Built site for AMR: 2.0.0.9024@f065945

404.html

@@ -36,7 +36,7 @@
     
     <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</small>
 
     
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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="">2.0.0.9023</small>
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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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</small>
 
     
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@@ -204,7 +204,7 @@
 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 27 May 2023.</p>
+generated on 22 June 2023.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -260,21 +260,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2023-05-27</td>
+<td align="center">2023-06-22</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">2023-05-27</td>
+<td align="center">2023-06-22</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">2023-05-27</td>
+<td align="center">2023-06-22</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -405,11 +405,11 @@ taxonomic codes. Let’s check this:</p>
 <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; 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;               argenteus (0.625), Staphylococcus aureus anaerobius (0.625), Salmonella</span></span>
-<span><span class="co">#&gt;               Streptomyces argenteolus (0.483), Streptomyces aureus (0.474),</span></span>
+<span><span class="co">#&gt;               Aurelianis (0.595), Salmonella Aarhus (0.588), Salmonella Amounderness</span></span>
-<span><span class="co">#&gt;               Streptomyces azureus (0.467), Streptomyces aureorectus (0.444),</span></span>
+<span><span class="co">#&gt;               (0.587), Selenomonas artemidis (0.571), Salmonella choleraesuis</span></span>
-<span><span class="co">#&gt;               Streptomyces auratus (0.433), Streptomyces aurantiogriseus (0.429), and</span></span>
+<span><span class="co">#&gt;               arizonae (0.562), Streptococcus anginosus anginosus (0.561), and</span></span>
-<span><span class="co">#&gt;               Streptomyces aureocirculatus (0.429)</span></span>
+<span><span class="co">#&gt;               Salmonella Abaetetuba (0.548)</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; Also matched: Streptococcus pseudopneumoniae (0.700), Serratia</span></span>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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 +216,7 @@ recommendations for reporting particular resistances.</em></p>
 <p>In Europe, a lot of medical microbiological laboratories already
 apply these rules (<a href="https://www.eurosurveillance.org/content/10.2807/1560-7917.ES2015.20.2.21008" class="external-link">Brown
 <em>et al.</em>, 2015</a>). Our package features their latest insights
-on intrinsic resistance and unusual phenotypes (v3.3, 2021).</p>
+on intrinsic resistance and unusual phenotypes (v3.1, 2016).</p>
 <p>Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function we use for this
 purpose can also apply additional rules, like forcing
 <help title="ATC: J01CA01">ampicillin</help> = R in isolates when

