Built site for AMR@3.0.0.9019: 60bd631

Built site for AMR@3.0.0.9018: 9b07a85
Built site for AMR@3.0.0.9017: fc72cf9
2025-09-02 08:20:54 +02:00 · 2025-09-01 15:07:43 +00:00 · 2025-08-07 14:35:23 +00:00 · 2025-07-28 10:32:15 +00:00 · 2025-07-23 20:25:40 +00:00 · 2025-07-19 12:16:34 +00:00
104 changed files with 439 additions and 418 deletions
--- a/404.html
+++ b/404.html
@@ -31,7 +31,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -91,7 +91,7 @@
 website update since they are based on randomly created values and the
 page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
 Markdown</a>. However, the methodology remains unchanged. This page was
-generated on 22 June 2025.</p>
+generated on 01 September 2025.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -147,21 +147,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2025-06-22</td>
+<td align="center">2025-09-01</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2025-06-22</td>
+<td align="center">2025-09-01</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2025-06-22</td>
+<td align="center">2025-09-01</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -263,17 +263,17 @@ user input can be used:</p>
 <p>Now we can thus clean our data:</p>
 <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Retrieved values from the </span><span style="color: #0000BB; background-color: #EEEEEE;">microorganisms.codes</span><span style="color: #0000BB;"> data set for "ESCCOL",</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Retrieved values from the </span><span style="color: #0000BB; background-color: #EEEEEE;">`microorganisms.codes`</span><span style="color: #0000BB;"> data set for "ESCCOL",</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   "KLEPNE", "STAAUR", and "STRPNE".</span></span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Microorganism translation was uncertain for four microorganisms. Run</span></span></span>
-<span><span class="co"><span style="color: #0000BB;">#&gt;   </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_uncertainties()</span><span style="color: #0000BB;"> to review these uncertainties, or use</span></span></span>
-<span><span class="co"><span style="color: #0000BB;">#&gt;   </span><span style="color: #0000BB; background-color: #EEEEEE;">add_custom_microorganisms()</span><span style="color: #0000BB;"> to add custom entries.</span></span></span></code></pre></div>
+<span><span class="co"><span style="color: #0000BB;">#&gt;   </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_uncertainties()`</span><span style="color: #0000BB;"> to review these uncertainties, or use</span></span></span>
+<span><span class="co"><span style="color: #0000BB;">#&gt;   </span><span style="color: #0000BB; background-color: #EEEEEE;">`add_custom_microorganisms()`</span><span style="color: #0000BB;"> to add custom entries.</span></span></span></code></pre></div>
 <p>Apparently, there was some uncertainty about the translation to
 taxonomic codes. Let’s check this:</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">Matching scores are based on the resemblance between the input and the full</span></span></span>
-<span><span class="co"><span style="color: #0000BB;">#&gt; taxonomic name, and the pathogenicity in humans. See </span><span style="color: #0000BB; background-color: #EEEEEE;">?mo_matching_score</span><span style="color: #0000BB;">.</span></span></span>
+<span><span class="co"><span style="color: #0000BB;">#&gt; taxonomic name, and the pathogenicity in humans. See </span><span style="color: #0000BB; background-color: #EEEEEE;">`?mo_matching_score`</span><span style="color: #0000BB;">.</span></span></span>
 <span><span class="co">#&gt; <span style="color: #0000BB;">Colour keys: </span><span style="color: #080808; background-color: #FFAFAF;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co">#&gt; <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span></span>
@@ -311,8 +311,8 @@ taxonomic codes. Let’s check this:</p>
 <span><span class="co"><span style="font-style: italic;">#&gt;               periodonticum</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFAFAF;">0.519</span>)</span></span>
 <span><span class="co">#&gt; </span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt; Only the first 10 other matches of each record are shown. Run</span></span></span>
-<span><span class="co"><span style="color: #0000BB;">#&gt; </span><span style="color: #0000BB; background-color: #EEEEEE;">print(mo_uncertainties(), n = ...)</span><span style="color: #0000BB;"> to view more entries, or save</span></span></span>
-<span><span class="co"><span style="color: #0000BB;">#&gt; </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_uncertainties()</span><span style="color: #0000BB;"> to an object.</span></span></span></code></pre></div>
+<span><span class="co"><span style="color: #0000BB;">#&gt; </span><span style="color: #0000BB; background-color: #EEEEEE;">`print(mo_uncertainties(), n = ...)`</span><span style="color: #0000BB;"> to view more entries, or save</span></span></span>
+<span><span class="co"><span style="color: #0000BB;">#&gt; </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_uncertainties()`</span><span style="color: #0000BB;"> to an object.</span></span></span></code></pre></div>
 <p>That’s all good.</p>
 </div>
 <div class="section level3">
@@ -400,9 +400,9 @@ the methods on the <code><a href="../reference/first_isolate.html">first_isolate
 <code class="sourceCode R"><span><span class="va">our_data</span> <span class="op">&lt;-</span> <span class="va">our_data</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/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">ℹ Determining first isolates using an episode length of </span><span style="color: #BB0000; font-weight: bold;">365 days</span></span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">col_mo</span><span style="color: #0000BB;">.</span></span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">col_date</span><span style="color: #0000BB;">.</span></span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient_id</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">col_patient_id</span><span style="color: #0000BB;">.</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">bacteria</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`col_mo`</span><span style="color: #0000BB;">.</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`col_date`</span><span style="color: #0000BB;">.</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient_id</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`col_patient_id`</span><span style="color: #0000BB;">.</span></span></span>
 <span><span class="co">#&gt; <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span></span>
 <span><span class="co"><span style="color: #BB0000;">#&gt;   of 2</span></span></span>
 <span><span class="co">#&gt; <span style="color: #080808;">=&gt; Found </span><span style="color: #080808; font-weight: bold;">2,724 'phenotype-based' first isolates</span><span style="color: #080808;"> (90.8% of total where a</span></span></span>
@@ -523,7 +523,7 @@ in:</p>
 <div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
-<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: #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>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span></span>
@@ -541,7 +541,7 @@ in:</p>
 <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_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">#&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>
 <span><span class="co">#&gt;    bacteria     AMX   AMC  </span></span>
@@ -578,7 +578,7 @@ in:</p>
 <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_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: #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>
 <span><span class="co">#&gt;    <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;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span></span></span>
@@ -596,7 +596,7 @@ in:</p>
 <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_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">#&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>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
@@ -615,7 +615,7 @@ in:</p>
 <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_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">#&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>
 <span><span class="co">#&gt;    patient_id hospital date       bacteria     AMX   AMC   CIP   GEN   first</span></span>
@@ -697,9 +697,9 @@ 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_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">#&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>
+<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>
 <table class="table">
 <colgroup>
 <col width="12%">
@@ -828,7 +828,7 @@ language to be Spanish using the <code>language</code> argument:</p>
 <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>
+<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></code></pre></div>
 <table class="table">
 <colgroup>
@@ -954,9 +954,9 @@ argument must be used. This can be any column in the data, or e.g. an
 <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_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">#&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>
+<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>
 <table class="table">
 <colgroup>
 <col width="10%">
--- a/articles/AMR_for_Python.html
+++ b/articles/AMR_for_Python.html
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -179,9 +179,9 @@ package.</p>
 <span>          mo <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">as.factor</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</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"># drop NAs - the ones without a Gramstain (fungi, etc.)</span></span>
 <span>  <span class="fu">drop_na</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">#&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;">betalactams()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></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;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</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 style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (piperacillin/tazobactam), '</span><span style="color: #0000BB; font-weight: bold;">CZO</span><span style="color: #0000BB;">' (cefazolin), '</span><span style="color: #0000BB; font-weight: bold;">FEP</span><span style="color: #0000BB;">' (cefepime), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">'</span></span></span>
@@ -227,9 +227,9 @@ we have with <code>step_corr()</code>, the necessary parameters can be
 estimated from a training set using <code>prep()</code>:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">prep</span><span class="op">(</span><span class="va">resistance_recipe</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">#&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;">betalactams()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></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;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</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 style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span></span>
 <span><span class="co"><span style="color: #0000BB;">#&gt;   (piperacillin/tazobactam), '</span><span style="color: #0000BB; font-weight: bold;">CZO</span><span style="color: #0000BB;">' (cefazolin), '</span><span style="color: #0000BB; font-weight: bold;">FEP</span><span style="color: #0000BB;">' (cefepime), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">'</span></span></span>
@@ -357,16 +357,16 @@ called since they are stored in the recipe.</p>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 394 × 24</span></span></span>
 <span><span class="co">#&gt;    .pred_class   `.pred_Gram-negative` `.pred_Gram-positive` mo        GEN   TOB</span></span>
 <span><span class="co">#&gt;    <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span>                         <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>                 <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;fct&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> Gram-positive              1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>              8.93<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p…     5     5</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> Gram-positive              3.17<span style="color: #949494;">e</span><span style="color: #BB0000;">- 8</span>              1.00<span style="color: #949494;">e</span>+ 0 Gram-p…     5     1</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gram-negative              9.99<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>              1.42<span style="color: #949494;">e</span><span style="color: #BB0000;">- 3</span> Gram-n…     5     5</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gram-positive              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span>              1   <span style="color: #949494;">e</span>+ 0 Gram-p…     5     5</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gram-negative              9.46<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>              5.42<span style="color: #949494;">e</span><span style="color: #BB0000;">- 2</span> Gram-n…     5     5</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gram-positive              1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>              8.93<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p…     5     5</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gram-positive              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span>              1   <span style="color: #949494;">e</span>+ 0 Gram-p…     1     5</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gram-positive              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span>              1   <span style="color: #949494;">e</span>+ 0 Gram-p…     4     4</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gram-negative              1   <span style="color: #949494;">e</span>+ 0              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> Gram-n…     1     1</span></span>
-<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gram-positive              6.05<span style="color: #949494;">e</span><span style="color: #BB0000;">-11</span>              1.00<span style="color: #949494;">e</span>+ 0 Gram-p…     4     4</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> Gram-positive              1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>             8.93 <span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> Gram-positive              3.17<span style="color: #949494;">e</span><span style="color: #BB0000;">- 8</span>             1.000<span style="color: #949494;">e</span>+ 0 Gram-p…     5     1</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> Gram-negative              9.99<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>             1.42 <span style="color: #949494;">e</span><span style="color: #BB0000;">- 3</span> Gram-n…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> Gram-positive              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span>             1    <span style="color: #949494;">e</span>+ 0 Gram-p…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> Gram-negative              9.46<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>             5.42 <span style="color: #949494;">e</span><span style="color: #BB0000;">- 2</span> Gram-n…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> Gram-positive              1.07<span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span>             8.93 <span style="color: #949494;">e</span><span style="color: #BB0000;">- 1</span> Gram-p…     5     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> Gram-positive              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span>             1    <span style="color: #949494;">e</span>+ 0 Gram-p…     1     5</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> Gram-positive              2.22<span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span>             1    <span style="color: #949494;">e</span>+ 0 Gram-p…     4     4</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> Gram-negative              1   <span style="color: #949494;">e</span>+ 0             2.22 <span style="color: #949494;">e</span><span style="color: #BB0000;">-16</span> Gram-n…     1     1</span></span>
+<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> Gram-positive              6.05<span style="color: #949494;">e</span><span style="color: #BB0000;">-11</span>             1.000<span style="color: #949494;">e</span>+ 0 Gram-p…     4     4</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 384 more rows</span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># ℹ 18 more variables: AMK &lt;int&gt;, KAN &lt;int&gt;, PEN &lt;int&gt;, OXA &lt;int&gt;, FLC &lt;int&gt;,</span></span></span>
 <span><span class="co">#&gt; <span style="color: #949494;">#   AMX &lt;int&gt;, AMC &lt;int&gt;, AMP &lt;int&gt;, TZP &lt;int&gt;, CZO &lt;int&gt;, FEP &lt;int&gt;,</span></span></span>
@@ -712,7 +712,7 @@ into a structured time-series format.</p>
 <span>                   .names <span class="op">=</span> <span class="st">"res_{.col}"</span><span class="op">)</span>, </span>
 <span>            .groups <span class="op">=</span> <span class="st">"drop"</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMX</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_AMC</span><span class="op">)</span> <span class="op">&amp;</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/NA.html" class="external-link">is.na</a></span><span class="op">(</span><span class="va">res_CIP</span><span class="op">)</span><span class="op">)</span> <span class="co"># Drop missing values</span></span>
-<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">col_mo</span><span style="color: #0000BB;">.</span></span></span>
+<span><span class="co">#&gt; <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`col_mo`</span><span style="color: #0000BB;">.</span></span></span>
 <span></span>
 <span><span class="va">data_time</span></span>
 <span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 32 × 5</span></span></span>
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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/WISCA.html
+++ b/articles/WISCA.html
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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
@@ -30,7 +30,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -80,7 +80,7 @@
  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.svg" class="logo" alt=""><h1>Download data sets for download / own use</h1>
            
