Built site for AMR@2.1.1.9151: ef02f4a

2025-04-27 16:43:55 +02:00 · 2025-02-15 20:00:11 +00:00 · 2025-02-15 20:00:11 +00:00 · 31e255491c
commit 31e255491c
parent db65f851b3
118 changed files with 333 additions and 316 deletions
--- a/404.html
+++ b/404.html
@ -32,7 +32,7 @@

    <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/LICENSE-text.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/AMR.html
+++ b/articles/AMR.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -519,7 +519,7 @@ columns based on the antibiotic class that your antibiotic 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_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</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>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
 <span><span class="co">#&gt;    date       GEN  </span></span>
@ -537,7 +537,7 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
 <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/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antimicrobial_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</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">bacteria</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">betalactams()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (amoxicillin/clavulanic acid)</span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
@ -574,7 +574,7 @@ in:</p>
 <span></span>
 <span><span class="co"># filtering using AB 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_class_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="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: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin)</span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
@ -592,7 +592,7 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 971 more rows</span></span></span>
 <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/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_class_selectors.html">betalactams</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="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/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</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: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">betalactams()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (amoxicillin/clavulanic acid)</span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
@ -611,7 +611,7 @@ in:</p>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 452 more rows</span></span></span>
 <span></span>
 <span><span class="co"># even works in base R (since R 3.0):</span></span>
-<span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_class_selectors.html">betalactams</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="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</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: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">betalactams()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin) and '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (amoxicillin/clavulanic acid)</span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
@ -693,7 +693,7 @@ should be used. The <code>antibiotics</code> argument in the
 previously mentioned antibiotic class selectors:</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <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>            antibiotics <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_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
+<span>            antibiotics <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">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span></span></code></pre></div>
@ -821,7 +821,7 @@ language to be Spanish using the <code>language</code> argument:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <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>            antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>            antibiotics <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>
 <span>            ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
 <span>            language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
@ -939,7 +939,7 @@ argument must be used. This can be any column in the data, or e.g. an
 <code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> with calculations based on certain columns:</p>
 <div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
 <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>            antibiotics <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_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
+<span>            antibiotics <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">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>            syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span></span>
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/AMR_with_tidymodels.html
+++ b/articles/AMR_with_tidymodels.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -95,7 +95,7 @@ question about the AMR package.</p>
 understanding resistance patterns is crucial for managing effective
 treatments. The <code>AMR</code> R package provides robust tools for
 analysing AMR data, including convenient antibiotic selector functions
-like <code><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_class_selectors.html">betalactams()</a></code>. In
+like <code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code>. In
 this post, we will explore how to use the <code>tidymodels</code>
 framework to predict resistance patterns in the
 <code>example_isolates</code> dataset.</p>
@ -112,7 +112,7 @@ antibiotic classes: aminoglycosides and beta-lactams.</p>
 microorganism based on microbial data. We will:</p>
 <ol style="list-style-type: decimal">
 <li>Preprocess data using the selector functions
-<code><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_class_selectors.html">betalactams()</a></code>.</li>
+<code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code>.</li>
 <li>Define a logistic regression model for prediction.</li>
 <li>Use a structured <code>tidymodels</code> workflow to preprocess,
 train, and evaluate the model.</li>
@ -142,7 +142,7 @@ package.</p>
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span>  masks <span style="color: #0000BB;">stats</span>::filter()</span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">lag()</span>     masks <span style="color: #0000BB;">stats</span>::lag()</span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">recipes</span>::<span style="color: #00BB00;">step()</span>  masks <span style="color: #0000BB;">stats</span>::step()</span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB;">•</span> Dig deeper into tidy modeling with R at <span style="color: #00BB00;">https://www.tmwr.org</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB;">•</span> Search for functions across packages at <span style="color: #00BB00;">https://www.tidymodels.org/find/</span></span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>          <span class="co"># For AMR data analysis</span></span>
 <span></span>
 <span><span class="co"># Load the example_isolates dataset</span></span>
@ -151,7 +151,7 @@ package.</p>
 <span><span class="co"># Select relevant columns for prediction</span></span>
 <span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="co"># select AB results dynamically</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">mo</span>, <span class="fu"><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</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/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</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">betalactams</a></span><span class="op">(</span><span class="op">)</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="co"># replace NAs with NI (not-interpretable)</span></span>
 <span>   <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</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://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span>
 <span>                 <span class="op">~</span><span class="fu">replace_na</span><span class="op">(</span><span class="va">.x</span>, <span class="st">"NI"</span><span class="op">)</span><span class="op">)</span>,</span>
@ -173,7 +173,7 @@ package.</p>
 <p><strong>Explanation:</strong></p>
 <ul>
 <li>
-<code><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_class_selectors.html">betalactams()</a></code>
+<code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code>
 dynamically select columns for antibiotics in these classes.</li>
 <li>
 <code>drop_na()</code> ensures the model receives complete cases for
@ -193,7 +193,7 @@ three steps: preprocessing, model specification, and fitting.</p>
 <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># Define the recipe for data preprocessing</span></span>
 <span><span class="va">resistance_recipe</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">mo</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">data</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">step_corr</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_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, threshold <span class="op">=</span> <span class="fl">0.9</span><span class="op">)</span></span>
+<span>  <span class="fu">step_corr</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">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, threshold <span class="op">=</span> <span class="fl">0.9</span><span class="op">)</span></span>
 <span><span class="va">resistance_recipe</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span></span>
@ -355,7 +355,7 @@ antibiotics. The ROC curve looks like this:</p>
 <p>In this post, we demonstrated how to build a machine learning
 pipeline with the <code>tidymodels</code> framework and the
 <code>AMR</code> package. By combining selector functions like
-<code><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_class_selectors.html">betalactams()</a></code> with
+<code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code> with
 <code>tidymodels</code>, we efficiently prepared data, trained a model,
 and evaluated its performance.</p>
 <p>This workflow is extensible to other antibiotic classes and
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/MDR.html
+++ b/articles/MDR.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/PCA.html
+++ b/articles/PCA.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/datasets.html
+++ b/articles/datasets.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/index.html
+++ b/articles/index.html
@ -7,7 +7,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/resistance_predict.html
+++ b/articles/resistance_predict.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/welcome_to_AMR.html
+++ b/articles/welcome_to_AMR.html
@ -31,7 +31,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/authors.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/index.html
+++ b/index.html
@ -34,7 +34,7 @@

