Built site for AMR@2.1.1.9227: d77ad6b

2025-07-27 14:27:53 +02:00 · 2025-03-27 14:46:09 +00:00
parent 5c912497a1
commit 1b88841880
82 changed files with 336 additions and 285 deletions
--- a/articles/AMR.html
+++ b/articles/AMR.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
@ -93,7 +93,7 @@
 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 20 March 2025.</p>
+generated on 27 March 2025.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@ -149,21 +149,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2025-03-20</td>
+<td align="center">2025-03-27</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">2025-03-20</td>
+<td align="center">2025-03-27</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">2025-03-20</td>
+<td align="center">2025-03-27</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -288,12 +288,12 @@ taxonomic codes. Let’s check this:</p>
 <span><span class="co"><span style="font-style: italic;">#&gt;               dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</span>)</span></span>
 <span><span class="co">#&gt; <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
 <span><span class="co">#&gt; "K. pneumoniae" -&gt; <span style="font-weight: bold; font-style: italic;">Klebsiella pneumoniae</span> (B_KLBSL_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.786</span>)</span></span>
-<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Klebsiella pneumoniae ozaenae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
-<span><span class="co"><span style="font-style: italic;">#&gt;               pneumoniae pneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.688</span>), <span style="font-style: italic;">Klebsiella pneumoniae rhinoscleromatis</span></span></span>
-<span><span class="co"><span style="color: #0000BB;">#&gt;               (</span><span style="color: #080808; background-color: #FFFF87;">0.658</span>), <span style="font-style: italic;">Klebsiella pasteurii</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.500</span>), <span style="font-style: italic;">Klebsiella planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.500</span>),</span></span>
-<span><span class="co">#&gt;               <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.400</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicale</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.386</span>),</span></span>
-<span><span class="co">#&gt;               <span style="font-style: italic;">Kluyveromyces pseudotropicalis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.363</span>), <span style="font-style: italic;">Kosakonia pseudosacchari</span></span></span>
-<span><span class="co"><span style="color: #0000BB;">#&gt;               (</span><span style="color: #080808; background-color: #FFAFAF;">0.361</span>), and <span style="font-style: italic;">Kluyveromyces pseudotropicalis pseudotropicalis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.361</span>)</span></span>
+<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Klebsiella pneumoniae</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
+<span><span class="co"><span style="font-style: italic;">#&gt;               pneumoniae ozaenae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae pneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.688</span>),</span></span>
+<span><span class="co">#&gt;               <span style="font-style: italic;">Klebsiella pneumoniae rhinoscleromatis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.658</span>), <span style="font-style: italic;">Klebsiella pasteurii</span></span></span>
+<span><span class="co"><span style="color: #0000BB;">#&gt;               (</span><span style="color: #080808; background-color: #FFAFAF;">0.500</span>), <span style="font-style: italic;">Klebsiella planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.500</span>), <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.400</span>),</span></span>
+<span><span class="co">#&gt;               <span style="font-style: italic;">Kluyveromyces pseudotropicale</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.386</span>), <span style="font-style: italic;">Kluyveromyces pseudotropicalis</span></span></span>
+<span><span class="co"><span style="color: #0000BB;">#&gt;               (</span><span style="color: #080808; background-color: #FFAFAF;">0.363</span>), and <span style="font-style: italic;">Kosakonia pseudosacchari</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.361</span>)</span></span>
 <span><span class="co">#&gt; <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
 <span><span class="co">#&gt; "S. aureus" -&gt; <span style="font-weight: bold; font-style: italic;">Staphylococcus aureus</span> (B_STPHY_AURS, <span style="color: #080808; background-color: #FFFF87;">0.690</span>)</span></span>
 <span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Staphylococcus aureus aureus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>), <span style="font-style: italic;">Staphylococcus</span></span></span>
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
--- a/articles/AMR_with_tidymodels.html
+++ b/articles/AMR_with_tidymodels.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
@ -133,7 +133,7 @@ package.</p>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>          <span class="co"># For AMR data analysis</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span>   <span class="co"># For machine learning workflows, and data manipulation (dplyr, tidyr, ...)</span></span>
 <span><span class="co">#&gt; ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.3.0 ──</span></span>
-<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom       </span> 1.0.7     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.2.0</span></span>
+<span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom       </span> 1.0.7     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.2.1</span></span>
 <span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials       </span> 1.4.0     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample     </span> 1.2.1</span></span>