-            <h4 data-toc-skip class="date">22 June 2025</h4>
+            <h4 data-toc-skip class="date">01 September 2025</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="d-none name"><code>datasets.Rmd</code></div>
@@ -115,7 +115,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
 <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 26 March 2025 16:19:17 UTC. Find more info
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>
@@ -417,15 +417,15 @@ all SNOMED codes as comma separated values.</p>
 <h2 id="antimicrobials-antibiotic-and-antifungal-drugs">
 <code>antimicrobials</code>: Antibiotic and Antifungal Drugs<a class="anchor" aria-label="anchor" href="#antimicrobials-antibiotic-and-antifungal-drugs"></a>
 </h2>
-<p>A data set with 497 rows and 14 columns, containing the following
+<p>A data set with 496 rows and 14 columns, containing the following
 column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>,
 <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>,
 <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>,
 <em>iv_ddd</em>, <em>iv_units</em>, and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antimicrobials</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 1 June 2025 09:54:40 UTC. Find more info about
-the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
+about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -602,7 +602,7 @@ column names:<br><em>guideline</em>, <em>type</em>, <em>host</em>, <em>method</e
 <em>breakpoint_R</em>, <em>uti</em>, and <em>is_SDD</em>.</p>
 <p>This data set is in R available as <code>clinical_breakpoints</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 20 April 2025 10:55:31 UTC. Find more info
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/clinical_breakpoints.html">data
 set here</a>.</p>
 <p><strong>Direct download links:</strong></p>
@@ -790,7 +790,7 @@ column names:<br><em>mo_group</em>, <em>mo</em>, <em>mo_group_name</em>, and
 <p>This data set is in R available as
 <code>microorganisms.groups</code>, after you load the <code>AMR</code>
 package.</p>
-<p>It was last updated on 26 March 2025 16:19:17 UTC. Find more info
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.groups.html">data
 set here</a>.</p>
 <p><strong>Direct download links:</strong></p>
@@ -880,7 +880,7 @@ Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intri
 column names:<br><em>mo</em> and <em>ab</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 28 March 2025 10:17:49 UTC. Find more info
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/intrinsic_resistant.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>
@@ -1156,7 +1156,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
 <em>original_txt</em>, and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you
 load the <code>AMR</code> package.</p>
-<p>It was last updated on 20 April 2025 10:55:31 UTC. Find more info
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/dosage.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>
@@ -1294,7 +1294,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
 <em>MUP</em>, and <em>RIF</em>.</p>
 <p>This data set is in R available as <code>example_isolates</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 15 June 2024 13:33:49 UTC. Find more info
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates.html">data set
 here</a>.</p>
 <p><strong>Example content</strong></p>
@@ -1700,7 +1700,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
 <p>This data set is in R available as
 <code>example_isolates_unclean</code>, after you load the
 <code>AMR</code> package.</p>
-<p>It was last updated on 27 August 2022 18:49:37 UTC. Find more info
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/example_isolates_unclean.html">data
 set here</a>.</p>
 <p><strong>Example content</strong></p>
@@ -1798,8 +1798,8 @@ set here</a>.</p>
 column names:<br><em>code</em> and <em>mo</em>.</p>
 <p>This data set is in R available as <code>microorganisms.codes</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 4 May 2025 16:50:25 UTC. Find more info about
-the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
+about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/microorganisms.codes.html">data
 set here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -1870,7 +1870,7 @@ column names:<br><em>av</em>, <em>name</em>, <em>atc</em>, <em>cid</em>,
 <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you
 load the <code>AMR</code> package.</p>
-<p>It was last updated on 20 October 2023 12:51:48 UTC. Find more info
+<p>It was last updated on 1 September 2025 15:00:00 UTC. Find more info
 about the contents, (scientific) source, and structure of this <a href="https://amr-for-r.org/reference/antimicrobials.html">data set
 here</a>.</p>
 <p><strong>Direct download links:</strong></p>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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/extra.css
+++ b/extra.css
@@ -190,6 +190,15 @@ this shows on top of every sidebar to the right
  }
 }

+.template-reference-topic h3,
+.template-reference-topic h3 code {
+  color: var(--amr-green-dark) !important;
+}
+.template-reference-topic h3 {
+  font-weight: normal;
+  margin-top: 2rem;
+}
+
 /* replace 'Developers' with 'Maintainers' */
 .developers h2 {
  display: none;
--- a/index.html
+++ b/index.html
@@ -33,7 +33,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -99,10 +99,10 @@
 </blockquote>
 <div style="display: flex; font-size: 0.8em;">
 <p style="text-align:left; width: 50%;">
-<small><a href="https://amr-for-r.org/">https://amr-for-r.org</a></small>
+<small><a href="https://amr-for-r.org/">amr-for-r.org</a></small>
 </p>
 <p style="text-align:right; width: 50%;">
-<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank" class="external-link">https://doi.org/10.18637/jss.v104.i03</a></small>
+<small><a href="https://doi.org/10.18637/jss.v104.i03" target="_blank" class="external-link">doi.org/10.18637/jss.v104.i03</a></small>
 </p>
 </div>
 <p><a href="./reference/clinical_breakpoints.html#response-from-clsi-and-eucast"><img src="./endorsement_clsi_eucast.jpg" class="endorse_img" align="right" height="120"></a></p>
@@ -142,14 +142,14 @@
 <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_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>
-<span><span class="co">#&gt; ℹ Using column 'mo' as input for mo_fullname()</span></span>
-<span><span class="co">#&gt; ℹ Using column 'mo' as input for mo_is_gram_negative()</span></span>
-<span><span class="co">#&gt; ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()</span></span>
+<span><span class="co">#&gt; ℹ Using column 'mo' as input for `mo_fullname()`</span></span>
+<span><span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_gram_negative()`</span></span>
+<span><span class="co">#&gt; ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span></span>
 <span><span class="co">#&gt; ℹ Determining intrinsic resistance based on 'EUCAST Expected Resistant</span></span>
 <span><span class="co">#&gt;   Phenotypes' v1.2 (2023). This note will be shown once per session.</span></span>
-<span><span class="co">#&gt; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
+<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span></span>
 <span><span class="co">#&gt;   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
-<span><span class="co">#&gt; ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span>
+<span><span class="co">#&gt; ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span>
 <span><span class="co">#&gt; # A tibble: 35 × 7</span></span>
 <span><span class="co">#&gt;    bacteria                     GEN   TOB   AMK   KAN   IPM   MEM  </span></span>
 <span><span class="co">#&gt;    &lt;chr&gt;                        &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span></span>
@@ -174,9 +174,9 @@
 <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>            antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="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; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
+<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span></span>
 <span><span class="co">#&gt;   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
-<span><span class="co">#&gt; ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></code></pre></div>
+<span><span class="co">#&gt; ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></code></pre></div>
 <table style="width:100%;" class="table">
 <colgroup>
 <col width="14%">
@@ -380,7 +380,7 @@
 <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_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">"grey30"</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>
@@ -407,9 +407,9 @@
 <span><span class="co">#&gt; # A tibble: 3 × 5</span></span>
 <span><span class="co">#&gt;   ward       GEN_total_R GEN_conf_int TOB_total_R TOB_conf_int</span></span>
 <span><span class="co">#&gt;   &lt;chr&gt;            &lt;dbl&gt; &lt;chr&gt;              &lt;dbl&gt; &lt;chr&gt;       </span></span>
-<span><span class="co">#&gt; 1 Clinical     0.2289362 0.205-0.254    0.3147503 0.284-0.347 </span></span>
-<span><span class="co">#&gt; 2 ICU          0.2902655 0.253-0.33     0.4004739 0.353-0.449 </span></span>
-<span><span class="co">#&gt; 3 Outpatient   0.2       0.131-0.285    0.3676471 0.254-0.493</span></span></code></pre></div>
+<span><span class="co">#&gt; 1 Clinical         0.229 0.205-0.254        0.315 0.284-0.347 </span></span>
+<span><span class="co">#&gt; 2 ICU              0.290 0.253-0.33         0.400 0.353-0.449 </span></span>
+<span><span class="co">#&gt; 3 Outpatient       0.2   0.131-0.285        0.368 0.254-0.493</span></span></code></pre></div>
 <p>Or use <a href="https://amr-for-r.org/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://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
@@ -421,40 +421,40 @@
 <span>  <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antimicrobial_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>            <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
-<span><span class="co">#&gt; ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span></span>
+<span><span class="co">#&gt; ℹ For `aminoglycosides()` using columns 'GEN' (gentamicin), 'TOB'</span></span>
 <span><span class="co">#&gt;   (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span></span>
-<span><span class="co">#&gt; ℹ For polymyxins() using column 'COL' (colistin)</span></span>
+<span><span class="co">#&gt; ℹ For `polymyxins()` using column 'COL' (colistin)</span></span>
 <span><span class="co">#&gt; Warning: There was 1 warning in `summarise()`.</span></span>
 <span><span class="co">#&gt; ℹ In argument: `across(c(aminoglycosides(), polymyxins()), resistance)`.</span></span>
 <span><span class="co">#&gt; ℹ In group 3: `ward = "Outpatient"`.</span></span>
 <span><span class="co">#&gt; Caused by warning:</span></span>
 <span><span class="co">#&gt; ! Introducing NA: only 23 results available for KAN in group: ward =</span></span>
-<span><span class="co">#&gt; "Outpatient" (minimum = 30).</span></span>
+<span><span class="co">#&gt; "Outpatient" (`minimum` = 30).</span></span>
 <span><span class="va">out</span></span>
 <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
-<span><span class="co">#&gt;   ward             GEN       TOB       AMK   KAN       COL</span></span>
-<span><span class="co">#&gt;   &lt;chr&gt;          &lt;dbl&gt;     &lt;dbl&gt;     &lt;dbl&gt; &lt;dbl&gt;     &lt;dbl&gt;</span></span>
-<span><span class="co">#&gt; 1 Clinical   0.2289362 0.3147503 0.6258993     1 0.7802956</span></span>
-<span><span class="co">#&gt; 2 ICU        0.2902655 0.4004739 0.6624473     1 0.8574144</span></span>
-<span><span class="co">#&gt; 3 Outpatient 0.2       0.3676471 0.6052632    NA 0.8888889</span></span></code></pre></div>
+<span><span class="co">#&gt;   ward         GEN   TOB   AMK   KAN   COL</span></span>
+<span><span class="co">#&gt;   &lt;chr&gt;      &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
+<span><span class="co">#&gt; 1 Clinical   0.229 0.315 0.626     1 0.780</span></span>
+<span><span class="co">#&gt; 2 ICU        0.290 0.400 0.662     1 0.857</span></span>
+<span><span class="co">#&gt; 3 Outpatient 0.2   0.368 0.605    NA 0.889</span></span></code></pre></div>
 <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>
 <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
-<span><span class="co">#&gt;   ward       gentamicin tobramycin  amikacin kanamycin  colistin</span></span>
-<span><span class="co">#&gt;   &lt;chr&gt;           &lt;dbl&gt;      &lt;dbl&gt;     &lt;dbl&gt;     &lt;dbl&gt;     &lt;dbl&gt;</span></span>
-<span><span class="co">#&gt; 1 Clinical    0.2289362  0.3147503 0.6258993         1 0.7802956</span></span>
-<span><span class="co">#&gt; 2 ICU         0.2902655  0.4004739 0.6624473         1 0.8574144</span></span>
-<span><span class="co">#&gt; 3 Outpatient  0.2        0.3676471 0.6052632        NA 0.8888889</span></span></code></pre></div>
+<span><span class="co">#&gt;   ward       gentamicin tobramycin amikacin kanamycin colistin</span></span>
+<span><span class="co">#&gt;   &lt;chr&gt;           &lt;dbl&gt;      &lt;dbl&gt;    &lt;dbl&gt;     &lt;dbl&gt;    &lt;dbl&gt;</span></span>
+<span><span class="co">#&gt; 1 Clinical        0.229      0.315    0.626         1    0.780</span></span>
+<span><span class="co">#&gt; 2 ICU             0.290      0.400    0.662         1    0.857</span></span>
+<span><span class="co">#&gt; 3 Outpatient      0.2        0.368    0.605        NA    0.889</span></span></code></pre></div>
 <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>
 <span><span class="co">#&gt; # A tibble: 3 × 6</span></span>
-<span><span class="co">#&gt;   ward         J01GB03   J01GB01   J01GB06 J01GB04   J01XB01</span></span>
-<span><span class="co">#&gt;   &lt;chr&gt;          &lt;dbl&gt;     &lt;dbl&gt;     &lt;dbl&gt;   &lt;dbl&gt;     &lt;dbl&gt;</span></span>
-<span><span class="co">#&gt; 1 Clinical   0.2289362 0.3147503 0.6258993       1 0.7802956</span></span>
-<span><span class="co">#&gt; 2 ICU        0.2902655 0.4004739 0.6624473       1 0.8574144</span></span>
-<span><span class="co">#&gt; 3 Outpatient 0.2       0.3676471 0.6052632      NA 0.8888889</span></span></code></pre></div>
+<span><span class="co">#&gt;   ward       J01GB03 J01GB01 J01GB06 J01GB04 J01XB01</span></span>
+<span><span class="co">#&gt;   &lt;chr&gt;        &lt;dbl&gt;   &lt;dbl&gt;   &lt;dbl&gt;   &lt;dbl&gt;   &lt;dbl&gt;</span></span>
+<span><span class="co">#&gt; 1 Clinical     0.229   0.315   0.626       1   0.780</span></span>
+<span><span class="co">#&gt; 2 ICU          0.290   0.400   0.662       1   0.857</span></span>
+<span><span class="co">#&gt; 3 Outpatient   0.2     0.368   0.605      NA   0.889</span></span></code></pre></div>
 </div>
 </div>
 <div class="section level2">
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -49,25 +49,36 @@
    </div>

