Built site for AMR@3.0.1.9091: aebad2a

404.html

@@ -31,7 +31,7 @@
 
     <a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -86,7 +86,7 @@ Content not found. Please use links in the navbar.
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

CLAUDE.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -134,6 +134,26 @@ _pkgdown.yml    # pkgdown website configuration</code></pre>
 <code>ggplot_sir.R</code> / <code>ggplot_pca.R</code> / <code>plotting.R</code> — visualisation functions</li>
 </ul></div>
 <div class="section level2">
+<h2 id="code-style">Code Style<a class="anchor" aria-label="anchor" href="#code-style"></a></h2>
+<p>Follow the <a href="https://style.tidyverse.org/" class="external-link">tidyverse style guide</a> precisely. Key rules:</p>
+<ul><li>2-space indentation; no tabs</li>
+<li>
+<code>&lt;-</code> for assignment, not <code>=</code>
+</li>
+<li>Spaces around all binary operators and after commas; no spaces inside parentheses</li>
+<li>When a function call must break across lines, place the first argument on a new line indented by 2 spaces, and put the closing <code>)</code> on its own line — <strong>never align arguments to the opening parenthesis</strong> (no hanging/forced mid-line indentation)</li>
+</ul><div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="co"># good</span></span>
+<span><span class="fu">stop_</span><span class="op">(</span></span>
+<span>  <span class="st">"some long message part one "</span>,</span>
+<span>  <span class="st">"part two"</span></span>
+<span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># bad — forces indentation to match the opening parenthesis</span></span>
+<span><span class="fu">stop_</span><span class="op">(</span><span class="st">"some long message part one "</span>,</span>
+<span>      <span class="st">"part two"</span><span class="op">)</span></span></code></pre></div>
+</div>
+<div class="section level2">
 <h2 id="custom-s3-classes">Custom S3 Classes<a class="anchor" aria-label="anchor" href="#custom-s3-classes"></a></h2>
 <p>The package defines five S3 classes with full print/format/plot/vctrs support:</p>
 <table class="table"><thead><tr><th>Class</th>
@@ -181,7 +201,7 @@ _pkgdown.yml    # pkgdown website configuration</code></pre>
 <div class="section level2">
 <h2 id="zero-dependency-design">Zero-Dependency Design<a class="anchor" aria-label="anchor" href="#zero-dependency-design"></a></h2>
 <p>The package has <strong>no <code>Imports</code></strong> in <code>DESCRIPTION</code>. All optional integrations (ggplot2, dplyr, data.table, tidymodels, cli, crayon, etc.) are listed in <code>Suggests</code> and guarded with:</p>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw">if</span> <span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"pkg"</span>, quietly <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span> <span class="va">...</span> <span class="op">}</span></span></code></pre></div>
 <p>Never add packages to <code>Imports</code>. If new functionality requires an external package, add it to <code>Suggests</code> and guard usage appropriately.</p>
 </div>
@@ -222,18 +242,18 @@ _pkgdown.yml    # pkgdown website configuration</code></pre>
 <div class="section level4">
 <h4 id="computing-the-correct-version-number">Computing the correct version number<a class="anchor" aria-label="anchor" href="#computing-the-correct-version-number"></a></h4>
 <p><strong>First, ensure <code>git</code> and <code>gh</code> are installed</strong> — both are required for the version computation and for pushing changes. Install them if missing before doing anything else:</p>
-<div class="sourceCode" id="cb5"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" tabindex="-1"></a><span class="fu">which</span> git <span class="kw">||</span> <span class="ex">apt-get</span> install <span class="at">-y</span> git</span>
-<span id="cb5-2"><a href="#cb5-2" tabindex="-1"></a><span class="fu">which</span> gh   <span class="kw">||</span> <span class="ex">apt-get</span> install <span class="at">-y</span> gh</span>
-<span id="cb5-3"><a href="#cb5-3" tabindex="-1"></a><span class="co"># Also ensure all tags are fetched so git describe works</span></span>
-<span id="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="fu">git</span> fetch <span class="at">--tags</span></span></code></pre></div>
+<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="fu">which</span> git <span class="kw">||</span> <span class="ex">apt-get</span> install <span class="at">-y</span> git</span>
+<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="fu">which</span> gh   <span class="kw">||</span> <span class="ex">apt-get</span> install <span class="at">-y</span> gh</span>
+<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="co"># Also ensure all tags are fetched so git describe works</span></span>
+<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="fu">git</span> fetch <span class="at">--tags</span></span></code></pre></div>
 <p>Then run the following from the repo root to determine the version string to use:</p>
-<div class="sourceCode" id="cb6"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb6-1"><a href="#cb6-1" tabindex="-1"></a><span class="va">currenttag</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0 <span class="kw">|</span> <span class="fu">sed</span> <span class="st">'s/v//'</span><span class="va">)</span></span>
-<span id="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0<span class="va">)</span></span>
-<span id="cb6-3"><a href="#cb6-3" tabindex="-1"></a><span class="va">defaultbranch</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> branch <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-c</span> 3- <span class="kw">|</span> <span class="fu">grep</span> <span class="at">-E</span> <span class="st">'^master$|^main$'</span><span class="va">)</span></span>
-<span id="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="fu">git</span> fetch origin <span class="va">${defaultbranch}</span> <span class="at">--quiet</span></span>
-<span id="cb6-5"><a href="#cb6-5" tabindex="-1"></a><span class="va">currentcommit</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> rev-list <span class="at">--count</span> <span class="va">${currenttagfull}</span>..origin/<span class="va">${defaultbranch})</span></span>
-<span id="cb6-6"><a href="#cb6-6" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span>
-<span id="cb6-7"><a href="#cb6-7" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
+<div class="sourceCode" id="cb7"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="va">currenttag</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0 <span class="kw">|</span> <span class="fu">sed</span> <span class="st">'s/v//'</span><span class="va">)</span></span>
+<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0<span class="va">)</span></span>
+<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a><span class="va">defaultbranch</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> branch <span class="kw">|</span> <span class="fu">cut</span> <span class="at">-c</span> 3- <span class="kw">|</span> <span class="fu">grep</span> <span class="at">-E</span> <span class="st">'^master$|^main$'</span><span class="va">)</span></span>
+<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="fu">git</span> fetch origin <span class="va">${defaultbranch}</span> <span class="at">--quiet</span></span>
+<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a><span class="va">currentcommit</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> rev-list <span class="at">--count</span> <span class="va">${currenttagfull}</span>..origin/<span class="va">${defaultbranch})</span></span>
+<span id="cb7-6"><a href="#cb7-6" tabindex="-1"></a><span class="va">currentversion</span><span class="op">=</span><span class="st">"</span><span class="va">${currenttag}</span><span class="st">.</span><span class="va">$((currentcommit</span> <span class="op">+</span> <span class="dv">9001</span> <span class="op">+</span> <span class="dv">1</span><span class="va">))</span><span class="st">"</span></span>
+<span id="cb7-7"><a href="#cb7-7" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
 <p>The <code>+ 1</code> accounts for the fact that this PR’s squash commit is not yet on the default branch. Set <strong>both</strong> of these files to the resulting version string (and only once per PR, even across multiple commits):</p>
 <ol style="list-style-type: decimal"><li><p><strong><code>DESCRIPTION</code></strong> — the <code>Version:</code> field</p></li>
 <li>
@@ -263,7 +283,7 @@ _pkgdown.yml    # pkgdown website configuration</code></pre>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

CLAUDE.md

@@ -90,6 +90,33 @@ R CMD check AMR
 - `ggplot_sir.R` / `ggplot_pca.R` / `plotting.R` — visualisation
   functions
 
+## Code Style
+
+Follow the [tidyverse style guide](https://style.tidyverse.org/)
+precisely. Key rules:
+
+- 2-space indentation; no tabs
+- `<-` for assignment, not `=`
+- Spaces around all binary operators and after commas; no spaces inside
+  parentheses
+- When a function call must break across lines, place the first argument
+  on a new line indented by 2 spaces, and put the closing `)` on its own
+  line — **never align arguments to the opening parenthesis** (no
+  hanging/forced mid-line indentation)
+
+``` r
+
+# good
+stop_(
+  "some long message part one ",
+  "part two"
+)
+
+# bad — forces indentation to match the opening parenthesis
+stop_("some long message part one ",
+      "part two")
+```
+
 ## Custom S3 Classes
 
 The package defines five S3 classes with full print/format/plot/vctrs

LICENSE-text.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -302,7 +302,7 @@ END OF TERMS AND CONDITIONS
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

articles/AMR.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -91,7 +91,7 @@
 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 26 June 2026.</p>
+generated on 08 September 2026.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2026-06-26</td>
+<td align="center">2026-09-08</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">2026-06-26</td>
+<td align="center">2026-09-08</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">2026-06-26</td>
+<td align="center">2026-09-08</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -284,11 +284,6 @@ taxonomic codes. Let’s check this:</p>
 <span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), and <span style="font-style: italic;">Enterobacter cloacae 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; <span style="color: #0000BB;">"K. pneumoniae"</span> -&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</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae</span></span></span>
-<span><span class="co">#&gt; <span style="font-style: italic;">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 style="font-style: italic;">Klebsiella</span></span></span>
-<span><span class="co">#&gt; <span style="font-style: italic;">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 style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
-<span><span class="co">#&gt; <span style="font-style: italic;">planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Kosakonia pseudosacchari</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.471</span>), <span style="font-style: italic;">Kaistella palustris</span></span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.435</span>), <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.435</span>), and <span style="font-style: italic;">Kocuria palustris</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.435</span>)</span></span>
 <span><span class="co">#&gt; <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">"S. aureus"</span> -&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 argenteus</span></span></span>
@@ -510,11 +505,11 @@ microorganisms:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae      319</span></span></code></pre></div>
 </div>
 <div class="section level3">
-<h3 id="select-and-filter-with-antibiotic-selectors">Select and filter with antibiotic selectors<a class="anchor" aria-label="anchor" href="#select-and-filter-with-antibiotic-selectors"></a>
+<h3 id="select-and-filter-with-antimicrobial-selectors">Select and filter with antimicrobial selectors<a class="anchor" aria-label="anchor" href="#select-and-filter-with-antimicrobial-selectors"></a>
 </h3>
-<p>Using so-called antibiotic class selectors, you can select or filter
-columns based on the antibiotic class that your antibiotic results are
-in:</p>
+<p>Using so-called antimicrobial class selectors, you can select or
+filter columns based on the antimicrobial class that your antimicrobial
+results are in:</p>
 <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
@@ -571,7 +566,7 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span> <span style="color: #080808; background-color: #5FD7AF;">  S  </span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
 <span></span>
-<span><span class="co"># filtering using AB selectors is also possible:</span></span>
+<span><span class="co"># filtering using antimicrobial selectors is also possible:</span></span>
 <span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column <span style="color: #00BB00; font-weight: bold;">GEN</span></span></span>
@@ -1325,10 +1320,6 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
 own:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
-<span><span class="co">#&gt;   category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
-<span><span class="co">#&gt;   option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
 <span><span class="co">#&gt; [1] 0.4203377</span></span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
 <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
@@ -1424,7 +1415,7 @@ values:</p>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

articles/AMR.md

@@ -3,7 +3,8 @@
 **Note:** values on this page will change with every website update
 since they are based on randomly created values and the page was written
 in [R Markdown](https://rmarkdown.rstudio.com/). However, the
-methodology remains unchanged. This page was generated on 26 June 2026.
+methodology remains unchanged. This page was generated on 08 September
+2026.
 
