Built site for AMR: 1.8.2.9111@aa48c6b

2026-08-29 23:18:53 +02:00 · 2023-02-08 16:01:47 +00:00
parent c43e91eaee
commit 769ace0b66
112 changed files with 1836 additions and 1173 deletions
--- a/404.html
+++ b/404.html
@@ -36,7 +36,7 @@
    <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -69,6 +69,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="https://msberends.github.io/AMR/reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="https://msberends.github.io/AMR/articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/articles/AMR.html
+++ b/articles/AMR.html
@@ -38,7 +38,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,6 +71,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -173,7 +178,7 @@
                        <h4 data-toc-skip class="author">Dr. Matthijs
 Berends</h4>
-            <h4 data-toc-skip class="date">24 January 2023</h4>
+            <h4 data-toc-skip class="date">08 February 2023</h4>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
      <div class="d-none name"><code>AMR.Rmd</code></div>
@@ -185,7 +190,7 @@ Berends</h4>
 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 24 January 2023.</p>
+generated on 08 February 2023.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -241,21 +246,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2023-01-24</td>
+<td align="center">2023-02-08</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2023-01-24</td>
+<td align="center">2023-02-08</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2023-01-24</td>
+<td align="center">2023-02-08</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -406,70 +411,70 @@ data set:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2018-01-01</td>
+<td align="center">2012-11-01</td>
-<td align="center">Y10</td>
+<td align="center">T4</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2012-02-22</td>
+<td align="center">2011-08-07</td>
-<td align="center">D10</td>
+<td align="center">Q3</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital A</td>
-<td align="center">Staphylococcus aureus</td>
+<td align="center">Escherichia coli</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">I</td>
-<td align="center">R</td>
+<td align="center">S</td>
-<td align="center">M</td>
+<td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2015-12-24</td>
+<td align="center">2015-04-08</td>
-<td align="center">H3</td>
+<td align="center">A9</td>
 <td align="center">Hospital C</td>
 <td align="center">Streptococcus pneumoniae</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2017-07-13</td>
 <td align="center">U7</td>
 <td align="center">Hospital D</td>
 <td align="center">Klebsiella pneumoniae</td>
-<td align="center">S</td>
+<td align="center">R</td>
-<td align="center">I</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
 <td align="center">2016-02-29</td>
 <td align="center">O4</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">I</td>
+<td align="center">M</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2016-02-09</td>
+<td align="center">2017-07-30</td>
-<td align="center">S1</td>
+<td align="center">I8</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">Klebsiella pneumoniae</td>
 <td align="center">I</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="odd">
 <td align="center">2012-01-05</td>
 <td align="center">M5</td>
 <td align="center">Hospital B</td>
 <td align="center">Streptococcus pneumoniae</td>
 <td align="center">I</td>
 <td align="center">R</td>
-<td align="center">F</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2015-02-21</td>
 <td align="center">E9</td>
 <td align="center">Hospital D</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">I</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 </tr>
 </tbody>
 </table>
@@ -505,18 +510,18 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,349</td>
+<td align="right">10,359</td>
-<td align="right">51.75%</td>
+<td align="right">51.80%</td>
-<td align="right">10,349</td>
+<td align="right">10,359</td>
-<td align="right">51.75%</td>
+<td align="right">51.8%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,651</td>
+<td align="right">9,641</td>
-<td align="right">48.26%</td>
+<td align="right">48.21%</td>
 <td align="right">20,000</td>
-<td align="right">100.00%</td>
+<td align="right">100.0%</td>
 </tr>
 </tbody>
 </table>
@@ -546,7 +551,7 @@ and <code><a href="https://dplyr.tidyverse.org/reference/across.html" class="ext
 <span><span class="co"># [1] "AMX" "AMC" "CIP" "GEN"</span></span>
 <span></span>
 <span><span class="va">data</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<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">where</span><span class="op">(</span><span class="va">is_sir_eligible</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
+<span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is_sir_eligible</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p>Finally, we will apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST
 rules</a> on our antimicrobial results. In Europe, most medical
 microbiological laboratories already apply these rules. Our package
@@ -627,9 +632,9 @@ takes into account the antimicrobial susceptibility test results using
 <span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
 <span><span class="co"># 2</span></span>
 <span><span class="co"># Including isolates from ICU.</span></span>
-<span><span class="co"># =&gt; Found 12,429 'phenotype-based' first isolates (62.1% of total where a</span></span>
+<span><span class="co"># =&gt; Found 20,000 'phenotype-based' first isolates (100.0% of total where a</span></span>
 <span><span class="co">#    microbial ID was available)</span></span></code></pre></div>
-<p>So only 62.1% is suitable for resistance analysis! We can now filter
+<p>So only 100% is suitable for resistance analysis! We can now filter
 on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
 <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@@ -638,15 +643,13 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
 <p>For future use, the above two syntaxes can be shortened:</p>
 <div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
-<span>  <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
+<span>  <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
-<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
+<p>So we end up with 20,000 isolates for analysis. Now our data looks
 <p>So we end up with 12,429 isolates for analysis. Now our data looks
 like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
-<table style="width:100%;" class="table">
+<table class="table">
 <colgroup>
 <col width="2%">
 <col width="9%">
 <col width="9%">
 <col width="9%">
@@ -662,7 +665,6 @@ like:</p>
 <col width="5%">
 </colgroup>
 <thead><tr class="header">
 <th align="left"></th>
 <th align="center">date</th>
 <th align="center">patient_id</th>
 <th align="center">hospital</th>
@@ -679,15 +681,14 @@ like:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
+<td align="center">2012-11-01</td>
-<td align="center">2018-01-01</td>
+<td align="center">T4</td>
-<td align="center">Y10</td>
+<td align="center">Hospital A</td>
 <td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
@@ -695,77 +696,27 @@ like:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">2</td>
+<td align="center">2011-08-07</td>
-<td align="center">2012-02-22</td>
+<td align="center">Q3</td>
-<td align="center">D10</td>
+<td align="center">Hospital A</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">I</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="center">2016-02-29</td>
 <td align="center">O4</td>
 <td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">6</td>
 <td align="center">2016-02-09</td>
 <td align="center">S1</td>
 <td align="center">Hospital B</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Klebsiella</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="left">7</td>
+<td align="center">2015-04-08</td>
-<td align="center">2013-02-22</td>
+<td align="center">A9</td>
 <td align="center">S5</td>
 <td align="center">Hospital D</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">9</td>
 <td align="center">2014-08-17</td>
 <td align="center">J7</td>
 <td align="center">Hospital D</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
@@ -774,6 +725,51 @@ like:</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2017-07-30</td>
 <td align="center">I8</td>
 <td align="center">Hospital D</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Klebsiella</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2012-01-05</td>
 <td align="center">M5</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2015-02-21</td>
 <td align="center">E9</td>
 <td align="center">Hospital D</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
 <p>Time for the analysis!</p>
@@ -807,8 +803,8 @@ readable:</p>
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 12,429<br>
+Length: 20,000<br>
-Available: 12,429 (100%, NA: 0 = 0%)<br>
+Available: 20,000 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -833,33 +829,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">5,950</td>
+<td align="right">9,956</td>
-<td align="right">47.87%</td>
+<td align="right">49.78%</td>
-<td align="right">5,950</td>
+<td align="right">9,956</td>
-<td align="right">47.87%</td>
+<td align="right">49.78%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">3,328</td>
+<td align="right">4,995</td>
-<td align="right">26.78%</td>
+<td align="right">24.98%</td>
-<td align="right">9,278</td>
+<td align="right">14,951</td>
-<td align="right">74.65%</td>
+<td align="right">74.76%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">1,809</td>
+<td align="right">3,001</td>
-<td align="right">14.55%</td>
+<td align="right">15.01%</td>
-<td align="right">11,087</td>
+<td align="right">17,952</td>
-<td align="right">89.20%</td>
+<td align="right">89.76%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,342</td>
+<td align="right">2,048</td>
-<td align="right">10.80%</td>
+<td align="right">10.24%</td>
-<td align="right">12,429</td>
+<td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -908,42 +904,12 @@ antibiotic class they are in:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2012-02-22</td>
+<td align="center">2015-04-08</td>
-<td align="center">D10</td>
+<td align="center">A9</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">I</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2016-02-09</td>
 <td align="center">S1</td>
 <td align="center">Hospital B</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Klebsiella</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2014-08-17</td>
 <td align="center">J7</td>
 <td align="center">Hospital D</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
@@ -953,50 +919,80 @@ antibiotic class they are in:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2013-05-07</td>
+<td align="center">2012-01-05</td>
-<td align="center">V6</td>
+<td align="center">M5</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">R</td>
-<td align="center">F</td>
+<td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2013-10-28</td>
+<td align="center">2015-02-21</td>
-<td align="center">P9</td>
+<td align="center">E9</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="center">B_STPHY_AURS</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
-<td align="center">F</td>
+<td align="center">S</td>
-<td align="center">Gram-negative</td>
+<td align="center">R</td>
-<td align="center">Escherichia</td>
+<td align="center">M</td>
-<td align="center">coli</td>
+<td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2017-04-15</td>
+<td align="center">2017-04-27</td>
-<td align="center">V10</td>
+<td align="center">C9</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">I</td>
 <td align="center">I</td>
 <td align="center">I</td>
 <td align="center">R</td>
-<td align="center">F</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2012-06-09</td>
 <td align="center">C6</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2011-12-09</td>
 <td align="center">W4</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
 <p>If you want to get a quick glance of the number of isolates in
@@ -1018,51 +1014,51 @@ different bug/drug combinations, you can use the
 <tbody>
 <tr class="odd">
 <td align="center">E. coli</td>
-<td align="center">AMX</td>
+<td align="center">AMC</td>
-<td align="center">1484</td>
+<td align="center">4463</td>
-<td align="center">1261</td>
+<td align="center">2199</td>
-<td align="center">3205</td>
+<td align="center">3294</td>
-<td align="center">5950</td>
+<td align="center">9956</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
-<td align="center">AMC</td>
+<td align="center">AMX</td>
-<td align="center">2726</td>
+<td align="center">2238</td>
-<td align="center">1214</td>
+<td align="center">2141</td>
-<td align="center">2010</td>
+<td align="center">5577</td>
-<td align="center">5950</td>
+<td align="center">9956</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">2026</td>
+<td align="center">3359</td>
-<td align="center">1824</td>
+<td align="center">3299</td>
-<td align="center">2100</td>
+<td align="center">3298</td>
-<td align="center">5950</td>
+<td align="center">9956</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">2016</td>
+<td align="center">3360</td>
-<td align="center">1853</td>
+<td align="center">3332</td>
-<td align="center">2081</td>
+<td align="center">3264</td>
-<td align="center">5950</td>
+<td align="center">9956</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
 <td align="center">886</td>
 <td align="center">446</td>
 <td align="center">716</td>
 <td align="center">2048</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1342</td>
+<td align="center">2048</td>
-<td align="center">1342</td>
+<td align="center">2048</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
 <td align="center">599</td>
 <td align="center">262</td>
 <td align="center">481</td>
 <td align="center">1342</td>
 </tr>
 </tbody>
 </table>
@@ -1084,34 +1080,34 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">2016</td>
+<td align="center">3360</td>
-<td align="center">1853</td>
+<td align="center">3332</td>
-<td align="center">2081</td>
+<td align="center">3264</td>
-<td align="center">5950</td>
+<td align="center">9956</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">468</td>
+<td align="center">682</td>
-<td align="center">429</td>
+<td align="center">656</td>
-<td align="center">445</td>
+<td align="center">710</td>
-<td align="center">1342</td>
+<td align="center">2048</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">1083</td>
+<td align="center">1668</td>
-<td align="center">1090</td>
+<td align="center">1653</td>
-<td align="center">1155</td>
+<td align="center">1674</td>
-<td align="center">3328</td>
+<td align="center">4995</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">GEN</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1809</td>
+<td align="center">3001</td>
-<td align="center">1809</td>
+<td align="center">3001</td>
 </tr>
 </tbody>
 </table>
@@ -1143,7 +1139,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
 own:</p>
 <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
-<span><span class="co"># [1] 0.5882211</span></span></code></pre></div>
+<span><span class="co"># [1] 0.60575</span></span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
 <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@@ -1158,19 +1154,19 @@ own:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5883152</td>
+<td align="center">0.6017567</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5836154</td>
+<td align="center">0.6139130</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5717427</td>
+<td align="center">0.6064538</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.6082433</td>
+<td align="center">0.5972906</td>
 </tr>
 </tbody>
 </table>
@@ -1195,23 +1191,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5883152</td>
+<td align="center">0.6017567</td>
-<td align="center">3680</td>
+<td align="center">6034</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5836154</td>
+<td align="center">0.6139130</td>
-<td align="center">4431</td>
+<td align="center">6900</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5717427</td>
+<td align="center">0.6064538</td>
-<td align="center">1819</td>
+<td align="center">3006</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.6082433</td>
+<td align="center">0.5972906</td>
-<td align="center">2499</td>
+<td align="center">4060</td>
 </tr>
 </tbody>
 </table>
@@ -1236,27 +1232,27 @@ therapies very easily:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.6621849</td>
+<td align="center">0.6691442</td>
-<td align="center">0.6502521</td>
+<td align="center">0.6721575</td>
-<td align="center">0.8878992</td>
+<td align="center">0.8938329</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.6415797</td>
+<td align="center">0.6503906</td>
-<td align="center">0.6684054</td>
+<td align="center">0.6533203</td>
-<td align="center">0.8941878</td>
+<td align="center">0.8803711</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.6676683</td>
+<td align="center">0.6654655</td>
-<td align="center">0.6529447</td>
+<td align="center">0.6648649</td>
-<td align="center">0.8846154</td>
+<td align="center">0.8852853</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.4693201</td>