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -402,19 +402,19 @@ 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          R         S            S          R            R            S</span></span>
+<span><span class="co">#&gt; 1          R         S            R          I            I            R</span></span>
-<span><span class="co">#&gt; 2          R         R            I          I            S            S</span></span>
+<span><span class="co">#&gt; 2          I         I            I          R            S            I</span></span>
-<span><span class="co">#&gt; 3          S         R            S          S            I            S</span></span>
+<span><span class="co">#&gt; 3          R         S            I          R            I            R</span></span>
-<span><span class="co">#&gt; 4          R         R            S          R            R            R</span></span>
+<span><span class="co">#&gt; 4          S         S            I          I            S            I</span></span>
-<span><span class="co">#&gt; 5          I         I            I          S            R            R</span></span>
+<span><span class="co">#&gt; 5          I         S            R          S            I            R</span></span>
-<span><span class="co">#&gt; 6          S         I            R          R            S            R</span></span>
+<span><span class="co">#&gt; 6          R         R            I          S            S            I</span></span>
 <span><span class="co">#&gt;   kanamycin</span></span>
-<span><span class="co">#&gt; 1         S</span></span>
+<span><span class="co">#&gt; 1         I</span></span>
-<span><span class="co">#&gt; 2         S</span></span>
+<span><span class="co">#&gt; 2         I</span></span>
-<span><span class="co">#&gt; 3         I</span></span>
+<span><span class="co">#&gt; 3         R</span></span>
-<span><span class="co">#&gt; 4         R</span></span>
+<span><span class="co">#&gt; 4         S</span></span>
-<span><span class="co">#&gt; 5         S</span></span>
+<span><span class="co">#&gt; 5         R</span></span>
-<span><span class="co">#&gt; 6         R</span></span></code></pre></div>
+<span><span class="co">#&gt; 6         S</span></span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can
 use:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@@ -455,40 +455,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3225</td>
+<td align="right">3262</td>
-<td align="right">64.50%</td>
+<td align="right">65.24%</td>
-<td align="right">3225</td>
+<td align="right">3262</td>
-<td align="right">64.50%</td>
+<td align="right">65.24%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">963</td>
+<td align="right">923</td>
-<td align="right">19.26%</td>
+<td align="right">18.46%</td>
-<td align="right">4188</td>
+<td align="right">4185</td>
-<td align="right">83.76%</td>
+<td align="right">83.70%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">478</td>
+<td align="right">446</td>
-<td align="right">9.56%</td>
+<td align="right">8.92%</td>
-<td align="right">4666</td>
+<td align="right">4631</td>
-<td align="right">93.32%</td>
+<td align="right">92.62%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">228</td>
+<td align="right">258</td>
-<td align="right">4.56%</td>
+<td align="right">5.16%</td>
-<td align="right">4894</td>
+<td align="right">4889</td>
-<td align="right">97.88%</td>
+<td align="right">97.78%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">106</td>
+<td align="right">111</td>
-<td align="right">2.12%</td>
+<td align="right">2.22%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -307,7 +307,7 @@ function:</p>
 <span><span class="co">#&gt; [1] "Caryophanales"    "Enterobacterales" "Lactobacillales"  "Pseudomonadales"</span></span>
 <span><span class="co">#&gt; Importance of components:</span></span>
 <span><span class="co">#&gt;                           PC1    PC2    PC3     PC4     PC5     PC6       PC7</span></span>
-<span><span class="co">#&gt; Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 9.577e-17</span></span>
+<span><span class="co">#&gt; Standard deviation     2.1539 1.6807 0.6138 0.33879 0.20808 0.03140 1.232e-16</span></span>
 <span><span class="co">#&gt; Proportion of Variance 0.5799 0.3531 0.0471 0.01435 0.00541 0.00012 0.000e+00</span></span>
 <span><span class="co">#&gt; Cumulative Proportion  0.5799 0.9330 0.9801 0.99446 0.99988 1.00000 1.000e+00</span></span></code></pre></div>
 <pre><code><span><span class="co">#&gt; Groups (n=4, named as 'order'):</span></span>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -193,7 +193,7 @@
   <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">27 May 2023</h4>
+            <h4 data-toc-skip class="date">22 June 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>
@@ -913,68 +913,70 @@ inhibitors</td>
 <code>clinical_breakpoints</code>: Interpretation from MIC values
 &amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
 </h2>
-<p>A data set with 18 271 rows and 11 columns, containing the following
+<p>A data set with 42 599 rows and 12 columns, containing the following
 column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
 <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
-<em>breakpoint_S</em>, <em>breakpoint_R</em>, and <em>uti</em>.</p>
+<em>breakpoint_S</em>, <em>breakpoint_R</em>, <em>ecoff</em>, and
+<em>uti</em>.</p>
 <p>This data set is in R available as <code>clinical_breakpoints</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
+<p>It was last updated on 22 June 2023 13:10:59 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/clinical_breakpoints.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/clinical_breakpoints.rds" class="external-link">original
-R Data Structure (RDS) file</a> (43 kB)<br>
+R Data Structure (RDS) file</a> (82 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.txt" class="external-link">tab-separated
-text file</a> (1.9 MB)<br>
+text file</a> (4.4 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.xlsx" class="external-link">Microsoft
-Excel workbook</a> (0.8 MB)<br>
+Excel workbook</a> (1.8 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.feather" class="external-link">Apache
-Feather file</a> (0.7 MB)<br>
+Feather file</a> (1.6 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.parquet" class="external-link">Apache
-Parquet file</a> (88 kB)<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/clinical_breakpoints.sas" class="external-link">SAS
 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>
+transport (XPT) file</a> (10.6 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>
+SPSS Statistics data file</a> (5.8 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/clinical_breakpoints.dta" class="external-link">Stata
-DTA file</a> (3.3 MB)</li>
+DTA file</a> (10.5 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-3">Source<a class="anchor" aria-label="anchor" href="#source-3"></a>
 </h3>
 <p>This data set contains interpretation rules for MIC values and disk
-diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
+diffusion diameters. Included guidelines are CLSI (2011-2023) and EUCAST
-(2013-2022).</p>
+(2011-2023).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-3">Example content<a class="anchor" aria-label="anchor" href="#example-content-3"></a>
 </h3>
 <table style="width:100%;" class="table">
 <colgroup>
-<col width="8%">
+<col width="7%">
-<col width="5%">
+<col width="4%">
 <col width="3%">
 <col width="8%">
 <col width="14%">
 <col width="7%">
 <col width="3%">
-<col width="10%">
+<col width="9%">
-<col width="8%">
 <col width="7%">
+<col width="6%">
 <col width="8%">
 <col width="8%">
 <col width="4%">
+<col width="4%">
 </colgroup>
 <thead><tr class="header">
 <th align="center">guideline</th>
@@ -989,11 +991,12 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
 <th align="center">disk_dose</th>
 <th align="center">breakpoint_S</th>
 <th align="center">breakpoint_R</th>
+<th align="center">ecoff</th>
 <th align="center">uti</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">EUCAST 2022</td>
+<td align="center">EUCAST 2023</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_ASPRG_MGTS</td>
@@ -1005,10 +1008,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
 <td align="center"></td>
 <td align="center">1</td>
 <td align="center">1</td>
+<td align="center"></td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
-<td align="center">EUCAST 2022</td>
+<td align="center">EUCAST 2023</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_ASPRG_NIGR</td>
@@ -1020,10 +1024,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
 <td align="center"></td>
 <td align="center">1</td>
 <td align="center">1</td>
+<td align="center"></td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="odd">
-<td align="center">EUCAST 2022</td>
+<td align="center">EUCAST 2023</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_CANDD_ALBC</td>
@@ -1035,10 +1040,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
 <td align="center"></td>
 <td align="center">1</td>
 <td align="center">1</td>
+<td align="center"></td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
-<td align="center">EUCAST 2022</td>
+<td align="center">EUCAST 2023</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_CANDD_DBLN</td>
@@ -1050,10 +1056,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
 <td align="center"></td>
 <td align="center">1</td>
 <td align="center">1</td>
+<td align="center"></td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="odd">
-<td align="center">EUCAST 2022</td>
+<td align="center">EUCAST 2023</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_CANDD_GLBR</td>
@@ -1065,10 +1072,11 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
 <td align="center"></td>
 <td align="center">1</td>
 <td align="center">1</td>
+<td align="center"></td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
-<td align="center">EUCAST 2022</td>
+<td align="center">EUCAST 2023</td>
 <td align="center">MIC</td>
 <td align="center"></td>
 <td align="center">F_CANDD_KRUS</td>
@@ -1080,6 +1088,7 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
 <td align="center"></td>
 <td align="center">1</td>
 <td align="center">1</td>
+<td align="center"></td>
 <td align="center">FALSE</td>
 </tr>
 </tbody>
@@ -1380,13 +1389,13 @@ v3.3</a> (2021).</p>
 <h2 id="dosage-dosage-guidelines-from-eucast">
 <code>dosage</code>: Dosage Guidelines from EUCAST<a class="anchor" aria-label="anchor" href="#dosage-dosage-guidelines-from-eucast"></a>
 </h2>
-<p>A data set with 336 rows and 9 columns, containing the following
+<p>A data set with 503 rows and 9 columns, containing the following
 column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
 <em>dose_times</em>, <em>administration</em>, <em>notes</em>,
 <em>original_txt</em>, and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you
 load the <code>AMR</code> package.</p>
-<p>It was last updated on 14 November 2022 14:20:39 UTC. Find more info
+<p>It was last updated on 22 June 2023 13:10:59 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -1394,28 +1403,28 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
 R Data Structure (RDS) file</a> (3 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">tab-separated
-text file</a> (29 kB)<br>
+text file</a> (43 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Microsoft
-Excel workbook</a> (19 kB)<br>
+Excel workbook</a> (25 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.feather" class="external-link">Apache
-Feather file</a> (16 kB)<br>
+Feather file</a> (21 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.parquet" class="external-link">Apache
-Parquet file</a> (8 kB)<br>
+Parquet file</a> (9 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 (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>
+transport (XPT) file</a> (0.1 MB)<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>
+SPSS Statistics data file</a> (64 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata
-DTA file</a> (82 kB)</li>
+DTA file</a> (0.1 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-5">Source<a class="anchor" aria-label="anchor" href="#source-5"></a>
@@ -1423,8 +1432,9 @@ DTA file</a> (82 kB)</li>
 <p>EUCAST breakpoints used in this package are based on the dosages in
 this data set.</p>
 <p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
-Breakpoint Tables’ v11.0</a> (2021) and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
+Breakpoint Tables’ v11.0</a> (2021), <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
-Breakpoint Tables’ v12.0</a> (2022).</p>
+Breakpoint Tables’ v12.0</a> (2022), and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical
+Breakpoint Tables’ v13.0</a> (2023).</p>
 </div>
 <div class="section level3">
 <h3 id="example-content-5">Example content<a class="anchor" aria-label="anchor" href="#example-content-5"></a>
@@ -1462,7 +1472,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
 <td align="center">iv</td>
 <td align="center"></td>
 <td align="center">25-30 mg/kg x 1 iv</td>
-<td align="center">12</td>
+<td align="center">13</td>
 </tr>
 <tr class="even">
 <td align="center">AMX</td>
@@ -1473,7 +1483,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
 <td align="center">iv</td>
 <td align="center"></td>
 <td align="center">2 g x 6 iv</td>
-<td align="center">12</td>
+<td align="center">13</td>
 </tr>
 <tr class="odd">
 <td align="center">AMX</td>
@@ -1484,7 +1494,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
 <td align="center">iv</td>
 <td align="center"></td>
 <td align="center">1 g x 3-4 iv</td>
-<td align="center">12</td>
+<td align="center">13</td>
 </tr>
 <tr class="even">
 <td align="center">AMX</td>
@@ -1495,7 +1505,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
 <td align="center">oral</td>
 <td align="center"></td>
 <td align="center">0.75-1 g x 3 oral</td>
-<td align="center">12</td>
+<td align="center">13</td>
 </tr>
 <tr class="odd">
 <td align="center">AMX</td>
@@ -1506,7 +1516,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
 <td align="center">oral</td>
 <td align="center"></td>
 <td align="center">0.5 g x 3 oral</td>
-<td align="center">12</td>
+<td align="center">13</td>
 </tr>
 <tr class="even">
 <td align="center">AMX</td>
@@ -1517,7 +1527,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
 <td align="center">oral</td>
 <td align="center"></td>
 <td align="center">0.5 g x 3 oral</td>
-<td align="center">12</td>
+<td align="center">13</td>
 </tr>
 </tbody>
 </table>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