    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -127,7 +127,7 @@
 <div class="section level4">
 <h4 id="filtering-and-selecting-data">Filtering and selecting data<a class="anchor" aria-label="anchor" href="#filtering-and-selecting-data"></a>
 </h4>
-<p>One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called <a href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">antimicrobial class selectors</a>, which work in base R, <code>dplyr</code> and <code>data.table</code>:</p>
+<p>One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antimicrobial columns. This can be done using the so-called <a href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">antimicrobial selectors</a>, which work in base R, <code>dplyr</code> and <code>data.table</code>.</p>
 <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
@ -140,9 +140,9 @@
 <span>         <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</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="co"># antimicrobial selectors:</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">bacteria</span>,</span>
-<span>         <span class="fu"><a href="reference/antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
-<span>         <span class="fu"><a href="reference/antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
-<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antimicrobial_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antimicrobial_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
+<span>         <span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>         <span class="fu"><a href="reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antimicrobial_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
 <table class="table">
 <thead><tr class="header">
 <th align="left">bacteria</th>
@ -246,34 +246,24 @@
 </tr>
 </tbody>
 </table>
-<p>A base R equivalent would be:</p>
-<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
-<span><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span></span>
-<span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span></span>
-<span>                         <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,</span>
-<span>                 <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"bacteria"</span>, <span class="fu"><a href="reference/antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></code></pre></div>
-<p>This base R code will work in any version of R since April 2013 (R-3.0). Moreover, this code works identically with the <code>data.table</code> package, only by starting with:</p>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op">&lt;-</span> <span class="fu">data.table</span><span class="fu">::</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></code></pre></div>
 </div>
 <div class="section level4">
 <h4 id="generating-antibiograms">Generating antibiograms<a class="anchor" aria-label="anchor" href="#generating-antibiograms"></a>
 </h4>
 <p>The <code>AMR</code> package supports generating traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA).</p>
-<p>If used inside R Markdown or Quarto, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<p>If used inside <a href="https://rmarkdown.rstudio.com" class="external-link">R Markdown</a> or <a href="https://quarto.org" class="external-link">Quarto</a>, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p>
+<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
 <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>            antibiotics <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_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
-<table style="width:100%;" class="table">
+<span>            antibiotics <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">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<table class="table">
 <colgroup>
-<col width="18%">
-<col width="13%">
-<col width="12%">
-<col width="13%">
-<col width="13%">
-<col width="13%">
-<col width="13%">
+<col width="16%">
+<col width="14%">
+<col width="14%">
+<col width="14%">
+<col width="10%">
+<col width="14%">
+<col width="14%">
 </colgroup>
 <thead><tr class="header">
 <th align="left">Pathogen</th>
@ -287,107 +277,107 @@
 <tbody>
 <tr class="odd">
 <td align="left">CoNS</td>
-<td align="center">0% (0/43)</td>
-<td align="center">86% (267/309)</td>
-<td align="center">52% (25/48)</td>
-<td align="center">0% (0/43)</td>
-<td align="center">52% (25/48)</td>
-<td align="center">22% (12/55)</td>
+<td align="center">0% (0-8%)</td>
+<td align="center">86% (82-90%)</td>
+<td align="center">52% (37-67%)</td>
+<td align="center">0% (0-8%)</td>
+<td align="center">52% (37-67%)</td>
+<td align="center">22% (12-35%)</td>
 </tr>
 <tr class="even">
 <td align="left"><em>E. coli</em></td>
-<td align="center">100% (171/171)</td>
-<td align="center">98% (451/460)</td>
-<td align="center">100% (422/422)</td>
+<td align="center">100% (98-100%)</td>
+<td align="center">98% (96-99%)</td>
+<td align="center">100% (99-100%)</td>
 <td align="center"></td>
-<td align="center">100% (418/418)</td>
-<td align="center">97% (450/462)</td>
+<td align="center">100% (99-100%)</td>
+<td align="center">97% (96-99%)</td>
 </tr>
 <tr class="odd">
 <td align="left"><em>E. faecalis</em></td>
-<td align="center">0% (0/39)</td>
-<td align="center">0% (0/39)</td>
-<td align="center">100% (38/38)</td>
-<td align="center">0% (0/39)</td>
+<td align="center">0% (0-9%)</td>
+<td align="center">0% (0-9%)</td>
+<td align="center">100% (91-100%)</td>
+<td align="center">0% (0-9%)</td>
 <td align="center"></td>
-<td align="center">0% (0/39)</td>
+<td align="center">0% (0-9%)</td>
 </tr>
 <tr class="even">
 <td align="left"><em>K. pneumoniae</em></td>
 <td align="center"></td>
-<td align="center">90% (52/58)</td>
-<td align="center">100% (51/51)</td>
+<td align="center">90% (79-96%)</td>
+<td align="center">100% (93-100%)</td>
 <td align="center"></td>
-<td align="center">100% (53/53)</td>
-<td align="center">90% (52/58)</td>
+<td align="center">100% (93-100%)</td>
+<td align="center">90% (79-96%)</td>
 </tr>
 <tr class="odd">
 <td align="left"><em>P. aeruginosa</em></td>
 <td align="center"></td>
-<td align="center">100% (30/30)</td>
+<td align="center">100% (88-100%)</td>
 <td align="center"></td>
-<td align="center">0% (0/30)</td>
+<td align="center">0% (0-12%)</td>
 <td align="center"></td>
-<td align="center">100% (30/30)</td>
+<td align="center">100% (88-100%)</td>
 </tr>
 <tr class="even">
 <td align="left"><em>P. mirabilis</em></td>
 <td align="center"></td>
-<td align="center">94% (32/34)</td>
-<td align="center">94% (30/32)</td>
+<td align="center">94% (80-99%)</td>
+<td align="center">94% (79-99%)</td>
 <td align="center"></td>
 <td align="center"></td>
-<td align="center">94% (32/34)</td>
+<td align="center">94% (80-99%)</td>
 </tr>
 <tr class="odd">
 <td align="left"><em>S. aureus</em></td>
 <td align="center"></td>
-<td align="center">99% (231/233)</td>
+<td align="center">99% (97-100%)</td>
 <td align="center"></td>
 <td align="center"></td>
 <td align="center"></td>
-<td align="center">98% (84/86)</td>
+<td align="center">98% (92-100%)</td>
 </tr>
 <tr class="even">
 <td align="left"><em>S. epidermidis</em></td>
-<td align="center">0% (0/44)</td>
-<td align="center">79% (128/163)</td>
+<td align="center">0% (0-8%)</td>
+<td align="center">79% (71-85%)</td>
 <td align="center"></td>
-<td align="center">0% (0/44)</td>
+<td align="center">0% (0-8%)</td>
 <td align="center"></td>
-<td align="center">51% (45/89)</td>
+<td align="center">51% (40-61%)</td>
 </tr>
 <tr class="odd">
 <td align="left"><em>S. hominis</em></td>
 <td align="center"></td>
-<td align="center">92% (74/80)</td>
+<td align="center">92% (84-97%)</td>
 <td align="center"></td>
 <td align="center"></td>
 <td align="center"></td>
-<td align="center">85% (53/62)</td>
+<td align="center">85% (74-93%)</td>
 </tr>
 <tr class="even">
 <td align="left"><em>S. pneumoniae</em></td>
-<td align="center">0% (0/117)</td>
-<td align="center">0% (0/117)</td>
+<td align="center">0% (0-3%)</td>
+<td align="center">0% (0-3%)</td>
 <td align="center"></td>
-<td align="center">0% (0/117)</td>
+<td align="center">0% (0-3%)</td>
 <td align="center"></td>
-<td align="center">0% (0/117)</td>
+<td align="center">0% (0-3%)</td>
 </tr>
 </tbody>
 </table>
 <p>In combination antibiograms, it is clear that combined antibiotics yield higher empiric coverage:</p>
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <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>            antibiotics <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>
 <span>            mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div>
-<table class="table">
+<table style="width:100%;" class="table">
 <colgroup>
 <col width="12%">
 <col width="21%">
 <col width="33%">
-<col width="32%">
+<col width="33%">
 </colgroup>
 <thead><tr class="header">
 <th align="left">Pathogen</th>
@ -398,32 +388,26 @@
 <tbody>
 <tr class="odd">
 <td align="left">Gram-negative</td>
-<td align="center">88% (565/641)</td>
-<td align="center">99% (681/691)</td>
-<td align="center">98% (679/693)</td>
+<td align="center">88% (85-91%)</td>
+<td align="center">99% (97-99%)</td>
+<td align="center">98% (97-99%)</td>
 </tr>
 <tr class="even">
 <td align="left">Gram-positive</td>
-<td align="center">86% (296/345)</td>