+<td align="center">0.4325225</td>
 <td align="center">0.0000000</td>
-<td align="center">0.4693201</td>
+<td align="center">0.4325225</td>
 </tr>
 </tbody>
 </table>
@@ -1284,23 +1280,23 @@ classes, use a antibiotic class selector such as
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">58.8%</td>
+<td align="right">60.2%</td>
-<td align="right">36.2%</td>
+<td align="right">36.8%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">58.4%</td>
+<td align="right">61.4%</td>
-<td align="right">36.9%</td>
+<td align="right">37.8%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">57.2%</td>
+<td align="right">60.6%</td>
-<td align="right">36.3%</td>
+<td align="right">36.6%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">60.8%</td>
+<td align="right">59.7%</td>
-<td align="right">37.1%</td>
+<td align="right">35.9%</td>
 </tr>
 </tbody>
 </table>
@@ -1416,16 +1412,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
 <code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
 <span><span class="va">mic_values</span></span>
 <span><span class="co"># Class 'mic'</span></span>
-<span><span class="co">#   [1] 256    64     0.001  0.01   8      8      1      0.5    0.5    16    </span></span>
+<span><span class="co">#   [1] 0.025   8       0.25    32      0.005   4       32      128     &lt;=0.001</span></span>
-<span><span class="co">#  [11] 0.125  256    0.5    0.002  2      0.005  1      1      256    0.002 </span></span>
+<span><span class="co">#  [10] 16      0.002   0.002   0.5     2       0.025   0.002   8       128    </span></span>
-<span><span class="co">#  [21] 0.002  0.01   0.25   2      256    64     0.125  128    0.001  4     </span></span>
+<span><span class="co">#  [19] 0.0625  1       0.125   128     0.5     2       1       8       0.025  </span></span>
-<span><span class="co">#  [31] 0.125  0.0625 1      64     256    0.25   128    0.5    0.5    32    </span></span>
+<span><span class="co">#  [28] 0.01    0.5     0.0625  64      0.25    0.025   64      0.005   128    </span></span>
-<span><span class="co">#  [41] 16     2      0.125  0.005  8      0.0625 0.01   0.25   0.125  0.025 </span></span>
+<span><span class="co">#  [37] &lt;=0.001 &lt;=0.001 0.25    2       16      0.125   0.125   0.002   0.125  </span></span>
-<span><span class="co">#  [51] 0.0625 4      0.125  8      0.002  0.5    0.01   0.025  0.125  0.025 </span></span>
+<span><span class="co">#  [46] 32      16      0.005   0.0625  0.0625  32      16      16      8      </span></span>
-<span><span class="co">#  [61] 0.001  16     1      0.25   0.5    2      8      0.01   8      0.0625</span></span>
+<span><span class="co">#  [55] 0.025   2       0.125   64      16      &lt;=0.001 64      &gt;=256   0.0625 </span></span>
-<span><span class="co">#  [71] 2      0.025  8      0.005  0.025  8      0.002  0.002  256    2     </span></span>
+<span><span class="co">#  [64] &gt;=256   0.002   &gt;=256   0.125   &gt;=256   0.0625  1       0.0625  0.002  </span></span>
-<span><span class="co">#  [81] 0.01   0.002  16     0.0625 64     8      0.005  32     0.125  0.001 </span></span>
+<span><span class="co">#  [73] &lt;=0.001 0.005   32      0.25    128     64      32      0.25    0.125  </span></span>
-<span><span class="co">#  [91] 0.002  2      0.125  8      1      128    0.01   1      0.001  0.025</span></span></code></pre></div>
+<span><span class="co">#  [82] &lt;=0.001 0.5     16      8       0.5     0.5     0.125   0.5     64     </span></span>
 <span><span class="co">#  [91] 1       0.0625  &gt;=256   0.005   128     &gt;=256   0.025   128     128    </span></span>
 <span><span class="co"># [100] 0.01</span></span></code></pre></div>
 <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># base R:</span></span>
 <span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@@ -1459,10 +1457,10 @@ plotting:</p>
 <code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
 <span><span class="va">disk_values</span></span>
 <span><span class="co"># Class 'disk'</span></span>
-<span><span class="co">#   [1] 25 20 25 25 26 18 20 24 23 28 30 18 27 27 25 20 28 21 19 23 27 28 28 24 28</span></span>
+<span><span class="co">#   [1] 24 18 24 25 18 27 25 21 28 26 18 23 21 30 27 21 20 30 29 20 29 27 17 31 25</span></span>
-<span><span class="co">#  [26] 17 25 19 23 30 22 17 31 23 31 24 28 25 28 28 27 31 20 24 18 18 24 29 17 31</span></span>
+<span><span class="co">#  [26] 25 20 29 24 30 18 31 31 20 17 30 22 29 27 19 31 25 23 21 26 25 30 28 30 21</span></span>
-<span><span class="co">#  [51] 17 28 23 26 19 25 18 22 24 18 17 27 26 26 25 18 23 21 21 28 17 25 30 29 29</span></span>
+<span><span class="co">#  [51] 24 24 21 27 24 17 19 27 21 21 21 26 30 24 27 24 24 27 28 18 29 17 26 19 21</span></span>
-<span><span class="co">#  [76] 18 31 20 22 28 23 26 24 27 28 20 25 19 19 17 24 24 17 18 17 30 24 21 29 27</span></span></code></pre></div>
+<span><span class="co">#  [76] 29 29 31 29 24 20 29 18 21 18 23 22 28 18 19 28 27 18 22 19 20 31 30 22 30</span></span></code></pre></div>
 <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># base R:</span></span>
 <span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
--- a/articles/AMR_files/figure-html/disk_plots-1.png
+++ b/articles/AMR_files/figure-html/disk_plots-1.png
--- a/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
+++ b/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
--- a/articles/AMR_files/figure-html/mic_plots-1.png
+++ b/articles/AMR_files/figure-html/mic_plots-1.png
--- a/articles/AMR_files/figure-html/mic_plots-2.png
+++ b/articles/AMR_files/figure-html/mic_plots-2.png
--- a/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
+++ b/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
--- a/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
+++ b/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@@ -38,7 +38,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,6 +71,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/articles/MDR.html
+++ b/articles/MDR.html
@@ -38,7 +38,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,6 +71,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -380,19 +385,19 @@ names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
 <span><span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
-<span><span class="co"># 1          S         S            R          I            I            R</span></span>
+<span><span class="co"># 1          I         S            I          I            S            I</span></span>
-<span><span class="co"># 2          R         R            S          S            I            I</span></span>
+<span><span class="co"># 2          S         S            S          S            I            S</span></span>
-<span><span class="co"># 3          S         R            S          S            I            S</span></span>
+<span><span class="co"># 3          R         R            I          S            I            R</span></span>
-<span><span class="co"># 4          R         I            R          S            S            R</span></span>
+<span><span class="co"># 4          I         I            R          S            S            R</span></span>
-<span><span class="co"># 5          R         I            R          I            S            S</span></span>
+<span><span class="co"># 5          R         I            S          S            I            S</span></span>
-<span><span class="co"># 6          I         I            I          R            S            I</span></span>
+<span><span class="co"># 6          R         S            R          I            R            I</span></span>
 <span><span class="co">#   kanamycin</span></span>
 <span><span class="co"># 1         I</span></span>
-<span><span class="co"># 2         R</span></span>
+<span><span class="co"># 2         S</span></span>
-<span><span class="co"># 3         R</span></span>
+<span><span class="co"># 3         S</span></span>
-<span><span class="co"># 4         I</span></span>
+<span><span class="co"># 4         S</span></span>
 <span><span class="co"># 5         R</span></span>
-<span><span class="co"># 6         R</span></span></code></pre></div>
+<span><span class="co"># 6         I</span></span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can
 use:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@@ -433,40 +438,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3174</td>
+<td align="right">3141</td>
-<td align="right">63.48%</td>
+<td align="right">62.82%</td>
-<td align="right">3174</td>
+<td align="right">3141</td>
-<td align="right">63.48%</td>
+<td align="right">62.82%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">1008</td>
+<td align="right">1012</td>
-<td align="right">20.16%</td>
+<td align="right">20.24%</td>
-<td align="right">4182</td>
+<td align="right">4153</td>
-<td align="right">83.64%</td>
+<td align="right">83.06%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">451</td>
+<td align="right">477</td>
-<td align="right">9.02%</td>
+<td align="right">9.54%</td>
-<td align="right">4633</td>
+<td align="right">4630</td>
-<td align="right">92.66%</td>
+<td align="right">92.60%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">255</td>
+<td align="right">257</td>
-<td align="right">5.10%</td>
+<td align="right">5.14%</td>
-<td align="right">4888</td>
+<td align="right">4887</td>
-<td align="right">97.76%</td>
+<td align="right">97.74%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">112</td>
+<td align="right">113</td>
-<td align="right">2.24%</td>
+<td align="right">2.26%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
--- a/articles/PCA.html
+++ b/articles/PCA.html
@@ -38,7 +38,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,6 +71,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/articles/SPSS.html
+++ b/articles/SPSS.html
@@ -38,7 +38,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,6 +71,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -173,7 +178,7 @@
                        <h4 data-toc-skip class="author">Dr. Matthijs
 Berends</h4>
-            <h4 data-toc-skip class="date">24 January 2023</h4>
+            <h4 data-toc-skip class="date">08 February 2023</h4>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
      <div class="d-none name"><code>SPSS.Rmd</code></div>
@@ -252,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed
 <li>
 <p><strong>R has a huge community.</strong></p>
 <p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
-online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">478,396
+online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">480,015
 R-related questions</a> have already been asked on this platform (that
 covers questions and answers for any programming language). In my own
 experience, most questions are answered within a couple of
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@@ -38,7 +38,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,6 +71,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/articles/datasets.html
+++ b/articles/datasets.html
@@ -38,7 +38,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,6 +71,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -171,7 +176,7 @@
  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
-            <h4 data-toc-skip class="date">24 January 2023</h4>
+            <h4 data-toc-skip class="date">08 February 2023</h4>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
      <div class="d-none name"><code>datasets.Rmd</code></div>
@@ -192,7 +197,7 @@ of the data sets look like.</p>
 <h2 id="microorganisms-full-microbial-taxonomy">
 <code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
 </h2>
-<p>A data set with 52,141 rows and 22 columns, containing the following
+<p>A data set with 52,142 rows and 22 columns, containing the following
 column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
 <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
 <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@@ -201,7 +206,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
 <em>gbif_renamed_to</em>, <em>prevalence</em> and <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 20 December 2022 15:14:04 UTC. Find more info
+<p>It was last updated on 6 February 2023 10:57:22 UTC. Find more info
 about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
@@ -278,7 +283,7 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
 </tr>
 <tr class="even">
 <td align="center">Bacteria</td>
-<td align="center">36,475</td>
+<td align="center">36,476</td>
 </tr>
 <tr class="odd">
 <td align="center">Fungi</td>
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/articles/resistance_predict.html
+++ b/articles/resistance_predict.html
@@ -38,7 +38,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,6 +71,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/articles/welcome_to_AMR.html
+++ b/articles/welcome_to_AMR.html
@@ -38,7 +38,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,6 +71,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/extra.css
+++ b/extra.css
@@ -49,6 +49,11 @@
  content: 'Maintainers';
 }
 /* marked words for after using the search box */
 mark, .mark {
  background: rgba(17, 143, 118, 0.25) !important;
 }
 /* SYNTAX */
 /* These are simple changes for the syntax highlighting */
--- a/index.html
+++ b/index.html
@@ -42,7 +42,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -75,6 +75,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -338,9 +343,148 @@
 <p>This base R snippet will work in any version of R since April 2013 (R-3.0).</p>
 </div>
 <div class="section level4">
 <h4 id="generating-antibiograms">Generating antibiograms<a class="anchor" aria-label="anchor" href="#generating-antibiograms"></a>
 </h4>
 <p>The <code>AMR</code> package supports generating traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA).</p>
 <p>If used inside R Markdown or Quarto, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
 <span>            antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
 <th align="left">Pathogen (N min-max)</th>
 <th align="right">AMK</th>
 <th align="right">GEN</th>
 <th align="right">IPM</th>
 <th align="right">KAN</th>
 <th align="right">MEM</th>
 <th align="right">TOB</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
 <td align="left">CoNS (43-309)</td>
 <td align="right">0</td>
 <td align="right">86</td>
 <td align="right">52</td>
 <td align="right">0</td>
 <td align="right">52</td>
 <td align="right">22</td>
 </tr>
 <tr class="even">
 <td align="left">E. coli (0-462)</td>
 <td align="right">100</td>
 <td align="right">98</td>
 <td align="right">100</td>
 <td align="right">NA</td>
 <td align="right">100</td>
 <td align="right">97</td>
 </tr>
 <tr class="odd">
 <td align="left">E. faecalis (0-39)</td>
 <td align="right">0</td>
 <td align="right">0</td>
 <td align="right">100</td>
 <td align="right">0</td>
 <td align="right">NA</td>
 <td align="right">0</td>
 </tr>
 <tr class="even">
 <td align="left">K. pneumoniae (0-58)</td>
 <td align="right">NA</td>
 <td align="right">90</td>
 <td align="right">100</td>
 <td align="right">NA</td>
 <td align="right">100</td>
 <td align="right">90</td>
 </tr>
 <tr class="odd">
 <td align="left">P. aeruginosa (17-30)</td>
 <td align="right">NA</td>
 <td align="right">100</td>
 <td align="right">NA</td>
 <td align="right">0</td>
 <td align="right">NA</td>
 <td align="right">100</td>
 </tr>
 <tr class="even">
 <td align="left">P. mirabilis (0-34)</td>
 <td align="right">NA</td>
 <td align="right">94</td>
 <td align="right">94</td>
 <td align="right">NA</td>
 <td align="right">NA</td>
 <td align="right">94</td>
 </tr>
 <tr class="odd">
 <td align="left">S. aureus (2-233)</td>
 <td align="right">NA</td>
 <td align="right">99</td>
 <td align="right">NA</td>
 <td align="right">NA</td>
 <td align="right">NA</td>
 <td align="right">98</td>
 </tr>
 <tr class="even">
 <td align="left">S. epidermidis (8-163)</td>
 <td align="right">0</td>
 <td align="right">79</td>
 <td align="right">NA</td>
 <td align="right">0</td>
 <td align="right">NA</td>
 <td align="right">51</td>
 </tr>
 <tr class="odd">
 <td align="left">S. hominis (3-80)</td>
 <td align="right">NA</td>
 <td align="right">92</td>
 <td align="right">NA</td>
 <td align="right">NA</td>
 <td align="right">NA</td>
 <td align="right">85</td>
 </tr>
 <tr class="even">
 <td align="left">S. pneumoniae (11-117)</td>
 <td align="right">0</td>
 <td align="right">0</td>
 <td align="right">NA</td>
 <td align="right">0</td>
 <td align="right">NA</td>
 <td align="right">0</td>
 </tr>
 </tbody>
 </table>
 <p>In combination antibiograms, it is clear that combined antibiotics yield higher empiric coverage:</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
 <span>            antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
 <span>            mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
 <thead><tr class="header">
 <th align="left">Pathogen (N min-max)</th>
 <th align="right">TZP</th>
 <th align="right">TZP + GEN</th>
 <th align="right">TZP + TOB</th>
 </tr></thead>
 <tbody>
 <tr class="odd">
 <td align="left">Gram-negative (641-693)</td>
 <td align="right">88</td>
 <td align="right">99</td>
 <td align="right">98</td>
 </tr>
 <tr class="even">
 <td align="left">Gram-positive (345-1044)</td>
 <td align="right">86</td>
 <td align="right">98</td>
 <td align="right">95</td>
 </tr>
 </tbody>
 </table>
 </div>
 <div class="section level4">
