \"\", \"custom\", \"\", defaults c(\"breakpoints\", \"expert\"). AMR_guideline  Used setting default guideline interpreting MIC values disk diffusion diameters .sir(). Can guideline name (e.g., \"CLSI\") name year (e.g. \"CLSI 2019\"). default latest implemented EUCAST guideline, currently \"EUCAST 2022\". Supported guideline currently EUCAST (2013-2022) CLSI (2013-2022). AMR_ignore_pattern  regular expression ignore (.e., make NA) match given .mo() mo_* functions. AMR_include_PKPD  logical use .sir(), indicate PK/PD clinical breakpoints must applied last resort - default TRUE. AMR_include_screening  logical use .sir(), indicate clinical breakpoints screening allowed - default FALSE. AMR_keep_synonyms  logical use .mo() mo_* functions, indicate old, previously valid taxonomic names must preserved corrected currently accepted names. default FALSE. AMR_cleaning_regex  regular expression (case-insensitive) use .mo() mo_* functions, clean user input. default outcome mo_cleaning_regex(), removes texts brackets texts \"species\" \"serovar\". AMR_locale  language use AMR package, can one supported language names ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), Ukrainian (uk). default current system language (supported). AMR_mo_source  file location manual code list used .mo() mo_* functions. explained set_mo_source().","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"saving-settings-between-sessions","dir":"Reference","previous_headings":"","what":"Saving Settings Between Sessions","title":"Options for the AMR package — AMR-options","text":"Settings R saved globally thus lost R exited. can save options .Rprofile file, user-specific file. can edit using:   file, can set options :   add Portuguese language support antibiotics, allow PK/PD rules interpreting MIC values .sir().","code":"utils::file.edit(\"~/.Rprofile\") options(AMR_locale = \"pt\")  options(AMR_include_PKPD = TRUE)"},{"path":"https://msberends.github.io/AMR/reference/AMR-options.html","id":"share-options-within-team","dir":"Reference","previous_headings":"","what":"Share Options Within Team","title":"Options for the AMR package — AMR-options","text":"global approach, e.g. within data team, save options file remote file location, shared network drive. work way: Save plain text file e.g. \"X:/team_folder/R_options.R\" fill preferred settings. user, open .Rprofile file using utils::file.edit(\"~/.Rprofile\") put :   Reload R/RStudio check settings getOption(), e.g. getOption(\"AMR_locale\") set value. Now team settings configured one place, can maintained .","code":"source(\"X:/team_folder/R_options.R\")"},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":null,"dir":"Reference","previous_headings":"","what":"The AMR Package — AMR","title":"The AMR Package — AMR","text":"Welcome AMR package. AMR package free open-source R package zero dependencies simplify analysis prediction Antimicrobial Resistance (AMR) work microbial antimicrobial data properties, using evidence-based methods. aim provide standard clean reproducible AMR data analysis, can therefore empower epidemiological analyses continuously enable surveillance treatment evaluation setting. Many different researchers around globe continually helping us make successful durable project! work published Journal Statistical Software (Volume 104(3); doi:jss.v104.i03 ) formed basis two PhD theses (doi:10.33612/diss.177417131  doi:10.33612/diss.192486375 ). installing package, R knows ~52 000 microorganisms (updated December 2022) ~600 antibiotic, antimycotic antiviral drugs name code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC SNOMED CT), knows valid SIR MIC values. integral breakpoint guidelines CLSI EUCAST included last 10 years. supports can read data format, including WHONET data. package works Windows, macOS Linux versions R since R-3.0 (April 2013). designed work setting, including limited resources. created routine data analysis academic research Faculty Medical Sciences University Groningen, collaboration non-profit organisations Certe Medical Diagnostics Advice Foundation University Medical Center Groningen. AMR package available English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, Ukrainian. Antimicrobial drug (group) names colloquial microorganism names provided languages.","code":""},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"The AMR Package — AMR","text":"cite AMR publications use: Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). \"AMR: R Package Working Antimicrobial Resistance Data.\" Journal Statistical Software, 104(3), 1-31. doi:10.18637/jss.v104.i03 . BibTeX entry LaTeX users :","code":"@Article{,   title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},   author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},   journal = {Journal of Statistical Software},   year = {2022},   volume = {104},   number = {3},   pages = {1--31},   doi = {10.18637/jss.v104.i03}, }"},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"The AMR Package — AMR","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/AMR.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"The AMR Package — AMR","text":"Maintainer: Matthijs S. Berends m.berends@certe.nl (ORCID) Authors: Christian F. Luz (ORCID) [contributor] Dennis Souverein (ORCID) [contributor] Erwin E. . Hassing [contributor] contributors: Casper J. Albers (ORCID) [thesis advisor] Peter Dutey-Magni (ORCID) [contributor] Judith M. Fonville [contributor] Alex W. Friedrich (ORCID) [thesis advisor] Corinna Glasner (ORCID) [thesis advisor] Eric H. L. C. M. Hazenberg [contributor] Gwen Knight (ORCID) [contributor] Annick Lenglet (ORCID) [contributor] Bart C. Meijer [contributor] Dmytro Mykhailenko [contributor] Anton Mymrikov [contributor] Andrew P. Norgan (ORCID) [contributor] Sofia Ny (ORCID) [contributor] Jonas Salm [contributor] Rogier P. Schade [contributor] Bhanu N. M. Sinha (ORCID) [thesis advisor] Anthony Underwood (ORCID) [contributor] Anita Williams (ORCID) [contributor]","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":null,"dir":"Reference","previous_headings":"","what":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"antimicrobial drugs official names, ATC codes, ATC groups defined daily dose (DDD) included package, using Collaborating Centre Drug Statistics Methodology.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHOCC.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"WHOCC: WHO Collaborating Centre for Drug Statistics Methodology — WHOCC","text":"","code":"as.ab(\"meropenem\") #> Class 'ab' #> [1] MEM ab_name(\"J01DH02\") #> [1] \"Meropenem\"  ab_tradenames(\"flucloxacillin\") #>  [1] \"culpen\"               \"floxacillin\"          \"floxacillin sodium\"   #>  [4] \"floxapen\"             \"floxapen sodium salt\" \"fluclox\"              #>  [7] \"flucloxacilina\"       \"flucloxacillin\"       \"flucloxacilline\"      #> [10] \"flucloxacillinum\"     \"fluorochloroxacillin\" \"staphylex\""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 500 Isolates - WHONET Example — WHONET","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"example data set exact structure export file WHONET. files can used package, example data set shows. antibiotic results example_isolates data set. patient names created using online surname generators place practice purposes.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"","code":"WHONET"},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"tibble 500 observations 53 variables: Identification number ID sample Specimen number ID specimen Organism Name microorganism. analysis, transform valid microbial class, using .mo(). Country Country origin Laboratory Name laboratory Last name Fictitious last name patient First name Fictitious initial patient Sex Fictitious gender patient Age Fictitious age patient Age category Age group, can also looked using age_groups() Date admissionDate hospital admission Specimen dateDate specimen received laboratory Specimen type Specimen type group Specimen type (Numeric) Translation \"Specimen type\" Reason Reason request Differential Diagnosis Isolate number ID isolate Organism type Type microorganism, can also looked using mo_type() Serotype Serotype microorganism Beta-lactamase Microorganism produces beta-lactamase? ESBL Microorganism produces extended spectrum beta-lactamase? Carbapenemase Microorganism produces carbapenemase? MRSA screening test Microorganism possible MRSA? Inducible clindamycin resistance Clindamycin can induced? Comment comments Date data entryDate data entered WHONET AMP_ND10:CIP_EE 28 different antibiotics. can lookup abbreviations antibiotics data set, use e.g. ab_name(\"AMP\") get official name immediately. analysis, transform valid antibiotic class, using .sir().","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/WHONET.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 500 Isolates - WHONET Example — WHONET","text":"","code":"WHONET #> # A tibble: 500 × 53 #>    `Identification number` `Specimen number` Organism Country         Laboratory #>    <chr>                               <int> <chr>    <chr>           <chr>      #>  1 fe41d7bafa                           1748 SPN      Belgium         National … #>  2 91f175ec37                           1767 eco      The Netherlands National … #>  3 cc4015056e                           1343 eco      The Netherlands National … #>  4 e864b692f5                           1894 MAP      Denmark         National … #>  5 3d051fe345                           1739 PVU      Belgium         National … #>  6 c80762a08d                           1846 103      The Netherlands National … #>  7 8022d3727c                           1628 103      Denmark         National … #>  8 f3dc5f553d                           1493 eco      The Netherlands National … #>  9 15add38f6c                           1847 eco      France          National … #> 10 fd41248def                           1458 eco      Germany         National … #> # ℹ 490 more rows #> # ℹ 48 more variables: `Last name` <chr>, `First name` <chr>, Sex <chr>, #> #   Age <dbl>, `Age category` <chr>, `Date of admission` <date>, #> #   `Specimen date` <date>, `Specimen type` <chr>, #> #   `Specimen type (Numeric)` <dbl>, Reason <chr>, `Isolate number` <int>, #> #   `Organism type` <chr>, Serotype <chr>, `Beta-lactamase` <lgl>, ESBL <lgl>, #> #   Carbapenemase <lgl>, `MRSA screening test` <lgl>, …"},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"Use function e.g. clinical texts health care records. returns list antimicrobial drugs, doses forms administration found texts.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"","code":"ab_from_text(   text,   type = c(\"drug\", \"dose\", \"administration\"),   collapse = NULL,   translate_ab = FALSE,   thorough_search = NULL,   info = interactive(),   ... )"},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"text text analyse type type property search , either \"drug\", \"dose\" \"administration\", see Examples collapse character pass paste(, collapse = ...) return one character per element text, see Examples translate_ab type = \"drug\": column name antibiotics data set translate antibiotic abbreviations , using ab_property(). default FALSE. Using TRUE equal using \"name\". thorough_search logical indicate whether input must extensively searched misspelling faulty input values. Setting TRUE take considerably time using FALSE. default, turn TRUE input elements contain maximum three words. info logical indicate whether progress bar printed - default TRUE interactive mode ... arguments passed .ab()","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"list,  character collapse NULL","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"function also internally used .ab(), although searches first drug name throw note drug names returned. Note: .ab() function may use long regular expression match brand names antimicrobial drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"argument-type","dir":"Reference","previous_headings":"","what":"Argument type","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"default, function search antimicrobial drug names. text elements searched official names, ATC codes brand names. uses .ab() internally, correct misspelling. type = \"dose\" (similar, like \"dosing\", \"doses\"), text elements searched numeric values higher 100 resemble years. output numeric. supports unit (g, mg, IE, etc.) multiple values one clinical text, see Examples. type = \"administration\" (abbreviations, like \"admin\", \"adm\"), text elements searched form drug administration. supports following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal vaginal. Abbreviations oral ('po', 'per os') become \"oral\", values intravenous ('iv', 'intraven') become \"iv\". supports multiple values one clinical text, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"argument-collapse","dir":"Reference","previous_headings":"","what":"Argument collapse","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"Without using collapse, function return list. can convenient use e.g. inside mutate()):df %>% mutate(abx = ab_from_text(clinical_text)) returned AB codes can transformed official names, groups, etc. ab_* functions ab_name() ab_group(), using translate_ab argument. using collapse, function return character:df %>% mutate(abx = ab_from_text(clinical_text, collapse = \"|\"))","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_from_text.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve Antimicrobial Drug Names and Doses from Clinical Text — ab_from_text","text":"","code":"# mind the bad spelling of amoxicillin in this line, # straight from a true health care record: ab_from_text(\"28/03/2020 regular amoxicilliin 500mg po tid\") #> [[1]] #> Class 'ab' #> [1] AMX #>   ab_from_text(\"500 mg amoxi po and 400mg cipro iv\") #> [[1]] #> Class 'ab' #> [1] AMX CIP #>  ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", type = \"dose\") #> [[1]] #> [1] 500 400 #>  ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", type = \"admin\") #> [[1]] #> [1] \"oral\" \"iv\"   #>   ab_from_text(\"500 mg amoxi po and 400mg cipro iv\", collapse = \", \") #> [1] \"AMX, CIP\" # \\donttest{ # if you want to know which antibiotic groups were administered, do e.g.: abx <- ab_from_text(\"500 mg amoxi po and 400mg cipro iv\") ab_group(abx[[1]]) #> [1] \"Beta-lactams/penicillins\" \"Quinolones\"                if (require(\"dplyr\")) {   tibble(clinical_text = c(     \"given 400mg cipro and 500 mg amox\",     \"started on doxy iv today\"   )) %>%     mutate(       abx_codes = ab_from_text(clinical_text),       abx_doses = ab_from_text(clinical_text, type = \"doses\"),       abx_admin = ab_from_text(clinical_text, type = \"admin\"),       abx_coll = ab_from_text(clinical_text, collapse = \"|\"),       abx_coll_names = ab_from_text(clinical_text,         collapse = \"|\",         translate_ab = \"name\"       ),       abx_coll_doses = ab_from_text(clinical_text,         type = \"doses\",         collapse = \"|\"       ),       abx_coll_admin = ab_from_text(clinical_text,         type = \"admin\",         collapse = \"|\"       )     ) } #> Loading required package: dplyr #>  #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union #> # A tibble: 2 × 8 #>   clinical_text            abx_codes abx_doses abx_admin abx_coll abx_coll_names #>   <chr>                    <list>    <list>    <list>    <chr>    <chr>          #> 1 given 400mg cipro and 5… <ab [2]>  <dbl [2]> <chr [1]> CIP|AMX  Ciprofloxacin… #> 2 started on doxy iv today <ab [1]>  <dbl [1]> <chr [1]> DOX      Doxycycline    #> # ℹ 2 more variables: abx_coll_doses <chr>, abx_coll_admin <chr> # }"},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Properties of an Antibiotic — ab_property","title":"Get Properties of an Antibiotic — ab_property","text":"Use functions return specific property antibiotic antibiotics data set. input values evaluated internally .ab().","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Properties of an Antibiotic — ab_property","text":"","code":"ab_name(x, language = get_AMR_locale(), tolower = FALSE, ...)  ab_cid(x, ...)  ab_synonyms(x, ...)  ab_tradenames(x, ...)  ab_group(x, language = get_AMR_locale(), ...)  ab_atc(x, only_first = FALSE, ...)  ab_atc_group1(x, language = get_AMR_locale(), ...)  ab_atc_group2(x, language = get_AMR_locale(), ...)  ab_loinc(x, ...)  ab_ddd(x, administration = \"oral\", ...)  ab_ddd_units(x, administration = \"oral\", ...)  ab_info(x, language = get_AMR_locale(), ...)  ab_url(x, open = FALSE, ...)  ab_property(x, property = \"name\", language = get_AMR_locale(), ...)  set_ab_names(   data,   ...,   property = \"name\",   language = get_AMR_locale(),   snake_case = NULL )"},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Properties of an Antibiotic — ab_property","text":"x (vector ) text can coerced valid antibiotic drug code .ab() language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. tolower logical indicate whether first character every output transformed lower case character. lead e.g. \"polymyxin B\" \"polymyxin b\". ... case set_ab_names() data data.frame: columns select (supports tidy selection column1:column4), otherwise arguments passed .ab() only_first logical indicate whether first ATC code must returned, giving preference J0-codes (.e., antimicrobial drug group) administration way administration, either \"oral\" \"iv\" open browse URL using utils::browseURL() property one column names one antibiotics data set: vector_or(colnames(antibiotics), sort = FALSE). data data.frame columns need renamed, character vector column names snake_case logical indicate whether names -called snake case: lower case spaces/slashes replaced underscore (_)","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Properties of an Antibiotic — ab_property","text":"integer case ab_cid() named list case ab_info() multiple ab_atc()/ab_synonyms()/ab_tradenames() double case ab_ddd() data.frame case set_ab_names() character cases","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Properties of an Antibiotic — ab_property","text":"output translated possible. function ab_url() return direct URL official website. warning returned required ATC code available. function set_ab_names() special column renaming function data.frames. renames columns names resemble antimicrobial drugs. always makes sure new column names unique. property = \"atc\" set, preference given ATC codes J-group.","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Properties of an Antibiotic — ab_property","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Get Properties of an Antibiotic — ab_property","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/ab_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Properties of an Antibiotic — ab_property","text":"","code":"# all properties: ab_name(\"AMX\") #> [1] \"Amoxicillin\" ab_atc(\"AMX\") #> [1] \"J01CA04\" ab_cid(\"AMX\") #> [1] 33613 ab_synonyms(\"AMX\") #>  [1] \"actimoxi\"            \"amoclen\"             \"amolin\"              #>  [4] \"amopen\"              \"amopenixin\"          \"amoxibiotic\"         #>  [7] \"amoxicaps\"           \"amoxicilina\"         \"amoxicillin\"         #> [10] \"amoxicillin hydrate\" \"amoxicilline\"        \"amoxicillinum\"       #> [13] \"amoxiden\"            \"amoxil\"              \"amoxivet\"            #> [16] \"amoxy\"               \"amoxycillin\"         \"amoxyke\"             #> [19] \"anemolin\"            \"aspenil\"             \"atoksilin\"           #> [22] \"biomox\"              \"bristamox\"           \"cemoxin\"             #> [25] \"clamoxyl\"            \"damoxy\"              \"delacillin\"          #> [28] \"demoksil\"            \"dispermox\"           \"efpenix\"             #> [31] \"flemoxin\"            \"hiconcil\"            \"histocillin\"         #> [34] \"hydroxyampicillin\"   \"ibiamox\"             \"imacillin\"           #> [37] \"lamoxy\"              \"largopen\"            \"metafarma capsules\"  #> [40] \"metifarma capsules\"  \"moksilin\"            \"moxacin\"             #> [43] \"moxatag\"             \"ospamox\"             \"pamoxicillin\"        #> [46] \"piramox\"             \"promoxil\"            \"remoxil\"             #> [49] \"robamox\"             \"sawamox pm\"          \"tolodina\"            #> [52] \"topramoxin\"          \"unicillin\"           \"utimox\"              #> [55] \"vetramox\"            ab_tradenames(\"AMX\") #>  [1] \"actimoxi\"            \"amoclen\"             \"amolin\"              #>  [4] \"amopen\"              \"amopenixin\"          \"amoxibiotic\"         #>  [7] \"amoxicaps\"           \"amoxicilina\"         \"amoxicillin\"         #> [10] \"amoxicillin hydrate\" \"amoxicilline\"        \"amoxicillinum\"       #> [13] \"amoxiden\"            \"amoxil\"              \"amoxivet\"            #> [16] \"amoxy\"               \"amoxycillin\"         \"amoxyke\"             #> [19] \"anemolin\"            \"aspenil\"             \"atoksilin\"           #> [22] \"biomox\"              \"bristamox\"           \"cemoxin\"             #> [25] \"clamoxyl\"            \"damoxy\"              \"delacillin\"          #> [28] \"demoksil\"            \"dispermox\"           \"efpenix\"             #> [31] \"flemoxin\"            \"hiconcil\"            \"histocillin\"         #> [34] \"hydroxyampicillin\"   \"ibiamox\"             \"imacillin\"           #> [37] \"lamoxy\"              \"largopen\"            \"metafarma capsules\"  #> [40] \"metifarma capsules\"  \"moksilin\"            \"moxacin\"             #> [43] \"moxatag\"             \"ospamox\"             \"pamoxicillin\"        #> [46] \"piramox\"             \"promoxil\"            \"remoxil\"             #> [49] \"robamox\"             \"sawamox pm\"          \"tolodina\"            #> [52] \"topramoxin\"          \"unicillin\"           \"utimox\"              #> [55] \"vetramox\"            ab_group(\"AMX\") #> [1] \"Beta-lactams/penicillins\" ab_atc_group1(\"AMX\") #> [1] \"Beta-lactam antibacterials, penicillins\" ab_atc_group2(\"AMX\") #> [1] \"Penicillins with extended spectrum\" ab_url(\"AMX\") #>                                                           Amoxicillin  #> \"https://www.whocc.no/atc_ddd_index/?code=J01CA04&showdescription=no\"   # smart lowercase tranformation ab_name(x = c(\"AMC\", \"PLB\")) #> [1] \"Amoxicillin/clavulanic acid\" \"Polymyxin B\"                 ab_name(x = c(\"AMC\", \"PLB\"), tolower = TRUE) #> [1] \"amoxicillin/clavulanic acid\" \"polymyxin B\"                  # defined daily doses (DDD) ab_ddd(\"AMX\", \"oral\") #> [1] 1.5 ab_ddd_units(\"AMX\", \"oral\") #> [1] \"g\" ab_ddd(\"AMX\", \"iv\") #> [1] 3 ab_ddd_units(\"AMX\", \"iv\") #> [1] \"g\"  ab_info(\"AMX\") # all properties as a list #> $ab #> [1] \"AMX\" #>  #> $cid #> [1] 33613 #>  #> $name #> [1] \"Amoxicillin\" #>  #> $group #> [1] \"Beta-lactams/penicillins\" #>  #> $atc #> [1] \"J01CA04\" #>  #> $atc_group1 #> [1] \"Beta-lactam antibacterials, penicillins\" #>  #> $atc_group2 #> [1] \"Penicillins with extended spectrum\" #>  #> $tradenames #>  [1] \"actimoxi\"            \"amoclen\"             \"amolin\"              #>  [4] \"amopen\"              \"amopenixin\"          \"amoxibiotic\"         #>  [7] \"amoxicaps\"           \"amoxicilina\"         \"amoxicillin\"         #> [10] \"amoxicillin hydrate\" \"amoxicilline\"        \"amoxicillinum\"       #> [13] \"amoxiden\"            \"amoxil\"              \"amoxivet\"            #> [16] \"amoxy\"               \"amoxycillin\"         \"amoxyke\"             #> [19] \"anemolin\"            \"aspenil\"             \"atoksilin\"           #> [22] \"biomox\"              \"bristamox\"           \"cemoxin\"             #> [25] \"clamoxyl\"            \"damoxy\"              \"delacillin\"          #> [28] \"demoksil\"            \"dispermox\"           \"efpenix\"             #> [31] \"flemoxin\"            \"hiconcil\"            \"histocillin\"         #> [34] \"hydroxyampicillin\"   \"ibiamox\"             \"imacillin\"           #> [37] \"lamoxy\"              \"largopen\"            \"metafarma capsules\"  #> [40] \"metifarma capsules\"  \"moksilin\"            \"moxacin\"             #> [43] \"moxatag\"             \"ospamox\"             \"pamoxicillin\"        #> [46] \"piramox\"             \"promoxil\"            \"remoxil\"             #> [49] \"robamox\"             \"sawamox pm\"          \"tolodina\"            #> [52] \"topramoxin\"          \"unicillin\"           \"utimox\"              #> [55] \"vetramox\"            #>  #> $loinc #> [1] \"16365-9\" \"25274-2\" \"3344-9\"  \"80133-2\" #>  #> $ddd #> $ddd$oral #> $ddd$oral$amount #> [1] 1.5 #>  #> $ddd$oral$units #> [1] \"g\" #>  #>  #> $ddd$iv #> $ddd$iv$amount #> [1] 3 #>  #> $ddd$iv$units #> [1] \"g\" #>  #>  #>   # all ab_* functions use as.ab() internally, so you can go from 'any' to 'any': ab_atc(\"AMP\") #> [1] \"J01CA01\" \"S01AA19\" ab_group(\"J01CA01\") #> [1] \"Beta-lactams/penicillins\" ab_loinc(\"ampicillin\") #> [1] \"21066-6\" \"3355-5\"  \"33562-0\" \"33919-2\" \"43883-8\" \"43884-6\" \"87604-5\" ab_name(\"21066-6\") #> [1] \"Ampicillin\" ab_name(6249) #> [1] \"Ampicillin\" ab_name(\"J01CA01\") #> [1] \"Ampicillin\"  # spelling from different languages and dyslexia are no problem ab_atc(\"ceftriaxon\") #> [1] \"J01DD04\" ab_atc(\"cephtriaxone\") #> [1] \"J01DD04\" ab_atc(\"cephthriaxone\") #> [1] \"J01DD04\" ab_atc(\"seephthriaaksone\") #> [1] \"J01DD04\"  # use set_ab_names() for renaming columns colnames(example_isolates) #>  [1] \"date\"    \"patient\" \"age\"     \"gender\"  \"ward\"    \"mo\"      \"PEN\"     #>  [8] \"OXA\"     \"FLC\"     \"AMX\"     \"AMC\"     \"AMP\"     \"TZP\"     \"CZO\"     #> [15] \"FEP\"     \"CXM\"     \"FOX\"     \"CTX\"     \"CAZ\"     \"CRO\"     \"GEN\"     #> [22] \"TOB\"     \"AMK\"     \"KAN\"     \"TMP\"     \"SXT\"     \"NIT\"     \"FOS\"     #> [29] \"LNZ\"     \"CIP\"     \"MFX\"     \"VAN\"     \"TEC\"     \"TCY\"     \"TGC\"     #> [36] \"DOX\"     \"ERY\"     \"CLI\"     \"AZM\"     \"IPM\"     \"MEM\"     \"MTR\"     #> [43] \"CHL\"     \"COL\"     \"MUP\"     \"RIF\"     colnames(set_ab_names(example_isolates)) #>  [1] \"date\"                          \"patient\"                       #>  [3] \"age\"                           \"gender\"                        #>  [5] \"ward\"                          \"mo\"                            #>  [7] \"benzylpenicillin\"              \"oxacillin\"                     #>  [9] \"flucloxacillin\"                \"amoxicillin\"                   #> [11] \"amoxicillin_clavulanic_acid\"   \"ampicillin\"                    #> [13] \"piperacillin_tazobactam\"       \"cefazolin\"                     #> [15] \"cefepime\"                      \"cefuroxime\"                    #> [17] \"cefoxitin\"                     \"cefotaxime\"                    #> [19] \"ceftazidime\"                   \"ceftriaxone\"                   #> [21] \"gentamicin\"                    \"tobramycin\"                    #> [23] \"amikacin\"                      \"kanamycin\"                     #> [25] \"trimethoprim\"                  \"trimethoprim_sulfamethoxazole\" #> [27] \"nitrofurantoin\"                \"fosfomycin\"                    #> [29] \"linezolid\"                     \"ciprofloxacin\"                 #> [31] \"moxifloxacin\"                  \"vancomycin\"                    #> [33] \"teicoplanin\"                   \"tetracycline\"                  #> [35] \"tigecycline\"                   \"doxycycline\"                   #> [37] \"erythromycin\"                  \"clindamycin\"                   #> [39] \"azithromycin\"                  \"imipenem\"                      #> [41] \"meropenem\"                     \"metronidazole\"                 #> [43] \"chloramphenicol\"               \"colistin\"                      #> [45] \"mupirocin\"                     \"rifampicin\"                    colnames(set_ab_names(example_isolates, NIT:VAN)) #>  [1] \"date\"           \"patient\"        \"age\"            \"gender\"         #>  [5] \"ward\"           \"mo\"             \"PEN\"            \"OXA\"            #>  [9] \"FLC\"            \"AMX\"            \"AMC\"            \"AMP\"            #> [13] \"TZP\"            \"CZO\"            \"FEP\"            \"CXM\"            #> [17] \"FOX\"            \"CTX\"            \"CAZ\"            \"CRO\"            #> [21] \"GEN\"            \"TOB\"            \"AMK\"            \"KAN\"            #> [25] \"TMP\"            \"SXT\"            \"nitrofurantoin\" \"fosfomycin\"     #> [29] \"linezolid\"      \"ciprofloxacin\"  \"moxifloxacin\"   \"vancomycin\"     #> [33] \"TEC\"            \"TCY\"            \"TGC\"            \"DOX\"            #> [37] \"ERY\"            \"CLI\"            \"AZM\"            \"IPM\"            #> [41] \"MEM\"            \"MTR\"            \"CHL\"            \"COL\"            #> [45] \"MUP\"            \"RIF\"            # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     set_ab_names()    # this does the same:   example_isolates %>%     rename_with(set_ab_names)    # set_ab_names() works with any AB property:   example_isolates %>%     set_ab_names(property = \"atc\")    example_isolates %>%     set_ab_names(where(is.sir)) %>%     colnames()    example_isolates %>%     set_ab_names(NIT:VAN) %>%     colnames() } #>  [1] \"date\"           \"patient\"        \"age\"            \"gender\"         #>  [5] \"ward\"           \"mo\"             \"PEN\"            \"OXA\"            #>  [9] \"FLC\"            \"AMX\"            \"AMC\"            \"AMP\"            #> [13] \"TZP\"            \"CZO\"            \"FEP\"            \"CXM\"            #> [17] \"FOX\"            \"CTX\"            \"CAZ\"            \"CRO\"            #> [21] \"GEN\"            \"TOB\"            \"AMK\"            \"KAN\"            #> [25] \"TMP\"            \"SXT\"            \"nitrofurantoin\" \"fosfomycin\"     #> [29] \"linezolid\"      \"ciprofloxacin\"  \"moxifloxacin\"   \"vancomycin\"     #> [33] \"TEC\"            \"TCY\"            \"TGC\"            \"DOX\"            #> [37] \"ERY\"            \"CLI\"            \"AZM\"            \"IPM\"            #> [41] \"MEM\"            \"MTR\"            \"CHL\"            \"COL\"            #> [45] \"MUP\"            \"RIF\"            # }"},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Custom Antimicrobials — add_custom_antimicrobials","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"add_custom_antimicrobials() can add custom antimicrobial drug names codes.","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"","code":"add_custom_antimicrobials(x)  clear_custom_antimicrobials()"},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"x data.frame resembling antibiotics data set, least containing columns \"ab\" \"name\"","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"Important: Due R works, add_custom_antimicrobials() function run every R session - added antimicrobials stored sessions thus lost R exited. two ways circumvent automate process adding antimicrobials: Method 1: Using package option AMR_custom_ab, preferred method. use method: Create data set structure antibiotics data set (containing least columns \"ab\" \"name\") save saveRDS() location choice, e.g. \"~/my_custom_ab.rds\", remote location. Set file location package option AMR_custom_ab: options(AMR_custom_ab = \"~/my_custom_ab.rds\"). can even remote file location, https URL. Since options saved R sessions, best save option .Rprofile file loaded start-R. , open .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"), add text save file:   Upon package load, file loaded run add_custom_antimicrobials() function. Method 2: Loading antimicrobial additions directly .Rprofile file. Note definitions stored user-specific R file, suboptimal workflow. use method: Edit .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"). Add text like save file:   Use clear_custom_antimicrobials() clear previously added antimicrobials.","code":"# Add custom antimicrobial codes: options(AMR_custom_ab = \"~/my_custom_ab.rds\") # Add custom antibiotic drug codes:  AMR::add_custom_antimicrobials(    data.frame(ab = \"TESTAB\",               name = \"Test Antibiotic\",               group = \"Test Group\")  )"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/add_custom_antimicrobials.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Custom Antimicrobials — add_custom_antimicrobials","text":"","code":"# \\donttest{  # returns NA and throws a warning (which is suppressed here): suppressWarnings(   as.ab(\"testab\") ) #> Class 'ab' #> [1] <NA>  # now add a custom entry - it will be considered by as.ab() and # all ab_*() functions add_custom_antimicrobials(   data.frame(     ab = \"TESTAB\",     name = \"Test Antibiotic\",     # you can add any property present in the     # 'antibiotics' data set, such as 'group':     group = \"Test Group\"   ) ) #> ℹ Added one record to the internal antibiotics data set.  # \"testab\" is now a new antibiotic: as.ab(\"testab\") #> Class 'ab' #> [1] TESTAB ab_name(\"testab\") #> [1] \"Test Antibiotic\" ab_group(\"testab\") #> [1] \"Test Group\"  ab_info(\"testab\") #> $ab #> [1] \"TESTAB\" #>  #> $cid #> [1] NA #>  #> $name #> [1] \"Test Antibiotic\" #>  #> $group #> [1] \"Test Group\" #>  #> $atc #> [1] NA #>  #> $atc_group1 #> [1] NA #>  #> $atc_group2 #> [1] NA #>  #> $tradenames #> [1] NA #>  #> $loinc #> [1] NA #>  #> $ddd #> $ddd$oral #> $ddd$oral$amount #> [1] NA #>  #> $ddd$oral$units #> [1] NA #>  #>  #> $ddd$iv #> $ddd$iv$amount #> [1] NA #>  #> $ddd$iv$units #> [1] NA #>  #>  #>    # Add Co-fluampicil, which is one of the many J01CR50 codes, see # https://www.whocc.no/ddd/list_of_ddds_combined_products/ add_custom_antimicrobials(   data.frame(     ab = \"COFLU\",     name = \"Co-fluampicil\",     atc = \"J01CR50\",     group = \"Beta-lactams/penicillins\"   ) ) #> ℹ Added one record to the internal antibiotics data set. ab_atc(\"Co-fluampicil\") #> [1] \"J01CR50\" ab_name(\"J01CR50\") #> [1] \"Co-fluampicil\"  # even antibiotic selectors work x <- data.frame(   random_column = \"some value\",   coflu = as.sir(\"S\"),   ampicillin = as.sir(\"R\") ) x #>   random_column coflu ampicillin #> 1    some value     S          R x[, betalactams()] #> ℹ For betalactams() using columns 'coflu' (co-fluampicil) and #>   'ampicillin' #>   coflu ampicillin #> 1     S          R # }"},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Custom Microorganisms — add_custom_microorganisms","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"add_custom_microorganisms() can add custom microorganisms, non-taxonomic outcome laboratory analysis.","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"","code":"add_custom_microorganisms(x)  clear_custom_microorganisms()"},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"x data.frame resembling microorganisms data set, least containing column \"genus\" (case-insensitive)","code":""},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"function fill missing taxonomy , specific taxonomic columns missing, see Examples. Important: Due R works, add_custom_microorganisms() function run every R session - added microorganisms stored sessions thus lost R exited. two ways circumvent automate process adding microorganisms: Method 1: Using package option AMR_custom_mo, preferred method. use method: Create data set structure microorganisms data set (containing least column \"genus\") save saveRDS() location choice, e.g. \"~/my_custom_mo.rds\", remote location. Set file location package option AMR_custom_mo: options(AMR_custom_mo = \"~/my_custom_mo.rds\"). can even remote file location, https URL. Since options saved R sessions, best save option .Rprofile file loaded start-R. , open .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"), add text save file:   Upon package load, file loaded run add_custom_microorganisms() function. Method 2: Loading microorganism directly .Rprofile file. Note definitions stored user-specific R file, suboptimal workflow. use method: Edit .Rprofile file using e.g. utils::file.edit(\"~/.Rprofile\"). Add text like save file:   Use clear_custom_microorganisms() clear previously added microorganisms.","code":"# Add custom microorganism codes: options(AMR_custom_mo = \"~/my_custom_mo.rds\") # Add custom antibiotic drug codes:  AMR::add_custom_microorganisms(    data.frame(genus = \"Enterobacter\",               species = \"asburiae/cloacae\")  )"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/add_custom_microorganisms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Custom Microorganisms — add_custom_microorganisms","text":"","code":"# \\donttest{ # a combination of species is not formal taxonomy, so # this will result in only \"Enterobacter asburiae\": mo_name(\"Enterobacter asburiae/cloacae\") #> [1] \"Enterobacter asburiae\"  # now add a custom entry - it will be considered by as.mo() and # all mo_*() functions add_custom_microorganisms(   data.frame(     genus = \"Enterobacter\",     species = \"asburiae/cloacae\"   ) ) #> ℹ Added Enterobacter asburiae/cloacae to the internal microorganisms data #>   set.  # E. asburiae/cloacae is now a new microorganism: mo_name(\"Enterobacter asburiae/cloacae\") #> [1] \"Enterobacter asburiae/cloacae\"  # its code: as.mo(\"Enterobacter asburiae/cloacae\") #> Class 'mo' #> [1] CUSTOM1_ENTRB_ASB/  # all internal algorithms will work as well: mo_name(\"Ent asburia cloacae\") #> [1] \"Enterobacter asburiae/cloacae\"  # and even the taxonomy was added based on the genus! mo_family(\"E. asburiae/cloacae\") #> [1] \"Enterobacteriaceae\" mo_gramstain(\"Enterobacter asburiae/cloacae\") #> [1] \"Gram-negative\"  mo_info(\"Enterobacter asburiae/cloacae\") #> $mo #> [1] \"CUSTOM1_ENTRB_ASB/\" #>  #> $kingdom #> [1] \"Bacteria\" #>  #> $phylum #> [1] \"Pseudomonadota\" #>  #> $class #> [1] \"Gammaproteobacteria\" #>  #> $order #> [1] \"Enterobacterales\" #>  #> $family #> [1] \"Enterobacteriaceae\" #>  #> $genus #> [1] \"Enterobacter\" #>  #> $species #> [1] \"asburiae/cloacae\" #>  #> $subspecies #> [1] \"\" #>  #> $status #> [1] \"accepted\" #>  #> $synonyms #> NULL #>  #> $gramstain #> [1] \"Gram-negative\" #>  #> $oxygen_tolerance #> [1] NA #>  #> $url #> [1] \"\" #>  #> $ref #> [1] \"Self-added, 2023\" #>  #> $snomed #> [1] NA #>  #> $lpsn #> [1] NA #>  #> $gbif #> [1] NA #>    # the function tries to be forgiving: add_custom_microorganisms(   data.frame(     GENUS = \"BACTEROIDES / PARABACTEROIDES SLASHLINE\",     SPECIES = \"SPECIES\"   ) ) #> ℹ Added Bacteroides/Parabacteroides to the internal microorganisms data #>   set. mo_name(\"BACTEROIDES / PARABACTEROIDES\") #> [1] \"Bacteroides/Parabacteroides\" mo_rank(\"BACTEROIDES / PARABACTEROIDES\") #> [1] \"genus\"  # taxonomy still works, although a slashline genus was given as input: mo_family(\"Bacteroides/Parabacteroides\") #> [1] \"Bacteroidaceae\"   # for groups and complexes, set them as species or subspecies: add_custom_microorganisms(   data.frame(     genus = \"Citrobacter\",     species = c(\"freundii\", \"braakii complex\"),     subspecies = c(\"complex\", \"\")   ) ) #> ℹ Added Citrobacter braakii complex and Citrobacter freundii complex to the #>   internal microorganisms data set. mo_name(c(\"C. freundii complex\", \"C. braakii complex\")) #> [1] \"Citrobacter freundii complex\" \"Citrobacter braakii complex\"  mo_species(c(\"C. freundii complex\", \"C. braakii complex\")) #> [1] \"freundii complex\" \"braakii complex\"  mo_gramstain(c(\"C. freundii complex\", \"C. braakii complex\")) #> [1] \"Gram-negative\" \"Gram-negative\" # }"},{"path":"https://msberends.github.io/AMR/reference/age.html","id":null,"dir":"Reference","previous_headings":"","what":"Age in Years of Individuals — age","title":"Age in Years of Individuals — age","text":"Calculates age years based reference date, system date default.","code":""},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Age in Years of Individuals — age","text":"","code":"age(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...)"},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Age in Years of Individuals — age","text":"x date(s), character (vectors) coerced .POSIXlt() reference reference date(s) (default today), character (vectors) coerced .POSIXlt() exact logical indicate whether age calculation exact, .e. decimals. divides number days year--date (YTD) x number days year reference (either 365 366). na.rm logical indicate whether missing values removed ... arguments passed .POSIXlt(), origin","code":""},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Age in Years of Individuals — age","text":"integer (decimals) exact = FALSE, double (decimals) otherwise","code":""},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Age in Years of Individuals — age","text":"Ages 0 returned NA warning. Ages 120 give warning. function vectorises x reference, meaning either can length 1 argument larger length.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/age.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Age in Years of Individuals — age","text":"","code":"# 10 random pre-Y2K birth dates df <- data.frame(birth_date = as.Date(\"2000-01-01\") - runif(10) * 25000)  # add ages df$age <- age(df$birth_date)  # add exact ages df$age_exact <- age(df$birth_date, exact = TRUE)  # add age at millenium switch df$age_at_y2k <- age(df$birth_date, \"2000-01-01\")  df #>    birth_date age age_exact age_at_y2k #> 1  1935-04-26  88  88.04384         64 #> 2  1939-12-20  83  83.39178         60 #> 3  1940-09-26  82  82.62466         59 #> 4  1981-04-16  42  42.07123         18 #> 5  1946-10-07  76  76.59452         53 #> 6  1974-10-27  48  48.53973         25 #> 7  1938-08-21  84  84.72329         61 #> 8  1941-05-13  81  81.99726         58 #> 9  1933-07-19  89  89.81370         66 #> 10 1977-01-31  46  46.27671         22"},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":null,"dir":"Reference","previous_headings":"","what":"Split Ages into Age Groups — age_groups","title":"Split Ages into Age Groups — age_groups","text":"Split ages age groups defined split argument. allows easier demographic (antimicrobial resistance) analysis.","code":""},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split Ages into Age Groups — age_groups","text":"","code":"age_groups(x, split_at = c(12, 25, 55, 75), na.rm = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split Ages into Age Groups — age_groups","text":"x age, e.g. calculated age() split_at values split x - default age groups 0-11, 12-24, 25-54, 55-74 75+. See Details. na.rm logical indicate whether missing values removed","code":""},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split Ages into Age Groups — age_groups","text":"Ordered factor","code":""},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Split Ages into Age Groups — age_groups","text":"split ages, input split_at argument can : numeric vector. value e.g. c(10, 20) split x 0-9, 10-19 20+. value 50 split x 0-49 50+. default split young children (0-11), youth (12-24), young adults (25-54), middle-aged adults (55-74) elderly (75+). character: \"children\" \"kids\", equivalent : c(0, 1, 2, 4, 6, 13, 18). split 0, 1, 2-3, 4-5, 6-12, 13-17 18+. \"elderly\" \"seniors\", equivalent : c(65, 75, 85). split 0-64, 65-74, 75-84, 85+. \"fives\", equivalent : 1:20 * 5. split 0-4, 5-9, ..., 95-99, 100+. \"tens\", equivalent : 1:10 * 10. split 0-9, 10-19, ..., 90-99, 100+.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/age_groups.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split Ages into Age Groups — age_groups","text":"","code":"ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)  # split into 0-49 and 50+ age_groups(ages, 50) #> [1] 0-49 0-49 0-49 50+  0-49 50+  50+  0-49 0-49 #> Levels: 0-49 < 50+  # split into 0-19, 20-49 and 50+ age_groups(ages, c(20, 50)) #> [1] 0-19  0-19  0-19  50+   20-49 50+   50+   20-49 20-49 #> Levels: 0-19 < 20-49 < 50+  # split into groups of ten years age_groups(ages, 1:10 * 10) #> [1] 0-9   0-9   10-19 50-59 30-39 70-79 100+  40-49 20-29 #> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+ age_groups(ages, split_at = \"tens\") #> [1] 0-9   0-9   10-19 50-59 30-39 70-79 100+  40-49 20-29 #> 11 Levels: 0-9 < 10-19 < 20-29 < 30-39 < 40-49 < 50-59 < 60-69 < ... < 100+  # split into groups of five years age_groups(ages, 1:20 * 5) #> [1] 0-4   5-9   15-19 50-54 30-34 75-79 100+  40-44 20-24 #> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+ age_groups(ages, split_at = \"fives\") #> [1] 0-4   5-9   15-19 50-54 30-34 75-79 100+  40-44 20-24 #> 21 Levels: 0-4 < 5-9 < 10-14 < 15-19 < 20-24 < 25-29 < 30-34 < ... < 100+  # split specifically for children age_groups(ages, c(1, 2, 4, 6, 13, 18)) #> [1] 2-3   6-12  13-17 18+   18+   18+   18+   18+   18+   #> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-17 < 18+ age_groups(ages, \"children\") #> [1] 2-3   6-12  13-17 18+   18+   18+   18+   18+   18+   #> Levels: 0 < 1 < 2-3 < 4-5 < 6-12 < 13-17 < 18+  # \\donttest{ # resistance of ciprofloxacin per age group if (require(\"dplyr\") && require(\"ggplot2\")) {   example_isolates %>%     filter_first_isolate() %>%     filter(mo == as.mo(\"Escherichia coli\")) %>%     group_by(age_group = age_groups(age)) %>%     select(age_group, CIP) %>%     ggplot_sir(       x = \"age_group\",       minimum = 0,       x.title = \"Age Group\",       title = \"Ciprofloxacin resistance per age group\"     ) } #> Loading required package: ggplot2  # }"},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"Generate antibiogram, communicate results plots tables. functions follow logic Klinker et al. Barbieri et al. (see Source), allow reporting e.g. R Markdown Quarto well.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"","code":"antibiogram(   x,   antibiotics = where(is.sir),   mo_transform = \"shortname\",   ab_transform = NULL,   syndromic_group = NULL,   add_total_n = TRUE,   only_all_tested = FALSE,   digits = 0,   col_mo = NULL,   language = get_AMR_locale(),   minimum = 30,   combine_SI = TRUE,   sep = \" + \",   info = interactive() )  # S3 method for antibiogram plot(x, ...)  # S3 method for antibiogram autoplot(object, ...)  # S3 method for antibiogram knit_print(   x,   italicise = TRUE,   na = getOption(\"knitr.kable.NA\", default = \"\"),   ... )"},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"Klinker KP et al. (2021). Antimicrobial stewardship antibiograms: importance moving beyond traditional antibiograms. Therapeutic Advances Infectious Disease, May 5;8:20499361211011373; doi:10.1177/20499361211011373 Barbieri E et al. (2021). Development Weighted-Incidence Syndromic Combination Antibiogram (WISCA) guide choice empiric antibiotic treatment urinary tract infection paediatric patients: Bayesian approach Antimicrobial Resistance & Infection Control May 1;10(1):74; doi:10.1186/s13756-021-00939-2 M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 5th Edition, 2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"x data.frame containing least column microorganisms columns antibiotic results (class 'sir', see .sir()) antibiotics vector antibiotic name code (evaluated .ab(), column name x, (combinations ) antibiotic selectors aminoglycosides() carbapenems(). combination antibiograms, can also set values separated \"+\", \"TZP+TOB\" \"cipro + genta\", given columns resembling antibiotics exist x. See Examples. mo_transform character transform microorganism input - must \"name\", \"shortname\", \"gramstain\", one column names microorganisms data set: \"mo\", \"fullname\", \"status\", \"kingdom\", \"phylum\", \"class\", \"order\", \"family\", \"genus\", \"species\", \"subspecies\", \"rank\", \"ref\", \"oxygen_tolerance\", \"source\", \"lpsn\", \"lpsn_parent\", \"lpsn_renamed_to\", \"gbif\", \"gbif_parent\", \"gbif_renamed_to\", \"prevalence\", \"snomed\". Can also NULL transform input. ab_transform character transform antibiotic input - must one column names antibiotics data set: \"ab\", \"cid\", \"name\", \"group\", \"atc\", \"atc_group1\", \"atc_group2\", \"abbreviations\", \"synonyms\", \"oral_ddd\", \"oral_units\", \"iv_ddd\", \"iv_units\", \"loinc\". Can also NULL transform input. syndromic_group column name x, values calculated split rows x, e.g. using ifelse() case_when(). See Examples. add_total_n logical indicate whether total available numbers per pathogen added table (default TRUE). add lowest highest number available isolate per antibiotic (e.g, E. coli 200 isolates available ciprofloxacin 150 amoxicillin, returned number \"150-200\"). only_all_tested (combination antibiograms): logical indicate isolates must tested antibiotics, see Details digits number digits use rounding col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). language language translate text, defaults system language (see get_AMR_locale()) minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. combine_SI logical indicate whether susceptibility determined results either S , instead S (default TRUE) sep separating character antibiotic columns combination antibiograms info logical indicate info printed - default TRUE interactive mode ... used R Markdown Quarto: arguments passed knitr::kable() (otherwise, use) object antibiogram() object italicise logical indicate whether microorganism names knitr table made italic, using italicise_taxonomy(). na character use showing NA values","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"function returns table values 0 100 susceptibility, resistance. Remember filter data let contain first isolates! needed exclude duplicates reduce selection bias. Use first_isolate() determine data set one four available algorithms. types antibiograms listed can plotted (using ggplot2::autoplot() base R plot()/barplot()). antibiogram object can also used directly R Markdown / Quarto (.e., knitr) reports. case, knitr::kable() applied automatically microorganism names even printed italics default (see argument italicise). can also use functions specific 'table reporting' packages transform output antibiogram() needs, e.g. flextable::as_flextable() gt::gt().","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"antibiogram-types","dir":"Reference","previous_headings":"","what":"Antibiogram Types","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"four antibiogram types, proposed Klinker et al. (2021, doi:10.1177/20499361211011373 ), supported antibiogram(): Traditional Antibiogram Case example: Susceptibility Pseudomonas aeruginosa piperacillin/tazobactam (TZP) Code example:   Combination Antibiogram Case example: Additional susceptibility Pseudomonas aeruginosa TZP + tobramycin versus TZP alone Code example:   Syndromic Antibiogram Case example: Susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) Code example:   Weighted-Incidence Syndromic Combination Antibiogram (WISCA) Case example: Susceptibility Pseudomonas aeruginosa TZP among respiratory specimens (obtained among ICU patients ) male patients age >=65 years heart failure Code example:   Note combination antibiograms, important realise susceptibility can calculated two ways, can set only_all_tested argument (default FALSE). See example two antibiotics, Drug Drug B, antibiogram() works calculate %SI:","code":"antibiogram(your_data,             antibiotics = \"TZP\") antibiogram(your_data,             antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\")) antibiogram(your_data,             antibiotics = penicillins(),             syndromic_group = \"ward\") library(dplyr) your_data %>%   filter(ward == \"ICU\" & specimen_type == \"Respiratory\") %>%   antibiogram(antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"),               syndromic_group = ifelse(.$age >= 65 &                                          .$gender == \"Male\" &                                          .