 ## Introduction
 
@@ -51,9 +52,9 @@ structure of your data generally look like this:
 
 |    date    | patient_id |        mo        | AMX | CIP |
 |:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-06-26 |    abcd    | Escherichia coli |  S  |  S  |
-| 2026-06-26 |    abcd    | Escherichia coli |  S  |  R  |
-| 2026-06-26 |    efgh    | Escherichia coli |  R  |  S  |
+| 2026-09-08 |    abcd    | Escherichia coli |  S  |  S  |
+| 2026-09-08 |    abcd    | Escherichia coli |  S  |  R  |
+| 2026-09-08 |    efgh    | Escherichia coli |  R  |  S  |
 
 ### Needed R packages
 
@@ -196,11 +197,6 @@ mo_uncertainties()
 #> (0.571), and Enterobacter cloacae dissolvens (0.565)
 #> -------------------------------------------------------------------------------
 #> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)
-#> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella pneumoniae
-#> ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688), Klebsiella
-#> pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii (0.500), Klebsiella
-#> planticola (0.500), Kosakonia pseudosacchari (0.471), Kaistella palustris
-#> (0.435), Kingella potus (0.435), and Kocuria palustris (0.435)
 #> -------------------------------------------------------------------------------
 #> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690)
 #> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus argenteus
@@ -450,11 +446,11 @@ our_data_1st %>%
 #> 4 Klebsiella pneumoniae      319
 ```
 
-### Select and filter with antibiotic selectors
+### Select and filter with antimicrobial selectors
 
-Using so-called antibiotic class selectors, you can select or filter
-columns based on the antibiotic class that your antibiotic results are
-in:
+Using so-called antimicrobial class selectors, you can select or filter
+columns based on the antimicrobial class that your antimicrobial results
+are in:
 
 ``` r
 
@@ -513,7 +509,7 @@ our_data_1st %>%
 #> 10 B_ESCHR_COLI   S     S     S     S  
 #> # ℹ 2,714 more rows
 
-# filtering using AB selectors is also possible:
+# filtering using antimicrobial selectors is also possible:
 our_data_1st %>%
   filter(any(aminoglycosides() == "R"))
 #> ℹ For `aminoglycosides()` using column GEN
@@ -912,10 +908,6 @@ These functions can be used on their own:
 ``` r
 
 our_data_1st %>% resistance(AMX)
-#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 #> [1] 0.4203377
 ```
 

articles/AMR_for_Python.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -619,6 +619,59 @@ frames:</p>
 </div>
 </div>
 <div class="section level2">
+<h2 id="installation-channels">Installation Channels<a class="anchor" aria-label="anchor" href="#installation-channels"></a>
+</h2>
+<div class="section level3">
+<h3 id="stable-release-cran">Stable Release (CRAN)<a class="anchor" aria-label="anchor" href="#stable-release-cran"></a>
+</h3>
+<p>The default <code>AMR</code> Python package uses the latest stable
+version of the <code>AMR</code> R package, published on CRAN. After
+running <code>pip install AMR</code>, import it as usual:</p>
+<div class="sourceCode" id="cb12"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" tabindex="-1"></a><span class="im">import</span> AMR</span>
+<span id="cb12-2"><a href="#cb12-2" tabindex="-1"></a></span>
+<span id="cb12-3"><a href="#cb12-3" tabindex="-1"></a>AMR.example_isolates</span></code></pre></div>
+</div>
+<div class="section level3">
+<h3 id="development-version-github">Development Version (GitHub)<a class="anchor" aria-label="anchor" href="#development-version-github"></a>
+</h3>
+<p>To use the latest development version of the <code>AMR</code> R
+package (sourced directly from GitHub), import the <code>beta</code>
+sub-package and alias it as <code>AMR</code>:</p>
+<div class="sourceCode" id="cb13"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb13-1"><a href="#cb13-1" tabindex="-1"></a><span class="im">import</span> AMR.beta <span class="im">as</span> AMR</span>
+<span id="cb13-2"><a href="#cb13-2" tabindex="-1"></a></span>
+<span id="cb13-3"><a href="#cb13-3" tabindex="-1"></a>AMR.example_isolates</span></code></pre></div>
+<p>Aliasing with <code>as AMR</code> keeps all downstream code identical
+to the stable import. Switching between the stable release and the
+development version requires changing only the import line — nothing
+else in your script needs to change.</p>
+</div>
+</div>
+<div class="section level2">
+<h2 id="sir-classification-with-as_sir">SIR Classification with <code>as_sir()</code><a class="anchor" aria-label="anchor" href="#sir-classification-with-as_sir"></a>
+</h2>
+<div class="section level3">
+<h3 id="using-enforce_method">Using <code>enforce_method</code><a class="anchor" aria-label="anchor" href="#using-enforce_method"></a>
+</h3>
+<p>The <code>as_sir()</code> function in R uses S3 method dispatch to
+select the correct calculation method based on the input class:
+<code>&lt;mic&gt;</code> for MIC values and <code>&lt;disk&gt;</code>
+for disk diffusion values. Because Python objects do not carry R class
+attributes through the <code>rpy2</code> bridge, this automatic dispatch
+may not resolve correctly.</p>
+<p>To explicitly specify the input type, use the
+<code>enforce_method</code> argument:</p>
+<div class="sourceCode" id="cb14"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb14-1"><a href="#cb14-1" tabindex="-1"></a><span class="co"># Treat the column as MIC values — maps to R's as.sir.mic()</span></span>
+<span id="cb14-2"><a href="#cb14-2" tabindex="-1"></a>AMR.as_sir(df[<span class="st">"MIC_col"</span>], mo<span class="op">=</span><span class="st">"E. coli"</span>, ab<span class="op">=</span><span class="st">"AMX"</span>, guideline<span class="op">=</span><span class="st">"EUCAST"</span>, enforce_method<span class="op">=</span><span class="st">"mic"</span>)</span>
+<span id="cb14-3"><a href="#cb14-3" tabindex="-1"></a></span>
+<span id="cb14-4"><a href="#cb14-4" tabindex="-1"></a><span class="co"># Treat the column as disk diffusion values — maps to R's as.sir.disk()</span></span>
+<span id="cb14-5"><a href="#cb14-5" tabindex="-1"></a>AMR.as_sir(df[<span class="st">"disk_col"</span>], mo<span class="op">=</span><span class="st">"E. coli"</span>, ab<span class="op">=</span><span class="st">"AMX"</span>, guideline<span class="op">=</span><span class="st">"EUCAST"</span>, enforce_method<span class="op">=</span><span class="st">"disk"</span>)</span></code></pre></div>
+<p>Without <code>enforce_method</code>, R falls back to class-based
+dispatch on the raw Python input, which may fail or return unexpected
+results. Always supply <code>enforce_method</code> when calling
+<code>as_sir()</code> from Python.</p>
+</div>
+</div>
+<div class="section level2">
 <h2 id="conclusion">Conclusion<a class="anchor" aria-label="anchor" href="#conclusion"></a>
 </h2>
 <p>With the <code>AMR</code> Python package, Python users can now
@@ -642,7 +695,7 @@ Python.</p>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

articles/AMR_for_Python.md

@@ -200,6 +200,61 @@ AMR.antimicrobials
 | ZID | 77846445.0 | Zidebactam | Other antibacterials | NaN | None | NaN | None |
 | ZFD | NaN | Zoliflodacin | None | NaN | None | NaN | None |
 
+## Installation Channels
+
+### Stable Release (CRAN)
+
+The default `AMR` Python package uses the latest stable version of the
+`AMR` R package, published on CRAN. After running `pip install AMR`,
+import it as usual:
+
+``` python
+import AMR
+
+AMR.example_isolates
+```
+
+### Development Version (GitHub)
+
+To use the latest development version of the `AMR` R package (sourced
+directly from GitHub), import the `beta` sub-package and alias it as
+`AMR`:
+
+``` python
+import AMR.beta as AMR
+
+AMR.example_isolates
+```
+
+Aliasing with `as AMR` keeps all downstream code identical to the stable
+import. Switching between the stable release and the development version
+requires changing only the import line — nothing else in your script
+needs to change.
+
+## SIR Classification with `as_sir()`
+
+### Using `enforce_method`
+
+The `as_sir()` function in R uses S3 method dispatch to select the
+correct calculation method based on the input class: `<mic>` for MIC
+values and `<disk>` for disk diffusion values. Because Python objects do
+not carry R class attributes through the `rpy2` bridge, this automatic
+dispatch may not resolve correctly.
+
+To explicitly specify the input type, use the `enforce_method` argument:
+
+``` python
+# Treat the column as MIC values — maps to R's as.sir.mic()
+AMR.as_sir(df["MIC_col"], mo="E. coli", ab="AMX", guideline="EUCAST", enforce_method="mic")
+
+# Treat the column as disk diffusion values — maps to R's as.sir.disk()
+AMR.as_sir(df["disk_col"], mo="E. coli", ab="AMX", guideline="EUCAST", enforce_method="disk")
+```
+
+Without `enforce_method`, R falls back to class-based dispatch on the
+raw Python input, which may fail or return unexpected results. Always
+supply `enforce_method` when calling `as_sir()` from Python.
+
 ## Conclusion
 
 With the `AMR` Python package, Python users can now effortlessly call R

articles/AMR_with_tidymodels.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -769,10 +769,6 @@ into a structured time-series format.</p>
 <span>  <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">mo</span> as input for `col_mo`.</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
-<span><span class="co">#&gt;   category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
-<span><span class="co">#&gt;   option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
 <span></span>
 <span><span class="va">data_time</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 32 × 5</span></span></span>
@@ -998,7 +994,7 @@ settings.</p>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

articles/AMR_with_tidymodels.md

@@ -684,10 +684,6 @@ data_time <- example_isolates %>%
   ) %>%
   filter(!is.na(res_AMX) & !is.na(res_AMC) & !is.na(res_CIP)) # Drop missing values
 #> ℹ Using column mo as input for `col_mo`.
-#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 
 data_time
 #> # A tibble: 32 × 5

articles/EUCAST.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -319,7 +319,7 @@ reading</em>, and is basically a form of imputation:</p>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

articles/PCA.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -163,10 +163,6 @@ per taxonomic order and genus:</p>
 <span>    <span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,</span>
 <span>    <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span></span>
 <span>  <span class="op">)</span> <span class="co"># and select only relevant columns</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
-<span><span class="co">#&gt;   category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
-<span><span class="co">#&gt;   option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
 <span></span>
 <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">resistance_data</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 6 × 10</span></span></span>
@@ -236,7 +232,7 @@ automatically adds the right labels and even groups:</p>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

articles/PCA.md

@@ -80,10 +80,6 @@ resistance_data <- example_isolates %>%
     order, genus, AMC, CXM, CTX,
     CAZ, GEN, TOB, TMP, SXT
   ) # and select only relevant columns
-#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 
 head(resistance_data)
 #> # A tibble: 6 × 10

articles/WHONET.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -254,11 +254,7 @@ Longest: 40</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># our transformed antibiotic columns</span></span>
 <span><span class="co"># amoxicillin/clavulanic acid (J01CR02) as an example</span></span>
-<span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> `susceptibility()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
-<span><span class="co">#&gt;   category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
-<span><span class="co">#&gt;   option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
-<span><span class="co">#&gt; <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span></code></pre></div>
+<span><span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">AMC_ND2</span><span class="op">)</span></span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered &gt; sir (numeric)<br>
 Length: 500<br>
@@ -325,7 +321,7 @@ using the included <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

articles/WHONET.md

@@ -106,10 +106,6 @@ Longest: 40
 # our transformed antibiotic columns
 # amoxicillin/clavulanic acid (J01CR02) as an example
 data %>% freq(AMC_ND2)
-#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 ```
 