 <h4 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a>
 </h4>
-<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
 <span></span>
@@ -388,7 +532,7 @@
 </tr>
 </tbody>
 </table>
-<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span>
 <span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
@@ -435,7 +579,7 @@
 </tr>
 </tbody>
 </table>
-<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span>
 <span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
@@ -515,7 +659,7 @@
 </h4>
 <p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
 <p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
-<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
 <p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
 <p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
@@ -529,13 +673,13 @@
 <ol style="list-style-type: decimal">
 <li>
 <p>Manually, using:</p>
-<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
 <span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
 </li>
 <li>
 <p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
-<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
+<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,</span>
 <span>                  msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
 <p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -137,39 +142,46 @@
    </div>
    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="1.8.2.9103" id="amr-1829103">AMR 1.8.2.9103<a class="anchor" aria-label="anchor" href="#amr-1829103"></a></h2>
+<h2 class="pkg-version" data-toc-text="1.8.2.9111" id="amr-1829111">AMR 1.8.2.9111<a class="anchor" aria-label="anchor" href="#amr-1829111"></a></h2>
 <p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p>
 <p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
 <p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
 <ul><li>All functions and arguments with ‘rsi’ were replaced with ‘sir’, such as the interpretation of MIC values (now <code><a href="../reference/as.sir.html">as.sir()</a></code> instead of <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>) - all old functions still work for now</li>
 <li>Many new interesting functions, such as <code><a href="../reference/antibiogram.html">antibiogram()</a></code> (for generating traditional/combined/syndromic/WISCA antibiograms), <code><a href="../reference/proportion.html">sir_confidence_interval()</a></code> and <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code>, and <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add custom microorganisms to this package</li>
 <li>Clinical breakpoints added for EUCAST 2022 and CLSI 2022</li>
 <li>Microbiological taxonomy (<code>microorganisms</code> data set) updated to 2022 and now based on LPSN and GBIF</li>
 <li>Much increased algorithms to translate user input to valid taxonomy, e.g. by using <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">recent scientific work</a> about per-species human pathogenicity</li>
 <li>Clinical breakpoints added for EUCAST 2022 and CLSI 2022</li>
 <li>20 new antibiotics added and updated all DDDs and ATC codes</li>
 <li>Extended support for antiviral agents (<code>antivirals</code> data set), with many new functions</li>
 <li>Now available in 16 languages</li>
 <li>Many new interesting functions, such as <code><a href="../reference/proportion.html">sir_confidence_interval()</a></code> and <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code>, and <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add custom microorganisms to this package</li>
 <li>Many small bug fixes</li>
 </ul><div class="section level3">
-<h3 id="new-1-8-2-9103">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9103"></a></h3>
+<h3 id="new-1-8-2-9111">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9111"></a></h3>
 <div class="section level4">
-<h4 id="sir-vs-rsi-1-8-2-9103">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9103"></a></h4>
+<h4 id="sir-vs-rsi-1-8-2-9111">SIR vs. RSI<a class="anchor" aria-label="anchor" href="#sir-vs-rsi-1-8-2-9111"></a></h4>
 <p>For this milestone version, we replaced all mentions of RSI with SIR, to comply with what is actually being commonly used in the field of clinical microbiology when it comes to this tri-form regarding AMR.</p>
 <p>While existing functions such as <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>, <code><a href="../reference/AMR-deprecated.html">rsi_df()</a></code> and <code><a href="../reference/AMR-deprecated.html">ggplot_rsi()</a></code> still work, their replacements <code><a href="../reference/as.sir.html">as.sir()</a></code>, <code><a href="../reference/proportion.html">sir_df()</a></code>, <code><a href="../reference/ggplot_sir.html">ggplot_sir()</a></code> are now the current functions for AMR data analysis. A warning will be thrown once a session to remind users about this. The data set <code>rsi_translation</code> is now called <code>clinical_breakpoints</code> to better reflect its content.</p>
 <p>The ‘RSI functions’ will be removed in a future version, but not before late 2023 / early 2024.</p>
 </div>
 <div class="section level4">
-<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9103">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9103"></a></h4>
+<h4 id="new-antibiogram-function-1-8-2-9111">New antibiogram function<a class="anchor" aria-label="anchor" href="#new-antibiogram-function-1-8-2-9111"></a></h4>
 <p>Klinker <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1177/20499361211011373" class="external-link">10.1177/20499361211011373</a>) and Barbieri <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">10.1186/s13756-021-00939-2</a>).</p>
 <p>With the new <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function, users can now generate traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA). With this, we follow the logic in the previously described work of Klinker <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1177/20499361211011373" class="external-link">10.1177/20499361211011373</a>) and Barbieri <em>et al.</em> (2021, DOI <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">10.1186/s13756-021-00939-2</a>).</p>
 <p>The help page for <code><a href="../reference/antibiogram.html">antibiogram()</a></code> extensively elaborates on use cases, and <code><a href="../reference/antibiogram.html">antibiogram()</a></code> also supports printing in R Markdown and Quarto, with support for 16 languages.</p>
 <p>Furthermore, different plotting methods were implemented to allow for graphical visualisations as well.</p>
 </div>
 <div class="section level4">
 <h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9111">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9111"></a></h4>
 <p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p>
 <p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p>
 </div>
 <div class="section level4">
-<h4 id="supported-languages-1-8-2-9103">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9103"></a></h4>
+<h4 id="supported-languages-1-8-2-9111">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9111"></a></h4>
 <p>We added support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user system language.</p>
 <p>We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages and according to download stats used in almost all countries in the world!</p>
 </div>
 <div class="section level4">
-<h4 id="microbiological-taxonomy-1-8-2-9103">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9103"></a></h4>
+<h4 id="microbiological-taxonomy-1-8-2-9111">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9111"></a></h4>
 <p>The <code>microorganisms</code> data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p>
 <p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p>
 <p>The new function <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> allows users to add custom microorganisms to the <code>AMR</code> package.</p>
@@ -193,7 +205,7 @@
 <li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li>
 </ul></div>
 <div class="section level4">
-<h4 id="antibiotic-agents-and-selectors-1-8-2-9103">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9103"></a></h4>
+<h4 id="antibiotic-agents-and-selectors-1-8-2-9111">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9111"></a></h4>
 <p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p>
 <p>The <code>antibiotics</code> data set was greatly updated:</p>
 <ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
@@ -205,14 +217,14 @@
 </ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p>
 </div>
 <div class="section level4">
-<h4 id="antiviral-agents-1-8-2-9103">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9103"></a></h4>
+<h4 id="antiviral-agents-1-8-2-9111">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9111"></a></h4>
 <p>We now added extensive support for antiviral agents! For the first time, the <code>AMR</code> package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.</p>
 <ul><li>The <code>antivirals</code> data set has been extended with 18 new drugs (also from the <a href="https://www.whocc.no/atc_ddd_index/?code=J05AJ&amp;showdescription=no" class="external-link">new J05AJ ATC group</a>) and now also contains antiviral identifiers and LOINC codes</li>
 <li>A new data type <code>av</code> (<em>antivirals</em>) has been added, which is functionally similar to <code>ab</code> for antibiotics</li>
 <li>Functions <code><a href="../reference/as.av.html">as.av()</a></code>, <code><a href="../reference/av_property.html">av_name()</a></code>, <code><a href="../reference/av_property.html">av_atc()</a></code>, <code><a href="../reference/av_property.html">av_synonyms()</a></code>, <code><a href="../reference/av_from_text.html">av_from_text()</a></code> have all been added as siblings to their <code>ab_*()</code> equivalents</li>
 </ul></div>
 <div class="section level4">
-<h4 id="other-new-functions-1-8-2-9103">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9103"></a></h4>
+<h4 id="other-new-functions-1-8-2-9111">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9111"></a></h4>
 <ul><li>Function <code><a href="../reference/proportion.html">sir_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li>
 <li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
 <li>Function <code><a href="../reference/as.sir.html">sir_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.sir.html">as.sir()</a></code> (previously <code><a href="../reference/AMR-deprecated.html">as.rsi()</a></code>). This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.sir.html">as.sir()</a></code> was run.</li>
@@ -221,10 +233,10 @@
 </ul></div>
 </div>
 <div class="section level3">
-<h3 id="changes-1-8-2-9103">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9103"></a></h3>
+<h3 id="changes-1-8-2-9111">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9111"></a></h3>
 <ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">sir_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
 <li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
-<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
+<li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://sfirke.github.io/janitor/reference/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">sir_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
 <li>All data sets in this package are now a <code>tibble</code>, instead of base R <code>data.frame</code>s. Older R versions are still supported, even if they do not support <code>tibble</code>s.</li>
 <li>Our data sets are now also continually exported to <strong>Apache Feather and Apache Parquet formats</strong>. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
 <li>For <code><a href="../reference/as.sir.html">as.sir()</a></code>:
@@ -258,9 +270,10 @@
 </li>
 <li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> in case of higher taxonomic ranks (order, class, phylum)</li>
 <li>Cleaning columns with <code><a href="../reference/as.sir.html">as.sir()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li>
 <li>Fix for using <code><a href="../reference/g.test.html">g.test()</a></code> with zeroes in a 2x2 table</li>
 </ul></div>
 <div class="section level3">
-<h3 id="other-1-8-2-9103">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9103"></a></h3>
+<h3 id="other-1-8-2-9111">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9111"></a></h3>
 <ul><li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, and Jonas Salm as contributors, to thank them for their valuable input</li>
 <li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
 <li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -11,7 +11,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2023-01-24T15:35Z
+last_built: 2023-02-08T15:58Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/AMR.html
+++ b/reference/AMR.html
@@ -18,7 +18,7 @@ The AMR package is available in English, Chinese, Danish, Dutch, French, German,
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -50,6 +50,11 @@ The AMR package is available in English, Chinese, Danish, Dutch, French, German,
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/Rplot003.png
+++ b/reference/Rplot003.png
--- a/reference/Rplot005.png
+++ b/reference/Rplot005.png
--- a/reference/Rplot006.png
+++ b/reference/Rplot006.png
--- a/reference/Rplot007.png
+++ b/reference/Rplot007.png
--- a/reference/Rplot008.png
+++ b/reference/Rplot008.png
--- a/reference/Rplot009.png
+++ b/reference/Rplot009.png
--- a/reference/WHOCC.html
+++ b/reference/WHOCC.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/WHONET.html
+++ b/reference/WHONET.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/ab_from_text.html
+++ b/reference/ab_from_text.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/ab_property.html
+++ b/reference/ab_property.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -469,22 +474,18 @@
 <span class="r-in"><span><span class="co"># \donttest{</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>    <span class="fu">set_ab_names</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">set_ab_names</span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="co"># this does the same:</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html" class="external-link">rename_with</a></span><span class="op">(</span><span class="va">set_ab_names</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/rename.html" class="external-link">rename_with</a></span><span class="op">(</span><span class="va">set_ab_names</span><span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="co"># set_ab_names() works with any AB property:</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>    <span class="fu">set_ab_names</span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</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_ab_names</span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>    <span class="fu">set_ab_names</span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.sir</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">set_ab_names</span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></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">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">set_ab_names</span><span class="op">(</span><span class="va">NIT</span><span class="op">:</span><span class="va">VAN</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>
--- a/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/add_custom_microorganisms.html
+++ b/reference/add_custom_microorganisms.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -260,7 +265,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Self-added, 2023"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $snomed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> character(0)</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] NA</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
--- a/reference/age.html
+++ b/reference/age.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -200,16 +205,16 @@
 <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  1941-04-16  81  81.77534         58</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1980-09-24  42  42.37534         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1966-08-03  56  56.47671         33</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1957-01-21  66  66.04932         42</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1980-02-04  42  42.96986         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1935-11-17  87  87.22740         64</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1967-03-18  55  55.85479         32</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1945-08-15  77  77.48493         54</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1947-05-25  75  75.66849         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1986-04-06  36  36.84384         13</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1948-08-19  74  74.43288         51</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1952-04-20  70  70.80548         47</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1933-07-04  89  89.55890         66</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1985-09-08  37  37.41918         14</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1954-12-03  68  68.14247         45</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1993-09-17  29  29.39452          6</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1956-07-25  66  66.50137         43</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1947-07-04  75  75.60000         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1998-12-10  24  24.12329          1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1943-09-17  79  79.39452         56</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/age_groups-1.png