$condition == \"Heart Disease\",                                        \"Study Group\", \"Control Group\")) --------------------------------------------------------------------                     only_all_tested = FALSE  only_all_tested = TRUE                     -----------------------  -----------------------  Drug A    Drug B   include as  include as   include as  include as                     numerator   denominator  numerator   denominator --------  --------  ----------  -----------  ----------  -----------  S or I    S or I       X            X            X            X    R       S or I       X            X            X            X   <NA>     S or I       X            X            -            -  S or I      R          X            X            X            X    R         R          -            X            -            X   <NA>       R          -            -            -            -  S or I     <NA>        X            X            -            -    R        <NA>        -            -            -            -   <NA>      <NA>        -            -            -            - --------------------------------------------------------------------"},{"path":"https://msberends.github.io/AMR/reference/antibiogram.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA) — antibiogram","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # \\donttest{ # Traditional antibiogram ----------------------------------------------  antibiogram(example_isolates,   antibiotics = c(aminoglycosides(), carbapenems()) ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 10 × 7 #>    `Pathogen (N min-max)`   AMK   GEN   IPM   KAN   MEM   TOB #>  * <chr>                  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1 CoNS (43-309)              0    86    52     0    52    22 #>  2 E. coli (0-462)          100    98   100    NA   100    97 #>  3 E. faecalis (0-39)         0     0   100     0    NA     0 #>  4 K. pneumoniae (0-58)      NA    90   100    NA   100    90 #>  5 P. aeruginosa (17-30)     NA   100    NA     0    NA   100 #>  6 P. mirabilis (0-34)       NA    94    94    NA    NA    94 #>  7 S. aureus (2-233)         NA    99    NA    NA    NA    98 #>  8 S. epidermidis (8-163)     0    79    NA     0    NA    51 #>  9 S. hominis (3-80)         NA    92    NA    NA    NA    85 #> 10 S. pneumoniae (11-117)     0     0    NA     0    NA     0  antibiogram(example_isolates,   antibiotics = aminoglycosides(),   ab_transform = \"atc\",   mo_transform = \"gramstain\" ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 2 × 5 #>   `Pathogen (N min-max)`   J01GB01 J01GB03 J01GB04 J01GB06 #> * <chr>                      <dbl>   <dbl>   <dbl>   <dbl> #> 1 Gram-negative (35-686)        96      96       0      98 #> 2 Gram-positive (436-1170)      34      63       0       0  antibiogram(example_isolates,   antibiotics = carbapenems(),   ab_transform = \"name\",   mo_transform = \"name\" ) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 5 × 3 #>   `Pathogen (N min-max)`                           Imipenem Meropenem #> * <chr>                                               <dbl>     <dbl> #> 1 Coagulase-negative Staphylococcus (CoNS) (48-48)       52        52 #> 2 Enterococcus faecalis (0-38)                          100        NA #> 3 Escherichia coli (418-422)                            100       100 #> 4 Klebsiella pneumoniae (51-53)                         100       100 #> 5 Proteus mirabilis (27-32)                              94        NA   # Combined antibiogram -------------------------------------------------  # combined antibiotics yield higher empiric coverage antibiogram(example_isolates,   antibiotics = c(\"TZP\", \"TZP+TOB\", \"TZP+GEN\"),   mo_transform = \"gramstain\" ) #> # A tibble: 2 × 4 #>   `Pathogen (N min-max)`     TZP `TZP + GEN` `TZP + TOB` #> * <chr>                    <dbl>       <dbl>       <dbl> #> 1 Gram-negative (641-693)     88          99          98 #> 2 Gram-positive (345-1044)    86          98          95  # names of antibiotics do not need to resemble columns exactly: antibiogram(example_isolates,   antibiotics = c(\"Cipro\", \"cipro + genta\"),   mo_transform = \"gramstain\",   ab_transform = \"name\",   sep = \" & \" ) #> # A tibble: 2 × 3 #>   `Pathogen (N min-max)`  Ciprofloxacin `Ciprofloxacin & Gentamicin` #> * <chr>                           <dbl>                        <dbl> #> 1 Gram-negative (684-694)            91                           99 #> 2 Gram-positive (724-847)            77                           93   # Syndromic antibiogram ------------------------------------------------  # the data set could contain a filter for e.g. respiratory specimens antibiogram(example_isolates,   antibiotics = c(aminoglycosides(), carbapenems()),   syndromic_group = \"ward\" ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 14 × 8 #>    `Syndromic Group` `Pathogen (N min-max)`   AMK   GEN   IPM   KAN   MEM   TOB #>  * <chr>             <chr>                  <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> #>  1 Clinical          CoNS (23-205)             NA    89    57    NA    57    26 #>  2 ICU               CoNS (10-73)              NA    79    NA    NA    NA    NA #>  3 Outpatient        CoNS (3-31)               NA    84    NA    NA    NA    NA #>  4 Clinical          E. coli (0-299)          100    98   100    NA   100    98 #>  5 ICU               E. coli (0-137)          100    99   100    NA   100    96 #>  6 Clinical          K. pneumoniae (0-51)      NA    92   100    NA   100    92 #>  7 Clinical          P. mirabilis (0-30)       NA   100    NA    NA    NA   100 #>  8 Clinical          S. aureus (2-150)         NA    99    NA    NA    NA    97 #>  9 ICU               S. aureus (0-66)          NA   100    NA    NA    NA    NA #> 10 Clinical          S. epidermidis (4-79)     NA    82    NA    NA    NA    55 #> 11 ICU               S. epidermidis (4-75)     NA    72    NA    NA    NA    41 #> 12 Clinical          S. hominis (1-45)         NA    96    NA    NA    NA    94 #> 13 Clinical          S. pneumoniae (5-78)       0     0    NA     0    NA     0 #> 14 ICU               S. pneumoniae (5-30)       0     0    NA     0    NA     0  # now define a data set with only E. coli ex1 <- example_isolates[which(mo_genus() == \"Escherichia\"), ] #> ℹ Using column 'mo' as input for mo_genus()  # with a custom language, though this will be determined automatically # (i.e., this table will be in Spanish on Spanish systems) antibiogram(ex1,   antibiotics = aminoglycosides(),   ab_transform = \"name\",   syndromic_group = ifelse(ex1$ward == \"ICU\",     \"UCI\", \"No UCI\"   ),   language = \"es\" ) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 2 × 5 #>   `Grupo sindrómico` `Patógeno (N min-max)` Amikacina Gentamicina Tobramicina #> * <chr>              <chr>                      <dbl>       <dbl>       <dbl> #> 1 No UCI             E. coli (0-325)              100          98          98 #> 2 UCI                E. coli (0-137)              100          99          96   # Weighted-incidence syndromic combination antibiogram (WISCA) ---------  # the data set could contain a filter for e.g. respiratory specimens/ICU antibiogram(example_isolates,   antibiotics = c(\"AMC\", \"AMC+CIP\", \"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\",   minimum = 10, # this should be >=30, but now just as example   syndromic_group = ifelse(example_isolates$age >= 65 &     example_isolates$gender == \"M\",   \"WISCA Group 1\", \"WISCA Group 2\"   ) ) #> # A tibble: 4 × 6 #>   `Syndromic Group` `Pathogen (N min-max)`    AMC `AMC + CIP`   TZP `TZP + TOB` #> * <chr>             <chr>                   <dbl>       <dbl> <dbl>       <dbl> #> 1 WISCA Group 1     Gram-negative (261-285)    76          95    89          99 #> 2 WISCA Group 2     Gram-negative (380-442)    76          98    88          98 #> 3 WISCA Group 1     Gram-positive (123-406)    76          89    81          95 #> 4 WISCA Group 2     Gram-positive (222-732)    76          89    88          95   # Print the output for R Markdown / Quarto -----------------------------  ureido <- antibiogram(example_isolates,   antibiotics = ureidopenicillins(),   ab_transform = \"name\" ) #> ℹ For ureidopenicillins() using column 'TZP' (piperacillin/tazobactam)  # in an Rmd file, you would just need to return `ureido` in a chunk, # but to be explicit here: if (requireNamespace(\"knitr\")) {   cat(knitr::knit_print(ureido)) } #>  #>  #> |Pathogen (N)          | Piperacillin/tazobactam| #> |:---------------------|-----------------------:| #> |CoNS (33)             |                      30| #> |*E. coli* (416)       |                      94| #> |*K. pneumoniae* (53)  |                      89| #> |*S. pneumoniae* (112) |                     100|   # Generate plots with ggplot2 or base R --------------------------------  ab1 <- antibiogram(example_isolates,   antibiotics = c(\"AMC\", \"CIP\", \"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\" ) ab2 <- antibiogram(example_isolates,   antibiotics = c(\"AMC\", \"CIP\", \"TZP\", \"TZP+TOB\"),   mo_transform = \"gramstain\",   syndromic_group = \"ward\" )  if (requireNamespace(\"ggplot2\")) {   ggplot2::autoplot(ab1) }  if (requireNamespace(\"ggplot2\")) {   ggplot2::autoplot(ab2) }   plot(ab1)  plot(ab2)  # }"},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":null,"dir":"Reference","previous_headings":"","what":"Antibiotic Selectors — antibiotic_class_selectors","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"functions allow filtering rows selecting columns based antibiotic test results specific antibiotic class group (according antibiotics data set), without need define columns antibiotic abbreviations. short, column name resembles antimicrobial drug, picked functions matches pharmaceutical class: \"cefazolin\", \"kefzol\", \"CZO\" \"J01DB04\" picked cephalosporins().","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"","code":"ab_class(ab_class, only_sir_columns = FALSE, only_treatable = TRUE, ...)  ab_selector(filter, only_sir_columns = FALSE, only_treatable = TRUE, ...)  aminoglycosides(only_sir_columns = FALSE, only_treatable = TRUE, ...)  aminopenicillins(only_sir_columns = FALSE, ...)  antifungals(only_sir_columns = FALSE, ...)  antimycobacterials(only_sir_columns = FALSE, ...)  betalactams(only_sir_columns = FALSE, only_treatable = TRUE, ...)  carbapenems(only_sir_columns = FALSE, only_treatable = TRUE, ...)  cephalosporins(only_sir_columns = FALSE, ...)  cephalosporins_1st(only_sir_columns = FALSE, ...)  cephalosporins_2nd(only_sir_columns = FALSE, ...)  cephalosporins_3rd(only_sir_columns = FALSE, ...)  cephalosporins_4th(only_sir_columns = FALSE, ...)  cephalosporins_5th(only_sir_columns = FALSE, ...)  fluoroquinolones(only_sir_columns = FALSE, ...)  glycopeptides(only_sir_columns = FALSE, ...)  lincosamides(only_sir_columns = FALSE, ...)  lipoglycopeptides(only_sir_columns = FALSE, ...)  macrolides(only_sir_columns = FALSE, ...)  oxazolidinones(only_sir_columns = FALSE, ...)  penicillins(only_sir_columns = FALSE, ...)  polymyxins(only_sir_columns = FALSE, only_treatable = TRUE, ...)  streptogramins(only_sir_columns = FALSE, ...)  quinolones(only_sir_columns = FALSE, ...)  tetracyclines(only_sir_columns = FALSE, ...)  trimethoprims(only_sir_columns = FALSE, ...)  ureidopenicillins(only_sir_columns = FALSE, ...)  administrable_per_os(only_sir_columns = FALSE, ...)  administrable_iv(only_sir_columns = FALSE, ...)  not_intrinsic_resistant(   only_sir_columns = FALSE,   col_mo = NULL,   version_expertrules = 3.3,   ... )"},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"ab_class antimicrobial class part , \"carba\" \"carbapenems\". columns group, atc_group1 atc_group2 antibiotics data set searched (case-insensitive) value. only_sir_columns logical indicate whether columns class sir must selected (default FALSE), see .sir() only_treatable logical indicate whether antimicrobial drugs excluded laboratory tests (default TRUE), gentamicin-high (GEH) imipenem/EDTA (IPE) ... ignored, place allow future extensions filter expression evaluated antibiotics data set, name %like% \"trim\" col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). version_expertrules version number use EUCAST Expert Rules Intrinsic Resistance guideline. Can either \"3.3\", \"3.2\", \"3.1\".","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"(internally) character vector column names, additional class \"ab_selector\"","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"functions can used data set calls selecting columns filtering rows. work base R, Tidyverse, data.table. heavily inspired Tidyverse selection helpers everything(), limited dplyr verbs. Nonetheless, convenient use dplyr functions select(), filter() summarise(), see Examples. columns data functions called searched known antibiotic names, abbreviations, brand names, codes (ATC, EARS-Net, , etc.) according antibiotics data set. means selector aminoglycosides() pick column names like 'gen', 'genta', 'J01GB03', 'tobra', 'Tobracin', etc. ab_class() function can used filter/select manually defined antibiotic class. searches results antibiotics data set within columns group, atc_group1 atc_group2. ab_selector() function can used internally filter antibiotics data set results, see Examples. allows filtering (part ) certain name, /group name even minimum DDDs oral treatment. function yields highest flexibility, also least user-friendly, since requires hard-coded filter set. administrable_per_os() administrable_iv() functions also rely antibiotics data set - antibiotic columns matched DDD (defined daily dose) resp. oral IV treatment available antibiotics data set. not_intrinsic_resistant() function can used select antibiotic columns pose intrinsic resistance microorganisms data set. example, data set contains microorganism codes names E. coli K. pneumoniae contains column \"vancomycin\", column removed (rather, unselected) using function. currently applies 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021) determine intrinsic resistance, using eucast_rules() function internally. determination, function quite slow terms performance.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"full-list-of-supported-antibiotic-classes","dir":"Reference","previous_headings":"","what":"Full list of supported (antibiotic) classes","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"aminoglycosides() can select:  amikacin (AMK), amikacin/fosfomycin (AKF), amphotericin B-high (AMH), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), tobramycin-high (TOH) aminopenicillins() can select:  amoxicillin (AMX) ampicillin (AMP) antifungals() can select:  amphotericin B (AMB), anidulafungin (ANI), butoconazole (), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), voriconazole (VOR) antimycobacterials() can select:  4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), viomycin (VIO) betalactams() can select:  amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC) carbapenems() can select:  biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), tebipenem (TBP) cephalosporins() can select:  cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening (FOX1), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), latamoxef (LTM), loracarbef (LOR) cephalosporins_1st() can select:  cefacetrile (CAC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefroxadine (CRD), ceftezole (CTL), cephradine (CED) cephalosporins_2nd() can select:  cefaclor (CEC), cefamandole (MAN), cefmetazole (CMZ), cefonicid (CID), ceforanide (CND), cefotetan (CTT), cefotiam (CTF), cefoxitin (FOX), cefoxitin screening (FOX1), cefprozil (CPR), cefuroxime (CXM), cefuroxime axetil (CXA), loracarbef (LOR) cephalosporins_3rd() can select:  cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefetamet (CAT), cefetamet pivoxil (CPI), cefixime (CFM), cefmenoxime (CMX), cefodizime (DIZ), cefoperazone (CFP), cefoperazone/sulbactam (CSL), cefotaxime (CTX), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotiam hexetil (CHE), cefovecin (FOV), cefpimizole (CFZ), cefpiramide (CPM), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefsulodin (CFS), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), latamoxef (LTM) cephalosporins_4th() can select:  cefepime (FEP), cefepime/clavulanic acid (CPC), cefepime/tazobactam (FPT), cefetecol (CCL), cefoselis (CSE), cefozopran (ZOP), cefpirome (CPO), cefquinome (CEQ) cephalosporins_5th() can select:  ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT) fluoroquinolones() can select:  besifloxacin (BES), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nifuroquine (NIF), norfloxacin (), ofloxacin (OFX), orbifloxacin (ORB), pazufloxacin (PAZ), pefloxacin (PEF), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), trovafloxacin (TVA) glycopeptides() can select:  avoparcin (AVO), dalbavancin (DAL), norvancomycin (NVA), oritavancin (ORI), ramoplanin (RAM), teicoplanin (TEC), teicoplanin-macromethod (TCM), telavancin (TLV), vancomycin (VAN), vancomycin-macromethod (VAM) lincosamides() can select:  acetylmidecamycin (ACM), acetylspiramycin (ASP), clindamycin (CLI), gamithromycin (GAM), kitasamycin (KIT), lincomycin (LIN), meleumycin (MEL), nafithromycin (ZWK), pirlimycin (PRL), primycin (PRM), solithromycin (SOL), tildipirosin (TIP), tilmicosin (TIL), tulathromycin (TUL), tylosin (TYL), tylvalosin (TYL1) lipoglycopeptides() can select:  dalbavancin (DAL), oritavancin (ORI), telavancin (TLV) macrolides() can select:  acetylmidecamycin (ACM), acetylspiramycin (ASP), azithromycin (AZM), clarithromycin (CLR), dirithromycin (DIR), erythromycin (ERY), flurithromycin (FLR1), gamithromycin (GAM), josamycin (JOS), kitasamycin (KIT), meleumycin (MEL), midecamycin (MID), miocamycin (MCM), nafithromycin (ZWK), oleandomycin (OLE), pirlimycin (PRL), primycin (PRM), rokitamycin (ROK), roxithromycin (RXT), solithromycin (SOL), spiramycin (SPI), telithromycin (TLT), tildipirosin (TIP), tilmicosin (TIL), troleandomycin (TRL), tulathromycin (TUL), tylosin (TYL), tylvalosin (TYL1) oxazolidinones() can select:  cadazolid (CDZ), cycloserine (CYC), linezolid (LNZ), tedizolid (TZD), thiacetazone (THA) penicillins() can select:  amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), avibactam (AVB), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), carbenicillin (CRB), carindacillin (CRN), cefepime/nacubactam (FNC), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), epicillin (EPC), flucloxacillin (FLC), hetacillin (HET), lenampicillin (LEN), mecillinam (MEC), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nacubactam (NAC), nafcillin (NAF), oxacillin (OXA), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), sarmoxicillin (SRX), sulbactam (SUL), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tazobactam (TAZ), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC) polymyxins() can select:  colistin (COL), polymyxin B (PLB), polymyxin B/polysorbate 80 (POP) quinolones() can select:  besifloxacin (BES), cinoxacin (CIN), ciprofloxacin (CIP), clinafloxacin (CLX), danofloxacin (DAN), delafloxacin (DFX), difloxacin (DIF), enoxacin (ENX), enrofloxacin (ENR), finafloxacin (FIN), fleroxacin (FLE), flumequine (FLM), garenoxacin (GRN), gatifloxacin (GAT), gemifloxacin (GEM), grepafloxacin (GRX), lascufloxacin (LSC), levofloxacin (LVX), levonadifloxacin (LND), lomefloxacin (LOM), marbofloxacin (MAR), metioxate (MXT), miloxacin (MIL), moxifloxacin (MFX), nadifloxacin (NAD), nalidixic acid (NAL), nemonoxacin (NEM), nifuroquine (NIF), nitroxoline (NTR), norfloxacin (), ofloxacin (OFX), orbifloxacin (ORB), oxolinic acid (OXO), pazufloxacin (PAZ), pefloxacin (PEF), pipemidic acid (PPA), piromidic acid (PIR), pradofloxacin (PRA), premafloxacin (PRX), prulifloxacin (PRU), rosoxacin (ROS), rufloxacin (RFL), sarafloxacin (SAR), sitafloxacin (SIT), sparfloxacin (SPX), temafloxacin (TMX), tilbroquinol (TBQ), tioxacin (TXC), tosufloxacin (TFX), trovafloxacin (TVA) streptogramins() can select:  pristinamycin (PRI) quinupristin/dalfopristin (QDA) tetracyclines() can select:  cetocycline (CTO), chlortetracycline (CTE), clomocycline (CLM1), demeclocycline (DEM), doxycycline (DOX), eravacycline (ERV), lymecycline (LYM), metacycline (MTC), minocycline (MNO), omadacycline (OMC), oxytetracycline (OXY), penimepicycline (PNM1), rolitetracycline (RLT), sarecycline (SRC), tetracycline (TCY), tigecycline (TGC) trimethoprims() can select:  brodimoprim (BDP), sulfadiazine (SDI), sulfadiazine/tetroxoprim (SLT), sulfadiazine/trimethoprim (SLT1), sulfadimethoxine (SUD), sulfadimidine (SDM), sulfadimidine/trimethoprim (SLT2), sulfafurazole (SLF), sulfaisodimidine (SLF1), sulfalene (SLF2), sulfamazone (SZO), sulfamerazine (SLF3), sulfamerazine/trimethoprim (SLT3), sulfamethizole (SLF4), sulfamethoxazole (SMX), sulfamethoxypyridazine (SLF5), sulfametomidine (SLF6), sulfametoxydiazine (SLF7), sulfametrole/trimethoprim (SLT4), sulfamoxole (SLF8), sulfamoxole/trimethoprim (SLT5), sulfanilamide (SLF9), sulfaperin (SLF10), sulfaphenazole (SLF11), sulfapyridine (SLF12), sulfathiazole (SUT), sulfathiourea (SLF13), trimethoprim (TMP), trimethoprim/sulfamethoxazole (SXT) ureidopenicillins() can select:  azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Antibiotic Selectors — antibiotic_class_selectors","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …   # Examples sections below are split into 'base R', 'dplyr', and 'data.table':   # base R ------------------------------------------------------------------  # select columns 'IPM' (imipenem) and 'MEM' (meropenem) example_isolates[, carbapenems()] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 2,000 × 2 #>    IPM   MEM   #>    <sir> <sir> #>  1 NA    NA    #>  2 NA    NA    #>  3 NA    NA    #>  4 NA    NA    #>  5 NA    NA    #>  6 NA    NA    #>  7 NA    NA    #>  8 NA    NA    #>  9 NA    NA    #> 10 NA    NA    #> # ℹ 1,990 more rows  # select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB' example_isolates[, c(\"mo\", aminoglycosides())] #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 2,000 × 5 #>    mo           GEN   TOB   AMK   KAN   #>    <mo>         <sir> <sir> <sir> <sir> #>  1 B_ESCHR_COLI NA    NA    NA    NA    #>  2 B_ESCHR_COLI NA    NA    NA    NA    #>  3 B_STPHY_EPDR NA    NA    NA    NA    #>  4 B_STPHY_EPDR NA    NA    NA    NA    #>  5 B_STPHY_EPDR NA    NA    NA    NA    #>  6 B_STPHY_EPDR NA    NA    NA    NA    #>  7 B_STPHY_AURS NA    S     NA    NA    #>  8 B_STPHY_AURS NA    S     NA    NA    #>  9 B_STPHY_EPDR NA    NA    NA    NA    #> 10 B_STPHY_EPDR NA    NA    NA    NA    #> # ℹ 1,990 more rows  # select only antibiotic columns with DDDs for oral treatment example_isolates[, administrable_per_os()] #> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC' #>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF' #>   (rifampicin) #> # A tibble: 2,000 × 23 #>    OXA   FLC   AMX   AMC   AMP   CXM   KAN   TMP   NIT   FOS   LNZ   CIP   MFX   #>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    I     NA    R     NA    NA    R     NA    NA    #>  2 NA    NA    NA    I     NA    I     NA    R     NA    NA    R     NA    NA    #>  3 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    NA    NA    #>  4 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    NA    NA    #>  5 NA    R     NA    NA    NA    R     NA    R     NA    NA    NA    NA    NA    #>  6 NA    R     NA    NA    NA    R     NA    R     NA    NA    NA    NA    NA    #>  7 NA    S     R     S     R     S     NA    R     NA    NA    NA    NA    NA    #>  8 NA    S     R     S     R     S     NA    R     NA    NA    NA    NA    NA    #>  9 NA    R     NA    NA    NA    R     NA    S     NA    NA    NA    S     NA    #> 10 NA    S     NA    NA    NA    S     NA    S     NA    NA    NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 10 more variables: VAN <sir>, TCY <sir>, DOX <sir>, ERY <sir>, CLI <sir>, #> #   AZM <sir>, MTR <sir>, CHL <sir>, COL <sir>, RIF <sir>  # filter using any() or all() example_isolates[any(carbapenems() == \"R\"), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 55 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  2 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  3 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R     #>  4 2005-04-21 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  5 2005-04-22 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  6 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  7 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  8 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  9 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> 10 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> # ℹ 45 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … subset(example_isolates, any(carbapenems() == \"R\")) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 55 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  2 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  3 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R     #>  4 2005-04-21 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  5 2005-04-22 452212     82 F      ICU      B_ENTRC      NA    NA    NA    NA    #>  6 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  7 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  8 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  9 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> 10 2008-01-22 1710B8     82 M      Clinical B_PROTS_MRBL R     NA    NA    NA    #> # ℹ 45 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # filter on any or all results in the carbapenem columns (i.e., IPM, MEM): example_isolates[any(carbapenems()), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Filtering any of columns 'IPM' and 'MEM' to contain value \"S\", \"I\" or \"R\" #> # A tibble: 962 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  4 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  5 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  6 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  7 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  8 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R     #>  9 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R     #> 10 2002-03-08 4FC193     69 M      Clinical B_ESCHR_COLI R     NA    NA    R     #> # ℹ 952 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … example_isolates[all(carbapenems()), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value \"S\", \"I\" or \"R\" #> # A tibble: 756 × 46 #>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir> #>  1 2002-04-14 F30196     73 M      Outpat… B_STRPT_GRPB  S     NA    S     S     #>  2 2003-04-08 114570     74 M      ICU     B_STRPT_PYGN  S     NA    S     S     #>  3 2003-04-08 114570     74 M      ICU     B_STRPT_GRPA  S     NA    S     S     #>  4 2003-04-08 114570     74 M      ICU     B_STRPT_GRPA  S     NA    S     S     #>  5 2003-08-14 F71508      0 F      Clinic… B_STRPT_GRPB  S     NA    S     S     #>  6 2003-10-16 650870     63 F      ICU     B_ESCHR_COLI  R     NA    NA    R     #>  7 2003-10-20 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  8 2003-10-20 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  9 2003-11-04 2FC253     87 F      ICU     B_ESCHR_COLI  R     NA    NA    NA    #> 10 2003-11-04 2FC253     87 F      ICU     B_ESCHR_COLI  R     NA    NA    NA    #> # ℹ 746 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # filter with multiple antibiotic selectors using c() example_isolates[all(c(carbapenems(), aminoglycosides()) == \"R\"), ] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 26 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2004-11-03 D65308     80 F      ICU      B_STNTR_MLTP R     NA    NA    R     #>  2 2005-04-22 452212     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  3 2007-02-21 8BBC46     61 F      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  4 2007-12-15 401043     72 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  5 2008-12-06 501361     43 F      Clinical B_STNTR_MLTP R     NA    NA    R     #>  6 2011-05-09 207325     82 F      ICU      B_ENTRC_FACM NA    NA    NA    NA    #>  7 2012-03-12 582258     80 M      ICU      B_STPHY_CONS R     R     R     R     #>  8 2012-05-19 C25552     89 F      Outpati… B_STPHY_CONS R     R     R     R     #>  9 2012-07-17 F05015     83 M      ICU      B_STPHY_CONS R     R     R     R     #> 10 2012-07-20 404299     66 F      Clinical B_STPHY_CONS R     R     R     R     #> # ℹ 16 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # filter + select in one go: get penicillins in carbapenem-resistant strains example_isolates[any(carbapenems() == \"R\"), penicillins()] #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP' #>   (piperacillin/tazobactam) #> # A tibble: 55 × 7 #>    PEN   OXA   FLC   AMX   AMC   AMP   TZP   #>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    NA    NA    NA    NA    #>  2 NA    NA    NA    NA    NA    NA    NA    #>  3 R     NA    NA    R     R     R     R     #>  4 NA    NA    NA    NA    NA    NA    R     #>  5 NA    NA    NA    NA    NA    NA    R     #>  6 NA    NA    NA    NA    NA    NA    R     #>  7 NA    NA    NA    NA    NA    NA    R     #>  8 NA    NA    NA    NA    NA    NA    R     #>  9 R     NA    NA    NA    S     NA    S     #> 10 R     NA    NA    NA    S     NA    S     #> # ℹ 45 more rows  # You can combine selectors with '&' to be more specific. For example, # penicillins() would select benzylpenicillin ('peni G') and # administrable_per_os() would select erythromycin. Yet, when combined these # drugs are both omitted since benzylpenicillin is not administrable per os # and erythromycin is not a penicillin: example_isolates[, penicillins() & administrable_per_os()] #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP' #>   (piperacillin/tazobactam) #> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC' #>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF' #>   (rifampicin) #> # A tibble: 2,000 × 5 #>    OXA   FLC   AMX   AMC   AMP   #>    <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    #>  2 NA    NA    NA    I     NA    #>  3 NA    R     NA    NA    NA    #>  4 NA    R     NA    NA    NA    #>  5 NA    R     NA    NA    NA    #>  6 NA    R     NA    NA    NA    #>  7 NA    S     R     S     R     #>  8 NA    S     R     S     R     #>  9 NA    R     NA    NA    NA    #> 10 NA    S     NA    NA    NA    #> # ℹ 1,990 more rows  # ab_selector() applies a filter in the `antibiotics` data set and is thus # very flexible. For instance, to select antibiotic columns with an oral DDD # of at least 1 gram: example_isolates[, ab_selector(oral_ddd > 1 & oral_units == \"g\")] #> ℹ For ab_selector(oral_ddd > 1 & oral_units == \"g\") using columns 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), 'KAN' (kanamycin), 'FOS' #>   (fosfomycin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'ERY' (erythromycin), #>   'CLI' (clindamycin), 'MTR' (metronidazole), and 'CHL' (chloramphenicol) #> # A tibble: 2,000 × 13 #>    OXA   FLC   AMX   AMC   AMP   KAN   FOS   LNZ   VAN   ERY   CLI   MTR   CHL   #>    <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    NA    NA    R     R     R     R     NA    NA    #>  2 NA    NA    NA    I     NA    NA    NA    R     R     R     R     NA    NA    #>  3 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #>  4 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #>  5 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #>  6 NA    R     NA    NA    NA    NA    NA    NA    S     R     R     NA    NA    #>  7 NA    S     R     S     R     NA    NA    NA    S     S     NA    NA    NA    #>  8 NA    S     R     S     R     NA    NA    NA    S     S     NA    NA    NA    #>  9 NA    R     NA    NA    NA    NA    NA    NA    S     R     NA    NA    NA    #> 10 NA    S     NA    NA    NA    NA    NA    NA    S     S     NA    NA    NA    #> # ℹ 1,990 more rows  # \\donttest{ # dplyr -------------------------------------------------------------------  if (require(\"dplyr\")) {   tibble(kefzol = random_sir(5)) %>%     select(cephalosporins()) } #> ℹ For cephalosporins() using column 'kefzol' (cefazolin) #> # A tibble: 5 × 1 #>   kefzol #>   <sir>  #> 1 I      #> 2 R      #> 3 R      #> 4 I      #> 5 R       if (require(\"dplyr\")) {   # get AMR for all aminoglycosides e.g., per ward:   example_isolates %>%     group_by(ward) %>%     summarise(across(aminoglycosides(), resistance)) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> Warning: There was 1 warning in `summarise()`. #> ℹ In argument: `across(aminoglycosides(), resistance)`. #> ℹ In group 3: `ward = \"Outpatient\"`. #> Caused by warning: #> ! Introducing NA: only 23 results available for KAN in group: ward = #> \"Outpatient\" (minimum = 30). #> # A tibble: 3 × 5 #>   ward         GEN   TOB   AMK   KAN #>   <chr>      <dbl> <dbl> <dbl> <dbl> #> 1 Clinical   0.229 0.315 0.626     1 #> 2 ICU        0.290 0.400 0.662     1 #> 3 Outpatient 0.2   0.368 0.605    NA if (require(\"dplyr\")) {   # You can combine selectors with '&' to be more specific:   example_isolates %>%     select(penicillins() & administrable_per_os()) } #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP' #>   (piperacillin/tazobactam) #> ℹ For administrable_per_os() using columns 'OXA' (oxacillin), 'FLC' #>   (flucloxacillin), 'AMX' (amoxicillin), 'AMC' (amoxicillin/clavulanic acid), #>   'AMP' (ampicillin), 'CXM' (cefuroxime), 'KAN' (kanamycin), 'TMP' #>   (trimethoprim), 'NIT' (nitrofurantoin), 'FOS' (fosfomycin), 'LNZ' #>   (linezolid), 'CIP' (ciprofloxacin), 'MFX' (moxifloxacin), 'VAN' #>   (vancomycin), 'TCY' (tetracycline), 'DOX' (doxycycline), 'ERY' #>   (erythromycin), 'CLI' (clindamycin), 'AZM' (azithromycin), 'MTR' #>   (metronidazole), 'CHL' (chloramphenicol), 'COL' (colistin), and 'RIF' #>   (rifampicin) #> # A tibble: 2,000 × 5 #>    OXA   FLC   AMX   AMC   AMP   #>    <sir> <sir> <sir> <sir> <sir> #>  1 NA    NA    NA    I     NA    #>  2 NA    NA    NA    I     NA    #>  3 NA    R     NA    NA    NA    #>  4 NA    R     NA    NA    NA    #>  5 NA    R     NA    NA    NA    #>  6 NA    R     NA    NA    NA    #>  7 NA    S     R     S     R     #>  8 NA    S     R     S     R     #>  9 NA    R     NA    NA    NA    #> 10 NA    S     NA    NA    NA    #> # ℹ 1,990 more rows if (require(\"dplyr\")) {   # get AMR for only drugs that matter - no intrinsic resistance:   example_isolates %>%     filter(mo_genus() %in% c(\"Escherichia\", \"Klebsiella\")) %>%     group_by(ward) %>%     summarise(across(not_intrinsic_resistant(), resistance)) } #> ℹ Using column 'mo' as input for mo_genus() #> ℹ For not_intrinsic_resistant() removing columns 'PEN' #>   (benzylpenicillin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'TEC' #>   (teicoplanin), 'ERY' (erythromycin), 'CLI' (clindamycin), 'AZM' #>   (azithromycin), and 'RIF' (rifampicin) #> Warning: There were 52 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `across(not_intrinsic_resistant(), resistance)`. #> ℹ In group 1: `ward = \"Clinical\"`. #> Caused by warning: #> ! Introducing NA: no results available for OXA in group: ward = \"Clinical\" #> (minimum = 30). #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 51 remaining warnings. #> # A tibble: 3 × 33 #>   ward    OXA   FLC    AMX    AMC    AMP     TZP     CZO     FEP     CXM     FOX #>   <chr> <dbl> <dbl>  <dbl>  <dbl>  <dbl>   <dbl>   <dbl>   <dbl>   <dbl>   <dbl> #> 1 Clin…    NA    NA  0.606  0.121  0.606  0.0504  0.0656  0.0159  0.0622  0.0648 #> 2 ICU      NA    NA  0.535  0.172  0.535  0.119  NA       0.0722  0.0828  0.0992 #> 3 Outp…    NA    NA NA     NA     NA     NA      NA      NA      NA      NA      #> # ℹ 22 more variables: CTX <dbl>, CAZ <dbl>, CRO <dbl>, GEN <dbl>, TOB <dbl>, #> #   AMK <dbl>, KAN <dbl>, TMP <dbl>, SXT <dbl>, NIT <dbl>, FOS <dbl>, #> #   CIP <dbl>, MFX <dbl>, TCY <dbl>, TGC <dbl>, DOX <dbl>, IPM <dbl>, #> #   MEM <dbl>, MTR <dbl>, CHL <dbl>, COL <dbl>, MUP <dbl> if (require(\"dplyr\")) {   # get susceptibility for antibiotics whose name contains \"trim\":   example_isolates %>%     filter(first_isolate()) %>%     group_by(ward) %>%     summarise(across(ab_selector(name %like% \"trim\"), susceptibility)) } #> ℹ For ab_selector(name %like% \"trim\") using columns 'TMP' (trimethoprim) #>   and 'SXT' (trimethoprim/sulfamethoxazole) #> # A tibble: 3 × 3 #>   ward         TMP   SXT #>   <chr>      <dbl> <dbl> #> 1 Clinical   0.627 0.808 #> 2 ICU        0.549 0.778 #> 3 Outpatient 0.667 0.821 if (require(\"dplyr\")) {   # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):   example_isolates %>%     select(carbapenems()) } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> # A tibble: 2,000 × 2 #>    IPM   MEM   #>    <sir> <sir> #>  1 NA    NA    #>  2 NA    NA    #>  3 NA    NA    #>  4 NA    NA    #>  5 NA    NA    #>  6 NA    NA    #>  7 NA    NA    #>  8 NA    NA    #>  9 NA    NA    #> 10 NA    NA    #> # ℹ 1,990 more rows if (require(\"dplyr\")) {   # this will select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB':   example_isolates %>%     select(mo, aminoglycosides()) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 2,000 × 5 #>    mo           GEN   TOB   AMK   KAN   #>    <mo>         <sir> <sir> <sir> <sir> #>  1 B_ESCHR_COLI NA    NA    NA    NA    #>  2 B_ESCHR_COLI NA    NA    NA    NA    #>  3 B_STPHY_EPDR NA    NA    NA    NA    #>  4 B_STPHY_EPDR NA    NA    NA    NA    #>  5 B_STPHY_EPDR NA    NA    NA    NA    #>  6 B_STPHY_EPDR NA    NA    NA    NA    #>  7 B_STPHY_AURS NA    S     NA    NA    #>  8 B_STPHY_AURS NA    S     NA    NA    #>  9 B_STPHY_EPDR NA    NA    NA    NA    #> 10 B_STPHY_EPDR NA    NA    NA    NA    #> # ℹ 1,990 more rows if (require(\"dplyr\")) {   # any() and all() work in dplyr's filter() too:   example_isolates %>%     filter(       any(aminoglycosides() == \"R\"),       all(cephalosporins_2nd() == \"R\")     ) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For cephalosporins_2nd() using columns 'CXM' (cefuroxime) and 'FOX' #>   (cefoxitin) #> # A tibble: 112 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  2 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R     #>  3 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  4 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA    #>  5 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA    #>  6 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R     #>  7 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R     #>  8 2003-08-13 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  9 2003-09-05 F35553     52 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #> 10 2004-06-09 529296     69 M      ICU      B_ENTRC_FACM NA    NA    NA    NA    #> # ℹ 102 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # also works with c():   example_isolates %>%     filter(any(c(carbapenems(), aminoglycosides()) == \"R\")) } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 531 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  2 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R     #>  3 2002-03-17 B30560     78 M      Clinical B_STPHY_CONS R     NA    R     R     #>  4 2002-04-04 E61143     67 M      Clinical B_STRPT_SNGN S     NA    NA    S     #>  5 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  6 2002-04-14 F30196     73 M      Outpati… B_STRPT_GRPB S     NA    S     S     #>  7 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  8 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  9 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #> 10 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #> # ℹ 521 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # not setting any/all will automatically apply all():   example_isolates %>%     filter(aminoglycosides() == \"R\") } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ Assuming a filter on all 4 aminoglycosides. Wrap around all() or #>   any() to prevent this note. #> # A tibble: 427 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinical B_ENTRC_FACM NA    NA    NA    NA    #>  2 2002-03-17 B30560     78 M      Clinical B_STPHY_CONS R     NA    R     R     #>  3 2002-04-04 E61143     67 M      Clinical B_STRPT_SNGN S     NA    NA    S     #>  4 2002-04-08 130252     78 M      ICU      B_ENTRC_FCLS NA    NA    NA    NA    #>  5 2002-04-14 F30196     73 M      Outpati… B_STRPT_GRPB S     NA    S     S     #>  6 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  7 2002-05-07 D91570     83 M      Clinical B_STPHY_CONS R     NA    R     R     #>  8 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #>  9 2002-05-14 077552     86 F      Clinical B_STRPT_PNMN S     NA    NA    S     #> 10 2002-05-16 D25302     65 F      ICU      B_STRPT_ANGN S     NA    NA    S     #> # ℹ 417 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # this will select columns 'mo' and all antimycobacterial drugs ('RIF'):   example_isolates %>%     select(mo, ab_class(\"mycobact\")) } #> ℹ For ab_class(\"mycobact\") using column 'RIF' (rifampicin) #> # A tibble: 2,000 × 2 #>    mo           RIF   #>    <mo>         <sir> #>  1 B_ESCHR_COLI R     #>  2 B_ESCHR_COLI R     #>  3 B_STPHY_EPDR NA    #>  4 B_STPHY_EPDR NA    #>  5 B_STPHY_EPDR NA    #>  6 B_STPHY_EPDR NA    #>  7 B_STPHY_AURS NA    #>  8 B_STPHY_AURS NA    #>  9 B_STPHY_EPDR NA    #> 10 B_STPHY_EPDR NA    #> # ℹ 1,990 more rows if (require(\"dplyr\")) {   # get bug/drug combinations for only glycopeptides in Gram-positives:   example_isolates %>%     filter(mo_is_gram_positive()) %>%     select(mo, glycopeptides()) %>%     bug_drug_combinations() %>%     format() } #> ℹ Using column 'mo' as input for mo_is_gram_positive() #> ℹ For glycopeptides() using columns 'VAN' (vancomycin) and 'TEC' #>   (teicoplanin) #> # A tibble: 2 × 8 #>   Group      Drug  CoNS  `E. faecalis` `S. aureus` `S. epidermidis` `S. hominis` #>   <chr>      <chr> <chr> <chr>         <chr>       <chr>            <chr>        #> 1 \"Glycopep… Teic… \"\"    \"\"            \" 0.0% (0/… \"64.1% (25/39)\"  \" 6.8% (4/5… #> 2 \"\"         Vanc… \" 0.… \" 0.0% (0/39… \" 0.0% (0/… \" 0.0% (0/171)\"  \" 0.0% (0/8… #> # ℹ 1 more variable: `S. pneumoniae` <chr> if (require(\"dplyr\")) {   data.frame(     some_column = \"some_value\",     J01CA01 = \"S\"   ) %>% # ATC code of ampicillin     select(penicillins()) # only the 'J01CA01' column will be selected } #> ℹ For penicillins() using column 'J01CA01' (ampicillin) #>   J01CA01 #> 1       S if (require(\"dplyr\")) {   # with recent versions of dplyr, this is all equal:   x <- example_isolates[carbapenems() == \"R\", ]   y <- example_isolates %>% filter(carbapenems() == \"R\")   z <- example_isolates %>% filter(if_all(carbapenems(), ~ .x == \"R\"))   identical(x, y) && identical(y, z) } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Assuming a filter on all 2 carbapenems. Wrap around all() or any() to #>   prevent this note. #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Assuming a filter on all 2 carbapenems. Wrap around all() or any() to #>   prevent this note. #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> [1] TRUE   # data.table --------------------------------------------------------------  # data.table is supported as well, just use it in the same way as with # base R, but add `with = FALSE` if using a single AB selector.  if (require(\"data.table\")) {   dt <- as.data.table(example_isolates)    # this does not work, it returns column *names*   dt[, carbapenems()] } #> Loading required package: data.table #>  #> Attaching package: ‘data.table’ #> The following objects are masked from ‘package:dplyr’: #>  #>     between, first, last #> The following objects are masked from ‘package:AMR’: #>  #>     %like%, like #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> [1] \"IPM\" \"MEM\" #> attr(,\"class\") #> [1] \"ab_selector\" \"character\"   if (require(\"data.table\")) {   # so `with = FALSE` is required   dt[, carbapenems(), with = FALSE] } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #>        IPM  MEM #>    1: <NA> <NA> #>    2: <NA> <NA> #>    3: <NA> <NA> #>    4: <NA> <NA> #>    5: <NA> <NA> #>   ---           #> 1996: <NA> <NA> #> 1997:    S    S #> 1998:    S    S #> 1999:    S    S #> 2000:    S    S  # for multiple selections or AB selectors, `with = FALSE` is not needed: if (require(\"data.table\")) {   dt[, c(\"mo\", aminoglycosides())] } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #>                 mo  GEN  TOB  AMK  KAN #>    1: B_ESCHR_COLI <NA> <NA> <NA> <NA> #>    2: B_ESCHR_COLI <NA> <NA> <NA> <NA> #>    3: B_STPHY_EPDR <NA> <NA> <NA> <NA> #>    4: B_STPHY_EPDR <NA> <NA> <NA> <NA> #>    5: B_STPHY_EPDR <NA> <NA> <NA> <NA> #>   ---                                  #> 1996: B_STRPT_PNMN    R    R    R    R #> 1997: B_ESCHR_COLI    S    S    S <NA> #> 1998: B_STPHY_CONS    S <NA> <NA> <NA> #> 1999: B_ESCHR_COLI    S    S <NA> <NA> #> 2000: B_KLBSL_PNMN    S    S <NA> <NA> if (require(\"data.table\")) {   dt[, c(carbapenems(), aminoglycosides())] } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #>        IPM  MEM  GEN  TOB  AMK  KAN #>    1: <NA> <NA> <NA> <NA> <NA> <NA> #>    2: <NA> <NA> <NA> <NA> <NA> <NA> #>    3: <NA> <NA> <NA> <NA> <NA> <NA> #>    4: <NA> <NA> <NA> <NA> <NA> <NA> #>    5: <NA> <NA> <NA> <NA> <NA> <NA> #>   ---                               #> 1996: <NA> <NA>    R    R    R    R #> 1997:    S    S    S    S    S <NA> #> 1998:    S    S    S <NA> <NA> <NA> #> 1999:    S    S    S    S <NA> <NA> #> 2000:    S    S    S    S <NA> <NA>  # row filters are also supported: if (require(\"data.table\")) {   dt[any(carbapenems() == \"S\"), ] } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #>            date patient age gender       ward           mo PEN  OXA  FLC  AMX #>   1: 2002-01-19  738003  71      M   Clinical B_ESCHR_COLI   R <NA> <NA> <NA> #>   2: 2002-01-19  738003  71      M   Clinical B_ESCHR_COLI   R <NA> <NA> <NA> #>   3: 2002-01-22  F35553  50      M        ICU B_PROTS_MRBL   R <NA> <NA> <NA> #>   4: 2002-01-22  F35553  50      M        ICU B_PROTS_MRBL   R <NA> <NA> <NA> #>   5: 2002-02-05  067927  45      F        ICU B_SERRT_MRCS   R <NA> <NA>    R #>  ---                                                                          #> 905: 2005-04-12  D71461  70      M        ICU B_ESCHR_COLI   R <NA> <NA>    S #> 906: 2009-11-12  650870  69      F Outpatient B_ESCHR_COLI   R <NA> <NA>    S #> 907: 2012-06-14  8CBCF2  41      F   Clinical B_STPHY_CONS   R    S    S <NA> #> 908: 2012-10-11  175532  78      M   Clinical B_ESCHR_COLI   R <NA> <NA>    R #> 909: 2013-11-23  A97263  77      M   Clinical B_KLBSL_PNMN   R <NA> <NA>    R #>      AMC  AMP  TZP  CZO  FEP CXM  FOX  CTX  CAZ  CRO  GEN  TOB  AMK  KAN  TMP #>   1:   I <NA> <NA> <NA> <NA>   S <NA>    S <NA>    S <NA>    S <NA> <NA>    S #>   2:   I <NA> <NA> <NA> <NA>   S <NA>    S <NA>    S <NA>    S <NA> <NA>    S #>   3:   I <NA> <NA> <NA> <NA>   S <NA>    S    S    S <NA> <NA> <NA> <NA>    S #>   4:   I <NA> <NA> <NA> <NA>   S <NA>    S    S    S <NA> <NA> <NA> <NA>    S #>   5:   R    R <NA>    R <NA>   R    R <NA> <NA> <NA> <NA> <NA> <NA> <NA>    S #>  ---                                                                          #> 905:   S    S    S <NA>    S   S    S    S    S    S    S    S    S <NA> <NA> #> 906:   S    S    S    S    S   S    S    S    S    S    S    S    S <NA>    S #> 907:   S <NA> <NA>    S    S   S    S    S    R    S    S <NA> <NA> <NA>    S #> 908:   S    R    S <NA>    S   R    R    S    S    S    S    S <NA> <NA>    R #> 909:   S    R    S <NA>    S   S    S    S    S    S    S    S <NA> <NA>    S #>      SXT  NIT  FOS  LNZ  CIP  MFX VAN  TEC  TCY  TGC  DOX ERY CLI AZM IPM  MEM #>   1:   S <NA> <NA>    R <NA> <NA>   R    R <NA> <NA> <NA>   R   R   R   S <NA> #>   2:   S <NA> <NA>    R <NA> <NA>   R    R <NA> <NA> <NA>   R   R   R   S <NA> #>   3:   S    R <NA>    R    S <NA>   R    R    R    R    R   R   R   R   S <NA> #>   4:   S    R <NA>    R    S <NA>   R    R    R    R    R   R   R   R   S <NA> #>   5:   S    R <NA>    R    S <NA>   R    R    R    R    R   R   R   R   S <NA> #>  ---                                                                           #> 905:   S    S <NA>    R    S <NA>   R    R <NA> <NA> <NA>   R   R   R   S    S #> 906:   S    S <NA>    R    S <NA>   R    R <NA> <NA> <NA>   R   R   R   S    S #> 907:   S <NA> <NA> <NA>    S <NA>   S <NA> <NA> <NA> <NA>   S   S   S   S    S #> 908:   R    R <NA>    R    R    R   R    R <NA> <NA> <NA>   R   R   R   S    S #> 909:   S    S <NA>    R    S <NA>   R    R <NA> <NA> <NA>   R   R   R   S    S #>       MTR  CHL  COL  MUP  RIF #>   1: <NA> <NA> <NA> <NA>    R #>   2: <NA> <NA> <NA> <NA>    R #>   3: <NA> <NA>    R <NA>    R #>   4: <NA> <NA>    R <NA>    R #>   5: <NA> <NA>    R <NA>    R #>  ---                          #> 905: <NA> <NA> <NA> <NA>    R #> 906: <NA> <NA> <NA> <NA>    R #> 907: <NA> <NA>    R <NA> <NA> #> 908: <NA> <NA>    S <NA>    R #> 909: <NA> <NA>    S <NA>    R if (require(\"data.table\")) {   dt[any(carbapenems() == \"S\"), penicillins(), with = FALSE] } #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ For penicillins() using columns 'PEN' (benzylpenicillin), 'OXA' #>   (oxacillin), 'FLC' (flucloxacillin), 'AMX' (amoxicillin), 'AMC' #>   (amoxicillin/clavulanic acid), 'AMP' (ampicillin), and 'TZP' #>   (piperacillin/tazobactam) #>      PEN  OXA  FLC  AMX AMC  AMP  TZP #>   1:   R <NA> <NA> <NA>   I <NA> <NA> #>   2:   R <NA> <NA> <NA>   I <NA> <NA> #>   3:   R <NA> <NA> <NA>   I <NA> <NA> #>   4:   R <NA> <NA> <NA>   I <NA> <NA> #>   5:   R <NA> <NA>    R   R    R <NA> #>  ---                                  #> 905:   R <NA> <NA>    S   S    S    S #> 906:   R <NA> <NA>    S   S    S    S #> 907:   R    S    S <NA>   S <NA> <NA> #> 908:   R <NA> <NA>    R   S    R    S #> 909:   R <NA> <NA>    R   S    R    S # }"},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Sets with 603 Antimicrobial Drugs — antibiotics","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"Two data sets containing antibiotics/antimycotics antivirals. Use .ab() one ab_* functions retrieve values antibiotics data set. Three identifiers included data set: antibiotic ID (ab, primarily used package) defined WHONET/EARS-Net, ATC code (atc) defined , Compound ID (cid) found PubChem. properties data set derived one codes. Note drugs multiple ATC codes.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"","code":"antibiotics  antivirals"},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"object class tbl_df (inherits tbl, data.frame) 120 rows 11 columns.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"for-the-antibiotics-data-set-a-tibble-with-observations-and-variables-","dir":"Reference","previous_headings":"","what":"For the antibiotics data set: a tibble with 483 observations and 14 variables:","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"ab Antibiotic ID used package (AMC), using official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes available cid Compound ID found PubChem name Official name used WHONET/EARS-Net group short concise group name, based WHONET WHOCC definitions atc ATC codes (Anatomical Therapeutic Chemical) defined WHOCC, like J01CR02 atc_group1 Official pharmacological subgroup (3rd level ATC code) defined WHOCC, like \"Macrolides, lincosamides streptogramins\" atc_group2 Official chemical subgroup (4th level ATC code) defined WHOCC, like \"Macrolides\" abbr List abbreviations used many countries, also antibiotic susceptibility testing (AST) synonyms Synonyms (often trade names) drug, found PubChem based compound ID oral_ddd Defined Daily Dose (DDD), oral treatment, currently available 174 drugs oral_units Units oral_ddd iv_ddd Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available 146 drugs iv_units Units iv_ddd loinc LOINC codes (Logical Observation Identifiers Names Codes) associated name antimicrobial drug. Use ab_loinc() retrieve quickly, see ab_property().","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"for-the-antivirals-data-set-a-tibble-with-observations-and-variables-","dir":"Reference","previous_headings":"","what":"For the antivirals data set: a tibble with 120 observations and 11 variables:","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"av Antibiotic ID used package (AMC), using official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes available name Official name used WHONET/EARS-Net atc ATC codes (Anatomical Therapeutic Chemical) defined WHOCC cid Compound ID found PubChem atc_group Official pharmacological subgroup (3rd level ATC code) defined WHOCC synonyms Synonyms (often trade names) drug, found PubChem based compound ID oral_ddd Defined Daily Dose (DDD), oral treatment oral_units Units oral_ddd iv_ddd Defined Daily Dose (DDD), parenteral treatment iv_units Units iv_ddd loinc LOINC codes (Logical Observation Identifiers Names Codes) associated name antimicrobial drug.