    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="3.0.0.9004" id="amr-3009004">AMR 3.0.0.9004<a class="anchor" aria-label="anchor" href="#amr-3009004"></a></h2>
+<h2 class="pkg-version" data-toc-text="3.0.0.9019" id="amr-3009019">AMR 3.0.0.9019<a class="anchor" aria-label="anchor" href="#amr-3009019"></a></h2>
+<p>This is primarily a bugfix release, though we added one nice feature too.</p>
 <div class="section level4">
-<h4 id="new-3-0-0-9004">New<a class="anchor" aria-label="anchor" href="#new-3-0-0-9004"></a></h4>
+<h4 id="new-3-0-0-9019">New<a class="anchor" aria-label="anchor" href="#new-3-0-0-9019"></a></h4>
 <ul><li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of MIC and SIR data in modelling pipelines via <code>recipes</code>
 <ul><li>
 <code><a href="../reference/amr-tidymodels.html">step_mic_log2()</a></code> to transform <code>&lt;mic&gt;</code> columns with log2, and <code><a href="../reference/amr-tidymodels.html">step_sir_numeric()</a></code> to convert <code>&lt;sir&gt;</code> columns to numeric</li>
-<li>
-<code>tidyselect</code> helpers: <code><a href="../reference/amr-tidymodels.html">all_mic()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic_predictors()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir_predictors()</a></code>
-</li>
-<li>Enables seamless use of MIC and SIR data in modelling pipelines via <code>recipes</code>
+<li>New <code>tidyselect</code> helpers: <code><a href="../reference/amr-tidymodels.html">all_mic()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_mic_predictors()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir()</a></code>, <code><a href="../reference/amr-tidymodels.html">all_sir_predictors()</a></code>
 </li>
 </ul></li>
 </ul></div>
 <div class="section level4">
-<h4 id="changed-3-0-0-9004">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-0-9004"></a></h4>
+<h4 id="changed-3-0-0-9019">Changed<a class="anchor" aria-label="anchor" href="#changed-3-0-0-9019"></a></h4>
 <ul><li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> for when no antimicrobials are set</li>
+<li>Fixed a bug in <code><a href="../reference/antibiogram.html">antibiogram()</a></code> to allow column names containing the <code>+</code> character (<a href="https://github.com/msberends/AMR/issues/222" class="external-link">#222</a>)</li>
 <li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> for antimicrobial codes with a number in it if they are preceded by a space</li>
 <li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> for using specific custom rules</li>
+<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> to allow any tidyselect language (<a href="https://github.com/msberends/AMR/issues/220" class="external-link">#220</a>)</li>
+<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> to pick right breakpoint when <code>uti = FALSE</code> (<a href="https://github.com/msberends/AMR/issues/216" class="external-link">#216</a>)</li>
+<li>Fixed a bug in <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> when using <code>combine_SI = FALSE</code> (<a href="https://github.com/msberends/AMR/issues/213" class="external-link">#213</a>)</li>
+<li>Fixed a bug the <code>antimicrobials</code> data set to remove statins (<a href="https://github.com/msberends/AMR/issues/229" class="external-link">#229</a>)</li>
+<li>Fixed a bug in <code><a href="../reference/mdro.html">mdro()</a></code> to make sure all genes specified in arguments are acknowledges</li>
+<li>Fixed ATC J01CR05 to map to piperacillin/tazobactam rather than piperacillin/sulbactam (<a href="https://github.com/msberends/AMR/issues/230" class="external-link">#230</a>)</li>
+<li>Fixed all plotting to contain a separate colour for SDD (susceptible dose-dependent) (<a href="https://github.com/msberends/AMR/issues/223" class="external-link">#223</a>)</li>
 <li>Fixed some specific Dutch translations for antimicrobials</li>
+<li>Added all reasons in verbose output of <code><a href="../reference/mdro.html">mdro()</a></code> (<a href="https://github.com/msberends/AMR/issues/227" class="external-link">#227</a>)</li>
+<li>Added <code>names</code> to <code><a href="../reference/age_groups.html">age_groups()</a></code> so that custom names can be given (<a href="https://github.com/msberends/AMR/issues/215" class="external-link">#215</a>)</li>
+<li>Added note to <code><a href="../reference/as.sir.html">as.sir()</a></code> to make it explicit when higher-level taxonomic breakpoints are used (<a href="https://github.com/msberends/AMR/issues/218" class="external-link">#218</a>)</li>
+<li>Added antibiotic codes from the Comprehensive Antibiotic Resistance Database (CARD) to the <code>antimicrobials</code> data set (<a href="https://github.com/msberends/AMR/issues/225" class="external-link">#225</a>)</li>
+<li>Updated Fosfomycin to be of antibiotic class ‘Phosphonics’ (<a href="https://github.com/msberends/AMR/issues/225" class="external-link">#225</a>)</li>
 <li>Updated <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code> to set skewedness of the distribution and allow multiple microorganisms</li>
 </ul></div>
 </div>
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
  PCA: PCA.html
  WHONET: WHONET.html
  WISCA: WISCA.html
-last_built: 2025-06-22T18:50Z
+last_built: 2025-09-01T15:03Z
 urls:
  reference: https://amr-for-r.org/reference
  article: https://amr-for-r.org/articles
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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, Arabic, Bengali, Chinese, Czech, Danish

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -111,7 +111,7 @@
 <span class="r-in"><span>    group <span class="op">=</span> <span class="st">"Test Group"</span></span></span>
 <span class="r-in"><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 Added one record to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">antimicrobials</span><span style="color: #0000BB;"> data set.</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added one record to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">`antimicrobials`</span><span style="color: #0000BB;"> data set.</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># "testab" is now a new antibiotic:</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
@@ -180,7 +180,7 @@
 <span class="r-in"><span>    group <span class="op">=</span> <span class="st">"Beta-lactams/penicillins"</span></span></span>
 <span class="r-in"><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 Added one record to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">antimicrobials</span><span style="color: #0000BB;"> data set.</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added one record to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">`antimicrobials`</span><span style="color: #0000BB;"> data set.</span></span>
 <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"Co-fluampicil"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CR50"</span>
 <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01CR50"</span><span class="op">)</span></span></span>
@@ -197,7 +197,7 @@
 <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_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;">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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1     S          R</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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -109,7 +109,7 @@
 <span class="r-in"><span>    species <span class="op">=</span> <span class="st">"asburiae/cloacae"</span></span></span>
 <span class="r-in"><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 Added </span><span style="color: #0000BB; font-style: italic;">Enterobacter asburiae/cloacae</span><span style="color: #0000BB;"> to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">microorganisms</span><span style="color: #0000BB;"> data</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added </span><span style="color: #0000BB; font-style: italic;">Enterobacter asburiae/cloacae</span><span style="color: #0000BB;"> to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">`microorganisms`</span><span style="color: #0000BB;"> data</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  set.</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># E. asburiae/cloacae is now a new microorganism:</span></span></span>
@@ -204,7 +204,7 @@
 <span class="r-in"><span>    SPECIES <span class="op">=</span> <span class="st">"SPECIES"</span></span></span>
 <span class="r-in"><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 Added </span><span style="color: #0000BB; font-style: italic;">Bacteroides/Parabacteroides</span><span style="color: #0000BB;"> to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">microorganisms</span><span style="color: #0000BB;"> data</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Added </span><span style="color: #0000BB; font-style: italic;">Bacteroides/Parabacteroides</span><span style="color: #0000BB;"> to the internal </span><span style="color: #0000BB; background-color: #EEEEEE;">`microorganisms`</span><span style="color: #0000BB;"> data</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  set.</span></span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"BACTEROIDES / PARABACTEROIDES"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteroides/Parabacteroides"</span>
@@ -225,7 +225,7 @@
 <span class="r-in"><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 Added </span><span style="color: #0000BB; font-style: italic;">Citrobacter braakii</span><span style="color: #0000BB;"> complex and </span><span style="color: #0000BB; font-style: italic;">Citrobacter freundii</span><span style="color: #0000BB;"> complex to the</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  internal </span><span style="color: #0000BB; background-color: #EEEEEE;">microorganisms</span><span style="color: #0000BB;"> data set.</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  internal </span><span style="color: #0000BB; background-color: #EEEEEE;">`microorganisms`</span><span style="color: #0000BB;"> data set.</span></span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</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="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Citrobacter freundii complex" "Citrobacter braakii complex" </span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_species</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="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -112,16 +112,16 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    birth_date age age_exact age_at_y2k</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1980-02-27  45  45.31507         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1953-07-26  71  71.90685         46</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-09-02  75  75.80274         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1986-08-03  38  38.88493         13</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1932-11-19  92  92.58904         67</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1949-03-30  76  76.23014         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1996-06-23  28  28.99726          3</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1963-09-16  61  61.76438         36</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1952-05-16  73  73.10137         47</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14  72  72.60274         47</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1980-02-27  45  45.50959         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1953-07-26  72  72.10137         46</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1949-09-02  75  75.99726         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1986-08-03  39  39.07945         13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1932-11-19  92  92.78356         67</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1949-03-30  76  76.42466         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1996-06-23  29  29.19178          3</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1963-09-16  61  61.95890         36</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1952-05-16  73  73.29589         47</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14  72  72.79726         47</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
--- a/reference/age_groups.html
+++ b/reference/age_groups.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>Split Ages into Age Groups — age_groups • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/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="Split Ages into Age Groups — age_groups"><meta name="description" content="Split ages into age groups defined by the split argument. This allows for easier demographic (antimicrobial resistance) analysis."><meta property="og:description" content="Split ages into age groups defined by the split argument. This allows for easier demographic (antimicrobial resistance) analysis."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
+<!-- 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>Split Ages into Age Groups — age_groups • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/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="Split Ages into Age Groups — age_groups"><meta name="description" content="Split ages into age groups defined by the split argument. This allows for easier demographic (antimicrobial resistance) analysis. The function returns an ordered factor."><meta property="og:description" content="Split ages into age groups defined by the split argument. This allows for easier demographic (antimicrobial resistance) analysis. The function returns an ordered factor."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>


@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -50,12 +50,13 @@
    </div>

    <div class="ref-description section level2">
-    <p>Split ages into age groups defined by the <code>split</code> argument. This allows for easier demographic (antimicrobial resistance) analysis.</p>
+    <p>Split ages into age groups defined by the <code>split</code> argument. This allows for easier demographic (antimicrobial resistance) analysis. The function returns an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a>.</p>
    </div>

    <div class="section level2">
    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">x</span>, split_at <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="fl">12</span>, <span class="fl">25</span>, <span class="fl">55</span>, <span class="fl">75</span><span class="op">)</span>, na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">x</span>, split_at <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="fl">0</span>, <span class="fl">12</span>, <span class="fl">25</span>, <span class="fl">55</span>, <span class="fl">75</span><span class="op">)</span>, names <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  na.rm <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
    </div>

    <div class="section level2">
@@ -70,6 +71,10 @@
 <dd><p>Values to split <code>x</code> at - the default is age groups 0-11, 12-24, 25-54, 55-74 and 75+. See <em>Details</em>.</p></dd>


+<dt id="arg-names">names<a class="anchor" aria-label="anchor" href="#arg-names"></a></dt>
+<dd><p>Optional names to be given to the various age groups.</p></dd>
+
+
 <dt id="arg-na-rm">na.rm<a class="anchor" aria-label="anchor" href="#arg-na-rm"></a></dt>
 <dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether missing values should be removed.</p></dd>

@@ -106,6 +111,10 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
 <span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</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="fl">20</span>, <span class="fl">50</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0-19  0-19  0-19  50+   20-49 50+   50+   20-49 20-49</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Levels: 0-19 &lt; 20-49 &lt; 50+</span>
+<span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</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="fl">20</span>, <span class="fl">50</span><span class="op">)</span>, names <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">"Under 20 years"</span>, <span class="st">"20 to 50 years"</span>, <span class="st">"Over 50 years"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] Under 20 years Under 20 years Under 20 years Over 50 years  20 to 50 years</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [6] Over 50 years  Over 50 years  20 to 50 years 20 to 50 years</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> Levels: Under 20 years &lt; 20 to 50 years &lt; Over 50 years</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># split into groups of ten years</span></span></span>
 <span class="r-in"><span><span class="fu">age_groups</span><span class="op">(</span><span class="va">ages</span>, <span class="fl">1</span><span class="op">:</span><span class="fl">10</span> <span class="op">*</span> <span class="fl">10</span><span class="op">)</span></span></span>
--- a/reference/amr-tidymodels.html
+++ b/reference/amr-tidymodels.html
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -121,100 +121,74 @@ may affect the computations for subsequent operations.</p></dd>

