Built site for AMR@3.0.1.9085: c4069da

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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">

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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">
@@ -73,7 +73,7 @@
 <span><span class="fu">pkgdown</span><span class="fu">::</span><span class="fu"><a href="https://pkgdown.r-lib.org/reference/build_site.html" class="external-link">build_site</a></span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># Code coverage report</span></span>
-<span><span class="fu">covr</span><span class="fu">::</span><span class="fu">package_coverage</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+<span><span class="fu">covr</span><span class="fu">::</span><span class="fu"><a href="http://covr.r-lib.org/reference/package_coverage.html" class="external-link">package_coverage</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <p>From the shell:</p>
 <div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co"># CRAN check from parent directory</span></span>
 <span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="ex">R</span> CMD check AMR</span></code></pre></div>
@@ -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>
+<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="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="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="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="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="cb5-4"><a href="#cb5-4" tabindex="-1"></a><span class="fu">git</span> fetch <span class="at">--tags</span></span></code></pre></div>
+<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">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0 <span class="kw">|</span> <span class="fu">sed</span> <span class="st">'s/v//'</span><span class="va">)</span></span>
+<div class="sourceCode" id="cb7"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" tabindex="-1"></a><span class="va">currenttag</span><span class="op">=</span><span class="va">$(</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="cb6-2"><a href="#cb6-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</span><span class="fu">git</span> describe <span class="at">--tags</span> <span class="at">--abbrev</span><span class="op">=</span>0<span class="va">)</span></span>
+<span id="cb7-2"><a href="#cb7-2" tabindex="-1"></a><span class="va">currenttagfull</span><span class="op">=</span><span class="va">$(</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="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$'</span><span class="va">)</span></span>
+<span id="cb7-3"><a href="#cb7-3" tabindex="-1"></a><span class="va">defaultbranch</span><span class="op">=</span><span class="va">$(</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="cb6-4"><a href="#cb6-4" tabindex="-1"></a><span class="fu">git</span> fetch origin <span class="va">${defaultbranch}</span> <span class="at">--quiet</span></span>
+<span id="cb7-4"><a href="#cb7-4" tabindex="-1"></a><span class="fu">git</span> fetch origin <span class="va">${defaultbranch}</span> <span class="at">--quiet</span></span>
-<span id="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">${defaultbranch})</span></span>
+<span id="cb7-5"><a href="#cb7-5" tabindex="-1"></a><span class="va">currentcommit</span><span class="op">=</span><span class="va">$(</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="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="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="cb6-7"><a href="#cb6-7" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$currentversion</span><span class="st">"</span></span></code></pre></div>
+<span id="cb7-7"><a href="#cb7-7" tabindex="-1"></a><span class="bu">echo</span> <span class="st">"</span><span class="va">$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>

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

articles/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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 09 July 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">2026-07-09</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">2026-07-09</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">2026-07-09</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
+<p>Using so-called antimicrobial class selectors, you can select or
-columns based on the antibiotic class that your antibiotic results are
+filter columns based on the antimicrobial class that your antimicrobial
-in:</p>
+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>

articles/AMR.md

@@ -3,7 +3,7 @@
 **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 09 July 2026.
 
 ## Introduction
 
@@ -51,9 +51,9 @@ structure of your data generally look like this:
 
 |    date    | patient_id |        mo        | AMX | CIP |
 |:----------:|:----------:|:----------------:|:---:|:---:|
-| 2026-06-26 |    abcd    | Escherichia coli |  S  |  S  |
+| 2026-07-09 |    abcd    | Escherichia coli |  S  |  S  |
-| 2026-06-26 |    abcd    | Escherichia coli |  S  |  R  |
+| 2026-07-09 |    abcd    | Escherichia coli |  S  |  R  |
-| 2026-06-26 |    efgh    | Escherichia coli |  R  |  S  |
+| 2026-07-09 |    efgh    | Escherichia coli |  R  |  S  |
 