-<td align="center">98% (1018/1044)</td>
-<td align="center">95% (524/550)</td>
+<td align="center">86% (82-89%)</td>
+<td align="center">98% (96-98%)</td>
+<td align="center">95% (93-97%)</td>
 </tr>
 </tbody>
 </table>
 <p>Like many other functions in this package, <code><a href="reference/antibiogram.html">antibiogram()</a></code> comes with support for 20 languages that are often detected automatically based on system language:</p>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <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>            antibiotics <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">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span>
 <span>            mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
 <span>            ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
 <span>            language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div>
 <table class="table">
-<colgroup>
-<col width="20%">
-<col width="27%">
-<col width="26%">
-<col width="25%">
-</colgroup>
 <thead><tr class="header">
 <th align="left">Збудник</th>
 <th align="center">Гентаміцин</th>
@ -433,24 +417,57 @@
 <tbody>
 <tr class="odd">
 <td align="left">Грамнегативні</td>
-<td align="center">96% (659/684)</td>
-<td align="center">96% (658/686)</td>
-<td align="center">91% (621/684)</td>
+<td align="center">96% (95-98%)</td>
+<td align="center">96% (94-97%)</td>
+<td align="center">91% (88-93%)</td>
 </tr>
 <tr class="even">
 <td align="left">Грампозитивні</td>
-<td align="center">63% (740/1170)</td>
-<td align="center">34% (228/665)</td>
-<td align="center">77% (560/724)</td>
+<td align="center">63% (60-66%)</td>
+<td align="center">34% (31-38%)</td>
+<td align="center">77% (74-80%)</td>
 </tr>
 </tbody>
 </table>
 </div>
 <div class="section level4">
+<h4 id="interpreting-and-plotting-mic-and-sir-values">Interpreting and plotting MIC and SIR values<a class="anchor" aria-label="anchor" href="#interpreting-and-plotting-mic-and-sir-values"></a>
+</h4>
+<p>The <code>AMR</code> package allows interpretation of MIC and disk diffusion values based on CLSI and EUCAST. Moreover, the <code>ggplot2</code> package is extended with new scale functions, to allow plotting of log2-distributed MIC values and SIR values.</p>
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span>
+<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># generate some random values</span></span>
+<span><span class="va">some_mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
+<span><span class="va">some_groups</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">5</span><span class="op">]</span>, <span class="fl">20</span>, replace <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span><span class="va">interpretation</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">some_mic_values</span>,</span>
+<span>                         guideline <span class="op">=</span> <span class="st">"EUCAST 2024"</span>,</span>
+<span>                         mo <span class="op">=</span> <span class="st">"E. coli"</span>, <span class="co"># or any code or name resembling a known species</span></span>
+<span>                         ab <span class="op">=</span> <span class="st">"Cipro"</span><span class="op">)</span>   <span class="co"># or any code or name resembling an antibiotic</span></span>
+<span></span>
+<span><span class="co"># create the plot</span></span>
+<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>mic <span class="op">=</span> <span class="va">some_mic_values</span>,</span>
+<span>                  group <span class="op">=</span> <span class="va">some_groups</span>,</span>
+<span>                  sir <span class="op">=</span> <span class="va">interpretation</span><span class="op">)</span>,</span>
+<span>       <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">group</span>, y <span class="op">=</span> <span class="va">mic</span>, colour <span class="op">=</span> <span class="va">sir</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggtheme.html" class="external-link">theme_minimal</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_boxplot.html" class="external-link">geom_boxplot</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="cn">NA</span>, colour <span class="op">=</span> <span class="st">"grey"</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_jitter.html" class="external-link">geom_jitter</a></span><span class="op">(</span>width <span class="op">=</span> <span class="fl">0.25</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  </span>
+<span>  <span class="co"># NEW scale function: plot MIC values to x, y, colour or fill</span></span>
+<span>  <span class="fu"><a href="reference/plot.html">scale_y_mic</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
+<span>  </span>
+<span>  <span class="co"># NEW scale function: write out S/I/R in any of the 20 supported languages</span></span>
+<span>  <span class="co">#                     and set colourblind-friendly colours</span></span>
+<span>  <span class="fu"><a href="reference/plot.html">scale_colour_sir</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
+<p><a href="./reference/plotting.html" title="Plotting Helpers for AMR Data Analysis"> <img src="./plot_readme.png" style="max-width: 600px;"></a></p>
+</div>
+<div class="section level4">
 <h4 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a>
 </h4>
 <p>For a manual approach, you can use the <code>resistance</code> or <code><a href="reference/proportion.html">susceptibility()</a></code> function:</p>
-<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="co"># group by ward:</span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -461,7 +478,7 @@
 <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></code></pre></div>
 <table class="table">
 <thead><tr class="header">
-<th align="center">ward</th>
+<th align="left">ward</th>
 <th align="center">GEN_total_R</th>
 <th align="center">GEN_conf_int</th>
 <th align="center">TOB_total_R</th>
@ -469,30 +486,30 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">Clinical</td>
-<td align="center">0.229</td>
+<td align="left">Clinical</td>
+<td align="center">0.2289362</td>
 <td align="center">0.205-0.254</td>
-<td align="center">0.315</td>
+<td align="center">0.3147503</td>
 <td align="center">0.284-0.347</td>
 </tr>
 <tr class="even">
-<td align="center">ICU</td>
-<td align="center">0.290</td>
-<td align="center">0.253-0.330</td>
-<td align="center">0.400</td>
+<td align="left">ICU</td>
+<td align="center">0.2902655</td>
+<td align="center">0.253-0.33</td>
+<td align="center">0.4004739</td>
 <td align="center">0.353-0.449</td>
 </tr>
 <tr class="odd">
-<td align="center">Outpatient</td>
-<td align="center">0.200</td>
+<td align="left">Outpatient</td>
+<td align="center">0.2000000</td>
 <td align="center">0.131-0.285</td>
-<td align="center">0.368</td>
+<td align="center">0.3676471</td>
 <td align="center">0.254-0.493</td>
 </tr>
 </tbody>
 </table>
-<p>Or use <a href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">antimicrobial class selectors</a> to select a series of antibiotic columns:</p>
-<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<p>Or use <a href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">antimicrobial selectors</a> to select a series of antibiotic columns:</p>
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
 <span></span>
@ -500,7 +517,7 @@
 <span>  <span class="co"># group by ward:</span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</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="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_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_class_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</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="va">out</span></span></code></pre></div>
 <table class="table">
@ -539,7 +556,7 @@
 </tr>
 </tbody>
 </table>
-<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span>
 <span><span class="va">out</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/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
@ -586,7 +603,7 @@
 </tr>
 </tbody>
 </table>
-<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span>
 <span><span class="va">out</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/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
@ -666,7 +683,7 @@
 </h4>
 <p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
 <p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
-<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
 <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
 <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
@ -680,13 +697,13 @@
 <ol style="list-style-type: decimal">
 <li>
 <p>Manually, using:</p>
-<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
 <span><span class="fu">remotes</span><span class="fu">::</span><span class="fu">install_github</span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
 </li>
 <li>
 <p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
-<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <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="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,</span>
 <span>                  msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
--- a/news/index.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -48,18 +48,18 @@
    </div>