articles/other_pkg.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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -221,7 +221,7 @@
 </h3>
 <p>The <code>AMR</code> package is a <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. <a href="./authors.html">Many different researchers</a> from around the globe are continually helping us to make this a successful and durable project!</p>
 <p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
-<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~52,000 distinct microbial species</strong></a> (updated December 2022) and all <a href="./reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
+<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~52,000 distinct microbial species</strong></a> (updated December 2022) and all <a href="./reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
 <div class="section level5">
 <h5 id="used-in-over-175-countries-translated-into-20-languages">Used in over 175 countries, translated into 20 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-translated-into-20-languages"></a>
 </h5>
@@ -738,7 +738,7 @@
 <p>This package was intended as a comprehensive toolbox for integrated AMR data analysis. This package can be used for:</p>
 <ul>
 <li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (<a href="(https://lpsn.dsmz.de)" class="external-link">LPSN</a>) and the Global Biodiversity Information Facility (<a href="https://www.gbif.org" class="external-link">GBIF</a>) (<a href="./reference/mo_property.html">manual</a>)</li>
-<li>Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline from the last 10 years (<a href="./reference/as.sir.html">manual</a>)</li>
+<li>Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline (<a href="./reference/as.sir.html">manual</a>)</li>
 <li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
 <li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
 <li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
@@ -779,7 +779,7 @@
 <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"><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>
+<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>
 </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>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -159,10 +159,13 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.0.0.9023" id="amr-2009023">AMR 2.0.0.9023<a class="anchor" aria-label="anchor" href="#amr-2009023"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.0.0.9024" id="amr-2009024">AMR 2.0.0.9024<a class="anchor" aria-label="anchor" href="#amr-2009024"></a></h2>
 <div class="section level3">
-<h3 id="changed-2-0-0-9023">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9023"></a></h3>
+<h3 id="new-2-0-0-9024">New<a class="anchor" aria-label="anchor" href="#new-2-0-0-9024"></a></h3>
-<ul><li>Added oxygen tolerance from BacDive to over 25,000 bacteria in the <code>microorganisms</code> data set
+<ul><li>Clinical breakpoints and intrinsic resistance of EUCAST 2023 and CLSI 2023 have been added for <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2023 (v13.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules.</li>
+<li>The EUCAST dosage guideline of v13.0 has been added to the <code>dosage</code> data set</li>
+<li>ECOFF: the <code>clinical_breakpoints</code> data set now contains the new column <code>ecoff</code>, in which the epidemiological cut-off (ECOFF) are available. These ECOFFs can be used for MIC/disk interpretation using <code>as.sir(..., ecoff = TRUE)</code>, which is an important new addition for veterinary microbiology.</li>
+<li>Added oxygen tolerance from BacDive 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 genera/species are obligate anaerobic bacteria</li>
 </ul></li>
@@ -170,7 +173,10 @@
 </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>
 <li>Added microbial codes for Gram-negative/positive anaerobic bacteria</li>
-<li>
+</ul></div>
+<div class="section level3">
+<h3 id="changed-2-0-0-9024">Changed<a class="anchor" aria-label="anchor" href="#changed-2-0-0-9024"></a></h3>
+<ul><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 formatting for <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code>
 </li>
@@ -179,7 +185,11 @@
 <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>Fixed usage of <code>icu_exclude</code> in <code>first_isolates()</code>
 </li>
-<li>Improved <code><a href="../reference/as.mo.html">as.mo()</a></code> algorithm for searching on only species names</li>
+<li>Improved <code><a href="../reference/as.mo.html">as.mo()</a></code> algorithm:
+<ul><li>Now allows searching on only species names</li>
+<li>Fix for using the <code>keep_synonyms</code> argument when using MO codes as input</li>
+<li>Fix for using the <code>minimum_matching_score</code> argument</li>
+</ul></li>
 <li>Updated the code table in <code>microorganisms.codes</code>
 </li>
 </ul></div>