 <span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dplyr       </span> 1.1.4     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble      </span> 3.2.1</span></span>
 <span><span class="co">#&gt; <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">ggplot2     </span> 3.5.1     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr       </span> 1.3.1</span></span>
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
@ -151,13 +151,13 @@ antimicrobials:</p>
 <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">"Klebsiella"</span>, <span class="st">"Escherichia"</span><span class="op">)</span>,</span>
 <span>  <span class="st">"ampicillin"</span></span>
 <span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1]  TRUE FALSE</span></span>
+<span><span class="co">#&gt; [1] FALSE FALSE</span></span>
 <span></span>
 <span><span class="fu"><a href="../reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span></span>
 <span>  <span class="st">"Klebsiella"</span>,</span>
 <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">"ampicillin"</span>, <span class="st">"kanamycin"</span><span class="op">)</span></span>
 <span><span class="op">)</span></span>
-<span><span class="co">#&gt; [1]  TRUE FALSE</span></span></code></pre></div>
+<span><span class="co">#&gt; [1] FALSE FALSE</span></span></code></pre></div>
 <p>EUCAST rules can not only be used for correction, they can also be
 used for filling in known resistance and susceptibility based on results
 of other antimicrobials drugs. This process is called <em>interpretive
@ -265,7 +265,7 @@ reading</em>, is basically a form of imputation, and is part of the
 <td align="left">Staphylococcus aureus</td>
 <td align="center">-</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">-</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -275,7 +275,7 @@ reading</em>, is basically a form of imputation, and is part of the
 <td align="left">Enterococcus faecalis</td>
 <td align="center">-</td>
 <td align="center">-</td>
-<td align="center">R</td>
+<td align="center">-</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
--- a/articles/MDR.html
+++ b/articles/MDR.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
@ -175,8 +175,8 @@ will help reading it if your console supports colours.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">custom</span></span>
 <span><span class="co">#&gt; A set of custom MDRO rules:</span></span>
-<span><span class="co">#&gt;   1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">CIP</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #080808;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type A</span></span></span>
-<span><span class="co">#&gt;   2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">ERY</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FF5F5F;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #080808;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type B</span></span></span>
+<span><span class="co">#&gt;   1. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">CIP</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFAFAF;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #080808;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type A</span></span></span>
+<span><span class="co">#&gt;   2. <span style="font-weight: bold;">If </span><span style="color: #0000BB;">ERY</span><span style="color: #080808;"> is </span><span style="color: #080808; background-color: #FFAFAF;"> R </span><span style="color: #080808; font-weight: bold;"> and </span><span style="color: #0000BB;">age</span><span style="color: #080808;"> is higher than </span><span style="color: #0000BB;">60</span><span style="font-weight: bold;"> then: </span><span style="color: #BB0000;">Elderly Type B</span></span></span>
 <span><span class="co">#&gt;   3. <span style="font-weight: bold;">Otherwise: </span><span style="color: #BB0000;">Negative</span></span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; Unmatched rows will return <span style="color: #BB0000;">NA</span>.</span></span>
--- a/articles/PCA.html
+++ b/articles/PCA.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
--- a/articles/datasets.html
+++ b/articles/datasets.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
@ -82,7 +82,7 @@
  <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">20 March 2025</h4>
+            <h4 data-toc-skip class="date">27 March 2025</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="d-none name"><code>datasets.Rmd</code></div>
@ -103,7 +103,7 @@ of the data sets look like.</p>
 <h2 id="microorganisms-full-microbial-taxonomy">
 <code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
 </h2>
-<p>A data set with 78 678 rows and 26 columns, containing the following
+<p>A data set with 78 679 rows and 26 columns, containing the following
 column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
 <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
 <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@ -114,7 +114,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
 <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 13 March 2025 13:30:14 UTC. Find more info
+<p>It was last updated on 26 March 2025 16:19:17 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@ -134,10 +134,10 @@ Feather file</a> (8.3 MB)<br>
 Parquet file</a> (3.8 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">IBM
-SPSS Statistics data file</a> (29 MB)<br>
+SPSS Statistics data file</a> (28.4 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
-DTA file</a> (92.5 MB)</li>
+DTA file</a> (89.5 MB)</li>
 </ul>
 <p><strong>NOTE: The exported files for SPSS and Stata contain only the
 first 50 SNOMED codes per record, as their file size would otherwise
@ -196,7 +196,7 @@ Set Name ‘Microorganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a hre
 </tr>
 <tr class="even">
 <td align="center">Bacteria</td>
-<td align="center">39 248</td>
+<td align="center">39 249</td>
 </tr>
 <tr class="odd">
 <td align="center">Chromista</td>
@ -1033,34 +1033,34 @@ use.</p>
 <code>intrinsic_resistant</code>: Intrinsic Bacterial
 Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
 </h2>