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology (WHOCC): https://www.whocc./atc_ddd_index/ Logical Observation Identifiers Names Codes (LOINC), Version 2.73 (8 August, 2022). Accessed https://loinc.org 30 October, 2022. European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"Properties based ATC code available ATC available. properties : atc_group1, atc_group2, oral_ddd, oral_units, iv_ddd iv_units. Synonyms (.e. trade names) derived PubChem Compound ID (column cid) consequently available CID available.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"Like data sets package, data sets publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/antibiotics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Sets with 603 Antimicrobial Drugs — antibiotics","text":"","code":"antibiotics #> # A tibble: 483 × 14 #>    ab        cid name   group atc   atc_group1 atc_group2 abbreviations synonyms #>    <ab>    <dbl> <chr>  <chr> <lis> <chr>      <chr>      <list>        <named > #>  1 AMA      4649 4-ami… Anti… <chr> Drugs for… Aminosali… <chr [1]>     <chr>    #>  2 ACM   6450012 Acety… Macr… <chr> NA         NA         <chr [1]>     <chr>    #>  3 ASP  49787020 Acety… Macr… <chr> NA         NA         <chr [1]>     <chr>    #>  4 ALS      8954 Aldes… Othe… <chr> Drugs for… Drugs for… <chr [1]>     <chr>    #>  5 AMK     37768 Amika… Amin… <chr> Aminoglyc… Other ami… <chr [5]>     <chr>    #>  6 AKF        NA Amika… Amin… <chr> NA         NA         <chr [1]>     <chr>    #>  7 AMX     33613 Amoxi… Beta… <chr> Beta-lact… Penicilli… <chr [3]>     <chr>    #>  8 AMC  23665637 Amoxi… Beta… <chr> Beta-lact… Combinati… <chr [5]>     <chr>    #>  9 AXS    465441 Amoxi… Beta… <chr> NA         NA         <chr [1]>     <chr>    #> 10 AMB   5280965 Ampho… Anti… <chr> Antimycot… Antibioti… <chr [3]>     <chr>    #> # ℹ 473 more rows #> # ℹ 5 more variables: oral_ddd <dbl>, oral_units <chr>, iv_ddd <dbl>, #> #   iv_units <chr>, loinc <list> antivirals #> # A tibble: 120 × 11 #>    av       name      atc      cid atc_group synonyms oral_ddd oral_units iv_ddd #>    <av>     <chr>     <chr>  <dbl> <chr>     <list>      <dbl> <chr>       <dbl> #>  1 ABA      Abacavir  J05A… 4.41e5 Nucleosi… <chr>         0.6 g              NA #>  2 ACI      Aciclovir J05A… 1.35e8 Nucleosi… <chr>         4   g               4 #>  3 ADD      Adefovir… J05A… 6.09e4 Nucleosi… <chr>        10   mg             NA #>  4 AME      Amenamev… J05A… 1.14e7 Other an… <chr>         0.4 g              NA #>  5 AMP      Amprenav… J05A… 6.50e4 Protease… <chr>         1.2 g              NA #>  6 ASU      Asunapre… J05A… 1.61e7 Antivira… <chr>         0.2 g              NA #>  7 ATA      Atazanav… J05A… 1.48e5 Protease… <chr>         0.3 g              NA #>  8 ATA+COBI Atazanav… J05A… 8.66e7 Antivira… <chr>        NA   NA             NA #>  9 ATA+RIT  Atazanav… J05A… 2.51e7 Antivira… <chr>         0.3 g              NA #> 10 BAM      Baloxavi… J05A… 1.24e8 Other an… <chr>        40   mg             NA #> # ℹ 110 more rows #> # ℹ 2 more variables: iv_units <chr>, loinc <list>"},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to an Antibiotic ID — as.ab","title":"Transform Input to an Antibiotic ID — as.ab","text":"Use function determine antibiotic drug code one antibiotics. data set antibiotics searched abbreviations, official names synonyms (brand names).","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to an Antibiotic ID — as.ab","text":"","code":"as.ab(x, flag_multiple_results = TRUE, info = interactive(), ...)  is.ab(x)"},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to an Antibiotic ID — as.ab","text":"x character vector determine antibiotic ID flag_multiple_results logical indicate whether note printed console probably one antibiotic drug code name can retrieved single input value. info logical indicate whether progress bar printed - default TRUE interactive mode ... arguments passed internal functions","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to an Antibiotic ID — as.ab","text":"character  vector additional class ab","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to an Antibiotic ID — as.ab","text":"entries antibiotics data set three different identifiers: human readable EARS-Net code (column ab, used ECDC WHONET), ATC code (column atc, used ), CID code (column cid, Compound ID, used PubChem). data set contains 5,000 official brand names many different countries, found PubChem. drugs contain multiple ATC codes. properties searched user input. .ab() can correct different forms misspelling: Wrong spelling drug names (\"tobramicin\" \"gentamycin\"), corrects audible similarities f/ph, x/ks, c/z/s, t/th, etc. many vowels consonants Switching two characters (\"mreopenem\", often case clinical data, doctors typed fast) Digitalised paper records, leaving artefacts like 0/o/O (zero O's), B/8, n/r, etc. Use ab_* functions get properties based returned antibiotic ID, see Examples. Note: .ab() ab_* functions may use long regular expression match brand names antimicrobial drugs. may fail systems. can add manual codes considered .ab() ab_* functions, see add_custom_antimicrobials().","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Transform Input to an Antibiotic ID — as.ab","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"Transform Input to an Antibiotic ID — as.ab","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Transform Input to an Antibiotic ID — as.ab","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.ab.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to an Antibiotic ID — as.ab","text":"","code":"# these examples all return \"ERY\", the ID of erythromycin: as.ab(\"J01FA01\") #> Class 'ab' #> [1] ERY as.ab(\"J 01 FA 01\") #> Class 'ab' #> [1] ERY as.ab(\"Erythromycin\") #> Class 'ab' #> [1] ERY as.ab(\"eryt\") #> Class 'ab' #> [1] ERY as.ab(\"   eryt 123\") #> Class 'ab' #> [1] ERY as.ab(\"ERYT\") #> Class 'ab' #> [1] ERY as.ab(\"ERY\") #> Class 'ab' #> [1] ERY as.ab(\"eritromicine\") # spelled wrong, yet works #> Class 'ab' #> [1] ERY as.ab(\"Erythrocin\") # trade name #> Class 'ab' #> [1] ERY as.ab(\"Romycin\") # trade name #> Class 'ab' #> [1] ERY  # spelling from different languages and dyslexia are no problem ab_atc(\"ceftriaxon\") #> [1] \"J01DD04\" ab_atc(\"cephtriaxone\") # small spelling error #> [1] \"J01DD04\" ab_atc(\"cephthriaxone\") # or a bit more severe #> [1] \"J01DD04\" ab_atc(\"seephthriaaksone\") # and even this works #> [1] \"J01DD04\"  # use ab_* functions to get a specific properties (see ?ab_property); # they use as.ab() internally: ab_name(\"J01FA01\") #> [1] \"Erythromycin\" ab_name(\"eryt\") #> [1] \"Erythromycin\"  # \\donttest{ if (require(\"dplyr\")) {   # you can quickly rename 'sir' columns using set_ab_names() with dplyr:   example_isolates %>%     set_ab_names(where(is.sir), property = \"atc\") } #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           J01CE01 J01CF04 J01CF05 #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir>   <sir>   <sir>   #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R       NA      NA      #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R       NA      NA      #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R       NA      S       #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R       NA      S       #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R       NA      R       #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R       NA      S       #> # ℹ 1,990 more rows #> # ℹ 37 more variables: J01CA04 <sir>, J01CR02 <sir>, J01CA01 <sir>, #> #   J01CR05 <sir>, J01DB04 <sir>, J01DE01 <sir>, J01DC02 <sir>, J01DC01 <sir>, #> #   J01DD01 <sir>, J01DD02 <sir>, J01DD04 <sir>, J01GB03 <sir>, J01GB01 <sir>, #> #   J01GB06 <sir>, J01GB04 <sir>, J01EA01 <sir>, J01EE01 <sir>, J01XE01 <sir>, #> #   J01XX01 <sir>, J01XX08 <sir>, J01MA02 <sir>, J01MA14 <sir>, J01XA01 <sir>, #> #   J01XA02 <sir>, J01AA07 <sir>, J01AA12 <sir>, J01AA02 <sir>, … # }"},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to an Antiviral Drug ID — as.av","title":"Transform Input to an Antiviral Drug ID — as.av","text":"Use function determine antiviral drug code one antiviral drugs. data set antivirals searched abbreviations, official names synonyms (brand names).","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to an Antiviral Drug ID — as.av","text":"","code":"as.av(x, flag_multiple_results = TRUE, info = interactive(), ...)  is.av(x)"},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to an Antiviral Drug ID — as.av","text":"x character vector determine antiviral drug ID flag_multiple_results logical indicate whether note printed console probably one antiviral drug code name can retrieved single input value. info logical indicate whether progress bar printed - default TRUE interactive mode ... arguments passed internal functions","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to an Antiviral Drug ID — as.av","text":"character  vector additional class ab","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to an Antiviral Drug ID — as.av","text":"entries antivirals data set three different identifiers: human readable EARS-Net code (column ab, used ECDC WHONET), ATC code (column atc, used ), CID code (column cid, Compound ID, used PubChem). data set contains 5,000 official brand names many different countries, found PubChem. drugs contain multiple ATC codes. properties searched user input. .av() can correct different forms misspelling: Wrong spelling drug names (\"acyclovir\"), corrects audible similarities f/ph, x/ks, c/z/s, t/th, etc. many vowels consonants Switching two characters (\"aycclovir\", often case clinical data, doctors typed fast) Digitalised paper records, leaving artefacts like 0/o/O (zero O's), B/8, n/r, etc. Use av_* functions get properties based returned antiviral drug ID, see Examples. Note: .av() av_* functions may use long regular expression match brand names antimicrobial drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Transform Input to an Antiviral Drug ID — as.av","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"whocc","dir":"Reference","previous_headings":"","what":"WHOCC","title":"Transform Input to an Antiviral Drug ID — as.av","text":"package contains ~550 antibiotic, antimycotic antiviral drugs Anatomical Therapeutic Chemical (ATC) codes, ATC groups Defined Daily Dose (DDD) World Health Organization Collaborating Centre Drug Statistics Methodology (WHOCC, https://www.whocc.) Pharmaceuticals Community Register European Commission (https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm). become gold standard international drug utilisation monitoring research. WHOCC located Oslo Norwegian Institute Public Health funded Norwegian government. European Commission executive European Union promotes general interest. NOTE: WHOCC copyright allow use commercial purposes, unlike info package. See https://www.whocc./copyright_disclaimer/.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Transform Input to an Antiviral Drug ID — as.av","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.av.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to an Antiviral Drug ID — as.av","text":"","code":"# these examples all return \"ACI\", the ID of aciclovir: as.av(\"J05AB01\") #> Class 'av' #> [1] ACI as.av(\"J 05 AB 01\") #> Class 'av' #> [1] ACI as.av(\"Aciclovir\") #> Class 'av' #> [1] ACI as.av(\"aciclo\") #> Class 'av' #> [1] ACI as.av(\"   aciclo 123\") #> Class 'av' #> [1] ACI as.av(\"ACICL\") #> Class 'av' #> [1] ACI as.av(\"ACI\") #> Class 'av' #> [1] ACI as.av(\"Virorax\") # trade name #> Class 'av' #> [1] ACI as.av(\"Zovirax\") # trade name #> Class 'av' #> [1] ACI  as.av(\"acyklofir\") # severe spelling error, yet works #> Class 'av' #> [1] ACI  # use av_* functions to get a specific properties (see ?av_property); # they use as.av() internally: av_name(\"J05AB01\") #> [1] \"Aciclovir\" av_name(\"acicl\") #> [1] \"Aciclovir\""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to Disk Diffusion Diameters — as.disk","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"transforms vector new class disk, disk diffusion growth zone size (around antibiotic disk) millimetres 6 50.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"","code":"as.disk(x, na.rm = FALSE)  NA_disk_  is.disk(x)"},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"object class disk (inherits integer) length 1.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"x vector na.rm logical indicating whether missing values removed","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"integer additional class disk","code":""},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"Interpret disk values SIR values .sir(). supports guidelines EUCAST CLSI. Disk diffusion growth zone sizes must 6 50 millimetres. Values higher 50 lower 100 maximised 50. others input values outside 6-50 range return NA. NA_disk_ missing value new disk class.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.disk.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to Disk Diffusion Diameters — as.disk","text":"","code":"# transform existing disk zones to the `disk` class (using base R) df <- data.frame(   microorganism = \"Escherichia coli\",   AMP = 20,   CIP = 14,   GEN = 18,   TOB = 16 ) df[, 2:5] <- lapply(df[, 2:5], as.disk) str(df) #> 'data.frame':\t1 obs. of  5 variables: #>  $ microorganism: chr \"Escherichia coli\" #>  $ AMP          : 'disk' int 20 #>  $ CIP          : 'disk' int 14 #>  $ GEN          : 'disk' int 18 #>  $ TOB          : 'disk' int 16  # \\donttest{ # transforming is easier with dplyr: if (require(\"dplyr\")) {   df %>% mutate(across(AMP:TOB, as.disk)) } #>      microorganism AMP CIP GEN TOB #> 1 Escherichia coli  20  14  18  16 # }  # interpret disk values, see ?as.sir as.sir(   x = as.disk(18),   mo = \"Strep pneu\", # `mo` will be coerced with as.mo()   ab = \"ampicillin\", # and `ab` with as.ab()   guideline = \"EUCAST\" ) #> => Interpreting disk diffusion zones of 'ampicillin' (AMP) according to #>    EUCAST 2022... #>  OK. #> Class 'sir' #> [1] R  # interpret whole data set, pretend to be all from urinary tract infections: as.sir(df, uti = TRUE) #> => Interpreting disk diffusion zones of column 'AMP' (ampicillin) according #>    to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'CIP' (ciprofloxacin) #>    according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'GEN' (gentamicin) according #>    to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according #>    to EUCAST 2022... #>  OK. #>      microorganism AMP CIP GEN TOB #> 1 Escherichia coli   S   R   S   S"},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"transforms vectors new class mic, treats input decimal numbers, maintaining operators (\">=\") allowing valid MIC values known field (medical) microbiology.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"","code":"as.mic(x, na.rm = FALSE)  NA_mic_  is.mic(x)  # S3 method for mic droplevels(x, as.mic = FALSE, ...)"},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"x character numeric vector na.rm logical indicating whether missing values removed .mic logical indicate whether mic class kept - default FALSE ... arguments passed methods","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"Ordered factor additional class mic, mathematical operations acts decimal numbers. Bare mind outcome mathematical operation MICs return numeric value.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"interpret MIC values SIR values, use .sir() MIC values. supports guidelines EUCAST (2013-2022) CLSI (2013-2022). class MIC values quite special data type: formally ordered factor valid MIC values factor levels (make sure valid MIC values retained), mathematical operation acts decimal numbers:   makes possible maintain operators often come MIC values, \">=\" \"<=\", even filtering using numeric values data analysis, e.g.:   following generic functions implemented MIC class: !, !=, %%, %/%, &, *, +, -, /, <, <=, ==, >, >=, ^, |, abs(), acos(), acosh(), (), (), asin(), asinh(), atan(), atanh(), ceiling(), cos(), cosh(), cospi(), cummax(), cummin(), cumprod(), cumsum(), digamma(), exp(), expm1(), floor(), gamma(), lgamma(), log(), log1p(), log2(), log10(), max(), mean(), min(), prod(), range(), round(), sign(), signif(), sin(), sinh(), sinpi(), sqrt(), sum(), tan(), tanh(), tanpi(), trigamma() trunc(). functions stats package also implemented: median(), quantile(), mad(), IQR(), fivenum(). Also, boxplot.stats() supported. Since sd() var() non-generic functions, extended. Use mad() alternative, use e.g. sd(.numeric(x)) x vector MIC values. Using .double() .numeric() MIC values remove operators return numeric vector. use .integer() MIC values R convention factors, return index factor levels (often useless regular users). Use droplevels() drop unused levels. default, return plain factor. Use droplevels(..., .mic = TRUE) maintain mic class. NA_mic_ missing value new mic class, analogous e.g. base R's NA_character_.","code":"x <- random_mic(10) x #> Class 'mic' #>  [1] 16     1      8      8      64     >=128  0.0625 32     32     16  is.factor(x) #> [1] TRUE  x[1] * 2 #> [1] 32  median(x) #> [1] 26 x[x > 4] #> Class 'mic' #> [1] 16    8     8     64    >=128 32    32    16  df <- data.frame(x, hospital = \"A\") subset(df, x > 4) # or with dplyr: df %>% filter(x > 4) #>        x hospital #> 1     16        A #> 5     64        A #> 6  >=128        A #> 8     32        A #> 9     32        A #> 10    16        A"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.mic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Input to Minimum Inhibitory Concentrations (MIC) — as.mic","text":"","code":"mic_data <- as.mic(c(\">=32\", \"1.0\", \"1\", \"1.00\", 8, \"<=0.128\", \"8\", \"16\", \"16\")) mic_data #> Class 'mic' #> [1] >=32    1       1       1       8       <=0.128 8       16      16      is.mic(mic_data) #> [1] TRUE  # this can also coerce combined MIC/SIR values: as.mic(\"<=0.002; S\") #> Class 'mic' #> [1] <=0.002  # mathematical processing treats MICs as numeric values fivenum(mic_data) #> [1]  0.128  1.000  8.000 16.000 32.000 quantile(mic_data) #>     0%    25%    50%    75%   100%  #>  0.128  1.000  8.000 16.000 32.000  all(mic_data < 512) #> [1] TRUE  # interpret MIC values as.sir(   x = as.mic(2),   mo = as.mo(\"Streptococcus pneumoniae\"),   ab = \"AMX\",   guideline = \"EUCAST\" ) #> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST #>    2022... #>  Note: #>    • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus #>      pneumoniae - assuming body site 'Meningitis'. #> Class 'sir' #> [1] R as.sir(   x = as.mic(c(0.01, 2, 4, 8)),   mo = as.mo(\"Streptococcus pneumoniae\"),   ab = \"AMX\",   guideline = \"EUCAST\" ) #> => Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST #>    2022... #>  Note: #>    • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus #>      pneumoniae - assuming body site 'Meningitis'. #> Class 'sir' #> [1] S R R R  # plot MIC values, see ?plot plot(mic_data)  plot(mic_data, mo = \"E. coli\", ab = \"cipro\")   if (require(\"ggplot2\")) {   autoplot(mic_data, mo = \"E. coli\", ab = \"cipro\") }  if (require(\"ggplot2\")) {   autoplot(mic_data, mo = \"E. coli\", ab = \"cipro\", language = \"nl\") # Dutch }  if (require(\"ggplot2\")) {   autoplot(mic_data, mo = \"E. coli\", ab = \"cipro\", language = \"uk\") # Ukrainian }"},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":null,"dir":"Reference","previous_headings":"","what":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"Use function get valid microorganism code (mo) based arbitrary user input. Determination done using intelligent rules complete taxonomic tree kingdoms Animalia, Archaea, Bacteria, Protozoa, microbial species kingdom Fungi (see Source). input can almost anything: full name (like \"Staphylococcus aureus\"), abbreviated name (\"S. aureus\"), abbreviation known field (\"MRSA\"), just genus. See Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"","code":"as.mo(   x,   Becker = FALSE,   Lancefield = FALSE,   minimum_matching_score = NULL,   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   reference_df = get_mo_source(),   ignore_pattern = getOption(\"AMR_ignore_pattern\", NULL),   cleaning_regex = getOption(\"AMR_cleaning_regex\", mo_cleaning_regex()),   language = get_AMR_locale(),   info = interactive(),   ... )  is.mo(x)  mo_uncertainties()  mo_renamed()  mo_failures()  mo_reset_session()  mo_cleaning_regex()"},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"x character vector data.frame one two columns Becker logical indicate whether staphylococci categorised coagulase-negative staphylococci (\"CoNS\") coagulase-positive staphylococci (\"CoPS\") instead species, according Karsten Becker et al. (see Source). Please see Details full list staphylococcal species converted. excludes Staphylococcus aureus default, use Becker = \"\" also categorise S. aureus \"CoPS\". Lancefield logical indicate whether beta-haemolytic Streptococcus categorised Lancefield groups instead species, according Rebecca C. Lancefield (see Source). streptococci categorised first group, e.g. Streptococcus dysgalactiae group C, although officially also categorised groups G L. . Please see Details full list streptococcal species converted. excludes enterococci default (group D), use Lancefield = \"\" also categorise enterococci group D. minimum_matching_score numeric value set lower limit MO matching score. left blank, determined automatically based character length x, taxonomic kingdom human pathogenicity. keep_synonyms logical indicate old, previously valid taxonomic names must preserved corrected currently accepted names. default FALSE, return note old taxonomic names processed. default can set package option AMR_keep_synonyms, .e. options(AMR_keep_synonyms = TRUE) options(AMR_keep_synonyms = FALSE). reference_df data.frame used extra reference translating x valid mo. See set_mo_source() get_mo_source() automate usage codes (e.g. used analysis organisation). ignore_pattern Perl-compatible regular expression (case-insensitive) matches x must return NA. can convenient exclude known non-relevant input can also set package option AMR_ignore_pattern, e.g. options(AMR_ignore_pattern = \"(reported|contaminated flora)\"). cleaning_regex Perl-compatible regular expression (case-insensitive) clean input x. Every matched part x removed. default, outcome mo_cleaning_regex(), removes texts brackets texts \"species\" \"serovar\". default can set package option AMR_cleaning_regex. language language translate text like \"growth\", defaults system language (see get_AMR_locale()) info logical indicate progress bar printed 25 items coerced - default TRUE interactive mode ... arguments passed functions","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"character  vector additional class mo","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"microorganism (MO) code package (class: mo) human readable typically looks like examples:   Values coerced considered 'unknown' returned MO code UNKNOWN warning. Use mo_* functions get properties based returned code, see Examples. .mo() function uses novel matching score algorithm (see Matching Score Microorganisms ) match input available microbial taxonomy package. lead effect e.g. \"E. coli\" (microorganism highly prevalent humans) return microbial ID Escherichia coli Entamoeba coli (microorganism less prevalent humans), although latter alphabetically come first. Becker = TRUE, following 85 staphylococci converted coagulase-negative group: S. argensis, S. arlettae, S. auricularis, S. borealis, S. caeli, S. caledonicus, S. canis, S. capitis, S. capitis capitis, S. capitis urealyticus, S. capitis ureolyticus, S. caprae, S. carnosus, S. carnosus carnosus, S. carnosus utilis, S. casei, S. caseolyticus, S. chromogenes, S. cohnii, S. cohnii cohnii, S. cohnii urealyticum, S. cohnii urealyticus, S. condimenti, S. croceilyticus, S. debuckii, S. devriesei, S. durrellii, S. edaphicus, S. epidermidis, S. equorum, S. equorum equorum, S. equorum linens, S. felis, S. fleurettii, S. gallinarum, S. haemolyticus, S. hominis, S. hominis hominis, S. hominis novobiosepticus, S. jettensis, S. kloosii, S. lentus, S. lloydii, S. lugdunensis, S. massiliensis, S. microti, S. muscae, S. nepalensis, S. pasteuri, S. petrasii, S. petrasii croceilyticus, S. petrasii jettensis, S. petrasii petrasii, S. petrasii pragensis, S. pettenkoferi, S. piscifermentans, S. pragensis, S. pseudoxylosus, S. pulvereri, S. ratti, S. rostri, S. saccharolyticus, S. saprophyticus, S. saprophyticus bovis, S. saprophyticus saprophyticus, S. schleiferi, S. schleiferi schleiferi, S. sciuri, S. sciuri carnaticus, S. sciuri lentus, S. sciuri rodentium, S. sciuri sciuri, S. simulans, S. stepanovicii, S. succinus, S. succinus casei, S. succinus succinus, S. taiwanensis, S. urealyticus, S. ureilyticus, S. veratri, S. vitulinus, S. vitulus, S. warneri, S. xylosus. following 16 staphylococci converted coagulase-positive group: S. agnetis, S. argenteus, S. coagulans, S. cornubiensis, S. delphini, S. hyicus, S. hyicus chromogenes, S. hyicus hyicus, S. intermedius, S. lutrae, S. pseudintermedius, S. roterodami, S. schleiferi coagulans, S. schweitzeri, S. simiae, S. singaporensis. Lancefield = TRUE, following streptococci converted corresponding Lancefield group: S. agalactiae (Group B), S. anginosus anginosus (Group F), S. anginosus whileyi (Group F), S. anginosus (Group F), S. canis (Group G), S. dysgalactiae dysgalactiae (Group C), S. dysgalactiae equisimilis (Group C), S. dysgalactiae (Group C), S. equi equi (Group C), S. equi ruminatorum (Group C), S. equi zooepidemicus (Group C), S. equi (Group C), S. pyogenes (Group ), S. salivarius salivarius (Group K), S. salivarius thermophilus (Group K), S. salivarius (Group K), S. sanguinis (Group H).","code":"Code               Full name   ---------------    --------------------------------------   B_KLBSL            Klebsiella   B_KLBSL_PNMN       Klebsiella pneumoniae   B_KLBSL_PNMN_RHNS  Klebsiella pneumoniae rhinoscleromatis   |   |    |    |   |   |    |    |   |   |    |    \\---> subspecies, a 3-5 letter acronym   |   |    \\----> species, a 3-6 letter acronym   |   \\----> genus, a 4-8 letter acronym   \\----> taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),                             F (Fungi), PL (Plantae), P (Protozoa)"},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"coping-with-uncertain-results","dir":"Reference","previous_headings":"","what":"Coping with Uncertain Results","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"Results non-exact taxonomic input based matching score. lowest allowed score can set minimum_matching_score argument. default determined based character length input, taxonomic kingdom human pathogenicity taxonomic outcome. values matched uncertainty, message shown suggest user evaluate results mo_uncertainties(), returns data.frame specifications. increase quality matching, cleaning_regex argument can used clean input (.e., x). must regular expression matches parts input removed input matched available microbial taxonomy. matched Perl-compatible case-insensitive. default value cleaning_regex outcome helper function mo_cleaning_regex(). three helper functions can run using .mo() function: Use mo_uncertainties() get data.frame prints pretty format taxonomic names guessed. output contains matching score matches (see Matching Score Microorganisms ). Use mo_failures() get character vector values coerced valid value. Use mo_renamed() get data.frame values coerced based old, previously accepted taxonomic names.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"microbial-prevalence-of-pathogens-in-humans","dir":"Reference","previous_headings":"","what":"Microbial Prevalence of Pathogens in Humans","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"coercion rules consider prevalence microorganisms humans, available prevalence column microorganisms data set. grouping human pathogenic prevalence explained section Matching Score Microorganisms .","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"Berends MS et al. (2022). AMR: R Package Working Antimicrobial Resistance Data. Journal Statistical Software, 104(3), 1-31; doi:10.18637/jss.v104.i03 Becker K et al. (2014). Coagulase-Negative Staphylococci. Clin Microbiol Rev. 27(4): 870-926; doi:10.1128/CMR.00109-13 Becker K et al. (2019). Implications identifying recently defined members S. aureus complex, S. argenteus S. schweitzeri: position paper members ESCMID Study Group staphylococci Staphylococcal Diseases (ESGS). Clin Microbiol Infect; doi:10.1016/j.cmi.2019.02.028 Becker K et al. (2020). Emergence coagulase-negative staphylococci. Expert Rev Anti Infect Ther. 18(4):349-366; doi:10.1080/14787210.2020.1730813 Lancefield RC (1933). serological differentiation human groups hemolytic streptococci. J Exp Med. 57(4): 571-95; doi:10.1084/jem.57.4.571 Berends MS et al. (2022). Trends Occurrence Phenotypic Resistance Coagulase-Negative Staphylococci (CoNS) Found Human Blood Northern Netherlands 2013 2019/ Micro.rganisms 10(9), 1801; doi:10.3390/microorganisms10091801 Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332 . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov Bartlett et al. (2022). comprehensive list bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269 Reimer et al. (2022). BacDive 2022: knowledge base standardized bacterial archaeal data.  Nucleic Acids Res. 2022 Jan 7;50(D1):D741-D746; doi:10.1093/nar/gkab961","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"matching-score-for-microorganisms","dir":"Reference","previous_headings":"","what":"Matching Score for Microorganisms","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"ambiguous user input .mo() mo_* functions, returned results chosen based matching score using mo_matching_score(). matching score \\(m\\), calculated :  : \\(x\\) user input; \\(n\\) taxonomic name (genus, species, subspecies); \\(l_n\\) length \\(n\\); \\(lev\\) Levenshtein distance function (counting insertion 1, deletion substitution 2) needed change \\(x\\) \\(n\\); \\(p_n\\) human pathogenic prevalence group \\(n\\), described ; \\(k_n\\) taxonomic kingdom \\(n\\), set Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5. grouping human pathogenic prevalence \\(p\\) based recent work Bartlett et al. (2022, doi:10.1099/mic.0.001269 ) extensively studied medical-scientific literature categorise bacterial species groups: Established, taxonomic species infected least three persons three references. records prevalence = 1.0 microorganisms data set; Putative, taxonomic species fewer three known cases. records prevalence = 1.25 microorganisms data set. Furthermore, genus present established list also prevalence = 1.0 microorganisms data set; genus present putative list prevalence = 1.25 microorganisms data set; species subspecies genus present two aforementioned groups, prevalence = 1.5 microorganisms data set; non-bacterial genus, species subspecies genus present following list, prevalence = 1.5 microorganisms data set: Absidia, Acanthamoeba, Acremonium, Aedes, Alternaria, Amoeba, Ancylostoma, Angiostrongylus, Anisakis, Anopheles, Apophysomyces, Aspergillus, Aureobasidium, Basidiobolus, Beauveria, Blastocystis, Blastomyces, Candida, Capillaria, Chaetomium, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Contracaecum, Cordylobia, Cryptococcus, Curvularia, Demodex, Dermatobia, Dientamoeba, Diphyllobothrium, Dirofilaria, Echinostoma, Entamoeba, Enterobius, Exophiala, Exserohilum, Fasciola, Fonsecaea, Fusarium, Giardia, Haloarcula, Halobacterium, Halococcus, Hendersonula, Heterophyes, Histomonas, Histoplasma, Hymenolepis, Hypomyces, Hysterothylacium, Leishmania, Malassezia, Malbranchea, Metagonimus, Meyerozyma, Microsporidium, Microsporum, Mortierella, Mucor, Mycocentrospora, Necator, Nectria, Ochroconis, Oesophagostomum, Oidiodendron, Opisthorchis, Pediculus, Penicillium, Phlebotomus, Phoma, Pichia, Piedraia, Pithomyces, Pityrosporum, Pneumocystis, Pseudallescheria, Pseudoterranova, Pulex, Rhizomucor, Rhizopus, Rhodotorula, Saccharomyces, Sarcoptes, Scolecobasidium, Scopulariopsis, Scytalidium, Spirometra, Sporobolomyces, Stachybotrys, Strongyloides, Syngamus, Taenia, Talaromyces, Toxocara, Trichinella, Trichobilharzia, Trichoderma, Trichomonas, Trichophyton, Trichosporon, Trichostrongylus, Trichuris, Tritirachium, Trombicula, Trypanosoma, Tunga, Wuchereria; records prevalence = 2.0 microorganisms data set. calculating matching score, characters \\(x\\) \\(n\\) ignored -Z, -z, 0-9, spaces parentheses. matches sorted descending matching score user input values, top match returned. lead effect e.g., \"E. coli\" return microbial ID Escherichia coli (\\(m = 0.688\\), highly prevalent microorganism found humans) Entamoeba coli (\\(m = 0.159\\), less prevalent microorganism humans), although latter alphabetically come first.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.mo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transform Arbitrary Input to Valid Microbial Taxonomy — as.mo","text":"","code":"# \\donttest{ # These examples all return \"B_STPHY_AURS\", the ID of S. aureus: as.mo(c(   \"sau\", # WHONET code   \"stau\",   \"STAU\",   \"staaur\",   \"S. aureus\",   \"S aureus\",   \"Sthafilokkockus aureus\", # handles incorrect spelling   \"Staphylococcus aureus (MRSA)\",   \"MRSA\", # Methicillin Resistant S. aureus   \"VISA\", # Vancomycin Intermediate S. aureus   \"VRSA\", # Vancomycin Resistant S. aureus   115329001 # SNOMED CT code )) #> Class 'mo' #>  [1] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS #>  [6] B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS B_STPHY_AURS #> [11] B_STPHY_AURS B_STPHY_AURS  # Dyslexia is no problem - these all work: as.mo(c(   \"Ureaplasma urealyticum\",   \"Ureaplasma urealyticus\",   \"Ureaplasmium urealytica\",   \"Ureaplazma urealitycium\" )) #> Class 'mo' #> [1] B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY B_URPLS_URLY  as.mo(\"Streptococcus group A\") #> Class 'mo' #> [1] B_STRPT_GRPA  as.mo(\"S. epidermidis\") # will remain species: B_STPHY_EPDR #> Class 'mo' #> [1] B_STPHY_EPDR as.mo(\"S. epidermidis\", Becker = TRUE) # will not remain species: B_STPHY_CONS #> Class 'mo' #> [1] B_STPHY_CONS  as.mo(\"S. pyogenes\") # will remain species: B_STRPT_PYGN #> Class 'mo' #> [1] B_STRPT_PYGN as.mo(\"S. pyogenes\", Lancefield = TRUE) # will not remain species: B_STRPT_GRPA #> Class 'mo' #> [1] B_STRPT_GRPA  # All mo_* functions use as.mo() internally too (see ?mo_property): mo_genus(\"E. coli\") #> [1] \"Escherichia\" mo_gramstain(\"ESCO\") #> [1] \"Gram-negative\" mo_is_intrinsic_resistant(\"ESCCOL\", ab = \"vanco\") #> ℹ Determining intrinsic resistance based on 'EUCAST Expert Rules' and #>   'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3 (2021). This note #>   will be shown once per session. #> [1] TRUE # }"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":null,"dir":"Reference","previous_headings":"","what":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"Interpret minimum inhibitory concentration (MIC) values disk diffusion diameters according EUCAST CLSI, clean existing SIR values. transforms input new class sir, ordered factor levels S < < R. breakpoints used interpretation publicly available clinical_breakpoints data set.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"","code":"as.sir(x, ...)  NA_sir_  is.sir(x)  is_sir_eligible(x, threshold = 0.05)  # S3 method for mic as.sir(   x,   mo = NULL,   ab = deparse(substitute(x)),   guideline = getOption(\"AMR_guideline\", \"EUCAST\"),   uti = NULL,   conserve_capped_values = FALSE,   add_intrinsic_resistance = FALSE,   reference_data = AMR::clinical_breakpoints,   include_screening = getOption(\"AMR_include_screening\", FALSE),   include_PKPD = getOption(\"AMR_include_PKPD\", TRUE),   ... )  # S3 method for disk as.sir(   x,   mo = NULL,   ab = deparse(substitute(x)),   guideline = getOption(\"AMR_guideline\", \"EUCAST\"),   uti = NULL,   add_intrinsic_resistance = FALSE,   reference_data = AMR::clinical_breakpoints,   include_screening = getOption(\"AMR_include_screening\", FALSE),   include_PKPD = getOption(\"AMR_include_PKPD\", TRUE),   ... )  # S3 method for data.frame as.sir(   x,   ...,   col_mo = NULL,   guideline = getOption(\"AMR_guideline\", \"EUCAST\"),   uti = NULL,   conserve_capped_values = FALSE,   add_intrinsic_resistance = FALSE,   reference_data = AMR::clinical_breakpoints,   include_screening = getOption(\"AMR_include_screening\", FALSE),   include_PKPD = getOption(\"AMR_include_PKPD\", TRUE) )  sir_interpretation_history(clean = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"object class sir (inherits ordered, factor) length 1.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"interpretations minimum inhibitory concentration (MIC) values disk diffusion diameters: M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 2013-2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/. M100 Performance Standard Antimicrobial Susceptibility Testing, 2013-2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m100/. Breakpoint tables interpretation MICs zone diameters, 2013-2022, European Committee Antimicrobial Susceptibility Testing (EUCAST). https://www.eucast.org/clinical_breakpoints.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"x vector values (class mic: MIC values mg/L, class disk: disk diffusion radius millimetres) ... using data.frame: names columns apply .sir() (supports tidy selection column1:column4). Otherwise: arguments passed methods. threshold maximum fraction invalid antimicrobial interpretations x, see Examples mo (vector ) text can coerced valid microorganism codes .mo(), can left empty determine automatically ab (vector ) text can coerced valid antimicrobial drug code .ab() guideline defaults EUCAST 2022 (latest implemented EUCAST guideline clinical_breakpoints data set), can set package option AMR_guideline. Currently supports EUCAST (2013-2022) CLSI (2013-2022), see Details. uti (Urinary Tract Infection) vector logicals (TRUE FALSE) specify whether UTI specific interpretation guideline chosen. using .sir() data.frame, can also column containing logicals left blank, data set searched column 'specimen', rows within column containing 'urin' ('urine', 'urina') regarded isolates UTI. See Examples. conserve_capped_values logical indicate MIC values starting \">\" (\">=\") must always return \"R\" , MIC values starting \"<\" (\"<=\") must always return \"S\" add_intrinsic_resistance (useful using EUCAST guideline) logical indicate whether intrinsic antibiotic resistance must also considered applicable bug-drug combinations, meaning e.g. ampicillin always return \"R\" Klebsiella species. Determination based intrinsic_resistant data set, based 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021). reference_data data.frame used interpretation, defaults clinical_breakpoints data set. Changing argument allows using interpretation guidelines. argument must contain data set equal structure clinical_breakpoints data set (column names column types). Please note guideline argument ignored reference_data manually set. include_screening logical indicate clinical breakpoints screening allowed - default FALSE. Can also set package option AMR_include_screening. include_PKPD logical indicate PK/PD clinical breakpoints must applied last resort - default TRUE. Can also set package option AMR_include_PKPD. col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). clean logical indicate whether previously stored results forgotten returning 'logbook' results","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"Ordered factor new class sir","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"NA_sir_ missing value new sir class, analogous e.g. base R's NA_character_.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"how-it-works","dir":"Reference","previous_headings":"","what":"How it Works","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":".sir() function works four ways: cleaning raw / untransformed data. data cleaned contain values S, R try best determine intelligence. example, mixed values SIR interpretations MIC values \"<0.25; S\" coerced \"S\". Combined interpretations multiple test methods (seen laboratory records) \"S; S\" coerced \"S\", value like \"S; \" return NA warning input unclear. interpreting minimum inhibitory concentration (MIC) values according EUCAST CLSI. must clean MIC values first using .mic(), also gives columns new data class mic. Also, sure column microorganism names codes. found automatically, can set manually using mo argument. Using dplyr, SIR interpretation can done easily either:   Operators like \"<=\" stripped interpretation. using conserve_capped_values = TRUE, MIC value e.g. \">2\" always return \"R\", even breakpoint according chosen guideline \">=4\". prevent capped values raw laboratory data treated conservatively. default behaviour (conserve_capped_values = FALSE) considers \">2\" lower \">=4\" might case return \"S\" \"\". interpreting disk diffusion diameters according EUCAST CLSI. must clean disk zones first using .disk(), also gives columns new data class disk. Also, sure column microorganism names codes. found automatically, can set manually using mo argument. Using dplyr, SIR interpretation can done easily either:   interpreting complete data set, automatic determination MIC values, disk diffusion diameters, microorganism names codes, antimicrobial test results. done simply running .sir(your_data). points 2, 3 4: Use sir_interpretation_history() retrieve data.frame (tibble tibble package installed) results last .sir() call.","code":"your_data %>% mutate_if(is.mic, as.sir) your_data %>% mutate(across(where(is.mic), as.sir)) your_data %>% mutate_if(is.disk, as.sir) your_data %>% mutate(across(where(is.disk), as.sir))"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"supported-guidelines","dir":"Reference","previous_headings":"","what":"Supported Guidelines","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"interpreting MIC values well disk diffusion diameters, currently implemented guidelines EUCAST (2013-2022) CLSI (2013-2022). Thus, guideline argument must set e.g., \"EUCAST 2022\" \"CLSI 2022\". simply using \"EUCAST\" (default) \"CLSI\" input, latest included version guideline automatically selected. can set data set using reference_data argument. guideline argument ignored. can set default guideline package option AMR_guideline (e.g. .Rprofile file), :","code":"options(AMR_guideline = \"CLSI\")   options(AMR_guideline = \"CLSI 2018\")   options(AMR_guideline = \"EUCAST 2020\")   # or to reset:   options(AMR_guideline = NULL)"},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"after-interpretation","dir":"Reference","previous_headings":"","what":"After Interpretation","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"using .sir(), can use eucast_rules() defined EUCAST (1) apply inferred susceptibility resistance based results antimicrobials (2) apply intrinsic resistance based taxonomic properties microorganism.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"machine-readable-clinical-breakpoints","dir":"Reference","previous_headings":"","what":"Machine-Readable Clinical Breakpoints","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"repository package contains machine-readable version guidelines. CSV file consisting 18 271 rows 11 columns. file machine-readable, since contains one row every unique combination test method (MIC disk diffusion), antimicrobial drug microorganism. allows easy implementation rules laboratory information systems (LIS). Note contains interpretation guidelines humans - interpretation guidelines CLSI animals removed.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"other","dir":"Reference","previous_headings":"","what":"Other","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"function .sir() detects input contains class sir. input data.frame, iterates columns returns logical vector. function is_sir_eligible() returns TRUE columns contains 5% invalid antimicrobial interpretations (S //R), FALSE otherwise. threshold 5% can set threshold argument. input data.frame, iterates columns returns logical vector.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/as.sir.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Translate MIC and Disk Diffusion to SIR, or Clean Existing SIR Data — as.sir","text":"","code":"example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … summary(example_isolates) # see all SIR results at a glance #>       date              patient               age           gender          #>  Min.   :2002-01-02   Length:2000        Min.   : 0.00   Length:2000        #>  1st Qu.:2005-07-31   Class :character   1st Qu.:63.00   Class :character   #>  Median :2009-07-31   Mode  :character   Median :74.00   Mode  :character   #>  Mean   :2009-11-20                      Mean   :70.69                      #>  3rd Qu.:2014-05-30                      3rd Qu.:82.00                      #>  Max.   :2017-12-28                      Max.   :97.00                      #>      ward                mo                  PEN                 #>  Length:2000        Class :mo             Class:sir              #>  Class :character   <NA>  :0              %R   :73.7% (n=1201)   #>  Mode  :character   Unique:90             %SI  :26.3% (n=428)    #>                     #1    :B_ESCHR_COLI   - %S :25.6% (n=417)    #>                     #2    :B_STPHY_CONS   - %I : 0.7% (n=11)     #>                     #3    :B_STPHY_AURS                          #>     OXA                   FLC                   AMX                #>  Class:sir             Class:sir             Class:sir             #>  %R   :31.2% (n=114)   %R   :29.5% (n=278)   %R   :59.6% (n=804)   #>  %SI  :68.8% (n=251)   %SI  :70.5% (n=665)   %SI  :40.4% (n=546)   #>  - %S :68.8% (n=251)   - %S :70.5% (n=665)   - %S :40.2% (n=543)   #>  - %I : 0.0% (n=0)     - %I : 0.0% (n=0)     - %I : 0.2% (n=3)     #>                                                                    #>     AMC                    AMP                   TZP                #>  Class:sir              Class:sir             Class:sir             #>  %R   :23.7% (n=446)    %R   :59.6% (n=804)   %R   :12.6% (n=126)   #>  %SI  :76.3% (n=1433)   %SI  :40.4% (n=546)   %SI  :87.4% (n=875)   #>  - %S :71.4% (n=1342)   - %S :40.2% (n=543)   - %S :86.1% (n=862)   #>  - %I : 4.8% (n=91)     - %I : 0.2% (n=3)     - %I : 1.3% (n=13)    #>                                                                     #>     CZO                   FEP                   CXM                 #>  Class:sir             Class:sir             Class:sir              #>  %R   :44.6% (n=199)   %R   :14.2% (n=103)   %R   :26.3% (n=470)    #>  %SI  :55.4% (n=247)   %SI  :85.8% (n=621)   %SI  :73.7% (n=1319)   #>  - %S :54.9% (n=245)   - %S :85.6% (n=620)   - %S :72.5% (n=1297)   #>  - %I : 0.4% (n=2)     - %I : 0.1% (n=1)     - %I : 1.2% (n=22)     #>                                                                     #>     FOX                   CTX                   CAZ                 #>  Class:sir             Class:sir             Class:sir              #>  %R   :27.4% (n=224)   %R   :15.5% (n=146)   %R   :66.5% (n=1204)   #>  %SI  :72.6% (n=594)   %SI  :84.5% (n=797)   %SI  :33.5% (n=607)    #>  - %S :71.6% (n=586)   - %S :84.4% (n=796)   - %S :33.5% (n=607)    #>  - %I : 1.0% (n=8)     - %I : 0.1% (n=1)     - %I : 0.0% (n=0)      #>                                                                     #>     CRO                   GEN                    TOB                #>  Class:sir             Class:sir              Class:sir             #>  %R   :15.5% (n=146)   %R   :24.6% (n=456)    %R   :34.4% (n=465)   #>  %SI  :84.5% (n=797)   %SI  :75.4% (n=1399)   %SI  :65.6% (n=886)   #>  - %S :84.4% (n=796)   - %S :74.0% (n=1372)   - %S :65.1% (n=879)   #>  - %I : 0.1% (n=1)     - %I : 1.5% (n=27)     - %I : 0.5% (n=7)     #>                                                                     #>     AMK                   KAN                    TMP                #>  Class:sir             Class:sir              Class:sir             #>  %R   :63.7% (n=441)   %R   :100.0% (n=471)   %R   :38.1% (n=571)   #>  %SI  :36.3% (n=251)   %SI  : 0.0% (n=0)      %SI  :61.9% (n=928)   #>  - %S :36.3% (n=251)   - %S : 0.0% (n=0)      - %S :61.2% (n=918)   #>  - %I : 0.0% (n=0)     - %I : 0.0% (n=0)      - %I : 0.7% (n=10)    #>                                                                     #>     SXT                    NIT                   FOS                #>  Class:sir              Class:sir             Class:sir             #>  %R   :20.5% (n=361)    %R   :17.1% (n=127)   %R   :42.2% (n=148)   #>  %SI  :79.5% (n=1398)   %SI  :82.9% (n=616)   %SI  :57.8% (n=203)   #>  - %S :79.1% (n=1392)   - %S :76.0% (n=565)   - %S :57.8% (n=203)   #>  - %I : 0.3% (n=6)      - %I : 6.9% (n=51)    - %I : 0.0% (n=0)     #>                                                                     #>     LNZ                   CIP                    MFX                #>  Class:sir             Class:sir              Class:sir             #>  %R   :69.3% (n=709)   %R   :16.2% (n=228)    %R   :33.6% (n=71)    #>  %SI  :30.7% (n=314)   %SI  :83.8% (n=1181)   %SI  :66.4% (n=140)   #>  - %S :30.7% (n=314)   - %S :78.9% (n=1112)   - %S :64.5% (n=136)   #>  - %I : 0.0% (n=0)     - %I : 4.9% (n=69)     - %I : 1.9% (n=4)     #>                                                                     #>     VAN                    TEC                   TCY                #>  Class:sir              Class:sir             Class:sir             #>  %R   :38.3% (n=712)    %R   :75.7% (n=739)   %R   :29.8% (n=357)   #>  %SI  :61.7% (n=1149)   %SI  :24.3% (n=237)   %SI  :70.3% (n=843)   #>  - %S :61.7% (n=1149)   - %S :24.3% (n=237)   - %S :68.3% (n=820)   #>  - %I : 0.0% (n=0)      - %I : 0.0% (n=0)     - %I : 1.9% (n=23)    #>                                                                     #>     TGC                   DOX                   ERY                 #>  Class:sir             Class:sir             Class:sir              #>  %R   :12.7% (n=101)   %R   :27.7% (n=315)   %R   :57.2% (n=1084)   #>  %SI  :87.3% (n=697)   %SI  :72.3% (n=821)   %SI  :42.8% (n=810)    #>  - %S :87.3% (n=697)   - %S :71.7% (n=814)   - %S :42.3% (n=801)    #>  - %I : 0.0% (n=0)     - %I : 0.6% (n=7)     - %I : 0.5% (n=9)      #>                                                                     #>     CLI                   AZM                    IPM                #>  Class:sir             Class:sir              Class:sir             #>  %R   :61.2% (n=930)   %R   :57.2% (n=1084)   %R   : 6.2% (n=55)    #>  %SI  :38.8% (n=590)   %SI  :42.8% (n=810)    %SI  :93.8% (n=834)   #>  - %S :38.6% (n=586)   - %S :42.3% (n=801)    - %S :92.7% (n=824)   #>  - %I : 0.3% (n=4)     - %I : 0.5% (n=9)      - %I : 1.1% (n=10)    #>                                                                     #>     MEM                   MTR                  CHL                #>  Class:sir             Class:sir            Class:sir             #>  %R   : 5.9% (n=49)    %R   :14.7% (n=5)    %R   :21.4% (n=33)    #>  %SI  :94.1% (n=780)   %SI  :85.3% (n=29)   %SI  :78.6% (n=121)   #>  - %S :94.1% (n=780)   - %S :85.3% (n=29)   - %S :78.6% (n=121)   #>  - %I : 0.0% (n=0)     - %I : 0.0% (n=0)    - %I : 0.0% (n=0)     #>                                                                   #>     COL                    MUP                   RIF                #>  Class:sir              Class:sir             Class:sir             #>  %R   :81.2% (n=1331)   %R   : 5.9% (n=16)    %R   :69.6% (n=698)   #>  %SI  :18.8% (n=309)    %SI  :94.1% (n=254)   %SI  :30.4% (n=305)   #>  - %S :18.8% (n=309)    - %S :93.0% (n=251)   - %S :30.2% (n=303)   #>  - %I : 0.0% (n=0)      - %I : 1.1% (n=3)     - %I : 0.2% (n=2)     #>                                                                      # For INTERPRETING disk diffusion and MIC values -----------------------  # a whole data set, even with combined MIC values and disk zones df <- data.frame(   microorganism = \"Escherichia coli\",   AMP = as.mic(8),   CIP = as.mic(0.256),   GEN = as.disk(18),   TOB = as.disk(16),   ERY = \"R\" ) as.sir(df) #> => Interpreting MIC values of column 'AMP' (ampicillin) according to EUCAST #>    2022... #>  OK. #> => Interpreting MIC values of column 'CIP' (ciprofloxacin) according to #>    EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of column 'GEN' (gentamicin) according #>    to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of column 'TOB' (tobramycin) according #>    to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Assigning class 'sir' to already clean column 'ERY' (erythromycin)... #>  OK. #>      microorganism AMP CIP GEN TOB ERY #> 1 Escherichia coli   S   I   S   S   R  # return a 'logbook' about the results: sir_interpretation_history() #> # A tibble: 50 × 12 #>    datetime            index ab_input ab_guideline mo_input     mo_guideline     #>    <dttm>              <int> <chr>    <ab>         <chr>        <mo>             #>  1 2023-05-12 08:40:42     1 TOB      TOB          Escherichia… B_[ORD]_ENTRBCTR #>  2 2023-05-12 08:40:42     1 GEN      GEN          Escherichia… B_[ORD]_ENTRBCTR #>  3 2023-05-12 08:40:42     1 CIP      CIP          Escherichia… B_[ORD]_ENTRBCTR #>  4 2023-05-12 08:40:41     1 AMP      AMP          Escherichia… B_[ORD]_ENTRBCTR #>  5 2023-05-12 08:40:37     1 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #>  6 2023-05-12 08:40:37     2 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #>  7 2023-05-12 08:40:37     3 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #>  8 2023-05-12 08:40:37     4 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #>  9 2023-05-12 08:40:37     5 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #> 10 2023-05-12 08:40:37     6 CIP      CIP          B_ESCHR_COLI B_[ORD]_ENTRBCTR #> # ℹ 40 more rows #> # ℹ 6 more variables: guideline <chr>, ref_table <chr>, method <chr>, #> #   input <dbl>, outcome <sir>, breakpoint_S_R <chr>  # for single values as.sir(   x = as.mic(2),   mo = as.mo(\"S. pneumoniae\"),   ab = \"AMP\",   guideline = \"EUCAST\" ) #> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST #>    2022... #>  Note: #>    • Multiple breakpoints available for ampicillin (AMP) in Streptococcus #>      pneumoniae - assuming body site 'Non-meningitis'. #> Class 'sir' #> [1] R  as.sir(   x = as.disk(18),   mo = \"Strep pneu\", # `mo` will be coerced with as.mo()   ab = \"ampicillin\", # and `ab` with as.ab()   guideline = \"EUCAST\" ) #> => Interpreting disk diffusion zones of 'ampicillin' (AMP) according to #>    EUCAST 2022... #>  OK. #> Class 'sir' #> [1] R  # \\donttest{ # the dplyr way if (require(\"dplyr\")) {   df %>% mutate_if(is.mic, as.sir)   df %>% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)   df %>% mutate(across(where(is.mic), as.sir))   df %>% mutate_at(vars(AMP:TOB), as.sir)   df %>% mutate(across(AMP:TOB, as.sir))    df %>%     mutate_at(vars(AMP:TOB), as.sir, mo = .