 **Frequency table**

articles/WISCA.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -654,7 +654,7 @@ of weighted-incidence syndromic combination antibiograms (WISCA).
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

articles/datasets.html

@@ -30,7 +30,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -80,7 +80,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">26 June 2026</h4>
+            <h4 data-toc-skip class="date">08 September 2026</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>
@@ -441,7 +441,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
 <em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antimicrobials</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 23 June 2026 12:38:59 UTC. Find more info
+<p>It was last updated on 13 August 2026 09:12:12 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>
@@ -612,20 +612,20 @@ 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 45 555 rows and 14 columns, containing the following
+<p>A data set with 45 735 rows and 14 columns, containing the following
 column names:<br><em>guideline</em>, <em>type</em>, <em>host</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>, <em>uti</em>, and <em>is_SDD</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 22 June 2026 23:38:13 UTC. Find more info
-about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
+<p>It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
+the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
 set 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/datasets/clinical_breakpoints.rds" class="external-link">original
-R Data Structure (RDS) file</a> (92 kB)<br>
+R Data Structure (RDS) file</a> (93 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt" class="external-link">tab-separated
 text file</a> (4.2 MB)<br>
@@ -637,7 +637,7 @@ Excel workbook</a> (2.7 MB)<br>
 Feather file</a> (2 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet" class="external-link">Apache
-Parquet file</a> (0.1 MB)<br>
+Parquet file</a> (0.2 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav" class="external-link">IBM
 SPSS Statistics data file</a> (7.5 MB)<br>
@@ -893,11 +893,11 @@ DTA file</a> (82 kB)</li>
 <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 294 079 rows and 2 columns, containing the following
-column names:<br><em>mo</em> and <em>ab</em>.</p>
+<p>A data set with 294 079 rows and 3 columns, containing the following
+column names:<br><em>mo</em>, <em>ab</em>, and <em>version</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 22 June 2026 23:38:13 UTC. Find more info
+<p>It was last updated on 3 September 2026 10:14:25 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/intrinsic_resistant.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>
@@ -2052,7 +2052,7 @@ inhibitors</td>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

articles/datasets.md

@@ -100,7 +100,7 @@ names:
 This data set is in R available as `antimicrobials`, after you load the
 `AMR` package.
 
-It was last updated on 23 June 2026 12:38:59 UTC. Find more info about
+It was last updated on 13 August 2026 09:12:12 UTC. Find more info about
 the contents, (scientific) source, and structure of this [data set
 here](https://amr-for-r.org/reference/antimicrobials.html).
 
@@ -147,7 +147,7 @@ as comma separated values.
 
 ## `clinical_breakpoints`: Interpretation from MIC values & disk diameters to SIR
 
-A data set with 45 555 rows and 14 columns, containing the following
+A data set with 45 735 rows and 14 columns, containing the following
 column names:  
 *guideline*, *type*, *host*, *method*, *site*, *mo*, *rank_index*, *ab*,
 *ref_tbl*, *disk_dose*, *breakpoint_S*, *breakpoint_R*, *uti*, and
@@ -156,7 +156,7 @@ column names:
 This data set is in R available as `clinical_breakpoints`, after you
 load the `AMR` package.
 
-It was last updated on 22 June 2026 23:38:13 UTC. Find more info about
+It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
 the contents, (scientific) source, and structure of this [data set
 here](https://amr-for-r.org/reference/clinical_breakpoints.html).
 
@@ -164,7 +164,7 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
 
 - Download as [original R Data Structure (RDS)
   file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.rds)
-  (92 kB)  
+  (93 kB)  
 - Download as [tab-separated text
   file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.txt)
   (4.2 MB)  
@@ -176,7 +176,7 @@ here](https://amr-for-r.org/reference/clinical_breakpoints.html).
   (2 MB)  
 - Download as [Apache Parquet
   file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.parquet)
-  (0.1 MB)  
+  (0.2 MB)  
 - Download as [IBM SPSS Statistics data
   file](https://github.com/msberends/AMR/raw/main/data-raw/datasets/clinical_breakpoints.sav)
   (7.5 MB)  
@@ -249,15 +249,15 @@ here](https://amr-for-r.org/reference/microorganisms.groups.html).
 
 ## `intrinsic_resistant`: Intrinsic Bacterial Resistance
 
-A data set with 294 079 rows and 2 columns, containing the following
+A data set with 294 079 rows and 3 columns, containing the following
 column names:  
-*mo* and *ab*.
+*mo*, *ab*, and *version*.
 
 This data set is in R available as `intrinsic_resistant`, after you load
 the `AMR` package.
 
-It was last updated on 22 June 2026 23:38:13 UTC. Find more info about
-the contents, (scientific) source, and structure of this [data set
+It was last updated on 3 September 2026 10:14:25 UTC. Find more info
+about the contents, (scientific) source, and structure of this [data set
 here](https://amr-for-r.org/reference/intrinsic_resistant.html).
 
 **Direct download links:**

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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -72,7 +72,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

authors.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -198,7 +198,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

extra.css

@@ -13,7 +13,7 @@
 # https://doi.org/10.18637/jss.v104.i03                                #
 #                                                                      #
 # Developed at the University of Groningen and the University Medical  #
-# Center Groningen in The Netherlands, in collaboration with many      #
+# Center Groningen in the Netherlands, in collaboration with many      #
 # colleagues from around the world, see our website.                   # 
 #                                                                      #
 # This R package is free software; you can freely use and distribute   #

extra.js

@@ -13,7 +13,7 @@
 # https://doi.org/10.18637/jss.v104.i03                                #
 #                                                                      #
 # Developed at the University of Groningen and the University Medical  #
-# Center Groningen in The Netherlands, in collaboration with many      #
+# Center Groningen in the Netherlands, in collaboration with many      #
 # colleagues from around the world, see our website.                   # 
 #                                                                      #
 # This R package is free software; you can freely use and distribute   #

index.html

@@ -33,7 +33,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -85,7 +85,7 @@
 <ul>
 <li>Provides an <strong>all-in-one solution</strong> for antimicrobial resistance (AMR) data analysis in a One Health approach</li>
 <li>
-<strong>Peer-reviewed</strong>, used in over 175 countries, available in 28 languages</li>
+<strong>Peer-reviewed</strong>, used in over 175 countries, cited over 100 times, available in 28 languages</li>
 <li>Generates <strong>antibiograms</strong> - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance</li>
 <li>Provides the <strong>full microbiological taxonomy</strong> of ~97 000 distinct species and extensive info of ~620 antimicrobial drugs</li>
 <li>Applies <strong>CLSI 2011-2026</strong> and <strong>EUCAST 2011-2026</strong> clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation</li>
@@ -111,8 +111,8 @@
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
-<p>The <code>AMR</code> package is a peer-reviewed, <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. We are a team of <a href="./authors.html">many different researchers</a> from around the globe 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>The <code>AMR</code> package is a peer-reviewed, <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.</p>
+<p><strong>Our aim has always been 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. We are a team of <a href="./authors.html">many different researchers</a> from around the globe to make this a successful and durable project! The <code>AMR</code> package was already cited <a href="https://scholar.google.com/citations?view_op=view_citation&amp;hl=en&amp;citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC" class="external-link">over 100 times</a> in scientific research.</p>
 <p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated May 2026) and all <a href="./reference/antimicrobials.html"><strong>~620 antimicrobial 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 2011-2026 and EUCAST 2011-2026 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> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
 <div class="section level3">
 <h3 id="used-in-over-175-countries-available-in-28-languages">Used in over 175 countries, available in 28 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-available-in-28-languages"></a>
@@ -146,10 +146,10 @@
 <span><span class="co">#&gt; ℹ Using column mo as input for `mo_fullname()`</span></span>
 <span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_gram_negative()`</span></span>
 <span><span class="co">#&gt; ℹ Using column mo as input for `mo_is_intrinsic_resistant()`</span></span>
-<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant</span></span>
-<span><span class="co">#&gt;   Phenotypes' v1.2 (2023). This note will be shown once per session.</span></span>
-<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
-<span><span class="co">#&gt;   (amikacin), and KAN (kanamycin)</span></span>
+<span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).</span></span>
+<span><span class="co">#&gt;   This note will be shown once per session.</span></span>
+<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN</span></span>
+<span><span class="co">#&gt;   (kanamycin)</span></span>
 <span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span>
 <span><span class="co">#&gt; # A tibble: 35 × 7</span></span>
 <span><span class="co">#&gt;    bacteria                     GEN   TOB   AMK   KAN   IPM   MEM  </span></span>
@@ -189,9 +189,9 @@
 <th align="left">Piperacillin/tazobactam + Tobramycin</th>
 </tr></thead>
 <tbody><tr>
-<td align="left">69.9% (64.7-75.2%)</td>
-<td align="left">93.7% (92.2-95.1%)</td>
-<td align="left">89.8% (86.8-92.3%)</td>
+<td align="left">70.2% (64.6-75.4%)</td>
+<td align="left">93.6% (92.1-95%)</td>
+<td align="left">89.9% (87-92.5%)</td>
 </tr></tbody>
 </table>
 <p>WISCA supports stratification by any clinical variable, so you can generate syndrome-specific or ward-specific coverage estimates:</p>
@@ -217,21 +217,21 @@
 <tbody>
 <tr>
 <td align="left">Clinical</td>
-<td align="left">74.6% (69-80.1%)</td>
-<td align="left">93.6% (91.9-95.1%)</td>
-<td align="left">90.5% (86.9-93%)</td>
+<td align="left">74.7% (68.9-80.8%)</td>
+<td align="left">93.7% (92.1-95.2%)</td>
+<td align="left">90.5% (87-93.2%)</td>
 </tr>
 <tr>
 <td align="left">ICU</td>
-<td align="left">57% (48.7-65.8%)</td>
-<td align="left">86.7% (83.7-89.7%)</td>
-<td align="left">82.8% (77.9-87.2%)</td>
+<td align="left">57% (48.2-65.7%)</td>
+<td align="left">86.8% (83.4-89.8%)</td>
+<td align="left">83% (78-87.6%)</td>
 </tr>
 <tr>
 <td align="left">Outpatient</td>
-<td align="left">57.5% (46.5-68.7%)</td>
-<td align="left">76.7% (70.6-82.4%)</td>
-<td align="left">67.5% (57.2-76.7%)</td>
+<td align="left">57.2% (46.2-68.9%)</td>
+<td align="left">76.6% (70.1-82.1%)</td>
+<td align="left">67.7% (57.6-77.5%)</td>
 </tr>
 </tbody>
 </table>
@@ -388,10 +388,6 @@
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></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="va">GEN</span>, <span class="va">TOB</span><span class="op">)</span>,</span>
 <span>                   <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>total_R <span class="op">=</span> <span class="va">resistance</span>,</span>
 <span>                        conf_int <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="reference/proportion.html">sir_confidence_interval</a></span><span class="op">(</span><span class="va">x</span>, collapse <span class="op">=</span> <span class="st">"-"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
-<span><span class="co">#&gt;   category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
-<span><span class="co">#&gt;   option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
-<span><span class="co">#&gt; ℹ This message will be shown once per session.</span></span>
 <span><span class="co">#&gt; # A tibble: 3 × 5</span></span>
 <span><span class="co">#&gt;   ward       GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span>
 <span><span class="co">#&gt;   &lt;chr&gt;            &lt;dbl&gt; &lt;chr&gt;              &lt;dbl&gt; &lt;chr&gt;       </span></span>
@@ -409,15 +405,15 @@
 <span>  <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></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="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>            <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
-<span><span class="co">#&gt;   (amikacin), and KAN (kanamycin)</span></span>
+<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN</span></span>
+<span><span class="co">#&gt;   (kanamycin)</span></span>
 <span><span class="co">#&gt; ℹ For `polymyxins()` using column COL (colistin)</span></span>
 <span><span class="co">#&gt; Warning: There was 1 warning in `summarise()`.</span></span>
 <span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
 <span><span class="co">#&gt; ℹ In group 3: `ward = "Outpatient"`.</span></span>
 <span><span class="co">#&gt; Caused by warning:</span></span>
-<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"</span></span>
-<span><span class="co">#&gt; (whilst `minimum = 30`).</span></span>
+<span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =</span></span>
+<span><span class="co">#&gt; 30`).</span></span>
 <span><span class="va">out</span></span>
 <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
 <span><span class="co">#&gt;   ward         GEN   TOB   AMK   KAN   COL</span></span>
@@ -556,7 +552,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