    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidymodels.tidymodels.org" class="external-link">tidymodels</a></span><span class="op">)</span></span></span>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://tidymodels.tidymodels.org" class="external-link">"tidymodels"</a></span><span class="op">)</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"># The below approach formed the basis for this paper: DOI 10.3389/fmicb.2025.1582703</span></span></span>
+<span class="r-in"><span>  <span class="co"># Presence of ESBL genes was predicted based on raw MIC values.</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># example data set in the AMR package</span></span></span>
+<span class="r-in"><span>  <span class="va">esbl_isolates</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># Prepare a binary outcome and convert to ordered factor</span></span></span>
+<span class="r-in"><span>  <span class="va">data</span> <span class="op">&lt;-</span> <span class="va">esbl_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/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>esbl <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">esbl</span>, levels <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="cn">FALSE</span>, <span class="cn">TRUE</span><span class="op">)</span>, ordered <span class="op">=</span> <span class="cn">TRUE</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"># Split into training and testing sets</span></span></span>
+<span class="r-in"><span>  <span class="va">split</span> <span class="op">&lt;-</span> <span class="fu">initial_split</span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">training_data</span> <span class="op">&lt;-</span> <span class="fu">training</span><span class="op">(</span><span class="va">split</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">testing_data</span> <span class="op">&lt;-</span> <span class="fu">testing</span><span class="op">(</span><span class="va">split</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># Create and prep a recipe with MIC log2 transformation</span></span></span>
+<span class="r-in"><span>  <span class="va">mic_recipe</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">esbl</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">training_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="r-in"><span></span></span>
+<span class="r-in"><span>    <span class="co"># Optionally remove non-predictive variables</span></span></span>
+<span class="r-in"><span>    <span class="fu">remove_role</span><span class="op">(</span><span class="va">genus</span>, old_role <span class="op">=</span> <span class="st">"predictor"</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></span>
+<span class="r-in"><span>    <span class="co"># Apply the log2 transformation to all MIC predictors</span></span></span>
+<span class="r-in"><span>    <span class="fu">step_mic_log2</span><span class="op">(</span><span class="fu">all_mic_predictors</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></span>
+<span class="r-in"><span>    <span class="co"># And apply the preparation steps</span></span></span>
+<span class="r-in"><span>    <span class="fu">prep</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"># View prepped recipe</span></span></span>
+<span class="r-in"><span>  <span class="va">mic_recipe</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># Apply the recipe to training and testing data</span></span></span>
+<span class="r-in"><span>  <span class="va">out_training</span> <span class="op">&lt;-</span> <span class="fu">bake</span><span class="op">(</span><span class="va">mic_recipe</span>, new_data <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">out_testing</span> <span class="op">&lt;-</span> <span class="fu">bake</span><span class="op">(</span><span class="va">mic_recipe</span>, new_data <span class="op">=</span> <span class="va">testing_data</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># Fit a logistic regression model</span></span></span>
+<span class="r-in"><span>  <span class="va">fitted</span> <span class="op">&lt;-</span> <span class="fu">logistic_reg</span><span class="op">(</span>mode <span class="op">=</span> <span class="st">"classification"</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">set_engine</span><span class="op">(</span><span class="st">"glm"</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">fit</span><span class="op">(</span><span class="va">esbl</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">out_training</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># Generate predictions on the test set</span></span></span>
+<span class="r-in"><span>  <span class="va">predictions</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">fitted</span>, <span class="va">out_testing</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/bind_cols.html" class="external-link">bind_cols</a></span><span class="op">(</span><span class="va">out_testing</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># Evaluate predictions using standard classification metrics</span></span></span>
+<span class="r-in"><span>  <span class="va">our_metrics</span> <span class="op">&lt;-</span> <span class="fu">metric_set</span><span class="op">(</span><span class="va">accuracy</span>, <span class="va">kap</span>, <span class="va">ppv</span>, <span class="va">npv</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="va">metrics</span> <span class="op">&lt;-</span> <span class="fu">our_metrics</span><span class="op">(</span><span class="va">predictions</span>, truth <span class="op">=</span> <span class="va">esbl</span>, estimate <span class="op">=</span> <span class="va">.pred_class</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span>  <span class="co"># Show performance</span></span></span>
+<span class="r-in"><span>  <span class="va">metrics</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> Loading required package: tidymodels</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Attaching packages</span> ────────────────────────────────────── tidymodels 1.3.0 ──</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom       </span> 1.0.8     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample     </span> 1.3.0</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials       </span> 1.4.0     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble      </span> 3.3.0</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer       </span> 1.0.8     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr       </span> 1.3.1</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata   </span> 1.4.0     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune        </span> 1.3.0</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip     </span> 1.3.2     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows   </span> 1.2.0</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr       </span> 1.0.4     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom       </span> 1.0.9     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample     </span> 1.3.1</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials       </span> 1.4.1     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tibble      </span> 3.3.0</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer       </span> 1.0.9     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr       </span> 1.3.1</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata   </span> 1.5.1     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune        </span> 1.3.0</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip     </span> 1.3.3     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows   </span> 1.3.0</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr       </span> 1.1.0     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes     </span> 1.3.1     <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick   </span> 1.3.2</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span>  masks <span style="color: #0000BB;">stats</span>::filter()</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">lag()</span>     masks <span style="color: #0000BB;">stats</span>::lag()</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <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 class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># The below approach formed the basis for this paper: DOI 10.3389/fmicb.2025.1582703</span></span></span>
-<span class="r-in"><span><span class="co"># Presence of ESBL genes was predicted based on raw MIC values.</span></span></span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># example data set in the AMR package</span></span></span>
-<span class="r-in"><span><span class="va">esbl_isolates</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 500 × 19</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    esbl  genus   AMC   AMP   TZP   CXM   FOX   CTX   CAZ   GEN   TOB   TMP   SXT</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mic&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> FALSE Esch…    32    32     4    64    64  8<span style="color: #BBBBBB;">.00</span>  8<span style="color: #BBBBBB;">.00</span>     1     1  16<span style="color: #BBBBBB;">.0</span>    20</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> FALSE Esch…    32    32     4    64    64  4<span style="color: #BBBBBB;">.00</span>  8<span style="color: #BBBBBB;">.00</span>     1     1  16<span style="color: #BBBBBB;">.0</span>   320</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> FALSE Esch…     4     2    64     8     4  8<span style="color: #BBBBBB;">.00</span>  0.12    16    16   0.5    20</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> FALSE Kleb…    32    32    16    64    64  8<span style="color: #BBBBBB;">.00</span>  8<span style="color: #BBBBBB;">.00</span>     1     1   0.5    20</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> FALSE Esch…    32    32     4     4     4  0.25  2<span style="color: #BBBBBB;">.00</span>     1     1  16<span style="color: #BBBBBB;">.0</span>   320</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> FALSE Citr…    32    32    16    64    64 64<span style="color: #BBBBBB;">.00</span> 32<span style="color: #BBBBBB;">.00</span>     1     1   0.5    20</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> FALSE Morg…    32    32     4    64    64 16<span style="color: #BBBBBB;">.00</span>  2<span style="color: #BBBBBB;">.00</span>     1     1   0.5    20</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> FALSE Prot…    16    32     4     1     4  8<span style="color: #BBBBBB;">.00</span>  0.12     1     1  16<span style="color: #BBBBBB;">.0</span>   320</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> FALSE Ente…    32    32     8    64    64 32<span style="color: #BBBBBB;">.00</span>  4<span style="color: #BBBBBB;">.00</span>     1     1   0.5    20</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> FALSE Citr…    32    32    32    64    64  8<span style="color: #BBBBBB;">.00</span> 64<span style="color: #BBBBBB;">.00</span>     1     1  16<span style="color: #BBBBBB;">.0</span>   320</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 490 more rows</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6 more variables: NIT &lt;mic&gt;, FOS &lt;mic&gt;, CIP &lt;mic&gt;, IPM &lt;mic&gt;, MEM &lt;mic&gt;,</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   COL &lt;mic&gt;</span></span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># Prepare a binary outcome and convert to ordered factor</span></span></span>
-<span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">esbl_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/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>esbl <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a></span><span class="op">(</span><span class="va">esbl</span>, levels <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="cn">FALSE</span>, <span class="cn">TRUE</span><span class="op">)</span>, ordered <span class="op">=</span> <span class="cn">TRUE</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"># Split into training and testing sets</span></span></span>
-<span class="r-in"><span><span class="va">split</span> <span class="op">&lt;-</span> <span class="fu">initial_split</span><span class="op">(</span><span class="va">data</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">training_data</span> <span class="op">&lt;-</span> <span class="fu">training</span><span class="op">(</span><span class="va">split</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">testing_data</span> <span class="op">&lt;-</span> <span class="fu">testing</span><span class="op">(</span><span class="va">split</span><span class="op">)</span></span></span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># Create and prep a recipe with MIC log2 transformation</span></span></span>
-<span class="r-in"><span><span class="va">mic_recipe</span> <span class="op">&lt;-</span> <span class="fu">recipe</span><span class="op">(</span><span class="va">esbl</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">training_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="r-in"><span>  <span class="co"># Optionally remove non-predictive variables</span></span></span>
-<span class="r-in"><span>  <span class="fu">remove_role</span><span class="op">(</span><span class="va">genus</span>, old_role <span class="op">=</span> <span class="st">"predictor"</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="co"># Apply the log2 transformation to all MIC predictors</span></span></span>
-<span class="r-in"><span>  <span class="fu">step_mic_log2</span><span class="op">(</span><span class="fu">all_mic_predictors</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">prep</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"># View prepped recipe</span></span></span>
-<span class="r-in"><span><span class="va">mic_recipe</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">──</span> <span style="font-weight: bold;">Recipe</span> <span style="color: #00BBBB;">──────────────────────────────────────────────────────────────────────</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ── Inputs </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Number of variables by role</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> outcome:          1</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> predictor:       17</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> undeclared role:  1</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ── Training information </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> Training data contained 375 data points and no incomplete rows.</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ── Operations </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">•</span> Log2 transformation of MIC columns: <span style="color: #0000BB;">AMC</span>, <span style="color: #0000BB;">AMP</span>, <span style="color: #0000BB;">TZP</span>, <span style="color: #0000BB;">CXM</span>, <span style="color: #0000BB;">FOX</span>, ... | <span style="font-style: italic;">Trained</span></span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># Apply the recipe to training and testing data</span></span></span>
-<span class="r-in"><span><span class="va">out_training</span> <span class="op">&lt;-</span> <span class="fu">bake</span><span class="op">(</span><span class="va">mic_recipe</span>, new_data <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">out_testing</span> <span class="op">&lt;-</span> <span class="fu">bake</span><span class="op">(</span><span class="va">mic_recipe</span>, new_data <span class="op">=</span> <span class="va">testing_data</span><span class="op">)</span></span></span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># Fit a logistic regression model</span></span></span>
-<span class="r-in"><span><span class="va">fitted</span> <span class="op">&lt;-</span> <span class="fu">logistic_reg</span><span class="op">(</span>mode <span class="op">=</span> <span class="st">"classification"</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">set_engine</span><span class="op">(</span><span class="st">"glm"</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">fit</span><span class="op">(</span><span class="va">esbl</span> <span class="op">~</span> <span class="va">.</span>, data <span class="op">=</span> <span class="va">out_training</span><span class="op">)</span></span></span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>glm.fit: fitted probabilities numerically 0 or 1 occurred</span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># Generate predictions on the test set</span></span></span>
-<span class="r-in"><span><span class="va">predictions</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/stats/predict.html" class="external-link">predict</a></span><span class="op">(</span><span class="va">fitted</span>, <span class="va">out_testing</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/bind_cols.html" class="external-link">bind_cols</a></span><span class="op">(</span><span class="va">out_testing</span><span class="op">)</span></span></span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># Evaluate predictions using standard classification metrics</span></span></span>
-<span class="r-in"><span><span class="va">our_metrics</span> <span class="op">&lt;-</span> <span class="fu">metric_set</span><span class="op">(</span><span class="va">accuracy</span>, <span class="va">kap</span>, <span class="va">ppv</span>, <span class="va">npv</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="va">metrics</span> <span class="op">&lt;-</span> <span class="fu">our_metrics</span><span class="op">(</span><span class="va">predictions</span>, truth <span class="op">=</span> <span class="va">esbl</span>, estimate <span class="op">=</span> <span class="va">.pred_class</span><span class="op">)</span></span></span>
-<span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># Show performance:</span></span></span>
-<span class="r-in"><span><span class="co"># - negative predictive value (NPV) of ~98%</span></span></span>
-<span class="r-in"><span><span class="co"># - positive predictive value (PPV) of ~94%</span></span></span>
-<span class="r-in"><span><span class="va">metrics</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 3</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   .metric  .estimator .estimate</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -408,9 +408,9 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <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>  antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="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;">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>
-<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>
+<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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 10 × 7</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type:           Non-WISCA with 95% CI</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    Pathogen       Amikacin    Gentamicin Imipenem Kanamycin Meropenem Tobramycin</span>
@@ -433,7 +433,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <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></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;">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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type:           Non-WISCA with 95% CI</span></span>
@@ -449,7 +449,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <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></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;">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 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 5 × 3</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type:           Non-WISCA with 95% CI</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   Pathogen                                 Imipenem             Meropenem       </span>
@@ -487,7 +487,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <span class="r-in"><span>  antimicrobials <span class="op">=</span> <span class="fu"><a href="antimicrobial_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">""</span>, <span class="st">"GEN"</span>, <span class="st">"tobra"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  mo_transform <span class="op">=</span> <span class="st">"gramstain"</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;">ureidopenicillins()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</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;">`ureidopenicillins()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 4</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type:           Non-WISCA with 95% CI</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   Pathogen  Piperacillin/tazobac…¹ Piperacillin/tazobac…² Piperacillin/tazobac…³</span>
@@ -524,9 +524,9 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <span class="r-in"><span>  antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="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></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;">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>
-<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>
+<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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 14 × 8</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type:           Non-WISCA with 95% CI</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    `Syndromic Group` Pathogen   Amikacin Gentamicin Imipenem Kanamycin Meropenem</span>
@@ -551,7 +551,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># now define a data set with only E. coli</span></span></span>
 <span class="r-in"><span><span class="va">ex1</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</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">"Escherichia"</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 Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_genus()</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_genus()`</span></span>
 <span class="r-in"><span></span></span>
 <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>
@@ -563,7 +563,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <span class="r-in"><span>  <span class="op">)</span>,</span></span>
 <span class="r-in"><span>  language <span class="op">=</span> <span class="st">"es"</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;">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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Type:           Non-WISCA with 95% CI</span></span>
@@ -603,7 +603,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
 <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></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;">ureidopenicillins()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</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;">`ureidopenicillins()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># in an Rmd file, you would just need to return `ureido` in a chunk,</span></span></span>
 <span class="r-in"><span><span class="co"># but to be explicit here:</span></span></span>
--- a/reference/antimicrobial_selectors.html
+++ b/reference/antimicrobial_selectors.html
@@ -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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -216,7 +216,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <ul><li><p><code>aminoglycosides()</code> can select: <br> amikacin (AMK), amikacin/fosfomycin (AKF), apramycin (APR), arbekacin (ARB), astromicin (AST), bekanamycin (BEK), dibekacin (DKB), framycetin (FRM), gentamicin (GEN), gentamicin-high (GEH), habekacin (HAB), hygromycin (HYG), isepamicin (ISE), kanamycin (KAN), kanamycin-high (KAH), kanamycin/cephalexin (KAC), micronomicin (MCR), neomycin (NEO), netilmicin (NET), pentisomicin (PIM), plazomicin (PLZ), propikacin (PKA), ribostamycin (RST), sisomicin (SIS), streptoduocin (STR), streptomycin (STR1), streptomycin-high (STH), tobramycin (TOB), and tobramycin-high (TOH)</p></li>