$microorganism)    # to include information about urinary tract infections (UTI)   data.frame(     mo = \"E. coli\",     NIT = c(\"<= 2\", 32),     from_the_bladder = c(TRUE, FALSE)   ) %>%     as.sir(uti = \"from_the_bladder\")    data.frame(     mo = \"E. coli\",     NIT = c(\"<= 2\", 32),     specimen = c(\"urine\", \"blood\")   ) %>%     as.sir() # automatically determines urine isolates    df %>%     mutate_at(vars(AMP:TOB), as.sir, mo = \"E. coli\", uti = TRUE) } #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of 'AMP' (ampicillin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) based on column #>    'microorganism' according to EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column #>    'microorganism' according to EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST #>    2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST #>    2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to #>    EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to #>    EUCAST 2022... #>  Note: #>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in #>      Escherichia coli - assuming non-UTI. Use argument uti to set which #>      isolates are from urine. See ?as.sir. #> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to #>    EUCAST 2022... #> Warning: in as.sir(): interpretation of nitrofurantoin (NIT) is only available for #> (uncomplicated) urinary tract infections (UTI) for some microorganisms, #> thus assuming uti = TRUE. See ?as.sir. #>  * WARNING * #> ℹ Assuming value \"urine\" in column 'specimen' reflects a urinary tract #>   infection. #>   Use as.sir(uti = FALSE) to prevent this. #> => Interpreting MIC values of column 'NIT' (nitrofurantoin) according to #>    EUCAST 2022... #> Warning: in as.sir(): interpretation of nitrofurantoin (NIT) is only available for #> (uncomplicated) urinary tract infections (UTI) for some microorganisms, #> thus assuming uti = TRUE. See ?as.sir. #>  * WARNING * #> => Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST #>    2022... #>  OK. #> => Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST #>    2022... #>  OK. #> => Interpreting disk diffusion zones of 'GEN' (gentamicin) according to #>    EUCAST 2022... #>  OK. #> => Interpreting disk diffusion zones of 'TOB' (tobramycin) according to #>    EUCAST 2022... #>  OK. #>      microorganism AMP CIP GEN TOB ERY #> 1 Escherichia coli   S   I   S   S   R  # For CLEANING existing SIR values ------------------------------------  as.sir(c(\"S\", \"I\", \"R\", \"A\", \"B\", \"C\")) #> Warning: in as.sir(): 3 results in column '24' truncated (50%) that were invalid #> antimicrobial interpretations: \"A\", \"B\", and \"C\" #> Class 'sir' #> [1] S    I    R    <NA> <NA> <NA> as.sir(\"<= 0.002; S\") # will return \"S\" #> Class 'sir' #> [1] S sir_data <- as.sir(c(rep(\"S\", 474), rep(\"I\", 36), rep(\"R\", 370))) is.sir(sir_data) #> [1] TRUE plot(sir_data) # for percentages  barplot(sir_data) # for frequencies   # the dplyr way if (require(\"dplyr\")) {   example_isolates %>%     mutate_at(vars(PEN:RIF), as.sir)   # same:   example_isolates %>%     as.sir(PEN:RIF)    # fastest way to transform all columns with already valid AMR results to class `sir`:   example_isolates %>%     mutate_if(is_sir_eligible, as.sir)    # since dplyr 1.0.0, this can also be:   # example_isolates %>%   #   mutate(across(where(is_sir_eligible), as.sir)) } #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … # }"},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":null,"dir":"Reference","previous_headings":"","what":"Get ATC Properties from WHOCC Website — atc_online_property","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"Gets data WHOCC website determine properties Anatomical Therapeutic Chemical (ATC) (e.g. antibiotic), name, defined daily dose (DDD) standard unit.","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"","code":"atc_online_property(   atc_code,   property,   administration = \"O\",   url = \"https://www.whocc.no/atc_ddd_index/?code=%s&showdescription=no\",   url_vet = \"https://www.whocc.no/atcvet/atcvet_index/?code=%s&showdescription=no\" )  atc_online_groups(atc_code, ...)  atc_online_ddd(atc_code, ...)  atc_online_ddd_units(atc_code, ...)"},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"https://www.whocc./atc_ddd_alterations__cumulative/ddd_alterations/abbrevations/","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"atc_code character (vector) ATC code(s) antibiotics, coerced .ab() ab_atc() internally valid ATC code property property ATC code. Valid values \"ATC\", \"Name\", \"DDD\", \"U\" (\"unit\"), \"Adm.R\", \"Note\" groups. last option, hierarchical groups ATC code returned, see Examples. administration type administration using property = \"Adm.R\", see Details url url website WHOCC. sign %s can used placeholder ATC codes. url_vet url website WHOCC veterinary medicine. sign %s can used placeholder ATC_vet codes (start \"Q\"). ... arguments pass atc_property","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"Options argument administration: \"Implant\" = Implant \"Inhal\" = Inhalation \"Instill\" = Instillation \"N\" = nasal \"O\" = oral \"P\" = parenteral \"R\" = rectal \"SL\" = sublingual/buccal \"TD\" = transdermal \"V\" = vaginal Abbreviations return values using property = \"U\" (unit): \"g\" = gram \"mg\" = milligram \"mcg\" = microgram \"U\" = unit \"TU\" = thousand units \"MU\" = million units \"mmol\" = millimole \"ml\" = millilitre (e.g. eyedrops) N.B. function requires internet connection works following packages installed: curl, rvest, xml2.","code":""},{"path":"https://msberends.github.io/AMR/reference/atc_online.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get ATC Properties from WHOCC Website — atc_online_property","text":"","code":"# \\donttest{ if (requireNamespace(\"curl\") && requireNamespace(\"rvest\") && requireNamespace(\"xml2\")) {   # oral DDD (Defined Daily Dose) of amoxicillin   atc_online_property(\"J01CA04\", \"DDD\", \"O\")   atc_online_ddd(ab_atc(\"amox\"))    # parenteral DDD (Defined Daily Dose) of amoxicillin   atc_online_property(\"J01CA04\", \"DDD\", \"P\")    atc_online_property(\"J01CA04\", property = \"groups\") # search hierarchical groups of amoxicillin } #> Loading required namespace: rvest #> [1] \"ANTIINFECTIVES FOR SYSTEMIC USE\"         #> [2] \"ANTIBACTERIALS FOR SYSTEMIC USE\"         #> [3] \"BETA-LACTAM ANTIBACTERIALS, PENICILLINS\" #> [4] \"Penicillins with extended spectrum\"      # }"},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"Use function e.g. clinical texts health care records. returns list antiviral drugs, doses forms administration found texts.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"","code":"av_from_text(   text,   type = c(\"drug\", \"dose\", \"administration\"),   collapse = NULL,   translate_av = FALSE,   thorough_search = NULL,   info = interactive(),   ... )"},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"text text analyse type type property search , either \"drug\", \"dose\" \"administration\", see Examples collapse character pass paste(, collapse = ...) return one character per element text, see Examples translate_av type = \"drug\": column name antivirals data set translate antibiotic abbreviations , using av_property(). default FALSE. Using TRUE equal using \"name\". thorough_search logical indicate whether input must extensively searched misspelling faulty input values. Setting TRUE take considerably time using FALSE. default, turn TRUE input elements contain maximum three words. info logical indicate whether progress bar printed - default TRUE interactive mode ... arguments passed .av()","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"list,  character collapse NULL","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"function also internally used .av(), although searches first drug name throw note drug names returned. Note: .av() function may use long regular expression match brand names antiviral drugs. may fail systems.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"argument-type","dir":"Reference","previous_headings":"","what":"Argument type","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"default, function search antiviral drug names. text elements searched official names, ATC codes brand names. uses .av() internally, correct misspelling. type = \"dose\" (similar, like \"dosing\", \"doses\"), text elements searched numeric values higher 100 resemble years. output numeric. supports unit (g, mg, IE, etc.) multiple values one clinical text, see Examples. type = \"administration\" (abbreviations, like \"admin\", \"adm\"), text elements searched form drug administration. supports following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal vaginal. Abbreviations oral ('po', 'per os') become \"oral\", values intravenous ('iv', 'intraven') become \"iv\". supports multiple values one clinical text, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"argument-collapse","dir":"Reference","previous_headings":"","what":"Argument collapse","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"Without using collapse, function return list. can convenient use e.g. inside mutate()):df %>% mutate(avx = av_from_text(clinical_text)) returned AV codes can transformed official names, groups, etc. av_* functions av_name() av_group(), using translate_av argument. using collapse, function return character:df %>% mutate(avx = av_from_text(clinical_text, collapse = \"|\"))","code":""},{"path":"https://msberends.github.io/AMR/reference/av_from_text.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Retrieve Antiviral Drug Names and Doses from Clinical Text — av_from_text","text":"","code":"av_from_text(\"28/03/2020 valaciclovir po tid\") #> [[1]] #> Class 'av' #> [1] VALA #>  av_from_text(\"28/03/2020 valaciclovir po tid\", type = \"admin\") #> [[1]] #> [1] \"oral\" #>"},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Properties of an Antiviral Drug — av_property","title":"Get Properties of an Antiviral Drug — av_property","text":"Use functions return specific property antiviral drug antivirals data set. input values evaluated internally .av().","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Properties of an Antiviral Drug — av_property","text":"","code":"av_name(x, language = get_AMR_locale(), tolower = FALSE, ...)  av_cid(x, ...)  av_synonyms(x, ...)  av_tradenames(x, ...)  av_group(x, language = get_AMR_locale(), ...)  av_atc(x, ...)  av_loinc(x, ...)  av_ddd(x, administration = \"oral\", ...)  av_ddd_units(x, administration = \"oral\", ...)  av_info(x, language = get_AMR_locale(), ...)  av_url(x, open = FALSE, ...)  av_property(x, property = \"name\", language = get_AMR_locale(), ...)"},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Properties of an Antiviral Drug — av_property","text":"x (vector ) text can coerced valid antiviral drug code .av() language language returned text - default system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. tolower logical indicate whether first character every output transformed lower case character. ... arguments passed .av() administration way administration, either \"oral\" \"iv\" open browse URL using utils::browseURL() property one column names one antivirals data set: vector_or(colnames(antivirals), sort = FALSE).","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Properties of an Antiviral Drug — av_property","text":"integer case av_cid() named list case av_info() multiple av_atc()/av_synonyms()/av_tradenames() double case av_ddd() character cases","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Properties of an Antiviral Drug — av_property","text":"output translated possible. function av_url() return direct URL official website. warning returned required ATC code available.","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Properties of an Antiviral Drug — av_property","text":"World Health Organization () Collaborating Centre Drug Statistics Methodology: https://www.whocc./atc_ddd_index/ European Commission Public Health PHARMACEUTICALS - COMMUNITY REGISTER: https://ec.europa.eu/health/documents/community-register/html/reg_hum_atc.htm","code":""},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Get Properties of an Antiviral Drug — av_property","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/av_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Properties of an Antiviral Drug — av_property","text":"","code":"# all properties: av_name(\"ACI\") #> [1] \"Aciclovir\" av_atc(\"ACI\") #> [1] \"J05AB01\" av_cid(\"ACI\") #> [1] 135398513 av_synonyms(\"ACI\") #>  [1] \"acicloftal\"        \"aciclovier\"        \"aciclovirum\"       #>  [4] \"activir\"           \"acyclofoam\"        \"acycloguanosine\"   #>  [7] \"acyclovir\"         \"acyclovir lauriad\" \"avaclyr\"           #> [10] \"cargosil\"          \"cyclovir\"          \"genvir\"            #> [13] \"gerpevir\"          \"hascovir\"          \"maynar\"            #> [16] \"novirus\"           \"poviral\"           \"sitavig\"           #> [19] \"sitavir\"           \"vipral\"            \"viropump\"          #> [22] \"virorax\"           \"zovirax\"           \"zyclir\"            av_tradenames(\"ACI\") #>  [1] \"acicloftal\"        \"aciclovier\"        \"aciclovirum\"       #>  [4] \"activir\"           \"acyclofoam\"        \"acycloguanosine\"   #>  [7] \"acyclovir\"         \"acyclovir lauriad\" \"avaclyr\"           #> [10] \"cargosil\"          \"cyclovir\"          \"genvir\"            #> [13] \"gerpevir\"          \"hascovir\"          \"maynar\"            #> [16] \"novirus\"           \"poviral\"           \"sitavig\"           #> [19] \"sitavir\"           \"vipral\"            \"viropump\"          #> [22] \"virorax\"           \"zovirax\"           \"zyclir\"            av_group(\"ACI\") #> [1] \"Nucleosides and nucleotides excl. reverse transcriptase inhibitors\" av_url(\"ACI\") #>                                                             Aciclovir  #> \"https://www.whocc.no/atc_ddd_index/?code=J05AB01&showdescription=no\"   # smart lowercase tranformation av_name(x = c(\"ACI\", \"VALA\")) #> [1] \"Aciclovir\"    \"Valaciclovir\" av_name(x = c(\"ACI\", \"VALA\"), tolower = TRUE) #> [1] \"aciclovir\"    \"valaciclovir\"  # defined daily doses (DDD) av_ddd(\"ACI\", \"oral\") #> [1] 4 av_ddd_units(\"ACI\", \"oral\") #> [1] \"g\" av_ddd(\"ACI\", \"iv\") #> [1] 4 av_ddd_units(\"ACI\", \"iv\") #> [1] \"g\"  av_info(\"ACI\") # all properties as a list #> $av #> [1] \"ACI\" #>  #> $cid #> [1] 135398513 #>  #> $name #> [1] \"Aciclovir\" #>  #> $group #> [1] \"Nucleosides and nucleotides excl. reverse transcriptase inhibitors\" #>  #> $atc #> [1] \"J05AB01\" #>  #> $tradenames #>  [1] \"acicloftal\"        \"aciclovier\"        \"aciclovirum\"       #>  [4] \"activir\"           \"acyclofoam\"        \"acycloguanosine\"   #>  [7] \"acyclovir\"         \"acyclovir lauriad\" \"avaclyr\"           #> [10] \"cargosil\"          \"cyclovir\"          \"genvir\"            #> [13] \"gerpevir\"          \"hascovir\"          \"maynar\"            #> [16] \"novirus\"           \"poviral\"           \"sitavig\"           #> [19] \"sitavir\"           \"vipral\"            \"viropump\"          #> [22] \"virorax\"           \"zovirax\"           \"zyclir\"            #>  #> $loinc #> [1] \"\" #>  #> $ddd #> $ddd$oral #> $ddd$oral$amount #> [1] 4 #>  #> $ddd$oral$units #> [1] \"g\" #>  #>  #> $ddd$iv #> $ddd$iv$amount #> [1] 4 #>  #> $ddd$iv$units #> [1] \"g\" #>  #>  #>   # all av_* functions use as.av() internally, so you can go from 'any' to 'any': av_atc(\"ACI\") #> [1] \"J05AB01\" av_group(\"J05AB01\") #> [1] \"Nucleosides and nucleotides excl. reverse transcriptase inhibitors\" av_loinc(\"abacavir\") #> [1] \"29113-8\" \"78772-1\" \"78773-9\" \"79134-3\" \"80118-3\" av_name(\"29113-8\") #> [1] \"Abacavir\" av_name(135398513) #> [1] \"Aciclovir\" av_name(\"J05AB01\") #> [1] \"Aciclovir\""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Availability of Columns — availability","title":"Check Availability of Columns — availability","text":"Easy check data availability columns data set. makes easy get idea antimicrobial combinations can used calculation e.g. susceptibility() resistance().","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Availability of Columns — availability","text":"","code":"availability(tbl, width = NULL)"},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Availability of Columns — availability","text":"tbl data.frame list width number characters present visual availability - default filling width console","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Availability of Columns — availability","text":"data.frame column names tbl row names","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check Availability of Columns — availability","text":"function returns data.frame columns \"resistant\" \"visual_resistance\". values columns calculated resistance().","code":""},{"path":"https://msberends.github.io/AMR/reference/availability.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Availability of Columns — availability","text":"","code":"availability(example_isolates) #>         count available     visual_availabilty resistant      visual_resistance #> date     2000    100.0% |####################|                                  #> patient  2000    100.0% |####################|                                  #> age      2000    100.0% |####################|                                  #> gender   2000    100.0% |####################|                                  #> ward     2000    100.0% |####################|                                  #> mo       2000    100.0% |####################|                                  #> PEN      1629     81.5% |################----|     73.7% |##############------| #> OXA       365     18.3% |###-----------------|     31.2% |######--------------| #> FLC       943     47.2% |#########-----------|     29.5% |#####---------------| #> AMX      1350     67.5% |#############-------|     59.6% |###########---------| #> AMC      1879     94.0% |##################--|     23.7% |####----------------| #> AMP      1350     67.5% |#############-------|     59.6% |###########---------| #> TZP      1001     50.0% |##########----------|     12.6% |##------------------| #> CZO       446     22.3% |####----------------|     44.6% |########------------| #> FEP       724     36.2% |#######-------------|     14.2% |##------------------| #> CXM      1789     89.5% |#################---|     26.3% |#####---------------| #> FOX       818     40.9% |########------------|     27.4% |#####---------------| #> CTX       943     47.2% |#########-----------|     15.5% |###-----------------| #> CAZ      1811     90.6% |##################--|     66.5% |#############-------| #> CRO       943     47.2% |#########-----------|     15.5% |###-----------------| #> GEN      1855     92.8% |##################--|     24.6% |####----------------| #> TOB      1351     67.6% |#############-------|     34.4% |######--------------| #> AMK       692     34.6% |######--------------|     63.7% |############--------| #> KAN       471     23.6% |####----------------|    100.0% |####################| #> TMP      1499     75.0% |###############-----|     38.1% |#######-------------| #> SXT      1759     88.0% |#################---|     20.5% |####----------------| #> NIT       743     37.2% |#######-------------|     17.1% |###-----------------| #> FOS       351     17.6% |###-----------------|     42.2% |########------------| #> LNZ      1023     51.2% |##########----------|     69.3% |#############-------| #> CIP      1409     70.5% |#############-------|     16.2% |###-----------------| #> MFX       211     10.6% |##------------------|     33.6% |######--------------| #> VAN      1861     93.1% |##################--|     38.3% |#######-------------| #> TEC       976     48.8% |#########-----------|     75.7% |###############-----| #> TCY      1200     60.0% |###########---------|     29.8% |#####---------------| #> TGC       798     39.9% |########------------|     12.7% |##------------------| #> DOX      1136     56.8% |###########---------|     27.7% |#####---------------| #> ERY      1894     94.7% |##################--|     57.2% |###########---------| #> CLI      1520     76.0% |###############-----|     61.2% |############--------| #> AZM      1894     94.7% |##################--|     57.2% |###########---------| #> IPM       889     44.5% |########------------|      6.2% |#-------------------| #> MEM       829     41.5% |########------------|      5.9% |#-------------------| #> MTR        34      1.7% |--------------------|     14.7% |##------------------| #> CHL       154      7.7% |#-------------------|     21.4% |####----------------| #> COL      1640     82.0% |################----|     81.2% |################----| #> MUP       270     13.5% |##------------------|      5.9% |#-------------------| #> RIF      1003     50.2% |##########----------|     69.6% |#############-------| # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     filter(mo == as.mo(\"Escherichia coli\")) %>%     select_if(is.sir) %>%     availability() } #>     count available       visual_availabilty resistant        visual_resistance #> PEN   467    100.0% |######################|    100.0% |######################| #> OXA     0      0.0% |----------------------|                                    #> FLC     0      0.0% |----------------------|                                    #> AMX   392     83.9% |##################----|     50.0% |###########-----------| #> AMC   467    100.0% |######################|     13.1% |##--------------------| #> AMP   392     83.9% |##################----|     50.0% |###########-----------| #> TZP   416     89.1% |###################---|      5.5% |#---------------------| #> CZO    82     17.6% |###-------------------|      2.4% |----------------------| #> FEP   317     67.9% |##############--------|      2.8% |----------------------| #> CXM   465     99.6% |######################|      5.4% |#---------------------| #> FOX   377     80.7% |#################-----|      6.9% |#---------------------| #> CTX   459     98.3% |#####################-|      2.4% |----------------------| #> CAZ   460     98.5% |#####################-|      2.4% |----------------------| #> CRO   459     98.3% |#####################-|      2.4% |----------------------| #> GEN   460     98.5% |#####################-|      2.0% |----------------------| #> TOB   462     98.9% |#####################-|      2.6% |----------------------| #> AMK   171     36.6% |########--------------|      0.0% |----------------------| #> KAN     0      0.0% |----------------------|                                    #> TMP   396     84.8% |##################----|     39.1% |########--------------| #> SXT   465     99.6% |######################|     31.6% |######----------------| #> NIT   458     98.1% |#####################-|      2.8% |----------------------| #> FOS    61     13.1% |##--------------------|      0.0% |----------------------| #> LNZ   467    100.0% |######################|    100.0% |######################| #> CIP   456     97.6% |#####################-|     12.5% |##--------------------| #> MFX    57     12.2% |##--------------------|    100.0% |######################| #> VAN   467    100.0% |######################|    100.0% |######################| #> TEC   467    100.0% |######################|    100.0% |######################| #> TCY     3      0.6% |----------------------|     66.7% |##############--------| #> TGC    68     14.6% |###-------------------|      0.0% |----------------------| #> DOX     0      0.0% |----------------------|                                    #> ERY   467    100.0% |######################|    100.0% |######################| #> CLI   467    100.0% |######################|    100.0% |######################| #> AZM   467    100.0% |######################|    100.0% |######################| #> IPM   422     90.4% |###################---|      0.0% |----------------------| #> MEM   418     89.5% |###################---|      0.0% |----------------------| #> MTR     2      0.4% |----------------------|      0.0% |----------------------| #> CHL     0      0.0% |----------------------|                                    #> COL   240     51.4% |###########-----------|      0.0% |----------------------| #> MUP     0      0.0% |----------------------|                                    #> RIF   467    100.0% |######################|    100.0% |######################| # }"},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Bug-Drug Combinations — bug_drug_combinations","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"Determine antimicrobial resistance (AMR) bug-drug combinations data set least 30 (default) isolates available per species. Use format() result prettify publishable/printable format, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"","code":"bug_drug_combinations(x, col_mo = NULL, FUN = mo_shortname, ...)  # S3 method for bug_drug_combinations format(   x,   translate_ab = \"name (ab, atc)\",   language = get_AMR_locale(),   minimum = 30,   combine_SI = TRUE,   add_ab_group = TRUE,   remove_intrinsic_resistant = FALSE,   decimal.mark = getOption(\"OutDec\"),   big.mark = ifelse(decimal.mark == \",\", \".\", \",\"),   ... )"},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"x data set antibiotic columns, amox, AMX AMC col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). FUN function call mo column transform microorganism codes - default mo_shortname() ... arguments passed FUN translate_ab character length 1 containing column names antibiotics data set language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. combine_SI logical indicate whether values S summed, resistance based R - default TRUE add_ab_group logical indicate group antimicrobials must included first column remove_intrinsic_resistant logical indicate rows columns 100% resistance tested antimicrobials must removed table decimal.mark character used indicate numeric     decimal point. big.mark character; empty used mark every     big.interval decimals (hence big)     decimal point.","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"function bug_drug_combinations() returns data.frame columns \"mo\", \"ab\", \"S\", \"\", \"R\" \"total\".","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"function format() calculates resistance per bug-drug combination returns table ready reporting/publishing. Use combine_SI = TRUE (default) test R vs. S+combine_SI = FALSE test R+vs. S. table can also directly used R Markdown / Quarto without need e.g. knitr::kable().","code":""},{"path":"https://msberends.github.io/AMR/reference/bug_drug_combinations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine Bug-Drug Combinations — bug_drug_combinations","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  # \\donttest{ x <- bug_drug_combinations(example_isolates) head(x) #> # A tibble: 6 × 6 #>   mo                ab        S     I     R total #>   <chr>             <chr> <int> <int> <int> <int> #> 1 (unknown species) AMC      15     0     0    15 #> 2 (unknown species) AMK       0     0     0     0 #> 3 (unknown species) AMP      15     0     1    16 #> 4 (unknown species) AMX      15     0     1    16 #> 5 (unknown species) AZM       3     0     3     6 #> 6 (unknown species) CAZ       0     0     0     0 #> Use 'format()' on this result to get a publishable/printable format. format(x, translate_ab = \"name (atc)\") #> # A tibble: 39 × 12 #>    Group     Drug  CoNS  `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa` #>    <chr>     <chr> <chr> <chr>     <chr>         <chr>           <chr>           #>  1 \"Aminogl… Amik… \"100… \"  0.0% … \"100.0% (39/… \"\"              \"\"              #>  2 \"\"        Gent… \" 13… \"  2.0% … \"100.0% (39/… \" 10.3% (6/58)\" \"  0.0% (0/30)\" #>  3 \"\"        Kana… \"100… \"\"        \"100.0% (39/… \"\"              \"100.0% (30/30… #>  4 \"\"        Tobr… \" 78… \"  2.6% … \"100.0% (39/… \" 10.3% (6/58)\" \"  0.0% (0/30)\" #>  5 \"Ampheni… Chlo… \"\"    \"\"        \"\"            \"\"              \"100.0% (30/30… #>  6 \"Antimyc… Rifa… \"\"    \"100.0% … \"\"            \"100.0% (58/58… \"100.0% (30/30… #>  7 \"Beta-la… Amox… \" 93… \" 50.0% … \"\"            \"100.0% (58/58… \"100.0% (30/30… #>  8 \"\"        Amox… \" 42… \" 13.1% … \"\"            \" 10.3% (6/58)\" \"100.0% (30/30… #>  9 \"\"        Ampi… \" 93… \" 50.0% … \"\"            \"100.0% (58/58… \"100.0% (30/30… #> 10 \"\"        Benz… \" 77… \"100.0% … \"\"            \"100.0% (58/58… \"100.0% (30/30… #> # ℹ 29 more rows #> # ℹ 5 more variables: `P. mirabilis` <chr>, `S. aureus` <chr>, #> #   `S. epidermidis` <chr>, `S. hominis` <chr>, `S. pneumoniae` <chr>  # Use FUN to change to transformation of microorganism codes bug_drug_combinations(example_isolates,   FUN = mo_gramstain ) #> # A tibble: 80 × 6 #>    mo            ab        S     I     R total #>  * <chr>         <chr> <int> <int> <int> <int> #>  1 Gram-negative AMC     463    89   174   726 #>  2 Gram-negative AMK     251     0     5   256 #>  3 Gram-negative AMP     226     0   405   631 #>  4 Gram-negative AMX     226     0   405   631 #>  5 Gram-negative AZM       1     2   696   699 #>  6 Gram-negative CAZ     607     0    27   634 #>  7 Gram-negative CHL       1     0    30    31 #>  8 Gram-negative CIP     610    11    63   684 #>  9 Gram-negative CLI      18     1   709   728 #> 10 Gram-negative COL     309     0    78   387 #> # ℹ 70 more rows #> Use 'format()' on this result to get a publishable/printable format.  bug_drug_combinations(example_isolates,   FUN = function(x) {     ifelse(x == as.mo(\"Escherichia coli\"),       \"E. coli\",       \"Others\"     )   } ) #> # A tibble: 80 × 6 #>    mo      ab        S     I     R total #>  * <chr>   <chr> <int> <int> <int> <int> #>  1 E. coli AMC     332    74    61   467 #>  2 E. coli AMK     171     0     0   171 #>  3 E. coli AMP     196     0   196   392 #>  4 E. coli AMX     196     0   196   392 #>  5 E. coli AZM       0     0   467   467 #>  6 E. coli CAZ     449     0    11   460 #>  7 E. coli CHL       0     0     0     0 #>  8 E. coli CIP     398     1    57   456 #>  9 E. coli CLI       0     0   467   467 #> 10 E. coli COL     240     0     0   240 #> # ℹ 70 more rows #> Use 'format()' on this result to get a publishable/printable format. # }"},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"Data set containing clinical breakpoints interpret MIC disk diffusion SIR values, according international guidelines. Currently implemented guidelines EUCAST (2013-2022) CLSI (2013-2022). Use .sir() transform MICs disks measurements SIR values.","code":""},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"","code":"clinical_breakpoints"},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"tibble 18 271 observations 11 variables: guideline Name guideline method Either \"DISK\" \"MIC\" site Body site, e.g. \"Oral\" \"Respiratory\" mo Microbial ID, see .mo() rank_index Taxonomic rank index mo 1 (subspecies/infraspecies) 5 (unknown microorganism) ab Antibiotic ID, see .ab() ref_tbl Info guideline rule can found disk_dose Dose used disk diffusion method breakpoint_S Lowest MIC value highest number millimetres leads \"S\" breakpoint_R Highest MIC value lowest number millimetres leads \"R\" uti logical value (TRUE/FALSE) indicate whether rule applies urinary tract infection (UTI)","code":""},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository. allow machine reading EUCAST CLSI guidelines, almost impossible MS Excel PDF files distributed EUCAST CLSI.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/clinical_breakpoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints","text":"","code":"clinical_breakpoints #> # A tibble: 18,271 × 11 #>    guideline   method site  mo               rank_index ab   ref_tbl   disk_dose #>    <chr>       <chr>  <chr> <mo>                  <dbl> <ab> <chr>     <chr>     #>  1 EUCAST 2022 MIC    NA    F_ASPRG_MGTS              2 AMB  Aspergil… NA        #>  2 EUCAST 2022 MIC    NA    F_ASPRG_NIGR              2 AMB  Aspergil… NA        #>  3 EUCAST 2022 MIC    NA    F_CANDD_ALBC              2 AMB  Candida   NA        #>  4 EUCAST 2022 MIC    NA    F_CANDD_DBLN              2 AMB  Candida   NA        #>  5 EUCAST 2022 MIC    NA    F_CANDD_GLBR              2 AMB  Candida   NA        #>  6 EUCAST 2022 MIC    NA    F_CANDD_KRUS              2 AMB  Candida   NA        #>  7 EUCAST 2022 MIC    NA    F_CANDD_PRPS              2 AMB  Candida   NA        #>  8 EUCAST 2022 MIC    NA    F_CANDD_TRPC              2 AMB  Candida   NA        #>  9 EUCAST 2022 MIC    NA    F_CRYPT_NFRM              2 AMB  Candida   NA        #> 10 EUCAST 2022 DISK   NA    B_[ORD]_ENTRBCTR          5 AMC  Enteroba… 20ug/10ug #> # ℹ 18,261 more rows #> # ℹ 3 more variables: breakpoint_S <dbl>, breakpoint_R <dbl>, uti <lgl>"},{"path":"https://msberends.github.io/AMR/reference/count.html","id":null,"dir":"Reference","previous_headings":"","what":"Count Available Isolates — count","title":"Count Available Isolates — count","text":"functions can used count resistant/susceptible microbial isolates. functions support quasiquotation pipes, can used summarise() dplyr package also support grouped variables, see Examples. count_resistant() used count resistant isolates, count_susceptible() used count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Count Available Isolates — count","text":"","code":"count_resistant(..., only_all_tested = FALSE)  count_susceptible(..., only_all_tested = FALSE)  count_R(..., only_all_tested = FALSE)  count_IR(..., only_all_tested = FALSE)  count_I(..., only_all_tested = FALSE)  count_SI(..., only_all_tested = FALSE)  count_S(..., only_all_tested = FALSE)  count_all(..., only_all_tested = FALSE)  n_sir(..., only_all_tested = FALSE)  count_df(   data,   translate_ab = \"name\",   language = get_AMR_locale(),   combine_SI = TRUE )"},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Count Available Isolates — count","text":"... one vectors (columns) antibiotic interpretations. transformed internally .sir() needed. only_all_tested (combination therapies, .e. using one variable ...): logical indicate isolates must tested antibiotics, see section Combination Therapy data data.frame containing columns class sir (see .sir()) translate_ab column name antibiotics data set translate antibiotic abbreviations , using ab_property() language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. combine_SI logical indicate whether values S must merged one, output consists S+vs. R (susceptible vs. resistant) - default TRUE","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Count Available Isolates — count","text":"integer","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Count Available Isolates — count","text":"functions meant count isolates. Use resistance()/susceptibility() functions calculate microbial resistance/susceptibility. function count_resistant() equal function count_R(). function count_susceptible() equal function count_SI(). function n_sir() alias count_all(). can used count available isolates, .e. input antibiotics available result (S, R). use equal n_distinct(). function equal count_susceptible(...) + count_resistant(...). function count_df() takes variable data sir class (created .sir()) counts number S's, 's R's. also supports grouped variables. function sir_df() works exactly like count_df(), adds percentage S, R.","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Count Available Isolates — count","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"combination-therapy","dir":"Reference","previous_headings":"","what":"Combination Therapy","title":"Count Available Isolates — count","text":"using one variable ... (= combination therapy), use only_all_tested count isolates tested antibiotics/variables test . See example two antibiotics, Drug Drug B, susceptibility() works calculate %SI:   Please note , combination therapies, only_all_tested = TRUE applies :   , combination therapies, only_all_tested = FALSE applies :   Using only_all_tested impact using one antibiotic input.","code":"--------------------------------------------------------------------                     only_all_tested = FALSE  only_all_tested = TRUE                     -----------------------  -----------------------  Drug A    Drug B   include as  include as   include as  include as                     numerator   denominator  numerator   denominator --------  --------  ----------  -----------  ----------  -----------  S or I    S or I       X            X            X            X    R       S or I       X            X            X            X   <NA>     S or I       X            X            -            -  S or I      R          X            X            X            X    R         R          -            X            -            X   <NA>       R          -            -            -            -  S or I     <NA>        X            X            -            -    R        <NA>        -            -            -            -   <NA>      <NA>        -            -            -            - -------------------------------------------------------------------- count_S()    +   count_I()    +   count_R()    = count_all()   proportion_S() + proportion_I() + proportion_R() = 1 count_S()    +   count_I()    +   count_R()    >= count_all()   proportion_S() + proportion_I() + proportion_R() >= 1"},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/count.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Count Available Isolates — count","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info.  # base R ------------------------------------------------------------ count_resistant(example_isolates$AMX) # counts \"R\" #> [1] 804 count_susceptible(example_isolates$AMX) # counts \"S\" and \"I\" #> [1] 546 count_all(example_isolates$AMX) # counts \"S\", \"I\" and \"R\" #> [1] 1350  # be more specific count_S(example_isolates$AMX) #> Using count_S() is discouraged; use count_susceptible() instead to also #> consider \"I\" being susceptible. This note will be shown once for this #> session. #> [1] 543 count_SI(example_isolates$AMX) #> [1] 546 count_I(example_isolates$AMX) #> [1] 3 count_IR(example_isolates$AMX) #> Using count_IR() is discouraged; use count_resistant() instead to not #> consider \"I\" being resistant. This note will be shown once for this #> session. #> [1] 807 count_R(example_isolates$AMX) #> [1] 804  # Count all available isolates count_all(example_isolates$AMX) #> [1] 1350 n_sir(example_isolates$AMX) #> [1] 1350  # n_sir() is an alias of count_all(). # Since it counts all available isolates, you can # calculate back to count e.g. susceptible isolates. # These results are the same: count_susceptible(example_isolates$AMX) #> [1] 546 susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX) #> [1] 546  # dplyr ------------------------------------------------------------- # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       R = count_R(CIP),       I = count_I(CIP),       S = count_S(CIP),       n1 = count_all(CIP), # the actual total; sum of all three       n2 = n_sir(CIP), # same - analogous to n_distinct       total = n()     ) # NOT the number of tested isolates!    # Number of available isolates for a whole antibiotic class   # (i.e., in this data set columns GEN, TOB, AMK, KAN)   example_isolates %>%     group_by(ward) %>%     summarise(across(aminoglycosides(), n_sir))    # Count co-resistance between amoxicillin/clav acid and gentamicin,   # so we can see that combination therapy does a lot more than mono therapy.   # Please mind that `susceptibility()` calculates percentages right away instead.   example_isolates %>% count_susceptible(AMC) # 1433   example_isolates %>% count_all(AMC) # 1879    example_isolates %>% count_susceptible(GEN) # 1399   example_isolates %>% count_all(GEN) # 1855    example_isolates %>% count_susceptible(AMC, GEN) # 1764   example_isolates %>% count_all(AMC, GEN) # 1936    # Get number of S+I vs. R immediately of selected columns   example_isolates %>%     select(AMX, CIP) %>%     count_df(translate = FALSE)    # It also supports grouping variables   example_isolates %>%     select(ward, AMX, CIP) %>%     group_by(ward) %>%     count_df(translate = FALSE) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> # A tibble: 12 × 4 #>    ward       antibiotic interpretation value #>  * <chr>      <chr>      <ord>          <int> #>  1 Clinical   AMX        SI               357 #>  2 Clinical   AMX        R                487 #>  3 Clinical   CIP        SI               741 #>  4 Clinical   CIP        R                128 #>  5 ICU        AMX        SI               158 #>  6 ICU        AMX        R                270 #>  7 ICU        CIP        SI               362 #>  8 ICU        CIP        R                 85 #>  9 Outpatient AMX        SI                31 #> 10 Outpatient AMX        R                 47 #> 11 Outpatient CIP        SI                78 #> 12 Outpatient CIP        R                 15 # }"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":null,"dir":"Reference","previous_headings":"","what":"Define Custom EUCAST Rules — custom_eucast_rules","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"Define custom EUCAST rules organisation specific analysis use output function eucast_rules().","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"","code":"custom_eucast_rules(...)"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"... rules formula notation, see Examples","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"list containing custom rules","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"organisations adoption EUCAST rules. function can used define custom EUCAST rules used eucast_rules() function.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"basics","dir":"Reference","previous_headings":"","what":"Basics","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"familiar case_when() function dplyr package, recognise input method set rules. Rules must set using R considers 'formula notation'. rule written tilde (~) consequence rule written tilde:   two custom EUCAST rules: TZP (piperacillin/tazobactam) \"S\", aminopenicillins (ampicillin amoxicillin) must made \"S\", TZP \"R\", aminopenicillins must made \"R\". rules can also printed console, immediately clear work:   rules (part tilde, example TZP == \"S\" TZP == \"R\") must evaluable data set: able run filter data set without errors. means example column TZP must exist. create sample data set test rules set:","code":"x <- custom_eucast_rules(TZP == \"S\" ~ aminopenicillins == \"S\",                          TZP == \"R\" ~ aminopenicillins == \"R\") x #> A set of custom EUCAST rules: #> #>   1. If TZP is \"S\" then set to  S : #>      amoxicillin (AMX), ampicillin (AMP) #> #>   2. If TZP is \"R\" then set to  R : #>      amoxicillin (AMX), ampicillin (AMP) df <- data.frame(mo = c(\"Escherichia coli\", \"Klebsiella pneumoniae\"),                  TZP = as.sir(\"R\"),                  ampi = as.sir(\"S\"),                  cipro = as.sir(\"S\")) df #>                      mo TZP ampi cipro #> 1      Escherichia coli   R    S     S #> 2 Klebsiella pneumoniae   R    S     S  eucast_rules(df, rules = \"custom\", custom_rules = x, info = FALSE) #>                      mo TZP ampi cipro #> 1      Escherichia coli   R    R     S #> 2 Klebsiella pneumoniae   R    R     S"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"using-taxonomic-properties-in-rules","dir":"Reference","previous_headings":"","what":"Using taxonomic properties in rules","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"one exception columns used rules: column names microorganisms data set can also used, exist data set. column names : \"mo\", \"fullname\", \"status\", \"kingdom\", \"phylum\", \"class\", \"order\", \"family\", \"genus\", \"species\", \"subspecies\", \"rank\", \"ref\", \"oxygen_tolerance\", \"source\", \"lpsn\", \"lpsn_parent\", \"lpsn_renamed_to\", \"gbif\", \"gbif_parent\", \"gbif_renamed_to\", \"prevalence\", \"snomed\". Thus, next example work well, despite fact df data set contain column genus:","code":"y <- custom_eucast_rules(TZP == \"S\" & genus == \"Klebsiella\" ~ aminopenicillins == \"S\",                          TZP == \"R\" & genus == \"Klebsiella\" ~ aminopenicillins == \"R\")  eucast_rules(df, rules = \"custom\", custom_rules = y, info = FALSE) #>                      mo TZP ampi cipro #> 1      Escherichia coli   R    S     S #> 2 Klebsiella pneumoniae   R    R     S"},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"usage-of-antibiotic-group-names","dir":"Reference","previous_headings":"","what":"Usage of antibiotic group names","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"possible define antibiotic groups instead single antibiotics rule consequence, part tilde. examples, antibiotic group aminopenicillins used include ampicillin amoxicillin. following groups allowed (case-insensitive). Within parentheses drugs matched running rule. \"aminoglycosides\"(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, tobramycin-high) \"aminopenicillins\"(amoxicillin ampicillin) \"antifungals\"(amphotericin B, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, voriconazole) \"antimycobacterials\"(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, viomycin) \"betalactams\"(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, biapenem, carbenicillin, carindacillin, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/nacubactam, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid) \"carbapenems\"(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, tebipenem) \"cephalosporins\"(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, loracarbef) \"cephalosporins_1st\"(cefacetrile, cefadroxil, cefalexin, cefaloridine, cefalotin, cefapirin, cefatrizine, cefazedone, cefazolin, cefroxadine, ceftezole, cephradine) \"cephalosporins_2nd\"(cefaclor, cefamandole, cefmetazole, cefonicid, ceforanide, cefotetan, cefotiam, cefoxitin, cefoxitin screening, cefprozil, cefuroxime, cefuroxime axetil, loracarbef) \"cephalosporins_3rd\"(cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefetamet, cefetamet pivoxil, cefixime, cefmenoxime, cefodizime, cefoperazone, cefoperazone/sulbactam, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotiam hexetil, cefovecin, cefpimizole, cefpiramide, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefsulodin, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, latamoxef) \"cephalosporins_4th\"(cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetecol, cefoselis, cefozopran, cefpirome, cefquinome) \"cephalosporins_5th\"(ceftaroline, ceftaroline/avibactam, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam) \"cephalosporins_except_caz\"(cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/clavulanic acid, cefepime/tazobactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, latamoxef, loracarbef) \"fluoroquinolones\"(besifloxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nifuroquine, norfloxacin, ofloxacin, orbifloxacin, pazufloxacin, pefloxacin, pradofloxacin, premafloxacin, prulifloxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin) \"glycopeptides\"(avoparcin, dalbavancin, norvancomycin, oritavancin, ramoplanin, teicoplanin, teicoplanin-macromethod, telavancin, vancomycin, vancomycin-macromethod) \"glycopeptides_except_lipo\"(avoparcin, norvancomycin, ramoplanin, teicoplanin, teicoplanin-macromethod, vancomycin, vancomycin-macromethod) \"lincosamides\"(acetylmidecamycin, acetylspiramycin, clindamycin, gamithromycin, kitasamycin, lincomycin, meleumycin, nafithromycin, pirlimycin, primycin, solithromycin, tildipirosin, tilmicosin, tulathromycin, tylosin, tylvalosin) \"lipoglycopeptides\"(dalbavancin, oritavancin, telavancin) \"macrolides\"(acetylmidecamycin, acetylspiramycin, azithromycin, clarithromycin, dirithromycin, erythromycin, flurithromycin, gamithromycin, josamycin, kitasamycin, meleumycin, midecamycin, miocamycin, nafithromycin, oleandomycin, pirlimycin, primycin, rokitamycin, roxithromycin, solithromycin, spiramycin, telithromycin, tildipirosin, tilmicosin, troleandomycin, tulathromycin, tylosin, tylvalosin) \"oxazolidinones\"(cadazolid, cycloserine, linezolid, tedizolid, thiacetazone) \"penicillins\"(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, avibactam, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, carbenicillin, carindacillin, cefepime/nacubactam, ciclacillin, clometocillin, cloxacillin, dicloxacillin, epicillin, flucloxacillin, hetacillin, lenampicillin, mecillinam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nacubactam, nafcillin, oxacillin, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, sarmoxicillin, sulbactam, sulbenicillin, sultamicillin, talampicillin, tazobactam, temocillin, ticarcillin, ticarcillin/clavulanic acid) \"polymyxins\"(colistin, polymyxin B, polymyxin B/polysorbate 80) \"quinolones\"(besifloxacin, cinoxacin, ciprofloxacin, clinafloxacin, danofloxacin, delafloxacin, difloxacin, enoxacin, enrofloxacin, finafloxacin, fleroxacin, flumequine, garenoxacin, gatifloxacin, gemifloxacin, grepafloxacin, lascufloxacin, levofloxacin, levonadifloxacin, lomefloxacin, marbofloxacin, metioxate, miloxacin, moxifloxacin, nadifloxacin, nalidixic acid, nemonoxacin, nifuroquine, nitroxoline, norfloxacin, ofloxacin, orbifloxacin, oxolinic acid, pazufloxacin, pefloxacin, pipemidic acid, piromidic acid, pradofloxacin, premafloxacin, prulifloxacin, rosoxacin, rufloxacin, sarafloxacin, sitafloxacin, sparfloxacin, temafloxacin, tilbroquinol, tioxacin, tosufloxacin, trovafloxacin) \"streptogramins\"(pristinamycin quinupristin/dalfopristin) \"tetracyclines\"(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline, tigecycline) \"tetracyclines_except_tgc\"(cetocycline, chlortetracycline, clomocycline, demeclocycline, doxycycline, eravacycline, lymecycline, metacycline, minocycline, omadacycline, oxytetracycline, penimepicycline, rolitetracycline, sarecycline, tetracycline) \"trimethoprims\"(brodimoprim, sulfadiazine, sulfadiazine/tetroxoprim, sulfadiazine/trimethoprim, sulfadimethoxine, sulfadimidine, sulfadimidine/trimethoprim, sulfafurazole, sulfaisodimidine, sulfalene, sulfamazone, sulfamerazine, sulfamerazine/trimethoprim, sulfamethizole, sulfamethoxazole, sulfamethoxypyridazine, sulfametomidine, sulfametoxydiazine, sulfametrole/trimethoprim, sulfamoxole, sulfamoxole/trimethoprim, sulfanilamide, sulfaperin, sulfaphenazole, sulfapyridine, sulfathiazole, sulfathiourea, trimethoprim, trimethoprim/sulfamethoxazole) \"ureidopenicillins\"(azlocillin, mezlocillin, piperacillin, piperacillin/tazobactam)","code":""},{"path":"https://msberends.github.io/AMR/reference/custom_eucast_rules.