    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="2.1.1.9150" id="amr-2119150">AMR 2.1.1.9150<a class="anchor" aria-label="anchor" href="#amr-2119150"></a></h2>
+<h2 class="pkg-version" data-toc-text="2.1.1.9151" id="amr-2119151">AMR 2.1.1.9151<a class="anchor" aria-label="anchor" href="#amr-2119151"></a></h2>
 <p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
 <div class="section level5">
-<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9150">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9150"></a></h5>
+<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9151">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9151"></a></h5>
 <p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
 </div>
 <div class="section level3">
-<h3 id="breaking-2-1-1-9150">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9150"></a></h3>
+<h3 id="breaking-2-1-1-9151">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9151"></a></h3>
 <ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents two years ago</li>
 </ul></div>
 <div class="section level3">
-<h3 id="new-2-1-1-9150">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9150"></a></h3>
+<h3 id="new-2-1-1-9151">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9151"></a></h3>
 <ul><li>
 <strong>One Health implementation</strong>
 <ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
@ -101,7 +101,7 @@
 </ul></li>
 <li>
 <strong>Support for <code>tidymodels</code></strong>
-<ul><li>All antimicrobial selectors (such as <code><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_class_selectors.html">betalactams()</a></code>) are now supported in <code>tidymodels</code> packages such as <code>recipe</code> and <code>parsnip</code>. See for more info <a href="https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html">our tutorial</a> on using these AMR functions for predictive modelling.</li>
+<ul><li>All antimicrobial selectors (such as <code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">betalactams()</a></code>) are now supported in <code>tidymodels</code> packages such as <code>recipe</code> and <code>parsnip</code>. See for more info <a href="https://msberends.github.io/AMR/articles/AMR_with_tidymodels.html">our tutorial</a> on using these AMR functions for predictive modelling.</li>
 </ul></li>
 <li>
 <strong>Other</strong>
@ -110,7 +110,7 @@
 </ul></li>
 </ul></div>
 <div class="section level3">
-<h3 id="changed-2-1-1-9150">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9150"></a></h3>
+<h3 id="changed-2-1-1-9151">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9151"></a></h3>
 <ul><li>SIR interpretation
 <ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
 <li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
@ -124,19 +124,19 @@
 <li>The <code>ab_transform</code> argument now defaults to <code>"name"</code>, displaying antibiotic column names instead of codes</li>
 </ul></li>
 <li>Antimicrobial selectors (previously: <em>antibiotic selectors</em>)
-<ul><li>‘Antibiotic selectors’ are now called ‘antimicrobial selectors’ since their scope is broader than just antibiotics. All documentation have been updated, and <code><a href="../reference/AMR-deprecated.html">ab_class()</a></code> and <code><a href="../reference/AMR-deprecated.html">ab_selector()</a></code> have been replaced with <code><a href="../reference/antimicrobial_class_selectors.html">amr_class()</a></code> and <code><a href="../reference/antimicrobial_class_selectors.html">amr_selector()</a></code>. The old functions are now deprecated and will be removed in a future version.</li>
-<li>Added selectors <code><a href="../reference/antimicrobial_class_selectors.html">isoxazolylpenicillins()</a></code>, <code><a href="../reference/antimicrobial_class_selectors.html">monobactams()</a></code>, <code><a href="../reference/antimicrobial_class_selectors.html">nitrofurans()</a></code>, <code><a href="../reference/antimicrobial_class_selectors.html">phenicols()</a></code>, and <code><a href="../reference/antimicrobial_class_selectors.html">rifamycins()</a></code>
+<ul><li>‘Antibiotic selectors’ are now called ‘antimicrobial selectors’ since their scope is broader than just antibiotics. All documentation have been updated, and <code><a href="../reference/AMR-deprecated.html">ab_class()</a></code> and <code><a href="../reference/AMR-deprecated.html">ab_selector()</a></code> have been replaced with <code><a href="../reference/antimicrobial_selectors.html">amr_class()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">amr_selector()</a></code>. The old functions are now deprecated and will be removed in a future version.</li>
+<li>Added selectors <code><a href="../reference/antimicrobial_selectors.html">isoxazolylpenicillins()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">monobactams()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">nitrofurans()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">phenicols()</a></code>, and <code><a href="../reference/antimicrobial_selectors.html">rifamycins()</a></code>
 </li>
-<li>When using antimicrobial selectors that exclude non-treatable drugs (such as gentamicin-high when using <code><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides()</a></code>), the function now always returns a warning that these can be included using <code>only_treatable = FALSE</code>
+<li>When using antimicrobial selectors that exclude non-treatable drugs (such as gentamicin-high when using <code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code>), the function now always returns a warning that these can be included using <code>only_treatable = FALSE</code>
 </li>
 <li>Added a new argument <code>return_all</code> to all selectors, which defaults to <code>TRUE</code> to include any match. With <code>FALSE</code>, the old behaviour, only the first hit for each unique antimicrobial is returned.</li>
 <li>All selectors can now be run as a separate command to retrieve a vector of all possible antimicrobials that the selector can select</li>
-<li>The selectors <code><a href="../reference/antimicrobial_class_selectors.html">lincosamides()</a></code> and <code><a href="../reference/antimicrobial_class_selectors.html">macrolides()</a></code> do not overlap anymore - each antibiotic is now classified as either of these and not both</li>
+<li>The selectors <code><a href="../reference/antimicrobial_selectors.html">lincosamides()</a></code> and <code><a href="../reference/antimicrobial_selectors.html">macrolides()</a></code> do not overlap anymore - each antibiotic is now classified as either of these and not both</li>
 </ul></li>
 <li>
 <code>antibiotics</code> data set
-<ul><li>Added “clindamycin inducible screening” as <code>CLI1</code>. Since clindamycin is a lincosamide, the antimicrobial selector <code><a href="../reference/antimicrobial_class_selectors.html">lincosamides()</a></code> now contains the argument <code>only_treatable = TRUE</code> (similar to other antibiotic selectors that contain non-treatable drugs)</li>
-<li>Added Amorolfine (<code>AMO</code>, D01AE16), which is now also part of the <code><a href="../reference/antimicrobial_class_selectors.html">antifungals()</a></code> selector</li>
+<ul><li>Added “clindamycin inducible screening” as <code>CLI1</code>. Since clindamycin is a lincosamide, the antimicrobial selector <code><a href="../reference/antimicrobial_selectors.html">lincosamides()</a></code> now contains the argument <code>only_treatable = TRUE</code> (similar to other antibiotic selectors that contain non-treatable drugs)</li>
+<li>Added Amorolfine (<code>AMO</code>, D01AE16), which is now also part of the <code><a href="../reference/antimicrobial_selectors.html">antifungals()</a></code> selector</li>
 <li>Added Efflux (<code>EFF</code>), to allow mapping to AMRFinderPlus</li>
 <li>Added Tigemonam (<code>TNM</code>), a monobactam</li>
 </ul></li>
@ -179,7 +179,7 @@
 <li>Added console colours support of <code>sir</code> class for Positron</li>
 </ul></div>
 <div class="section level3">
-<h3 id="other-2-1-1-9150">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9150"></a></h3>
+<h3 id="other-2-1-1-9151">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9151"></a></h3>
 <ul><li>Added Dr. Larisse Bolton as contributor for her fantastic implementation of WISCA in a mathematically solid way</li>
 <li>Added Matthew Saab, Dr. Jordan Stull, and Prof. Javier Sanchez as contributors for their tremendous input on veterinary breakpoints and interpretations</li>
 <li>Greatly improved <code>vctrs</code> integration, a Tidyverse package working in the background for many Tidyverse functions. For users, this means that functions such as <code>dplyr</code>’s <code><a href="https://dplyr.tidyverse.org/reference/bind_rows.html" class="external-link">bind_rows()</a></code>, <code><a href="https://dplyr.tidyverse.org/reference/rowwise.html" class="external-link">rowwise()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/c_across.html" class="external-link">c_across()</a></code> are now supported for e.g. columns of class <code>mic</code>. Despite this, this <code>AMR</code> package is still zero-dependent on any other package, including <code>dplyr</code> and <code>vctrs</code>.</li>
@ -187,7 +187,7 @@
 <li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
 </ul></div>
 <div class="section level3">
-<h3 id="older-versions-2-1-1-9150">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9150"></a></h3>
+<h3 id="older-versions-2-1-1-9151">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9151"></a></h3>
 <p>This changelog only contains changes from AMR v3.0 (February 2025) and later.</p>
 <ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
 <li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
--- a/pkgdown.yml
+++ b/pkgdown.yml
@ -12,7 +12,7 @@ articles:
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
  WHONET: WHONET.html
-last_built: 2025-02-15T12:46Z
+last_built: 2025-02-15T19:56Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
--- a/plot_readme.png
+++ b/plot_readme.png
--- a/reference/AMR-deprecated.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@ -7,7 +7,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/AMR.html
+++ b/reference/AMR.html
@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/WHOCC.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/WHONET.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ab_from_text.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ab_property.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/add_custom_antimicrobials.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -197,7 +197,7 @@
 <span class="r-in"><span><span class="va">x</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   random_column coflu ampicillin</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1    some value     S          R</span>
-<span class="r-in"><span><span class="va">x</span><span class="op">[</span>, <span class="fu"><a href="antimicrobial_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
+<span class="r-in"><span><span class="va">x</span><span class="op">[</span>, <span class="fu"><a href="antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">betalactams()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">coflu</span><span style="color: #0000BB;">' (co-fluampicil) and</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  '</span><span style="color: #0000BB; font-weight: bold;">ampicillin</span><span style="color: #0000BB;">'</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   coflu ampicillin</span>
--- a/reference/add_custom_microorganisms.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/administrable_iv.html
+++ b/reference/administrable_iv.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/administrable_per_os.html
+++ b/reference/administrable_per_os.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/age.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/age_groups.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/aminoglycosides.html
+++ b/reference/aminoglycosides.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/aminopenicillins.html
+++ b/reference/aminopenicillins.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/amr_class.html
+++ b/reference/amr_class.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/amr_selector.html
+++ b/reference/amr_selector.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/antibiogram.html
+++ b/reference/antibiogram.html
@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -106,7 +106,7 @@ Adhering to previously described approaches (see Source) and especially the Baye