index.md

@@ -2,8 +2,8 @@
 
 - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
   data analysis in a One Health approach
-- **Peer-reviewed**, used in over 175 countries, available in 28
-  languages
+- **Peer-reviewed**, used in over 175 countries, cited over 100 times,
+  available in 28 languages
 - Generates **antibiograms** - WISCA for empiric coverage estimates, or
   traditional/syndromic for AMR surveillance
 - Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -36,19 +36,17 @@ R package with [zero
 dependencies](https://en.wikipedia.org/wiki/Dependency_hell) 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
+evidence-based methods.
+
+**Our aim has always been 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. We are a team of [many different
 researchers](https://amr-for-r.org/authors.md) from around the globe to
-make this a successful and durable project!
-
-This work was published in the Journal of Statistical Software (Volume
-104(3); [DOI
-10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and
-formed the basis of two PhD theses ([DOI
-10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and
-[DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
+make this a successful and durable project! The `AMR` package was
+already cited [over 100
+times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC)
+in scientific research.
 
 After installing this package, R knows [**~97 000 distinct microbial
 species**](https://amr-for-r.org/reference/microorganisms.md) (updated
@@ -118,10 +116,10 @@ example_isolates %>%
 #> ℹ Using column mo as input for `mo_fullname()`
 #> ℹ Using column mo as input for `mo_is_gram_negative()`
 #> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
-#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
-#>   Phenotypes' v1.2 (2023). This note will be shown once per session.
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
-#>   (amikacin), and KAN (kanamycin)
+#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).
+#>   This note will be shown once per session.
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
+#>   (kanamycin)
 #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
 #> # A tibble: 35 × 7
 #>    bacteria                     GEN   TOB   AMK   KAN   IPM   MEM  
@@ -181,7 +179,7 @@ wisca(example_isolates,
 
 | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|
-| 69.9% (64.7-75.2%) | 93.7% (92.2-95.1%) | 89.8% (86.8-92.3%) |
+| 70.2% (64.6-75.4%) | 93.6% (92.1-95%) | 89.9% (87-92.5%) |
 
 WISCA supports stratification by any clinical variable, so you can
 generate syndrome-specific or ward-specific coverage estimates:
@@ -197,9 +195,9 @@ wisca(example_isolates,
 
 | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|:---|
-| Clinical | 74.6% (69-80.1%) | 93.6% (91.9-95.1%) | 90.5% (86.9-93%) |
-| ICU | 57% (48.7-65.8%) | 86.7% (83.7-89.7%) | 82.8% (77.9-87.2%) |
-| Outpatient | 57.5% (46.5-68.7%) | 76.7% (70.6-82.4%) | 67.5% (57.2-76.7%) |
+| Clinical | 74.7% (68.9-80.8%) | 93.7% (92.1-95.2%) | 90.5% (87-93.2%) |
+| ICU | 57% (48.2-65.7%) | 86.8% (83.4-89.8%) | 83% (78-87.6%) |
+| Outpatient | 57.2% (46.2-68.9%) | 76.6% (70.1-82.1%) | 67.7% (57.6-77.5%) |
 
 **For AMR surveillance**, traditional antibiograms remain the right tool
 for tracking resistance per species over time:
@@ -307,10 +305,6 @@ example_isolates %>%
   summarise(across(c(GEN, TOB),
                    list(total_R = resistance,
                         conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
-#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 #> # A tibble: 3 × 5
 #>   ward       GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
 #>   <chr>            <dbl> <chr>              <dbl> <chr>       
@@ -334,15 +328,15 @@ out <- example_isolates %>%
   # calculate AMR using resistance(), over all aminoglycosides and polymyxins:
   summarise(across(c(aminoglycosides(), polymyxins()),
             resistance))
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
-#>   (amikacin), and KAN (kanamycin)
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
+#>   (kanamycin)
 #> ℹ For `polymyxins()` using column COL (colistin)
 #> Warning: There was 1 warning in `summarise()`.
 #> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
 #> ℹ In group 3: `ward = "Outpatient"`.
 #> Caused by warning:
-#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"
-#> (whilst `minimum = 30`).
+#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =
+#> 30`).
 out
 #> # A tibble: 3 × 6
 #>   ward         GEN   TOB   AMK   KAN   COL

llms.txt

@@ -2,8 +2,8 @@
 
 - Provides an **all-in-one solution** for antimicrobial resistance (AMR)
   data analysis in a One Health approach
-- **Peer-reviewed**, used in over 175 countries, available in 28
-  languages
+- **Peer-reviewed**, used in over 175 countries, cited over 100 times,
+  available in 28 languages
 - Generates **antibiograms** - WISCA for empiric coverage estimates, or
   traditional/syndromic for AMR surveillance
 - Provides the **full microbiological taxonomy** of ~97 000 distinct
@@ -36,19 +36,17 @@ R package with [zero
 dependencies](https://en.wikipedia.org/wiki/Dependency_hell) 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
+evidence-based methods.
+
+**Our aim has always been 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. We are a team of [many different
 researchers](https://amr-for-r.org/authors.md) from around the globe to
-make this a successful and durable project!
-
-This work was published in the Journal of Statistical Software (Volume
-104(3); [DOI
-10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and
-formed the basis of two PhD theses ([DOI
-10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and
-[DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).
+make this a successful and durable project! The `AMR` package was
+already cited [over 100
+times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC)
+in scientific research.
 
 After installing this package, R knows [**~97 000 distinct microbial
 species**](https://amr-for-r.org/reference/microorganisms.md) (updated
@@ -118,10 +116,10 @@ example_isolates %>%
 #> ℹ Using column mo as input for `mo_fullname()`
 #> ℹ Using column mo as input for `mo_is_gram_negative()`
 #> ℹ Using column mo as input for `mo_is_intrinsic_resistant()`
-#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant
-#>   Phenotypes' v1.2 (2023). This note will be shown once per session.
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
-#>   (amikacin), and KAN (kanamycin)
+#> ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant Phenotypes' v1.2 (2023).
+#>   This note will be shown once per session.
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
+#>   (kanamycin)
 #> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
 #> # A tibble: 35 × 7
 #>    bacteria                     GEN   TOB   AMK   KAN   IPM   MEM  
@@ -181,7 +179,7 @@ wisca(example_isolates,
 
 | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|
-| 69.9% (64.7-75.2%) | 93.7% (92.2-95.1%) | 89.8% (86.8-92.3%) |
+| 70.2% (64.6-75.4%) | 93.6% (92.1-95%) | 89.9% (87-92.5%) |
 
 WISCA supports stratification by any clinical variable, so you can
 generate syndrome-specific or ward-specific coverage estimates:
@@ -197,9 +195,9 @@ wisca(example_isolates,
 
 | Syndromic Group | Piperacillin/tazobactam | Piperacillin/tazobactam + Gentamicin | Piperacillin/tazobactam + Tobramycin |
 |:---|:---|:---|:---|
-| Clinical | 74.6% (69-80.1%) | 93.6% (91.9-95.1%) | 90.5% (86.9-93%) |
-| ICU | 57% (48.7-65.8%) | 86.7% (83.7-89.7%) | 82.8% (77.9-87.2%) |
-| Outpatient | 57.5% (46.5-68.7%) | 76.7% (70.6-82.4%) | 67.5% (57.2-76.7%) |
+| Clinical | 74.7% (68.9-80.8%) | 93.7% (92.1-95.2%) | 90.5% (87-93.2%) |
+| ICU | 57% (48.2-65.7%) | 86.8% (83.4-89.8%) | 83% (78-87.6%) |
+| Outpatient | 57.2% (46.2-68.9%) | 76.6% (70.1-82.1%) | 67.7% (57.6-77.5%) |
 
 **For AMR surveillance**, traditional antibiograms remain the right tool
 for tracking resistance per species over time:
@@ -307,10 +305,6 @@ example_isolates %>%
   summarise(across(c(GEN, TOB),
                    list(total_R = resistance,
                         conf_int = function(x) sir_confidence_interval(x, collapse = "-"))))
-#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 #> # A tibble: 3 × 5
 #>   ward       GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int
 #>   <chr>            <dbl> <chr>              <dbl> <chr>       
@@ -334,15 +328,15 @@ out <- example_isolates %>%
   # calculate AMR using resistance(), over all aminoglycosides and polymyxins:
   summarise(across(c(aminoglycosides(), polymyxins()),
             resistance))
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
-#>   (amikacin), and KAN (kanamycin)
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK (amikacin), and KAN
+#>   (kanamycin)
 #> ℹ For `polymyxins()` using column COL (colistin)
 #> Warning: There was 1 warning in `summarise()`.
 #> ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.
 #> ℹ In group 3: `ward = "Outpatient"`.
 #> Caused by warning:
-#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient"
-#> (whilst `minimum = 30`).
+#> ! Introducing NA: only 23 results available for KAN in group: ward = "Outpatient" (whilst `minimum =
+#> 30`).
 out
 #> # A tibble: 3 × 6
 #>   ward         GEN   TOB   AMK   KAN   COL