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Define Custom EUCAST Rules — custom_eucast_rules","text":"","code":"x <- custom_eucast_rules(   AMC == \"R\" & genus == \"Klebsiella\" ~ aminopenicillins == \"R\",   AMC == \"I\" & genus == \"Klebsiella\" ~ aminopenicillins == \"I\" ) x #> A set of custom EUCAST rules: #>  #>   1. If AMC is \"R\" and genus is \"Klebsiella\" then set to  R : #>      amoxicillin (AMX), ampicillin (AMP) #>  #>   2. If AMC is \"I\" and genus is \"Klebsiella\" then set to  I : #>      amoxicillin (AMX), ampicillin (AMP)  # run the custom rule set (verbose = TRUE will return a logbook instead of the data set): eucast_rules(example_isolates,   rules = \"custom\",   custom_rules = x,   info = FALSE,   verbose = TRUE ) #> # A tibble: 8 × 9 #>     row col   mo_fullname     old   new   rule  rule_group rule_name rule_source #>   <int> <chr> <chr>           <ord> <chr> <chr> <chr>      <chr>     <chr>       #> 1    33 AMP   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 2    33 AMX   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 3    34 AMP   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 4    34 AMX   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 5   531 AMP   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 6   531 AMX   Klebsiella pne… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 7  1485 AMP   Klebsiella oxy… R     I     \"rep… Custom EU… Custom E… Object 'x'… #> 8  1485 AMX   Klebsiella oxy… R     I     \"rep… Custom EU… Custom E… Object 'x'…  # combine rule sets x2 <- c(   x,   custom_eucast_rules(TZP == \"R\" ~ carbapenems == \"R\") ) x2 #> A set of custom EUCAST rules: #>  #>   1. If AMC is \"R\" and genus is \"Klebsiella\" then set to  R : #>      amoxicillin (AMX), ampicillin (AMP) #>  #>   2. If AMC is \"I\" and genus is \"Klebsiella\" then set to  I : #>      amoxicillin (AMX), ampicillin (AMP) #>  #>   3. If TZP is \"R\" then set to  R : #>      biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), #>      imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), #>      meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), #>      razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), tebipenem (TBP)"},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"EUCAST breakpoints used package based dosages data set. can retrieved eucast_dosage().","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"","code":"dosage"},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"tibble 336 observations 9 variables: ab Antibiotic ID used package (AMC), using official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes available name Official name antimicrobial drug used WHONET/EARS-Net type Type dosage, either \"high_dosage\", \"standard_dosage\", \"uncomplicated_uti\" dose Dose, \"2 g\" \"25 mg/kg\" dose_times Number times dose must administered administration Route administration, either \"im\", \"iv\", \"oral\" notes Additional dosage notes original_txt Original text PDF file EUCAST eucast_version Version number EUCAST Clinical Breakpoints guideline dosages apply","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"data set based 'EUCAST Clinical Breakpoint Tables' v12.0 (2022) 'EUCAST Clinical Breakpoint Tables' v11.0 (2021).","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/dosage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Treatment Dosages as Defined by EUCAST — dosage","text":"","code":"dosage #> # A tibble: 336 × 9 #>    ab   name            type  dose  dose_times administration notes original_txt #>    <ab> <chr>           <chr> <chr>      <int> <chr>          <chr> <chr>        #>  1 AMK  Amikacin        stan… 25-3…          1 iv             \"\"    25-30 mg/kg… #>  2 AMX  Amoxicillin     high… 2 g            6 iv             \"\"    2 g x 6 iv   #>  3 AMX  Amoxicillin     stan… 1 g            3 iv             \"\"    1 g x 3-4 iv #>  4 AMX  Amoxicillin     high… 0.75…          3 oral           \"\"    0.75-1 g x … #>  5 AMX  Amoxicillin     stan… 0.5 g          3 oral           \"\"    0.5 g x 3 o… #>  6 AMX  Amoxicillin     unco… 0.5 g          3 oral           \"\"    0.5 g x 3 o… #>  7 AMC  Amoxicillin/cl… high… 2 g …          3 iv             \"\"    (2 g amoxic… #>  8 AMC  Amoxicillin/cl… stan… 1 g …          3 iv             \"\"    (1 g amoxic… #>  9 AMC  Amoxicillin/cl… high… 0.87…          3 oral           \"\"    (0.875 g am… #> 10 AMC  Amoxicillin/cl… stan… 0.5 …          3 oral           \"\"    (0.5 g amox… #> # ℹ 326 more rows #> # ℹ 1 more variable: eucast_version <dbl>"},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply EUCAST Rules — eucast_rules","title":"Apply EUCAST Rules — eucast_rules","text":"Apply rules clinical breakpoints intrinsic resistance defined European Committee Antimicrobial Susceptibility Testing (EUCAST, https://www.eucast.org), see Source. Use eucast_dosage() get data.frame advised dosages certain bug-drug combination, based dosage data set. improve interpretation antibiogram EUCAST rules applied, non-EUCAST rules can applied default, see Details.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply EUCAST Rules — eucast_rules","text":"","code":"eucast_rules(   x,   col_mo = NULL,   info = interactive(),   rules = getOption(\"AMR_eucastrules\", default = c(\"breakpoints\", \"expert\")),   verbose = FALSE,   version_breakpoints = 12,   version_expertrules = 3.3,   ampc_cephalosporin_resistance = NA,   only_sir_columns = FALSE,   custom_rules = NULL,   ... )  eucast_dosage(ab, administration = \"iv\", version_breakpoints = 12)"},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Apply EUCAST Rules — eucast_rules","text":"EUCAST Expert Rules. Version 2.0, 2012. Leclercq et al. EUCAST expert rules antimicrobial susceptibility testing. Clin Microbiol Infect. 2013;19(2):141-60; doi:10.1111/j.1469-0691.2011.03703.x EUCAST Expert Rules, Intrinsic Resistance Exceptional Phenotypes Tables. Version 3.1, 2016. (link) EUCAST Intrinsic Resistance Unusual Phenotypes. Version 3.2, 2020. (link) EUCAST Intrinsic Resistance Unusual Phenotypes. Version 3.3, 2021. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 9.0, 2019. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 10.0, 2020. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 11.0, 2021. (link) EUCAST Breakpoint tables interpretation MICs zone diameters. Version 12.0, 2022. (link)","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply EUCAST Rules — eucast_rules","text":"x data set antibiotic columns, amox, AMX AMC col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). info logical indicate whether progress printed console - default print interactive sessions rules character vector specifies rules applied. Must one \"breakpoints\", \"expert\", \"\", \"custom\", \"\", defaults c(\"breakpoints\", \"expert\"). default value can set another value using package option AMR_eucastrules: options(AMR_eucastrules = \"\"). using \"custom\", sure fill argument custom_rules . Custom rules can created custom_eucast_rules(). verbose logical turn Verbose mode (default ). Verbose mode, function apply rules data, instead returns data set logbook form extensive info rows columns effected way. Using Verbose mode takes lot time. version_breakpoints version number use EUCAST Clinical Breakpoints guideline. Can either \"12.0\", \"11.0\", \"10.0\". version_expertrules version number use EUCAST Expert Rules Intrinsic Resistance guideline. Can either \"3.3\", \"3.2\", \"3.1\". ampc_cephalosporin_resistance character value applied cefotaxime, ceftriaxone ceftazidime AmpC de-repressed cephalosporin-resistant mutants - default NA. Currently works version_expertrules 3.2 higher; version 'EUCAST Expert Rules Enterobacterales' state results cefotaxime, ceftriaxone ceftazidime reported note, results suppressed (emptied) three drugs. value NA (default) argument remove results three drugs, e.g. value \"R\" make results drugs resistant. Use NULL FALSE alter results three drugs AmpC de-repressed cephalosporin-resistant mutants. Using TRUE equal using \"R\".  EUCAST Expert Rules v3.2, rule applies : Citrobacter braakii, Citrobacter freundii, Citrobacter gillenii, Citrobacter murliniae, Citrobacter rodenticum, Citrobacter sedlakii, Citrobacter werkmanii, Citrobacter youngae, Enterobacter, Hafnia alvei, Klebsiella aerogenes, Morganella morganii, Providencia, Serratia. only_sir_columns logical indicate whether antibiotic columns must detected transformed class sir (see .sir()) beforehand (default FALSE) custom_rules custom rules apply, created custom_eucast_rules() ... column name antibiotic, see section Antibiotics ab (vector ) text can coerced valid antibiotic drug code .ab() administration route administration, either \"im\", \"iv\", \"oral\"","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply EUCAST Rules — eucast_rules","text":"input x, possibly edited values antibiotics. , verbose = TRUE, data.frame original new values affected bug-drug combinations.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Apply EUCAST Rules — eucast_rules","text":"Note: function translate MIC values SIR values. Use .sir() . Note: ampicillin (AMP, J01CA01) available amoxicillin (AMX, J01CA04) , latter used rules dependency ampicillin. drugs interchangeable comes expression antimicrobial resistance. file containing EUCAST rules located : https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv.  Note: Old taxonomic names replaced current taxonomy applicable. example, Ochrobactrum anthropi renamed Brucella anthropi 2020; original EUCAST rules v3.1 v3.2 yet contain new taxonomic name. AMR package contains full microbial taxonomy updated 11 December, 2022, see microorganisms.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"custom-rules","dir":"Reference","previous_headings":"","what":"Custom Rules","title":"Apply EUCAST Rules — eucast_rules","text":"Custom rules can created using custom_eucast_rules(), e.g.:","code":"x <- custom_eucast_rules(AMC == \"R\" & genus == \"Klebsiella\" ~ aminopenicillins == \"R\",                          AMC == \"I\" & genus == \"Klebsiella\" ~ aminopenicillins == \"I\")  eucast_rules(example_isolates, rules = \"custom\", custom_rules = x)"},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"-other-rules","dir":"Reference","previous_headings":"","what":"'Other' Rules","title":"Apply EUCAST Rules — eucast_rules","text":"processing, two non-EUCAST rules drug combinations can applied improve efficacy EUCAST rules, reliability data (analysis). rules : drug enzyme inhibitor set S drug without enzyme inhibitor S drug without enzyme inhibitor set R drug enzyme inhibitor R Important examples include amoxicillin amoxicillin/clavulanic acid, trimethoprim trimethoprim/sulfamethoxazole. Needless say, rules work, drugs must available data set. Since rules officially approved EUCAST, applied default. use rules, include \"\" rules argument, use eucast_rules(..., rules = \"\"). can also set package option AMR_eucastrules, .e. run options(AMR_eucastrules = \"\").","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"antibiotics","dir":"Reference","previous_headings":"","what":"Antibiotics","title":"Apply EUCAST Rules — eucast_rules","text":"define antibiotics column names, leave determine automatically guess_ab_col() input text (case-insensitive), use NULL skip column (e.g. TIC = NULL skip ticarcillin). Manually defined non-existing columns skipped warning. following antibiotics eligible functions eucast_rules() mdro(). shown format 'name (antimicrobial ID, ATC code)', sorted alphabetically: Amikacin (AMK, J01GB06), amoxicillin (AMX, J01CA04), amoxicillin/clavulanic acid (AMC, J01CR02), ampicillin (AMP, J01CA01), ampicillin/sulbactam (SAM, J01CR01), arbekacin (ARB, J01GB12), aspoxicillin (APX, J01CA19), azidocillin (AZD, J01CE04), azithromycin (AZM, J01FA10), azlocillin (AZL, J01CA09), aztreonam (ATM, J01DF01), bacampicillin (BAM, J01CA06), bekanamycin (BEK, J01GB13), benzathine benzylpenicillin (BNB, J01CE08), benzathine phenoxymethylpenicillin (BNP, J01CE10), benzylpenicillin (PEN, J01CE01), besifloxacin (BES, S01AE08), biapenem (BIA, J01DH05), carbenicillin (CRB, J01CA03), carindacillin (CRN, J01CA05), cefacetrile (CAC, J01DB10), cefaclor (CEC, J01DC04), cefadroxil (CFR, J01DB05), cefalexin (LEX, J01DB01), cefaloridine (RID, J01DB02), cefalotin (CEP, J01DB03), cefamandole (MAN, J01DC03), cefapirin (HAP, J01DB08), cefatrizine (CTZ, J01DB07), cefazedone (CZD, J01DB06), cefazolin (CZO, J01DB04), cefcapene (CCP, J01DD17), cefdinir (CDR, J01DD15), cefditoren (DIT, J01DD16), cefepime (FEP, J01DE01), cefetamet (CAT, J01DD10), cefixime (CFM, J01DD08), cefmenoxime (CMX, J01DD05), cefmetazole (CMZ, J01DC09), cefodizime (DIZ, J01DD09), cefonicid (CID, J01DC06), cefoperazone (CFP, J01DD12), cefoperazone/sulbactam (CSL, J01DD62), ceforanide (CND, J01DC11), cefotaxime (CTX, J01DD01), cefotaxime/clavulanic acid (CTC, J01DD51), cefotetan (CTT, J01DC05), cefotiam (CTF, J01DC07), cefoxitin (FOX, J01DC01), cefozopran (ZOP, J01DE03), cefpiramide (CPM, J01DD11), cefpirome (CPO, J01DE02), cefpodoxime (CPD, J01DD13), cefprozil (CPR, J01DC10), cefroxadine (CRD, J01DB11), cefsulodin (CFS, J01DD03), ceftaroline (CPT, J01DI02), ceftazidime (CAZ, J01DD02), ceftazidime/clavulanic acid (CCV, J01DD52), cefteram (CEM, J01DD18), ceftezole (CTL, J01DB12), ceftibuten (CTB, J01DD14), ceftizoxime (CZX, J01DD07), ceftobiprole medocaril (CFM1, J01DI01), ceftolozane/tazobactam (CZT, J01DI54), ceftriaxone (CRO, J01DD04), ceftriaxone/beta-lactamase inhibitor (CEB, J01DD63), cefuroxime (CXM, J01DC02), cephradine (CED, J01DB09), chloramphenicol (CHL, J01BA01), ciprofloxacin (CIP, J01MA02), clarithromycin (CLR, J01FA09), clindamycin (CLI, J01FF01), clometocillin (CLM, J01CE07), cloxacillin (CLO, J01CF02), colistin (COL, J01XB01), cycloserine (CYC, J04AB01), dalbavancin (DAL, J01XA04), daptomycin (DAP, J01XX09), delafloxacin (DFX, J01MA23), dibekacin (DKB, J01GB09), dicloxacillin (DIC, J01CF01), dirithromycin (DIR, J01FA13), doripenem (DOR, J01DH04), doxycycline (DOX, J01AA02), enoxacin (ENX, J01MA04), epicillin (EPC, J01CA07), ertapenem (ETP, J01DH03), erythromycin (ERY, J01FA01), fleroxacin (FLE, J01MA08), flucloxacillin (FLC, J01CF05), flurithromycin (FLR1, J01FA14), fosfomycin (FOS, J01XX01), framycetin (FRM, D09AA01), fusidic acid (FUS, J01XC01), garenoxacin (GRN, J01MA19), gatifloxacin (GAT, J01MA16), gemifloxacin (GEM, J01MA15), gentamicin (GEN, J01GB03), grepafloxacin (GRX, J01MA11), hetacillin (HET, J01CA18), imipenem (IPM, J01DH51), imipenem/relebactam (IMR, J01DH56), isepamicin (ISE, J01GB11), josamycin (JOS, J01FA07), kanamycin (KAN, J01GB04), lascufloxacin (LSC, J01MA25), latamoxef (LTM, J01DD06), levofloxacin (LVX, J01MA12), levonadifloxacin (LND, J01MA24), lincomycin (LIN, J01FF02), linezolid (LNZ, J01XX08), lomefloxacin (LOM, J01MA07), loracarbef (LOR, J01DC08), mecillinam (MEC, J01CA11), meropenem (MEM, J01DH02), meropenem/vaborbactam (MEV, J01DH52), metampicillin (MTM, J01CA14), meticillin (MET, J01CF03), mezlocillin (MEZ, J01CA10), micronomicin (MCR, S01AA22), midecamycin (MID, J01FA03), minocycline (MNO, J01AA08), miocamycin (MCM, J01FA11), moxifloxacin (MFX, J01MA14), nadifloxacin (NAD, D10AF05), nafcillin (NAF, J01CF06), nalidixic acid (NAL, J01MB02), neomycin (NEO, J01GB05), netilmicin (NET, J01GB07), nitrofurantoin (NIT, J01XE01), norfloxacin (, J01MA06), ofloxacin (OFX, J01MA01), oleandomycin (OLE, J01FA05), oritavancin (ORI, J01XA05), oxacillin (OXA, J01CF04), panipenem (PAN, J01DH55), pazufloxacin (PAZ, J01MA18), pefloxacin (PEF, J01MA03), penamecillin (PNM, J01CE06), pheneticillin (PHE, J01CE05), phenoxymethylpenicillin (PHN, J01CE02), piperacillin (PIP, J01CA12), piperacillin/tazobactam (TZP, J01CR05), pivampicillin (PVM, J01CA02), pivmecillinam (PME, J01CA08), plazomicin (PLZ, J01GB14), polymyxin B (PLB, J01XB02), pristinamycin (PRI, J01FG01), procaine benzylpenicillin (PRB, J01CE09), propicillin (PRP, J01CE03), prulifloxacin (PRU, J01MA17), quinupristin/dalfopristin (QDA, J01FG02), ribostamycin (RST, J01GB10), rifampicin (RIF, J04AB02), rokitamycin (ROK, J01FA12), roxithromycin (RXT, J01FA06), rufloxacin (RFL, J01MA10), sisomicin (SIS, J01GB08), sitafloxacin (SIT, J01MA21), solithromycin (SOL, J01FA16), sparfloxacin (SPX, J01MA09), spiramycin (SPI, J01FA02), streptoduocin (STR, J01GA02), streptomycin (STR1, J01GA01), sulbactam (SUL, J01CG01), sulbenicillin (SBC, J01CA16), sulfadiazine (SDI, J01EC02), sulfadiazine/trimethoprim (SLT1, J01EE02), sulfadimethoxine (SUD, J01ED01), sulfadimidine (SDM, J01EB03), sulfadimidine/trimethoprim (SLT2, J01EE05), sulfafurazole (SLF, J01EB05), sulfaisodimidine (SLF1, J01EB01), sulfalene (SLF2, J01ED02), sulfamazone (SZO, J01ED09), sulfamerazine (SLF3, J01ED07), sulfamerazine/trimethoprim (SLT3, J01EE07), sulfamethizole (SLF4, J01EB02), sulfamethoxazole (SMX, J01EC01), sulfamethoxypyridazine (SLF5, J01ED05), sulfametomidine (SLF6, J01ED03), sulfametoxydiazine (SLF7, J01ED04), sulfametrole/trimethoprim (SLT4, J01EE03), sulfamoxole (SLF8, J01EC03), sulfamoxole/trimethoprim (SLT5, J01EE04), sulfanilamide (SLF9, J01EB06), sulfaperin (SLF10, J01ED06), sulfaphenazole (SLF11, J01ED08), sulfapyridine (SLF12, J01EB04), sulfathiazole (SUT, J01EB07), sulfathiourea (SLF13, J01EB08), sultamicillin (SLT6, J01CR04), talampicillin (TAL, J01CA15), tazobactam (TAZ, J01CG02), tebipenem (TBP, J01DH06), tedizolid (TZD, J01XX11), teicoplanin (TEC, J01XA02), telavancin (TLV, J01XA03), telithromycin (TLT, J01FA15), temafloxacin (TMX, J01MA05), temocillin (TEM, J01CA17), tetracycline (TCY, J01AA07), ticarcillin (TIC, J01CA13), ticarcillin/clavulanic acid (TCC, J01CR03), tigecycline (TGC, J01AA12), tilbroquinol (TBQ, P01AA05), tobramycin (TOB, J01GB01), tosufloxacin (TFX, J01MA22), trimethoprim (TMP, J01EA01), trimethoprim/sulfamethoxazole (SXT, J01EE01), troleandomycin (TRL, J01FA08), trovafloxacin (TVA, J01MA13), vancomycin (VAN, J01XA01)","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Apply EUCAST Rules — eucast_rules","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/eucast_rules.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply EUCAST Rules — eucast_rules","text":"","code":"# \\donttest{ a <- data.frame(   mo = c(     \"Staphylococcus aureus\",     \"Enterococcus faecalis\",     \"Escherichia coli\",     \"Klebsiella pneumoniae\",     \"Pseudomonas aeruginosa\"   ),   VAN = \"-\", # Vancomycin   AMX = \"-\", # Amoxicillin   COL = \"-\", # Colistin   CAZ = \"-\", # Ceftazidime   CXM = \"-\", # Cefuroxime   PEN = \"S\", # Benzylpenicillin   FOX = \"S\", # Cefoxitin   stringsAsFactors = FALSE )  head(a) #>                       mo VAN AMX COL CAZ CXM PEN FOX #> 1  Staphylococcus aureus   -   -   -   -   -   S   S #> 2  Enterococcus faecalis   -   -   -   -   -   S   S #> 3       Escherichia coli   -   -   -   -   -   S   S #> 4  Klebsiella pneumoniae   -   -   -   -   -   S   S #> 5 Pseudomonas aeruginosa   -   -   -   -   -   S   S   # apply EUCAST rules: some results wil be changed b <- eucast_rules(a) #> Warning: in eucast_rules(): not all columns with antimicrobial results are of #> class 'sir'. Transform them on beforehand, with e.g.: #>   - a %>% as.sir(CXM:AMX) #>   - a %>% mutate_if(is_sir_eligible, as.sir) #>   - a %>% mutate(across(where(is_sir_eligible), as.sir))  head(b) #>                       mo VAN AMX COL CAZ CXM PEN FOX #> 1  Staphylococcus aureus   -   S   R   S   S   S   S #> 2  Enterococcus faecalis   -   -   R   R   R   S   R #> 3       Escherichia coli   R   -   -   -   -   R   S #> 4  Klebsiella pneumoniae   R   R   -   -   -   R   S #> 5 Pseudomonas aeruginosa   R   R   -   -   R   R   R   # do not apply EUCAST rules, but rather get a data.frame # containing all details about the transformations: c <- eucast_rules(a, verbose = TRUE) #> Warning: in eucast_rules(): not all columns with antimicrobial results are of #> class 'sir'. Transform them on beforehand, with e.g.: #>   - a %>% as.sir(CXM:AMX) #>   - a %>% mutate_if(is_sir_eligible, as.sir) #>   - a %>% mutate(across(where(is_sir_eligible), as.sir)) head(c) #>   row col           mo_fullname old new rule   rule_group #> 1   1 AMX Staphylococcus aureus   -   S       Breakpoints #> 2   1 CXM Staphylococcus aureus   -   S       Breakpoints #> 3   1 CAZ Staphylococcus aureus   R   S      Expert Rules #> 4   1 CAZ Staphylococcus aureus   -   R      Expert Rules #> 5   1 COL Staphylococcus aureus   -   R      Expert Rules #> 6   2 CAZ Enterococcus faecalis   -   R      Expert Rules #>                                                 rule_name #> 1                                          Staphylococcus #> 2                                          Staphylococcus #> 3                          Expert Rules on Staphylococcus #> 4 Table 4: Intrinsic resistance in gram-positive bacteria #> 5 Table 4: Intrinsic resistance in gram-positive bacteria #> 6 Table 4: Intrinsic resistance in gram-positive bacteria #>                                                                                 rule_source #> 1                                           'EUCAST Clinical Breakpoint Tables' v12.0, 2022 #> 2                                           'EUCAST Clinical Breakpoint Tables' v12.0, 2022 #> 3 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 #> 4 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 #> 5 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 #> 6 'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.3, 2021 # }  # Dosage guidelines:  eucast_dosage(c(\"tobra\", \"genta\", \"cipro\"), \"iv\") #> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint #>   Tables' v12.0 (2022). This note will be shown once per session. #> # A tibble: 3 × 4 #>   ab   name          standard_dosage  high_dosage  #>   <ab> <chr>         <chr>            <chr>        #> 1 TOB  Tobramycin    6-7 mg/kg x 1 iv NA           #> 2 GEN  Gentamicin    6-7 mg/kg x 1 iv NA           #> 3 CIP  Ciprofloxacin 0.4 g x 2 iv     0.4 g x 3 iv  eucast_dosage(c(\"tobra\", \"genta\", \"cipro\"), \"iv\", version_breakpoints = 10) #> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint #>   Tables' v10.0 (2020). This note will be shown once per session. #> # A tibble: 3 × 4 #>   ab   name          standard_dosage  high_dosage  #>   <ab> <chr>         <chr>            <chr>        #> 1 TOB  Tobramycin    6-7 mg/kg x 1 iv NA           #> 2 GEN  Gentamicin    6-7 mg/kg x 1 iv NA           #> 3 CIP  Ciprofloxacin 0.4 g x 2 iv     0.4 g x 3 iv"},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 2 000 Example Isolates — example_isolates","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"data set containing 2 000 microbial isolates full antibiograms. data set contains randomised fictitious data, reflects reality can used practise AMR data analysis. examples, please read tutorial website.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"","code":"example_isolates"},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"tibble 2 000 observations 46 variables: date Date receipt laboratory patient ID patient age Age patient gender Gender patient, either \"F\" \"M\" ward Ward type patient admitted, either \"Clinical\", \"ICU\", \"Outpatient\" mo ID microorganism created .mo(), see also microorganisms data set PEN:RIF 40 different antibiotics class sir (see .sir()); column names occur antibiotics data set can translated set_ab_names() ab_name()","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 2 000 Example Isolates — example_isolates","text":"","code":"example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …"},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Unclean Data — example_isolates_unclean","title":"Data Set with Unclean Data — example_isolates_unclean","text":"data set containing 3 000 microbial isolates cleaned consequently ready AMR data analysis. data set can used practice.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Unclean Data — example_isolates_unclean","text":"","code":"example_isolates_unclean"},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Unclean Data — example_isolates_unclean","text":"tibble 3 000 observations 8 variables: patient_id ID patient date date receipt laboratory hospital ID hospital, C bacteria info microorganism can transformed .mo(), see also microorganisms AMX:GEN 4 different antibiotics transformed .sir()","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Unclean Data — example_isolates_unclean","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/example_isolates_unclean.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Unclean Data — example_isolates_unclean","text":"","code":"example_isolates_unclean #> # A tibble: 3,000 × 8 #>    patient_id hospital date       bacteria      AMX   AMC   CIP   GEN   #>    <chr>      <chr>    <date>     <chr>         <chr> <chr> <chr> <chr> #>  1 J3         A        2012-11-21 E. coli       R     I     S     S     #>  2 R7         A        2018-04-03 K. pneumoniae R     I     S     S     #>  3 P3         A        2014-09-19 E. coli       R     S     S     S     #>  4 P10        A        2015-12-10 E. coli       S     I     S     S     #>  5 B7         A        2015-03-02 E. coli       S     S     S     S     #>  6 W3         A        2018-03-31 S. aureus     R     S     R     S     #>  7 J8         A        2016-06-14 E. coli       R     S     S     S     #>  8 M3         A        2015-10-25 E. coli       R     S     S     S     #>  9 J3         A        2019-06-19 E. coli       S     S     S     S     #> 10 G6         A        2015-04-27 S. aureus     S     S     S     S     #> # ℹ 2,990 more rows"},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine First Isolates — first_isolate","title":"Determine First Isolates — first_isolate","text":"Determine first isolates microorganisms every patient per episode (needed) per specimen type. functions support four methods summarised Hindler et al. 2007 (doi:10.1086/511864 ). determine patient episodes necessarily based microorganisms, use is_new_episode() also supports grouping dplyr package.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine First Isolates — first_isolate","text":"","code":"first_isolate(   x = NULL,   col_date = NULL,   col_patient_id = NULL,   col_mo = NULL,   col_testcode = NULL,   col_specimen = NULL,   col_icu = NULL,   col_keyantimicrobials = NULL,   episode_days = 365,   testcodes_exclude = NULL,   icu_exclude = FALSE,   specimen_group = NULL,   type = \"points\",   method = c(\"phenotype-based\", \"episode-based\", \"patient-based\", \"isolate-based\"),   ignore_I = TRUE,   points_threshold = 2,   info = interactive(),   include_unknown = FALSE,   include_untested_sir = TRUE,   ... )  filter_first_isolate(   x = NULL,   col_date = NULL,   col_patient_id = NULL,   col_mo = NULL,   episode_days = 365,   method = c(\"phenotype-based\", \"episode-based\", \"patient-based\", \"isolate-based\"),   ... )"},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Determine First Isolates — first_isolate","text":"Methodology function strictly based : M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 5th Edition, 2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/. Hindler JF Stelling J (2007). Analysis Presentation Cumulative Antibiograms: New Consensus Guideline Clinical Laboratory Standards Institute. Clinical Infectious Diseases, 44(6), 867-873. doi:10.1086/511864","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine First Isolates — first_isolate","text":"x data.frame containing isolates. Can left blank automatic determination, see Examples. col_date column name result date (date received lab) - default first column date class col_patient_id column name unique IDs patients - default first column starts 'patient' 'patid' (case insensitive) col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). col_testcode column name test codes. Use col_testcode = NULL exclude certain test codes (test codes screening). case testcodes_exclude ignored. col_specimen column name specimen type group col_icu column name logicals (TRUE/FALSE) whether ward department Intensive Care Unit (ICU). can also logical vector length rows x. col_keyantimicrobials (useful method = \"phenotype-based\") column name key antimicrobials determine first isolates, see key_antimicrobials(). default first column starts 'key' followed 'ab' 'antibiotics' 'antimicrobials' (case insensitive). Use col_keyantimicrobials = FALSE prevent . Can also output key_antimicrobials(). episode_days episode days genus/species combination determined 'first isolate' . default 365 days based guideline CLSI, see Source. testcodes_exclude character vector test codes excluded (case-insensitive) icu_exclude logical indicate whether ICU isolates excluded (rows value TRUE column set col_icu) specimen_group value column set col_specimen filter type type determine weighed isolates; can \"keyantimicrobials\" \"points\", see Details method method apply, either \"phenotype-based\", \"episode-based\", \"patient-based\" \"isolate-based\" (can abbreviated), see Details. default \"phenotype-based\" antimicrobial test results present data, \"episode-based\" otherwise. ignore_I logical indicate whether antibiotic interpretations \"\" ignored type = \"keyantimicrobials\", see Details points_threshold minimum number points require differences antibiogram lead inclusion isolate type = \"points\", see Details info logical indicate info printed - default TRUE interactive mode include_unknown logical indicate whether 'unknown' microorganisms included , .e. microbial code \"UNKNOWN\", defaults FALSE. WHONET users, means records organism code \"con\" (contamination) excluded default. Isolates microbial ID NA always excluded first isolate. include_untested_sir logical indicate whether also rows without antibiotic results still eligible becoming first isolate. Use include_untested_sir = FALSE always return FALSE rows. checks data set columns class sir consequently requires transforming columns antibiotic results using .sir() first. ... arguments passed first_isolate() using filter_first_isolate(), otherwise arguments passed key_antimicrobials() (universal, gram_negative, gram_positive)","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine First Isolates — first_isolate","text":"logical vector","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine First Isolates — first_isolate","text":"conduct epidemiological analyses antimicrobial resistance data, -called first isolates included prevent overestimation underestimation antimicrobial resistance. Different methods can used , see . functions context-aware. means x argument can left blank used inside data.frame call, see Examples. first_isolate() function wrapper around is_new_episode() function, efficient data sets containing microorganism codes names. isolates microbial ID NA excluded first isolate.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"different-methods","dir":"Reference","previous_headings":"","what":"Different methods","title":"Determine First Isolates — first_isolate","text":"According Hindler et al. (2007, doi:10.1086/511864 ), different methods (algorithms) select first isolates increasing reliability: isolate-based, patient-based, episode-based phenotype-based. methods select combination taxonomic genus species (subspecies). mentioned methods covered first_isolate() function:","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"isolate-based","dir":"Reference","previous_headings":"","what":"Isolate-based","title":"Determine First Isolates — first_isolate","text":"method require selection, isolates included. , however, respect arguments set first_isolate() function. example, default setting include_unknown (FALSE) omit selection rows without microbial ID.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"patient-based","dir":"Reference","previous_headings":"","what":"Patient-based","title":"Determine First Isolates — first_isolate","text":"include every genus-species combination per patient , set episode_days Inf. Although often inappropriate, method makes sure duplicate isolates selected patient. large longitudinal data set, mean isolates excluded found years initial isolate.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"episode-based","dir":"Reference","previous_headings":"","what":"Episode-based","title":"Determine First Isolates — first_isolate","text":"include every genus-species combination per patient episode , set episode_days sensible number days. Depending type analysis, 14, 30, 60 365. Short episodes common analysing specific hospital ward data, long episodes common analysing regional national data. common method correct duplicate isolates. Patients categorised episodes based ID dates (e.g., date specimen receipt laboratory result). common method, take account antimicrobial test results. means e.g. methicillin-resistant Staphylococcus aureus (MRSA) isolate differentiated wildtype Staphylococcus aureus isolate.","code":""},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"phenotype-based","dir":"Reference","previous_headings":"","what":"Phenotype-based","title":"Determine First Isolates — first_isolate","text":"reliable method, since also weighs antibiogram (antimicrobial test results) yielding -called 'first weighted isolates'. two different methods weigh antibiogram: Using type = \"points\" argument points_threshold (default) method weighs antimicrobial drugs available data set. difference S R (vice versa) counts 0.5 points, difference S R (vice versa) counts 1 point. sum points exceeds points_threshold, defaults 2, isolate selected first weighted isolate. antimicrobials internally selected using all_antimicrobials() function. output function need passed first_isolate() function. Using type = \"keyantimicrobials\" argument ignore_I method weighs specific antimicrobial drugs, called key antimicrobials. difference S R (vice versa) key antimicrobials select isolate first weighted isolate. ignore_I = FALSE, also differences S R (vice versa) lead . Key antimicrobials internally selected using key_antimicrobials() function, can also added manually variable data set col_keyantimicrobials argument. Another option pass output key_antimicrobials() function directly col_keyantimicrobials argument. default method phenotype-based (using type = \"points\") episode-based (using episode_days = 365). makes sure every genus-species combination selected per patient per year, taking account antimicrobial test results. antimicrobial test results available data set, episode-based method applied default.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/first_isolate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine First Isolates — first_isolate","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  example_isolates[first_isolate(info = TRUE), ] #> Determining first isolates using an episode length of 365 days #> ℹ Using column 'date' as input for col_date. #> ℹ Using column 'patient' as input for col_patient_id. #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a #>    microbial ID was available) #> # A tibble: 1,379 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  3 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  4 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #>  5 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA    #>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  7 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  8 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  9 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA    #> 10 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA    #> # ℹ 1,369 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … # \\donttest{ # get all first Gram-negatives example_isolates[which(first_isolate(info = FALSE) & mo_is_gram_negative()), ] #> ℹ Using column 'mo' as input for mo_is_gram_negative() #> # A tibble: 437 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  4 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  5 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R     #>  6 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R     #>  7 2002-03-08 4FC193     69 M      Clinical B_ESCHR_COLI R     NA    NA    R     #>  8 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R     #>  9 2002-04-01 496896     46 F      ICU      B_ESCHR_COLI R     NA    NA    NA    #> 10 2002-04-23 EE2510     69 F      ICU      B_ESCHR_COLI R     NA    NA    NA    #> # ℹ 427 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  if (require(\"dplyr\")) {   # filter on first isolates using dplyr:   example_isolates %>%     filter(first_isolate(info = TRUE)) } #> Determining first isolates using an episode length of 365 days #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 1,379 'phenotype-based' first isolates (69.0% of total where a #>    microbial ID was available) #> # A tibble: 1,379 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  3 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  4 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #>  5 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA    #>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  7 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  8 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  9 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA    #> 10 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA    #> # ℹ 1,369 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # short-hand version:   example_isolates %>%     filter_first_isolate(info = FALSE) } #> # A tibble: 1,379 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  3 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  4 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #>  5 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA    #>  6 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  7 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R     #>  8 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA    #>  9 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA    #> 10 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA    #> # ℹ 1,369 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … if (require(\"dplyr\")) {   # flag the first isolates per group:   example_isolates %>%     group_by(ward) %>%     mutate(first = first_isolate(info = TRUE)) %>%     select(ward, date, patient, mo, first) } #> Determining first isolates using an episode length of 365 days #> Basing inclusion on all antimicrobial results, using a points threshold of #> 2 #> Including isolates from ICU. #>  #> Group: ward = \"Clinical\" #> ℹ Excluded 9 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 861 'phenotype-based' first isolates (69.8% of total where a #>    microbial ID was available) #> Including isolates from ICU. #>  #> Group: ward = \"ICU\" #> ℹ Excluded 6 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 449 'phenotype-based' first isolates (69.6% within scope and 69.5% #>    of total where a microbial ID was available) #> Including isolates from ICU. #>  #> Group: ward = \"Outpatient\" #> ℹ Excluded 1 isolates with a microbial ID 'UNKNOWN' (in column 'mo') #> => Found 98 'phenotype-based' first isolates (82.4% within scope and 81.7% #>    of total where a microbial ID was available) #> # A tibble: 2,000 × 5 #> # Groups:   ward [3] #>    ward     date       patient mo           first #>    <chr>    <date>     <chr>   <mo>         <lgl> #>  1 Clinical 2002-01-02 A77334  B_ESCHR_COLI TRUE  #>  2 Clinical 2002-01-03 A77334  B_ESCHR_COLI FALSE #>  3 ICU      2002-01-07 067927  B_STPHY_EPDR TRUE  #>  4 ICU      2002-01-07 067927  B_STPHY_EPDR FALSE #>  5 ICU      2002-01-13 067927  B_STPHY_EPDR FALSE #>  6 ICU      2002-01-13 067927  B_STPHY_EPDR FALSE #>  7 Clinical 2002-01-14 462729  B_STPHY_AURS TRUE  #>  8 Clinical 2002-01-14 462729  B_STPHY_AURS FALSE #>  9 ICU      2002-01-16 067927  B_STPHY_EPDR FALSE #> 10 ICU      2002-01-17 858515  B_STPHY_EPDR TRUE  #> # ℹ 1,990 more rows # }"},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":null,"dir":"Reference","previous_headings":"","what":"G-test for Count Data — g.test","title":"G-test for Count Data — g.test","text":"g.test() performs chi-squared contingency table tests goodness--fit tests, just like chisq.test() reliable (1). G-test can used see whether number observations category fits theoretical expectation (called G-test goodness--fit), see whether proportions one variable different different values variable (called G-test independence).","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"G-test for Count Data — g.test","text":"","code":"g.test(x, y = NULL, p = rep(1/length(x), length(x)), rescale.p = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"G-test for Count Data — g.test","text":"code function identical chisq.test(), except : calculation statistic changed \\(2 * sum(x * log(x / E))\\) Yates' continuity correction removed apply G-test possibility simulate p values simulate.p.value removed","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"G-test for Count Data — g.test","text":"x numeric vector matrix. x y can also     factors. y numeric vector; ignored x matrix.      x factor, y factor length. p vector probabilities length x.     error given entry p negative. rescale.p logical scalar; TRUE p rescaled     (necessary) sum 1.  rescale.p FALSE,     p sum 1, error given.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"G-test for Count Data — g.test","text":"list class \"htest\" containing following   components: statistic value chi-squared test statistic. parameter degrees freedom approximate     chi-squared distribution test statistic, NA     p-value computed Monte Carlo simulation. p.value p-value test. method character string indicating type test     performed, whether Monte Carlo simulation continuity     correction used. data.name character string giving name(s) data. observed observed counts. expected expected counts null hypothesis. residuals Pearson residuals,     (observed - expected) / sqrt(expected). stdres standardized residuals,     (observed - expected) / sqrt(V), V residual cell variance (Agresti, 2007,     section 2.4.5 case x matrix, n * p * (1 - p) otherwise).","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"G-test for Count Data — g.test","text":"x matrix one row column, x vector y given, goodness--fit test performed (x treated one-dimensional contingency table). entries x must non-negative integers. case, hypothesis tested whether population probabilities equal p, equal p given. x matrix least two rows columns, taken two-dimensional contingency table: entries x must non-negative integers.  Otherwise, x y must vectors factors length; cases missing values removed, objects coerced factors, contingency table computed .  Pearson's chi-squared test performed null hypothesis joint distribution cell counts 2-dimensional contingency table product row column marginals. p-value computed asymptotic chi-squared distribution test statistic. contingency table case simulation done random sampling set contingency tables given marginals, works marginals strictly positive. Note usual sampling situation assumed chi-squared test (G-test) rather Fisher's exact test. goodness--fit case simulation done random sampling discrete distribution specified p, sample size n = sum(x). simulation done R may slow.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"g-test-of-goodness-of-fit-likelihood-ratio-test-","dir":"Reference","previous_headings":"","what":"G-test Of Goodness-of-Fit (Likelihood Ratio Test)","title":"G-test for Count Data — g.test","text":"Use G-test goodness--fit one nominal variable two values (male female, red, pink white flowers). compare observed counts numbers observations category expected counts, calculate using kind theoretical expectation (1:1 sex ratio 1:2:1 ratio genetic cross). expected number observations category small, G-test may give inaccurate results, use exact test instead (fisher.test()). G-test goodness--fit alternative chi-square test goodness--fit (chisq.test()); tests advantages disadvantages, results two tests usually similar.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"g-test-of-independence","dir":"Reference","previous_headings":"","what":"G-test of Independence","title":"G-test for Count Data — g.test","text":"Use G-test independence two nominal variables, two possible values. want know whether proportions one variable different among values variable. also possible G-test independence two nominal variables. example, Jackson et al. (2013) also data children 3, analysis old vs. young, thigh vs. arm, reaction vs. reaction, analyzed together. Fisher's exact test (fisher.test()) exact test, G-test still approximation. 2x2 table, Fisher's Exact test may slower still run seconds, even sum observations multiple millions. G-test independence alternative chi-square test independence (chisq.test()), give approximately results.","code":""},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"how-the-test-works","dir":"Reference","previous_headings":"","what":"How the Test Works","title":"G-test for Count Data — g.test","text":"Unlike exact test goodness--fit (fisher.test()), G-test directly calculate probability obtaining observed results something extreme. Instead, like almost statistical tests, G-test intermediate step; uses data calculate test statistic measures far observed data null expectation. use mathematical relationship, case chi-square distribution, estimate probability obtaining value test statistic. G-test uses log ratio two likelihoods test statistic, also called likelihood ratio test log-likelihood ratio test. formula calculate G-statistic : \\(G = 2 * sum(x * log(x / E))\\) E expected values. Since chi-square distributed, p value can calculated R :   df degrees freedom. two categories want find ones significantly different null expectation, can use method testing category vs. sum categories, Bonferroni correction. use G-tests category, course.","code":"p <- stats::pchisq(G, df, lower.tail = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"G-test for Count Data — g.test","text":"McDonald, J.H. 2014. Handbook Biological Statistics (3rd ed.). Sparky House Publishing, Baltimore, Maryland. http://www.biostathandbook.com/gtestgof.html.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/g.test.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"G-test for Count Data — g.test","text":"","code":"# = EXAMPLE 1 = # Shivrain et al. (2006) crossed clearfield rice (which are resistant # to the herbicide imazethapyr) with red rice (which are susceptible to # imazethapyr). They then crossed the hybrid offspring and examined the # F2 generation, where they found 772 resistant plants, 1611 moderately # resistant plants, and 737 susceptible plants. If resistance is controlled # by a single gene with two co-dominant alleles, you would expect a 1:2:1 # ratio.  x <- c(772, 1611, 737) g.test(x, p = c(1, 2, 1) / 4) #>  #> \tG-test of goodness-of-fit (likelihood ratio test) #>  #> data:  x #> X-squared = 4.1471, p-value = 0.1257 #>   # There is no significant difference from a 1:2:1 ratio. # Meaning: resistance controlled by a single gene with two co-dominant # alleles, is plausible.   # = EXAMPLE 2 = # Red crossbills (Loxia curvirostra) have the tip of the upper bill either # right or left of the lower bill, which helps them extract seeds from pine # cones. Some have hypothesized that frequency-dependent selection would # keep the number of right and left-billed birds at a 1:1 ratio. Groth (1992) # observed 1752 right-billed and 1895 left-billed crossbills.  x <- c(1752, 1895) g.test(x) #>  #> \tG-test of goodness-of-fit (likelihood ratio test) #>  #> data:  x #> X-squared = 5.6085, p-value = 0.01787 #>   # There is a significant difference from a 1:1 ratio. # Meaning: there are significantly more left-billed birds."},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Clinical or Epidemic Episodes — get_episode","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"functions determine items vector can considered (start ) new episode. can used determine clinical episodes epidemiological analysis. get_episode() function returns index number episode per group, is_new_episode() function returns TRUE every new get_episode() index. absolute relative episode determination supported.","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"","code":"get_episode(x, episode_days = NULL, case_free_days = NULL, ...)  is_new_episode(x, episode_days = NULL, case_free_days = NULL, ...)"},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"x vector dates (class Date POSIXt), sorted internally determine episodes episode_days episode length days specify time period new episode begins, can also less day Inf, see Details case_free_days (inter-epidemic) interval length days new episode start, can also less day Inf, see Details ... ignored, place allow future extensions","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"get_episode(): integer vector is_new_episode(): logical vector","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"Episodes can determined two ways: absolute relative. Absolute method uses episode_days define episode length days, new episode start. common use case AMR data analysis microbial epidemiology: episodes S. aureus bacteraemia ICU patients example. episode length 30 days, new S. aureus isolates ICU episode 30 days considered different (new) episode. Thus, method counts since start previous episode. Relative method uses case_free_days quantify duration case-free days (inter-epidemic interval), new episode start. common use case infectious disease epidemiology: episodes norovirus outbreaks hospital example. case-free period 14 days, new norovirus cases time considered different (new) episode. Thus, methods counts since last case previous episode. table: ** marks start new episode, 8 January 2023 7 days since start previous episode (1 January 2023).  *** marks start new episode, 21 January 2023 7 days since last case previous episode (8 January 2023). Either episode_days case_free_days must provided function.","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"difference-between-get-episode-and-is-new-episode-","dir":"Reference","previous_headings":"","what":"Difference between get_episode() and is_new_episode()","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"get_episode() function returns index number episode, cases/patients/isolates first episode number 1, cases/patients/isolates second episode number 2, etc. is_new_episode() function hand, returns TRUE every new get_episode() index. specify, setting episode_days = 365 (using method 1 explained ), two functions differ:","code":""},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"other","dir":"Reference","previous_headings":"","what":"Other","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"first_isolate() function wrapper around is_new_episode() function, efficient data sets containing microorganism codes names allows different isolate selection methods. dplyr package required functions work, episode functions support variable grouping work conveniently inside dplyr verbs filter(), mutate() summarise().","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/get_episode.