 <dt id="arg-antibiotics">antibiotics<a class="anchor" aria-label="anchor" href="#arg-antibiotics"></a></dt>
-<dd><p>vector of any antimicrobial name or code (will be evaluated with <code><a href="as.ab.html">as.ab()</a></code>, column name of <code>x</code>, or (any combinations of) <a href="antimicrobial_class_selectors.html">antimicrobial selectors</a> such as <code><a href="antimicrobial_class_selectors.html">aminoglycosides()</a></code> or <code><a href="antimicrobial_class_selectors.html">carbapenems()</a></code>. For combination antibiograms, this can also be set to values separated with <code>"+"</code>, such as <code>"TZP+TOB"</code> or <code>"cipro + genta"</code>, given that columns resembling such antimicrobials exist in <code>x</code>. See <em>Examples</em>.</p></dd>
+<dd><p>vector of any antimicrobial name or code (will be evaluated with <code><a href="as.ab.html">as.ab()</a></code>, column name of <code>x</code>, or (any combinations of) <a href="antimicrobial_selectors.html">antimicrobial selectors</a> such as <code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> or <code><a href="antimicrobial_selectors.html">carbapenems()</a></code>. For combination antibiograms, this can also be set to values separated with <code>"+"</code>, such as <code>"TZP+TOB"</code> or <code>"cipro + genta"</code>, given that columns resembling such antimicrobials exist in <code>x</code>. See <em>Examples</em>.</p></dd>