pkgdown.yml

@@ -11,7 +11,7 @@ articles:
   other_pkg: other_pkg.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2023-05-27T08:50Z
+last_built: 2023-06-22T13:15Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -171,9 +171,10 @@
 <ul><li><p><code>AMR_custom_ab</code> <br> Allows to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
 <li><p><code>AMR_custom_mo</code> <br> Allows to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>
 <li><p><code>AMR_eucastrules</code> <br> Used for setting the default types of rules for <code><a href="eucast_rules.html">eucast_rules()</a></code> function, must be one or more of: <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>.</p></li>
-<li><p><code>AMR_guideline</code> <br> Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2022"</code>. Supported guideline are currently EUCAST (2013-2022) and CLSI (2013-2022).</p></li>
+<li><p><code>AMR_guideline</code> <br> Used for setting the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2023"</code>. Supported guideline are currently EUCAST (2011-2023) and CLSI (2011-2023).</p></li>
 <li><p><code>AMR_ignore_pattern</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to ignore (i.e., make <code>NA</code>) any match given in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions.</p></li>
 <li><p><code>AMR_include_PKPD</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>.</p></li>
+<li><p><code>AMR_ecoff</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that ECOFF (Epidemiological Cut-Off) values must be used - the default is <code>FALSE</code>.</p></li>
 <li><p><code>AMR_include_screening</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that clinical breakpoints for screening are allowed - the default is <code>FALSE</code>.</p></li>
 <li><p><code>AMR_keep_synonyms</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to indicate if old, previously valid taxonomic names must be preserved and not be corrected to currently accepted names. The default is <code>FALSE</code>.</p></li>
 <li><p><code>AMR_cleaning_regex</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> (case-insensitive) to use in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions, to clean the user input. The default is the outcome of <code><a href="as.mo.html">mo_cleaning_regex()</a></code>, which removes texts between brackets and texts such as "species" and "serovar".</p></li>

reference/AMR.html

@@ -5,14 +5,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
 ) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
  and doi:10.33612/diss.192486375
 ).
-After installing this package, R knows ~52 000 microorganisms (updated December 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
+After installing this package, R knows ~52 000 microorganisms (updated December 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
 The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><title>The AMR Package — AMR • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.6/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="The AMR Package — AMR"><meta property="og:description" content="Welcome to the AMR package.
 The AMR package is a free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. Many different researchers from around the globe are continually helping us to make this a successful and durable project!
 This work was published in the Journal of Statistical Software (Volume 104(3); doi:jss.v104.i03
 ) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
  and doi:10.33612/diss.192486375
 ).
-After installing this package, R knows ~52 000 microorganisms (updated December 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
+After installing this package, R knows ~52 000 microorganisms (updated December 2022) and all ~600 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen.
 The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
@@ -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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -180,7 +180,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
 ) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
  and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
 ).</p>
-<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~52 000 microorganisms</strong></a> (updated December 2022) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
+<p>After installing this package, R knows <a href="https://msberends.github.io/AMR/reference/microorganisms.html"><strong>~52 000 microorganisms</strong></a> (updated December 2022) and all <a href="https://msberends.github.io/AMR/reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
 <p>The <code>AMR</code> package is available in English, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish, Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
     </div>
 

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -222,16 +222,16 @@
 <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  1989-07-11  33  33.87671         10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1989-09-05  33  33.79452         10</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1976-01-27  47  47.32877         23</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1978-12-23  44  44.49589         21</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1952-06-04  70  70.97808         47</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1982-12-24  40  40.49315         17</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1975-04-14  48  48.11781         24</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1958-08-14  64  64.85479         41</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1980-05-09  43  43.04932         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1968-12-14  54  54.52055         31</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1959-05-20  64  64.01918         40</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1992-02-12  31  31.35616          7</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1956-11-01  66  66.56712         43</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1988-05-22  35  35.08493         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1986-10-27  36  36.58082         13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1950-02-15  73  73.34795         49</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1989-06-17  33  33.94247         10</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1937-05-17  86  86.09863         62</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1965-07-30  57  57.82466         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1965-11-25  57  57.57260         34</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -261,7 +261,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
 
 
 <dt>version_expertrules</dt>
-<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2", or "3.1".</p></dd>
+<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".</p></dd>
 