 ### Needed R packages
 
@@ -196,11 +196,6 @@ 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 +445,11 @@ 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
+Using so-called antimicrobial class selectors, you can select or filter
-columns based on the antibiotic class that your antibiotic results are
+columns based on the antimicrobial class that your antimicrobial results
-in:
+are in:
 
 ``` r
 
@@ -513,7 +508,7 @@ 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 +907,6 @@ 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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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>

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

articles/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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>

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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="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>
-<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>
 <p><strong>Frequency table</strong></p>
 <p>Class: factor &gt; ordered &gt; sir (numeric)<br>
 Length: 500<br>

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

articles/datasets.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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">09 July 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>
@@ -441,8 +441,8 @@ 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 9 July 2026 19:05:33 UTC. Find more info about
-about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
+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>
 <ul>
@@ -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
+<p>It was last updated on 9 July 2026 15:14:59 UTC. Find more info about
-about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
+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>

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 9 July 2026 19:05:33 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)  

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

authors.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

index.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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>
@@ -111,9 +111,9 @@
 <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>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>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><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>
+<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated mei 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>
 </h3>
@@ -146,11 +146,13 @@
 <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; ℹ Determining intrinsic resistance based on 'EUCAST Expected</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;   Resistant Phenotypes' v1.2 (2023). This note will be shown</span></span>
-<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK</span></span>
+<span><span class="co">#&gt;   once per session.</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</span></span>
-<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span>
+<span><span class="co">#&gt;   (tobramycin), AMK (amikacin), and KAN (kanamycin)</span></span>
+<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
+<span><span class="co">#&gt;   (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>
 <span><span class="co">#&gt;    &lt;chr&gt;                        &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span></span>
@@ -179,9 +181,9 @@
 <span><span class="co">#&gt; Warning: invalid microorganism code, NA generated</span></span></code></pre></div>
 <table class="table">
 <colgroup>
-<col width="33%">
+<col width="24%">
-<col width="33%">
+<col width="37%">
-<col width="33%">
+<col width="37%">
 </colgroup>
 <thead><tr>
 <th align="left">Piperacillin/tazobactam</th>
@@ -189,9 +191,9 @@
 <th align="left">Piperacillin/tazobactam + Tobramycin</th>
 </tr></thead>
 <tbody><tr>
-<td align="left">69.9% (64.7-75.2%)</td>
+<td align="left">70% (64.8-75.1%)</td>
-<td align="left">93.7% (92.2-95.1%)</td>
+<td align="left">93.6% (92.1-95%)</td>
-<td align="left">89.8% (86.8-92.3%)</td>
+<td align="left">89.9% (86.9-92.3%)</td>
 </tr></tbody>
 </table>
 <p>WISCA supports stratification by any clinical variable, so you can generate syndrome-specific or ward-specific coverage estimates:</p>
@@ -203,10 +205,10 @@
 <span><span class="co">#&gt; Warning: invalid microorganism code, NA generated</span></span></code></pre></div>
 <table class="table">
 <colgroup>
-<col width="25%">
+<col width="14%">
-<col width="25%">
+<col width="21%">
-<col width="25%">
+<col width="32%">
-<col width="25%">
+<col width="32%">
 </colgroup>
 <thead><tr>
 <th align="left">Syndromic Group</th>
@@ -217,21 +219,21 @@
 <tbody>
 <tr>
 <td align="left">Clinical</td>
-<td align="left">74.6% (69-80.1%)</td>
+<td align="left">74.7% (69-80.3%)</td>
-<td align="left">93.6% (91.9-95.1%)</td>
+<td align="left">93.6% (92-95.2%)</td>
-<td align="left">90.5% (86.9-93%)</td>
+<td align="left">90.4% (86.8-93.1%)</td>
 </tr>
 <tr>
 <td align="left">ICU</td>
-<td align="left">57% (48.7-65.8%)</td>
+<td align="left">56.9% (48.7-66%)</td>
-<td align="left">86.7% (83.7-89.7%)</td>
+<td align="left">86.8% (83.6-90%)</td>
-<td align="left">82.8% (77.9-87.2%)</td>
+<td align="left">82.8% (78.3-87.3%)</td>