news/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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -49,15 +49,63 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="3.0.1.9075" id="amr-3019075">AMR 3.0.1.9075<a class="anchor" aria-label="anchor" href="#amr-3019075"></a></h2>
-<p>Planned as v3.1.0, end of June 2026.</p>
+<h2 class="pkg-version" data-toc-text="3.0.1.9091" id="amr-3019091">AMR 3.0.1.9091<a class="anchor" aria-label="anchor" href="#amr-3019091"></a></h2>
+<p>Planned as v3.1.0, end of September 2026.</p>
 <div class="section level4">
-<h4 id="breaking-changes-3-0-1-9075">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9075"></a></h4>
-<ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li>
-<li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li>
+<h4 id="breaking-changes-3-0-1-9091">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9091"></a></h4>
+<ul><li>
+<p>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</p>
+<table class="table"><colgroup><col width="33%"><col width="29%"><col width="37%"></colgroup><thead><tr><th>
+<code><a href="../reference/mo_property.html">mo_kingdom()</a></code> &lt; 3.1.0</th>
+<th>
+<code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now</th>
+<th>
+<code><a href="../reference/mo_property.html">mo_domain()</a></code> (unchanged)</th>
+</tr></thead><tbody><tr><td>Bacteria</td>
+<td>Bacillati</td>
+<td>Bacteria</td>
+</tr><tr><td></td>
+<td>Fusobacteriati</td>
+<td>Bacteria</td>
+</tr><tr><td></td>
+<td>Pseudomonadati</td>
+<td>Bacteria</td>
+</tr><tr><td></td>
+<td>Thermotogati</td>
+<td>Bacteria</td>
+</tr><tr><td></td>
+<td></td>
+<td></td>
+</tr><tr><td>Archaea</td>
+<td>Methanobacteriati</td>
+<td>Archaea</td>
+</tr><tr><td></td>
+<td>Nanobdellati</td>
+<td>Archaea</td>
+</tr><tr><td></td>
+<td>Promethearchaeati</td>
+<td>Archaea</td>
+</tr><tr><td></td>
+<td>Thermoproteati</td>
+<td>Archaea</td>
+</tr><tr><td></td>
+<td></td>
+<td></td>
+</tr><tr><td>Fungi</td>
+<td>Fungi</td>
+<td>Fungi</td>
+</tr><tr><td></td>
+<td></td>
+<td></td>
+</tr><tr><td>Protozoa</td>
+<td>Protozoa</td>
+<td>Protozoa</td>
+</tr></tbody></table><p>Thus, <code><a href="../reference/mo_property.html">mo_domain()</a></code> was previously an alias of <code><a href="../reference/mo_property.html">mo_kingdom()</a></code>; it is now a distinct function returning the domain. Output of <code><a href="../reference/mo_property.html">mo_domain()</a></code> is therefore unchanged, while <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal, new kingdom.</p>
+</li>
+<li><p>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</p></li>
 </ul></div>
 <div class="section level4">
-<h4 id="new-3-0-1-9075">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9075"></a></h4>
+<h4 id="new-3-0-1-9091">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9091"></a></h4>
 <ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
 <li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
 <li>
@@ -74,8 +122,9 @@
 <li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li>
 </ul></div>
 <div class="section level4">
-<h4 id="fixed-3-0-1-9075">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9075"></a></h4>
-<ul><li>
+<h4 id="fixed-3-0-1-9091">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9091"></a></h4>
+<ul><li>Setting <code>options(AMR_guideline = "EUCAST 2012")</code> or any year-qualified value no longer causes errors or silent wrong behaviour in <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, <code><a href="../reference/proportion.html">resistance()</a></code>, <code><a href="../reference/proportion.html">susceptibility()</a></code>, <code><a href="../reference/count.html">count_resistant()</a></code>, <code><a href="../reference/count.html">count_susceptible()</a></code>, and SIR plotting/printing functions (<a href="https://github.com/msberends/AMR/issues/298" class="external-link">#298</a>)</li>
+<li>
 <code><a href="../reference/as.sir.html">as.sir()</a></code>
 <ul><li>On data frames: already-converted SIR columns no longer dropped on re-run (<a href="https://github.com/msberends/AMR/issues/278" class="external-link">#278</a>)</li>
 <li>Metadata columns (e.g. <code>patient</code>, <code>ward</code>) no longer misidentified as antibiotic columns</li>
@@ -92,6 +141,7 @@
 <code><a href="../reference/as.mo.html">as.mo()</a></code>:
 <ul><li>Input of the form <code>"X complex"</code> now falls back to <code>"X"</code> when the complex is not a distinct taxon in the database, preventing <code>NA</code> results for valid clinical descriptions such as <code>"Proteus vulgaris complex"</code> (<a href="https://github.com/msberends/AMR/issues/287" class="external-link">#287</a>)</li>
 <li>Abbreviated-genus input (e.g. <code>"S. apiospermum"</code>) now correctly ranks candidates whose species epithet exactly matches the input above more-prevalent organisms whose species does not match; fixes <code>"S. apiospermum"</code> resolving to <em>Staphylococcus</em> instead of <em>Scedosporium apiospermum</em> (<a href="https://github.com/msberends/AMR/issues/288" class="external-link">#288</a>)</li>
+<li>Abbreviated-genus input for species that have subspecies (e.g. <code>"P. ovale"</code>) now collapses to the species-rank record instead of incorrectly matching a more-prevalent organism; explicit subspecies queries (e.g. <code>"P. ovale curtisi"</code>) are preserved (<a href="https://github.com/msberends/AMR/issues/288" class="external-link">#288</a>)</li>
 </ul></li>
 <li>
 <code>get_author_year()</code> in the microorganism reproduction script now strips <code>emend.</code> and everything after it, so <code>ref</code> reflects the combination authority rather than the emendation author (e.g. <em>Rhodococcus equi</em> now returns “Goodfellow et al., 1977” instead of “Nouioui et al., 2018”)</li>
@@ -101,8 +151,10 @@
 </li>
 </ul></div>
 <div class="section level4">
-<h4 id="updated-3-0-1-9075">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9075"></a></h4>
-<ul><li>Taxonomic update for all microorganisms, now updated to June 2026</li>
+<h4 id="updated-3-0-1-9091">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9091"></a></h4>
+<ul><li>
+<code><a href="../reference/top_n_microorganisms.html">top_n_microorganisms()</a></code>: new <code>property_for_each</code> argument for sub-grouping within top <em>n</em> groups; rank ordering enforced (only lower taxonomic ranks allowed); fixed <code>property = NULL</code> not being accepted; inner filter now tracks original row indices to prevent cross-group contamination</li>
+<li>Taxonomic update for all microorganisms, now updated to June 2026</li>
 <li>
 <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal taxonomic kingdom; a one-time note per session explains the change when querying bacterial or archaeal records.</li>
 <li>
@@ -127,6 +179,8 @@
 <code><a href="../reference/as.disk.html">as.disk()</a></code>: input validation is now more strict, rejecting values that are not recognisable as a numeric disk zone diameter</li>
 <li>
 <code><a href="../reference/as.sir.html">as.sir()</a></code> gains an <code>enforce_method</code> argument (<code>"auto"</code>, <code>"mic"</code>, or <code>"disk"</code>) to force the interpretation method when S3 class information is lost, e.g. when called from Python (<a href="https://github.com/msberends/AMR/issues/291" class="external-link">#291</a>)</li>
+<li>
+<code>AMR for Python</code> vignette: added sections on installation channels (stable CRAN vs. development GitHub via <code>AMR.beta</code>) and on using <code>enforce_method</code> in <code>as_sir()</code> from Python</li>
 </ul></div>
 </div>
     <div class="section level2">
@@ -339,7 +393,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

news/index.md

@@ -1,8 +1,8 @@
 # Changelog
 
-## AMR 3.0.1.9075
+## AMR 3.0.1.9091
 
-Planned as v3.1.0, end of June 2026.
+Planned as v3.1.0, end of September 2026.
 
 #### Breaking Changes
 
@@ -17,6 +17,32 @@ Planned as v3.1.0, end of June 2026.
   [`mo_domain()`](https://amr-for-r.org/reference/mo_property.md) for
   the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa,
   etc.), `kingdom` and `domain` are identical.
+
+  | [`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md) \< 3.1.0 | [`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md) now | [`mo_domain()`](https://amr-for-r.org/reference/mo_property.md) (unchanged) |
+  |----|----|----|
+  | Bacteria | Bacillati | Bacteria |
+  |  | Fusobacteriati | Bacteria |
+  |  | Pseudomonadati | Bacteria |
+  |  | Thermotogati | Bacteria |
+  |  |  |  |
+  | Archaea | Methanobacteriati | Archaea |
+  |  | Nanobdellati | Archaea |
+  |  | Promethearchaeati | Archaea |
+  |  | Thermoproteati | Archaea |
+  |  |  |  |
+  | Fungi | Fungi | Fungi |
+  |  |  |  |
+  | Protozoa | Protozoa | Protozoa |
+
+  Thus, [`mo_domain()`](https://amr-for-r.org/reference/mo_property.md)
+  was previously an alias of
+  [`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md); it
+  is now a distinct function returning the domain. Output of
+  [`mo_domain()`](https://amr-for-r.org/reference/mo_property.md) is
+  therefore unchanged, while
+  [`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md) now
+  returns the formal, new kingdom.
+
 - Faster parallel computing via the `future` package for
   [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) and
   [`wisca()`](https://amr-for-r.org/reference/antibiogram.md): a
@@ -77,6 +103,15 @@ Planned as v3.1.0, end of June 2026.
 
 #### Fixed
 
+- Setting `options(AMR_guideline = "EUCAST 2012")` or any year-qualified
+  value no longer causes errors or silent wrong behaviour in
+  [`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md),
+  [`resistance()`](https://amr-for-r.org/reference/proportion.md),
+  [`susceptibility()`](https://amr-for-r.org/reference/proportion.md),
+  [`count_resistant()`](https://amr-for-r.org/reference/count.md),
+  [`count_susceptible()`](https://amr-for-r.org/reference/count.md), and
+  SIR plotting/printing functions
+  ([\#298](https://github.com/msberends/AMR/issues/298))
 - [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
   - On data frames: already-converted SIR columns no longer dropped on
     re-run ([\#278](https://github.com/msberends/AMR/issues/278))
@@ -108,6 +143,11 @@ Planned as v3.1.0, end of June 2026.
     `"S. apiospermum"` resolving to *Staphylococcus* instead of
     *Scedosporium apiospermum*
     ([\#288](https://github.com/msberends/AMR/issues/288))
+  - Abbreviated-genus input for species that have subspecies
+    (e.g. `"P. ovale"`) now collapses to the species-rank record instead
+    of incorrectly matching a more-prevalent organism; explicit
+    subspecies queries (e.g. `"P. ovale curtisi"`) are preserved
+    ([\#288](https://github.com/msberends/AMR/issues/288))
 - `get_author_year()` in the microorganism reproduction script now
   strips `emend.` and everything after it, so `ref` reflects the
   combination authority rather than the emendation author
@@ -125,6 +165,11 @@ Planned as v3.1.0, end of June 2026.
 