 </dl></div>
     <div class="section level2">
@@ -626,11 +626,11 @@ 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> I     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> R     </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> 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;">4</span> S     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> S     </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>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -241,7 +241,7 @@
 <span class="r-in"><span>  guideline <span class="op">=</span> <span class="st">"EUCAST"</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> =&gt; Interpreting disk diffusion zones of 'ampicillin' (AMP) according to</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</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] R</span>
@@ -249,16 +249,16 @@
 <span class="r-in"><span><span class="co"># interpret whole data set, pretend to be all from urinary tract infections:</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">df</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'AMP' (ampicillin) according</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'CIP' (ciprofloxacin)</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    according to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'GEN' (gentamicin) according</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'TOB' (tobramycin) according</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      microorganism AMP CIP GEN TOB</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli   S   R   S   S</span>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -201,7 +201,7 @@
     </div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>To interpret MIC values as SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2013-2022) and CLSI (2013-2022).</p>
+    <p>To interpret MIC values as SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2023) and CLSI (2011-2023).</p>
 <p>This class for MIC values is a quite a special data type: formally it is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with valid MIC values as <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p>
 <p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>x <span class="ot">&lt;-</span> <span class="fu">random_mic</span>(<span class="dv">10</span>)</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>x</span>
@@ -271,7 +271,7 @@
 <span class="r-in"><span>  guideline <span class="op">=</span> <span class="st">"EUCAST"</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> =&gt; Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      pneumoniae - assuming body site 'Meningitis'.</span>
@@ -284,7 +284,7 @@
 <span class="r-in"><span>  guideline <span class="op">=</span> <span class="st">"EUCAST"</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> =&gt; Interpreting MIC values of 'AMX' (amoxicillin) according to EUCAST</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for amoxicillin (AMX) in Streptococcus</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      pneumoniae - assuming body site 'Meningitis'.</span>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -188,6 +188,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
 <span>  reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
 <span>  include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
 <span>  include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
+<span>  ecoff <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_ecoff"</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>
@@ -202,6 +203,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
 <span>  reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
 <span>  include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
 <span>  include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
+<span>  ecoff <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_ecoff"</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>
@@ -216,7 +218,8 @@ All breakpoints used for interpretation are publicly available in the clinical_b
 <span>  add_intrinsic_resistance <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  reference_data <span class="op">=</span> <span class="fu">AMR</span><span class="fu">::</span><span class="va"><a href="clinical_breakpoints.html">clinical_breakpoints</a></span>,</span>
 <span>  include_screening <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_include_screening"</span>, <span class="cn">FALSE</span><span class="op">)</span>,</span>
-<span>  include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span></span>
+<span>  include_PKPD <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_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
+<span>  ecoff <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_ecoff"</span>, <span class="cn">FALSE</span><span class="op">)</span></span>
 <span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">sir_interpretation_history</span><span class="op">(</span>clean <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
@@ -228,9 +231,9 @@ All breakpoints used for interpretation are publicly available in the clinical_b
     </div>
     <div class="section level2">
     <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
-    <p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2013-2022, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
+    <p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
-<li><p><strong>M100 Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2013-2022, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
+<li><p><strong>M100 Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2023, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
-<li><p><strong>Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2013-2022, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
+<li><p><strong>Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2023, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/clinical_breakpoints" class="external-link">https://www.eucast.org/clinical_breakpoints</a>.</p></li>
 </ul></div>
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
@@ -255,7 +258,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
 
 
 <dt>guideline</dt>
-<dd><p>defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2013-2022) and CLSI (2013-2022), see <em>Details</em>.</p></dd>
+<dd><p>defaults to EUCAST 2023 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2023) and CLSI (2011-2023), see <em>Details</em>.</p></dd>
 
 
 <dt>uti</dt>
@@ -282,6 +285,10 @@ All breakpoints used for interpretation are publicly available in the clinical_b
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_include_PKPD</a></code>.</p></dd>
 
 
+<dt>ecoff</dt>
+<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that ECOFF (Epidemiological Cut-Off) values must be used <strong>instead</strong> of other clinical breakpoints - the default is <code>FALSE</code>. Can also be set with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_ecoff</a></code>.</p></dd>
+
+
 <dt>col_mo</dt>
 <dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 
@@ -323,8 +330,8 @@ All breakpoints used for interpretation are publicly available in the clinical_b
 <h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
 
 
-<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022).</p>
+<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023).</p>
-<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2022"</code> or <code>"CLSI 2022"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
+<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2023"</code> or <code>"CLSI 2023"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
 <p>You can set the default guideline with the <a href="AMR-options.html">package option</a> <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
 <p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a>  <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>  <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI 2018"</span>)</span>
@@ -344,7 +351,7 @@ All breakpoints used for interpretation are publicly available in the clinical_b
 <h3 id="machine-readable-clinical-breakpoints">Machine-Readable Clinical Breakpoints<a class="anchor" aria-label="anchor" href="#machine-readable-clinical-breakpoints"></a></h3>
 
 
-<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 18 271 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
+<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 42 599 rows and 12 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
 </div>
 
 <div class="section">
@@ -524,19 +531,24 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'AMP' (ampicillin) according to EUCAST</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'CIP' (ciprofloxacin) according to</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      - assuming body site 'Non-meningitis'.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'GEN' (gentamicin) according</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of column 'TOB' (tobramycin) according</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
@@ -551,16 +563,16 @@ 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> 2023-05-27 <span style="color: #949494;">08:50:58</span>     1 TOB      TOB          Escherichia… B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-06-22 <span style="color: #949494;">13:16:45</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> 2023-05-27 <span style="color: #949494;">08:50:58</span>     1 GEN      GEN          Escherichia… B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-06-22 <span style="color: #949494;">13:16:45</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> 2023-05-27 <span style="color: #949494;">08:50:57</span>     1 CIP      CIP          Escherichia… B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-06-22 <span style="color: #949494;">13:16:44</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> 2023-05-27 <span style="color: #949494;">08:50:57</span>     1 AMP      AMP          Escherichia… B_[ORD]_ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-06-22 <span style="color: #949494;">13:16:43</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> 2023-05-27 <span style="color: #949494;">08:50:52</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;"> 5</span> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-05-27 <span style="color: #949494;">08:50:52</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;"> 6</span> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-05-27 <span style="color: #949494;">08:50:52</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;"> 7</span> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-05-27 <span style="color: #949494;">08:50:52</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;"> 8</span> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-05-27 <span style="color: #949494;">08:50:52</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;"> 9</span> 2023-06-22 <span style="color: #949494;">13:16:36</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> 2023-05-27 <span style="color: #949494;">08:50:52</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;">10</span> 2023-06-22 <span style="color: #949494;">13:16:36</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>
@@ -573,7 +585,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><span>  guideline <span class="op">=</span> <span class="st">"EUCAST"</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> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for ampicillin (AMP) in Streptococcus</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      pneumoniae - assuming body site 'Non-meningitis'.</span>
@@ -587,7 +599,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><span>  guideline <span class="op">=</span> <span class="st">"EUCAST"</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> =&gt; Interpreting disk diffusion zones of 'ampicillin' (AMP) according to</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</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] R</span>
@@ -623,91 +635,121 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMP</span><span class="op">:</span><span class="va">TOB</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</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> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      - assuming body site 'Non-meningitis'.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      - assuming body site 'Non-meningitis'.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      - assuming body site 'Non-meningitis'.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      - assuming body site 'Non-meningitis'.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      - assuming body site 'Non-meningitis'.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) based on column</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    'microorganism' according to EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for ampicillin (AMP) in</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      - assuming body site 'Non-meningitis'.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for gentamicin (GEN) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    • Breakpoints for UTI and non-UTI available for tobramycin (TOB) in</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      Escherichia coli - assuming non-UTI. Use argument uti to set which</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>      isolates are from urine. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2023...</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>
@@ -716,22 +758,24 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   infection.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   Use as.sir(uti = FALSE) to prevent this.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of column 'NIT' (nitrofurantoin) according to</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2023...</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in as.sir(): interpretation of nitrofurantoin (NIT) is only available for</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (uncomplicated) urinary tract infections (UTI) for some microorganisms,</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> thus assuming uti = TRUE. See ?as.sir.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  * WARNING *</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'AMP' (ampicillin) according to EUCAST</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting MIC values of 'CIP' (ciprofloxacin) according to EUCAST</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    2023...</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>  Note:</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>      - assuming body site 'Non-meningitis'.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'GEN' (gentamicin) according to</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Interpreting disk diffusion zones of 'TOB' (tobramycin) according to</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2022...</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>    EUCAST 2023...</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>  OK.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      microorganism AMP CIP GEN TOB ERY</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli   S   I   S   S   R</span>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