+++ b/reference/age_groups-1.png
--- a/reference/age_groups.html
+++ b/reference/age_groups.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -237,7 +242,6 @@ The default is to split on young children (0-11), youth (12-24), young adults (2
 <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> Loading required package: ggplot2</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
 <span class="r-plt img"><img src="age_groups-1.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
--- a/reference/antibiogram-1.png
+++ b/reference/antibiogram-1.png
--- a/reference/antibiogram-2.png
+++ b/reference/antibiogram-2.png
--- a/reference/antibiogram-3.png
+++ b/reference/antibiogram-3.png
--- a/reference/antibiogram-4.png
+++ b/reference/antibiogram-4.png
--- a/reference/antibiogram.html
+++ b/reference/antibiogram.html
@@ -0,0 +1,526 @@
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  <main id="main" class="col-md-9"><div class="page-header">
      <img src="../logo.svg" class="logo" alt=""><h1>Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/antibiogram.R" class="external-link"><code>R/antibiogram.R</code></a></small>
      <div class="d-none name"><code>antibiogram.Rd</code></div>
    </div>
    <div class="ref-description section level2">
    <p>Generate an antibiogram, and communicate the results in plots or tables. These functions follow the logic of Klinker <em>et al.</em> (2021, <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a>
 ) and Barbieri <em>et al.</em> (2021, <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">doi:10.1186/s13756-021-00939-2</a>
 ), and allow reporting in e.g. R Markdown and Quarto as well.</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">antibiogram</span><span class="op">(</span></span>
 <span>  <span class="va">x</span>,</span>
 <span>  antibiotics <span class="op">=</span> <span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>,</span>
 <span>  mo_transform <span class="op">=</span> <span class="st">"shortname"</span>,</span>
 <span>  ab_transform <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  syndromic_group <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  add_total_n <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  only_all_tested <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  digits <span class="op">=</span> <span class="fl">0</span>,</span>
 <span>  col_mo <span class="op">=</span> <span class="cn">NULL</span>,</span>
 <span>  language <span class="op">=</span> <span class="fu"><a href="translate.html">get_AMR_locale</a></span><span class="op">(</span><span class="op">)</span>,</span>
 <span>  minimum <span class="op">=</span> <span class="fl">30</span>,</span>
 <span>  combine_SI <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  sep <span class="op">=</span> <span class="st">" + "</span></span>
 <span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for antibiogram</span></span>
 <span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for antibiogram</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>, <span class="va">...</span><span class="op">)</span></span>
 <span></span>
 <span><span class="co"># S3 method for antibiogram</span></span>
 <span><span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="va">x</span>, as_kable <span class="op">=</span> <span class="op">!</span><span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span></code></pre></div>
    </div>
    <div class="section level2">
    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
 <ul><li><p>Klinker KP <em>et al.</em> (2021). <strong>Antimicrobial stewardship and antibiograms: importance of moving beyond traditional antibiograms</strong>. <em>Therapeutic Advances in Infectious Disease</em>, May 5;8:20499361211011373; <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a></p></li>
 <li><p>Barbieri E <em>et al.</em> (2021). <strong>Development of a Weighted-Incidence Syndromic Combination Antibiogram (WISCA) to guide the choice of the empiric antibiotic treatment for urinary tract infection in paediatric patients: a Bayesian approach</strong> <em>Antimicrobial Resistance &amp; Infection Control</em> May 1;10(1):74; <a href="https://doi.org/10.1186/s13756-021-00939-2" class="external-link">doi:10.1186/s13756-021-00939-2</a></p></li>
 <li><p><strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 5th Edition</strong>, 2022, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
 </ul></div>
    <div class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
    <dl><dt>x</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing at least a column with microorganisms and columns with antibiotic results (class 'sir', see <code><a href="as.sir.html">as.sir()</a></code>)</p></dd>
 <dt>antibiotics</dt>
 <dd><p>vector of column names, or (any combinations of) <a href="antibiotic_class_selectors.html">antibiotic selectors</a> such as <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> or <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code>. For combination antibiograms, this can also be column names separated with <code>"+"</code>, such as "TZP+TOB" given that the data set contains columns "TZP" and "TOB". See <em>Examples</em>.</p></dd>
 <dt>mo_transform</dt>
 <dd><p>a character to transform microorganism input - must be "name", "shortname", "gramstain", or one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" or "snomed". Can also be <code>NULL</code> to not transform the input.</p></dd>
 <dt>ab_transform</dt>
 <dd><p>a character to transform antibiotic input - must be one of the column names of the <a href="antibiotics.html">antibiotics</a> data set: "ab", "cid", "name", "group", "atc", "atc_group1", "atc_group2", "abbreviations", "synonyms", "oral_ddd", "oral_units", "iv_ddd", "iv_units" or "loinc". Can also be <code>NULL</code> to not transform the input.</p></dd>
 <dt>syndromic_group</dt>
 <dd><p>a column name of <code>x</code>, or values calculated to split rows of <code>x</code>, e.g. by using <code><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse()</a></code> or <code><a href="https://dplyr.tidyverse.org/reference/case_when.html" class="external-link">case_when()</a></code>. See <em>Examples</em>.</p></dd>
 <dt>add_total_n</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether total available numbers per pathogen should be added to the table (defaults to <code>TRUE</code>). This will add the lowest and highest number of available isolate per antibiotic (e.g, if for <em>E. coli</em> 200 isolates are available for ciprofloxacin and 150 for amoxicillin, the returned number will be "150-200").</p></dd>
 <dt>only_all_tested</dt>
 <dd><p>(for combination antibiograms): a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate that isolates must be tested for all antibiotics, see <em>Details</em></p></dd>
 <dt>digits</dt>
 <dd><p>number of digits to use for rounding</p></dd>
 <dt>col_mo</dt>
 <dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 <dt>language</dt>
 <dd><p>language to translate text, which defaults to the system language (see <code><a href="translate.html">get_AMR_locale()</a></code>)</p></dd>
 <dt>minimum</dt>
 <dd><p>the minimum allowed number of available (tested) isolates. Any isolate count lower than <code>minimum</code> will return <code>NA</code> with a warning. The default number of <code>30</code> isolates is advised by the Clinical and Laboratory Standards Institute (CLSI) as best practice, see <em>Source</em>.</p></dd>
 <dt>combine_SI</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether all susceptibility should be determined by results of either S or I, instead of only S (defaults to <code>TRUE</code>)</p></dd>
 <dt>sep</dt>
 <dd><p>a separating character for antibiotic columns in combination antibiograms</p></dd>
 <dt>...</dt>
 <dd><p>method extensions</p></dd>
 <dt>object</dt>
 <dd><p>an <code>antibiogram()</code> object</p></dd>
 <dt>as_kable</dt>
 <dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the printing should be done using <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code> (which is the default in non-interactive sessions)</p></dd>
 </dl></div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
    <p>This function returns a table with values between 0 and 100 for <em>susceptibility</em>, not resistance.</p>
 <p><strong>Remember that you should filter your data to let it contain only first isolates!</strong> This is needed to exclude duplicates and to reduce selection bias. Use <code><a href="first_isolate.html">first_isolate()</a></code> to determine them in your data set with one of the four available algorithms.</p>
 <p>There are four antibiogram types, as proposed by Klinker <em>et al.</em> (2021, <a href="https://doi.org/10.1177/20499361211011373" class="external-link">doi:10.1177/20499361211011373</a>
 ), and they are all supported by <code>antibiogram()</code>:</p><ol><li><p><strong>Traditional Antibiogram</strong></p>
 <p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to piperacillin/tazobactam (TZP)</p>
 <p>Code example:</p>
 <p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
 <span>            antibiotics <span class="op">=</span> <span class="st">"TZP"</span><span class="op">)</span></span></code></pre><p></p></div></li>
 <li><p><strong>Combination Antibiogram</strong></p>
 <p>Case example: Additional susceptibility of <em>Pseudomonas aeruginosa</em> to TZP + tobramycin versus TZP alone</p>
 <p>Code example:</p>
 <p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
 <span>            antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div></li>
 <li><p><strong>Syndromic Antibiogram</strong></p>
 <p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to TZP among respiratory specimens (obtained among ICU patients only)</p>
 <p>Code example:</p>
 <p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
 <span>            antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antibiotic_class_selectors.html">penicillins</a></span><span class="op">(</span><span class="op">)</span>,</span>
 <span>            syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></code></pre><p></p></div></li>
 <li><p><strong>Weighted-Incidence Syndromic Combination Antibiogram (WISCA)</strong></p>
 <p>Case example: Susceptibility of <em>Pseudomonas aeruginosa</em> to TZP among respiratory specimens (obtained among ICU patients only) for male patients age &gt;=65 years with heart failure</p>
 <p>Code example:</p>
 <p></p><div class="sourceCode r"><pre><code><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">your_data</span>,</span>
 <span>            antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
 <span>            syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">your_data</span><span class="op">$</span><span class="va">age</span> <span class="op">&gt;=</span> <span class="fl">65</span> <span class="op">&amp;</span> <span class="va">your_data</span><span class="op">$</span><span class="va">gender</span> <span class="op">==</span> <span class="st">"Male"</span>,</span>
 <span>                                     <span class="st">"Group 1"</span>, <span class="st">"Group 2"</span><span class="op">)</span><span class="op">)</span></span></code></pre><p></p></div></li>
 </ol><p>All types of antibiograms can be generated with the functions as described on this page, and can be plotted (using <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">ggplot2::autoplot()</a></code> or base <span style="R">R</span> <code><a href="plot.html">plot()</a></code>/<code><a href="https://rdrr.io/r/graphics/barplot.html" class="external-link">barplot()</a></code>) or printed into R Markdown / Quarto formats for reports. Use functions from specific 'table reporting' packages to transform the output of <code>antibiogram()</code> to your needs, e.g. <code>flextable::as_flextable()</code> or <code>gt::gt()</code>.</p>
 <p>Note that for combination antibiograms, it is important to realise that susceptibility can be calculated in two ways, which can be set with the <code>only_all_tested</code> argument (defaults to <code>FALSE</code>). See this example for two antibiotics, Drug A and Drug B, about how <code>antibiogram()</code> works to calculate the %SI:</p>
 <p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>                    only_all_tested <span class="ot">=</span> <span class="cn">FALSE</span>  only_all_tested <span class="ot">=</span> <span class="cn">TRUE</span></span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>                    <span class="sc">-----------------------</span>  <span class="sc">-----------------------</span></span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a> Drug A    Drug B   include as  include as   include as  include as</span>
 <span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>                    numerator   denominator  numerator   denominator</span>
 <span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="sc">--------</span>  <span class="sc">--------</span>  <span class="sc">----------</span>  <span class="sc">-----------</span>  <span class="sc">----------</span>  <span class="sc">-----------</span></span>
 <span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a> S or I    S or I       X            X            X            X</span>
 <span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>   R       S or I       X            X            X            X</span>
 <span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>  <span class="sc">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span>     S or I       X            X            <span class="sc">-</span>            <span class="sc">-</span></span>
 <span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a> S or I      R          X            X            X            X</span>
 <span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a>   R         R          <span class="sc">-</span>            X            <span class="sc">-</span>            X</span>
 <span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a>  <span class="sc">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span>       R          <span class="sc">-</span>            <span class="sc">-</span>            <span class="sc">-</span>            <span class="sc">-</span></span>
 <span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a> S or I     <span class="sc">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span>        X            X            <span class="sc">-</span>            <span class="sc">-</span></span>
 <span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a>   R        <span class="sc">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span>        <span class="sc">-</span>            <span class="sc">-</span>            <span class="sc">-</span>            <span class="sc">-</span></span>
 <span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a>  <span class="er">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span>      <span class="er">&lt;</span><span class="cn">NA</span><span class="sc">&gt;</span>        <span class="sc">-</span>            <span class="sc">-</span>            <span class="sc">-</span>            <span class="sc">-</span></span>
 <span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="sc">--------------------------------------------------------------------</span></span></code></pre><p></p></div>
 <p>Printing the antibiogram in non-interactive sessions will be done by <code><a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">knitr::kable()</a></code>, with support for <a href="https://rdrr.io/pkg/knitr/man/kable.html" class="external-link">all their implemented formats</a>, such as "markdown". The knitr format will be automatically determined if printed inside a knitr document (LaTeX, HTML, etc.).</p>
    </div>
    <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="co"># example_isolates is a data set available in the AMR package.</span></span></span>