 <li><p><code>aminopenicillins()</code> can select: <br> amoxicillin (AMX) and ampicillin (AMP)</p></li>
 <li><p><code>antifungals()</code> can select: <br> amorolfine (AMO), amphotericin B (AMB), amphotericin B-high (AMH), anidulafungin (ANI), butoconazole (BUT), caspofungin (CAS), ciclopirox (CIX), clotrimazole (CTR), econazole (ECO), fluconazole (FLU), flucytosine (FCT), fosfluconazole (FFL), griseofulvin (GRI), hachimycin (HCH), ibrexafungerp (IBX), isavuconazole (ISV), isoconazole (ISO), itraconazole (ITR), ketoconazole (KET), manogepix (MGX), micafungin (MIF), miconazole (MCZ), nystatin (NYS), oteseconazole (OTE), pimaricin (PMR), posaconazole (POS), rezafungin (RZF), ribociclib (RBC), sulconazole (SUC), terbinafine (TRB), terconazole (TRC), and voriconazole (VOR)</p></li>
-<li><p><code>antimycobacterials()</code> can select: <br> 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), simvastatin/fenofibrate (SMF), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)</p></li>
+<li><p><code>antimycobacterials()</code> can select: <br> 4-aminosalicylic acid (AMA), calcium aminosalicylate (CLA), capreomycin (CAP), clofazimine (CLF), delamanid (DLM), enviomycin (ENV), ethambutol (ETH), ethambutol/isoniazid (ETI), ethionamide (ETI1), isoniazid (INH), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), morinamide (MRN), p-aminosalicylic acid (PAS), pretomanid (PMD), protionamide (PTH), pyrazinamide (PZA), rifabutin (RIB), rifampicin (RIF), rifampicin/ethambutol/isoniazid (REI), rifampicin/isoniazid (RFI), rifampicin/pyrazinamide/ethambutol/isoniazid (RPEI), rifampicin/pyrazinamide/isoniazid (RPI), rifamycin (RFM), rifapentine (RFP), sodium aminosalicylate (SDA), streptomycin/isoniazid (STI), terizidone (TRZ), thioacetazone (TAT), thioacetazone/isoniazid (THI1), tiocarlide (TCR), and viomycin (VIO)</p></li>
 <li><p><code>betalactams()</code> can select: <br> amoxicillin (AMX), amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin (AMP), ampicillin/sulbactam (SAM), apalcillin (APL), aspoxicillin (APX), azidocillin (AZD), azlocillin (AZL), aztreonam (ATM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), bacampicillin (BAM), benzathine benzylpenicillin (BNB), benzathine phenoxymethylpenicillin (BNP), benzylpenicillin (PEN), benzylpenicillin screening test (PEN-S), biapenem (BIA), carbenicillin (CRB), carindacillin (CRN), carumonam (CAR), cefacetrile (CAC), cefaclor (CEC), cefadroxil (CFR), cefalexin (LEX), cefaloridine (RID), cefalotin (CEP), cefamandole (MAN), cefapirin (HAP), cefatrizine (CTZ), cefazedone (CZD), cefazolin (CZO), cefcapene (CCP), cefcapene pivoxil (CCX), cefdinir (CDR), cefditoren (DIT), cefditoren pivoxil (DIX), cefepime (FEP), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefetamet (CAT), cefetamet pivoxil (CPI), cefetecol (CCL), cefetrizole (CZL), cefiderocol (FDC), cefixime (CFM), cefmenoxime (CMX), cefmetazole (CMZ), cefodizime (DIZ), cefonicid (CID), cefoperazone (CFP), cefoperazone/sulbactam (CSL), ceforanide (CND), cefoselis (CSE), cefotaxime (CTX), cefotaxime screening test (CTX-S), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefotetan (CTT), cefotiam (CTF), cefotiam hexetil (CHE), cefovecin (FOV), cefoxitin (FOX), cefoxitin screening test (FOX-S), cefozopran (ZOP), cefpimizole (CFZ), cefpiramide (CPM), cefpirome (CPO), cefpodoxime (CPD), cefpodoxime proxetil (CPX), cefpodoxime/clavulanic acid (CDC), cefprozil (CPR), cefquinome (CEQ), cefroxadine (CRD), cefsulodin (CFS), cefsumide (CSU), ceftaroline (CPT), ceftaroline/avibactam (CPA), ceftazidime (CAZ), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), cefteram (CEM), cefteram pivoxil (CPL), ceftezole (CTL), ceftibuten (CTB), ceftiofur (TIO), ceftizoxime (CZX), ceftizoxime alapivoxil (CZP), ceftobiprole (BPR), ceftobiprole medocaril (CFM1), ceftolozane/tazobactam (CZT), ceftriaxone (CRO), ceftriaxone/beta-lactamase inhibitor (CEB), cefuroxime (CXM), cefuroxime axetil (CXA), cephradine (CED), ciclacillin (CIC), clometocillin (CLM), cloxacillin (CLO), dicloxacillin (DIC), doripenem (DOR), epicillin (EPC), ertapenem (ETP), flucloxacillin (FLC), hetacillin (HET), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), latamoxef (LTM), lenampicillin (LEN), loracarbef (LOR), mecillinam (MEC), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), metampicillin (MTM), meticillin (MET), mezlocillin (MEZ), mezlocillin/sulbactam (MSU), nafcillin (NAF), oxacillin (OXA), oxacillin screening test (OXA-S), panipenem (PAN), penamecillin (PNM), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), pheneticillin (PHE), phenoxymethylpenicillin (PHN), piperacillin (PIP), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), piridicillin (PRC), pivampicillin (PVM), pivmecillinam (PME), procaine benzylpenicillin (PRB), propicillin (PRP), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), sarmoxicillin (SRX), sulbenicillin (SBC), sultamicillin (SLT6), talampicillin (TAL), tebipenem (TBP), temocillin (TEM), ticarcillin (TIC), ticarcillin/clavulanic acid (TCC), and tigemonam (TMN)</p></li>
 <li><p><code>betalactams_with_inhibitor()</code> can select: <br> amoxicillin/clavulanic acid (AMC), amoxicillin/sulbactam (AXS), ampicillin/sulbactam (SAM), aztreonam/avibactam (AZA), aztreonam/nacubactam (ANC), cefepime/amikacin (CFA), cefepime/clavulanic acid (CPC), cefepime/enmetazobactam (FPE), cefepime/nacubactam (FNC), cefepime/tazobactam (FPT), cefepime/zidebactam (FPZ), cefoperazone/sulbactam (CSL), cefotaxime/clavulanic acid (CTC), cefotaxime/sulbactam (CTS), cefpodoxime/clavulanic acid (CDC), ceftaroline/avibactam (CPA), ceftazidime/avibactam (CZA), ceftazidime/clavulanic acid (CCV), ceftolozane/tazobactam (CZT), ceftriaxone/beta-lactamase inhibitor (CEB), imipenem/relebactam (IMR), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), mezlocillin/sulbactam (MSU), penicillin/novobiocin (PNO), penicillin/sulbactam (PSU), piperacillin/sulbactam (PIS), piperacillin/tazobactam (TZP), and ticarcillin/clavulanic acid (TCC)</p></li>
 <li><p><code>carbapenems()</code> can select: <br> biapenem (BIA), doripenem (DOR), ertapenem (ETP), imipenem (IPM), imipenem/EDTA (IPE), imipenem/relebactam (IMR), meropenem (MEM), meropenem/nacubactam (MNC), meropenem/vaborbactam (MEV), panipenem (PAN), razupenem (RZM), ritipenem (RIT), ritipenem acoxil (RIA), and tebipenem (TBP)</p></li>
@@ -284,10 +284,10 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># you can use the selectors separately to retrieve all possible antimicrobials:</span></span></span>
 <span class="r-in"><span><span class="fu">carbapenems</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 in </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;">: Imipenem/EDTA (</span><span style="color: #0000BB; background-color: #EEEEEE;">IPE</span><span style="color: #0000BB;">) and meropenem/nacubactam</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (</span><span style="color: #0000BB; background-color: #EEEEEE;">MNC</span><span style="color: #0000BB;">) are not included since </span><span style="color: #0000BB; background-color: #EEEEEE;">only_treatable = TRUE</span><span style="color: #0000BB;">.</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This 'ab' vector was retrieved using </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;">, which should</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  normally be used inside a </span><span style="color: #0000BB; background-color: #EEEEEE;">dplyr</span><span style="color: #0000BB;"> verb or </span><span style="color: #0000BB; background-color: #EEEEEE;">data.frame</span><span style="color: #0000BB;"> call, e.g.:</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;">: Imipenem/EDTA (</span><span style="color: #0000BB; background-color: #EEEEEE;">`IPE`</span><span style="color: #0000BB;">) and meropenem/nacubactam</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (</span><span style="color: #0000BB; background-color: #EEEEEE;">`MNC`</span><span style="color: #0000BB;">) are not included since </span><span style="color: #0000BB; background-color: #EEEEEE;">`only_treatable = TRUE`</span><span style="color: #0000BB;">.</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ This 'ab' vector was retrieved using </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;">, which should</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  normally be used inside a </span><span style="color: #0000BB; background-color: #EEEEEE;">`dplyr`</span><span style="color: #0000BB;"> verb or </span><span style="color: #0000BB; background-color: #EEEEEE;">`data.frame`</span><span style="color: #0000BB;"> call, e.g.:</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  • your_data %&gt;% select(carbapenems())</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  • your_data %&gt;% select(column_a, column_b, carbapenems())</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  • your_data %&gt;% filter(any(carbapenems() == "R"))</span></span>
@@ -392,7 +392,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># select columns 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">carbapenems</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;">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 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    IPM   MEM  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -410,7 +410,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
-<span class="r-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;">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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    mo           GEN   TOB   AMK   KAN  </span>
@@ -429,7 +429,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># select only antimicrobials with DDDs for oral treatment</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">administrable_per_os</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;">administrable_per_os()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</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;">`administrable_per_os()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">' (amoxicillin/clavulanic acid),</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;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin), '</span><span style="color: #0000BB; font-weight: bold;">TMP</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (trimethoprim), '</span><span style="color: #0000BB; font-weight: bold;">NIT</span><span style="color: #0000BB;">' (nitrofurantoin), '</span><span style="color: #0000BB; font-weight: bold;">FOS</span><span style="color: #0000BB;">' (fosfomycin), '</span><span style="color: #0000BB; font-weight: bold;">LNZ</span><span style="color: #0000BB;">'</span></span>
@@ -457,7 +457,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter using any() or all()</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</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">carbapenems</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="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>
+<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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -479,7 +479,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">example_isolates</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">carbapenems</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="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>
+<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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 55 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -503,7 +503,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter on any or all results in the carbapenem columns (i.e., IPM, MEM):</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</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">carbapenems</span><span class="op">(</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;">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 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>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Filtering any of columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' to contain value "S", "I" or "R"</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 962 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
@@ -526,7 +526,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;, CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, …</span></span>
 <span class="r-in"><span><span class="va">example_isolates</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">carbapenems</span><span class="op">(</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;">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 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>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Filtering all of columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' to contain value "S", "I" or "R"</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 756 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX  </span>
@@ -551,8 +551,8 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter with multiple antimicrobial selectors using c()</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</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="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</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="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>
-<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;">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 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 26 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
@@ -577,8 +577,8 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenem-resistant strains</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</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">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="fu">penicillins</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;">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 class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">penicillins()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</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>
+<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;">`penicillins()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), and '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (piperacillin/tazobactam)</span></span>
@@ -603,11 +603,11 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span><span class="co"># drugs are both omitted since benzylpenicillin is not administrable per os</span></span></span>
 <span class="r-in"><span><span class="co"># and erythromycin is not a penicillin:</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu">administrable_per_os</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;">penicillins()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</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;">`penicillins()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), and '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (piperacillin/tazobactam)</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;">administrable_per_os()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</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;">`administrable_per_os()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">' (amoxicillin/clavulanic acid),</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;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin), '</span><span style="color: #0000BB; font-weight: bold;">TMP</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (trimethoprim), '</span><span style="color: #0000BB; font-weight: bold;">NIT</span><span style="color: #0000BB;">' (nitrofurantoin), '</span><span style="color: #0000BB; font-weight: bold;">FOS</span><span style="color: #0000BB;">' (fosfomycin), '</span><span style="color: #0000BB; font-weight: bold;">LNZ</span><span style="color: #0000BB;">'</span></span>
@@ -635,7 +635,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span><span class="co"># very flexible. For instance, to select antimicrobials with an oral DDD</span></span></span>
 <span class="r-in"><span><span class="co"># of at least 1 gram:</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">amr_selector</span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">&gt;</span> <span class="fl">1</span> <span class="op">&amp;</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</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;">amr_selector(oral_ddd &gt; 1 &amp; oral_units == "g")</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</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;">`amr_selector(oral_ddd &gt; 1 &amp; oral_units == "g")`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin), '</span><span style="color: #0000BB; font-weight: bold;">FOS</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (fosfomycin), '</span><span style="color: #0000BB; font-weight: bold;">LNZ</span><span style="color: #0000BB;">' (linezolid), '</span><span style="color: #0000BB; font-weight: bold;">VAN</span><span style="color: #0000BB;">' (vancomycin), '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">' (erythromycin),</span></span>
@@ -679,17 +679,17 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-msg co"><span class="r-pr">#&gt;</span> The following objects are masked from ‘package:AMR’:</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>     %like%, like</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>
+<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>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>It should never be needed to print an antimicrobial selector class. Are you</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> using data.table? Then add the argument <span style="background-color: #EEEEEE;">with = FALSE</span>, see our examples at</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="background-color: #EEEEEE;">?amr_selector</span>.</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> using data.table? Then add the argument <span style="background-color: #EEEEEE;">`with = FALSE`</span>, see our examples at</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="background-color: #EEEEEE;">`?amr_selector`</span>.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'amr_selector'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] IPM MEM</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># so `with = FALSE` is required</span></span></span>
 <span class="r-in"><span>  <span class="va">dt</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, with <span class="op">=</span> <span class="cn">FALSE</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;">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 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         IPM   MEM</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       &lt;sir&gt; &lt;sir&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    1:  &lt;NA&gt;  &lt;NA&gt;</span>
@@ -708,7 +708,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">dt</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<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;">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>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                 mo   GEN   TOB   AMK   KAN</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
@@ -726,8 +726,8 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">dt</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<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>
-<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;">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 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span>         IPM   MEM   GEN   TOB   AMK   KAN</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>       &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
@@ -747,7 +747,7 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">dt</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"S"</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;">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 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span>            date patient   age gender       ward           mo   PEN   OXA   FLC</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>          &lt;Date&gt;  &lt;char&gt; &lt;num&gt; &lt;char&gt;     &lt;char&gt;         &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   1: 2002-01-19  738003    71      M   Clinical B_ESCHR_COLI     R  &lt;NA&gt;  &lt;NA&gt;</span>
@@ -816,8 +816,8 @@ my_data_with_all_these_columns %&amp;gt;%
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">dt</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"S"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span>, with <span class="op">=</span> <span class="cn">FALSE</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;">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 class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">penicillins()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</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>
+<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;">`penicillins()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), and '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (piperacillin/tazobactam)</span></span>
--- a/reference/antimicrobials.html
+++ b/reference/antimicrobials.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>Data Sets with 617 Antimicrobial Drugs — antimicrobials • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/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="Data Sets with 617 Antimicrobial Drugs — antimicrobials"><meta name="description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
+<!-- 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>Data Sets with 616 Antimicrobial Drugs — antimicrobials • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><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-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/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="Data Sets with 616 Antimicrobial Drugs — antimicrobials"><meta name="description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
 The antibiotics data set has been renamed to antimicrobials. The old name will be removed in a future version."><meta property="og:description" content="Two data sets containing all antimicrobials and antivirals. Use as.ab() or one of the ab_* functions to retrieve values from the antimicrobials data set. Three identifiers are included in this data set: an antimicrobial ID (ab, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (atc) as defined by the WHO, and a Compound ID (cid) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.
 The antibiotics data set has been renamed to antimicrobials. The old name will be removed in a future version."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -46,7 +46,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
 </nav><div class="container template-reference-topic">
 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 617 Antimicrobial Drugs</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Data Sets with 616 Antimicrobial Drugs</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
      <div class="d-none name"><code>antimicrobials.Rd</code></div>
    </div>
@@ -69,7 +69,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>