 <dt id="arg-mo-transform">mo_transform<a class="anchor" aria-label="anchor" href="#arg-mo-transform"></a></dt>
@ -253,7 +253,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to TZP among respiratory specimens (obtained among ICU patients only)</p>
 <p>Code example:</p>
 <p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
-<span>            antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antimicrobial_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>            antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antimicrobial_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span>,</span>
 <span>            syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></code></pre><p></p></div></li>
 <li><p><strong>Weighted-Incidence Syndromic Combination Antibiogram (WISCA)</strong></p>
 <p>WISCA can be applied to any antibiogram, see the section <em>Explaining WISCA</em> on this page for more information.</p>
@ -406,7 +406,7 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
 <span class="r-in"><span><span class="co"># Traditional antibiogram ----------------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
-<span class="r-in"><span>  antibiotics <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="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  antibiotics <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="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></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>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
@ -428,7 +428,7 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
-<span class="r-in"><span>  antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  ab_transform <span class="op">=</span> <span class="st">"atc"</span>,</span></span>
 <span class="r-in"><span>  mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
@ -442,7 +442,7 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
-<span class="r-in"><span>  antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
 <span class="r-in"><span>  mo_transform <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
@ -494,7 +494,7 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># the data set could contain a filter for e.g. respiratory specimens</span></span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
-<span class="r-in"><span>  antibiotics <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="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  antibiotics <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="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
@ -527,7 +527,7 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
 <span class="r-in"><span><span class="co"># with a custom language, though this will be determined automatically</span></span></span>
 <span class="r-in"><span><span class="co"># (i.e., this table will be in Spanish on Spanish systems)</span></span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">ex1</span>,</span></span>
-<span class="r-in"><span>  antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
 <span class="r-in"><span>  syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">ex1</span><span class="op">$</span><span class="va">ward</span> <span class="op">==</span> <span class="st">"ICU"</span>,</span></span>
 <span class="r-in"><span>    <span class="st">"UCI"</span>, <span class="st">"No UCI"</span></span></span>
@ -568,7 +568,7 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
 <span class="r-in"><span><span class="co"># Print the output for R Markdown / Quarto -----------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">ureido</span> <span class="op">&lt;-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
-<span class="r-in"><span>  antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_class_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  syndromic_group <span class="op">=</span> <span class="st">"ward"</span>,</span></span>
 <span class="r-in"><span>  wisca <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>WISCA must be based on the species level as WISCA parameters are based on</span>
--- a/reference/antibiotics.html
+++ b/reference/antibiotics.html
@ -7,7 +7,7 @@