 <span class="r-in"><span><span class="co"># run ?example_isolates for more info.</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;, FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   MFX &lt;sir&gt;, VAN &lt;sir&gt;, TEC &lt;sir&gt;, TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;, IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, RIF &lt;sir&gt;</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Traditional antibiogram ----------------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>            antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antibiotic_class_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="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 502 combinations had less than minimum = 30 results and were ignored</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 10 × 7</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    `Pathogen (N min-max)`   AMK   GEN   IPM   KAN   MEM   TOB</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> CoNS (43-309)              0     0     0     0     0     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli (0-462)            0     0     0    <span style="color: #BB0000;">NA</span>     0     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. faecalis (0-39)         0     0     0     0    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae (0-58)      <span style="color: #BB0000;">NA</span>     0     0    <span style="color: #BB0000;">NA</span>     0     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa (17-30)     <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis (0-34)       <span style="color: #BB0000;">NA</span>     0     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> S. aureus (2-233)         <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis (8-163)     0     0    <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> S. hominis (3-80)         <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> S. pneumoniae (11-117)     0     0    <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-in"><span>            </span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>            antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>            ab_transform <span class="op">=</span> <span class="st">"atc"</span>,</span></span>
 <span class="r-in"><span>            mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 4 combinations had less than minimum = 30 results and were ignored</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   `Pathogen (N min-max)`   J01GB01 J01GB03 J01GB04 J01GB06</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (35-686)         0       0       0       0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (436-1170)       0       0       0       0</span>
 <span class="r-in"><span>            </span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>            antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>            ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
 <span class="r-in"><span>            mo_transform <span class="op">=</span> <span class="st">"name"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 172 combinations had less than minimum = 30 results and were ignored</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 5 × 3</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   `Pathogen (N min-max)`                           Imipenem Meropenem</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) (48-48)        2         2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis (0-38)                            3        <span style="color: #BB0000;">NA</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Escherichia coli (418-422)                              0         0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae (51-53)                           2         2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis (27-32)                               3        <span style="color: #BB0000;">NA</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Combined antibiogram -------------------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># combined antibiotics yield higher empiric coverage</span></span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>            antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>            mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 3 combinations had less than minimum = 30 results and were ignored</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 4</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   `Pathogen (N min-max)`     TZP `TZP + GEN` `TZP + TOB`</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693)      2           2           2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-1044)     4           1           3</span>
 <span class="r-in"><span>            </span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>            antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</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>            ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
 <span class="r-in"><span>            sep <span class="op">=</span> <span class="st">" &amp; "</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 2 combinations had less than minimum = 30 results and were ignored</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 3</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   `Pathogen (N min-max)`  `Piperacillin/tazobactam` Piperacillin/tazobactam &amp; …¹</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693)                         2                            2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-550)                         4                            3</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with abbreviated variable name ¹`Piperacillin/tazobactam &amp; Tobramycin`</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Syndromic antibiogram ------------------------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># the data set could contain a filter for e.g. respiratory specimens</span></span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>            antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>            syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 897 combinations had less than minimum = 30 results and were ignored</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 14 × 8</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    `Syndromic Group` `Pathogen (N min-max)`   AMK   GEN   IPM   KAN   MEM   TOB</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;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 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical          CoNS (23-205)             <span style="color: #BB0000;">NA</span>     0     0    <span style="color: #BB0000;">NA</span>     0     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU               CoNS (10-73)              <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Outpatient        CoNS (3-31)               <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical          E. coli (0-299)            0     0     0    <span style="color: #BB0000;">NA</span>     0     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU               E. coli (0-137)            0     0     0    <span style="color: #BB0000;">NA</span>     0     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical          K. pneumoniae (0-51)      <span style="color: #BB0000;">NA</span>     0     0    <span style="color: #BB0000;">NA</span>     0     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical          P. mirabilis (0-30)       <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical          S. aureus (2-150)         <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU               S. aureus (0-66)          <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical          S. epidermidis (4-79)     <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">11</span> ICU               S. epidermidis (4-75)     <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">12</span> Clinical          S. hominis (1-45)         <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">13</span> Clinical          S. pneumoniae (5-78)       0     0    <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">14</span> ICU               S. pneumoniae (5-30)       0     0    <span style="color: #BB0000;">NA</span>     0    <span style="color: #BB0000;">NA</span>     0</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>
 <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> ℹ Using column 'mo' as input for mo_genus()</span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">ex1</span>,</span></span>
 <span class="r-in"><span>            antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>            ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
 <span class="r-in"><span>            syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">ex1</span><span class="op">$</span><span class="va">ward</span> <span class="op">==</span> <span class="st">"ICU"</span>,</span></span>
 <span class="r-in"><span>                                     <span class="st">"UCI"</span>, <span class="st">"No UCI"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>            language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 2 combinations had less than minimum = 30 results and were ignored</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   `Grupo sindrómico` `Patógeno (N min-max)` Amikacina Gentamicina Tobramicina</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;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 style="color: #949494; font-style: italic;">&lt;dbl&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> No UCI             E. coli (0-325)              100          37          37</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> UCI                E. coli (0-137)              229          87          87</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Weighted-incidence syndromic combination antibiogram (WISCA) ---------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># the data set could contain a filter for e.g. respiratory specimens</span></span></span>
 <span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>            antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"AMC+CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</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>            minimum <span class="op">=</span> <span class="fl">10</span>, <span class="co"># this should be &gt;= 30, but now just as example</span></span></span>
 <span class="r-in"><span>            syndromic_group <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">age</span> <span class="op">&gt;=</span> <span class="fl">65</span> <span class="op">&amp;</span></span></span>
 <span class="r-in"><span>                                       <span class="va">example_isolates</span><span class="op">$</span><span class="va">gender</span> <span class="op">==</span> <span class="st">"M"</span>,</span></span>
 <span class="r-in"><span>                                     <span class="st">"WISCA Group 1"</span>, <span class="st">"WISCA Group 2"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 8 combinations had less than minimum = 10 results and were ignored</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 6</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   `Syndromic Group` `Pathogen (N min-max)`    AMC `AMC + CIP`   TZP `TZP + TOB`</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;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 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> WISCA Group 1     Gram-negative (261-285)     3           3     3           3</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> WISCA Group 2     Gram-negative (380-442)     2           2     2           2</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> WISCA Group 1     Gram-positive (123-406)     2           2     7           5</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> WISCA Group 2     Gram-positive (222-732)     1           1     4           3</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Generate plots with ggplot2 or base R --------------------------------</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">ab1</span> <span class="op">&lt;-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>                   antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>                   mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 4 combinations had less than minimum = 30 results and were ignored</span>
 <span class="r-in"><span><span class="va">ab2</span> <span class="op">&lt;-</span> <span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>                   antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"AMC"</span>, <span class="st">"CIP"</span>, <span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</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>                   syndromic_group <span class="op">=</span> <span class="st">"ward"</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ 16 combinations had less than minimum = 30 results and were ignored</span>
 <span class="r-in"><span>                   </span></span>
 <span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ab1</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="antibiogram-1.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="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">ggplot2</span><span class="fu">::</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">ab1</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="antibiogram-2.png" alt="" width="700" height="433"></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu"><a href="plot.html">plot</a></span><span class="op">(</span><span class="va">ab2</span><span class="op">)</span></span></span>
 <span class="r-plt img"><img src="antibiogram-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="fu"><a href="https://rdrr.io/r/base/ns-load.html" class="external-link">requireNamespace</a></span><span class="op">(</span><span class="st">"ggplot2"</span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="fu">ggplot2</span><span class="fu">::</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">ab2</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="antibiogram-4.png" alt="" width="700" height="433"></span>
 </code></pre></div>
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  <p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
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--- a/reference/antibiotic_class_selectors.html
+++ b/reference/antibiotic_class_selectors.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -232,7 +237,7 @@
 <dt>col_mo</dt>
-<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
+<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 <dt>version_expertrules</dt>
@@ -596,7 +601,11 @@
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   (tobramycin), 'AMK' (amikacin) and 'KAN' (kanamycin)</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for KAN in group: ward =</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: `across(aminoglycosides(), resistance)`.</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" (minimum = 30).</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward         GEN   TOB   AMK   KAN</span>
@@ -648,110 +657,14 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   (benzylpenicillin), 'LNZ' (linezolid), 'VAN' (vancomycin), 'TEC'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   (teicoplanin), 'ERY' (erythromycin), 'CLI' (clindamycin), 'AZM'</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   (azithromycin) and 'RIF' (rifampicin)</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: ward = "Clinical"</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 52 warnings in `summarise()`.</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: ward = "ICU"</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `across(not_intrinsic_resistant(), resistance)`.</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In group 1: `ward = "Clinical"`.</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: 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> (minimum = 30).</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> Introducing NA: no results available for OXA in group: ward = "Clinical"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: ward = "Clinical"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: ward = "Outpatient"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for AMX in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for AMC in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for AMP in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 24 results available for TZP in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for CZO in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 10 results available for CZO in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 20 results available for FEP in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for CXM in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 22 results available for FOX in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for CTX in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for CAZ in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for CRO in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for GEN in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for TOB in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 15 results available for AMK in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: ward = "Clinical"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: ward = "Outpatient"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 22 results available for TMP in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for SXT in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for NIT in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for FOS in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for FOS in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for CIP in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 15 results available for MFX in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 4 results available for MFX in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 5 results available for TCY in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Clinical" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for TCY in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for TCY in group: ward = "Outpatient"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 13 results available for TGC in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for TGC in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: ward = "Clinical"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: ward = "Outpatient"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 24 results available for IPM in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for MEM in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for MTR in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Clinical" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: ward = "Outpatient"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: ward = "Clinical"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: ward = "Outpatient"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 9 results available for COL in group: ward =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Outpatient" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: ward = "Clinical"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: ward = "ICU"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: ward = "Outpatient"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> (minimum = 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 51 remaining warnings.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 33</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward    OXA   FLC    AMX    AMC    AMP     TZP     CZO     FEP     CXM     FOX</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 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>