reference/clinical_breakpoints.html

@@ -1,5 +1,5 @@
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@@ -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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -160,7 +160,7 @@
     </div>
 
     <div class="ref-description section level2">
-    <p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2013-2022) and CLSI (2013-2022). Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
+    <p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2023) and CLSI (2011-2023). Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
     </div>
 
     <div class="section level2">
@@ -170,7 +170,7 @@
 
     <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 18 271 observations and 11 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 42 599 observations and 12 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
 <li><p><code>method</code><br> Either "DISK" or "MIC"</p></li>
 <li><p><code>site</code><br> Body site, e.g. "Oral" or "Respiratory"</p></li>
 <li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
@@ -180,11 +180,13 @@
 <li><p><code>disk_dose</code><br> Dose of the used disk diffusion method</p></li>
 <li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
 <li><p><code>breakpoint_R</code><br> Highest MIC value or lowest number of millimetres that leads to "R"</p></li>
+<li><p><code>ecoff</code><br> Epidemiological cut-off (ECOFF) value, used in antimicrobial susceptibility testing to differentiate between wild-type and non-wild-type strains of bacteria or fungi (use <code><a href="as.sir.html">as.sir(..., ecoff = TRUE)</a></code> to interpret raw data using ECOFF values)</p></li>
 <li><p><code>uti</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the rule applies to a urinary tract infection (UTI)</p></li>
 </ul></div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
+    <p>Clinical breakpoints are validated through <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>.</p>
+<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
 <p>They <strong>allow for machine reading EUCAST and CLSI guidelines</strong>, which is almost impossible with the MS Excel and PDF files distributed by EUCAST and CLSI.</p>
     </div>
     <div class="section level2">
@@ -195,21 +197,22 @@
     <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">clinical_breakpoints</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 18,271 × 11</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 42,599 × 12</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    guideline   method site  mo               rank_index ab   ref_tbl   disk_dose</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    guideline   method site  mo           rank_index ab   ref_tbl       disk_dose</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;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;dbl&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;chr&gt;</span>    </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;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;dbl&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;chr&gt;</span>    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2022 MIC    <span style="color: #BB0000;">NA</span>    F_ASPRG_MGTS              2 AMB  Aspergil… <span style="color: #BB0000;">NA</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    F_ASPRG_MGTS          2 AMB  Aspergillus   <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2022 MIC    <span style="color: #BB0000;">NA</span>    F_ASPRG_NIGR              2 AMB  Aspergil… <span style="color: #BB0000;">NA</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    F_ASPRG_NIGR          2 AMB  Aspergillus   <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2022 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_ALBC              2 AMB  Candida   <span style="color: #BB0000;">NA</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_ALBC          2 AMB  Candida       <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2022 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_DBLN              2 AMB  Candida   <span style="color: #BB0000;">NA</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_DBLN          2 AMB  Candida       <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2022 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_GLBR              2 AMB  Candida   <span style="color: #BB0000;">NA</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_GLBR          2 AMB  Candida       <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2022 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_KRUS              2 AMB  Candida   <span style="color: #BB0000;">NA</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_KRUS          2 AMB  Candida       <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2022 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_PRPS              2 AMB  Candida   <span style="color: #BB0000;">NA</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_PRPS          2 AMB  Candida       <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2022 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_TRPC              2 AMB  Candida   <span style="color: #BB0000;">NA</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    F_CANDD_TRPC          2 AMB  Candida       <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2022 MIC    <span style="color: #BB0000;">NA</span>    F_CRYPT_NFRM              2 AMB  Candida   <span style="color: #BB0000;">NA</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    F_CRYPT_NFRM          2 AMB  Candida       <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2022 DISK   <span style="color: #BB0000;">NA</span>    B_[ORD]_ENTRBCTR          5 AMC  Enteroba… 20ug/10ug</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2023 MIC    <span style="color: #BB0000;">NA</span>    B_ANAER-NEG           6 AMC  Gram-negativ… <span style="color: #BB0000;">NA</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 18,261 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 42,589 more rows</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 3 more variables: breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, uti &lt;lgl&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4 more variables: breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, ecoff &lt;dbl&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   uti &lt;lgl&gt;</span></span>
 </code></pre></div>
     </div>
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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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -170,7 +170,7 @@
 
     <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 336 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 503 observations and 9 variables:</p><ul><li><p><code>ab</code><br> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
 <li><p><code>name</code><br> Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO</p></li>
 <li><p><code>type</code><br> Type of the dosage, either "high_dosage", "standard_dosage", or "uncomplicated_uti"</p></li>
 <li><p><code>dose</code><br> Dose, such as "2 g" or "25 mg/kg"</p></li>
@@ -178,23 +178,17 @@
 <li><p><code>administration</code><br> Route of administration, either "im", "iv", or "oral"</p></li>
 <li><p><code>notes</code><br> Additional dosage notes</p></li>
 <li><p><code>original_txt</code><br> Original text in the PDF file of EUCAST</p></li>
-<li><p><code>eucast_version</code><br> Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply</p></li>
+<li><p><code>eucast_version</code><br> Version number of the EUCAST Clinical Breakpoints guideline to which these dosages apply, either 13, 12, or 11</p></li>
 </ul></div>
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>This data set is based on <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">'EUCAST Clinical Breakpoint Tables' v12.0</a> (2022) and <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">'EUCAST Clinical Breakpoint Tables' v11.0</a> (2021).</p><div class="section">
+    <p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
-<h3 id="direct-download">Direct download<a class="anchor" aria-label="anchor" href="#direct-download"></a></h3>
-
-
-<p>Like all data sets in this package, this data set is publicly available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. Please visit <a href="https://msberends.github.io/AMR/articles/datasets.html">our website for the download links</a>. The actual files are of course available on <a href="https://github.com/msberends/AMR/tree/main/data-raw" class="external-link">our GitHub repository</a>.</p>
-</div>
-
     </div>
 