 </tr>
 <tr>
 <td align="left">Outpatient</td>
-<td align="left">57.5% (46.5-68.7%)</td>
+<td align="left">57.2% (46-68.2%)</td>
-<td align="left">76.7% (70.6-82.4%)</td>
+<td align="left">76.5% (70.3-82.2%)</td>
-<td align="left">67.5% (57.2-76.7%)</td>
+<td align="left">67.7% (57.3-77.2%)</td>
 </tr>
 </tbody>
 </table>
@@ -240,14 +242,15 @@
 <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
 <span>            mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
 <span>            antimicrobials <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">"AMC"</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>, <span class="st">"TZP"</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)</span></span></code></pre></div>
+<span><span class="co">#&gt; ℹ For `carbapenems()` using columns IPM (imipenem) and MEM</span></span>
+<span><span class="co">#&gt;   (meropenem)</span></span></code></pre></div>
 <table class="table">
 <colgroup>
-<col width="20%">
+<col width="13%">
-<col width="20%">
+<col width="25%">
-<col width="20%">
+<col width="18%">
-<col width="20%">
+<col width="19%">
-<col width="20%">
+<col width="22%">
 </colgroup>
 <thead><tr>
 <th align="left">Pathogen</th>
@@ -280,10 +283,10 @@
 <span>            antimicrobials <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">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <colgroup>
-<col width="25%">
+<col width="12%">
-<col width="25%">
+<col width="21%">
-<col width="25%">
+<col width="32%">
-<col width="25%">
+<col width="32%">
 </colgroup>
 <thead><tr>
 <th align="left">Pathogen</th>
@@ -388,10 +391,6 @@
 <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 +408,16 @@
 <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; ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB</span></span>
-<span><span class="co">#&gt;   (amikacin), and KAN (kanamycin)</span></span>
+<span><span class="co">#&gt;   (tobramycin), AMK (amikacin), and KAN (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 argument: `across(c(aminoglycosides(), polymyxins()),</span></span>
+<span><span class="co">#&gt;   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; ! Introducing NA: only 23 results available for KAN in group:</span></span>
-<span><span class="co">#&gt; (whilst `minimum = 30`).</span></span>
+<span><span class="co">#&gt; ward = "Outpatient" (whilst `minimum = 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>

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
+- **Peer-reviewed**, used in over 175 countries, cited over 100 times,
-  languages
+  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
@@ -36,23 +36,21 @@ 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
+evidence-based methods.
-and reproducible AMR data analysis, that can therefore empower
+
+**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!
+make this a successful and durable project! The `AMR` package was
-
+already cited [over 100
-This work was published in the Journal of Statistical Software (Volume
+times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC)
-104(3); [DOI
+in scientific research.
-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)).
 
 After installing this package, R knows [**~97 000 distinct microbial
 species**](https://amr-for-r.org/reference/microorganisms.md) (updated
-May 2026) and all [**~620 antimicrobial and antiviral
+mei 2026) and all [**~620 antimicrobial and antiviral
 drugs**](https://amr-for-r.org/reference/antimicrobials.md) 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
@@ -118,11 +116,13 @@ 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
+#> ℹ Determining intrinsic resistance based on 'EUCAST Expected
-#>   Phenotypes' v1.2 (2023). This note will be shown once per session.
+#>   Resistant Phenotypes' v1.2 (2023). This note will be shown
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
+#>   once per session.
-#>   (amikacin), and KAN (kanamycin)
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
-#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
+#>   (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  
 #>    <chr>                        <sir> <sir> <sir> <sir> <sir> <sir>
@@ -181,7 +181,7 @@ 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% (64.8-75.1%) | 93.6% (92.1-95%) | 89.9% (86.9-92.3%) |
 
 WISCA supports stratification by any clinical variable, so you can
 generate syndrome-specific or ward-specific coverage estimates:
@@ -197,9 +197,9 @@ 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%) |
+| Clinical | 74.7% (69-80.3%) | 93.6% (92-95.2%) | 90.4% (86.8-93.1%) |
-| ICU | 57% (48.7-65.8%) | 86.7% (83.7-89.7%) | 82.8% (77.9-87.2%) |
+| ICU | 56.9% (48.7-66%) | 86.8% (83.6-90%) | 82.8% (78.3-87.3%) |
-| Outpatient | 57.5% (46.5-68.7%) | 76.7% (70.6-82.4%) | 67.5% (57.2-76.7%) |
+| Outpatient | 57.2% (46-68.2%) | 76.5% (70.3-82.2%) | 67.7% (57.3-77.2%) |
 
 **For AMR surveillance**, traditional antibiograms remain the right tool
 for tracking resistance per species over time:
@@ -209,7 +209,8 @@ for tracking resistance per species over time:
 antibiogram(example_isolates,
             mo_transform = "gramstain",
             antimicrobials = c("AMC", carbapenems(), "TZP"))
-#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
+#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
+#>   (meropenem)
 ```
 
 | Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
@@ -307,10 +308,6 @@ 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 +331,16 @@ 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
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
-#>   (amikacin), and KAN (kanamycin)
+#>   (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 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"
+#> ! Introducing NA: only 23 results available for KAN in group:
-#> (whilst `minimum = 30`).
+#> 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
+- **Peer-reviewed**, used in over 175 countries, cited over 100 times,
-  languages
+  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
@@ -36,23 +36,21 @@ 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
+evidence-based methods.
-and reproducible AMR data analysis, that can therefore empower
+
+**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!
+make this a successful and durable project! The `AMR` package was
-
+already cited [over 100
-This work was published in the Journal of Statistical Software (Volume
+times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC)
-104(3); [DOI
+in scientific research.
-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)).
 
 After installing this package, R knows [**~97 000 distinct microbial
 species**](https://amr-for-r.org/reference/microorganisms.md) (updated
-May 2026) and all [**~620 antimicrobial and antiviral
+mei 2026) and all [**~620 antimicrobial and antiviral
 drugs**](https://amr-for-r.org/reference/antimicrobials.md) 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
@@ -118,11 +116,13 @@ 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
+#> ℹ Determining intrinsic resistance based on 'EUCAST Expected
-#>   Phenotypes' v1.2 (2023). This note will be shown once per session.
+#>   Resistant Phenotypes' v1.2 (2023). This note will be shown
-#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB (tobramycin), AMK
+#>   once per session.
-#>   (amikacin), and KAN (kanamycin)
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
-#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
+#>   (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  
 #>    <chr>                        <sir> <sir> <sir> <sir> <sir> <sir>
@@ -181,7 +181,7 @@ 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% (64.8-75.1%) | 93.6% (92.1-95%) | 89.9% (86.9-92.3%) |
 
 WISCA supports stratification by any clinical variable, so you can
 generate syndrome-specific or ward-specific coverage estimates:
@@ -197,9 +197,9 @@ 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%) |
+| Clinical | 74.7% (69-80.3%) | 93.6% (92-95.2%) | 90.4% (86.8-93.1%) |
-| ICU | 57% (48.7-65.8%) | 86.7% (83.7-89.7%) | 82.8% (77.9-87.2%) |
+| ICU | 56.9% (48.7-66%) | 86.8% (83.6-90%) | 82.8% (78.3-87.3%) |
-| Outpatient | 57.5% (46.5-68.7%) | 76.7% (70.6-82.4%) | 67.5% (57.2-76.7%) |
+| Outpatient | 57.2% (46-68.2%) | 76.5% (70.3-82.2%) | 67.7% (57.3-77.2%) |
 