 <div class="section">
-<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 497 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>
+<h3 id="for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-">For the antimicrobials data set: a <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 496 observations and 14 variables:<a class="anchor" aria-label="anchor" href="#for-the-antimicrobials-data-set-a-tibble-with-observations-and-variables-"></a></h3>

 <ul><li><p><code>ab</code><br> antimicrobial ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available. <em><strong>This is a unique identifier.</strong></em></p></li>
 <li><p><code>cid</code><br> Compound ID as found in PubChem. <em><strong>This is a unique identifier.</strong></em></p></li>
@@ -103,7 +103,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
 <li><p><code>loinc</code><br> All codes associated with the name of the antiviral drug from Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023). Use <code><a href="av_property.html">av_loinc()</a></code> to retrieve them quickly, see <code><a href="av_property.html">av_property()</a></code>.</p></li>
 </ul></div>

-<p>An object of class <code>deprecated_amr_dataset</code> (inherits from <code>tbl_df</code>, <code>tbl</code>, <code>data.frame</code>) with 497 rows and 14 columns.</p>
+<p>An object of class <code>deprecated_amr_dataset</code> (inherits from <code>tbl_df</code>, <code>tbl</code>, <code>data.frame</code>) with 496 rows and 14 columns.</p>
 <p>An object of class <code>tbl_df</code> (inherits from <code>tbl</code>, <code>data.frame</code>) with 120 rows and 11 columns.</p>
    </div>
    <div class="section level2">
@@ -145,7 +145,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">antimicrobials</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 497 × 14</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 496 × 14</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    ab        cid name   group atc   atc_group1 atc_group2 abbreviations synonyms</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lis&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;list&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;named &gt;</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> AMA      <span style="text-decoration: underline;">4</span>649 4-ami… Anti… <span style="color: #949494;">&lt;chr&gt;</span> Drugs for… Aminosali… <span style="color: #949494;">&lt;chr [1]&gt;</span>     <span style="color: #949494;">&lt;chr&gt;</span>   </span>
@@ -158,7 +158,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> AMX     <span style="text-decoration: underline;">33</span>613 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Penicilli… <span style="color: #949494;">&lt;chr [4]&gt;</span>     <span style="color: #949494;">&lt;chr&gt;</span>   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> AMC  23<span style="text-decoration: underline;">665</span>637 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> Beta-lact… Combinati… <span style="color: #949494;">&lt;chr [6]&gt;</span>     <span style="color: #949494;">&lt;chr&gt;</span>   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> AXS    <span style="text-decoration: underline;">465</span>441 Amoxi… Beta… <span style="color: #949494;">&lt;chr&gt;</span> <span style="color: #BB0000;">NA</span>         <span style="color: #BB0000;">NA</span>         <span style="color: #949494;">&lt;chr [1]&gt;</span>     <span style="color: #949494;">&lt;chr&gt;</span>   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 487 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 486 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: oral_ddd &lt;dbl&gt;, oral_units &lt;chr&gt;, iv_ddd &lt;dbl&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   iv_units &lt;chr&gt;, loinc &lt;list&gt;</span></span>
 <span class="r-in"><span><span class="va">antivirals</span></span></span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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
@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -128,7 +128,8 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,


 <dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
-<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: names of columns to apply <code>as.sir()</code> on (supports tidy selection such as <code>column1:column4</code>). Otherwise: arguments passed on to methods.</p></dd>
+<dd><p>For using on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: selection of columns to apply <code>as.sir()</code> to. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</code>, and can thus also be <a href="antimicrobial_selectors.html">antimicrobial selectors</a> such as <code>as.sir(df, penicillins())</code>.</p>
+<p>Otherwise: arguments passed on to methods.</p></dd>


 <dt id="arg-threshold">threshold<a class="anchor" aria-label="anchor" href="#arg-threshold"></a></dt>
@@ -414,10 +415,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   datetime            index method ab_given    mo_given   host_given input_given</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-06-22 <span style="color: #949494;">18:51:08</span>     1 MIC    amoxicillin Escherich… human      8          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-06-22 <span style="color: #949494;">18:51:08</span>     1 MIC    cipro       Escherich… human      0.256      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-06-22 <span style="color: #949494;">18:51:08</span>     1 DISK   tobra       Escherich… human      16         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-06-22 <span style="color: #949494;">18:51:08</span>     1 DISK   genta       Escherich… human      18         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2025-09-01 <span style="color: #949494;">15:04:18</span>     1 MIC    amoxicillin Escherich… human      8          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2025-09-01 <span style="color: #949494;">15:04:19</span>     1 MIC    cipro       Escherich… human      0.256      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2025-09-01 <span style="color: #949494;">15:04:19</span>     1 DISK   tobra       Escherich… human      16         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2025-09-01 <span style="color: #949494;">15:04:19</span>     1 DISK   genta       Escherich… human      18         </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>
@@ -426,7 +427,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-in"><span><span class="co"># using parallel computing, which is available in base R:</span></span></span>
 <span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="va">df_wide</span>, parallel <span class="op">=</span> <span class="cn">TRUE</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Returning previously coerced values for various antimicrobials. Run</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  </span><span style="color: #0000BB; background-color: #EEEEEE;">ab_reset_session()</span><span style="color: #0000BB;"> to reset this. This note will be shown once per</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  </span><span style="color: #0000BB; background-color: #EEEEEE;">`ab_reset_session()`</span><span style="color: #0000BB;"> to reset this. This note will be shown once per</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  session.</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Running in parallel mode using 3 out of 4 cores, on columns '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">',</span></span>
@@ -434,7 +435,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #080808; background-color: #5FD7AF;"> DONE</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">sir_interpretation_history()</span><span style="color: #00BB00;"> to retrieve a logbook with all details</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">ℹ Run </span><span style="color: #00BB00; background-color: #EEEEEE;">`sir_interpretation_history()`</span><span style="color: #00BB00;"> to retrieve a logbook with all details</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">  of the breakpoint interpretations.</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      microorganism amoxicillin cipro tobra genta ERY</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1 Escherichia coli           S     I     S     S   R</span>
@@ -446,9 +447,12 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is.mic</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><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="as.mic.html">is.mic</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">|</span> <span class="fu"><a href="as.disk.html">is.disk</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://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.mic</span><span class="op">)</span>, <span class="va">as.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="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">amoxicillin</span><span class="op">:</span><span class="va">tobra</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://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="va">amoxicillin</span><span class="op">:</span><span class="va">tobra</span>, <span class="va">as.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="va">df_wide</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://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="antimicrobial_selectors.html">aminopenicillins</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">as.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"># approaches that all work with additional arguments:</span></span></span>
 <span class="r-in"><span>  <span class="va">df_long</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="co"># given a certain data type, e.g. MIC values</span></span></span>
@@ -544,6 +548,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-in"><span>  <span class="va">df_wide</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_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">cipro</span><span class="op">:</span><span class="va">genta</span><span class="op">)</span>, <span class="va">as.sir</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, uti <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`aminopenicillins()`</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">amoxicillin</span><span style="color: #0000BB;">'</span></span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(...)`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
@@ -614,7 +619,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-in"><span><span class="co"># For CLEANING existing SIR values -------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">as.sir</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"S"</span>, <span class="st">"SDD"</span>, <span class="st">"I"</span>, <span class="st">"R"</span>, <span class="st">"NI"</span>, <span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">as.sir()</span>: 3 results in index '21' truncated (38%) that were invalid</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">`as.sir()`</span>: 3 results in index '21' truncated (38%) that were invalid</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial interpretations: "A", "B", and "C"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'sir'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] S    SDD  I    R    NI   &lt;NA&gt; &lt;NA&gt; &lt;NA&gt;</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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -135,10 +135,10 @@
 <span class="r-in"><span>  <span class="fu">atc_online_property</span><span class="op">(</span><span class="st">"J01CA04"</span>, property <span class="op">=</span> <span class="st">"groups"</span><span class="op">)</span> <span class="co"># search hierarchical groups of amoxicillin</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> Loading required namespace: rvest</span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">atc_online_property()</span><span style="color: #0000BB;">: no properties found for ATC QG51AA03. Please</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">`atc_online_property()`</span><span style="color: #0000BB;">: no properties found for ATC QG51AA03. Please</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  check</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  https://atcddd.fhi.no/atcvet/atcvet_index/?code=QG51AA03&amp;showdescription=no.</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">atc_online_property()</span><span style="color: #0000BB;">: no properties found for ATC QJ01CA04. Please</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">`atc_online_property()`</span><span style="color: #0000BB;">: no properties found for ATC QJ01CA04. Please</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  check</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  https://atcddd.fhi.no/atcvet/atcvet_index/?code=QJ01CA04&amp;showdescription=no.</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "ANTIINFECTIVES FOR SYSTEMIC USE"        </span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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/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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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/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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -243,7 +243,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
 <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">count_df</span><span class="op">(</span>translate <span class="op">=</span> <span class="cn">FALSE</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;">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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 12 × 4</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    ward       antibiotic interpretation value</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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -150,7 +150,7 @@
 <p>These 35 antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:</p><ul><li><p>aminoglycosides<br>(amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high)</p></li>
 <li><p>aminopenicillins<br>(amoxicillin and ampicillin)</p></li>
 <li><p>antifungals<br>(amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole)</p></li>
-<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
+<li><p>antimycobacterials<br>(4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin)</p></li>
 <li><p>betalactams<br>(amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam)</p></li>
 <li><p>betalactams_with_inhibitor<br>(amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid)</p></li>
 <li><p>carbapenems<br>(biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem)</p></li>
--- a/reference/custom_mdro_guideline.html
+++ b/reference/custom_mdro_guideline.html
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -147,7 +147,7 @@
 <p>All 35 antimicrobial selectors are supported for use in the rules:</p><ul><li><p><code><a href="antimicrobial_selectors.html">aminoglycosides()</a></code> can select: <br> amikacin, amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin, and tobramycin-high</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">aminopenicillins()</a></code> can select: <br> amoxicillin and ampicillin</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">antifungals()</a></code> can select: <br> amorolfine, amphotericin B, amphotericin B-high, anidulafungin, butoconazole, caspofungin, ciclopirox, clotrimazole, econazole, fluconazole, flucytosine, fosfluconazole, griseofulvin, hachimycin, ibrexafungerp, isavuconazole, isoconazole, itraconazole, ketoconazole, manogepix, micafungin, miconazole, nystatin, oteseconazole, pimaricin, posaconazole, rezafungin, ribociclib, sulconazole, terbinafine, terconazole, and voriconazole</p></li>
-<li><p><code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> can select: <br> 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, simvastatin/fenofibrate, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin</p></li>
+<li><p><code><a href="antimicrobial_selectors.html">antimycobacterials()</a></code> can select: <br> 4-aminosalicylic acid, calcium aminosalicylate, capreomycin, clofazimine, delamanid, enviomycin, ethambutol, ethambutol/isoniazid, ethionamide, isoniazid, isoniazid/sulfamethoxazole/trimethoprim/pyridoxine, morinamide, p-aminosalicylic acid, pretomanid, protionamide, pyrazinamide, rifabutin, rifampicin, rifampicin/ethambutol/isoniazid, rifampicin/isoniazid, rifampicin/pyrazinamide/ethambutol/isoniazid, rifampicin/pyrazinamide/isoniazid, rifamycin, rifapentine, sodium aminosalicylate, streptomycin/isoniazid, terizidone, thioacetazone, thioacetazone/isoniazid, tiocarlide, and viomycin</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">betalactams()</a></code> can select: <br> amoxicillin, amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin, ampicillin/sulbactam, apalcillin, aspoxicillin, azidocillin, azlocillin, aztreonam, aztreonam/avibactam, aztreonam/nacubactam, bacampicillin, benzathine benzylpenicillin, benzathine phenoxymethylpenicillin, benzylpenicillin, benzylpenicillin screening test, biapenem, carbenicillin, carindacillin, carumonam, cefacetrile, cefaclor, cefadroxil, cefalexin, cefaloridine, cefalotin, cefamandole, cefapirin, cefatrizine, cefazedone, cefazolin, cefcapene, cefcapene pivoxil, cefdinir, cefditoren, cefditoren pivoxil, cefepime, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefetamet, cefetamet pivoxil, cefetecol, cefetrizole, cefiderocol, cefixime, cefmenoxime, cefmetazole, cefodizime, cefonicid, cefoperazone, cefoperazone/sulbactam, ceforanide, cefoselis, cefotaxime, cefotaxime screening test, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefotetan, cefotiam, cefotiam hexetil, cefovecin, cefoxitin, cefoxitin screening test, cefozopran, cefpimizole, cefpiramide, cefpirome, cefpodoxime, cefpodoxime proxetil, cefpodoxime/clavulanic acid, cefprozil, cefquinome, cefroxadine, cefsulodin, cefsumide, ceftaroline, ceftaroline/avibactam, ceftazidime, ceftazidime/avibactam, ceftazidime/clavulanic acid, cefteram, cefteram pivoxil, ceftezole, ceftibuten, ceftiofur, ceftizoxime, ceftizoxime alapivoxil, ceftobiprole, ceftobiprole medocaril, ceftolozane/tazobactam, ceftriaxone, ceftriaxone/beta-lactamase inhibitor, cefuroxime, cefuroxime axetil, cephradine, ciclacillin, clometocillin, cloxacillin, dicloxacillin, doripenem, epicillin, ertapenem, flucloxacillin, hetacillin, imipenem, imipenem/EDTA, imipenem/relebactam, latamoxef, lenampicillin, loracarbef, mecillinam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, metampicillin, meticillin, mezlocillin, mezlocillin/sulbactam, nafcillin, oxacillin, oxacillin screening test, panipenem, penamecillin, penicillin/novobiocin, penicillin/sulbactam, pheneticillin, phenoxymethylpenicillin, piperacillin, piperacillin/sulbactam, piperacillin/tazobactam, piridicillin, pivampicillin, pivmecillinam, procaine benzylpenicillin, propicillin, razupenem, ritipenem, ritipenem acoxil, sarmoxicillin, sulbenicillin, sultamicillin, talampicillin, tebipenem, temocillin, ticarcillin, ticarcillin/clavulanic acid, and tigemonam</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">betalactams_with_inhibitor()</a></code> can select: <br> amoxicillin/clavulanic acid, amoxicillin/sulbactam, ampicillin/sulbactam, aztreonam/avibactam, aztreonam/nacubactam, cefepime/amikacin, cefepime/clavulanic acid, cefepime/enmetazobactam, cefepime/nacubactam, cefepime/tazobactam, cefepime/zidebactam, cefoperazone/sulbactam, cefotaxime/clavulanic acid, cefotaxime/sulbactam, cefpodoxime/clavulanic acid, ceftaroline/avibactam, ceftazidime/avibactam, ceftazidime/clavulanic acid, ceftolozane/tazobactam, ceftriaxone/beta-lactamase inhibitor, imipenem/relebactam, meropenem/nacubactam, meropenem/vaborbactam, mezlocillin/sulbactam, penicillin/novobiocin, penicillin/sulbactam, piperacillin/sulbactam, piperacillin/tazobactam, and ticarcillin/clavulanic acid</p></li>
 <li><p><code><a href="antimicrobial_selectors.html">carbapenems()</a></code> can select: <br> biapenem, doripenem, ertapenem, imipenem, imipenem/EDTA, imipenem/relebactam, meropenem, meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem, ritipenem, ritipenem acoxil, and tebipenem</p></li>
@@ -241,10 +241,18 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> Results will be of class 'factor', with ordered levels: Negative &lt; Custom MDRO 1 &lt; Custom MDRO 2</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu"><a href="mdro.html">mdro</a></span><span class="op">(</span><span class="va">example_isolates</span>, guideline <span class="op">=</span> <span class="va">my_guideline</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;">cephalosporins_2nd()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime) and '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">'</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">esbl</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  it seems to be tazobactam (TAZ)</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">mecC</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  it seems to be mecillinam (MEC)</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">vanA</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  it seems to be lenampicillin (LEN)</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Column '</span><span style="color: #0000BB; font-weight: bold;">vanB</span><span style="color: #0000BB;">' is SIR eligible (despite only having empty values), since</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  it seems to be metronidazole (MTR)</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;">`cephalosporins_2nd()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime) and '</span><span style="color: #0000BB; font-weight: bold;">FOX</span><span style="color: #0000BB;">'</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  (cefoxitin)</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around </span><span style="color: #0000BB; background-color: #EEEEEE;">all()</span><span style="color: #0000BB;"> or</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  </span><span style="color: #0000BB; background-color: #EEEEEE;">any()</span><span style="color: #0000BB;"> to prevent this note.</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Assuming a filter on all 2 cephalosporins_2nd. Wrap around </span><span style="color: #0000BB; background-color: #EEEEEE;">`all()`</span><span style="color: #0000BB;"> or</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">  </span><span style="color: #0000BB; background-color: #EEEEEE;">`any()`</span><span style="color: #0000BB;"> to prevent this note.</span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> out</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>      Negative Custom MDRO 1 Custom MDRO 2 </span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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/esbl_isolates.html
+++ b/reference/esbl_isolates.html
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -215,7 +215,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># apply EUCAST rules: some results wil be changed</span></span></span>
 <span class="r-in"><span><span class="va">b</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <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>in <span style="background-color: #EEEEEE;">eucast_rules()</span>: not all columns with antimicrobial results are of</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">`eucast_rules()`</span>: not all columns with antimicrobial results are of</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> class 'sir'. Transform them on beforehand, with e.g.:</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span>   - a %&gt;% as.sir(CXM:AMX)</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span>   - a %&gt;% mutate_if(is_sir_eligible, as.sir)</span>
@@ -233,7 +233,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 <span class="r-in"><span><span class="co"># do not apply EUCAST rules, but rather get a data.frame</span></span></span>
 <span class="r-in"><span><span class="co"># containing all details about the transformations:</span></span></span>
 <span class="r-in"><span><span class="va">c</span> <span class="op">&lt;-</span> <span class="fu">eucast_rules</span><span class="op">(</span><span class="va">a</span>, overwrite <span class="op">=</span> <span class="cn">TRUE</span>, verbose <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>in <span style="background-color: #EEEEEE;">eucast_rules()</span>: not all columns with antimicrobial results are of</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">`eucast_rules()`</span>: not all columns with antimicrobial results are of</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> class 'sir'. Transform them on beforehand, with e.g.:</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span>   - a %&gt;% as.sir(CXM:AMX)</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span>   - a %&gt;% mutate_if(is_sir_eligible, as.sir)</span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -227,8 +227,8 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span><span class="fu">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</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: #BB0000;">ℹ Determining first isolates using an episode length of </span><span style="color: #BB0000; font-weight: bold;">365 days</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">col_date</span><span style="color: #0000BB;">.</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">col_patient_id</span><span style="color: #0000BB;">.</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">date</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`col_date`</span><span style="color: #0000BB;">.</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">patient</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`col_patient_id`</span><span style="color: #0000BB;">.</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">ℹ Basing inclusion on all antimicrobial results, using a points threshold</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">  of 2</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">ℹ Excluding 16 isolates with a microbial ID 'UNKNOWN' (in column '</span><span style="color: #BB0000; font-weight: bold;">mo</span><span style="color: #BB0000;">')</span></span>
@@ -257,7 +257,7 @@
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="co"># get all first Gram-negatives</span></span></span>
 <span class="r-in"><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">first_isolate</span><span class="op">(</span>info <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_is_gram_negative</a></span><span class="op">(</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 Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_is_gram_negative()</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_is_gram_negative()`</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 441 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -224,7 +224,7 @@
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"` `genus = "Enterococcus"`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (<span style="background-color: #EEEEEE;">minimum</span> = 30).</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (<span style="background-color: #EEEEEE;">`minimum`</span> = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Columns selected for PCA: "</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">SXT</span><span style="color: #0000BB;">",</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;">TMP</span><span style="color: #0000BB;">", and "</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">". Total observations available: 7.</span></span>
--- a/reference/ggplot_sir-5.png
+++ b/reference/ggplot_sir-5.png
--- a/reference/ggplot_sir-6.png
+++ b/reference/ggplot_sir-6.png
--- a/reference/ggplot_sir-9.png
+++ b/reference/ggplot_sir-9.png
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -59,10 +59,10 @@
 <span>  fill <span class="op">=</span> <span class="st">"interpretation"</span>, facet <span class="op">=</span> <span class="cn">NULL</span>, breaks <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fl">1</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
 <span>  limits <span class="op">=</span> <span class="cn">NULL</span>, translate_ab <span class="op">=</span> <span class="st">"name"</span>, combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  minimum <span class="op">=</span> <span class="fl">30</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="cn">NULL</span>, colours <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S</span>
-<span>  <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SI <span class="op">=</span> <span class="st">"#3CAEA3"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, IR <span class="op">=</span> <span class="st">"#ED553B"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
-<span>  datalabels <span class="op">=</span> <span class="cn">TRUE</span>, datalabels.size <span class="op">=</span> <span class="fl">2.5</span>, datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span>,</span>
-<span>  title <span class="op">=</span> <span class="cn">NULL</span>, subtitle <span class="op">=</span> <span class="cn">NULL</span>, caption <span class="op">=</span> <span class="cn">NULL</span>,</span>
-<span>  x.title <span class="op">=</span> <span class="st">"Antimicrobial"</span>, y.title <span class="op">=</span> <span class="st">"Proportion"</span>, <span class="va">...</span><span class="op">)</span></span>
+<span>  <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, SI <span class="op">=</span> <span class="st">"#3CAEA3"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, IR <span class="op">=</span> <span class="st">"#ED553B"</span>,</span>
+<span>  R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, datalabels <span class="op">=</span> <span class="cn">TRUE</span>, datalabels.size <span class="op">=</span> <span class="fl">2.5</span>,</span>
+<span>  datalabels.colour <span class="op">=</span> <span class="st">"grey15"</span>, title <span class="op">=</span> <span class="cn">NULL</span>, subtitle <span class="op">=</span> <span class="cn">NULL</span>,</span>
+<span>  caption <span class="op">=</span> <span class="cn">NULL</span>, x.title <span class="op">=</span> <span class="st">"Antimicrobial"</span>, y.title <span class="op">=</span> <span class="st">"Proportion"</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">geom_sir</span><span class="op">(</span>position <span class="op">=</span> <span class="cn">NULL</span>, x <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">"antibiotic"</span>, <span class="st">"interpretation"</span><span class="op">)</span>,</span>
 <span>  fill <span class="op">=</span> <span class="st">"interpretation"</span>, translate_ab <span class="op">=</span> <span class="st">"name"</span>, minimum <span class="op">=</span> <span class="fl">30</span>,</span>
@@ -284,7 +284,7 @@
 <span class="r-in"><span>      datalabels <span class="op">=</span> <span class="cn">FALSE</span></span></span>
 <span class="r-in"><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 Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_is_gram_negative()</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_is_gram_negative()`</span></span>
 <span class="r-plt img"><img src="ggplot_sir-10.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -373,7 +373,7 @@
          <code><a href="antimicrobials.html">antimicrobials</a></code> <code><a href="antimicrobials.html">antibiotics</a></code> <code><a href="antimicrobials.html">antivirals</a></code>