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/antifungals.html
+++ b/reference/antifungals.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/antimicrobial_class_selectors.html
+++ b/reference/antimicrobial_class_selectors.html
@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Antimicrobial Selectors — antimicrobial_class_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antimicrobial Selectors — antimicrobial_class_selectors"><meta name="description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations.
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Antimicrobial Selectors — antimicrobial_selectors • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.9/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Antimicrobial Selectors — antimicrobial_selectors"><meta name="description" content='These functions allow for filtering rows and selecting columns based on antimicrobial test results that are of a specific antimicrobial class or group, without the need to define the columns or antimicrobial abbreviations.
 In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using:
 library(dplyr)
 my_data_with_all_these_columns %&amp;gt;%
@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -55,7 +55,7 @@ my_data_with_all_these_columns %&amp;gt;%
  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.svg" class="logo" alt=""><h1>Antimicrobial Selectors</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/amr_selectors.R" class="external-link"><code>R/amr_selectors.R</code></a></small>
-      <div class="d-none name"><code>antimicrobial_class_selectors.Rd</code></div>
+      <div class="d-none name"><code>antimicrobial_selectors.Rd</code></div>
    </div>

    <div class="ref-description section level2">
@ -63,7 +63,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <p>In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "kefzol", "CZO" and "J01DB04" will all be picked up using:</p>
 <p></p><div class="sourceCode r"><pre><code><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
 <span><span class="va">my_data_with_all_these_columns</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="fu"><a href="../reference/antimicrobial_class_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">cephalosporins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div>
    </div>

    <div class="section level2">
--- a/reference/antimycobacterials.html
+++ b/reference/antimycobacterials.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
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+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/as.ab.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.av.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.disk.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.mic.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.mo.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.sir.html
+++ b/reference/as.sir.html
@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -782,16 +782,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_given mo_given host_given ab   mo              </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  <span style="color: #BCBCBC;">*</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;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>            </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-02-15 <span style="color: #949494;">12:47:31</span>     4 AMX      B_STRPT… human      AMX  <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-02-15 <span style="color: #949494;">12:47:38</span>     4 genta    Escheri… human      GEN  <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-02-15 <span style="color: #949494;">12:47:38</span>     4 genta    Escheri… human      GEN  <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-02-15 <span style="color: #949494;">12:47:39</span>     4 genta    Escheri… cattle     GEN  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-02-15 <span style="color: #949494;">12:47:39</span>     4 genta    Escheri… cattle     GEN  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-02-15 <span style="color: #949494;">12:47:31</span>     3 AMX      B_STRPT… human      AMX  <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-02-15 <span style="color: #949494;">12:47:38</span>     3 tobra    Escheri… human      TOB  <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-02-15 <span style="color: #949494;">12:47:38</span>     3 tobra    Escheri… human      TOB  <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-02-15 <span style="color: #949494;">12:47:39</span>     3 tobra    Escheri… horses     TOB  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-02-15 <span style="color: #949494;">12:47:39</span>     3 tobra    Escheri… horses     TOB  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-02-15 <span style="color: #949494;">19:57:31</span>     4 AMX      B_STRPT… human      AMX  <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-02-15 <span style="color: #949494;">19:57:38</span>     4 genta    Escheri… human      GEN  <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-02-15 <span style="color: #949494;">19:57:38</span>     4 genta    Escheri… human      GEN  <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-02-15 <span style="color: #949494;">19:57:39</span>     4 genta    Escheri… cattle     GEN  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-02-15 <span style="color: #949494;">19:57:39</span>     4 genta    Escheri… cattle     GEN  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-02-15 <span style="color: #949494;">19:57:31</span>     3 AMX      B_STRPT… human      AMX  <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-02-15 <span style="color: #949494;">19:57:38</span>     3 tobra    Escheri… human      TOB  <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-02-15 <span style="color: #949494;">19:57:38</span>     3 tobra    Escheri… human      TOB  <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-02-15 <span style="color: #949494;">19:57:39</span>     3 tobra    Escheri… horses     TOB  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-02-15 <span style="color: #949494;">19:57:39</span>     3 tobra    Escheri… horses     TOB  <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;, outcome &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
--- a/reference/atc_online.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/av_from_text.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/av_property.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/availability.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/betalactams.html
+++ b/reference/betalactams.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/betalactams_with_inhibitor.html
+++ b/reference/betalactams_with_inhibitor.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/bug_drug_combinations.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/carbapenems.html
+++ b/reference/carbapenems.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/cephalosporins.html
+++ b/reference/cephalosporins.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
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+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/cephalosporins_1st.html
+++ b/reference/cephalosporins_1st.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
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+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/cephalosporins_2nd.html
+++ b/reference/cephalosporins_2nd.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
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+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/cephalosporins_3rd.html
+++ b/reference/cephalosporins_3rd.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
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+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/cephalosporins_4th.html
+++ b/reference/cephalosporins_4th.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
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+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/cephalosporins_5th.html
+++ b/reference/cephalosporins_5th.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/clinical_breakpoints.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/count.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -233,7 +233,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-in"><span>  <span class="co"># (i.e., in this data set columns GEN, TOB, AMK, KAN)</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</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="r-in"><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="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">n_sir</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><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="antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">n_sir</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="co"># Count co-resistance between amoxicillin/clav acid and gentamicin,</span></span></span>
 <span class="r-in"><span>  <span class="co"># so we can see that combination therapy does a lot more than mono therapy.</span></span></span>
--- a/reference/custom_eucast_rules.html
+++ b/reference/custom_eucast_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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/dosage.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/eucast_rules.html
+++ b/reference/eucast_rules.html
@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/example_isolates.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/example_isolates_unclean.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/export_ncbi_biosample.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/first_isolate.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/fluoroquinolones.html
+++ b/reference/fluoroquinolones.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/g.test.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/get_episode.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ggplot_pca.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ggplot_sir.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/glycopeptides.html
+++ b/reference/glycopeptides.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/guess_ab_col.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/index.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -183,7 +183,7 @@
      </dl></div><div class="section level2">
      <h2 id="analysing-data">Analysing data<a class="anchor" aria-label="anchor" href="#analysing-data"></a></h2>

-      <div class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. With <code><a href="../reference/antibiogram.html">antibiogram()</a></code>, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination antibiogram (WISCA). This function also comes with support for R Markdown and Quarto. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antimicrobial_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antimicrobial_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></div>
+      <div class="section-desc"><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. With <code><a href="../reference/antibiogram.html">antibiogram()</a></code>, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination antibiogram (WISCA). This function also comes with support for R Markdown and Quarto. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antimicrobial_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antimicrobial_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p></div>


    </div><div class="section level2">
@ -241,7 +241,7 @@
        <dd>Determine Bug-Drug Combinations</dd>
      </dl><dl><dt>