-<p>A data set with 301 583 rows and 2 columns, containing the following
+<p>A data set with 196 665 rows and 2 columns, containing the following
 column names:<br><em>mo</em> and <em>ab</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
+<p>It was last updated on 27 March 2025 14:20:22 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.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/intrinsic_resistant.rds" class="external-link">original
-R Data Structure (RDS) file</a> (0.1 MB)<br>
+R Data Structure (RDS) file</a> (33 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">tab-separated
-text file</a> (10.9 MB)<br>
+text file</a> (7.3 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Microsoft
-Excel workbook</a> (3 MB)<br>
+Excel workbook</a> (2.1 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.feather" class="external-link">Apache
-Feather file</a> (2.5 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/intrinsic_resistant.parquet" class="external-link">Apache
-Parquet file</a> (0.3 MB)<br>
+Parquet file</a> (66 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">IBM
-SPSS Statistics data file</a> (16.2 MB)<br>
+SPSS Statistics data file</a> (10.7 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata
-DTA file</a> (25 MB)</li>
+DTA file</a> (15.6 MB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-4">Source<a class="anchor" aria-label="anchor" href="#source-4"></a>
@ -1118,115 +1118,115 @@ v3.3</a> (2021).</p>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Cadazolid</td>
+<td align="center">Bleomycin</td>
 </tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
+<td align="center">Cadazolid</td>
+</tr>
+<tr class="even">
+<td align="center">Enterobacter cloacae</td>
 <td align="center">Cefadroxil</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Cefalexin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Cefalotin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Cefazolin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Cefoxitin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Clarithromycin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Clindamycin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Cycloserine</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Dalbavancin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Dirithromycin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Erythromycin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Flurithromycin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Fusidic acid</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Gamithromycin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Josamycin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Kitasamycin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Lincomycin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Linezolid</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Meleumycin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Midecamycin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Miocamycin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Nafithromycin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Norvancomycin</td>
 </tr>
-<tr class="even">
+<tr class="odd">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Oleandomycin</td>
 </tr>
-<tr class="odd">
+<tr class="even">
 <td align="center">Enterobacter cloacae</td>
 <td align="center">Oritavancin</td>
 </tr>
-<tr class="even">
-<td align="center">Enterobacter cloacae</td>
-<td align="center">Pirlimycin</td>
-</tr>
 <tr class="odd">
 <td align="center">Enterobacter cloacae</td>
-<td align="center">Primycin</td>
+<td align="center">Pirlimycin</td>
 </tr>
 <tr class="even">
 <td align="center">Enterobacter cloacae</td>
@ -1985,24 +1985,24 @@ reality and can be used to practise AMR data analysis.</p>
 <code>microorganisms.groups</code>: Species Groups and
 Microbiological Complexes<a class="anchor" aria-label="anchor" href="#microorganisms-groups-species-groups-and-microbiological-complexes"></a>
 </h2>
-<p>A data set with 521 rows and 4 columns, containing the following
+<p>A data set with 534 rows and 4 columns, containing the following
 column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
 <em>mo_name</em>.</p>
 <p>This data set is in R available as
 <code>microorganisms.groups</code>, after you load the <code>AMR</code>
 package.</p>
-<p>It was last updated on 29 September 2024 20:17:56 UTC. Find more info
+<p>It was last updated on 26 March 2025 16:19:17 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.groups.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.rds" class="external-link">original
-R Data Structure (RDS) file</a> (5 kB)<br>
+R Data Structure (RDS) file</a> (6 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.txt" class="external-link">tab-separated
-text file</a> (49 kB)<br>
+text file</a> (50 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.xlsx" class="external-link">Microsoft
-Excel workbook</a> (19 kB)<br>
+Excel workbook</a> (20 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.feather" class="external-link">Apache
 Feather file</a> (19 kB)<br>
@ -2011,10 +2011,10 @@ Feather file</a> (19 kB)<br>
 Parquet file</a> (13 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.sav" class="external-link">IBM
-SPSS Statistics data file</a> (63 kB)<br>
+SPSS Statistics data file</a> (65 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.groups.dta" class="external-link">Stata
-DTA file</a> (81 kB)</li>
+DTA file</a> (83 kB)</li>
 </ul>
 <div class="section level3">
 <h3 id="source-8">Source<a class="anchor" aria-label="anchor" href="#source-8"></a>
--- a/articles/index.html
+++ b/articles/index.html
@ -7,7 +7,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
--- a/articles/resistance_predict.html
+++ b/articles/resistance_predict.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">
--- a/articles/welcome_to_AMR.html
+++ b/articles/welcome_to_AMR.html
@ -31,7 +31,7 @@

    <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="">2.1.1.9224</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9227</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">