        </dt>
-        <dd>Data Sets with 617 Antimicrobial Drugs</dd>
+        <dd>Data Sets with 616 Antimicrobial Drugs</dd>
      </dl><dl><dt>

          <code><a href="clinical_breakpoints.html">clinical_breakpoints</a></code>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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/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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -133,7 +133,7 @@
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="co"># get isolates whose name start with 'Entero' (case-insensitive)</span></span></span>
 <span class="r-in"><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="mo_property.html">mo_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^entero"</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 Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_name()</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_name()`</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
@@ -159,7 +159,7 @@
 <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_name</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%like%</span> <span class="st">"^ent"</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 Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_name()</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_name()`</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 106 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    date       patient   age gender ward    mo            PEN   OXA   FLC   AMX  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span> <span style="color: #949494; font-style: italic;">&lt;sir&gt;</span></span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -126,7 +126,7 @@


 <dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
-<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.</p></dd>
+<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function returns a data set with the MDRO results in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.</p></dd>


 <dt id="arg-only-sir-columns">only_sir_columns<a class="anchor" aria-label="anchor" href="#arg-only-sir-columns"></a></dt>
@@ -205,8 +205,8 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">out</span> <span class="op">&lt;-</span> <span class="fu">mdro</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">mdro()</span>: NA introduced for isolates where the available percentage of</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with <span style="background-color: #EEEEEE;">pct_required_classes</span>)</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">`mdro()`</span>: NA introduced for isolates where the available percentage of</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with <span style="background-color: #EEEEEE;">`pct_required_classes`</span>)</span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  Ord.factor w/ 4 levels "Negative"&lt;"Multi-drug-resistant (MDR)"&lt;..: NA NA 1 1 1 1 NA NA 1 1 ...</span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/table.html" class="external-link">table</a></span><span class="op">(</span><span class="va">out</span><span class="op">)</span></span></span>
@@ -232,8 +232,8 @@ Ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">facto
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `mutate()`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `MDRO = mdro()`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in <span style="background-color: #EEEEEE;">mdro()</span>: NA introduced for isolates where the available percentage of</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with <span style="background-color: #EEEEEE;">pct_required_classes</span>)</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in <span style="background-color: #EEEEEE;">`mdro()`</span>: NA introduced for isolates where the available percentage of</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> antimicrobial classes was below 50% (set with <span style="background-color: #EEEEEE;">`pct_required_classes`</span>)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 2</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   MDRO                           n</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;ord&gt;</span>                      <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -75,7 +75,7 @@