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine Clinical or Epidemic Episodes — get_episode","text":"","code":"# difference between absolute and relative determination of episodes: x <- data.frame(dates = as.Date(c(   \"2021-01-01\",   \"2021-01-02\",   \"2021-01-05\",   \"2021-01-08\",   \"2021-02-21\",   \"2021-02-22\",   \"2021-02-23\",   \"2021-02-24\",   \"2021-03-01\",   \"2021-03-01\" ))) x$absolute <- get_episode(x$dates, episode_days = 7) x$relative <- get_episode(x$dates, case_free_days = 7) x #>         dates absolute relative #> 1  2021-01-01        1        1 #> 2  2021-01-02        1        1 #> 3  2021-01-05        1        1 #> 4  2021-01-08        2        1 #> 5  2021-02-21        3        2 #> 6  2021-02-22        3        2 #> 7  2021-02-23        3        2 #> 8  2021-02-24        3        2 #> 9  2021-03-01        4        2 #> 10 2021-03-01        4        2   # `example_isolates` is a data set available in the AMR package. # See ?example_isolates df <- example_isolates[sample(seq_len(2000), size = 100), ]  get_episode(df$date, episode_days = 60) # indices #>   [1] 45 13 42 35 36 17 26 23 21 32 27 48 22 10 19  4 37  5 18 11  7 15  3 38 28 #>  [26] 47 51 35  6 41 16 25 24 26  4 38 24 35  2 26 10 44 43  1 46 19 12 15 49 41 #>  [51] 29  5 31 11 33 18  9 48 12 20 25 47 36 46 16 52  8 30 34 51  7 27 50 40 47 #>  [76] 39 34 35 15 32 27 10 26 36 26 11 34 44 37 50 48 14 22  2 45  5 26 30 51  5 is_new_episode(df$date, episode_days = 60) # TRUE/FALSE #>   [1]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE #>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE #>  [25]  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE #>  [37] FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE #>  [49]  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE #>  [61] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE #>  [73]  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE #>  [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE #>  [97] FALSE FALSE FALSE FALSE  # filter on results from the third 60-day episode only, using base R df[which(get_episode(df$date, 60) == 3), ] #> # A tibble: 1 × 46 #>   date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>   <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #> 1 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R     #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, RIF <sir>  # the functions also work for less than a day, e.g. to include one per hour: get_episode(   c(     Sys.time(),     Sys.time() + 60 * 60   ),   episode_days = 1 / 24 ) #> [1] 1 2  # \\donttest{ if (require(\"dplyr\")) {   # is_new_episode() can also be used in dplyr verbs to determine patient   # episodes based on any (combination of) grouping variables:   df %>%     mutate(condition = sample(       x = c(\"A\", \"B\", \"C\"),       size = 100,       replace = TRUE     )) %>%     group_by(patient, condition) %>%     mutate(new_episode = is_new_episode(date, 365)) %>%     select(patient, date, condition, new_episode) %>%     arrange(patient, condition, date) } #> # A tibble: 100 × 4 #> # Groups:   patient, condition [99] #>    patient date       condition new_episode #>    <chr>   <date>     <chr>     <lgl>       #>  1 023456  2009-11-02 A         TRUE        #>  2 036063  2010-01-28 B         TRUE        #>  3 0DBB93  2003-10-02 A         TRUE        #>  4 0DBF93  2015-10-12 B         TRUE        #>  5 0E2483  2007-06-21 A         TRUE        #>  6 114570  2003-04-08 B         TRUE        #>  7 14D826  2006-09-14 A         TRUE        #>  8 156730  2012-04-12 B         TRUE        #>  9 1710B8  2008-01-22 C         TRUE        #> 10 180928  2008-06-13 A         TRUE        #> # ℹ 90 more rows  if (require(\"dplyr\")) {   df %>%     group_by(ward, patient) %>%     transmute(date,       patient,       new_index = get_episode(date, 60),       new_logical = is_new_episode(date, 60)     ) %>%     arrange(patient, ward, date) } #> # A tibble: 100 × 5 #> # Groups:   ward, patient [94] #>    ward     date       patient new_index new_logical #>    <chr>    <date>     <chr>       <int> <lgl>       #>  1 Clinical 2009-11-02 023456          1 TRUE        #>  2 Clinical 2010-01-28 036063          1 TRUE        #>  3 ICU      2003-10-02 0DBB93          1 TRUE        #>  4 Clinical 2015-10-12 0DBF93          1 TRUE        #>  5 ICU      2007-06-21 0E2483          1 TRUE        #>  6 ICU      2003-04-08 114570          1 TRUE        #>  7 Clinical 2006-09-14 14D826          1 TRUE        #>  8 Clinical 2012-04-12 156730          1 TRUE        #>  9 Clinical 2008-01-22 1710B8          1 TRUE        #> 10 Clinical 2008-06-14 180928          1 FALSE       #> # ℹ 90 more rows  if (require(\"dplyr\")) {   df %>%     group_by(ward) %>%     summarise(       n_patients = n_distinct(patient),       n_episodes_365 = sum(is_new_episode(date, episode_days = 365)),       n_episodes_60 = sum(is_new_episode(date, episode_days = 60)),       n_episodes_30 = sum(is_new_episode(date, episode_days = 30))     ) } #> # A tibble: 3 × 5 #>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30 #>   <chr>           <int>          <int>         <int>         <int> #> 1 Clinical           64             14            40            49 #> 2 ICU                23              9            20            21 #> 3 Outpatient          7              5             6             7  # grouping on patients and microorganisms leads to the same # results as first_isolate() when using 'episode-based': if (require(\"dplyr\")) {   x <- df %>%     filter_first_isolate(       include_unknown = TRUE,       method = \"episode-based\"     )    y <- df %>%     group_by(patient, mo) %>%     filter(is_new_episode(date, 365)) %>%     ungroup()    identical(x, y) } #> [1] FALSE  # but is_new_episode() has a lot more flexibility than first_isolate(), # since you can now group on anything that seems relevant: if (require(\"dplyr\")) {   df %>%     group_by(patient, mo, ward) %>%     mutate(flag_episode = is_new_episode(date, 365)) %>%     select(group_vars(.), flag_episode) } #> # A tibble: 100 × 4 #> # Groups:   patient, mo, ward [98] #>    patient mo           ward     flag_episode #>    <chr>   <mo>         <chr>    <lgl>        #>  1 A76045  B_ENTRC_FACM ICU      TRUE         #>  2 452212  B_ENTRC_FACM ICU      TRUE         #>  3 419568  B_STRPT_PNMN Clinical TRUE         #>  4 BC9909  B_ESCHR_COLI Clinical TRUE         #>  5 443847  B_KLBSL_PNMN Clinical TRUE         #>  6 F32657  B_STPHY_EPDR ICU      TRUE         #>  7 180928  B_STRPT_AGLC Clinical TRUE         #>  8 B82692  B_STPHY_CONS Clinical TRUE         #>  9 89F578  B_STPHY_CONS Clinical TRUE         #> 10 597301  B_ESCHR_COLI ICU      TRUE         #> # ℹ 90 more rows # }"},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":null,"dir":"Reference","previous_headings":"","what":"PCA Biplot with ggplot2 — ggplot_pca","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"Produces ggplot2 variant -called biplot PCA (principal component analysis), flexible appealing base R biplot() function.","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"","code":"ggplot_pca(   x,   choices = 1:2,   scale = 1,   pc.biplot = TRUE,   labels = NULL,   labels_textsize = 3,   labels_text_placement = 1.5,   groups = NULL,   ellipse = TRUE,   ellipse_prob = 0.68,   ellipse_size = 0.5,   ellipse_alpha = 0.5,   points_size = 2,   points_alpha = 0.25,   arrows = TRUE,   arrows_colour = \"darkblue\",   arrows_size = 0.5,   arrows_textsize = 3,   arrows_textangled = TRUE,   arrows_alpha = 0.75,   base_textsize = 10,   ... )"},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"ggplot_pca() function based ggbiplot() function ggbiplot package Vince Vu, found GitHub: https://github.com/vqv/ggbiplot (retrieved: 2 March 2020, latest commit: 7325e88; 12 February 2015). per GPL-2 licence demands documentation code changes, changes made based source code : Rewritten code remove dependency packages plyr, scales grid Parametrised options, like arrow ellipse settings Hardened input possibilities defining exact type user input every argument Added total amount explained variance caption plot Cleaned syntax based lintr package, fixed grammatical errors added integrity checks Updated documentation","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"x object returned pca(), prcomp() princomp() choices length 2 vector specifying components plot. default     biplot strict sense. scale variables scaled lambda ^ scale     observations scaled lambda ^ (1-scale)     lambda singular values computed     princomp. Normally 0 <= scale <= 1, warning     issued specified scale outside range. pc.biplot true, use Gabriel (1971) refers \"principal component     biplot\", lambda = 1 observations scaled sqrt(n)     variables scaled sqrt(n).  inner products     variables approximate covariances distances observations     approximate Mahalanobis distance. labels optional vector labels observations. set, labels placed respective points. using pca() function input x, determined automatically based attribute non_numeric_cols, see pca(). labels_textsize size text used labels labels_text_placement adjustment factor placement variable names (>=1 means away arrow head) groups optional vector groups labels, length labels. set, points labels coloured according groups. using pca() function input x, determined automatically based attribute non_numeric_cols, see pca(). ellipse logical indicate whether normal data ellipse drawn group (set groups) ellipse_prob statistical size ellipse normal probability ellipse_size size ellipse line ellipse_alpha alpha (transparency) ellipse line points_size size points points_alpha alpha (transparency) points arrows logical indicate whether arrows drawn arrows_colour colour arrow text arrows_size size (thickness) arrow lines arrows_textsize size text end arrows arrows_textangled logical whether text end arrows angled arrows_alpha alpha (transparency) arrows text base_textsize text size plot elements except labels arrows ... arguments passed functions","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"colours labels points can changed adding another scale layer colour, scale_colour_viridis_d() scale_colour_brewer().","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"PCA Biplot with ggplot2 — ggplot_pca","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  # \\donttest{ if (require(\"dplyr\")) {   # calculate the resistance per group first   resistance_data <- example_isolates %>%     group_by(       order = mo_order(mo), # group on anything, like order       genus = mo_genus(mo)     ) %>% #   and genus as we do here;     filter(n() >= 30) %>% # filter on only 30 results per group     summarise_if(is.sir, resistance) # then get resistance of all drugs    # now conduct PCA for certain antimicrobial drugs   pca_result <- resistance_data %>%     pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)    summary(pca_result)    # old base R plotting method:   biplot(pca_result)    # new ggplot2 plotting method using this package:   if (require(\"ggplot2\")) {     ggplot_pca(pca_result)      # still extendible with any ggplot2 function     ggplot_pca(pca_result) +       scale_colour_viridis_d() +       labs(title = \"Title here\")   } } #> Warning: There were 73 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE, #>   only_all_tested = FALSE) ...`. #> ℹ In group 5: `order = \"Lactobacillales\"`, `genus = \"Enterococcus\"`. #> Caused by warning: #> ! Introducing NA: only 14 results available for PEN in group: order = #> \"Lactobacillales\", genus = \"Enterococcus\" (minimum = 30). #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings. #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", #>   \"TMP\", and \"TOB\". Total observations available: 7. #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\"  #>    # }"},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":null,"dir":"Reference","previous_headings":"","what":"AMR Plots with ggplot2 — ggplot_sir","title":"AMR Plots with ggplot2 — ggplot_sir","text":"Use functions create bar plots AMR data analysis. functions rely ggplot2 functions.","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"AMR Plots with ggplot2 — ggplot_sir","text":"","code":"ggplot_sir(   data,   position = NULL,   x = \"antibiotic\",   fill = \"interpretation\",   facet = NULL,   breaks = seq(0, 1, 0.1),   limits = NULL,   translate_ab = \"name\",   combine_SI = TRUE,   minimum = 30,   language = get_AMR_locale(),   nrow = NULL,   colours = c(S = \"#3CAEA3\", SI = \"#3CAEA3\", I = \"#F6D55C\", IR = \"#ED553B\", R =     \"#ED553B\"),   datalabels = TRUE,   datalabels.size = 2.5,   datalabels.colour = \"grey15\",   title = NULL,   subtitle = NULL,   caption = NULL,   x.title = \"Antimicrobial\",   y.title = \"Proportion\",   ... )  geom_sir(   position = NULL,   x = c(\"antibiotic\", \"interpretation\"),   fill = \"interpretation\",   translate_ab = \"name\",   minimum = 30,   language = get_AMR_locale(),   combine_SI = TRUE,   ... )  facet_sir(facet = c(\"interpretation\", \"antibiotic\"), nrow = NULL)  scale_y_percent(breaks = seq(0, 1, 0.1), limits = NULL)  scale_sir_colours(..., aesthetics = \"fill\")  theme_sir()  labels_sir_count(   position = NULL,   x = \"antibiotic\",   translate_ab = \"name\",   minimum = 30,   language = get_AMR_locale(),   combine_SI = TRUE,   datalabels.size = 3,   datalabels.colour = \"grey15\" )"},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"AMR Plots with ggplot2 — ggplot_sir","text":"data data.frame column(s) class sir (see .sir()) position position adjustment bars, either \"fill\", \"stack\" \"dodge\" x variable show x axis, either \"antibiotic\" (default) \"interpretation\" grouping variable fill variable categorise using plots legend, either \"antibiotic\" (default) \"interpretation\" grouping variable facet variable split plots , either \"interpretation\" (default) \"antibiotic\" grouping variable breaks numeric vector positions limits numeric vector length two providing limits scale, use NA refer existing minimum maximum translate_ab column name antibiotics data set translate antibiotic abbreviations , using ab_property() combine_SI logical indicate whether values S must merged one, output consists S+vs. R (susceptible vs. resistant) - default TRUE minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. nrow (using facet) number rows colours named vactor colour used filling. default colours colour-blind friendly. datalabels show datalabels using labels_sir_count() datalabels.size size datalabels datalabels.colour colour datalabels title text show title plot subtitle text show subtitle plot caption text show caption plot x.title text show x axis description y.title text show y axis description ... arguments passed geom_sir() , case scale_sir_colours(), named values set colours. default colours colour-blind friendly, maintaining convention e.g. 'susceptible' green 'resistant' red. See Examples. aesthetics aesthetics apply colours - default \"fill\" can also (combination ) \"alpha\", \"colour\", \"fill\", \"linetype\", \"shape\" \"size\"","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"AMR Plots with ggplot2 — ggplot_sir","text":"default, names antibiotics shown plots using ab_name(). can set translate_ab argument. See count_df().","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"the-functions","dir":"Reference","previous_headings":"","what":"The Functions","title":"AMR Plots with ggplot2 — ggplot_sir","text":"geom_sir() take variable data sir class (created .sir()) using sir_df() plot bars percentage S, , R. default behaviour bars stacked different antibiotics x axis. facet_sir() creates 2d plots (default based S//R) using ggplot2::facet_wrap(). scale_y_percent() transforms y axis 0 100% range using ggplot2::scale_y_continuous(). scale_sir_colours() sets colours bars (green S, yellow , red R). multilingual support. default colours colour-blind friendly, maintaining convention e.g. 'susceptible' green 'resistant' red. theme_sir() [ggplot2 theme][ggplot2::theme() minimal distraction. labels_sir_count() print datalabels bars percentage amount isolates using ggplot2::geom_text(). ggplot_sir() wrapper around functions uses data first input. makes possible use function pipe (%>%). See Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/ggplot_sir.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"AMR Plots with ggplot2 — ggplot_sir","text":"","code":"# \\donttest{ if (require(\"ggplot2\") && require(\"dplyr\")) {   # get antimicrobial results for drugs against a UTI:   ggplot(example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)) +     geom_sir() }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # prettify the plot using some additional functions:   df <- example_isolates %>% select(AMX, NIT, FOS, TMP, CIP)   ggplot(df) +     geom_sir() +     scale_y_percent() +     scale_sir_colours() +     labels_sir_count() +     theme_sir() }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # or better yet, simplify this using the wrapper function - a single command:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir() }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # get only proportions and no counts:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir(datalabels = FALSE) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # add other ggplot2 arguments as you like:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir(       width = 0.5,       colour = \"black\",       size = 1,       linetype = 2,       alpha = 0.25     ) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # you can alter the colours with colour names:   example_isolates %>%     select(AMX) %>%     ggplot_sir(colours = c(SI = \"yellow\")) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # but you can also use the built-in colour-blind friendly colours for   # your plots, where \"S\" is green, \"I\" is yellow and \"R\" is red:   data.frame(     x = c(\"Value1\", \"Value2\", \"Value3\"),     y = c(1, 2, 3),     z = c(\"Value4\", \"Value5\", \"Value6\")   ) %>%     ggplot() +     geom_col(aes(x = x, y = y, fill = z)) +     scale_sir_colours(Value4 = \"S\", Value5 = \"I\", Value6 = \"R\") }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # resistance of ciprofloxacine per age group   example_isolates %>%     mutate(first_isolate = first_isolate()) %>%     filter(       first_isolate == TRUE,       mo == as.mo(\"Escherichia coli\")     ) %>%     # age_groups() is also a function in this AMR package:     group_by(age_group = age_groups(age)) %>%     select(age_group, CIP) %>%     ggplot_sir(x = \"age_group\") } #> Warning: Removed 6 rows containing missing values (`position_stack()`). #> Warning: Removed 6 rows containing missing values (`position_stack()`).  if (require(\"ggplot2\") && require(\"dplyr\")) {   # a shorter version which also adjusts data label colours:   example_isolates %>%     select(AMX, NIT, FOS, TMP, CIP) %>%     ggplot_sir(colours = FALSE) }  if (require(\"ggplot2\") && require(\"dplyr\")) {   # it also supports groups (don't forget to use the group var on `x` or `facet`):   example_isolates %>%     filter(mo_is_gram_negative(), ward != \"Outpatient\") %>%     # select only UTI-specific drugs     select(ward, AMX, NIT, FOS, TMP, CIP) %>%     group_by(ward) %>%     ggplot_sir(       x = \"ward\",       facet = \"antibiotic\",       nrow = 1,       title = \"AMR of Anti-UTI Drugs Per Ward\",       x.title = \"Ward\",       datalabels = FALSE     ) } #> ℹ Using column 'mo' as input for mo_is_gram_negative()  # }"},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Guess Antibiotic Column — guess_ab_col","title":"Guess Antibiotic Column — guess_ab_col","text":"tries find column name data set based information antibiotics data set. Also supports WHONET abbreviations.","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Guess Antibiotic Column — guess_ab_col","text":"","code":"guess_ab_col(   x = NULL,   search_string = NULL,   verbose = FALSE,   only_sir_columns = FALSE )"},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Guess Antibiotic Column — guess_ab_col","text":"x data.frame search_string text search x , checked .ab() value column x verbose logical indicate whether additional info printed only_sir_columns logical indicate whether antibiotic columns must detected transformed class sir (see .sir()) beforehand (default FALSE)","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Guess Antibiotic Column — guess_ab_col","text":"column name x, NULL result found.","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Guess Antibiotic Column — guess_ab_col","text":"can look antibiotic (trade) name abbreviation search x antibiotics data set column containing name code antibiotic.","code":""},{"path":"https://msberends.github.io/AMR/reference/guess_ab_col.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Guess Antibiotic Column — guess_ab_col","text":"","code":"df <- data.frame(   amox = \"S\",   tetr = \"R\" )  guess_ab_col(df, \"amoxicillin\") #> [1] \"amox\" guess_ab_col(df, \"J01AA07\") # ATC code of tetracycline #> [1] \"tetr\"  guess_ab_col(df, \"J01AA07\", verbose = TRUE) #> Auto-guessing columns suitable for analysis #> ... #>  OK. #> ℹ Using column 'amox' as input for AMX (amoxicillin). #> ℹ Using column 'tetr' as input for TCY (tetracycline). #> ℹ Using column 'tetr' as input for J01AA07 (tetracycline). #> [1] \"tetr\" # NOTE: Using column 'tetr' as input for J01AA07 (tetracycline).  # WHONET codes df <- data.frame(   AMP_ND10 = \"R\",   AMC_ED20 = \"S\" ) guess_ab_col(df, \"ampicillin\") #> [1] \"AMP_ND10\" guess_ab_col(df, \"J01CR02\") #> [1] \"AMC_ED20\" guess_ab_col(df, as.ab(\"augmentin\")) #> [1] \"AMC_ED20\""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"Data set containing defined intrinsic resistance EUCAST bug-drug combinations.","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"","code":"intrinsic_resistant"},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"tibble 134 634 observations 2 variables: mo Microorganism ID ab Antibiotic ID","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"data set based 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021).","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository. allow machine reading EUCAST CLSI guidelines, almost impossible MS Excel PDF files distributed EUCAST CLSI.","code":""},{"path":"https://msberends.github.io/AMR/reference/intrinsic_resistant.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with Bacterial Intrinsic Resistance — intrinsic_resistant","text":"","code":"intrinsic_resistant #> # A tibble: 134,634 × 2 #>    mo      ab    #>    <mo>    <chr> #>  1 B_GRAMP ATM   #>  2 B_GRAMP COL   #>  3 B_GRAMP NAL   #>  4 B_GRAMP PLB   #>  5 B_GRAMP TEM   #>  6 B_ABTRP ATM   #>  7 B_ABTRP COL   #>  8 B_ABTRP NAL   #>  9 B_ABTRP PLB   #> 10 B_ABTRP TEM   #> # ℹ 134,624 more rows"},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":null,"dir":"Reference","previous_headings":"","what":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"According binomial nomenclature, lowest four taxonomic levels (family, genus, species, subspecies) printed italics. function finds taxonomic names within strings makes italic.","code":""},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"","code":"italicise_taxonomy(string, type = c(\"markdown\", \"ansi\"))  italicize_taxonomy(string, type = c(\"markdown\", \"ansi\"))"},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"string character (vector) type type conversion taxonomic names, either \"markdown\" \"ansi\", see Details","code":""},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"function finds taxonomic names makes italic based microorganisms data set. taxonomic names can italicised using markdown (default) adding * taxonomic names, using ANSI colours adding \\033[3m \\033[23m taxonomic names. multiple ANSI colours available, conversion occur. function also supports abbreviation genus followed species, \"E. coli\" \"K. pneumoniae ozaenae\".","code":""},{"path":"https://msberends.github.io/AMR/reference/italicise_taxonomy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Italicise Taxonomic Families, Genera, Species, Subspecies — italicise_taxonomy","text":"","code":"italicise_taxonomy(\"An overview of Staphylococcus aureus isolates\") #> [1] \"An overview of *Staphylococcus aureus* isolates\" italicise_taxonomy(\"An overview of S. aureus isolates\") #> [1] \"An overview of *S. aureus* isolates\"  cat(italicise_taxonomy(\"An overview of S. aureus isolates\", type = \"ansi\")) #> An overview of S. aureus isolates"},{"path":"https://msberends.github.io/AMR/reference/join.html","id":null,"dir":"Reference","previous_headings":"","what":"Join microorganisms to a Data Set — join","title":"Join microorganisms to a Data Set — join","text":"Join data set microorganisms easily existing data set character vector.","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Join microorganisms to a Data Set — join","text":"","code":"inner_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  left_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  right_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  full_join_microorganisms(x, by = NULL, suffix = c(\"2\", \"\"), ...)  semi_join_microorganisms(x, by = NULL, ...)  anti_join_microorganisms(x, by = NULL, ...)"},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Join microorganisms to a Data Set — join","text":"x existing data set join, character vector. case character vector, resulting data.frame contain column 'x' values. variable join - left empty search column class mo (created .mo()) \"mo\" column name exists x, otherwise column name x values exist microorganisms$mo (= \"bacteria_id\"), another column microorganisms (named, like = c(\"bacteria_id\" = \"fullname\")) suffix non-joined duplicate variables x y, suffixes added output disambiguate . character vector length 2. ... ignored, place allow future extensions","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Join microorganisms to a Data Set — join","text":"data.frame","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Join microorganisms to a Data Set — join","text":"Note: opposed join() functions dplyr, character vectors supported default existing columns get suffix \"2\" newly joined columns get suffix. dplyr package installed, join functions used. Otherwise, much slower merge() interaction() functions base R used.","code":""},{"path":"https://msberends.github.io/AMR/reference/join.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Join microorganisms to a Data Set — join","text":"","code":"left_join_microorganisms(as.mo(\"K. pneumoniae\")) #> # A tibble: 1 × 23 #>   mo           fullname   status kingdom phylum class order family genus species #>   <mo>         <chr>      <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>   #> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo… #> # ℹ 13 more variables: subspecies <chr>, rank <chr>, ref <chr>, #> #   oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>, #> #   lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>, #> #   gbif_renamed_to <chr>, prevalence <dbl>, snomed <list> left_join_microorganisms(\"B_KLBSL_PNMN\") #> # A tibble: 1 × 23 #>   mo           fullname   status kingdom phylum class order family genus species #>   <mo>         <chr>      <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> <chr>   #> 1 B_KLBSL_PNMN Klebsiell… accep… Bacter… Pseud… Gamm… Ente… Enter… Kleb… pneumo… #> # ℹ 13 more variables: subspecies <chr>, rank <chr>, ref <chr>, #> #   oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>, #> #   lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>, #> #   gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>  df <- data.frame(   date = seq(     from = as.Date(\"2018-01-01\"),     to = as.Date(\"2018-01-07\"),     by = 1   ),   bacteria = as.mo(c(     \"S. aureus\", \"MRSA\", \"MSSA\", \"STAAUR\",     \"E. coli\", \"E. coli\", \"E. coli\"   )),   stringsAsFactors = FALSE ) colnames(df) #> [1] \"date\"     \"bacteria\"  df_joined <- left_join_microorganisms(df, \"bacteria\") colnames(df_joined) #>  [1] \"date\"             \"bacteria\"         \"fullname\"         \"status\"           #>  [5] \"kingdom\"          \"phylum\"           \"class\"            \"order\"            #>  [9] \"family\"           \"genus\"            \"species\"          \"subspecies\"       #> [13] \"rank\"             \"ref\"              \"oxygen_tolerance\" \"source\"           #> [17] \"lpsn\"             \"lpsn_parent\"      \"lpsn_renamed_to\"  \"gbif\"             #> [21] \"gbif_parent\"      \"gbif_renamed_to\"  \"prevalence\"       \"snomed\"            # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     left_join_microorganisms() %>%     colnames() } #> Joining, by = \"mo\" #>  [1] \"date\"             \"patient\"          \"age\"              \"gender\"           #>  [5] \"ward\"             \"mo\"               \"PEN\"              \"OXA\"              #>  [9] \"FLC\"              \"AMX\"              \"AMC\"              \"AMP\"              #> [13] \"TZP\"              \"CZO\"              \"FEP\"              \"CXM\"              #> [17] \"FOX\"              \"CTX\"              \"CAZ\"              \"CRO\"              #> [21] \"GEN\"              \"TOB\"              \"AMK\"              \"KAN\"              #> [25] \"TMP\"              \"SXT\"              \"NIT\"              \"FOS\"              #> [29] \"LNZ\"              \"CIP\"              \"MFX\"              \"VAN\"              #> [33] \"TEC\"              \"TCY\"              \"TGC\"              \"DOX\"              #> [37] \"ERY\"              \"CLI\"              \"AZM\"              \"IPM\"              #> [41] \"MEM\"              \"MTR\"              \"CHL\"              \"COL\"              #> [45] \"MUP\"              \"RIF\"              \"fullname\"         \"status\"           #> [49] \"kingdom\"          \"phylum\"           \"class\"            \"order\"            #> [53] \"family\"           \"genus\"            \"species\"          \"subspecies\"       #> [57] \"rank\"             \"ref\"              \"oxygen_tolerance\" \"source\"           #> [61] \"lpsn\"             \"lpsn_parent\"      \"lpsn_renamed_to\"  \"gbif\"             #> [65] \"gbif_parent\"      \"gbif_renamed_to\"  \"prevalence\"       \"snomed\"           # }"},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":null,"dir":"Reference","previous_headings":"","what":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"functions can used determine first weighted isolates considering phenotype isolate selection (see first_isolate()). Using phenotype-based method determine first isolates reliable methods disregard phenotypes.","code":""},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"","code":"key_antimicrobials(   x = NULL,   col_mo = NULL,   universal = c(\"ampicillin\", \"amoxicillin/clavulanic acid\", \"cefuroxime\",     \"piperacillin/tazobactam\", \"ciprofloxacin\", \"trimethoprim/sulfamethoxazole\"),   gram_negative = c(\"gentamicin\", \"tobramycin\", \"colistin\", \"cefotaxime\", \"ceftazidime\",     \"meropenem\"),   gram_positive = c(\"vancomycin\", \"teicoplanin\", \"tetracycline\", \"erythromycin\",     \"oxacillin\", \"rifampin\"),   antifungal = c(\"anidulafungin\", \"caspofungin\", \"fluconazole\", \"miconazole\", \"nystatin\",     \"voriconazole\"),   only_sir_columns = FALSE,   ... )  all_antimicrobials(x = NULL, only_sir_columns = FALSE, ...)  antimicrobials_equal(   y,   z,   type = c(\"points\", \"keyantimicrobials\"),   ignore_I = TRUE,   points_threshold = 2,   ... )"},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"x data.frame antibiotics columns, like AMX amox. Can left blank determine automatically col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). universal names broad-spectrum antimicrobial drugs, case-insensitive. Set NULL ignore. See Details default antimicrobial drugs gram_negative names antibiotic drugs Gram-positives, case-insensitive. Set NULL ignore. See Details default antibiotic drugs gram_positive names antibiotic drugs Gram-negatives, case-insensitive. Set NULL ignore. See Details default antibiotic drugs antifungal names antifungal drugs fungi, case-insensitive. Set NULL ignore. See Details default antifungal drugs only_sir_columns logical indicate whether columns must included transformed class sir (see .sir()) beforehand (default FALSE) ... ignored, place allow future extensions y, z character vectors compare type type determine weighed isolates; can \"keyantimicrobials\" \"points\", see Details ignore_I logical indicate whether antibiotic interpretations \"\" ignored type = \"keyantimicrobials\", see Details points_threshold minimum number points require differences antibiogram lead inclusion isolate type = \"points\", see Details","code":""},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"key_antimicrobials() all_antimicrobials() functions context-aware. means x argument can left blank used inside data.frame call, see Examples. function key_antimicrobials() returns character vector 12 antimicrobial results every isolate. function all_antimicrobials() returns character vector antimicrobial drug results every isolate. vectors can compared using antimicrobials_equal(), check two isolates generally antibiogram. Missing invalid values replaced dot (\".\") key_antimicrobials() ignored antimicrobials_equal(). Please see first_isolate() function important functions enable 'phenotype-based' method determination first isolates. default antimicrobial drugs used rows (set universal) : Ampicillin Amoxicillin/clavulanic acid Cefuroxime Ciprofloxacin Piperacillin/tazobactam Trimethoprim/sulfamethoxazole default antimicrobial drugs used Gram-negative bacteria (set gram_negative) : Cefotaxime Ceftazidime Colistin Gentamicin Meropenem Tobramycin default antimicrobial drugs used Gram-positive bacteria (set gram_positive) : Erythromycin Oxacillin Rifampin Teicoplanin Tetracycline Vancomycin default antimicrobial drugs used fungi (set antifungal) : Anidulafungin Caspofungin Fluconazole Miconazole Nystatin Voriconazole","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/key_antimicrobials.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"(Key) Antimicrobials for First Weighted Isolates — key_antimicrobials","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  # output of the `key_antimicrobials()` function could be like this: strainA <- \"SSSRR.S.R..S\" strainB <- \"SSSIRSSSRSSS\"  # those strings can be compared with: antimicrobials_equal(strainA, strainB, type = \"keyantimicrobials\") #> [1] TRUE # TRUE, because I is ignored (as well as missing values)  antimicrobials_equal(strainA, strainB, type = \"keyantimicrobials\", ignore_I = FALSE) #> [1] FALSE # FALSE, because I is not ignored and so the 4th [character] differs  # \\donttest{ if (require(\"dplyr\")) {   # set key antibiotics to a new variable   my_patients <- example_isolates %>%     mutate(keyab = key_antimicrobials(antifungal = NULL)) %>% # no need to define `x`     mutate(       # now calculate first isolates       first_regular = first_isolate(col_keyantimicrobials = FALSE),       # and first WEIGHTED isolates       first_weighted = first_isolate(col_keyantimicrobials = \"keyab\")     )    # Check the difference in this data set, 'weighted' results in more isolates:   sum(my_patients$first_regular, na.rm = TRUE)   sum(my_patients$first_weighted, na.rm = TRUE) } #> [1] 1395 # }"},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":null,"dir":"Reference","previous_headings":"","what":"Kurtosis of the Sample — kurtosis","title":"Kurtosis of the Sample — kurtosis","text":"Kurtosis measure \"tailedness\" probability distribution real-valued random variable. normal distribution kurtosis 3 excess kurtosis 0.","code":""},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Kurtosis of the Sample — kurtosis","text":"","code":"kurtosis(x, na.rm = FALSE, excess = FALSE)  # S3 method for default kurtosis(x, na.rm = FALSE, excess = FALSE)  # S3 method for matrix kurtosis(x, na.rm = FALSE, excess = FALSE)  # S3 method for data.frame kurtosis(x, na.rm = FALSE, excess = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Kurtosis of the Sample — kurtosis","text":"x vector values, matrix data.frame na.rm logical indicate whether NA values stripped computation proceeds excess logical indicate whether excess kurtosis returned, defined kurtosis minus 3.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/kurtosis.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Kurtosis of the Sample — kurtosis","text":"","code":"kurtosis(rnorm(10000)) #> [1] 3.027601 kurtosis(rnorm(10000), excess = TRUE) #> [1] 0.04687044"},{"path":"https://msberends.github.io/AMR/reference/like.html","id":null,"dir":"Reference","previous_headings":"","what":"Vectorised Pattern Matching with Keyboard Shortcut — like","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"Convenient wrapper around grepl() match pattern: x %like% pattern. always returns logical vector always case-insensitive (use x %like_case% pattern case-sensitive matching). Also, pattern can long x compare items index vectors, can length iterate cases.","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"","code":"like(x, pattern, ignore.case = TRUE)  x %like% pattern  x %unlike% pattern  x %like_case% pattern  x %unlike_case% pattern"},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"Idea like function data.table package, although altered explained Details.","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"x character vector matches sought, object can coerced .character() character vector. pattern character vector containing regular expressions (character string fixed = TRUE) matched given character vector. Coerced .character() character string possible. ignore.case FALSE, pattern matching case sensitive TRUE, case ignored matching.","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"logical vector","code":""},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"like() %like%/%unlike% functions: case-insensitive (use %like_case%/%unlike_case% case-sensitive matching) Support multiple patterns Check pattern valid regular expression sets fixed = TRUE , greatly improve speed (vectorised pattern) Always use compatibility Perl unless fixed = TRUE, greatly improve speed Using RStudio? %like%/%unlike% functions can also directly inserted code Addins menu can keyboard shortcut like Shift+Ctrl+L Shift+Cmd+L (see menu Tools > Modify Keyboard Shortcuts...). keep pressing shortcut, inserted text iterated %like% -> %unlike% -> %like_case% -> %unlike_case%.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/like.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Vectorised Pattern Matching with Keyboard Shortcut — like","text":"","code":"# data.table has a more limited version of %like%, so unload it: try(detach(\"package:data.table\", unload = TRUE), silent = TRUE)  a <- \"This is a test\" b <- \"TEST\" a %like% b #> [1] TRUE b %like% a #> [1] FALSE  # also supports multiple patterns a <- c(\"Test case\", \"Something different\", \"Yet another thing\") b <- c(\"case\", \"diff\", \"yet\") a %like% b #> [1] TRUE TRUE TRUE a %unlike% b #> [1] FALSE FALSE FALSE  a[1] %like% b #> [1]  TRUE FALSE FALSE a %like% b[1] #> [1]  TRUE FALSE FALSE  # \\donttest{ # get isolates whose name start with 'Entero' (case-insensitive) example_isolates[which(mo_name() %like% \"^entero\"), ] #> ℹ Using column 'mo' as input for mo_name() #> # A tibble: 106 × 46 #>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinic… B_ENTRC_FACM  NA    NA    NA    NA    #>  2 2002-04-08 130252     78 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  3 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  4 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  5 2003-04-20 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  6 2003-04-21 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  7 2003-08-13 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  8 2003-08-13 F35553     52 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  9 2003-09-05 F35553     52 M      ICU     B_ENTRC       NA    NA    NA    NA    #> 10 2003-09-05 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #> # ℹ 96 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …  if (require(\"dplyr\")) {   example_isolates %>%     filter(mo_name() %like% \"^ent\") } #> ℹ Using column 'mo' as input for mo_name() #> # A tibble: 106 × 46 #>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>   <mo>          <sir> <sir> <sir> <sir> #>  1 2002-02-21 4FC193     69 M      Clinic… B_ENTRC_FACM  NA    NA    NA    NA    #>  2 2002-04-08 130252     78 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  3 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  4 2002-06-23 798871     82 M      Clinic… B_ENTRC_FCLS  NA    NA    NA    NA    #>  5 2003-04-20 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  6 2003-04-21 6BC362     62 M      ICU     B_ENTRC       NA    NA    NA    NA    #>  7 2003-08-13 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #>  8 2003-08-13 F35553     52 M      ICU     B_ENTRC_FCLS  NA    NA    NA    NA    #>  9 2003-09-05 F35553     52 M      ICU     B_ENTRC       NA    NA    NA    NA    #> 10 2003-09-05 F35553     52 M      ICU     B_ENTRBC_CLOC R     NA    NA    R     #> # ℹ 96 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, … # }"},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":null,"dir":"Reference","previous_headings":"","what":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"Determine isolates multidrug-resistant organisms (MDRO) according international, national custom guidelines.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"","code":"mdro(   x = NULL,   guideline = \"CMI2012\",   col_mo = NULL,   info = interactive(),   pct_required_classes = 0.5,   combine_SI = TRUE,   verbose = FALSE,   only_sir_columns = FALSE,   ... )  custom_mdro_guideline(..., as_factor = TRUE)  brmo(x = NULL, only_sir_columns = FALSE, ...)  mrgn(x = NULL, only_sir_columns = FALSE, ...)  mdr_tb(x = NULL, only_sir_columns = FALSE, ...)  mdr_cmi2012(x = NULL, only_sir_columns = FALSE, ...)  eucast_exceptional_phenotypes(x = NULL, only_sir_columns = FALSE, ...)"},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"See supported guidelines list publications used function.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"x data.frame antibiotics columns, like AMX amox. Can left blank automatic determination. guideline specific guideline follow, see sections Supported international / national guidelines Using Custom Guidelines . left empty, publication Magiorakos et al. (see ) followed. col_mo column name names codes microorganisms (see .mo()) - default first column class mo. Values coerced using .mo(). info logical indicate whether progress printed console - default print interactive sessions pct_required_classes minimal required percentage antimicrobial classes must available per isolate, rounded . example, default guideline, 17 antimicrobial classes must available S. aureus. Setting pct_required_classes argument 0.5 (default) means every S. aureus isolate least 8 different classes must available. lower number available classes return NA isolate. combine_SI logical indicate whether values S must merged one, resistance considered isolates R, . default behaviour mdro() function, follows redefinition EUCAST interpretation (increased exposure) 2019, see section 'Interpretation S, R' . using combine_SI = FALSE, resistance considered isolates R . verbose logical turn Verbose mode (default ). Verbose mode, function return MDRO results, instead returns data set logbook form extensive info isolates MDRO-positive, . only_sir_columns logical indicate whether antibiotic columns must detected transformed class sir (see .sir()) beforehand (default FALSE) ... case custom_mdro_guideline(): set rules, see section Using Custom Guidelines . Otherwise: column name antibiotic, see section Antibiotics . as_factor logical indicate whether returned value ordered factor (TRUE, default), otherwise character vector","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"CMI 2012 paper - function mdr_cmi2012() mdro(): Ordered factor levels Negative < Multi-drug-resistant (MDR) < Extensively drug-resistant (XDR) < Pandrug-resistant (PDR) TB guideline - function mdr_tb() mdro(..., guideline = \"TB\"): Ordered factor levels Negative < Mono-resistant < Poly-resistant < Multi-drug-resistant < Extensively drug-resistant German guideline - function mrgn() mdro(..., guideline = \"MRGN\"): Ordered factor levels Negative < 3MRGN < 4MRGN Everything else, except custom guidelines: Ordered factor levels Negative < Positive, unconfirmed < Positive. value \"Positive, unconfirmed\" means , according guideline, entirely sure isolate multi-drug resistant confirmed additional (e.g. molecular) tests","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"functions context-aware. means x argument can left blank used inside data.frame call, see Examples. pct_required_classes argument, values 1 divided 100. support fractions (0.75 3/4) percentages (75). Note: Every test involves Enterobacteriaceae family, internally performed using newly named order Enterobacterales, since Enterobacteriaceae family taxonomically reclassified Adeolu et al. 2016. , Enterobacteriaceae family Enterobacteriales () order. species old Enterobacteriaceae family still new Enterobacterales (without ) order, divided multiple families. way tests performed now mdro() function makes sure results 2016 2016 identical.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"supported-international-national-guidelines","dir":"Reference","previous_headings":"","what":"Supported International / National Guidelines","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"Currently supported guidelines (case-insensitive): guideline = \"CMI2012\" (default) Magiorakos AP, Srinivasan et al. \"Multidrug-resistant, extensively drug-resistant pandrug-resistant bacteria: international expert proposal interim standard definitions acquired resistance.\" Clinical Microbiology Infection (2012) (link) guideline = \"EUCAST3.3\" (simply guideline = \"EUCAST\") European international guideline - EUCAST Expert Rules Version 3.3 \"Intrinsic Resistance Unusual Phenotypes\" (link) guideline = \"EUCAST3.2\" European international guideline - EUCAST Expert Rules Version 3.2 \"Intrinsic Resistance Unusual Phenotypes\" (link) guideline = \"EUCAST3.1\" European international guideline - EUCAST Expert Rules Version 3.1 \"Intrinsic Resistance Exceptional Phenotypes Tables\" (link) guideline = \"TB\" international guideline multi-drug resistant tuberculosis - World Health Organization \"Companion handbook guidelines programmatic management drug-resistant tuberculosis\" (link) guideline = \"MRGN\" German national guideline - Mueller et al. (2015) Antimicrobial Resistance Infection Control 4:7; doi:10.1186/s13756-015-0047-6 guideline = \"BRMO\" Dutch national guideline - Rijksinstituut voor Volksgezondheid en Milieu \"WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) (ZKH)\" (link) Please suggest (country-specific) guidelines letting us know: https://github.com/msberends/AMR/issues/new.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"using-custom-guidelines","dir":"Reference","previous_headings":"","what":"Using Custom Guidelines","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"Custom guidelines can set custom_mdro_guideline() function. great importance custom rules determine MDROs hospital, e.g., rules dependent ward, state contact isolation variables data. familiar case_when() function dplyr package, recognise input method set rules. Rules must set using R considers 'formula notation'. rule written tilde (~) consequence rule written tilde:   row/isolate matches first rule, value first ~ (case 'Elderly Type ') set MDRO value. Otherwise, second rule tried . number rules unlimited. can print rules set console overview. Colours help reading console supports colours.   outcome function can used guideline argument mdro() function:   Rules can also combined custom rules using c():   rules set (custom object case) exported shared file location using saveRDS() collaborate multiple users. custom rules set imported using readRDS().","code":"custom <- custom_mdro_guideline(CIP == \"R\" & age > 60 ~ \"Elderly Type A\",                                 ERY == \"R\" & age > 60 ~ \"Elderly Type B\") custom #> A set of custom MDRO rules: #>   1. CIP is \"R\" and age is higher than 60 -> Elderly Type A #>   2. ERY is \"R\" and age is higher than 60 -> Elderly Type B #>   3. Otherwise -> Negative #> #> Unmatched rows will return NA. x <- mdro(example_isolates,           guideline = custom) table(x) #>       Negative Elderly Type A Elderly Type B #>           1070            198            732 x <- mdro(example_isolates,           guideline = c(custom,                         custom_mdro_guideline(ERY == \"R\" & age > 50 ~ \"Elderly Type C\"))) table(x) #>       Negative Elderly Type A Elderly Type B Elderly Type C #>            961            198            732            109"},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"antibiotics","dir":"Reference","previous_headings":"","what":"Antibiotics","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"define antibiotics column names, leave determine automatically guess_ab_col() input text (case-insensitive), use NULL skip column (e.g. TIC = NULL skip ticarcillin). Manually defined non-existing columns skipped warning. following antibiotics eligible functions eucast_rules() mdro(). shown format 'name (antimicrobial ID, ATC code)', sorted alphabetically: Amikacin (AMK, J01GB06), amoxicillin (AMX, J01CA04), amoxicillin/clavulanic acid (AMC, J01CR02), ampicillin (AMP, J01CA01), ampicillin/sulbactam (SAM, J01CR01), arbekacin (ARB, J01GB12), aspoxicillin (APX, J01CA19), azidocillin (AZD, J01CE04), azithromycin (AZM, J01FA10), azlocillin (AZL, J01CA09), aztreonam (ATM, J01DF01), bacampicillin (BAM, J01CA06), bekanamycin (BEK, J01GB13), benzathine benzylpenicillin (BNB, J01CE08), benzathine phenoxymethylpenicillin (BNP, J01CE10), benzylpenicillin (PEN, J01CE01), besifloxacin (BES, S01AE08), biapenem (BIA, J01DH05), carbenicillin (CRB, J01CA03), carindacillin (CRN, J01CA05), cefacetrile (CAC, J01DB10), cefaclor (CEC, J01DC04), cefadroxil (CFR, J01DB05), cefalexin (LEX, J01DB01), cefaloridine (RID, J01DB02), cefalotin (CEP, J01DB03), cefamandole (MAN, J01DC03), cefapirin (HAP, J01DB08), cefatrizine (CTZ, J01DB07), cefazedone (CZD, J01DB06), cefazolin (CZO, J01DB04), cefcapene (CCP, J01DD17), cefdinir (CDR, J01DD15), cefditoren (DIT, J01DD16), cefepime (FEP, J01DE01), cefetamet (CAT, J01DD10), cefixime (CFM, J01DD08), cefmenoxime (CMX, J01DD05), cefmetazole (CMZ, J01DC09), cefodizime (DIZ, J01DD09), cefonicid (CID, J01DC06), cefoperazone (CFP, J01DD12), cefoperazone/sulbactam (CSL, J01DD62), ceforanide (CND, J01DC11), cefotaxime (CTX, J01DD01), cefotaxime/clavulanic acid (CTC, J01DD51), cefotetan (CTT, J01DC05), cefotiam (CTF, J01DC07), cefoxitin (FOX, J01DC01), cefozopran (ZOP, J01DE03), cefpiramide (CPM, J01DD11), cefpirome (CPO, J01DE02), cefpodoxime (CPD, J01DD13), cefprozil (CPR, J01DC10), cefroxadine (CRD, J01DB11), cefsulodin (CFS, J01DD03), ceftaroline (CPT, J01DI02), ceftazidime (CAZ, J01DD02), ceftazidime/clavulanic acid (CCV, J01DD52), cefteram (CEM, J01DD18), ceftezole (CTL, J01DB12), ceftibuten (CTB, J01DD14), ceftizoxime (CZX, J01DD07), ceftobiprole medocaril (CFM1, J01DI01), ceftolozane/tazobactam (CZT, J01DI54), ceftriaxone (CRO, J01DD04), ceftriaxone/beta-lactamase inhibitor (CEB, J01DD63), cefuroxime (CXM, J01DC02), cephradine (CED, J01DB09), chloramphenicol (CHL, J01BA01), ciprofloxacin (CIP, J01MA02), clarithromycin (CLR, J01FA09), clindamycin (CLI, J01FF01), clometocillin (CLM, J01CE07), cloxacillin (CLO, J01CF02), colistin (COL, J01XB01), cycloserine (CYC, J04AB01), dalbavancin (DAL, J01XA04), daptomycin (DAP, J01XX09), delafloxacin (DFX, J01MA23), dibekacin (DKB, J01GB09), dicloxacillin (DIC, J01CF01), dirithromycin (DIR, J01FA13), doripenem (DOR, J01DH04), doxycycline (DOX, J01AA02), enoxacin (ENX, J01MA04), epicillin (EPC, J01CA07), ertapenem (ETP, J01DH03), erythromycin (ERY, J01FA01), fleroxacin (FLE, J01MA08), flucloxacillin (FLC, J01CF05), flurithromycin (FLR1, J01FA14), fosfomycin (FOS, J01XX01), framycetin (FRM, D09AA01), fusidic acid (FUS, J01XC01), garenoxacin (GRN, J01MA19), gatifloxacin (GAT, J01MA16), gemifloxacin (GEM, J01MA15), gentamicin (GEN, J01GB03), grepafloxacin (GRX, J01MA11), hetacillin (HET, J01CA18), imipenem (IPM, J01DH51), imipenem/relebactam (IMR, J01DH56), isepamicin (ISE, J01GB11), josamycin (JOS, J01FA07), kanamycin (KAN, J01GB04), lascufloxacin (LSC, J01MA25), latamoxef (LTM, J01DD06), levofloxacin (LVX, J01MA12), levonadifloxacin (LND, J01MA24), lincomycin (LIN, J01FF02), linezolid (LNZ, J01XX08), lomefloxacin (LOM, J01MA07), loracarbef (LOR, J01DC08), mecillinam (MEC, J01CA11), meropenem (MEM, J01DH02), meropenem/vaborbactam (MEV, J01DH52), metampicillin (MTM, J01CA14), meticillin (MET, J01CF03), mezlocillin (MEZ, J01CA10), micronomicin (MCR, S01AA22), midecamycin (MID, J01FA03), minocycline (MNO, J01AA08), miocamycin (MCM, J01FA11), moxifloxacin (MFX, J01MA14), nadifloxacin (NAD, D10AF05), nafcillin (NAF, J01CF06), nalidixic acid (NAL, J01MB02), neomycin (NEO, J01GB05), netilmicin (NET, J01GB07), nitrofurantoin (NIT, J01XE01), norfloxacin (, J01MA06), ofloxacin (OFX, J01MA01), oleandomycin (OLE, J01FA05), oritavancin (ORI, J01XA05), oxacillin (OXA, J01CF04), panipenem (PAN, J01DH55), pazufloxacin (PAZ, J01MA18), pefloxacin (PEF, J01MA03), penamecillin (PNM, J01CE06), pheneticillin (PHE, J01CE05), phenoxymethylpenicillin (PHN, J01CE02), piperacillin (PIP, J01CA12), piperacillin/tazobactam (TZP, J01CR05), pivampicillin (PVM, J01CA02), pivmecillinam (PME, J01CA08), plazomicin (PLZ, J01GB14), polymyxin B (PLB, J01XB02), pristinamycin (PRI, J01FG01), procaine benzylpenicillin (PRB, J01CE09), propicillin (PRP, J01CE03), prulifloxacin (PRU, J01MA17), quinupristin/dalfopristin (QDA, J01FG02), ribostamycin (RST, J01GB10), rifampicin (RIF, J04AB02), rokitamycin (ROK, J01FA12), roxithromycin (RXT, J01FA06), rufloxacin (RFL, J01MA10), sisomicin (SIS, J01GB08), sitafloxacin (SIT, J01MA21), solithromycin (SOL, J01FA16), sparfloxacin (SPX, J01MA09), spiramycin (SPI, J01FA02), streptoduocin (STR, J01GA02), streptomycin (STR1, J01GA01), sulbactam (SUL, J01CG01), sulbenicillin (SBC, J01CA16), sulfadiazine (SDI, J01EC02), sulfadiazine/trimethoprim (SLT1, J01EE02), sulfadimethoxine (SUD, J01ED01), sulfadimidine (SDM, J01EB03), sulfadimidine/trimethoprim (SLT2, J01EE05), sulfafurazole (SLF, J01EB05), sulfaisodimidine (SLF1, J01EB01), sulfalene (SLF2, J01ED02), sulfamazone (SZO, J01ED09), sulfamerazine (SLF3, J01ED07), sulfamerazine/trimethoprim (SLT3, J01EE07), sulfamethizole (SLF4, J01EB02), sulfamethoxazole (SMX, J01EC01), sulfamethoxypyridazine (SLF5, J01ED05), sulfametomidine (SLF6, J01ED03), sulfametoxydiazine (SLF7, J01ED04), sulfametrole/trimethoprim (SLT4, J01EE03), sulfamoxole (SLF8, J01EC03), sulfamoxole/trimethoprim (SLT5, J01EE04), sulfanilamide (SLF9, J01EB06), sulfaperin (SLF10, J01ED06), sulfaphenazole (SLF11, J01ED08), sulfapyridine (SLF12, J01EB04), sulfathiazole (SUT, J01EB07), sulfathiourea (SLF13, J01EB08), sultamicillin (SLT6, J01CR04), talampicillin (TAL, J01CA15), tazobactam (TAZ, J01CG02), tebipenem (TBP, J01DH06), tedizolid (TZD, J01XX11), teicoplanin (TEC, J01XA02), telavancin (TLV, J01XA03), telithromycin (TLT, J01FA15), temafloxacin (TMX, J01MA05), temocillin (TEM, J01CA17), tetracycline (TCY, J01AA07), ticarcillin (TIC, J01CA13), ticarcillin/clavulanic acid (TCC, J01CR03), tigecycline (TGC, J01AA12), tilbroquinol (TBQ, P01AA05), tobramycin (TOB, J01GB01), tosufloxacin (TFX, J01MA22), trimethoprim (TMP, J01EA01), trimethoprim/sulfamethoxazole (SXT, J01EE01), troleandomycin (TRL, J01FA08), trovafloxacin (TVA, J01MA13), vancomycin (VAN, J01XA01)","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/mdro.