 **For AMR surveillance**, traditional antibiograms remain the right tool
 for tracking resistance per species over time:
@@ -209,7 +209,8 @@ for tracking resistance per species over time:
 antibiogram(example_isolates,
             mo_transform = "gramstain",
             antimicrobials = c("AMC", carbapenems(), "TZP"))
-#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM (meropenem)
+#> ℹ For `carbapenems()` using columns IPM (imipenem) and MEM
+#>   (meropenem)
 ```
 
 | Pathogen | Amoxicillin/clavulanic acid | Imipenem | Meropenem | Piperacillin/tazobactam |
@@ -307,10 +308,6 @@ 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 +331,16 @@ 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
+#> ℹ For `aminoglycosides()` using columns GEN (gentamicin), TOB
-#>   (amikacin), and KAN (kanamycin)
+#>   (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 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"
+#> ! Introducing NA: only 23 results available for KAN in group:
-#> (whilst `minimum = 30`).
+#> 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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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 +49,15 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="3.0.1.9070" id="amr-3019070">AMR 3.0.1.9070<a class="anchor" aria-label="anchor" href="#amr-3019070"></a></h2>
+<h2 class="pkg-version" data-toc-text="3.0.1.9085" id="amr-3019085">AMR 3.0.1.9085<a class="anchor" aria-label="anchor" href="#amr-3019085"></a></h2>
 <p>Planned as v3.1.0, end of June 2026.</p>
 <div class="section level4">
-<h4 id="breaking-changes-3-0-1-9070">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9070"></a></h4>
+<h4 id="breaking-changes-3-0-1-9085">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9085"></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>
 </ul></div>
 <div class="section level4">
-<h4 id="new-3-0-1-9070">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9070"></a></h4>
+<h4 id="new-3-0-1-9085">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9085"></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 +74,9 @@
 <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-3-0-1-9070">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9070"></a></h4>
+<h4 id="fixed-3-0-1-9085">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9085"></a></h4>
-<ul><li>
+<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 +93,7 @@
 <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 +103,10 @@
 </li>
 </ul></div>
 <div class="section level4">
-<h4 id="updated-3-0-1-9070">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9070"></a></h4>
+<h4 id="updated-3-0-1-9085">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9085"></a></h4>
-<ul><li>Taxonomic update for all microorganisms, now updated to June 2026</li>
+<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 +131,8 @@
 <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">

news/index.md

@@ -1,6 +1,6 @@
 # Changelog
 
-## AMR 3.0.1.9070
+## AMR 3.0.1.9085
 
 Planned as v3.1.0, end of June 2026.
 
@@ -77,6 +77,15 @@ 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 +117,11 @@ 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 +139,11 @@ 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 +199,9 @@ 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: 2026-06-26T07:29Z
+last_built: 2026-07-09T19:12Z
 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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/AMR-options.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/AMR.html

@@ -5,14 +5,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
 ) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
  and doi:10.33612/diss.192486375
 ).
-After installing this package, R knows ~97 000 distinct microbial species (updated May 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 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). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
+After installing this package, R knows ~97 000 distinct microbial species (updated mei 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 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). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
 The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
 The AMR package is a peer-reviewed, free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of many different researchers 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
 ) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
  and doi:10.33612/diss.192486375
 ).
-After installing this package, R knows ~97 000 distinct microbial species (updated May 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 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). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
+After installing this package, R knows ~97 000 distinct microbial species (updated mei 2026) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 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). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
 The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
 
@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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">
@@ -70,7 +70,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
 ) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
  and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
 ).</p>
-<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated May 2026) and all <a href="https://amr-for-r.org/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>
+<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~97 000 distinct microbial species</strong></a> (updated mei 2026) and all <a href="https://amr-for-r.org/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>
 <p>The <code>AMR</code> package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
     </div>
 

reference/AMR.md

@@ -25,7 +25,7 @@ and
 
 After installing this package, R knows [**~97 000 distinct microbial
 species**](https://amr-for-r.org/reference/microorganisms.html) (updated
-May 2026) and all [**~620 antimicrobial and antiviral
+mei 2026) and all [**~620 antimicrobial and antiviral
 drugs**](https://amr-for-r.org/reference/antimicrobials.html) 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