 #### Updated
 
+- [`top_n_microorganisms()`](https://amr-for-r.org/reference/top_n_microorganisms.md):
+  new `property_for_each` argument for sub-grouping within top *n*
+  groups; rank ordering enforced (only lower taxonomic ranks allowed);
+  fixed `property = NULL` not being accepted; inner filter now tracks
+  original row indices to prevent cross-group contamination
 - Taxonomic update for all microorganisms, now updated to June 2026
 - [`mo_kingdom()`](https://amr-for-r.org/reference/mo_property.md) now
   returns the formal taxonomic kingdom; a one-time note per session
@@ -180,6 +225,9 @@ Planned as v3.1.0, end of June 2026.
   the interpretation method when S3 class information is lost, e.g. when
   called from Python
   ([\#291](https://github.com/msberends/AMR/issues/291))
+- `AMR for Python` vignette: added sections on installation channels
+  (stable CRAN vs. development GitHub via `AMR.beta`) and on using
+  `enforce_method` in `as_sir()` from Python
 
 ## AMR 3.0.1
 

pkgdown.yml

@@ -1,5 +1,5 @@
 pandoc: 3.8.3
-pkgdown: 2.2.0
+pkgdown: 2.2.1
 pkgdown_sha: ~
 articles:
   AMR_for_Python: AMR_for_Python.html
@@ -10,7 +10,7 @@ articles:
   PCA: PCA.html
   WHONET: WHONET.html
   WISCA: WISCA.html
-last_built: 2026-06-26T10:08Z
+last_built: 2026-09-08T13:07Z
 urls:
   reference: https://amr-for-r.org/reference
   article: https://amr-for-r.org/articles

reference/AMR-deprecated.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -67,7 +67,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/AMR-options.html

@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -109,7 +109,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/AMR.html

@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -112,7 +112,8 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
     <div class="section level2">
     <h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
     <p><strong>Maintainer</strong>: Matthijs S. Berends <a href="mailto:m.s.berends@umcg.nl">m.s.berends@umcg.nl</a> (<a href="https://orcid.org/0000-0001-7620-1800" class="external-link">ORCID</a>)</p>
-<p>Authors:</p><ul><li><p>Dennis Souverein (<a href="https://orcid.org/0000-0003-0455-0336" class="external-link">ORCID</a>) [contributor]</p></li>
+<p>Authors:</p><ul><li><p>Matthijs S. Berends <a href="mailto:m.s.berends@umcg.nl">m.s.berends@umcg.nl</a> (<a href="https://orcid.org/0000-0001-7620-1800" class="external-link">ORCID</a>)</p></li>
+<li><p>Dennis Souverein (<a href="https://orcid.org/0000-0003-0455-0336" class="external-link">ORCID</a>) [contributor]</p></li>
 <li><p>Erwin E. A. Hassing [contributor]</p></li>
 </ul><p>Other contributors:</p><ul><li><p>Aislinn Cook (<a href="https://orcid.org/0000-0002-9189-7815" class="external-link">ORCID</a>) [contributor]</p></li>
 <li><p>Andrew P. Norgan (<a href="https://orcid.org/0000-0002-2955-2066" class="external-link">ORCID</a>) [contributor]</p></li>
@@ -148,7 +149,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/AMR.md

@@ -102,6 +102,9 @@ Useful links:
 
 Authors:
 
+- Matthijs S. Berends <m.s.berends@umcg.nl>
+  ([ORCID](https://orcid.org/0000-0001-7620-1800))
+
 - Dennis Souverein ([ORCID](https://orcid.org/0000-0003-0455-0336))
   \[contributor\]
 

reference/WHOCC.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -87,7 +87,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/WHONET.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -126,7 +126,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/ab_from_text.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -203,7 +203,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/ab_property.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -449,7 +449,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/add_custom_antimicrobials.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -208,7 +208,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/add_custom_microorganisms.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -245,7 +245,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/age.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -112,16 +112,16 @@
 <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  1999-06-30  26  26.98904          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1968-01-29  58  58.40548         31</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1965-12-05  60  60.55616         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-03-01  46  46.32055         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1949-11-01  76  76.64932         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-02-14  79  79.36164         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-02-19  86  86.34795         59</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1988-01-10  38  38.45753         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-08-27  28  28.83014          2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.41370         21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1999-06-30  27  27.19178          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1968-01-29  58  58.60822         31</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1965-12-05  60  60.75890         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-03-01  46  46.52329         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1949-11-01  76  76.85205         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-02-14  79  79.56438         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-02-19  86  86.55068         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1988-01-10  38  38.66027         11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-08-27  29  29.03288          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.61644         21</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
@@ -129,7 +129,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/age.md

@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
 
 df
 #>    birth_date age age_exact age_at_y2k
-#> 1  1999-06-30  26  26.98904          0
-#> 2  1968-01-29  58  58.40548         31
-#> 3  1965-12-05  60  60.55616         34
-#> 4  1980-03-01  46  46.32055         19
-#> 5  1949-11-01  76  76.64932         50
-#> 6  1947-02-14  79  79.36164         52
-#> 7  1940-02-19  86  86.34795         59
-#> 8  1988-01-10  38  38.45753         11
-#> 9  1997-08-27  28  28.83014          2
-#> 10 1978-01-26  48  48.41370         21
+#> 1  1999-06-30  27  27.19178          0
+#> 2  1968-01-29  58  58.60822         31
+#> 3  1965-12-05  60  60.75890         34
+#> 4  1980-03-01  46  46.52329         19
+#> 5  1949-11-01  76  76.85205         50
+#> 6  1947-02-14  79  79.56438         52
+#> 7  1940-02-19  86  86.55068         59
+#> 8  1988-01-10  38  38.66027         11
+#> 9  1997-08-27  29  29.03288          2
+#> 10 1978-01-26  48  48.61644         21
 ```

reference/age_groups.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -164,7 +164,7 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/amr-tidymodels.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -202,10 +202,10 @@ may affect the computations for subsequent operations.</p></dd>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom       </span> 1.0.13     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample     </span> 1.3.2 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials       </span> 1.4.4      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tailor      </span> 0.1.0 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer       </span> 1.1.0      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr       </span> 1.3.2 </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata   </span> 1.5.1      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune        </span> 2.1.0 </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata   </span> 1.6.0      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune        </span> 2.1.0 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip     </span> 1.6.0      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows   </span> 1.3.0 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr       </span> 1.2.2      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1 </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.3.3      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick   </span> 1.4.0 </span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.4.0      <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick   </span> 1.4.0 </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span>  masks <span style="color: #0000BB;">stats</span>::filter()</span>
@@ -229,7 +229,7 @@ may affect the computations for subsequent operations.</p></dd>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/amr-tidymodels.md

@@ -181,10 +181,10 @@ if (require("tidymodels")) {
 #> ✔ broom        1.0.13     ✔ rsample      1.3.2 
 #> ✔ dials        1.4.4      ✔ tailor       0.1.0 
 #> ✔ infer        1.1.0      ✔ tidyr        1.3.2 
-#> ✔ modeldata    1.5.1      ✔ tune         2.1.0 
+#> ✔ modeldata    1.6.0      ✔ tune         2.1.0 
 #> ✔ parsnip      1.6.0      ✔ workflows    1.3.0 
 #> ✔ purrr        1.2.2      ✔ workflowsets 1.1.1 
-#> ✔ recipes      1.3.3      ✔ yardstick    1.4.0 
+#> ✔ recipes      1.4.0      ✔ yardstick    1.4.0 
 #> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
 #> ✖ purrr::discard() masks scales::discard()
 #> ✖ dplyr::filter()  masks stats::filter()

reference/amr_course.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -102,7 +102,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/antibiogram.html

@@ -13,7 +13,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -744,7 +744,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/antimicrobial_selectors.html

@@ -17,7 +17,7 @@ my_data_with_all_these_columns %>%
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -724,7 +724,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span><span class="co"># data.table --------------------------------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># data.table is supported as well, just use it in the same way as with</span></span></span>
-<span class="r-in"><span><span class="co"># base R, but add `with = FALSE` if using a single AB selector.</span></span></span>
+<span class="r-in"><span><span class="co"># base R, but add `with = FALSE` if using a single AMR selector.</span></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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">dt</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/pkg/data.table/man/as.data.table.html" class="external-link">as.data.table</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
@@ -772,7 +772,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1999:     S     S</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2000:     S     S</span>
 <span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># for multiple selections or AB selectors, `with = FALSE` is not needed:</span></span></span>
+<span class="r-in"><span><span class="co"># for multiple selections or AMR selectors, `with = FALSE` is not needed:</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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">dt</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">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
@@ -909,7 +909,7 @@ my_data_with_all_these_columns %&amp;gt;%
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/antimicrobial_selectors.md

@@ -1097,7 +1097,7 @@ example_isolates[, amr_selector(oral_ddd > 1 & oral_units == "g")]
 # data.table --------------------------------------------------------------
 
 # data.table is supported as well, just use it in the same way as with
-# base R, but add `with = FALSE` if using a single AB selector.
+# base R, but add `with = FALSE` if using a single AMR selector.
 
 if (require("data.table")) {
   dt <- as.data.table(example_isolates)
@@ -1145,7 +1145,7 @@ if (require("data.table")) {
 #> 1999:     S     S
 #> 2000:     S     S
 
-# for multiple selections or AB selectors, `with = FALSE` is not needed:
+# for multiple selections or AMR selectors, `with = FALSE` is not needed:
 if (require("data.table")) {
   dt[, c("mo", aminoglycosides())]
 }

reference/antimicrobials.html

@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will 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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -184,7 +184,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/as.ab.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/as.av.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -174,7 +174,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/as.disk.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -62,10 +62,6 @@
 <span><span class="fu">is.disk</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
     </div>
 
-    <div class="section level2">
-    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>An object of class <code>disk</code> (inherits from <code>integer</code>) of length 1.</p>
-    </div>
     <div class="section level2">
     <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
 
@@ -142,7 +138,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/as.disk.md

@@ -14,10 +14,6 @@ NA_disk_
 is.disk(x)
 ```
 
-## Format
-
-An object of class `disk` (inherits from `integer`) of length 1.
-
 ## Arguments
 
 - x:

reference/as.mic.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -232,7 +232,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/as.mo.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -339,7 +339,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/as.sir.html

@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -462,10 +462,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   datetime            index method ab_given    mo_given   host_given input_given</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;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-06-26 <span style="color: #949494;">10:11:05</span>     1 MIC    amoxicillin Escherich… human      8          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-06-26 <span style="color: #949494;">10:11:06</span>     1 MIC    cipro       Escherich… human      0.256      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-06-26 <span style="color: #949494;">10:11:06</span>     1 DISK   tobra       Escherich… human      16         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-06-26 <span style="color: #949494;">10:11:06</span>     1 DISK   genta       Escherich… human      18         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-09-08 <span style="color: #949494;">13:09:34</span>     1 MIC    amoxicillin Escherich… human      8          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-09-08 <span style="color: #949494;">13:09:34</span>     1 MIC    cipro       Escherich… human      0.256      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-09-08 <span style="color: #949494;">13:09:35</span>     1 DISK   tobra       Escherich… human      16         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-09-08 <span style="color: #949494;">13:09:35</span>     1 DISK   genta       Escherich… human      18         </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@@ -722,7 +722,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/as.sir.md