     <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">dosage</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 336 × 9</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 503 × 9</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    ab   name            type  dose  dose_times administration notes original_txt</span>
 <span class="r-out co"><span class="r-pr">#&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;chr&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;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> AMK  Amikacin        stan… 25-3…          1 iv             <span style="color: #949494;">""</span>    25-30 mg/kg…</span>
@@ -207,7 +201,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMC  Amoxicillin/cl… stan… 1 g …          3 iv             <span style="color: #949494;">""</span>    (1 g amoxic…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC  Amoxicillin/cl… high… 0.87…          3 oral           <span style="color: #949494;">""</span>    (0.875 g am…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AMC  Amoxicillin/cl… stan… 0.5 …          3 oral           <span style="color: #949494;">""</span>    (0.5 g amox…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 326 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 493 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 1 more variable: eucast_version &lt;dbl&gt;</span></span>
 </code></pre></div>
     </div>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -176,13 +176,14 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
 <span>  verbose <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  version_breakpoints <span class="op">=</span> <span class="fl">12</span>,</span>
 <span>  version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
+<span>  version_resistant_phenotypes <span class="op">=</span> <span class="fl">1.2</span>,</span>
 <span>  ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>,</span>
 <span>  only_sir_columns <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  custom_rules <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">12</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">13</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -221,11 +222,15 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 
 
 <dt>version_breakpoints</dt>
-<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "12.0", "11.0", or "10.0".</p></dd>
+<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be "13.0", "12.0", "11.0", or "10.0".</p></dd>
 
 
 <dt>version_expertrules</dt>
-<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2", or "3.1".</p></dd>
+<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be "3.3", "3.2", or "3.1".</p></dd>
+
+
+<dt>version_resistant_phenotypes</dt>
+<dd><p>the version number to use for the EUCAST Expected Resistant Phenotypes. Can be "1.2".</p></dd>
 
 
 <dt>ampc_cephalosporin_resistance</dt>
@@ -381,7 +386,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"tobra"</span>, <span class="st">"genta"</span>, <span class="st">"cipro"</span><span class="op">)</span>, <span class="st">"iv"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Dosages for antimicrobial drugs, as meant for 'EUCAST Clinical Breakpoint</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   Tables' v12.0 (2022). This note will be shown once per session.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   Tables' v13.0 (2023). This note will be shown once per session.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 4</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ab   name          standard_dosage  high_dosage </span>
 <span class="r-out co"><span class="r-pr">#&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;chr&gt;</span>            <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       </span>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -263,27 +263,29 @@
 <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">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 34 32 18 15 11  8 45 29  7  7 46 31 27 44 20 38 47 11 42  3 46  4 13 37  4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 12 24 43 42 22 36 23 19  6 36 30 18  2 25 41 27 13 45 31 16  4  6 21 29 18</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26]  9 35  5 46 26 44 40 16 20 21 20 24 27 14 41 20 41 28 27 42 24 22 35 30 22</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 10 29 30 35 28  9  2 14 31 38 24 20 33 37 35 33  9 46 23  1 44 30  2 48  3</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 16 44 25 35 30  6 12 13 38  8 33 46 29  6 23  6 34 47 11  1 16 40 27 46  5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 41 17 31 40 36 40 17 43 42 38  8 36 40  3 47 29 34 37 10 43  6  7 22 32 10</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 10  2 39 48  4 23 46 25 36 19 12 43 17 22  9 47 11  2 45 17 15 42 37 28  8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 31 12 14 34 39  1 35 42 45 26 11 38  5 15  3 28 39 45  8 15  9  7  1 41 32</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</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  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE FALSE  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 FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37]  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37]  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49]  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49]  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61]  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61]  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85]  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85]  TRUE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE 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> <span style="color: #949494;"># A tibble: 3 × 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>   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: #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> 2002-08-19 A49852     70 M      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-12-13 285137     78 F      ICU       B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-11-11 D80753     74 F      Outpatie… B_STPHY_CONS R     NA    R     R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2003-01-08 783073     83 M      Clinical  B_STPHY_CONS R     NA    S     NA   </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>
@@ -317,19 +319,19 @@
 <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 [99]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, condition [98]</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> 006827  2009-07-24 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 005088  2007-08-22 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 021648  2004-08-21 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 008268  2007-02-20 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 023456  2011-04-25 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 097186  2015-10-28 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 032343  2003-06-09 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 0C0688  2014-09-05 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 074321  2015-09-20 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 0DBB93  2009-05-08 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0D7D34  2011-03-19 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0E2483  2007-05-29 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 0E2483  2007-08-10 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 0F9638  2014-09-22 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 164466  2009-10-07 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 12CB58  2017-09-23 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 16DC39  2015-11-19 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1343BD  2016-04-02 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 189564  2009-12-22 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 141061  2014-10-22 B         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>
@@ -343,19 +345,19 @@
 <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 [97]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [95]</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 2009-07-24 006827          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2007-08-22 005088          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2004-08-21 021648          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU      2007-02-20 008268          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-04-25 023456          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2015-10-28 097186          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</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 2014-09-05 0C0688          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU      2015-09-20 074321          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2009-05-08 0DBB93          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2011-03-19 0D7D34          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2007-05-29 0E2483          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU      2007-08-10 0E2483          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2014-09-22 0F9638          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2009-10-07 164466          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU      2017-09-23 12CB58          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU      2015-11-19 16DC39          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2016-04-02 1343BD          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU      2009-12-22 189564          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2014-10-22 141061          1 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>
@@ -371,9 +373,9 @@
 <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           60             13            37            45</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical           67             13            41            51</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                31             12            22            27</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                23             10            19            21</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          6              3             5             5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          5              5             5             5</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>
@@ -403,18 +405,18 @@
 <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 [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>    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: #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> 451000  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 838694  B_ACNTB      Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 741413  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 699321  B_STPHY_CONS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 8BBC46  B_ENTRC_FACM Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C6F894  B_STPHY_EPDR Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F09078  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D10538  B_ESCHR_COLI ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> C56827  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 164466  B_STPHY_CONS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> D27410  B_BCTRD_FRGL Outpatient TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 0C0688  B_ESCHR_COLI Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D38469    UNKNOWN    ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 317826  B_ESCHR_COLI ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 023456  B_PROTS_MRBL Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 195736  B_STPHY_AURS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2FC253  B_ESCHR_COLI ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 288260  B_STPHY_EPDR ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EB1709  B_STRPT_PNMN ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 141061  B_STPHY_HMNS Clinical 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>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -413,7 +413,7 @@
           