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/WHONET.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/ab_from_text.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/ab_property.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/add_custom_antimicrobials.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/add_custom_microorganisms.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/age.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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> 1  1999-06-30  27  27.02466          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> 2  1968-01-29  58  58.44110         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> 3  1965-12-05  60  60.59178         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> 4  1980-03-01  46  46.35616         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> 5  1949-11-01  76  76.68493         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> 6  1947-02-14  79  79.39726         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> 7  1940-02-19  86  86.38356         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> 8  1988-01-10  38  38.49315         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> 9  1997-08-27  28  28.86575          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> 10 1978-01-26  48  48.44932         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>

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
+#> 1  1999-06-30  27  27.02466          0
-#> 2  1968-01-29  58  58.40548         31
+#> 2  1968-01-29  58  58.44110         31
-#> 3  1965-12-05  60  60.55616         34
+#> 3  1965-12-05  60  60.59178         34
-#> 4  1980-03-01  46  46.32055         19
+#> 4  1980-03-01  46  46.35616         19
-#> 5  1949-11-01  76  76.64932         50
+#> 5  1949-11-01  76  76.68493         50
-#> 6  1947-02-14  79  79.36164         52
+#> 6  1947-02-14  79  79.39726         52
-#> 7  1940-02-19  86  86.34795         59
+#> 7  1940-02-19  86  86.38356         59
-#> 8  1988-01-10  38  38.45753         11
+#> 8  1988-01-10  38  38.49315         11
-#> 9  1997-08-27  28  28.83014          2
+#> 9  1997-08-27  28  28.86575          2
-#> 10 1978-01-26  48  48.41370         21
+#> 10 1978-01-26  48  48.44932         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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/amr-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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/amr_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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/antibiogram.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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>

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.ab.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.av.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.disk.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/as.sir.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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;">07:32:01</span>     1 MIC    amoxicillin Escherich… human      8          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-07-09 <span style="color: #949494;">19:14:46</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;">07:32:01</span>     1 MIC    cipro       Escherich… human      0.256      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-07-09 <span style="color: #949494;">19:14:46</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;">07:32:01</span>     1 DISK   tobra       Escherich… human      16         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-07-09 <span style="color: #949494;">19:14:47</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;">07:32:02</span>     1 DISK   genta       Escherich… human      18         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-07-09 <span style="color: #949494;">19:14:47</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>

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 07:32:01     1 MIC    amoxicillin Escherich… human      8          
+#> 1 2026-07-09 19:14:46     1 MIC    amoxicillin Escherich… human      8          
-#> 2 2026-06-26 07:32:01     1 MIC    cipro       Escherich… human      0.256      
+#> 2 2026-07-09 19:14:46     1 MIC    cipro       Escherich… human      0.256      
-#> 3 2026-06-26 07:32:01     1 DISK   tobra       Escherich… human      16         
+#> 3 2026-07-09 19:14:47     1 DISK   tobra       Escherich… human      16         
-#> 4 2026-06-26 07:32:02     1 DISK   genta       Escherich… human      18         
+#> 4 2026-07-09 19:14:47     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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/av_from_text.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/av_property.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/availability.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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>

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/clinical_breakpoints.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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>
@@ -143,7 +143,7 @@ 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 +156,7 @@ 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>

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
@@ -154,7 +154,7 @@ 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 +167,7 @@ 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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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>

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/custom_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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/dosage.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/example_isolates.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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/example_isolates_unclean.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/first_isolate.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/g.test.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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">
@@ -125,7 +125,7 @@
   <dt>stdres</dt>
 <dd><p>standardized residuals,
     <code>(observed - expected) / sqrt(V)</code>, where <code>V</code> is the
-    residual cell variance (Agresti, 2007, section 2.4.5
+    residual cell variance (<a href="#reference+chisq.test.Rd+R+3AAgresti+3A2007" class="citation">Agresti 2007</a>, section 2.4.5)
     for the case where <code>x</code> is a matrix, <code>n * p * (1 - p)</code> otherwise).</p></dd>
 
 </dl></div>

reference/g.test.md

@@ -93,8 +93,9 @@ A list with class `"htest"` containing the following components:
 - stdres:
 
   standardized residuals, `(observed - expected) / sqrt(V)`, where `V`
-  is the residual cell variance (Agresti, 2007, section 2.4.5 for the
+  is the residual cell variance ([Agresti
-  case where `x` is a matrix, `n * p * (1 - p)` otherwise).
+  2007](#reference+chisq.test.Rd+R+3AAgresti+3A2007), section 2.4.5) for
+  the case where `x` is a matrix, `n * p * (1 - p)` otherwise).
 