@@ -712,10 +712,10 @@ sir_interpretation_history()
 #> # A tibble: 4 × 18
 #>   datetime            index method ab_given    mo_given   host_given input_given
 #>   <dttm>              <int> <chr>  <chr>       <chr>      <chr>      <chr>      
-#> 1 2026-06-26 10:11:05     1 MIC    amoxicillin Escherich… human      8          
-#> 2 2026-06-26 10:11:06     1 MIC    cipro       Escherich… human      0.256      
-#> 3 2026-06-26 10:11:06     1 DISK   tobra       Escherich… human      16         
-#> 4 2026-06-26 10:11:06     1 DISK   genta       Escherich… human      18         
+#> 1 2026-09-08 13:09:34     1 MIC    amoxicillin Escherich… human      8          
+#> 2 2026-09-08 13:09:34     1 MIC    cipro       Escherich… human      0.256      
+#> 3 2026-09-08 13:09:35     1 DISK   tobra       Escherich… human      16         
+#> 4 2026-09-08 13:09:35     1 DISK   genta       Escherich… human      18         
 #> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
 #> #   outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
 #> #   breakpoint_S_R <chr>, site <chr>

reference/atc_online.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -157,7 +157,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/av_from_text.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -142,7 +142,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/av_property.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -263,7 +263,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/availability.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -82,10 +82,6 @@
     <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">availability</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   option to either "CLSI" or "EUCAST", see `?AMR-options`.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         count available     visual_availabilty resistant      visual_resistance</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> date     2000    100.0% |####################|                                 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> patient  2000    100.0% |####################|                                 </span>
@@ -189,7 +185,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/availability.md

@@ -41,10 +41,6 @@ calculated with
 
 ``` r
 availability(example_isolates)
-#> ℹ `resistance()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 #>         count available     visual_availabilty resistant      visual_resistance
 #> date     2000    100.0% |####################|                                 
 #> patient  2000    100.0% |####################|                                 

reference/bug_drug_combinations.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -254,7 +254,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/clinical_breakpoints.html

@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -78,7 +78,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
 
     <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 45 555 observations and 14 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 45 735 observations and 14 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
 <li><p><code>type</code><br> Breakpoint type, either <code>"ECOFF"</code>, <code>"animal"</code>, or <code>"human"</code></p></li>
 <li><p><code>host</code><br> Host of infectious agent. This is mostly useful for veterinary breakpoints and is either <code>"ECOFF"</code>, <code>"aquatic"</code>, <code>"cats"</code>, <code>"cattle"</code>, <code>"dogs"</code>, <code>"horse"</code>, <code>"human"</code>, <code>"poultry"</code>, or <code>"swine"</code></p></li>
 <li><p><code>method</code><br> Testing method, either <code>"DISK"</code> or <code>"MIC"</code></p></li>
@@ -108,7 +108,10 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
 <h3 id="imported-from-whonet">Imported From WHONET<a class="anchor" aria-label="anchor" href="#imported-from-whonet"></a></h3>
 
 
-<p>Clinical breakpoints in this package were validated through and imported from <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>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.</p>
+<p>Some breakpoints in this package were validated through and imported from <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>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.</p>
+<p>From WHONET, imported were:</p><ul><li><p>All CLSI breakpoints, including ECOFF</p></li>
+<li><p>EUCAST breakpoints between  2011 and 2018</p></li>
+</ul><p>EUCAST breakpoints from 2019 onwards, were retrieved directly from <a href="https://www.eucast.org" class="external-link">https://www.eucast.org</a>.</p>
 <p>Our import and reproduction script can be found here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R</a>.</p>
 </div>
 
@@ -143,7 +146,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
     <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: 45,555 × 14</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 45,735 × 14</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    guideline   type  host  method site    mo            rank_index ab   ref_tbl </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;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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2026 human human DISK   <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 MEM  A. xylo…</span>
@@ -156,7 +159,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2026 human human DISK   Uncomp… <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2026 human human MIC    <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2026 human human MIC    Uncomp… <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45,545 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45,725 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: disk_dose &lt;chr&gt;, breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   uti &lt;lgl&gt;, is_SDD &lt;lgl&gt;</span></span>
 </code></pre></div>
@@ -166,7 +169,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/clinical_breakpoints.md

@@ -26,7 +26,7 @@ clinical_breakpoints
 ## Format
 
 A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 45
-555 observations and 14 variables:
+735 observations and 14 variables:
 
 - `guideline`  
   Name of the guideline
@@ -100,7 +100,7 @@ to interpret raw data using a specific breakpoint type, e.g.
 
 ### Imported From WHONET
 
-Clinical breakpoints in this package were validated through and imported
+Some breakpoints in this package were validated through and imported
 from [WHONET](https://whonet.org), a free desktop Windows application
 developed and supported by the WHO Collaborating Centre for Surveillance
 of Antimicrobial Resistance. More can be read on [their
@@ -108,6 +108,15 @@ website](https://whonet.org). The developers of WHONET and this `AMR`
 package have been in contact about sharing their work. We highly
 appreciate their great development on the WHONET software.
 
+From WHONET, imported were:
+
+- All CLSI breakpoints, including ECOFF
+
+- EUCAST breakpoints between 2011 and 2018
+
+EUCAST breakpoints from 2019 onwards, were retrieved directly from
+<https://www.eucast.org>.
+
 Our import and reproduction script can be found here:
 <https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R>.
 
@@ -154,7 +163,7 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
 