           <code><a href="microorganisms.codes.html">microorganisms.codes</a></code> 
         </dt>
-        <dd>Data Set with 4 909 Common Microorganism Codes</dd>
+        <dd>Data Set with 4 942 Common Microorganism Codes</dd>
       </dl><dl><dt>
           
           <code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> 

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -199,9 +199,9 @@
     <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] 3.010824</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.980956</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] 0.1430003</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02318823</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -218,30 +218,30 @@
     <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 R I S I I S S</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] I R I I R R R I R I</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] -0.4743416 -0.4743416  1.8973666  1.8973666 -0.4743416 -0.4743416</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] -0.4743416 -0.4743416 -0.4743416 -0.4743416</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] 8     &gt;=16  0.002 &gt;=16  0.025 &gt;=16  0.002 2     2     2    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 256   0.01  4     64    8     1     1     0.002 0.125 256  </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]  0.6738475  0.8649910 -1.6133339  0.8649910 -0.9168346  0.8649910</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  1.2331707 -1.2886091  0.1999266  0.8887560  0.3721339 -0.1444882</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -1.6133339  0.2915606  0.2915606  0.2915606</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.1444882 -1.6884622 -0.6611102  1.2331707</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]  0.6738475  0.8649910 -1.6133339  0.8649910 -0.9168346  0.8649910</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  1.2331707 -1.2886091  0.1999266  0.8887560  0.3721339 -0.1444882</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -1.6133339  0.2915606  0.2915606  0.2915606</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.1444882 -1.6884622 -0.6611102  1.2331707</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] 39 15 22 38 19 50 29 46 40 18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 25  6 45 23 39 45 20 49  8 43</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]  0.5869812 -1.3167417 -0.7614892  0.5076595 -0.9994545  1.4595209</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.3319640 -1.5220235  0.9207303 -0.4572334  0.5449220  0.9207303</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.2062367  1.1422338  0.6663030 -1.0787763</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.6451375  1.1712691 -1.3967541  0.7954608</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>
@@ -251,22 +251,22 @@
 <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>    id amox cipr  gent   tobr</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    I   17    8    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    R   27     1    0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    S   31    2    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    R   29     1    0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    R   19   16    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    I   19 &lt;=0.5      4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    S   18    8    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    I   27     1 &lt;=0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   19   16    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   30 &lt;=0.5      4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    I   31   16    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    I   22     1      1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    I   24  &lt;=1    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    I   26     1      1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    S   24  &lt;=1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    R   22     1      2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   22    4    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    I   21     4    0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   20    2  0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   29     1 &lt;=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] -0.06628516  0.31654289  0.46727798 -0.49122694 -0.05027119  0.77969806</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.27087972  0.39969323 -0.52646026 -0.38265093  0.18201405 -0.36586924</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.42081207 -0.65798290  0.54387830 -0.42081897</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.10824222  0.28766141  0.01268871  0.23028550</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>
@@ -282,17 +282,17 @@
 <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>    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   19   16    2   0.46727798 0.00000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    I   19 &lt;=0.5      4  -0.52646026  0.0000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   I    R   22    4    4   0.54387830 0.07660032</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   D    I   27     1 &lt;=0.25  -0.38265093  0.1438093</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   B    S   31    2    4   0.31654289 0.15073509</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   F    I   22     1      1  -0.36586924  0.1605910</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   F    I   31   16    4   0.77969806 0.31242008</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   G    I   26     1      1  -0.10824222  0.4182180</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   19   16    2  -0.05027119 0.51754917</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   I    I   21     4    0.5   0.01268871  0.5391490</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   A    I   17    8    4  -0.06628516 0.53356314</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   E    S   30 &lt;=0.5      4   0.18201405  0.7084743</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    I   24  &lt;=1    2  -0.42081207 0.88809005</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   J    R   29     1 &lt;=0.25   0.23028550  0.7567458</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   J    R   20    2  0.5  -0.42081897 0.88809695</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   A    R   27     1    0.5   0.27087972  0.7973400</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   D    S   18    8    1  -0.49122694 0.95850492</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   H    R   22     1      2   0.28766141  0.8141217</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  H    S   24  &lt;=1    1  -0.65798290 1.12526088</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  B    R   29     1    0.5   0.39969323  0.9261535</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>

reference/microorganisms.codes.html

@@ -1,5 +1,5 @@
 <!DOCTYPE html>
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@@ -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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">
@@ -154,7 +154,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
   <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>Data Set with 4 909 Common Microorganism Codes</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Data Set with 4 942 Common Microorganism Codes</h1>
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
       <div class="d-none name"><code>microorganisms.codes.Rd</code></div>
     </div>
@@ -170,7 +170,7 @@
 
     <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 4 909 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 4 942 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
 <li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
 </ul></div>
     <div class="section level2">
@@ -185,7 +185,7 @@
     <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.codes</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4,909 × 2</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4,942 × 2</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    code  mo          </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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 1011  B_GRAMP     </span>
@@ -198,7 +198,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 1100  B_STRPT     </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101  B_STRPT_VIRI</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102  B_STRPT_HAEM</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,899 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 4,932 more rows</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span>
 <span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</span>, <span class="op">]</span></span></span>

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">

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="">2.0.0.9023</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9024</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">