 ## Details
 

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/ggplot_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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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">
@@ -113,8 +113,9 @@
 
 
 <dt id="arg-pc-biplot">pc.biplot<a class="anchor" aria-label="anchor" href="#arg-pc-biplot"></a></dt>
-<dd><p>If true, use what Gabriel (1971) refers to as a "principal component
+<dd><p>If true, use what <cite></cite><a href="#reference+biplot.princomp.Rd+R+3AGabriel+3A1971" class="citation">Gabriel (1971)</a> refers to as a
-    biplot", with <code>lambda = 1</code> and observations scaled up by sqrt(n) and
+    “principal component biplot”,
+    with <code>lambda = 1</code> and observations scaled up by sqrt(n) and
     variables scaled down by sqrt(n).  Then inner products between
     variables approximate covariances and distances between observations
     approximate Mahalanobis distance.</p></dd>

reference/ggplot_pca.md

@@ -85,11 +85,12 @@ the changes made based on the source code were:
 
 - pc.biplot:
 
-  If true, use what Gabriel (1971) refers to as a "principal component
+  If true, use what [Gabriel
-  biplot", with `lambda = 1` and observations scaled up by sqrt(n) and
+  (1971)](#reference+biplot.princomp.Rd+R+3AGabriel+3A1971) refers to as
-  variables scaled down by sqrt(n). Then inner products between
+  a “principal component biplot”, with `lambda = 1` and observations
-  variables approximate covariances and distances between observations
+  scaled up by sqrt(n) and variables scaled down by sqrt(n). Then inner
-  approximate Mahalanobis distance.
+  products between variables approximate covariances and distances
+  between observations approximate Mahalanobis distance.
 
 - labels:
 

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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/guess_ab_col.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/index.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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">
@@ -212,13 +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 Expected Phenotypes. <a href="https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/" 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 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>
-<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>
 </ul></div>
 
     <div class="section level2">

reference/interpretive_rules.md

@@ -280,31 +280,12 @@ 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
+- EUCAST Expected Phenotypes.
-  Tables. Version 3.1, 2016.
+  [(link)](https://www.eucast.org/bacteria/important-additional-information/expected-phenotypes/)
-  [(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 Breakpoint tables for interpretation of MICs and zone
-  diameters. Version 9.0, 2019.
+  diameters.
-  [(link)](https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx)
+  [(link)](https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/)
-
-- 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)
 
 ## 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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/italicise_taxonomy.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/join.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/key_antimicrobials.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/kurtosis.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/mdro.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/mean_amr_distance.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/microorganisms.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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/mo_matching_score.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/mo_property.html

@@ -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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/mo_source.html

@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/plot.html

@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 
     <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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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">
@@ -69,21 +69,21 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span><span class="fu">scale_x_sir</span><span class="op">(</span></span>
 <span>  colours_SIR <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>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
 <span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>,</span>
+<span>  eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"EUCAST"</span>,</span>
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">scale_colour_sir</span><span class="op">(</span></span>
 <span>  colours_SIR <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>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
 <span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>,</span>
+<span>  eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"EUCAST"</span>,</span>
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">scale_fill_sir</span><span class="op">(</span></span>
 <span>  colours_SIR <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>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
 <span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>  eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>,</span>
+<span>  eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"EUCAST"</span>,</span>
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span>
 <span></span>

reference/plot.md

@@ -21,21 +21,21 @@ scale_fill_mic(keep_operators = "edges", mic_range = NULL, ...)
 scale_x_sir(
   colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
   language = get_AMR_locale(),
-  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
+  eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
   ...
 )
 
 scale_colour_sir(
   colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
   language = get_AMR_locale(),
-  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
+  eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
   ...
 )
 
 scale_fill_sir(
   colours_SIR = c(S = "#3CAEA3", SDD = "#8FD6C4", I = "#F6D55C", R = "#ED553B"),
   language = get_AMR_locale(),
-  eucast_I = getOption("AMR_guideline", "EUCAST") == "EUCAST",
+  eucast_I = getOption("AMR_guideline", "EUCAST") %like% "EUCAST",
   ...
 )
 

reference/proportion.html

@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
 
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/random.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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/resistance_predict.html

@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
 
     <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="">3.0.1.9070</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9085</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">