 <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_selectors.html">antimicrobial selectors</a>.</p></dd>
+<dd><p>Variables to select. Supports <a href="https://tidyselect.r-lib.org/reference/starts_with.html" class="external-link">tidyselect language</a> such as <code>where(is.mic)</code>, <code>starts_with(...)</code>, or <code>column1:column4</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>
@@ -204,9 +204,9 @@
 <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>
 <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 Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_genus()</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_species()</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>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_genus()`</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_species()`</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>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Calculating mean AMR distance based on columns "TCY", "IPM", and "MEM"</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   mo [4]</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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -120,7 +120,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_ESCHR_COLI</span>
 <span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Matching scores are based on the resemblance between the input and the full</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">taxonomic name, and the pathogenicity in humans. See </span><span style="color: #0000BB; background-color: #EEEEEE;">?mo_matching_score</span><span style="color: #0000BB;">.</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">taxonomic name, and the pathogenicity in humans. See </span><span style="color: #0000BB; background-color: #EEEEEE;">`?mo_matching_score`</span><span style="color: #0000BB;">.</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Colour keys: </span><span style="color: #080808; background-color: #FFAFAF;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #B2B2B2;">--------------------------------------------------------------------------------</span></span>
@@ -133,8 +133,8 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="font-style: italic;">              dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</span>)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">Only the first 10 other matches of each record are shown. Run</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; background-color: #EEEEEE;">print(mo_uncertainties(), n = ...)</span><span style="color: #0000BB;"> to view more entries, or save</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; background-color: #EEEEEE;">mo_uncertainties()</span><span style="color: #0000BB;"> to an object.</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; background-color: #EEEEEE;">`print(mo_uncertainties(), n = ...)`</span><span style="color: #0000BB;"> to view more entries, or save</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB; background-color: #EEEEEE;">`mo_uncertainties()`</span><span style="color: #0000BB;"> to an object.</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -367,9 +367,9 @@
 <span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida krusei"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "337013"</span>
 <span class="r-in"><span><span class="fu">mo_mycobank</span><span class="op">(</span><span class="st">"Candida krusei"</span>, keep_synonyms <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>Function <span style="background-color: #EEEEEE;">as.mo()</span> returned one old taxonomic name. Use <span style="background-color: #EEEEEE;">as.mo(...,</span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="background-color: #EEEEEE;">keep_synonyms = FALSE)</span> to clean the input to currently accepted taxonomic</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> names, or set the R option <span style="background-color: #EEEEEE;">AMR_keep_synonyms</span> to <span style="background-color: #EEEEEE;">FALSE</span>. This warning</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Function <span style="background-color: #EEEEEE;">`as.mo()`</span> returned one old taxonomic name. Use <span style="background-color: #EEEEEE;">`as.mo(...,</span></span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="background-color: #EEEEEE;">keep_synonyms = FALSE)`</span> to clean the input to currently accepted taxonomic</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> names, or set the R option <span style="background-color: #EEEEEE;">`AMR_keep_synonyms`</span> to <span style="background-color: #EEEEEE;">`FALSE`</span>. This warning</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> will be shown once per session.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "268707"</span>
 <span class="r-in"><span></span></span>
@@ -462,8 +462,8 @@
 <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">mo_is_gram_positive</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="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_is_gram_positive()</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_genus()</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_is_gram_positive()`</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_genus()`</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 18 × 2</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    `mo_genus()`        n</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
@@ -490,8 +490,8 @@
 <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">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</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="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_is_intrinsic_resistant()</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_genus()</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_is_intrinsic_resistant()`</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">`mo_genus()`</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 19 × 2</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    `mo_genus()`         n</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>            <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
--- 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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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/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="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -152,7 +152,7 @@
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 5: `order = "Lactobacillales"` `genus = "Enterococcus"`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 14 results available for PEN in group: order =</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (<span style="background-color: #EEEEEE;">minimum</span> = 30).</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (<span style="background-color: #EEEEEE;">`minimum`</span> = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 72 remaining warnings.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #0000BB;">ℹ Columns selected for PCA: "</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CAZ</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CTX</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">", "</span><span style="color: #0000BB; font-weight: bold;">SXT</span><span style="color: #0000BB;">",</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;">TMP</span><span style="color: #0000BB;">", and "</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">". Total observations available: 7.</span></span>
--- a/reference/plot-10.png
+++ b/reference/plot-10.png
--- a/reference/plot-11.png
+++ b/reference/plot-11.png
--- a/reference/plot-12.png
+++ b/reference/plot-12.png
--- a/reference/plot-13.png
+++ b/reference/plot-13.png
--- a/reference/plot-14.png
+++ b/reference/plot-14.png
--- a/reference/plot-15.png
+++ b/reference/plot-15.png
--- a/reference/plot-16.png
+++ b/reference/plot-16.png
--- a/reference/plot-17.png
+++ b/reference/plot-17.png
--- a/reference/plot-18.png
+++ b/reference/plot-18.png
--- a/reference/plot-19.png
+++ b/reference/plot-19.png
--- a/reference/plot-20.png
+++ b/reference/plot-20.png
--- a/reference/plot-21.png
+++ b/reference/plot-21.png
--- a/reference/plot-3.png
+++ b/reference/plot-3.png
--- a/reference/plot-4.png
+++ b/reference/plot-4.png
--- a/reference/plot-5.png
+++ b/reference/plot-5.png
--- a/reference/plot-6.png
+++ b/reference/plot-6.png
--- a/reference/plot-7.png
+++ b/reference/plot-7.png
--- a/reference/plot-8.png
+++ b/reference/plot-8.png
--- a/reference/plot-9.png
+++ b/reference/plot-9.png
--- a/reference/plot.html
+++ b/reference/plot.html
@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -66,17 +66,17 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span></span>
 <span><span class="fu">scale_fill_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"edges"</span>, mic_range <span class="op">=</span> <span class="cn">NULL</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">scale_x_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
-<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>,</span>
-<span>  <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">scale_x_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R</span>
+<span>  <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">scale_colour_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
-<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>,</span>
-<span>  <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">scale_colour_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span></span>
+<span>  <span class="st">"#F6D55C"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">scale_fill_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
-<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>,</span>
-<span>  <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
+<span><span class="fu">scale_fill_sir</span><span class="op">(</span>colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>,</span>
+<span>  R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
+<span>  eucast_I <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span> <span class="op">==</span> <span class="st">"EUCAST"</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for class 'mic'</span></span>
 <span><span class="fu">plot</span><span class="op">(</span><span class="va">x</span>, mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>,</span>
@@ -84,8 +84,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span>  main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language</span>
 <span>  <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <span class="op">=</span></span>
-<span>  <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
-<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R</span>
+<span>  <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span>  breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -95,8 +95,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span>  title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>,</span>
 <span>  language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>, language <span class="op">=</span></span>
-<span>  <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
-<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R</span>
+<span>  <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span>  breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -105,8 +105,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span>  ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Disk diffusion diameter (mm)"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
 <span>  mo <span class="op">=</span> <span class="cn">NULL</span>, ab <span class="op">=</span> <span class="cn">NULL</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
-<span>  colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
-<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span></span>
+<span>  <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span>  breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -115,8 +115,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span>  title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>, ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>,</span>
 <span>  language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Disk diffusion diameter (mm)"</span>,</span>
 <span>  language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
-<span>  colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
-<span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
+<span>  colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span></span>
+<span>  <span class="st">"#ED553B"</span><span class="op">)</span>, language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, expand <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  include_PKPD <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_include_PKPD"</span>, <span class="cn">TRUE</span><span class="op">)</span>,</span>
 <span>  breakpoint_type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_breakpoint_type"</span>, <span class="st">"human"</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
@@ -129,8 +129,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span><span class="co"># S3 method for class 'sir'</span></span>
 <span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">object</span>, title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span>,</span>
 <span>  xlab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Antimicrobial Interpretation"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
-<span>  ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>,</span>
-<span>  colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>, <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
+<span>  ylab <span class="op">=</span> <span class="fu"><a href="translate.html">translate_AMR</a></span><span class="op">(</span><span class="st">"Frequency"</span>, language <span class="op">=</span> <span class="va">language</span><span class="op">)</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S</span>
+<span>  <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span> <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span>,</span>
 <span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">facet_sir</span><span class="op">(</span>facet <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">"interpretation"</span>, <span class="st">"antibiotic"</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span>
@@ -138,8 +138,8 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span><span class="fu">scale_y_percent</span><span class="op">(</span>breaks <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="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span><span class="fl">0</span>, <span class="fu"><a href="https://rdrr.io/r/base/Extremes.html" class="external-link">max</a></span><span class="op">(</span><span class="va">x</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span>, <span class="fl">0.1</span><span class="op">)</span>,</span>
 <span>  limits <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="fl">0</span>, <span class="cn">NA</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
-<span><span class="fu">scale_sir_colours</span><span class="op">(</span><span class="va">...</span>, <span class="va">aesthetics</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span>,</span>
-<span>  <span class="st">"#ED553B"</span><span class="op">)</span><span class="op">)</span></span>
+<span><span class="fu">scale_sir_colours</span><span class="op">(</span><span class="va">...</span>, <span class="va">aesthetics</span>, colours_SIR <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span>S <span class="op">=</span> <span class="st">"#3CAEA3"</span>, SDD <span class="op">=</span></span>
+<span>  <span class="st">"#8FD6C4"</span>, I <span class="op">=</span> <span class="st">"#F6D55C"</span>, R <span class="op">=</span> <span class="st">"#ED553B"</span><span class="op">)</span><span class="op">)</span></span>
 <span></span>
 <span><span class="fu">theme_sir</span><span class="op">(</span><span class="op">)</span></span>
 <span></span>
@@ -310,6 +310,11 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-plt img"><img src="plot-2.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_mic_values</span>, mo <span class="op">=</span> <span class="st">"Staph aureus"</span>, ab <span class="op">=</span> <span class="st">"Ceftaroline"</span>, guideline <span class="op">=</span> <span class="st">"CLSI"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
+<span class="r-plt img"><img src="plot-3.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span></span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># support for 27 languages, various guidelines, and many options</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">some_disk_values</span>,</span></span>
 <span class="r-in"><span>    mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>,</span></span>
@@ -317,7 +322,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span>    title <span class="op">=</span> <span class="st">"Disk diffusion from the North"</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-3.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-4.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Plotting using scale_x_mic() -----------------------------------------</span></span></span>
@@ -333,31 +338,31 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span>  <span class="va">mic_plot</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"without scale_x_mic()"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-4.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-5.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">mic_plot</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_x_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic()"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-5.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-6.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">mic_plot</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_x_mic</span><span class="op">(</span>keep_operators <span class="op">=</span> <span class="st">"all"</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() keeping all operators"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-6.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-7.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">mic_plot</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <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="fl">1</span>, <span class="fl">16</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual 'within' range"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-7.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">mic_plot</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_x_mic</span><span class="op">(</span>mic_range <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="fl">0.032</span>, <span class="fl">256</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span>title <span class="op">=</span> <span class="st">"with scale_x_mic() using a manual 'outside' range"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-8.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Plotting using scale_y_mic() -----------------------------------------</span></span></span>
@@ -372,10 +377,10 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">group</span>, <span class="va">mic</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><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><span class="op">)</span> <span class="op">+</span></span></span>
-<span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span>linetype <span class="op">=</span> <span class="fl">2</span>, colour <span class="op">=</span> <span class="st">"grey"</span>, fill <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="op">+</span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span>linetype <span class="op">=</span> <span class="fl">2</span>, colour <span class="op">=</span> <span class="st">"grey30"</span>, fill <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_y_mic</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-plt img"><img src="plot-9.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-10.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
@@ -385,10 +390,10 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span><span class="va">group</span>, <span class="va">mic</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><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><span class="op">)</span> <span class="op">+</span></span></span>
-<span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span>linetype <span class="op">=</span> <span class="fl">2</span>, colour <span class="op">=</span> <span class="st">"grey"</span>, fill <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="op">+</span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_violin.html" class="external-link">geom_violin</a></span><span class="op">(</span>linetype <span class="op">=</span> <span class="fl">2</span>, colour <span class="op">=</span> <span class="st">"grey30"</span>, fill <span class="op">=</span> <span class="cn">NA</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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="cn">NA</span>, <span class="fl">0.25</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-plt img"><img src="plot-10.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Plotting using scale_x_sir() -----------------------------------------</span></span></span>
@@ -403,7 +408,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span>    <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_bar.html" class="external-link">geom_col</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_x_sir</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-plt img"><img src="plot-11.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Plotting using scale_y_mic() and scale_colour_sir() ------------------</span></span></span>
@@ -420,19 +425,19 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><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></span>
 <span class="r-in"><span>  <span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><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="r-in"><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="r-in"><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">"grey30"</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><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></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="va">plain</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-12.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-13.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># and now with our MIC and SIR scale functions:</span></span></span>
 <span class="r-in"><span>  <span class="va">plain</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_y_mic</span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_colour_sir</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-plt img"><img src="plot-13.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://ggplot2.tidyverse.org" class="external-link">"ggplot2"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">plain</span> <span class="op">+</span></span></span>
 <span class="r-in"><span>    <span class="fu">scale_y_mic</span><span class="op">(</span>mic_range <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="fl">0.005</span>, <span class="fl">32</span><span class="op">)</span>, name <span class="op">=</span> <span class="st">"Our MICs!"</span><span class="op">)</span> <span class="op">+</span></span></span>
@@ -441,26 +446,26 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <span class="r-in"><span>      name <span class="op">=</span> <span class="st">"Support in 27 languages"</span></span></span>
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
-<span class="r-plt img"><img src="plot-14.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Plotting using base R's plot() ---------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_mic_values</span><span class="op">)</span></span></span>
-<span class="r-plt img"><img src="plot-15.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-16.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="co"># when providing the microorganism and antibiotic, colours will show interpretations:</span></span></span>
 <span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_mic_values</span>, mo <span class="op">=</span> <span class="st">"S. aureus"</span>, ab <span class="op">=</span> <span class="st">"ampicillin"</span><span class="op">)</span></span></span>
-<span class="r-plt img"><img src="plot-16.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span><span class="op">)</span></span></span>
-<span class="r-plt img"><img src="plot-17.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="plot-18.png" alt="" width="700" height="433"></span>
-<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="plot-19.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_disk_values</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">plot</span><span class="op">(</span><span class="va">some_sir_values</span><span class="op">)</span></span></span>
-<span class="r-plt img"><img src="plot-20.png" alt="" width="700" height="433"></span>
+<span class="r-plt img"><img src="plot-21.png" alt="" width="700" height="433"></span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
--- a/reference/proportion.html
+++ b/reference/proportion.html
@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -306,16 +306,16 @@ resistance() should be used to calculate resistance, susceptibility() should be
 <span class="r-in"><span>      <span class="va">resistance</span></span></span>
 <span class="r-in"><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;">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>
-<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>
+<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>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There was 1 warning in `summarise()`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `KAN = (function (..., minimum = 30, as_percent = FALSE,</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span>   only_all_tested = FALSE) ...`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 3: `ward = "Outpatient"`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: only 23 results available for KAN in group: ward =</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (<span style="background-color: #EEEEEE;">minimum</span> = 30).</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (<span style="background-color: #EEEEEE;">`minimum`</span> = 30).</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 7</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward         GEN   TOB   AMK   KAN    IPM    MEM</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
--- a/reference/random.html
+++ b/reference/random.html
@@ -7,7 +7,7 @@

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <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/resistance_predict.html
+++ b/reference/resistance_predict.html
@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us

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

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9004</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9019</small>


    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -179,8 +179,8 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
 <span class="r-in"><span>  year_min <span class="op">=</span> <span class="fl">2010</span>,</span></span>
 <span class="r-in"><span>  model <span class="op">=</span> <span class="st">"binomial"</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The <span style="background-color: #EEEEEE;">resistance_predict()</span> function is deprecated and will be removed in a</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> future version, see <span style="background-color: #EEEEEE;">?AMR-deprecated</span>. Use the tidymodels framework</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The <span style="background-color: #EEEEEE;">`resistance_predict()`</span> function is deprecated and will be removed in a</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> future version, see <span style="background-color: #EEEEEE;">`?AMR-deprecated`</span>. Use the tidymodels framework</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> instead, for which we have written a basic and short introduction on our</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> website: https://amr-for-r.org/articles/AMR_with_tidymodels.html</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> This warning will be shown once per session.</span>
--- a/Show More
+++ b/Show More
Author	SHA1	Message	Date
github-actions	43285cb936	Built site for AMR@3.0.0.9019: `60bd631`	2025-09-01 15:07:43 +00:00
github-actions	4542802e26	Built site for AMR@3.0.0.9018: `9b07a85`	2025-08-07 14:35:23 +00:00
github-actions	e8a82b62b7	Built site for AMR@3.0.0.9017: `fc72cf9`	2025-07-28 10:32:15 +00:00
github-actions	501395d46e	Built site for AMR@3.0.0.9016: `2f86698`	2025-07-23 20:25:40 +00:00
github-actions	a09b81fb58	Built site for AMR@3.0.0.9015: `6cb724a`	2025-07-19 12:16:34 +00:00
github-actions	3be689a8db	Built site for AMR@3.0.0.9014: `49274f0`	2025-07-18 14:05:50 +00:00
github-actions	7f9aacb56b	Built site for AMR@3.0.0.9012: `8da0f52`	2025-07-17 21:05:56 +00:00
github-actions	5791bfb45d	Built site for AMR@3.0.0.9012: `68442f3`	2025-07-17 17:54:16 +00:00
github-actions	b993fdd12f	Built site for AMR@3.0.0.9011: `39ea5f6`	2025-07-17 17:42:41 +00:00
github-actions	eb889b5de5	Built site for AMR@3.0.0.9010: `65ec098`	2025-07-17 17:19:09 +00:00
github-actions	7d4c4ecffc	Built site for AMR@3.0.0.9009: `e9e3de4`	2025-07-17 15:23:46 +00:00
github-actions	758fc341e8	Built site for AMR@3.0.0.9008: `d94bdd2`	2025-07-17 15:16:31 +00:00