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Determine Multidrug-Resistant Organisms (MDRO) — mdro","text":"","code":"out <- mdro(example_isolates, guideline = \"EUCAST\") #>  (16 isolates had no test results) str(out) #>  Ord.factor w/ 3 levels \"Negative\"<\"Positive, unconfirmed\"<..: 1 1 1 1 1 1 1 1 1 1 ... table(out) #> out #>              Negative Positive, unconfirmed              Positive  #>                  1978                     0                     6   out <- mdro(example_isolates,   guideline = custom_mdro_guideline(     AMX == \"R\" ~ \"Custom MDRO 1\",     VAN == \"R\" ~ \"Custom MDRO 2\"   ) ) table(out) #> out #>      Negative Custom MDRO 1 Custom MDRO 2  #>           870           804           326   # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     mdro() %>%     table()    # no need to define `x` when used inside dplyr verbs:   example_isolates %>%     mutate(MDRO = mdro()) %>%     pull(MDRO) %>%     table() } #>  (16 isolates had no test results) #> Warning: in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) #>  (16 isolates had no test results) #> Warning: There was 1 warning in `mutate()`. #> ℹ In argument: `MDRO = mdro()`. #> Caused by warning: #> ! in mdro(): NA introduced for isolates where the available percentage of #> antimicrobial classes was below 50% (set with pct_required_classes) #> . #>                         Negative       Multi-drug-resistant (MDR)  #>                             1601                              128  #> Extensively drug-resistant (XDR)          Pandrug-resistant (PDR)  #>                                0                                0  # }"},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the Mean AMR Distance — mean_amr_distance","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"Calculates normalised mean antimicrobial resistance multiple observations, help identify similar isolates without comparing antibiograms hand.","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"","code":"mean_amr_distance(x, ...)  # S3 method for sir mean_amr_distance(x, ..., combine_SI = TRUE)  # S3 method for data.frame mean_amr_distance(x, ..., combine_SI = TRUE)  amr_distance_from_row(amr_distance, row)"},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"x vector class sir, mic disk, data.frame containing columns classes ... variables select (supports tidyselect language column1:column4 (.mic), can thus also antibiotic selectors combine_SI logical indicate whether values S must merged one, input consists S+vs. R (susceptible vs. resistant) - default TRUE amr_distance outcome mean_amr_distance() row index, row number","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"mean AMR distance effectively Z-score; normalised numeric value compare AMR test results can help identify similar isolates, without comparing antibiograms hand. MIC values (see .mic()) transformed log2() first; distance thus calculated (log2(x) - mean(log2(x))) / sd(log2(x)). SIR values (see .sir()) transformed using \"S\" = 1, \"\" = 2, \"R\" = 3. combine_SI TRUE (default), \"\" considered 1. data sets, mean AMR distance calculated per column, mean per row returned, see Examples. Use amr_distance_from_row() subtract distances distance one row, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"interpretation","dir":"Reference","previous_headings":"","what":"Interpretation","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"Isolates distances less 0.01 difference considered similar. Differences lower 0.025 considered suspicious.","code":""},{"path":"https://msberends.github.io/AMR/reference/mean_amr_distance.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the Mean AMR Distance — mean_amr_distance","text":"","code":"sir <- random_sir(10) sir #> Class 'sir' #>  [1] R R R I S R S I S R mean_amr_distance(sir) #>  [1]  0.9486833  0.9486833  0.9486833 -0.9486833 -0.9486833  0.9486833 #>  [7] -0.9486833 -0.9486833 -0.9486833  0.9486833  mic <- random_mic(10) mic #> Class 'mic' #>  [1] 4     128   0.5   0.025 0.002 32    128   16    0.5   128   mean_amr_distance(mic) #>  [1]  0.07714511  0.97675198 -0.46261901 -1.24022626 -1.89583387  0.61690923 #>  [7]  0.97675198  0.43698786 -0.46261901  0.97675198 # equal to the Z-score of their log2: (log2(mic) - mean(log2(mic))) / sd(log2(mic)) #>  [1]  0.07714511  0.97675198 -0.46261901 -1.24022626 -1.89583387  0.61690923 #>  [7]  0.97675198  0.43698786 -0.46261901  0.97675198  disk <- random_disk(10) disk #> Class 'disk' #>  [1]  9 46 37 23 13 47 10 23  6 38 mean_amr_distance(disk) #>  [1] -1.0287932  1.3209197  0.7493679 -0.1397127 -0.7747702  1.3844254 #>  [7] -0.9652875 -0.1397127 -1.2193105  0.8128737  y <- data.frame(   id = LETTERS[1:10],   amox = random_sir(10, ab = \"amox\", mo = \"Escherichia coli\"),   cipr = random_disk(10, ab = \"cipr\", mo = \"Escherichia coli\"),   gent = random_mic(10, ab = \"gent\", mo = \"Escherichia coli\"),   tobr = random_mic(10, ab = \"tobr\", mo = \"Escherichia coli\") ) y #>    id amox cipr  gent tobr #> 1   A    I   18     4    2 #> 2   B    I   23    16 0.25 #> 3   C    R   20     2    1 #> 4   D    I   20     8    2 #> 5   E    S   25 <=0.5    2 #> 6   F    R   22     1    1 #> 7   G    I   26     1 0.25 #> 8   H    R   22     2    2 #> 9   I    I   31     2 0.25 #> 10  J    R   19     8 0.25 mean_amr_distance(y) #> ℹ Calculating mean AMR distance based on columns \"amox\", \"cipr\", \"gent\", #>   and \"tobr\" #>  [1] -0.14918777 -0.03570087  0.13005928  0.13771386 -0.17506383  0.10002806 #>  [7] -0.47691376  0.43333913  0.00264067  0.03308522 y$amr_distance <- mean_amr_distance(y, where(is.mic)) #> Error in .subset(x, j): invalid subscript type 'list' y[order(y$amr_distance), ] #> Error in order(y$amr_distance): argument 1 is not a vector  if (require(\"dplyr\")) {   y %>%     mutate(       amr_distance = mean_amr_distance(y),       check_id_C = amr_distance_from_row(amr_distance, id == \"C\")     ) %>%     arrange(check_id_C) } #> ℹ Calculating mean AMR distance based on columns \"amox\", \"cipr\", \"gent\", #>   and \"tobr\" #>    id amox cipr  gent tobr amr_distance  check_id_C #> 1   C    R   20     2    1   0.13005928 0.000000000 #> 2   D    I   20     8    2   0.13771386 0.007654579 #> 3   F    R   22     1    1   0.10002806 0.030031221 #> 4   J    R   19     8 0.25   0.03308522 0.096974059 #> 5   I    I   31     2 0.25   0.00264067 0.127418609 #> 6   B    I   23    16 0.25  -0.03570087 0.165760150 #> 7   A    I   18     4    2  -0.14918777 0.279247046 #> 8   H    R   22     2    2   0.43333913 0.303279854 #> 9   E    S   25 <=0.5    2  -0.17506383 0.305123107 #> 10  G    I   26     1 0.25  -0.47691376 0.606973037 if (require(\"dplyr\")) {   # support for groups   example_isolates %>%     filter(mo_genus() == \"Enterococcus\" & mo_species() != \"\") %>%     select(mo, TCY, carbapenems()) %>%     group_by(mo) %>%     mutate(dist = mean_amr_distance(.)) %>%     arrange(mo, dist) } #> ℹ Using column 'mo' as input for mo_genus() #> ℹ Using column 'mo' as input for mo_species() #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> ℹ Calculating mean AMR distance based on columns \"TCY\", \"IPM\", and \"MEM\" #> # A tibble: 63 × 5 #> # Groups:   mo [4] #>    mo           TCY   IPM   MEM     dist #>    <mo>         <sir> <sir> <sir>  <dbl> #>  1 B_ENTRC_AVIM S     S     NA     0     #>  2 B_ENTRC_AVIM S     S     NA     0     #>  3 B_ENTRC_CSSL NA    S     NA    NA     #>  4 B_ENTRC_FACM S     S     NA    -2.66  #>  5 B_ENTRC_FACM S     R     R     -0.423 #>  6 B_ENTRC_FACM S     R     R     -0.423 #>  7 B_ENTRC_FACM NA    R     R      0.224 #>  8 B_ENTRC_FACM NA    R     R      0.224 #>  9 B_ENTRC_FACM NA    R     R      0.224 #> 10 B_ENTRC_FACM NA    R     R      0.224 #> # ℹ 53 more rows"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"data set containing commonly used codes microorganisms, laboratory systems WHONET. Define set_mo_source(). searched using .mo() consequently mo_* functions.","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"","code":"microorganisms.codes"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"tibble 5 754 observations 2 variables: code Commonly used code microorganism mo ID microorganism microorganisms data set","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/microorganisms.codes.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 5 754 Common Microorganism Codes — microorganisms.codes","text":"","code":"microorganisms.codes #> # A tibble: 5,754 × 2 #>    code    mo        #>    <chr>   <mo>      #>  1 _FAM_A- B_GRAMN   #>  2 _FAM_A+ B_GRAMP   #>  3 _FAM_AC B_GRAMP   #>  4 _FAM_AE B_GRAMN   #>  5 _FAM_AN B_GRAMN   #>  6 _FAM_AO B_GRAMP   #>  7 _FAM_AP   UNKNOWN #>  8 _FAM_AS F_FUNGUS  #>  9 _FAM_AT   UNKNOWN #> 10 _FAM_AV   UNKNOWN #> # ℹ 5,744 more rows"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":null,"dir":"Reference","previous_headings":"","what":"Data Set with 52 151 Microorganisms — microorganisms","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"data set containing full microbial taxonomy (last updated: 11 December, 2022) five kingdoms List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF). data set backbone AMR package. MO codes can looked using .mo().","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"","code":"microorganisms"},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"tibble 52 151 observations 23 variables: mo ID microorganism used package fullname Full name, like \"Escherichia coli\". taxonomic ranks genus, species subspecies, 'pasted' text genus, species, subspecies. taxonomic ranks higher genus, name taxon. status  Status taxon, either \"accepted\" \"synonym\" kingdom, phylum, class, order, family, genus, species, subspecies Taxonomic rank microorganism rank Text taxonomic rank microorganism, \"species\" \"genus\" ref Author(s) year related scientific publication. contains first surname year latest authors, e.g. \"Wallis et al. 2006 emend. Smith Jones 2018\" becomes \"Smith et al., 2018\". field directly retrieved source specified column source. Moreover, accents removed comply CRAN allows ASCII characters, e.g. \"Váňová\" becomes \"Vanova\". lpsn Identifier ('Record number') List Prokaryotic names Standing Nomenclature (LPSN). first/highest LPSN identifier keep one identifier per row. example, Acetobacter ascendens LPSN Record number 7864 11011. first available microorganisms data set. oxygen_tolerance  Oxygen tolerance, either \"aerobe\", \"anaerobe\", \"anaerobe/microaerophile\", \"facultative anaerobe\", \"likely facultative anaerobe\", \"microaerophile\". data retrieved BacDive (see Source). Items contain \"likely\" missing BacDive extrapolated species within genus guess oxygen tolerance. Currently 73.4% ~36 000 bacteria data set contain oxygen tolerance. lpsn_parent LPSN identifier parent taxon lpsn_renamed_to LPSN identifier currently valid taxon gbif Identifier ('taxonID') Global Biodiversity Information Facility (GBIF) gbif_parent GBIF identifier parent taxon gbif_renamed_to GBIF identifier currently valid taxon source Either \"GBIF\", \"LPSN\", \"manually added\" (see Source) prevalence Prevalence microorganism according Bartlett et al. (2022, doi:10.1099/mic.0.001269 ), see mo_matching_score() full explanation snomed Systematized Nomenclature Medicine (SNOMED) code microorganism, version 1 July, 2021 (see Source). Use mo_snomed() retrieve quickly, see mo_property().","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332 . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov Grimont et al. (2007). Antigenic Formulae Salmonella Serovars, 9th Edition. Collaborating Centre Reference Research Salmonella (WHOCC-SALM). Bartlett et al. (2022). comprehensive list bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269 Reimer et al. (2022). BacDive 2022: knowledge base standardized bacterial archaeal data.  Nucleic Acids Res. 2022 Jan 7;50(D1):D741-D746; doi:10.1093/nar/gkab961","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"Please note entries based List Prokaryotic names Standing Nomenclature (LPSN) Global Biodiversity Information Facility (GBIF) (see ). Since sources incorporate entries based (recent) publications International Journal Systematic Evolutionary Microbiology (IJSEM), can happen year publication sometimes later one might expect. example, Staphylococcus pettenkoferi described first time Diagnostic Microbiology Infectious Disease 2002 (doi:10.1016/s0732-8893(02)00399-1 ), 2007 publication IJSEM followed (doi:10.1099/ijs.0.64381-0 ). Consequently, AMR package returns 2007 mo_year(\"S. pettenkoferi\").","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"included-taxa","dir":"Reference","previous_headings":"","what":"Included Taxa","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"Included taxonomic data : ~36 000 (sub)species kingdoms Archaea Bacteria ~7 900 (sub)species kingdom Fungi. kingdom Fungi large taxon almost 300,000 different (sub)species, microbial (rather macroscopic, like mushrooms). , fungi fit scope package. relevant fungi covered (species Aspergillus, Candida, Cryptococcus, Histoplasma, Pneumocystis, Saccharomyces Trichophyton). ~5 100 (sub)species kingdom Protozoa ~1 400 (sub)species 43 relevant genera kingdom Animalia (Strongyloides Taenia) ~9 800 previously accepted names included (sub)species (taxonomically renamed) complete taxonomic tree included (sub)species: kingdom subspecies identifier parent taxons year first author related scientific publication","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"manual-additions","dir":"Reference","previous_headings":"","what":"Manual additions","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"convenience, entries added manually: ~1 500 entries Salmonella, city-like serovars groups H 15 entries Streptococcus, beta-haemolytic groups K, viridans, milleri 2 entries Staphylococcus (coagulase-negative (CoNS) coagulase-positive (CoPS)) 1 entry Blastocystis (B.  hominis), although officially exist (Noel et al. 2005, PMID 15634993) 1 entry Moraxella (M. catarrhalis), formally named Branhamella catarrhalis (Catlin, 1970) though change never accepted within field clinical microbiology 8 'undefined' entries (unknown, unknown Gram-negatives, unknown Gram-positives, unknown yeast, unknown fungus, unknown anaerobic Gram-pos/Gram-neg bacteria) syntax used transform original data cleansed R format, can found : https://github.com/msberends/AMR/blob/main/data-raw/reproduction_of_microorganisms.R.","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"direct-download","dir":"Reference","previous_headings":"","what":"Direct download","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"Like data sets package, data set publicly available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"about-the-records-from-lpsn-see-source-","dir":"Reference","previous_headings":"","what":"About the Records from LPSN (see Source)","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"LPSN main source bacteriological taxonomy AMR package. List Prokaryotic names Standing Nomenclature (LPSN) provides comprehensive information nomenclature prokaryotes. LPSN free use service founded Jean P. Euzeby 1997 later maintained Aidan C. Parte.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/microorganisms.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Data Set with 52 151 Microorganisms — microorganisms","text":"","code":"microorganisms #> # A tibble: 52,151 × 23 #>    mo               fullname      status kingdom phylum class order family genus #>    <mo>             <chr>         <chr>  <chr>   <chr>  <chr> <chr> <chr>  <chr> #>  1 B_GRAMN          (unknown Gra… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  2 B_GRAMP          (unknown Gra… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  3 B_ANAER-NEG      (unknown ana… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  4 B_ANAER-POS      (unknown ana… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  5 B_ANAER          (unknown ana… accep… Bacter… (unkn… (unk… (unk… \"(unk… \"(un… #>  6 F_FUNGUS         (unknown fun… accep… Fungi   (unkn… (unk… (unk… \"(unk… \"(un… #>  7   UNKNOWN        (unknown nam… accep… (unkno… (unkn… (unk… (unk… \"(unk… \"(un… #>  8 F_YEAST          (unknown yea… accep… Fungi   (unkn… (unk… (unk… \"(unk… \"(un… #>  9 B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… Abdi… \"Abdi… \"\"    #> 10 B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… Abdi… Abdi… \"\"     \"\"    #> # ℹ 52,141 more rows #> # ℹ 14 more variables: species <chr>, subspecies <chr>, rank <chr>, ref <chr>, #> #   oxygen_tolerance <chr>, source <chr>, lpsn <chr>, lpsn_parent <chr>, #> #   lpsn_renamed_to <chr>, gbif <chr>, gbif_parent <chr>, #> #   gbif_renamed_to <chr>, prevalence <dbl>, snomed <list>"},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate the Matching Score for Microorganisms — mo_matching_score","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"algorithm used .mo() mo_* functions determine probable match taxonomic records based user input.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"","code":"mo_matching_score(x, n)"},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"x user input value(s) n full taxonomic name, exists microorganisms$fullname","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"note","dir":"Reference","previous_headings":"","what":"Note","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"algorithm originally described : Berends MS et al. (2022). AMR: R Package Working Antimicrobial Resistance Data. Journal Statistical Software, 104(3), 1-31; doi:10.18637/jss.v104.i03 . Later, work Bartlett et al. bacterial pathogens infecting humans (2022, doi:10.1099/mic.0.001269 ) incorporated.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"matching-score-for-microorganisms","dir":"Reference","previous_headings":"","what":"Matching Score for Microorganisms","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"ambiguous user input .mo() mo_* functions, returned results chosen based matching score using mo_matching_score(). matching score \\(m\\), calculated :  : \\(x\\) user input; \\(n\\) taxonomic name (genus, species, subspecies); \\(l_n\\) length \\(n\\); \\(lev\\) Levenshtein distance function (counting insertion 1, deletion substitution 2) needed change \\(x\\) \\(n\\); \\(p_n\\) human pathogenic prevalence group \\(n\\), described ; \\(k_n\\) taxonomic kingdom \\(n\\), set Bacteria = 1, Fungi = 2, Protozoa = 3, Archaea = 4, others = 5. grouping human pathogenic prevalence \\(p\\) based recent work Bartlett et al. (2022, doi:10.1099/mic.0.001269 ) extensively studied medical-scientific literature categorise bacterial species groups: Established, taxonomic species infected least three persons three references. records prevalence = 1.0 microorganisms data set; Putative, taxonomic species fewer three known cases. records prevalence = 1.25 microorganisms data set. Furthermore, genus present established list also prevalence = 1.0 microorganisms data set; genus present putative list prevalence = 1.25 microorganisms data set; species subspecies genus present two aforementioned groups, prevalence = 1.5 microorganisms data set; non-bacterial genus, species subspecies genus present following list, prevalence = 1.5 microorganisms data set: Absidia, Acanthamoeba, Acremonium, Aedes, Alternaria, Amoeba, Ancylostoma, Angiostrongylus, Anisakis, Anopheles, Apophysomyces, Aspergillus, Aureobasidium, Basidiobolus, Beauveria, Blastocystis, Blastomyces, Candida, Capillaria, Chaetomium, Chrysonilia, Cladophialophora, Cladosporium, Conidiobolus, Contracaecum, Cordylobia, Cryptococcus, Curvularia, Demodex, Dermatobia, Dientamoeba, Diphyllobothrium, Dirofilaria, Echinostoma, Entamoeba, Enterobius, Exophiala, Exserohilum, Fasciola, Fonsecaea, Fusarium, Giardia, Haloarcula, Halobacterium, Halococcus, Hendersonula, Heterophyes, Histomonas, Histoplasma, Hymenolepis, Hypomyces, Hysterothylacium, Leishmania, Malassezia, Malbranchea, Metagonimus, Meyerozyma, Microsporidium, Microsporum, Mortierella, Mucor, Mycocentrospora, Necator, Nectria, Ochroconis, Oesophagostomum, Oidiodendron, Opisthorchis, Pediculus, Penicillium, Phlebotomus, Phoma, Pichia, Piedraia, Pithomyces, Pityrosporum, Pneumocystis, Pseudallescheria, Pseudoterranova, Pulex, Rhizomucor, Rhizopus, Rhodotorula, Saccharomyces, Sarcoptes, Scolecobasidium, Scopulariopsis, Scytalidium, Spirometra, Sporobolomyces, Stachybotrys, Strongyloides, Syngamus, Taenia, Talaromyces, Toxocara, Trichinella, Trichobilharzia, Trichoderma, Trichomonas, Trichophyton, Trichosporon, Trichostrongylus, Trichuris, Tritirachium, Trombicula, Trypanosoma, Tunga, Wuchereria; records prevalence = 2.0 microorganisms data set. calculating matching score, characters \\(x\\) \\(n\\) ignored -Z, -z, 0-9, spaces parentheses. matches sorted descending matching score user input values, top match returned. lead effect e.g., \"E. coli\" return microbial ID Escherichia coli (\\(m = 0.688\\), highly prevalent microorganism found humans) Entamoeba coli (\\(m = 0.159\\), less prevalent microorganism humans), although latter alphabetically come first.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"Dr. Matthijs Berends, 2018","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_matching_score.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate the Matching Score for Microorganisms — mo_matching_score","text":"","code":"mo_reset_session() #> ℹ Reset 17 previously matched input values.  as.mo(\"E. coli\") #> Class 'mo' #> [1] B_ESCHR_COLI mo_uncertainties() #> Matching scores are based on the resemblance between the input and the full #> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score. #>  #> -------------------------------------------------------------------------------- #> \"E. coli\" -> Escherichia coli (B_ESCHR_COLI, 0.688) #> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii #>               (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi #>               (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides #>               (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae #>               cloacae (0.571), Ehrlichia canis (0.567), and Enterobacter cloacae #>               dissolvens (0.565) #>  #> Only the first 10 other matches of each record are shown. Run #> print(mo_uncertainties(), n = ...) to view more entries, or save #> mo_uncertainties() to an object.  mo_matching_score(   x = \"E. coli\",   n = c(\"Escherichia coli\", \"Entamoeba coli\") ) #> [1] 0.6875000 0.1587302"},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Properties of a Microorganism — mo_property","title":"Get Properties of a Microorganism — mo_property","text":"Use functions return specific property microorganism based latest accepted taxonomy. input values evaluated internally .mo(), makes possible use microbial abbreviations, codes names input. See Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Properties of a Microorganism — mo_property","text":"","code":"mo_name(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_fullname(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_shortname(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_subspecies(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_species(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_genus(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_family(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_order(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_class(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_phylum(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_kingdom(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_domain(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_type(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_status(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_pathogenicity(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_gramstain(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_gram_negative(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_gram_positive(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_yeast(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_intrinsic_resistant(   x,   ab,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_oxygen_tolerance(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_is_anaerobic(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_snomed(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_ref(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_authors(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_year(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_lpsn(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_gbif(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_rank(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_taxonomy(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_synonyms(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_current(x, language = get_AMR_locale(), ...)  mo_info(   x,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_url(   x,   open = FALSE,   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )  mo_property(   x,   property = \"fullname\",   language = get_AMR_locale(),   keep_synonyms = getOption(\"AMR_keep_synonyms\", FALSE),   ... )"},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Properties of a Microorganism — mo_property","text":"x character (vector) can coerced valid microorganism code .mo(). Can left blank auto-guessing column containing microorganism codes used data set, see Examples. language language translate text like \"growth\", defaults system language (see get_AMR_locale()) keep_synonyms logical indicate old, previously valid taxonomic names must preserved corrected currently accepted names. default FALSE, return note old taxonomic names processed. default can set package option AMR_keep_synonyms, .e. options(AMR_keep_synonyms = TRUE) options(AMR_keep_synonyms = FALSE). ... arguments passed .mo(), 'minimum_matching_score', 'ignore_pattern', 'remove_from_input' ab (vector ) text can coerced valid antibiotic drug code .ab() open browse URL using browseURL() property one column names microorganisms data set: \"mo\", \"fullname\", \"status\", \"kingdom\", \"phylum\", \"class\", \"order\", \"family\", \"genus\", \"species\", \"subspecies\", \"rank\", \"ref\", \"oxygen_tolerance\", \"source\", \"lpsn\", \"lpsn_parent\", \"lpsn_renamed_to\", \"gbif\", \"gbif_parent\", \"gbif_renamed_to\", \"prevalence\", \"snomed\", must \"shortname\"","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Properties of a Microorganism — mo_property","text":"integer case mo_year() ordered factor case mo_pathogenicity() list case mo_taxonomy(), mo_synonyms(), mo_snomed() mo_info() named character case mo_url() character cases","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Get Properties of a Microorganism — mo_property","text":"functions , default, keep old taxonomic properties, synonyms automatically replaced current taxonomy. Take example Enterobacter aerogenes, initially named 1960 renamed Klebsiella aerogenes 2017: mo_genus(\"Enterobacter aerogenes\") return \"Klebsiella\" (note renaming) mo_genus(\"Enterobacter aerogenes\", keep_synonyms = TRUE) return \"Enterobacter\" (-per-session warning name outdated) mo_ref(\"Enterobacter aerogenes\") return \"Tindall et al., 2017\" (note) mo_ref(\"Enterobacter aerogenes\", keep_synonyms = TRUE) return \"Hormaeche et al., 1960\" (warning) short name (mo_shortname()) returns first character genus full species, \"E. coli\", species subspecies. Exceptions abbreviations staphylococci (\"CoNS\", Coagulase-Negative Staphylococci) beta-haemolytic streptococci (\"GBS\", Group B Streptococci). Please bear mind e.g. E. coli mean Escherichia coli (kingdom Bacteria) well Entamoeba coli (kingdom Protozoa). Returning full name done using .mo() internally, giving priority bacteria human pathogens, .e. \"E. coli\" considered Escherichia coli. result, mo_fullname(mo_shortname(\"Entamoeba coli\")) returns \"Escherichia coli\". Since top-level taxonomy sometimes referred 'kingdom' sometimes 'domain', functions mo_kingdom() mo_domain() return exact results. Determination human pathogenicity (mo_pathogenicity()) strongly based Bartlett et al. (2022, doi:10.1099/mic.0.001269 ). function returns factor levels Pathogenic, Potentially pathogenic, Non-pathogenic, Unknown. Determination Gram stain (mo_gramstain()) based taxonomic kingdom phylum. Originally, Cavalier-Smith defined -called subkingdoms Negibacteria Posibacteria (2002, PMID 11837318), considered phyla Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, Tenericutes. phyla later renamed Actinomycetota, Chloroflexota, Bacillota, Mycoplasmatota (2021, PMID 34694987). Bacteria phyla considered Gram-positive AMR package, except members class Negativicutes (within phylum Bacillota) Gram-negative. bacteria considered Gram-negative. Species outside kingdom Bacteria return value NA. Functions mo_is_gram_negative() mo_is_gram_positive() always return TRUE FALSE (NA input NA MO code UNKNOWN), thus always return FALSE species outside taxonomic kingdom Bacteria. Determination yeasts (mo_is_yeast()) based taxonomic kingdom class. Budding yeasts fungi phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes). True yeasts aggregated underlying order Saccharomycetales. Thus, microorganisms member taxonomic class Saccharomycetes, function return TRUE. returns FALSE otherwise (NA input NA MO code UNKNOWN). Determination intrinsic resistance (mo_is_intrinsic_resistant()) based intrinsic_resistant data set, based 'EUCAST Expert Rules' 'EUCAST Intrinsic Resistance Unusual Phenotypes' v3.3 (2021). mo_is_intrinsic_resistant() function can vectorised argument x (input microorganisms) ab (input antibiotics). Determination bacterial oxygen tolerance (mo_oxygen_tolerance()) based BacDive, see Source. function mo_is_anaerobic() returns TRUE oxygen tolerance \"anaerobe\", indicting obligate anaerobic species genus. always returns FALSE species outside taxonomic kingdom Bacteria. function mo_url() return direct URL online database entry, also shows scientific reference concerned species. SNOMED codes (mo_snomed()) version 1 July, 2021. See Source microorganisms data set info. Old taxonomic names (-called 'synonyms') can retrieved mo_synonyms() (scientific reference name), current taxonomic name can retrieved mo_current(). functions return full names. output translated possible.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"matching-score-for-microorganisms","dir":"Reference","previous_headings":"","what":"Matching Score for Microorganisms","title":"Get Properties of a Microorganism — mo_property","text":"function uses .mo() internally, uses advanced algorithm translate arbitrary user input valid taxonomy using -called matching score. can read public algorithm MO matching score page.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Get Properties of a Microorganism — mo_property","text":"Berends MS et al. (2022). AMR: R Package Working Antimicrobial Resistance Data. Journal Statistical Software, 104(3), 1-31; doi:10.18637/jss.v104.i03 Becker K et al. (2014). Coagulase-Negative Staphylococci. Clin Microbiol Rev. 27(4): 870-926; doi:10.1128/CMR.00109-13 Becker K et al. (2019). Implications identifying recently defined members S. aureus complex, S. argenteus S. schweitzeri: position paper members ESCMID Study Group staphylococci Staphylococcal Diseases (ESGS). Clin Microbiol Infect; doi:10.1016/j.cmi.2019.02.028 Becker K et al. (2020). Emergence coagulase-negative staphylococci. Expert Rev Anti Infect Ther. 18(4):349-366; doi:10.1080/14787210.2020.1730813 Lancefield RC (1933). serological differentiation human groups hemolytic streptococci. J Exp Med. 57(4): 571-95; doi:10.1084/jem.57.4.571 Berends MS et al. (2022). Trends Occurrence Phenotypic Resistance Coagulase-Negative Staphylococci (CoNS) Found Human Blood Northern Netherlands 2013 2019/ Micro.rganisms 10(9), 1801; doi:10.3390/microorganisms10091801 Parte, AC et al. (2020). List Prokaryotic names Standing Nomenclature (LPSN) moves DSMZ. International Journal Systematic Evolutionary Microbiology, 70, 5607-5612; doi:10.1099/ijsem.0.004332 . Accessed https://lpsn.dsmz.de 11 December, 2022. GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset doi:10.15468/39omei . Accessed https://www.gbif.org 11 December, 2022. Public Health Information Network Vocabulary Access Distribution System (PHIN VADS). US Edition SNOMED CT 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12). URL: https://phinvads.cdc.gov Bartlett et al. (2022). comprehensive list bacterial pathogens infecting humans Microbiology 168:001269; doi:10.1099/mic.0.001269 Reimer et al. (2022). BacDive 2022: knowledge base standardized bacterial archaeal data.  Nucleic Acids Res. 2022 Jan 7;50(D1):D741-D746; doi:10.1093/nar/gkab961","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"reference-data-publicly-available","dir":"Reference","previous_headings":"","what":"Reference Data Publicly Available","title":"Get Properties of a Microorganism — mo_property","text":"data sets AMR package (microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) publicly freely available download following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, Stata. also provide tab-separated plain text files machine-readable suitable input software program, laboratory information systems. Please visit website download links. actual files course available GitHub repository.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/mo_property.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get Properties of a Microorganism — mo_property","text":"","code":"# taxonomic tree -----------------------------------------------------------  mo_kingdom(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_phylum(\"Klebsiella pneumoniae\") #> [1] \"Pseudomonadota\" mo_class(\"Klebsiella pneumoniae\") #> [1] \"Gammaproteobacteria\" mo_order(\"Klebsiella pneumoniae\") #> [1] \"Enterobacterales\" mo_family(\"Klebsiella pneumoniae\") #> [1] \"Enterobacteriaceae\" mo_genus(\"Klebsiella pneumoniae\") #> [1] \"Klebsiella\" mo_species(\"Klebsiella pneumoniae\") #> [1] \"pneumoniae\" mo_subspecies(\"Klebsiella pneumoniae\") #> [1] \"\"   # full names and short names -----------------------------------------------  mo_name(\"Klebsiella pneumoniae\") #> [1] \"Klebsiella pneumoniae\" mo_fullname(\"Klebsiella pneumoniae\") #> [1] \"Klebsiella pneumoniae\" mo_shortname(\"Klebsiella pneumoniae\") #> [1] \"K. pneumoniae\"   # other properties ---------------------------------------------------------  mo_pathogenicity(\"Klebsiella pneumoniae\") #> [1] Pathogenic #> Levels: Pathogenic < Potentially pathogenic < Non-pathogenic < Unknown mo_gramstain(\"Klebsiella pneumoniae\") #> [1] \"Gram-negative\" mo_snomed(\"Klebsiella pneumoniae\") #> [[1]] #> [1] \"1098101000112102\" \"446870005\"        \"1098201000112108\" \"409801009\"        #> [5] \"56415008\"         \"714315002\"        \"713926009\"        #>  mo_type(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_rank(\"Klebsiella pneumoniae\") #> [1] \"species\" mo_url(\"Klebsiella pneumoniae\") #>                                Klebsiella pneumoniae  #> \"https://lpsn.dsmz.de/species/klebsiella-pneumoniae\"  mo_is_yeast(c(\"Candida\", \"Trichophyton\", \"Klebsiella\")) #> [1]  TRUE FALSE FALSE   # scientific reference -----------------------------------------------------  mo_ref(\"Klebsiella aerogenes\") #> [1] \"Tindall et al., 2017\" mo_authors(\"Klebsiella aerogenes\") #> [1] \"Tindall et al.\" mo_year(\"Klebsiella aerogenes\") #> [1] 2017 mo_lpsn(\"Klebsiella aerogenes\") #> [1] \"777146\" mo_gbif(\"Klebsiella aerogenes\") #> [1] \"9281703\" mo_synonyms(\"Klebsiella aerogenes\") #>   Hormaeche et al., 1960     Bascomb et al., 1971  #> \"Enterobacter aerogenes\"     \"Klebsiella mobilis\"    # abbreviations known in the field -----------------------------------------  mo_genus(\"MRSA\") #> [1] \"Staphylococcus\" mo_species(\"MRSA\") #> [1] \"aureus\" mo_shortname(\"VISA\") #> [1] \"S. aureus\" mo_gramstain(\"VISA\") #> [1] \"Gram-positive\"  mo_genus(\"EHEC\") #> [1] \"Escherichia\" mo_species(\"EIEC\") #> [1] \"coli\" mo_name(\"UPEC\") #> [1] \"Escherichia coli\"   # known subspecies ---------------------------------------------------------  mo_fullname(\"K. pneu rh\") #> [1] \"Klebsiella pneumoniae rhinoscleromatis\" mo_shortname(\"K. pneu rh\") #> [1] \"K. pneumoniae\"  # \\donttest{ # Becker classification, see ?as.mo ----------------------------------------  mo_fullname(\"Staph epidermidis\") #> [1] \"Staphylococcus epidermidis\" mo_fullname(\"Staph epidermidis\", Becker = TRUE) #> [1] \"Coagulase-negative Staphylococcus (CoNS)\" mo_shortname(\"Staph epidermidis\") #> [1] \"S. epidermidis\" mo_shortname(\"Staph epidermidis\", Becker = TRUE) #> [1] \"CoNS\"   # Lancefield classification, see ?as.mo ------------------------------------  mo_fullname(\"Strep agalactiae\") #> [1] \"Streptococcus agalactiae\" mo_fullname(\"Strep agalactiae\", Lancefield = TRUE) #> [1] \"Streptococcus Group B\" mo_shortname(\"Strep agalactiae\") #> [1] \"S. agalactiae\" mo_shortname(\"Strep agalactiae\", Lancefield = TRUE) #> [1] \"GBS\"   # language support  --------------------------------------------------------  mo_gramstain(\"Klebsiella pneumoniae\", language = \"de\") # German #> [1] \"Gramnegativ\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"nl\") # Dutch #> [1] \"Gram-negatief\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"es\") # Spanish #> [1] \"Gram negativo\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"el\") # Greek #> [1] \"Αρνητικό κατά Gram\" mo_gramstain(\"Klebsiella pneumoniae\", language = \"uk\") # Ukrainian #> [1] \"Грамнегативні\"  # mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated mo_kingdom(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_type(\"Klebsiella pneumoniae\") #> [1] \"Bacteria\" mo_kingdom(\"Klebsiella pneumoniae\", language = \"zh\") # Chinese, no effect #> [1] \"Bacteria\" mo_type(\"Klebsiella pneumoniae\", language = \"zh\") # Chinese, translated #> [1] \"细菌\"  mo_fullname(\"S. pyogenes\", Lancefield = TRUE, language = \"de\") #> [1] \"Streptococcus Gruppe A\" mo_fullname(\"S. pyogenes\", Lancefield = TRUE, language = \"uk\") #> [1] \"Streptococcus Група A\"   # other --------------------------------------------------------------------  # gram stains and intrinsic resistance can be used as a filter in dplyr verbs if (require(\"dplyr\")) {   example_isolates %>%     filter(mo_is_gram_positive()) %>%     count(mo_genus(), sort = TRUE) } #> ℹ Using column 'mo' as input for mo_is_gram_positive() #> ℹ Using column 'mo' as input for mo_genus() #> # A tibble: 18 × 2 #>    `mo_genus()`        n #>    <chr>           <int> #>  1 Staphylococcus    840 #>  2 Streptococcus     275 #>  3 Enterococcus       83 #>  4 Corynebacterium    17 #>  5 Micrococcus         6 #>  6 Gemella             3 #>  7 Aerococcus          2 #>  8 Cutibacterium       1 #>  9 Dermabacter         1 #> 10 Fusibacter          1 #> 11 Globicatella        1 #> 12 Granulicatella      1 #> 13 Lactobacillus       1 #> 14 Leuconostoc         1 #> 15 Listeria            1 #> 16 Paenibacillus       1 #> 17 Rothia              1 #> 18 Schaalia            1 if (require(\"dplyr\")) {   example_isolates %>%     filter(mo_is_intrinsic_resistant(ab = \"vanco\")) %>%     count(mo_genus(), sort = TRUE) } #> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant() #> ℹ Using column 'mo' as input for mo_genus() #> # A tibble: 20 × 2 #>    `mo_genus()`         n #>    <chr>            <int> #>  1 Escherichia        467 #>  2 Klebsiella          77 #>  3 Proteus             39 #>  4 Pseudomonas         30 #>  5 Serratia            25 #>  6 Enterobacter        23 #>  7 Citrobacter         11 #>  8 Haemophilus          8 #>  9 Acinetobacter        6 #> 10 Morganella           6 #> 11 Pantoea              4 #> 12 Salmonella           3 #> 13 Neisseria            2 #> 14 Stenotrophomonas     2 #> 15 Campylobacter        1 #> 16 Enterococcus         1 #> 17 Hafnia               1 #> 18 Lactobacillus        1 #> 19 Leuconostoc          1 #> 20 Pseudescherichia     1  # get a list with the complete taxonomy (from kingdom to subspecies) mo_taxonomy(\"Klebsiella pneumoniae\") #> $kingdom #> [1] \"Bacteria\" #>  #> $phylum #> [1] \"Pseudomonadota\" #>  #> $class #> [1] \"Gammaproteobacteria\" #>  #> $order #> [1] \"Enterobacterales\" #>  #> $family #> [1] \"Enterobacteriaceae\" #>  #> $genus #> [1] \"Klebsiella\" #>  #> $species #> [1] \"pneumoniae\" #>  #> $subspecies #> [1] \"\" #>   # get a list with the taxonomy, the authors, Gram-stain, # SNOMED codes, and URL to the online database mo_info(\"Klebsiella pneumoniae\") #> $mo #> [1] \"B_KLBSL_PNMN\" #>  #> $kingdom #> [1] \"Bacteria\" #>  #> $phylum #> [1] \"Pseudomonadota\" #>  #> $class #> [1] \"Gammaproteobacteria\" #>  #> $order #> [1] \"Enterobacterales\" #>  #> $family #> [1] \"Enterobacteriaceae\" #>  #> $genus #> [1] \"Klebsiella\" #>  #> $species #> [1] \"pneumoniae\" #>  #> $subspecies #> [1] \"\" #>  #> $status #> [1] \"accepted\" #>  #> $synonyms #> NULL #>  #> $gramstain #> [1] \"Gram-negative\" #>  #> $oxygen_tolerance #> [1] \"aerobe\" #>  #> $url #> [1] \"https://lpsn.dsmz.de/species/klebsiella-pneumoniae\" #>  #> $ref #> [1] \"Trevisan, 1887\" #>  #> $snomed #> [1] \"1098101000112102\" \"446870005\"        \"1098201000112108\" \"409801009\"        #> [5] \"56415008\"         \"714315002\"        \"713926009\"        #>  #> $lpsn #> [1] \"777151\" #>  #> $gbif #> [1] \"3221874\" #>  # }"},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":null,"dir":"Reference","previous_headings":"","what":"User-Defined Reference Data Set for Microorganisms — mo_source","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"functions can used predefine reference used .mo() consequently mo_* functions (mo_genus() mo_gramstain()). fastest way organisation (analysis) specific codes picked translated package, since bother setting .","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"","code":"set_mo_source(   path,   destination = getOption(\"AMR_mo_source\", \"~/mo_source.rds\") )  get_mo_source(destination = getOption(\"AMR_mo_source\", \"~/mo_source.rds\"))"},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"path location reference file, can text file (comma-, tab- pipe-separated) Excel file (see Details). Can also \"\", NULL FALSE delete reference file. destination destination compressed data file - default user's home directory.","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"reference file can text file separated commas (CSV) tabs pipes, Excel file (either 'xls' 'xlsx' format) R object file (extension '.rds'). use Excel file, need readxl package installed. set_mo_source() check file validity: must data.frame, must column named \"mo\" contains values microorganisms$mo microorganisms$fullname must reference column defined values. tests pass, set_mo_source() read file R ask export \"~/mo_source.rds\". CRAN policy disallows packages write file system, although 'exceptions may allowed interactive sessions package obtains confirmation user'. reason, function works interactive sessions user can specifically confirm allow file created. destination file can set destination argument defaults user's home directory. can also set package option AMR_mo_source, e.g. options(AMR_mo_source = \"/location/file.rds\"). created compressed data file \"mo_source.rds\" used default MO determination (function .mo() consequently mo_* functions like mo_genus() mo_gramstain()). location timestamp original file saved attribute compressed data file. function get_mo_source() return data set reading \"mo_source.rds\" readRDS(). original file changed (checking location timestamp original file), call set_mo_source() update data file automatically used interactive session. Reading Excel file (.xlsx) one row size 8-9 kB. compressed file created set_mo_source() size 0.1 kB can read get_mo_source() couple microseconds (millionths second).","code":""},{"path":"https://msberends.github.io/AMR/reference/mo_source.html","id":"how-to-setup","dir":"Reference","previous_headings":"","what":"How to Setup","title":"User-Defined Reference Data Set for Microorganisms — mo_source","text":"Imagine data sheet Excel file. first column contains organisation specific codes, second column contains valid taxonomic names:   save \"home//ourcodes.xlsx\". Now set source:   now created file \"~/mo_source.rds\" contents Excel file. first column foreign values 'mo' column kept creating RDS file. now can use functions:   edit Excel file , say, adding row 4 like :   ...new usage MO function package update data file:   delete reference data file, just use \"\", NULL FALSE input set_mo_source():   original file (previous case Excel file) moved deleted, mo_source.rds file removed upon next use .mo() mo_* function.","code":"|         A          |            B          | --|--------------------|-----------------------| 1 | Organisation XYZ   | mo                    | 2 | lab_mo_ecoli       | Escherichia coli      | 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae | 4 |                    |                       | set_mo_source(\"home/me/ourcodes.xlsx\") #> NOTE: Created mo_source file '/Users/me/mo_source.rds' (0.3 kB) from #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns #>       \"Organisation XYZ\" and \"mo\" as.mo(\"lab_mo_ecoli\") #> Class 'mo' #> [1] B_ESCHR_COLI  mo_genus(\"lab_mo_kpneumoniae\") #> [1] \"Klebsiella\"  # other input values still work too as.mo(c(\"Escherichia coli\", \"E. coli\", \"lab_mo_ecoli\")) #> NOTE: Translation to one microorganism was guessed with uncertainty. #>       Use mo_uncertainties() to review it. #> Class 'mo' #> [1] B_ESCHR_COLI B_ESCHR_COLI B_ESCHR_COLI |         A          |            B          | --|--------------------|-----------------------| 1 | Organisation XYZ   | mo                    | 2 | lab_mo_ecoli       | Escherichia coli      | 3 | lab_mo_kpneumoniae | Klebsiella pneumoniae | 4 | lab_Staph_aureus   | Staphylococcus aureus | 5 |                    |                       | as.mo(\"lab_mo_ecoli\") #> NOTE: Updated mo_source file '/Users/me/mo_source.rds' (0.3 kB) from #>       '/Users/me/Documents/ourcodes.xlsx' (9 kB), columns #>        \"Organisation XYZ\" and \"mo\" #> Class 'mo' #> [1] B_ESCHR_COLI  mo_genus(\"lab_Staph_aureus\") #> [1] \"Staphylococcus\" set_mo_source(NULL) #> Removed mo_source file '/Users/me/mo_source.rds'"},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":null,"dir":"Reference","previous_headings":"","what":"Principal Component Analysis (for AMR) — pca","title":"Principal Component Analysis (for AMR) — pca","text":"Performs principal component analysis (PCA) based data set automatic determination afterwards plotting groups labels, automatic filtering suitable (.e. non-empty numeric) variables.","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Principal Component Analysis (for AMR) — pca","text":"","code":"pca(   x,   ...,   retx = TRUE,   center = TRUE,   scale. = TRUE,   tol = NULL,   rank. = NULL )"},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Principal Component Analysis (for AMR) — pca","text":"x data.frame containing numeric columns ... columns x selected PCA, can unquoted since supports quasiquotation. retx logical value indicating whether rotated variables     returned. center logical value indicating whether variables     shifted zero centered. Alternately, vector     length equal number columns x can supplied.     value passed scale. scale. logical value indicating whether variables     scaled unit variance analysis takes     place.  default FALSE consistency S,     general scaling advisable.  Alternatively, vector length     equal number columns x can supplied.      value passed scale. tol value indicating magnitude components     omitted. (Components omitted     standard deviations less equal tol times     standard deviation first component.)  default null     setting, components omitted (unless rank. specified     less min(dim(x)).).  settings tol     tol = 0 tol = sqrt(.Machine$double.eps),     omit essentially constant components. rank. optionally, number specifying maximal rank, .e.,     maximal number principal components used.  