-          <code><a href="antimicrobial_class_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_class_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_class_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_class_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_class_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_class_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_class_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_class_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_class_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_class_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_class_selectors.html">isoxazolylpenicillins()</a></code> <code><a href="antimicrobial_class_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_class_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_class_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_class_selectors.html">monobactams()</a></code> <code><a href="antimicrobial_class_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_class_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_class_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_class_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_class_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_class_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_class_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_class_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_class_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_class_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_class_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_class_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_class_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_class_selectors.html">not_intrinsic_resistant()</a></code>
+          <code><a href="antimicrobial_selectors.html">amr_class()</a></code> <code><a href="antimicrobial_selectors.html">amr_selector()</a></code> <code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> <code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">antifungals()</a></code> <code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> <code><a href="antimicrobial_selectors.html">betalactams()</a></code> <code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> <code><a href="antimicrobial_selectors.html">carbapenems()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_1st()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_4th()</a></code> <code><a href="antimicrobial_selectors.html">cephalosporins_5th()</a></code> <code><a href="antimicrobial_selectors.html">fluoroquinolones()</a></code> <code><a href="antimicrobial_selectors.html">glycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">isoxazolylpenicillins()</a></code> <code><a href="antimicrobial_selectors.html">lincosamides()</a></code> <code><a href="antimicrobial_selectors.html">lipoglycopeptides()</a></code> <code><a href="antimicrobial_selectors.html">macrolides()</a></code> <code><a href="antimicrobial_selectors.html">monobactams()</a></code> <code><a href="antimicrobial_selectors.html">nitrofurans()</a></code> <code><a href="antimicrobial_selectors.html">oxazolidinones()</a></code> <code><a href="antimicrobial_selectors.html">penicillins()</a></code> <code><a href="antimicrobial_selectors.html">phenicols()</a></code> <code><a href="antimicrobial_selectors.html">polymyxins()</a></code> <code><a href="antimicrobial_selectors.html">quinolones()</a></code> <code><a href="antimicrobial_selectors.html">rifamycins()</a></code> <code><a href="antimicrobial_selectors.html">streptogramins()</a></code> <code><a href="antimicrobial_selectors.html">tetracyclines()</a></code> <code><a href="antimicrobial_selectors.html">trimethoprims()</a></code> <code><a href="antimicrobial_selectors.html">ureidopenicillins()</a></code> <code><a href="antimicrobial_selectors.html">administrable_per_os()</a></code> <code><a href="antimicrobial_selectors.html">administrable_iv()</a></code> <code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code>

        </dt>
        <dd>Antimicrobial Selectors</dd>
@ -272,7 +272,7 @@
      </dl></div><div class="section level2">
      <h2 id="plotting-data">Plotting data<a class="anchor" aria-label="anchor" href="#plotting-data"></a></h2>

-      <div class="section-desc"><p>Use these functions for the plotting part. The <code>scale_*_mic()</code> functions extend the ggplot2 package to allow plotting of MIC values, even within a manually set range. If using <code><a href="../reference/plot.html">plot()</a></code> (base R) or <code>autoplot()</code> (ggplot2) on MIC values or disk diffusion values, the user can set the interpretation guideline to give the bars the right SIR colours. The <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> function is a short wrapper for users not much accustomed to ggplot2 yet. The <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function is a specific function to plot so-called biplots for PCA (principal component analysis).</p></div>
+      <div class="section-desc"><p>Use these functions for the plotting part. The <code>scale_*_mic()</code> functions extend the ggplot2 package to allow plotting of MIC values, even within a manually set range. If using <code><a href="../reference/plot.html">plot()</a></code> (base R) or <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> (ggplot2) on MIC values or disk diffusion values, the user can set the interpretation guideline to give the bars the right SIR colours. The <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> function is a short wrapper for users not much accustomed to ggplot2 yet. The <code><a href="../reference/ggplot_pca.html">ggplot_pca()</a></code> function is a specific function to plot so-called biplots for PCA (principal component analysis).</p></div>


    </div><div class="section level2">
--- a/reference/intrinsic_resistant.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/isoxazolylpenicillins.html
+++ b/reference/isoxazolylpenicillins.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/italicise_taxonomy.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/join.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/key_antimicrobials.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/kurtosis.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/like.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/lincosamides.html
+++ b/reference/lincosamides.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/lipoglycopeptides.html
+++ b/reference/lipoglycopeptides.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/macrolides.html
+++ b/reference/macrolides.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/mdro.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mean_amr_distance.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -74,7 +74,7 @@


 <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
-<dd><p>variables to select (supports <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">tidyselect language</a> such as <code>column1:column4</code> and <code>where(is.mic)</code>, and can thus also be <a href="antimicrobial_class_selectors.html">antimicrobial selectors</a></p></dd>
+<dd><p>variables to select (supports <a href="https://tidyselect.r-lib.org/reference/language.html" class="external-link">tidyselect language</a> such as <code>column1:column4</code> and <code>where(is.mic)</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a></p></dd>


 <dt id="arg-combine-si">combine_SI<a class="anchor" aria-label="anchor" href="#arg-combine-si"></a></dt>
@ -188,7 +188,7 @@
 <span class="r-in"><span>  <span class="co"># support for groups</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><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="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterococcus"</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_species</a></span><span class="op">(</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</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="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">TCY</span>, <span class="fu"><a href="antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</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="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">TCY</span>, <span class="fu"><a href="antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</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="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">mo</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="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span><span class="op">)</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="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">dist</span><span class="op">)</span></span></span>
--- a/reference/microorganisms.codes.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/microorganisms.groups.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/microorganisms.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_matching_score.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_property.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_source.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/monobactams.html
+++ b/reference/monobactams.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/nitrofurans.html
+++ b/reference/nitrofurans.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/not_intrinsic_resistant.html
+++ b/reference/not_intrinsic_resistant.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/oxazolidinones.html
+++ b/reference/oxazolidinones.html
@ -1,8 +1,8 @@
 <html>
  <head>
-    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html" />
+    <meta http-equiv="refresh" content="0;URL=https://msberends.github.io/AMR/reference/antimicrobial_selectors.html" />
    <meta name="robots" content="noindex">
-    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_class_selectors.html">
+    <link rel="canonical" href="https://msberends.github.io/AMR/reference/antimicrobial_selectors.html">
  </head>
 </html>

--- a/reference/pca.html
+++ b/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="">2.1.1.9150</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9151</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/Show More
+++ b/Show More