 ``` r
 clinical_breakpoints
-#> # A tibble: 45,555 × 14
+#> # A tibble: 45,735 × 14
 #>    guideline   type  host  method site    mo            rank_index ab   ref_tbl 
 #>    <chr>       <chr> <chr> <chr>  <chr>   <mo>               <dbl> <ab> <chr>   
 #>  1 EUCAST 2026 human human DISK   NA      B_ACHRMB_XYLS          2 MEM  A. xylo…
@@ -167,7 +176,7 @@ clinical_breakpoints
 #>  8 EUCAST 2026 human human DISK   Uncomp… B_ACNTB                3 AMK  Acineto…
 #>  9 EUCAST 2026 human human MIC    NA      B_ACNTB                3 AMK  Acineto…
 #> 10 EUCAST 2026 human human MIC    Uncomp… B_ACNTB                3 AMK  Acineto…
-#> # ℹ 45,545 more rows
+#> # ℹ 45,725 more rows
 #> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
 #> #   uti <lgl>, is_SDD <lgl>
 ```

reference/count.html

@@ -9,7 +9,7 @@ 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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -184,16 +184,8 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># base R ------------------------------------------------------------</span></span></span>
 <span class="r-in"><span><span class="fu">count_resistant</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "R"</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `count_resistant()` assumes the EUCAST guideline and thus considers the 'I'</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   option to either "CLSI" or "EUCAST", see `?AMR-options`.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 804</span>
 <span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S" and "I"</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `count_susceptible()` assumes the EUCAST guideline and thus considers the 'I'</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   option to either "CLSI" or "EUCAST", see `?AMR-options`.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
 <span class="r-in"><span><span class="fu">count_all</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="co"># counts "S", "I" and "R"</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1350</span>
@@ -223,10 +215,6 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
 <span class="r-in"><span><span class="fu">count_susceptible</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
 <span class="r-in"><span><span class="fu"><a href="proportion.html">susceptibility</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span> <span class="op">*</span> <span class="fu">n_sir</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">AMX</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> `susceptibility()` assumes the EUCAST guideline and thus considers the 'I'</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   category susceptible. Set the `guideline` argument or the `AMR_guideline`</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   option to either "CLSI" or "EUCAST", see `?AMR-options`.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 546</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># dplyr -------------------------------------------------------------</span></span></span>
@@ -297,7 +285,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/count.md

@@ -198,16 +198,8 @@ calculate microbial resistance and susceptibility.
 
 # base R ------------------------------------------------------------
 count_resistant(example_isolates$AMX) # counts "R"
-#> ℹ `count_resistant()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 #> [1] 804
 count_susceptible(example_isolates$AMX) # counts "S" and "I"
-#> ℹ `count_susceptible()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 #> [1] 546
 count_all(example_isolates$AMX) # counts "S", "I" and "R"
 #> [1] 1350
@@ -237,10 +229,6 @@ n_sir(example_isolates$AMX)
 count_susceptible(example_isolates$AMX)
 #> [1] 546
 susceptibility(example_isolates$AMX) * n_sir(example_isolates$AMX)
-#> ℹ `susceptibility()` assumes the EUCAST guideline and thus considers the 'I'
-#>   category susceptible. Set the `guideline` argument or the `AMR_guideline`
-#>   option to either "CLSI" or "EUCAST", see `?AMR-options`.
-#> ℹ This message will be shown once per session.
 #> [1] 546
 
 # dplyr -------------------------------------------------------------

reference/custom_interpretive_rules.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -252,7 +252,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/custom_mdro_guideline.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -259,7 +259,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/dosage.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -104,7 +104,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/esbl_isolates.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -95,7 +95,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/example_isolates.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -107,7 +107,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/example_isolates_unclean.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -99,7 +99,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/export_ncbi_biosample.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -86,7 +86,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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 <div class="pkgdown-footer-right">

reference/first_isolate.html

@@ -9,7 +9,7 @@
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -381,7 +381,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/g.test.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -228,7 +228,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/get_episode.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -315,7 +315,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/ggplot_pca.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -260,7 +260,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/ggplot_sir.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</small>
 
 
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@@ -319,7 +319,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/guess_ab_col.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</small>
 
 
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@@ -129,7 +129,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -609,7 +609,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/interpretive_rules.html

@@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -135,11 +135,11 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
 
 
 <dt id="arg-version-expertrules">version_expertrules<a class="anchor" aria-label="anchor" href="#arg-version-expertrules"></a></dt>
-<dd><p>The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be <code>"3.3"</code>, <code>"3.2"</code>, or <code>"3.1"</code>.</p></dd>
+<dd><p>The version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be <code>"3.3"</code>.</p></dd>
 
 
 <dt id="arg-ampc-cephalosporin-resistance">ampc_cephalosporin_resistance<a class="anchor" aria-label="anchor" href="#arg-ampc-cephalosporin-resistance"></a></dt>
-<dd><p>(only applies when <code>rules</code> contains <code>"expert"</code> or <code>"all"</code>) a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code> and higher; these versions of '<em>EUCAST Expert Rules on Enterobacterales</em>' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of <code>NA</code> (the default) for this argument will remove results for these three drugs, while e.g. a value of <code>"R"</code> will make the results for these drugs resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using <code>TRUE</code> is equal to using <code>"R"</code>. <br> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Citrobacter braakii</em>, <em>Citrobacter freundii</em>, <em>Citrobacter gillenii</em>, <em>Citrobacter murliniae</em>, <em>Citrobacter rodenticum</em>, <em>Citrobacter sedlakii</em>, <em>Citrobacter werkmanii</em>, <em>Citrobacter youngae</em>, <em>Enterobacter</em>, <em>Hafnia alvei</em>, <em>Klebsiella aerogenes</em>, <em>Morganella morganii</em>, <em>Providencia</em>, and <em>Serratia</em>.</p></dd>
+<dd><p>(only applies when <code>rules</code> contains <code>"expert"</code> or <code>"all"</code>) a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants - the default is <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code> and higher; these versions of '<em>EUCAST Expert Rules on Enterobacterales</em>' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of <code>NA</code> (the default) for this argument will remove results for these three drugs, while e.g. a value of <code>"R"</code> will make the results for these drugs resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using <code>TRUE</code> is equal to using <code>"R"</code>. <br> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Citrobacter braakii</em>, <em>Citrobacter freundii</em>, <em>Citrobacter gillenii</em>, <em>Citrobacter murliniae</em>, <em>Citrobacter rodenticum</em>, <em>Citrobacter sedlakii</em>, <em>Citrobacter werkmanii</em>, <em>Citrobacter youngae</em>, <em>Enterobacter</em>, <em>Hafnia alvei</em>, and <em>Klebsiella aerogenes</em>.</p></dd>
 
 
 <dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
@@ -177,7 +177,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
     <div class="section level2">
     <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
     <p><strong>Note:</strong> This function does not translate MIC or disk values to SIR values. Use <code><a href="as.sir.html">as.sir()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
-<p>The file containing all interpretive rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv</a>.  <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until 7th of May, 2026, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
+<p>The file containing all interpretive rules is located here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv</a>.  <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; older interpretive rules may not yet contain this new taxonomic name. The <code>AMR</code> package contains the full microbial taxonomy updated until 7th of May, 2026, see <a href="microorganisms.html">microorganisms</a>.</p><div class="section">
 <h3 id="custom-rules">Custom Rules<a class="anchor" aria-label="anchor" href="#custom-rules"></a></h3>
 
 
@@ -212,13 +212,8 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
 
 <ul><li><p>EUCAST Expert Rules. Version 2.0, 2012.<br>
 Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility testing.</strong> <em>Clin Microbiol Infect.</em> 2013;19(2):141-60; <a href="https://doi.org/10.1111/j.1469-0691.2011.03703.x" class="external-link">doi:10.1111/j.1469-0691.2011.03703.x</a></p></li>
-<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf" class="external-link">(link)</a></p></li>
-<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf" class="external-link">(link)</a></p></li>
-<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf" class="external-link">(link)</a></p></li>
-<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
-<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
-<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
-<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 12.0, 2022. <a href="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx" class="external-link">(link)</a></p></li>
+<li><p>EUCAST Expected Phenotypes. <a href="https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/" class="external-link">(link)</a></p></li>
+<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" class="external-link">(link)</a></p></li>
 </ul></div>
 
     <div class="section level2">
@@ -332,7 +327,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/interpretive_rules.md

@@ -118,7 +118,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
 - version_expertrules:
 
   The version number to use for the EUCAST Expert Rules and Intrinsic
-  Resistance guideline. Can be `"3.3"`, `"3.2"`, or `"3.1"`.
+  Resistance guideline. Can be `"3.3"`.
 
 - ampc_cephalosporin_resistance:
 
@@ -140,8 +140,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
   braakii*, *Citrobacter freundii*, *Citrobacter gillenii*, *Citrobacter
   murliniae*, *Citrobacter rodenticum*, *Citrobacter sedlakii*,
   *Citrobacter werkmanii*, *Citrobacter youngae*, *Enterobacter*,
-  *Hafnia alvei*, *Klebsiella aerogenes*, *Morganella morganii*,
-  *Providencia*, and *Serratia*.
+  *Hafnia alvei*, and *Klebsiella aerogenes*.
 
 - only_sir_columns:
 
@@ -218,9 +217,9 @@ The file containing all interpretive rules is located here:
 <https://github.com/msberends/AMR/blob/main/data-raw/interpretive_rules.tsv>.
 **Note:** Old taxonomic names are replaced with the current taxonomy
 where applicable. For example, *Ochrobactrum anthropi* was renamed to
-*Brucella anthropi* in 2020; the original EUCAST rules v3.1 and v3.2 did
-not yet contain this new taxonomic name. The `AMR` package contains the
-full microbial taxonomy updated until 7th of May, 2026, see
+*Brucella anthropi* in 2020; older interpretive rules may not yet
+contain this new taxonomic name. The `AMR` package contains the full
+microbial taxonomy updated until 7th of May, 2026, see
 [microorganisms](https://amr-for-r.org/reference/microorganisms.md).
 
 ### Custom Rules
@@ -280,31 +279,12 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
   testing.** *Clin Microbiol Infect.* 2013;19(2):141-60;
   [doi:10.1111/j.1469-0691.2011.03703.x](https://doi.org/10.1111/j.1469-0691.2011.03703.x)
 
-- EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes
-  Tables. Version 3.1, 2016.
-  [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf)
-
-- EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020.
-  [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf)
-
-- EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021.
-  [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf)
+- EUCAST Expected Phenotypes.
+  [(link)](https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/)
 
 - EUCAST Breakpoint tables for interpretation of MICs and zone
-  diameters. Version 9.0, 2019.
-  [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
-
-- EUCAST Breakpoint tables for interpretation of MICs and zone
-  diameters. Version 10.0, 2020.
-  [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx)
-
-- EUCAST Breakpoint tables for interpretation of MICs and zone
-  diameters. Version 11.0, 2021.
-  [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx)
-
-- EUCAST Breakpoint tables for interpretation of MICs and zone
-  diameters. Version 12.0, 2022.
-  [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_12.0_Breakpoint_Tables.xlsx)
+  diameters.
+  [(link)](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/)
 
 ## Examples
 

reference/intrinsic_resistant.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -60,12 +60,13 @@
 
     <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 294 079 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID which occurs in <code><a href="microorganisms.html">microorganisms$mo</a></code>. Names can be retrieved using <code><a href="mo_property.html">mo_name()</a></code>.</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 294 079 observations and 3 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID which occurs in <code><a href="microorganisms.html">microorganisms$mo</a></code>. Names can be retrieved using <code><a href="mo_property.html">mo_name()</a></code>.</p></li>
 <li><p><code>ab</code><br> Antimicrobial ID which occurs in <code><a href="antimicrobials.html">antimicrobials$ab</a></code>. Names can be retrieved using <code><a href="ab_property.html">ab_name()</a></code>.</p></li>
+<li><p><code>version</code><br> Guideline name and version.</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 currently based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023).</p>
+    <p>This data set is currently strictly follows <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The</p>
 <p>This data set is internally used by:</p><ul><li><p><code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code> (an <a href="antimicrobial_selectors.html">antimicrobial selector</a>)</p></li>
 <li><p><code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code></p></li>
 <li><p><code><a href="antibiogram.html">wisca()</a></code> to model \(\beta(1, 9999)\) for resistant bug-drug combinations, per <a href="https://doi.org/10.1093/jac/dkv397" class="external-link">doi:10.1093/jac/dkv397</a></p></li>
@@ -82,19 +83,19 @@
     <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">intrinsic_resistant</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 294,079 × 2</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    mo          ab  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>GRAMP     ATM </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>GRAMP     COL </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>GRAMP     NAL </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>GRAMP     PLB </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>GRAMP     TEM </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>ANAER-POS ATM </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ANAER-POS COL </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ANAER-POS NAL </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>ANAER-POS PLB </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ANAER-POS TEM </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 294,079 × 3</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    mo          ab   version                                    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;ab&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> <span style="color: #949494;">B_</span>GRAMP     ATM  'EUCAST Expected Resistant Phenotypes' v1.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>GRAMP     COL  'EUCAST Expected Resistant Phenotypes' v1.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>GRAMP     NAL  'EUCAST Expected Resistant Phenotypes' v1.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>GRAMP     PLB  'EUCAST Expected Resistant Phenotypes' v1.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>GRAMP     TEM  'EUCAST Expected Resistant Phenotypes' v1.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>ANAER-POS ATM  'EUCAST Expected Resistant Phenotypes' v1.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ANAER-POS COL  'EUCAST Expected Resistant Phenotypes' v1.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ANAER-POS NAL  'EUCAST Expected Resistant Phenotypes' v1.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>ANAER-POS PLB  'EUCAST Expected Resistant Phenotypes' v1.2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ANAER-POS TEM  'EUCAST Expected Resistant Phenotypes' v1.2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 294,069 more rows</span></span>
 </code></pre></div>
     </div>
@@ -103,7 +104,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/intrinsic_resistant.md

@@ -15,7 +15,7 @@ intrinsic_resistant
 ## Format
 
 A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 294
-079 observations and 2 variables:
+079 observations and 3 variables:
 
 - `mo`  
   Microorganism ID which occurs in
@@ -29,12 +29,15 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 294
   Names can be retrieved using
   [`ab_name()`](https://amr-for-r.org/reference/ab_property.md).
 
+- `version`  
+  Guideline name and version.
+
 ## Details
 
-This data set is currently based on ['EUCAST Expected Resistant
+This data set is currently strictly follows ['EUCAST Expected Resistant
 Phenotypes'
 v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
-(2023).
+(2023). The
 
 This data set is internally used by:
 
@@ -68,18 +71,18 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
 
 ``` r
 intrinsic_resistant
-#> # A tibble: 294,079 × 2
-#>    mo          ab  
-#>    <mo>        <ab>
-#>  1 B_GRAMP     ATM 
-#>  2 B_GRAMP     COL 
-#>  3 B_GRAMP     NAL 
-#>  4 B_GRAMP     PLB 
-#>  5 B_GRAMP     TEM 
-#>  6 B_ANAER-POS ATM 
-#>  7 B_ANAER-POS COL 
-#>  8 B_ANAER-POS NAL 
-#>  9 B_ANAER-POS PLB 
-#> 10 B_ANAER-POS TEM 
+#> # A tibble: 294,079 × 3
+#>    mo          ab   version                                    
+#>    <mo>        <ab> <chr>                                      
+#>  1 B_GRAMP     ATM  'EUCAST Expected Resistant Phenotypes' v1.2
+#>  2 B_GRAMP     COL  'EUCAST Expected Resistant Phenotypes' v1.2
+#>  3 B_GRAMP     NAL  'EUCAST Expected Resistant Phenotypes' v1.2
+#>  4 B_GRAMP     PLB  'EUCAST Expected Resistant Phenotypes' v1.2
+#>  5 B_GRAMP     TEM  'EUCAST Expected Resistant Phenotypes' v1.2
+#>  6 B_ANAER-POS ATM  'EUCAST Expected Resistant Phenotypes' v1.2
+#>  7 B_ANAER-POS COL  'EUCAST Expected Resistant Phenotypes' v1.2
+#>  8 B_ANAER-POS NAL  'EUCAST Expected Resistant Phenotypes' v1.2
+#>  9 B_ANAER-POS PLB  'EUCAST Expected Resistant Phenotypes' v1.2
+#> 10 B_ANAER-POS TEM  'EUCAST Expected Resistant Phenotypes' v1.2
 #> # ℹ 294,069 more rows
 ```

reference/italicise_taxonomy.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -95,7 +95,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/join.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -189,7 +189,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/key_antimicrobials.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -212,7 +212,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
 </div>
 
 <div class="pkgdown-footer-right">

reference/kurtosis.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</small>
 
 
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@@ -101,7 +101,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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 <div class="pkgdown-footer-right">

reference/like.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -188,7 +188,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/mdro.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -269,7 +269,7 @@ Ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-l
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/mean_amr_distance.html

@@ -7,7 +7,7 @@
 
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@@ -231,7 +231,7 @@
 
 
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-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/microorganisms.codes.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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -190,7 +190,7 @@
 
 
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+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/microorganisms.groups.html

@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</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">
@@ -113,7 +113,7 @@
 
 
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-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/microorganisms.html

@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
 
     <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="">3.0.1.9075</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9091</small>
 
 
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@@ -178,7 +178,7 @@ Public Health Information Network Vocabulary Access and Distribution System (PHI
 
 
     <footer><div class="pkgdown-footer-left">
-  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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reference/mo_matching_score.html

@@ -7,7 +7,7 @@
 
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@@ -146,7 +146,7 @@
 
 
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+  <p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU GPL 2.0</a>. Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in the Netherlands, in collaboration with <a href="https://amr-for-r.org/authors.html">many colleagues from around the world</a>.</p>
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