Can set     alternative addition tol, useful notably     desired rank considerably smaller dimensions matrix.","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Principal Component Analysis (for AMR) — pca","text":"object classes pca prcomp","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Principal Component Analysis (for AMR) — pca","text":"pca() function takes data.frame input performs actual PCA R function prcomp(). result pca() function prcomp object, additional attribute non_numeric_cols vector column names columns contain numeric values. probably groups labels, used ggplot_pca().","code":""},{"path":"https://msberends.github.io/AMR/reference/pca.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Principal Component Analysis (for AMR) — pca","text":"","code":"# `example_isolates` is a data set available in the AMR package. # See ?example_isolates.  # \\donttest{ if (require(\"dplyr\")) {   # calculate the resistance per group first   resistance_data <- example_isolates %>%     group_by(       order = mo_order(mo), # group on anything, like order       genus = mo_genus(mo)     ) %>% #   and genus as we do here;     filter(n() >= 30) %>% # filter on only 30 results per group     summarise_if(is.sir, resistance) # then get resistance of all drugs    # now conduct PCA for certain antimicrobial drugs   pca_result <- resistance_data %>%     pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)    pca_result   summary(pca_result)    # old base R plotting method:   biplot(pca_result)   # new ggplot2 plotting method using this package:   if (require(\"ggplot2\")) {     ggplot_pca(pca_result)      ggplot_pca(pca_result) +       scale_colour_viridis_d() +       labs(title = \"Title here\")   } } #> Warning: There were 73 warnings in `summarise()`. #> The first warning was: #> ℹ In argument: `PEN = (function (..., minimum = 30, as_percent = FALSE, #>   only_all_tested = FALSE) ...`. #> ℹ In group 5: `order = \"Lactobacillales\"`, `genus = \"Enterococcus\"`. #> Caused by warning: #> ! Introducing NA: only 14 results available for PEN in group: order = #> \"Lactobacillales\", genus = \"Enterococcus\" (minimum = 30). #> ℹ Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings. #> ℹ Columns selected for PCA: \"AMC\", \"CAZ\", \"CTX\", \"CXM\", \"GEN\", \"SXT\", #>   \"TMP\", and \"TOB\". Total observations available: 7. #> Groups (n=4, named as 'order'): #> [1] \"Caryophanales\"    \"Enterobacterales\" \"Lactobacillales\"  \"Pseudomonadales\"  #>    # }"},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":null,"dir":"Reference","previous_headings":"","what":"Plotting for Classes sir, mic and disk — plot","title":"Plotting for Classes sir, mic and disk — plot","text":"Functions plot classes sir, mic disk, support base R ggplot2.","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plotting for Classes sir, mic and disk — plot","text":"","code":"# S3 method for mic plot(   x,   mo = NULL,   ab = NULL,   guideline = \"EUCAST\",   main = deparse(substitute(x)),   ylab = translate_AMR(\"Frequency\", language = language),   xlab = translate_AMR(\"Minimum Inhibitory Concentration (mg/L)\", language = language),   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for mic autoplot(   object,   mo = NULL,   ab = NULL,   guideline = \"EUCAST\",   title = deparse(substitute(object)),   ylab = translate_AMR(\"Frequency\", language = language),   xlab = translate_AMR(\"Minimum Inhibitory Concentration (mg/L)\", language = language),   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for mic fortify(object, ...)  # S3 method for disk plot(   x,   main = deparse(substitute(x)),   ylab = translate_AMR(\"Frequency\", language = language),   xlab = translate_AMR(\"Disk diffusion diameter (mm)\", language = language),   mo = NULL,   ab = NULL,   guideline = \"EUCAST\",   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for disk autoplot(   object,   mo = NULL,   ab = NULL,   title = deparse(substitute(object)),   ylab = translate_AMR(\"Frequency\", language = language),   xlab = translate_AMR(\"Disk diffusion diameter (mm)\", language = language),   guideline = \"EUCAST\",   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   expand = TRUE,   ... )  # S3 method for disk fortify(object, ...)  # S3 method for sir plot(   x,   ylab = translate_AMR(\"Percentage\", language = language),   xlab = translate_AMR(\"Antimicrobial Interpretation\", language = language),   main = deparse(substitute(x)),   language = get_AMR_locale(),   ... )  # S3 method for sir autoplot(   object,   title = deparse(substitute(object)),   xlab = translate_AMR(\"Antimicrobial Interpretation\", language = language),   ylab = translate_AMR(\"Frequency\", language = language),   colours_SIR = c(\"#3CAEA3\", \"#F6D55C\", \"#ED553B\"),   language = get_AMR_locale(),   ... )  # S3 method for sir fortify(object, ...)"},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plotting for Classes sir, mic and disk — plot","text":"x, object values created .mic(), .disk() .sir() (random_* variants, random_mic()) mo (vector ) text can coerced valid microorganism code .mo() ab (vector ) text can coerced valid antimicrobial drug code .ab() guideline interpretation guideline use - default latest included EUCAST guideline, see Details main, title title plot xlab, ylab axis title colours_SIR colours use filling bars, must vector three values (order S, R). default colours colour-blind friendly. language language used translate 'Susceptible', 'Increased exposure'/'Intermediate' 'Resistant' - default system language (see get_AMR_locale()) can overwritten setting package option AMR_locale, e.g. options(AMR_locale = \"de\"), see translate. Use language = NULL language = \"\" prevent translation. expand logical indicate whether range x axis expanded lowest highest value. MIC values, intermediate values factors 2 starting highest MIC value. disk diameters, whole diameter range filled. ... arguments passed methods","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plotting for Classes sir, mic and disk — plot","text":"autoplot() functions return ggplot model extendible ggplot2 function. fortify() functions return data.frame extension usage ggplot2::ggplot() function.","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plotting for Classes sir, mic and disk — plot","text":"interpretation \"\" named \"Increased exposure\" EUCAST guidelines since 2019, named \"Intermediate\" cases. interpreting MIC values well disk diffusion diameters, supported guidelines used input guideline argument : \"EUCAST 2022\", \"EUCAST 2021\", \"EUCAST 2020\", \"EUCAST 2019\", \"EUCAST 2018\", \"EUCAST 2017\", \"EUCAST 2016\", \"EUCAST 2015\", \"EUCAST 2014\", \"EUCAST 2013\", \"CLSI 2022\", \"CLSI 2021\", \"CLSI 2020\", \"CLSI 2019\", \"CLSI 2018\", \"CLSI 2017\", \"CLSI 2016\", \"CLSI 2015\", \"CLSI 2014\", \"CLSI 2013\". Simply using \"CLSI\" \"EUCAST\" input automatically select latest version guideline.","code":""},{"path":"https://msberends.github.io/AMR/reference/plot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plotting for Classes sir, mic and disk — plot","text":"","code":"some_mic_values <- random_mic(size = 100) some_disk_values <- random_disk(size = 100, mo = \"Escherichia coli\", ab = \"cipro\") some_sir_values <- random_sir(50, prob_SIR = c(0.55, 0.05, 0.30))  plot(some_mic_values)  plot(some_disk_values)  plot(some_sir_values)   # when providing the microorganism and antibiotic, colours will show interpretations: plot(some_mic_values, mo = \"S. aureus\", ab = \"ampicillin\")  plot(some_disk_values, mo = \"Escherichia coli\", ab = \"cipro\")  plot(some_disk_values, mo = \"Escherichia coli\", ab = \"cipro\", language = \"uk\")   # \\donttest{ if (require(\"ggplot2\")) {   autoplot(some_mic_values) }  if (require(\"ggplot2\")) {   autoplot(some_disk_values, mo = \"Escherichia coli\", ab = \"cipro\") }  if (require(\"ggplot2\")) {   autoplot(some_sir_values) }  # }"},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate Antimicrobial Resistance — proportion","title":"Calculate Antimicrobial Resistance — proportion","text":"functions can used calculate (co-)resistance susceptibility microbial isolates (.e. percentage S, SI, , IR R). functions support quasiquotation pipes, can used summarise() dplyr package also support grouped variables, see Examples. resistance() used calculate resistance, susceptibility() used calculate susceptibility.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate Antimicrobial Resistance — proportion","text":"","code":"resistance(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  susceptibility(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  sir_confidence_interval(   ...,   ab_result = \"R\",   minimum = 30,   as_percent = FALSE,   only_all_tested = FALSE,   confidence_level = 0.95,   side = \"both\",   collapse = FALSE )  proportion_R(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_IR(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_I(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_SI(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_S(..., minimum = 30, as_percent = FALSE, only_all_tested = FALSE)  proportion_df(   data,   translate_ab = \"name\",   language = get_AMR_locale(),   minimum = 30,   as_percent = FALSE,   combine_SI = TRUE,   confidence_level = 0.95 )  sir_df(   data,   translate_ab = \"name\",   language = get_AMR_locale(),   minimum = 30,   as_percent = FALSE,   combine_SI = TRUE,   confidence_level = 0.95 )"},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"Calculate Antimicrobial Resistance — proportion","text":"M39 Analysis Presentation Cumulative Antimicrobial Susceptibility Test Data, 5th Edition, 2022, Clinical Laboratory Standards Institute (CLSI). https://clsi.org/standards/products/microbiology/documents/m39/.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate Antimicrobial Resistance — proportion","text":"... one vectors (columns) antibiotic interpretations. transformed internally .sir() needed. Use multiple columns calculate (lack ) co-resistance: probability one two drugs resistant susceptible result. See Examples. minimum minimum allowed number available (tested) isolates. isolate count lower minimum return NA warning. default number 30 isolates advised Clinical Laboratory Standards Institute (CLSI) best practice, see Source. as_percent logical indicate whether output must returned hundred fold % sign (character). value 0.123456 returned \"12.3%\". only_all_tested (combination therapies, .e. using one variable ...): logical indicate isolates must tested antibiotics, see section Combination Therapy ab_result antibiotic results test , must one values \"S\", \"\", \"R\" confidence_level confidence level returned confidence interval. calculation, number S SI isolates, R isolates compared total number available isolates R, S, using binom.test(), .e., Clopper-Pearson method. side side confidence interval return. default \"\" length 2 vector, can also (abbreviated ) \"min\"/\"left\"/\"lower\"/\"less\" \"max\"/\"right\"/\"higher\"/\"greater\". collapse logical indicate whether output values 'collapsed', .e. merged together one value, character value use collapsing data data.frame containing columns class sir (see .sir()) translate_ab column name antibiotics data set translate antibiotic abbreviations , using ab_property() language language returned text - default current system language (see get_AMR_locale()) can also set package option AMR_locale. Use language = NULL language = \"\" prevent translation. combine_SI logical indicate whether values S must merged one, output consists S+vs. R (susceptible vs. resistant) - default TRUE","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate Antimicrobial Resistance — proportion","text":"double , as_percent = TRUE, character.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate Antimicrobial Resistance — proportion","text":"function resistance() equal function proportion_R(). function susceptibility() equal function proportion_SI(). Use sir_confidence_interval() calculate confidence interval, relies binom.test(), .e., Clopper-Pearson method. function returns vector length 2 default antimicrobial resistance. Change side argument \"left\"/\"min\" \"right\"/\"max\" return single value, change ab_result argument e.g. c(\"S\", \"\") test antimicrobial susceptibility, see Examples. Remember filter data let contain first isolates! needed exclude duplicates reduce selection bias. Use first_isolate() determine data set one four available algorithms. functions meant count isolates, calculate proportion resistance/susceptibility. Use count() functions count isolates. function susceptibility() essentially equal count_susceptible() / count_all(). Low counts can influence outcome - proportion functions may camouflage , since return proportion (albeit dependent minimum argument). function proportion_df() takes variable data sir class (created .sir()) calculates proportions S, , R. also supports grouped variables. function sir_df() works exactly like proportion_df(), adds number isolates.","code":""},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"combination-therapy","dir":"Reference","previous_headings":"","what":"Combination Therapy","title":"Calculate Antimicrobial Resistance — proportion","text":"using one variable ... (= combination therapy), use only_all_tested count isolates tested antibiotics/variables test . See example two antibiotics, Drug Drug B, susceptibility() works calculate %SI:   Please note , combination therapies, only_all_tested = TRUE applies :   , combination therapies, only_all_tested = FALSE applies :   Using only_all_tested impact using one antibiotic input.","code":"--------------------------------------------------------------------                     only_all_tested = FALSE  only_all_tested = TRUE                     -----------------------  -----------------------  Drug A    Drug B   include as  include as   include as  include as                     numerator   denominator  numerator   denominator --------  --------  ----------  -----------  ----------  -----------  S or I    S or I       X            X            X            X    R       S or I       X            X            X            X   <NA>     S or I       X            X            -            -  S or I      R          X            X            X            X    R         R          -            X            -            X   <NA>       R          -            -            -            -  S or I     <NA>        X            X            -            -    R        <NA>        -            -            -            -   <NA>      <NA>        -            -            -            - -------------------------------------------------------------------- count_S()    +   count_I()    +   count_R()    = count_all()   proportion_S() + proportion_I() + proportion_R() = 1 count_S()    +   count_I()    +   count_R()    >= count_all()   proportion_S() + proportion_I() + proportion_R() >= 1"},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Calculate Antimicrobial Resistance — proportion","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/proportion.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate Antimicrobial Resistance — proportion","text":"","code":"# example_isolates is a data set available in the AMR package. # run ?example_isolates for more info. example_isolates #> # A tibble: 2,000 × 46 #>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX   #>    <date>     <chr>   <dbl> <chr>  <chr>    <mo>         <sir> <sir> <sir> <sir> #>  1 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  2 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA    #>  3 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  4 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  5 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  6 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #>  7 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  8 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R     #>  9 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA    #> 10 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA    #> # ℹ 1,990 more rows #> # ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>, #> #   CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>, #> #   TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>, #> #   FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>, #> #   TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>, #> #   IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …   # base R ------------------------------------------------------------ # determines %R resistance(example_isolates$AMX) #> [1] 0.5955556 sir_confidence_interval(example_isolates$AMX) #> [1] 0.5688204 0.6218738 sir_confidence_interval(example_isolates$AMX,   confidence_level = 0.975 ) #> [1] 0.5650148 0.6255670 sir_confidence_interval(example_isolates$AMX,   confidence_level = 0.975,   collapse = \", \" ) #> [1] \"0.565, 0.626\"  # determines %S+I: susceptibility(example_isolates$AMX) #> [1] 0.4044444 sir_confidence_interval(example_isolates$AMX,   ab_result = c(\"S\", \"I\") ) #> [1] 0.3781262 0.4311796  # be more specific proportion_S(example_isolates$AMX) #> [1] 0.4022222 proportion_SI(example_isolates$AMX) #> [1] 0.4044444 proportion_I(example_isolates$AMX) #> [1] 0.002222222 proportion_IR(example_isolates$AMX) #> [1] 0.5977778 proportion_R(example_isolates$AMX) #> [1] 0.5955556  # dplyr ------------------------------------------------------------- # \\donttest{ if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       r = resistance(CIP),       n = n_sir(CIP)     ) # n_sir works like n_distinct in dplyr, see ?n_sir } #> # A tibble: 3 × 3 #>   ward           r     n #>   <chr>      <dbl> <int> #> 1 Clinical   0.147   869 #> 2 ICU        0.190   447 #> 3 Outpatient 0.161    93 if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       cipro_R = resistance(CIP),       ci_min = sir_confidence_interval(CIP, side = \"min\"),       ci_max = sir_confidence_interval(CIP, side = \"max\"),     ) } #> # A tibble: 3 × 4 #>   ward       cipro_R ci_min ci_max #>   <chr>        <dbl>  <dbl>  <dbl> #> 1 Clinical     0.147 0.124   0.173 #> 2 ICU          0.190 0.155   0.230 #> 3 Outpatient   0.161 0.0932  0.252 if (require(\"dplyr\")) {   # scoped dplyr verbs with antibiotic selectors   # (you could also use across() of course)   example_isolates %>%     group_by(ward) %>%     summarise_at(       c(aminoglycosides(), carbapenems()),       resistance     ) } #> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB' #>   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin) #> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem) #> Warning: There was 1 warning in `summarise()`. #> ℹ In argument: `KAN = (function (..., minimum = 30, as_percent = FALSE, #>   only_all_tested = FALSE) ...`. #> ℹ In group 3: `ward = \"Outpatient\"`. #> Caused by warning: #> ! Introducing NA: only 23 results available for KAN in group: ward = #> \"Outpatient\" (minimum = 30). #> # A tibble: 3 × 7 #>   ward         GEN   TOB   AMK   KAN    IPM    MEM #>   <chr>      <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl> #> 1 Clinical   0.229 0.315 0.626     1 0.0498 0.0458 #> 2 ICU        0.290 0.400 0.662     1 0.0862 0.0894 #> 3 Outpatient 0.2   0.368 0.605    NA 0.0541 0.0541 if (require(\"dplyr\")) {   example_isolates %>%     group_by(ward) %>%     summarise(       R = resistance(CIP, as_percent = TRUE),       SI = susceptibility(CIP, as_percent = TRUE),       n1 = count_all(CIP), # the actual total; sum of all three       n2 = n_sir(CIP), # same - analogous to n_distinct       total = n()     ) # NOT the number of tested isolates!    # Calculate co-resistance between amoxicillin/clav acid and gentamicin,   # so we can see that combination therapy does a lot more than mono therapy:   example_isolates %>% susceptibility(AMC) # %SI = 76.3%   example_isolates %>% count_all(AMC) #   n = 1879    example_isolates %>% susceptibility(GEN) # %SI = 75.4%   example_isolates %>% count_all(GEN) #   n = 1855    example_isolates %>% susceptibility(AMC, GEN) # %SI = 94.1%   example_isolates %>% count_all(AMC, GEN) #   n = 1939     # See Details on how `only_all_tested` works. Example:   example_isolates %>%     summarise(       numerator = count_susceptible(AMC, GEN),       denominator = count_all(AMC, GEN),       proportion = susceptibility(AMC, GEN)     )    example_isolates %>%     summarise(       numerator = count_susceptible(AMC, GEN, only_all_tested = TRUE),       denominator = count_all(AMC, GEN, only_all_tested = TRUE),       proportion = susceptibility(AMC, GEN, only_all_tested = TRUE)     )     example_isolates %>%     group_by(ward) %>%     summarise(       cipro_p = susceptibility(CIP, as_percent = TRUE),       cipro_n = count_all(CIP),       genta_p = susceptibility(GEN, as_percent = TRUE),       genta_n = count_all(GEN),       combination_p = susceptibility(CIP, GEN, as_percent = TRUE),       combination_n = count_all(CIP, GEN)     )    # Get proportions S/I/R immediately of all sir columns   example_isolates %>%     select(AMX, CIP) %>%     proportion_df(translate = FALSE)    # It also supports grouping variables   # (use sir_df to also include the count)   example_isolates %>%     select(ward, AMX, CIP) %>%     group_by(ward) %>%     sir_df(translate = FALSE) } #> # A tibble: 12 × 7 #>    ward       antibiotic interpretation value ci_min ci_max isolates #>  * <chr>      <chr>      <ord>          <dbl>  <dbl>  <dbl>    <int> #>  1 Clinical   AMX        SI             0.423 0.389   0.457      357 #>  2 Clinical   AMX        R              0.577 0.543   0.611      487 #>  3 Clinical   CIP        SI             0.853 0.827   0.876      741 #>  4 Clinical   CIP        R              0.147 0.124   0.173      128 #>  5 ICU        AMX        SI             0.369 0.323   0.417      158 #>  6 ICU        AMX        R              0.631 0.583   0.677      270 #>  7 ICU        CIP        SI             0.810 0.770   0.845      362 #>  8 ICU        CIP        R              0.190 0.155   0.230       85 #>  9 Outpatient AMX        SI             0.397 0.288   0.515       31 #> 10 Outpatient AMX        R              0.603 0.485   0.712       47 #> 11 Outpatient CIP        SI             0.839 0.748   0.907       78 #> 12 Outpatient CIP        R              0.161 0.0932  0.252       15 # }"},{"path":"https://msberends.github.io/AMR/reference/random.html","id":null,"dir":"Reference","previous_headings":"","what":"Random MIC Values/Disk Zones/SIR Generation — random","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"functions can used generating random MIC values disk diffusion diameters, AMR data analysis practice. providing microorganism antimicrobial drug, generated results reflect reality much possible.","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"","code":"random_mic(size = NULL, mo = NULL, ab = NULL, ...)  random_disk(size = NULL, mo = NULL, ab = NULL, ...)  random_sir(size = NULL, prob_SIR = c(0.33, 0.33, 0.33), ...)"},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"size desired size returned vector. used data.frame call dplyr verb, get current (group) size left blank. mo character can coerced valid microorganism code .mo() ab character can coerced valid antimicrobial drug code .ab() ... ignored, place allow future extensions prob_SIR vector length 3: probabilities \"S\" (1st value), \"\" (2nd value) \"R\" (3rd value)","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"class mic random_mic() (see .mic()) class disk random_disk() (see .disk())","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"base R function sample() used generating values. Generated values based EUCAST 2022 guideline implemented clinical_breakpoints data set. create specific generated values per bug drug, set mo /ab argument.","code":""},{"path":"https://msberends.github.io/AMR/reference/random.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Random MIC Values/Disk Zones/SIR Generation — random","text":"","code":"random_mic(25) #> Class 'mic' #>  [1] 4     4     128   4     4     2     0.25  0.002 2     128   1     0.25  #> [13] 128   0.5   0.005 0.025 4     256   64    16    16    0.01  0.25  0.001 #> [25] 0.002 random_disk(25) #> Class 'disk' #>  [1] 42  9 27 42 18  9 46 39 38 20 26 48  6 47 40 23 13 29 22  6  8 16 40 20 16 random_sir(25) #> Class 'sir' #>  [1] S S I I S S S I R R I R I I S R R R R I I S R I I  # \\donttest{ # make the random generation more realistic by setting a bug and/or drug: random_mic(25, \"Klebsiella pneumoniae\") # range 0.0625-64 #> Class 'mic' #>  [1] 32    0.125 0.025 0.001 0.01  64    0.125 0.01  2     2     64    1     #> [13] 0.025 0.25  0.125 16    8     0.125 0.002 4     0.025 128   256   0.002 #> [25] 16    random_mic(25, \"Klebsiella pneumoniae\", \"meropenem\") # range 0.0625-16 #> Class 'mic' #>  [1] 16 32 1  16 2  4  32 32 32 2  4  2  16 1  16 16 2  16 2  8  8  1  8  32 2  random_mic(25, \"Streptococcus pneumoniae\", \"meropenem\") # range 0.0625-4 #> Class 'mic' #>  [1] <=0.0625 0.25     4        0.5      0.5      2        16       1        #>  [9] 0.5      <=0.0625 <=0.0625 0.25     0.125    8        1        0.125    #> [17] 0.25     0.25     0.5      4        <=0.0625 0.5      2        0.5      #> [25] <=0.0625  random_disk(25, \"Klebsiella pneumoniae\") # range 8-50 #> Class 'disk' #>  [1] 15 40 46 17 10 19 38 43 35 33 44  9 22 30 24 49 11 48  8 18  8 12 21 24 33 random_disk(25, \"Klebsiella pneumoniae\", \"ampicillin\") # range 11-17 #> Class 'disk' #>  [1] 12 13 15 12 15 17 11 14 17 15 15 13 13 13 13 13 11 17 16 13 12 13 13 12 17 random_disk(25, \"Streptococcus pneumoniae\", \"ampicillin\") # range 12-27 #> Class 'disk' #>  [1] 21 23 23 18 25 24 16 19 20 22 15 22 23 24 21 24 23 17 22 17 23 27 23 26 19 # }"},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":null,"dir":"Reference","previous_headings":"","what":"Predict Antimicrobial Resistance — resistance_predict","title":"Predict Antimicrobial Resistance — resistance_predict","text":"Create prediction model predict antimicrobial resistance next years statistical solid ground. Standard errors (SE) returned columns se_min se_max. See Examples real live example.","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Predict Antimicrobial Resistance — resistance_predict","text":"","code":"resistance_predict(   x,   col_ab,   col_date = NULL,   year_min = NULL,   year_max = NULL,   year_every = 1,   minimum = 30,   model = NULL,   I_as_S = TRUE,   preserve_measurements = TRUE,   info = interactive(),   ... )  sir_predict(   x,   col_ab,   col_date = NULL,   year_min = NULL,   year_max = NULL,   year_every = 1,   minimum = 30,   model = NULL,   I_as_S = TRUE,   preserve_measurements = TRUE,   info = interactive(),   ... )  # S3 method for resistance_predict plot(x, main = paste(\"Resistance Prediction of\", x_name), ...)  ggplot_sir_predict(   x,   main = paste(\"Resistance Prediction of\", x_name),   ribbon = TRUE,   ... )  # S3 method for resistance_predict autoplot(   object,   main = paste(\"Resistance Prediction of\", x_name),   ribbon = TRUE,   ... )"},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Predict Antimicrobial Resistance — resistance_predict","text":"x data.frame containing isolates. Can left blank automatic determination, see Examples. col_ab column name x containing antimicrobial interpretations (\"R\", \"\" \"S\") col_date column name date, used calculate years column consist years already - default first column date class year_min lowest year use prediction model, dafaults lowest year col_date year_max highest year use prediction model - default 10 years today year_every unit sequence lowest year found data year_max minimum minimal amount available isolates per year include. Years containing less observations estimated model. model statistical model choice. generalised linear regression model binomial distribution (.e. using glm(..., family = binomial), assuming period zero resistance followed period increasing resistance leading slowly resistance. See Details valid options. I_as_S logical indicate whether values \"\" treated \"S\" (otherwise treated \"R\"). default, TRUE, follows redefinition EUCAST interpretation (increased exposure) 2019, see section Interpretation S, R . preserve_measurements logical indicate whether predictions years actually available data overwritten original data. standard errors years NA. info logical indicate whether textual analysis printed name summary() statistical model. ... arguments passed functions main title plot ribbon logical indicate whether ribbon shown (default) error bars object model data plotted","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Predict Antimicrobial Resistance — resistance_predict","text":"data.frame extra class resistance_predict columns: year value, estimated preserve_measurements = FALSE, combination observed estimated otherwise se_min, lower bound standard error minimum 0 (standard error never go 0%) se_max upper bound standard error maximum 1 (standard error never go 100%) observations, total number available observations year, .e. \\(S + + R\\) observed, original observed resistant percentages estimated, estimated resistant percentages, calculated model Furthermore, model available attribute: attributes(x)$model, see Examples.","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Predict Antimicrobial Resistance — resistance_predict","text":"Valid options statistical model (argument model) : \"binomial\" \"binom\" \"logit\": generalised linear regression model binomial distribution \"loglin\" \"poisson\": generalised log-linear regression model poisson distribution \"lin\" \"linear\": linear regression model","code":""},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"interpretation-of-sir","dir":"Reference","previous_headings":"","what":"Interpretation of SIR","title":"Predict Antimicrobial Resistance — resistance_predict","text":"2019, European Committee Antimicrobial Susceptibility Testing (EUCAST) decided change definitions susceptibility testing categories S, , R shown (https://www.eucast.org/newsiandr/): S - Susceptible, standard dosing regimen microorganism categorised \"Susceptible, standard dosing regimen\", high likelihood therapeutic success using standard dosing regimen agent. - Susceptible, increased exposure  microorganism categorised \"Susceptible, Increased exposure\" high likelihood therapeutic success exposure agent increased adjusting dosing regimen concentration site infection. R = Resistant microorganism categorised \"Resistant\" high likelihood therapeutic failure even increased exposure. Exposure function mode administration, dose, dosing interval, infusion time, well distribution excretion antimicrobial agent influence infecting organism site infection. AMR package honours insight. Use susceptibility() (equal proportion_SI()) determine antimicrobial susceptibility count_susceptible() (equal count_SI()) count susceptible isolates.","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/resistance_predict.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Predict Antimicrobial Resistance — resistance_predict","text":"","code":"x <- resistance_predict(example_isolates,   col_ab = \"AMX\",   year_min = 2010,   model = \"binomial\" ) plot(x)  # \\donttest{ if (require(\"ggplot2\")) {   ggplot_sir_predict(x) }   # using dplyr: if (require(\"dplyr\")) {   x <- example_isolates %>%     filter_first_isolate() %>%     filter(mo_genus(mo) == \"Staphylococcus\") %>%     resistance_predict(\"PEN\", model = \"binomial\")   print(plot(x))    # get the model from the object   mymodel <- attributes(x)$model   summary(mymodel) }  #> NULL #>  #> Call: #> glm(formula = df_matrix ~ year, family = binomial) #>  #> Coefficients: #>             Estimate Std. Error z value Pr(>|z|) #> (Intercept) 47.02915   72.98739   0.644    0.519 #> year        -0.02280    0.03637  -0.627    0.531 #>  #> (Dispersion parameter for binomial family taken to be 1) #>  #>     Null deviance: 5.9620  on 11  degrees of freedom #> Residual deviance: 5.5701  on 10  degrees of freedom #> AIC: 50.533 #>  #> Number of Fisher Scoring iterations: 4 #>   # create nice plots with ggplot2 yourself if (require(\"dplyr\") && require(\"ggplot2\")) {   data <- example_isolates %>%     filter(mo == as.mo(\"E. coli\")) %>%     resistance_predict(       col_ab = \"AMX\",       col_date = \"date\",       model = \"binomial\",       info = FALSE,       minimum = 15     )   head(data)   autoplot(data) }  # }"},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":null,"dir":"Reference","previous_headings":"","what":"Skewness of the Sample — skewness","title":"Skewness of the Sample — skewness","text":"Skewness measure asymmetry probability distribution real-valued random variable mean. negative ('left-skewed'): left tail longer; mass distribution concentrated right histogram. positive ('right-skewed'): right tail longer; mass distribution concentrated left histogram. normal distribution skewness 0.","code":""},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Skewness of the Sample — skewness","text":"","code":"skewness(x, na.rm = FALSE)  # S3 method for default skewness(x, na.rm = FALSE)  # S3 method for matrix skewness(x, na.rm = FALSE)  # S3 method for data.frame skewness(x, na.rm = FALSE)"},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Skewness of the Sample — skewness","text":"x vector values, matrix data.frame na.rm logical value indicating whether NA values stripped computation proceeds","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/reference/skewness.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Skewness of the Sample — skewness","text":"","code":"skewness(runif(1000)) #> [1] 0.02857046"},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":null,"dir":"Reference","previous_headings":"","what":"Translate Strings from the AMR Package — translate","title":"Translate Strings from the AMR Package — translate","text":"language-dependent output AMR functions, mo_name(), mo_gramstain(), mo_type() ab_name().","code":""},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Translate Strings from the AMR Package — translate","text":"","code":"get_AMR_locale()  set_AMR_locale(language)  reset_AMR_locale()  translate_AMR(x, language = get_AMR_locale())"},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Translate Strings from the AMR Package — translate","text":"language language choose. Use one supported language names ISO-639-1 codes: English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), Ukrainian (uk). x text translate","code":""},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Translate Strings from the AMR Package — translate","text":"currently 20 supported languages English (en), Chinese (zh), Czech (cs), Danish (da), Dutch (nl), Finnish (fi), French (fr), German (de), Greek (el), Italian (), Japanese (ja), Norwegian (), Polish (pl), Portuguese (pt), Romanian (ro), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr), Ukrainian (uk). languages translations available antimicrobial drugs colloquial microorganism names. permanently silence -per-session language note non-English operating system, can set package option AMR_locale .Rprofile file like :   save file. Please read adding updating language Wiki.","code":"# Open .Rprofile file utils::file.edit(\"~/.Rprofile\")  # Then add e.g. Italian support to that file using: options(AMR_locale = \"Italian\")"},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"changing-the-default-language","dir":"Reference","previous_headings":"","what":"Changing the Default Language","title":"Translate Strings from the AMR Package — translate","text":"system language used default (returned Sys.getenv(\"LANG\") , LANG set, Sys.getlocale(\"LC_COLLATE\")), language supported. language used can overwritten two ways checked order: Setting package option AMR_locale, either using e.g. set_AMR_locale(\"German\") running e.g. options(AMR_locale = \"German\"). Note setting R option works session. Save command options(AMR_locale = \"(language)\") .Rprofile file apply every session. Run utils::file.edit(\"~/.Rprofile\") edit .Rprofile file. Setting system variable LANGUAGE LANG, e.g. adding LANGUAGE=\"de_DE.utf8\" .Renviron file home directory. Thus, package option AMR_locale set, system variables LANGUAGE LANG ignored.","code":""},{"path":"https://msberends.github.io/AMR/reference/translate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Translate Strings from the AMR Package — translate","text":"","code":"# Current settings (based on system language) ab_name(\"Ciprofloxacin\") #> [1] \"Ciprofloxacin\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Coagulase-negative Staphylococcus (CoNS)\"  # setting another language set_AMR_locale(\"Spanish\") #> ℹ Using Spanish (Español) for the AMR package for this session. ab_name(\"Ciprofloxacin\") #> [1] \"Ciprofloxacina\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Staphylococcus coagulasa negativo (SCN)\"  # setting yet another language set_AMR_locale(\"Greek\") #> ℹ Using Greek (Ελληνικά) for the AMR package for this session. ab_name(\"Ciprofloxacin\") #> [1] \"Σιπροφλοξασίνη\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Σταφυλόκοκκος με αρνητική πηκτικότητα (CoNS)\"  # setting yet another language set_AMR_locale(\"Ukrainian\") #> ℹ Using Ukrainian (Українська) for the AMR package for this session. ab_name(\"Ciprofloxacin\") #> [1] \"Ципрофлоксацин\" mo_name(\"Coagulase-negative Staphylococcus (CoNS)\") #> [1] \"Коагулазонегативний стафілокок (КНС)\"  # set_AMR_locale() understands endonyms, English exonyms, and ISO-639-1: set_AMR_locale(\"Deutsch\") #> ℹ Using German (Deutsch) for the AMR package for this session. set_AMR_locale(\"German\") #> ℹ Using German (Deutsch) for the AMR package for this session. set_AMR_locale(\"de\") #> ℹ Using German (Deutsch) for the AMR package for this session. ab_name(\"amox/clav\") #> ℹ More than one result was found for item 1: amoxicillin and clavulansäure #> [1] \"Amoxicillin/Clavulansäure\"  # reset to system default reset_AMR_locale() #> ℹ Using the English language (English) for the AMR package for this #>   session. ab_name(\"amox/clav\") #> [1] \"Amoxicillin/clavulanic acid\""},{"path":[]},{"path":"https://msberends.github.io/AMR/news/index.html","id":"changed-2-0-0-9015","dir":"Changelog","previous_headings":"","what":"Changed","title":"AMR 2.0.0.9015","text":"Added mo_oxygen_tolerance() retrieve values Added mo_is_anaerobic() determine species obligate anaerobic bacteria Added LPSN GBIF identifiers, oxygen tolerance mo_info() formatting fix sir_interpretation_history() Fixed WHONET codes microorganisms consequently couple entries clinical_breakpoints Added microbial codes Gram-negative/positive anaerobic bacteria mo_rank() now returns NA ‘unknown’ microorganisms (B_ANAER, B_ANAER-NEG, B_ANAER-POS, B_GRAMN, B_GRAMP, F_FUNGUS, F_YEAST, UNKNOWN) Fixed bug .mo() led coercion NA values using custom microorganism codes Added SAS Transport files (file extension .xpt) download page use SAS software","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"amr-200","dir":"Changelog","previous_headings":"","what":"AMR 2.0.0","title":"AMR 2.0.0","text":"CRAN release: 2023-03-12 new major release AMR package, great new additions also breaking changes current users. listed . TL;DR functions arguments ‘rsi’ replaced ‘sir’, interpretation MIC values (now .sir() instead .rsi()) - old functions still work now Many new interesting functions, antibiogram() (generating traditional/combined/syndromic/WISCA antibiograms), sir_confidence_interval() mean_amr_distance(), add_custom_microorganisms() add custom microorganisms package Clinical breakpoints added EUCAST 2022 CLSI 2022 Microbiological taxonomy (microorganisms data set) updated 2022 now based LPSN GBIF Much increased algorithms translate user input valid taxonomy, e.g. using recent scientific work per-species human pathogenicity 20 new antibiotics added updated DDDs ATC codes Extended support antiviral agents (antivirals data set), many new functions Now available 20 languages Many small bug fixes","code":""},{"path":[]},{"path":"https://msberends.github.io/AMR/news/index.html","id":"sir-vs-rsi-2-0-0","dir":"Changelog","previous_headings":"New","what":"SIR vs. RSI","title":"AMR 2.0.0","text":"milestone version, replaced mentions RSI SIR, comply actually commonly used field clinical microbiology comes tri-form regarding AMR. existing functions .rsi(), rsi_df() ggplot_rsi() still work, replacements .sir(), sir_df(), ggplot_sir() now current functions AMR data analysis. warning thrown session remind users . data set rsi_translation now called clinical_breakpoints better reflect content. ‘RSI functions’ removed future version, late 2023 / early 2024.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"new-antibiogram-function-2-0-0","dir":"Changelog","previous_headings":"New","what":"New antibiogram function","title":"AMR 2.0.0","text":"new antibiogram() function, users can now generate traditional, combined, syndromic, even weighted-incidence syndromic combination antibiograms (WISCA). , follow logic previously described work Klinker et al. (2021, DOI 10.1177/20499361211011373) Barbieri et al. (2021, DOI 10.1186/s13756-021-00939-2). help page antibiogram() extensively elaborates use cases, antibiogram() also supports printing R Markdown Quarto, support 20 languages. Furthermore, different plotting methods implemented allow graphical visualisations well.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"interpretation-of-mic-and-disk-diffusion-values-2-0-0","dir":"Changelog","previous_headings":"New","what":"Interpretation of MIC and disk diffusion values","title":"AMR 2.0.0","text":"clinical breakpoints intrinsic resistance EUCAST 2022 CLSI 2022 added .sir(). EUCAST 2022 (v12.0) now new default guideline MIC disks diffusion interpretations, eucast_rules() apply EUCAST Expert Rules. default guideline (EUCAST) can now changed new AMR_guideline option, : options(AMR_guideline = \"CLSI 2020\"). new arguments include_PKPD (default: TRUE) include_screening (default: FALSE), users can now specify whether breakpoints screening PK/PD table included interpreting MICs disks diffusion values. options can set globally, can read new manual. Interpretation guidelines older 10 years removed, oldest now included guidelines EUCAST CLSI 2013.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"supported-languages-2-0-0","dir":"Changelog","previous_headings":"New","what":"Supported languages","title":"AMR 2.0.0","text":"added support following ten languages: Chinese (simplified), Czech, Finnish, Greek, Japanese, Norwegian (bokmål), Polish, Romanian, Turkish Ukrainian. antibiotic names now available languages, AMR package automatically determine supported language based user’s system language. grateful valuable input colleagues countries. AMR package now available 20 languages total, according download stats used almost countries world!","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"outbreak-management-2-0-0","dir":"Changelog","previous_headings":"New","what":"Outbreak management","title":"AMR 2.0.0","text":"analysis outbreak management, updated get_episode() is_new_episode() functions: now contain argument case_free_days. argument can used quantify duration case-free days (inter-epidemic interval), new episode start. common requirement outbreak management, e.g. determining number norovirus outbreaks hospital. case-free period 14 28 days, new norovirus cases time considered different (new) episode.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"microbiological-taxonomy-2-0-0","dir":"Changelog","previous_headings":"New","what":"Microbiological taxonomy","title":"AMR 2.0.0","text":"microorganisms data set longer relies Catalogue Life, List Prokaryotic names Standing Nomenclature (LPSN) supplemented ‘backbone taxonomy’ Global Biodiversity Information Facility (GBIF). structure data set changed include separate LPSN GBIF identifiers. Almost previous MO codes retained. contains 1,400 taxonomic names 2022. previously relied experience categorise species pathogenic groups, happy encounter recent work Bartlett et al. (2022, DOI 10.1099/mic.0.001269) extensively studied medical-scientific literature categorise bacterial species groups. See mo_matching_score() work incorporated prevalence column microorganisms data set. Using results, .mo() mo_*() functions now much better capable converting user input valid taxonomic records. new function add_custom_microorganisms() allows users add custom microorganisms AMR package. also made following changes regarding included taxonomy microorganisms functions: Updated full microbiological taxonomy according latest daily LPSN data set (December 2022) latest yearly GBIF taxonomy backbone (November 2022) Added function mo_current() get currently valid taxonomic name microorganism Support 1,516 city-like serovars Salmonella, Salmonella Goldcoast. Formally, serovars belonging S. enterica species, reported name genus city. reason, serovars subspecies column microorganisms data set “enterica” species column, full name contain species name (enterica). new argument keep_synonyms allows correct updated taxonomy, favour now deleted argument allow_uncertain increased tremendously speed returns generally consequent results Sequential coercion now extremely fast results stored package environment, although coercion unknown values must run per session. Previous results can reset/removed new mo_reset_session() function. Support microorganism codes ASIan Antimicrobial Resistance Surveillance Network (ASIARS-Net) MO matching score algorithm (mo_matching_score()) now counts deletions substitutions 2 instead 1, impacts outcome .mo() mo_*() function CRAN allows packages around 5 MB maximum, packages exempted package one Chromista relevant comes antimicrobial resistance, thus lacking primary scope package Chromista almost never clinically relevant, thus lacking secondary scope package microorganisms.old data set removed, previously accepted names now included microorganisms data set. new column status contains \"accepted\" currently accepted names \"synonym\" taxonomic synonyms; currently invalid names. previously accepted names now microorganisms ID - available - LPSN, GBIF SNOMED CT identifier.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"antibiotic-agents-and-selectors-2-0-0","dir":"Changelog","previous_headings":"New","what":"Antibiotic agents and selectors","title":"AMR 2.0.0","text":"new function add_custom_antimicrobials() allows users add custom antimicrobial codes names AMR package. antibiotics data set greatly updated: following 20 antibiotics added (also includes new J01RA ATC group): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), thioacetazone (TAT) Added missing ATC codes Updated DDDs PubChem Compound IDs Updated antibiotic name spelling, now used WHOCC (cephalexin -> cefalexin, phenethicillin -> pheneticillin) Antibiotic code “CEI” ceftolozane/tazobactam replaced “CZT” comply EARS-Net WHONET 2022. old code still work cases using .ab() ab_*() functions. Support antimicrobial interpretation anaerobic bacteria, adding ‘placeholder’ code B_ANAER microorganisms data set adding breakpoints anaerobics clinical_breakpoints data set, used .sir() interpretion MIC disk diffusion values Also, added support using antibiotic selectors scoped dplyr verbs (without using vars()), : ... %>% summarise_at(aminoglycosides(), resistance), please see resistance() examples.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"antiviral-agents-2-0-0","dir":"Changelog","previous_headings":"New","what":"Antiviral agents","title":"AMR 2.0.0","text":"now added extensive support antiviral agents! first time, AMR package extensive support antiviral drugs work names, codes data way. antivirals data set extended 18 new drugs (also new J05AJ ATC group) now also contains antiviral identifiers LOINC codes new data type av (antivirals) added, functionally similar ab antibiotics Functions .av(), av_name(), av_atc(), av_synonyms(), av_from_text() added siblings ab_*() equivalents","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"other-new-functions-2-0-0","dir":"Changelog","previous_headings":"New","what":"Other new functions","title":"AMR 2.0.0","text":"Function sir_confidence_interval() add confidence intervals AMR calculation. now also included sir_df() proportion_df(). Function mean_amr_distance() calculate mean AMR distance. mean AMR distance normalised numeric value compare AMR test results can help identify similar isolates, without comparing antibiograms hand. Function sir_interpretation_history() view history previous runs .sir() (previously .rsi()). returns ‘logbook’ selected guideline, reference table specific interpretation row data set .sir() run.","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"changes-2-0-0","dir":"Changelog","previous_headings":"","what":"Changes","title":"AMR 2.0.0","text":"Fix working NA values Fix unsorted dates length 2 Now returns class integer instead numeric since always whole numbers Argument combine_IR removed package (affecting functions count_df(), proportion_df(), sir_df() plotting functions), since replaced combine_SI three years ago Using units ab_ddd(..., units = \"...\") deprecated time now supported anymore. Use ab_ddd_units() instead. Support data.frame-enhancing R packages, specifically: data.table::data.table, janitor::tabyl, tibble::tibble, tsibble::tsibble. AMR package functions data set output (sir_df() bug_drug_combinations()), now return data type input. data sets package now tibble, instead base R data.frames. Older R versions still supported, even support tibbles. data sets now also continually exported Apache Feather Apache Parquet formats. can find info article website. Fixed certain EUCAST breakpoints MIC values Allow NA values (e.g. .sir(.disk(NA), ...)) Fix bug-drug combinations multiple breakpoints different body sites Interpretation MIC disk zones now informative availability breakpoints robust Removed .integer() method MIC values, since MIC integer values running table() MIC values consequently failed able retrieve level position (’s normally .integer() factors work) Fixed determination Gram stains (mo_gramstain()), since taxonomic phyla Actinobacteria, Chloroflexi, Firmicutes, Tenericutes renamed respectively Actinomycetota, Chloroflexota, Bacillota, Mycoplasmatota 2021 droplevels() MIC now return common factor default lose mic class. Use droplevels(..., .mic = TRUE) keep mic class. Small fix using ab_from_text() Fixes reading text files using set_mo_source(), now also allows source file contain valid taxonomic names instead valid microorganism ID package Fixed bug mdro() using similar column names Magiorakos guideline Using random_*() function (random_mic()) now possible directly calling package without loading first: AMR::random_mic(10) Extended support vctrs package, used internally tidyverse. allows change values class mic, disk, sir, mo ab tibbles, use antibiotic selectors selecting/filtering, e.g. df[carbapenems() == \"R\", ] Fix using info = FALSE mdro() interpretation guidelines using .sir() amoxicillin, rules ampicillin used amoxicillin rules available Fix using ab_atc() non-existing ATC codes Black white message texts now reversed colour using RStudio dark theme mo_snomed() now returns class character, numeric anymore (make long SNOMED codes readable) Fix using .ab() NA values Updated support WHONET 2022 microorganism codes Antimicrobial interpretation ‘SDD’ (susceptible dose-dependent, coined CLSI) interpreted ‘’ comply EUCAST’s ‘’ .sir() Fix mo_shortname() case higher taxonomic ranks (order, class, phylum) Cleaning columns .sir(), .mic(), .disk() now show column name warning invalid results Fix using g.test() zeroes 2x2 table mo_synonyns() now contains scientific reference names","code":""},{"path":"https://msberends.github.io/AMR/news/index.html","id":"other-2-0-0","dir":"Changelog","previous_headings":"","what":"Other","title":"AMR 2.0.0","text":"Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, Jonas Salm, Anita Williams contributors, thank valuable input New website make use new Bootstrap 5 pkgdown 2.0. website now contains results examples automatically regenerated every change repository, using GitHub Actions R Rmd files project now styled using styler package Set scalar conditional expressions (&& ||) possible comply upcoming R 4.3 enormous lot code cleaning, fixing small bugs along way changelog contains changes AMR v2.0 later. prior versions, please see archive.","code":""}]