@@ -769,15 +682,14 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">ab_selector</span><span class="op">(</span><span class="va">name</span> <span class="op"><a href="like.html">%like%</a></span> <span class="st">"trim"</span><span class="op">)</span>, <span class="va">susceptibility</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> Including isolates from ICU.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For ab_selector(name %like% "trim") using columns 'TMP' (trimethoprim)</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   and 'SXT' (trimethoprim/sulfamethoxazole)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 3</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward         TMP   SXT</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>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical   0.627 0.808</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical   0.633 0.793</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU        0.549 0.778</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU        0.578 0.792</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 0.667 0.821</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient 0.705 0.835</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># this will select columns 'IPM' (imipenem) and 'MEM' (meropenem):</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
--- a/reference/antibiotics.html
+++ b/reference/antibiotics.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/as.ab.html
+++ b/reference/as.ab.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -272,7 +277,7 @@
 <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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># you can quickly rename 'sir' columns using set_ab_names() with dplyr:</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>    <span class="fu"><a href="ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    date       patient   age gender ward     mo           J01CE01 J01CF04 J01CF05</span>
--- a/reference/as.av.html
+++ b/reference/as.av.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/as.disk.html
+++ b/reference/as.disk.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/as.mic-4.png
+++ b/reference/as.mic-4.png
--- a/reference/as.mic-5.png
+++ b/reference/as.mic-5.png
--- a/reference/as.mic.html
+++ b/reference/as.mic.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/as.mo.html
+++ b/reference/as.mo.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/as.sir.html
+++ b/reference/as.sir.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -251,7 +256,7 @@
 <dt>col_mo</dt>
-<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
+<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 <dt>clean</dt>
@@ -312,7 +317,7 @@
 <h3 id="machine-readable-interpretation-guidelines">Machine-Readable Interpretation Guidelines<a class="anchor" aria-label="anchor" href="#machine-readable-interpretation-guidelines"></a></h3>
-<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 18,308 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
+<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/clinical_breakpoints.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 18 308 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
 </div>
 <div class="section">
@@ -519,16 +524,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_input ab_guid…¹ mo_in…² mo_guideline     guide…³</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;ab&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;chr&gt;</span>  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-01-24 <span style="color: #949494;">15:36:22</span>     1 TOB      TOB       Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-02-08 <span style="color: #949494;">15:59:02</span>     1 TOB      TOB       Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-01-24 <span style="color: #949494;">15:36:22</span>     1 GEN      GEN       Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-02-08 <span style="color: #949494;">15:59:02</span>     1 GEN      GEN       Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-01-24 <span style="color: #949494;">15:36:21</span>     1 CIP      CIP       Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-02-08 <span style="color: #949494;">15:59:01</span>     1 CIP      CIP       Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-01-24 <span style="color: #949494;">15:36:21</span>     1 AMP      AMP       Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-02-08 <span style="color: #949494;">15:59:01</span>     1 AMP      AMP       Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-01-24 <span style="color: #949494;">15:36:15</span>     1 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-02-08 <span style="color: #949494;">15:58:56</span>     1 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-01-24 <span style="color: #949494;">15:36:15</span>     2 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-02-08 <span style="color: #949494;">15:58:56</span>     2 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-01-24 <span style="color: #949494;">15:36:15</span>     3 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-02-08 <span style="color: #949494;">15:58:56</span>     3 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-01-24 <span style="color: #949494;">15:36:15</span>     4 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-02-08 <span style="color: #949494;">15:58:56</span>     4 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-01-24 <span style="color: #949494;">15:36:15</span>     5 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-02-08 <span style="color: #949494;">15:58:56</span>     5 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-01-24 <span style="color: #949494;">15:36:15</span>     6 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-02-08 <span style="color: #949494;">15:58:56</span>     6 CIP      CIP       B_ESCH… B_[ORD]_ENTRBCTR EUCAST…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 5 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   input &lt;dbl&gt;, outcome &lt;sir&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   names ¹ab_guideline, ²mo_input, ³guideline</span></span>
@@ -565,7 +570,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">df</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</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</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">where</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 class="va">df</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 class="va">df</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">AMP</span><span class="op">:</span><span class="va">TOB</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</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">AMP</span><span class="op">:</span><span class="va">TOB</span>, <span class="va">as.sir</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/av_from_text.html
+++ b/reference/av_from_text.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/av_property.html
+++ b/reference/av_property.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/availability.html
+++ b/reference/availability.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/bug_drug_combinations.html
+++ b/reference/bug_drug_combinations.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -155,7 +160,7 @@
 <span>  add_ab_group <span class="op">=</span> <span class="cn">TRUE</span>,</span>
 <span>  remove_intrinsic_resistant <span class="op">=</span> <span class="cn">FALSE</span>,</span>
 <span>  decimal.mark <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">"OutDec"</span><span class="op">)</span>,</span>
-<span>  big.mark <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">decimal.mark</span> <span class="op">==</span> <span class="st">","</span>, <span class="st">"."</span>, <span class="st">","</span><span class="op">)</span>,</span>
+<span>  big.mark <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">decimal.mark</span> <span class="op">==</span> <span class="st">","</span>, <span class="st">" "</span>, <span class="st">","</span><span class="op">)</span>,</span>
 <span>  <span class="va">...</span></span>
 <span><span class="op">)</span></span></code></pre></div>
    </div>
@@ -167,7 +172,7 @@
 <dt>col_mo</dt>
-<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
+<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 <dt>FUN</dt>
@@ -227,18 +232,31 @@
    <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="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="co">#' # example_isolates is a data set available in the AMR package.</span></span></span>
 <span class="r-in"><span><span class="co"># run ?example_isolates for more info.</span></span></span>
 <span class="r-in"><span><span class="va">example_isolates</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;, FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   MFX &lt;sir&gt;, VAN &lt;sir&gt;, TEC &lt;sir&gt;, TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   ERY &lt;sir&gt;, CLI &lt;sir&gt;, AZM &lt;sir&gt;, IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, RIF &lt;sir&gt;</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6 × 6</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   mo                ab        S     I     R total</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;int&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 style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> (unknown species) PEN      14     0     1    15</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> (unknown species) OXA       0     0     1     1</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> (unknown species) FLC       0     0     0     0</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX      15     0     1    16</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> (unknown species) AMC      15     0     0    15</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> (unknown species) AMP      15     0     1    16</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    Group     Drug  CoNS  E. co…¹ E. fa…² K. pn…³ P. ae…⁴ P. mi…⁵ S. au…⁶ S. ep…⁷</span>
@@ -262,20 +280,20 @@
 <span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
 <span class="r-in"><span>  FUN <span class="op">=</span> <span class="va">mo_gramstain</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 120 × 6</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    mo            ab        S     I     R total</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&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 style="color: #949494; font-style: italic;">&lt;int&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 class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative PEN       8     0   717   725</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative AMC     463    89   174   726</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative OXA       6     0     0     6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative AMK     251     0     5   256</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative FLC       6     0     0     6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative AMP     226     0   405   631</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX     226     0   405   631</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AMC     463    89   174   726</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AZM       1     2   696   699</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative AMP     226     0   405   631</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative CAZ     607     0    27   634</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative TZP     554    11    76   641</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative CHL       1     0    30    31</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CZO      94     2   110   206</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CIP     610    11    63   684</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative FEP     470     1    14   485</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI      18     1   709   728</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative CXM     539    22   142   703</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative COL     309     0    78   387</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 70 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 110 more rows</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
@@ -289,16 +307,16 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    mo      ab        S     I     R total</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&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 style="color: #949494; font-style: italic;">&lt;int&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 class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E. coli PEN       0     0   467   467</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E. coli AMC     332    74    61   467</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli OXA       0     0     0     0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli AMK     171     0     0   171</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. coli FLC       0     0     0     0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. coli AMP     196     0   196   392</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E. coli AMX     196     0   196   392</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E. coli AMC     332    74    61   467</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E. coli AZM       0     0   467   467</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E. coli AMP     196     0   196   392</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E. coli CAZ     449     0    11   460</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E. coli TZP     388     5    23   416</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E. coli CHL       0     0     0     0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E. coli CZO      79     1     2    82</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E. coli CIP     398     1    57   456</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E. coli FEP     308     0     9   317</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E. coli CLI       0     0   467   467</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E. coli CXM     425    15    25   465</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E. coli COL     240     0     0   240</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 70 more rows</span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
--- a/reference/clinical_breakpoints.html
+++ b/reference/clinical_breakpoints.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -148,7 +153,7 @@
    <div class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 18,308 observations and 11 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 18 308 observations and 11 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
 <li><p><code>method</code><br> Either "DISK" or "MIC"</p></li>
 <li><p><code>site</code><br> Body site, e.g. "Oral" or "Respiratory"</p></li>
 <li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
--- a/reference/count.html
+++ b/reference/count.html
@@ -12,7 +12,7 @@ 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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -44,6 +44,11 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/custom_eucast_rules.html
+++ b/reference/custom_eucast_rules.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/dosage.html
+++ b/reference/dosage.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/eucast_rules.html
+++ b/reference/eucast_rules.html
@@ -12,7 +12,7 @@ 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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -44,6 +44,11 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -183,7 +188,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
 <dt>col_mo</dt>
-<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
+<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 <dt>info</dt>
--- a/reference/example_isolates.html
+++ b/reference/example_isolates.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"><meta name="description" content="A data set containing 2,000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read the tutorial on our website."><title>Data Set with 2,000 Example Isolates — example_isolates • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 2,000 Example Isolates — example_isolates"><meta property="og:description" content="A data set containing 2,000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read the tutorial on our website."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- 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"><meta name="description" content="A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read the tutorial on our website."><title>Data Set with 2 000 Example Isolates — example_isolates • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 2 000 Example Isolates — example_isolates"><meta property="og:description" content="A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read the tutorial on our website."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -132,13 +137,13 @@
 </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 Set with 2,000 Example Isolates</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Data Set with 2 000 Example Isolates</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
      <div class="d-none name"><code>example_isolates.Rd</code></div>
    </div>
    <div class="ref-description section level2">
-    <p>A data set containing 2,000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read <a href="https://msberends.github.io/AMR/articles/AMR.html">the tutorial on our website</a>.</p>
+    <p>A data set containing 2 000 microbial isolates with their full antibiograms. This data set contains randomised fictitious data, but reflects reality and can be used to practise AMR data analysis. For examples, please read <a href="https://msberends.github.io/AMR/articles/AMR.html">the tutorial on our website</a>.</p>
    </div>
    <div class="section level2">
@@ -148,7 +153,7 @@
    <div class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 2,000 observations and 46 variables:</p><ul><li><p><code>date</code><br> Date of receipt at the laboratory</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 2 000 observations and 46 variables:</p><ul><li><p><code>date</code><br> Date of receipt at the laboratory</p></li>
 <li><p><code>patient</code><br> ID of the patient</p></li>
 <li><p><code>age</code><br> Age of the patient</p></li>
 <li><p><code>gender</code><br> Gender of the patient, either "F" or "M"</p></li>
--- a/reference/example_isolates_unclean.html
+++ b/reference/example_isolates_unclean.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
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+<!-- 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"><meta name="description" content="A data set containing 3 000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice."><title>Data Set with Unclean Data — example_isolates_unclean • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with Unclean Data — example_isolates_unclean"><meta property="og:description" content="A data set containing 3 000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -138,7 +143,7 @@
    </div>
    <div class="ref-description section level2">
-    <p>A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.</p>
+    <p>A data set containing 3 000 microbial isolates that are not cleaned up and consequently not ready for AMR data analysis. This data set can be used for practice.</p>
    </div>
    <div class="section level2">
@@ -148,7 +153,7 @@
    <div class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 3,000 observations and 8 variables:</p><ul><li><p><code>patient_id</code><br> ID of the patient</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 3 000 observations and 8 variables:</p><ul><li><p><code>patient_id</code><br> ID of the patient</p></li>
 <li><p><code>date</code><br> date of receipt at the laboratory</p></li>
 <li><p><code>hospital</code><br> ID of the hospital, from A to C</p></li>
 <li><p><code>bacteria</code><br> info about microorganism that can be transformed with <code><a href="as.mo.html">as.mo()</a></code>, see also <a href="microorganisms.html">microorganisms</a></p></li>
--- a/reference/first_isolate.html
+++ b/reference/first_isolate.html
@@ -12,7 +12,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -44,6 +44,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -200,7 +205,7 @@
 <dt>col_mo</dt>
-<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
+<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 <dt>col_testcode</dt>
@@ -284,7 +289,7 @@
 <p>According to Hindler <em>et al.</em> (2007, <a href="https://doi.org/10.1086/511864" class="external-link">doi:10.1086/511864</a>
 ), there are different methods (algorithms) to select first isolates with increasing reliability: isolate-based, patient-based, episode-based and phenotype-based. All methods select on a combination of the taxonomic genus and species (not subspecies).</p>
-<p>All mentioned methods are covered in the <code>first_isolate()</code> function:</p><table class="table table"><tr><td><strong>Method</strong></td><td><strong>Function to apply</strong></td></tr><tr><td><strong>Isolate-based</strong></td><td><code>first_isolate(x, method = "isolate-based")</code></td></tr><tr><td><em>(= all isolates)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Patient-based</strong></td><td><code>first_isolate(x, method = "patient-based")</code></td></tr><tr><td><em>(= first isolate per patient)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Episode-based</strong></td><td><code>first_isolate(x, method = "episode-based")</code>, or:</td></tr><tr><td><em>(= first isolate per episode)</em></td><td></td></tr><tr><td>- 7-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 7)</code></td></tr><tr><td>- 30-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 30)</code></td></tr><tr><td></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Phenotype-based</strong></td><td><code>first_isolate(x, method = "phenotype-based")</code>, or:</td></tr><tr><td><em>(= first isolate per phenotype)</em></td><td></td></tr><tr><td>- Major difference in any antimicrobial result</td><td>- <code>first_isolate(x, type = "points")</code></td></tr><tr><td>- Any difference in key antimicrobial results</td><td>- <code>first_isolate(x, type = "keyantimicrobials")</code></td></tr></table></div>
+<p>All mentioned methods are covered in the <code>first_isolate()</code> function:</p><table class="table table"><tr><td><strong>Method</strong></td><td><strong>Function to apply</strong></td></tr><tr><td><strong>Isolate-based</strong></td><td><code>first_isolate(x, method = "isolate-based")</code></td></tr><tr><td><em>(= all isolates)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Patient-based</strong></td><td><code>first_isolate(x, method = "patient-based")</code></td></tr><tr><td><em>(= first isolate per patient)</em></td><td></td></tr><tr><td></td><td></td></tr><tr><td><strong>Episode-based</strong></td><td><code>first_isolate(x, method = "episode-based")</code>, or:</td></tr><tr><td><em>(= first isolate per episode)</em></td><td></td></tr><tr><td>- 7-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 7)</code></td></tr><tr><td>- 30-Day interval from initial isolate</td><td>- <code>first_isolate(x, method = "e", episode_days = 30)</code></td></tr><tr><td></td><td></td></tr><tr><td><strong>Phenotype-based</strong></td><td><code>first_isolate(x, method = "phenotype-based")</code>, or:</td></tr><tr><td><em>(= first isolate per phenotype)</em></td><td></td></tr><tr><td>- Major difference in any antimicrobial result</td><td>- <code>first_isolate(x, type = "points")</code></td></tr><tr><td>- Any difference in key antimicrobial results</td><td>- <code>first_isolate(x, type = "keyantimicrobials")</code></td></tr></table></div>
 <div class="section">
 <h3 id="isolate-based">Isolate-based<a class="anchor" aria-label="anchor" href="#isolate-based"></a></h3>
@@ -332,22 +337,30 @@
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># `example_isolates` is a data set available in the AMR package.</span></span></span>
 <span class="r-in"><span><span class="co"># See ?example_isolates.</span></span></span>
 <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><span class="op">)</span>, <span class="op">]</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> Determining first isolates using an episode length of 365 days</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'date' as input for col_date.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'patient' as input for col_patient_id.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Basing inclusion on all antimicrobial results, using a points threshold of</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 2</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 1,984 'phenotype-based' first isolates (99.2% of total where a</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    microbial ID was available)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,984 × 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,369 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,974 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;, FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;,</span></span>
@@ -357,22 +370,21 @@
 <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> Including isolates from ICU.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_is_gram_negative()</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 437 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 731 × 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-02-27 066895     85 F      Clinical B_KLBSL_PNMN R     NA    NA    R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-03-08 4FC193     69 M      Clinical B_ESCHR_COLI R     NA    NA    R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-03-16 4FC193     69 M      Clinical B_PSDMN_AERG R     NA    NA    R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-04-01 496896     46 F      ICU      B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-04-23 EE2510     69 F      ICU      B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-05 067927     45 F      ICU      B_SERRT_MRCS R     NA    NA    R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 427 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 721 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CZO &lt;sir&gt;, FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;, CAZ &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CRO &lt;sir&gt;, GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;, TMP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   SXT &lt;sir&gt;, NIT &lt;sir&gt;, FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;, MFX &lt;sir&gt;,</span></span>
@@ -383,23 +395,29 @@
 <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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># filter on first isolates using dplyr:</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">first_isolate</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://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></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-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Determining first isolates using an episode length of 365 days</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Basing inclusion on all antimicrobial results, using a points threshold of</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> 2</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,379 × 46</span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Excluded 16 isolates with a microbial ID 'UNKNOWN' (in column 'mo')</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> =&gt; Found 1,984 'phenotype-based' first isolates (99.2% of total where a</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>    microbial ID was available)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,984 × 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,369 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,974 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;, FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;,</span></span>
@@ -411,21 +429,20 @@
 <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">filter_first_isolate</span><span class="op">(</span>info <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> Including isolates from ICU.</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,984 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1,379 × 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>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334     65 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-17 495616     67 M      Clinical B_STPHY_EPDR R     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-19 738003     71 M      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-21 462081     75 F      Clinical B_CTRBC_FRND R     NA    NA    R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-22 F35553     50 M      ICU      B_PROTS_MRBL R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729     78 M      Clinical B_STPHY_AURS R     NA    S     R    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-02-03 481442     76 M      ICU      B_STPHY_CONS R     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927     45 F      ICU      B_STPHY_EPDR R     NA    R     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-02-05 023456     50 M      Clinical B_STPHY_HMNS S     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515     79 F      ICU      B_STPHY_EPDR R     NA    S     NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,369 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,974 more rows, and 36 more variables: AMC &lt;sir&gt;, AMP &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TZP &lt;sir&gt;, CZO &lt;sir&gt;, FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;, KAN &lt;sir&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;, FOS &lt;sir&gt;, LNZ &lt;sir&gt;, CIP &lt;sir&gt;,</span></span>
@@ -436,25 +453,22 @@
 <span class="r-in"><span>  <span class="co"># flag the first isolates per group:</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu">first_isolate</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <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">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">ward</span>, <span class="va">date</span>, <span class="va">patient</span>, <span class="va">mo</span>, <span class="va">first</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> Including isolates from ICU.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</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> <span style="color: #949494;"># Groups:   ward [3]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    ward     date       patient mo           first</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;date&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;lgl&gt;</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2002-01-02 A77334  B_ESCHR_COLI TRUE </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2002-01-03 A77334  B_ESCHR_COLI FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2002-01-03 A77334  B_ESCHR_COLI TRUE </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU      2002-01-07 067927  B_STPHY_EPDR TRUE </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU      2002-01-07 067927  B_STPHY_EPDR FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU      2002-01-07 067927  B_STPHY_EPDR TRUE </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU      2002-01-13 067927  B_STPHY_EPDR FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU      2002-01-13 067927  B_STPHY_EPDR TRUE </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2002-01-13 067927  B_STPHY_EPDR FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2002-01-13 067927  B_STPHY_EPDR TRUE </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2002-01-14 462729  B_STPHY_AURS TRUE </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2002-01-14 462729  B_STPHY_AURS FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2002-01-14 462729  B_STPHY_AURS TRUE </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU      2002-01-16 067927  B_STPHY_EPDR FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU      2002-01-16 067927  B_STPHY_EPDR TRUE </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU      2002-01-17 858515  B_STPHY_EPDR TRUE </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 1,990 more rows</span></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
--- a/reference/g.test.html
+++ b/reference/g.test.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/get_episode.html
+++ b/reference/get_episode.html
--- a/reference/ggplot_pca.html
+++ b/reference/ggplot_pca.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -318,152 +323,15 @@
 <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">"Title here"</span><span class="op">)</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-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 14 results available for PEN in group: order =</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 73 warnings in `summarise()`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `PEN = (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 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" (minimum = 30).</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: order =</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-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 13 results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 15 results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 13 results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 26 results available for AMX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 26 results available for AMP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for TZP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 12 results available for CZO in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 5 results available for CZO in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for FEP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for FEP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 29 results available for FOX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 26 results available for AMK in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 6 results available for AMK in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 17 results available for AMK in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 6 results available for NIT in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 17 results available for NIT in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 8 results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 7 results available for LNZ in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 5 results available for CIP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for CIP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 7 results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 6 results available for TEC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 3 results available for TCY in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for TCY in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 18 results available for TGC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 7 results available for TGC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for DOX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for IPM in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for MEM in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 26 results available for MEM in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Caryophanales", genus = "Staphylococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 9 results available for COL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for RIF in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for RIF in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   and "TOB". Total observations available: 7.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Groups (n=4, named as 'order'):</span>
--- a/reference/ggplot_sir-8.png
+++ b/reference/ggplot_sir-8.png
--- a/reference/ggplot_sir.html
+++ b/reference/ggplot_sir.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -391,9 +396,8 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">age_group</span>, <span class="va">CIP</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">ggplot_sir</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"age_group"</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> Including isolates from ICU.</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 4 rows containing missing values (`position_stack()`).</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values (`position_stack()`).</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 4 rows containing missing values (`position_stack()`).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values (`position_stack()`).</span>
 <span class="r-plt img"><img src="ggplot_sir-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">&amp;&amp;</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># a shorter version which also adjusts data label colours:</span></span></span>
--- a/reference/guess_ab_col.html
+++ b/reference/guess_ab_col.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -241,7 +246,7 @@
      </dl></div><div class="section level2">
      <h2 id="analysing-data-antimicrobial-resistance">Analysing data: antimicrobial resistance<a class="anchor" aria-label="anchor" href="#analysing-data-antimicrobial-resistance"></a></h2>
-      <p class="section-desc"></p><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
+      <p class="section-desc"></p><p>Use these function for the analysis part. You can use <code><a href="../reference/proportion.html">susceptibility()</a></code> or <code><a href="../reference/proportion.html">resistance()</a></code> on any antibiotic column. With <code><a href="../reference/antibiogram.html">antibiogram()</a></code>, you can generate a traditional, combined, syndromic, or weighted-incidence syndromic combination antibiogram(WISCA). This function also comes with support for R Markdown and Quarto. Be sure to first select the isolates that are appropiate for analysis, by using <code><a href="../reference/first_isolate.html">first_isolate()</a></code> or <code><a href="../reference/get_episode.html">is_new_episode()</a></code>. You can also filter your data on certain resistance in certain antibiotic classes (<code><a href="../reference/antibiotic_class_selectors.html">carbapenems()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">aminoglycosides()</a></code>), or determine multi-drug resistant microorganisms (MDRO, <code><a href="../reference/mdro.html">mdro()</a></code>).</p>
    </div><div id="" class="section level2">
@@ -251,9 +256,14 @@
      <dl><dt>
          <code><a href="antibiogram.html">antibiogram()</a></code> <code><a href="antibiogram.html">plot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">autoplot(<i>&lt;antibiogram&gt;</i>)</a></code> <code><a href="antibiogram.html">print(<i>&lt;antibiogram&gt;</i>)</a></code> 
        </dt>
        <dd>Generate Antibiogram: Traditional, Combined, Syndromic, or Weighted-Incidence Syndromic Combination (WISCA)</dd>
      </dl><dl><dt>
          <code><a href="proportion.html">resistance()</a></code> <code><a href="proportion.html">susceptibility()</a></code> <code><a href="proportion.html">sir_confidence_interval()</a></code> <code><a href="proportion.html">proportion_R()</a></code> <code><a href="proportion.html">proportion_IR()</a></code> <code><a href="proportion.html">proportion_I()</a></code> <code><a href="proportion.html">proportion_SI()</a></code> <code><a href="proportion.html">proportion_S()</a></code> <code><a href="proportion.html">proportion_df()</a></code> <code><a href="proportion.html">sir_df()</a></code> 
        </dt>
-        <dd>Calculate Microbial Resistance</dd>
+        <dd>Calculate Antimicrobial Resistance</dd>
      </dl><dl><dt>
          <code><a href="count.html">count_resistant()</a></code> <code><a href="count.html">count_susceptible()</a></code> <code><a href="count.html">count_R()</a></code> <code><a href="count.html">count_IR()</a></code> <code><a href="count.html">count_I()</a></code> <code><a href="count.html">count_SI()</a></code> <code><a href="count.html">count_S()</a></code> <code><a href="count.html">count_all()</a></code> <code><a href="count.html">n_sir()</a></code> <code><a href="count.html">count_df()</a></code> 
@@ -376,17 +386,17 @@
          <code><a href="example_isolates.html">example_isolates</a></code> 
        </dt>
-        <dd>Data Set with 2,000 Example Isolates</dd>
+        <dd>Data Set with 2 000 Example Isolates</dd>
      </dl><dl><dt>
          <code><a href="microorganisms.html">microorganisms</a></code> 
        </dt>
-        <dd>Data Set with 52,141 Microorganisms</dd>
+        <dd>Data Set with 52 142 Microorganisms</dd>
      </dl><dl><dt>
          <code><a href="microorganisms.codes.html">microorganisms.codes</a></code> 
        </dt>
-        <dd>Data Set with 5,910 Common Microorganism Codes</dd>
+        <dd>Data Set with 5 910 Common Microorganism Codes</dd>
      </dl><dl><dt>
          <code><a href="antibiotics.html">antibiotics</a></code> <code><a href="antibiotics.html">antivirals</a></code> 
--- a/reference/intrinsic_resistant.html
+++ b/reference/intrinsic_resistant.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -148,7 +153,7 @@
    <div class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 134,634 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 134 634 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID</p></li>
 <li><p><code>ab</code><br> Antibiotic ID</p></li>
 </ul></div>
    <div class="section level2">
--- a/reference/italicise_taxonomy.html
+++ b/reference/italicise_taxonomy.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/join.html
+++ b/reference/join.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/key_antimicrobials.html
+++ b/reference/key_antimicrobials.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -177,7 +182,7 @@
 <dt>col_mo</dt>
-<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
+<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 <dt>universal</dt>
@@ -289,9 +294,7 @@
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <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> Including isolates from ICU.</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1984</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1395</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
    </div>
--- a/reference/kurtosis.html
+++ b/reference/kurtosis.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -177,9 +182,9 @@
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.880473</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.938161</span>
 <span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span>, excess <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.007374585</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0159802</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/like.html
+++ b/reference/like.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/mdro.html
+++ b/reference/mdro.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -183,7 +188,7 @@
 <dt>col_mo</dt>
-<dd><p>column name of the IDs of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
+<dd><p>column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
 <dt>info</dt>
@@ -347,7 +352,10 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in mdro(): 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 pct_required_classes)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  (16 isolates had no test results)</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in mdro(): NA introduced for isolates where the available percentage of</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: `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 mdro(): 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 pct_required_classes)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> .</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>                         Negative       Multi-drug-resistant (MDR) </span>
--- a/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -196,31 +201,31 @@
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sir</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_sir</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">sir</span></span></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 I R I S R R I R S</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] R S R R S R I S I R</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">sir</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.7745967 -0.7745967  1.1618950 -0.7745967 -0.7745967  1.1618950</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.9486833 -0.9486833  0.9486833  0.9486833 -0.9486833  0.9486833</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  1.1618950 -0.7745967  1.1618950 -0.7745967</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.9486833 -0.9486833 -0.9486833  0.9486833</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">mic</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.5     0.005   4       0.005   4       16      8       &gt;=128   &lt;=0.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] &lt;=0.001 8       2       &lt;=0.001 16      &lt;=0.001 0.25    128     0.125  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.125  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &lt;=0.001</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.004555148 -1.189296722  0.543632982 -1.189296722  0.543632982</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.052079574  0.902371938  0.600893605 -1.052079574  1.053111104</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6]  0.903018205  0.723325594  1.442096040 -1.426837433 -0.354830075</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6] -1.052079574  0.148676107  1.505328602 -0.002063059 -1.052079574</span>
 <span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
 <span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.004555148 -1.189296722  0.543632982 -1.189296722  0.543632982</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.052079574  0.902371938  0.600893605 -1.052079574  1.053111104</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6]  0.903018205  0.723325594  1.442096040 -1.426837433 -0.354830075</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6] -1.052079574  0.148676107  1.505328602 -0.002063059 -1.052079574</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">disk</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  8 32 43 15 44 37 16 14 29 29</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 38  7 36 29 48 15 25 50 50 39</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.4621577  0.4144083  1.2745011 -0.9148259  1.3526913  0.8053596</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.2922699 -1.8147922  0.1563304 -0.3194578  0.9719673 -1.2710342</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.8366357 -0.9930162  0.1798376  0.1798376</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.5913368  1.1079068  1.1079068  0.3602396</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</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>
 <span class="r-in"><span>  id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@@ -231,35 +236,25 @@
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">y</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr  gent   tobr</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    I   25   16 0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    S   26 &lt;=0.5    0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    I   30   16 0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    I   20  &gt;=16      2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    I   28  0.5    8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    R   22     1    0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    I   26   16 0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    S   25  &gt;=16    &gt;=8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   26    8  0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    I   18  &gt;=16    0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    R   21   16 0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    S   18 &lt;=0.5 &lt;=0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    S   19    2    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    S   19     2 &lt;=0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    I   27    8    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    S   21     8    0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   19    8    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   25     1 &lt;=0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   28    8    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    S   25 &lt;=0.5 &lt;=0.25</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.19598774  0.12451337 -0.09209741 -0.13188752 -0.14956959  0.06516053</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.08308833  0.31310698  0.30459906  1.01959980 -0.15475222 -0.87382971</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.63363528  0.05123363  0.05598101  0.90628900</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.56840820 -0.02905708  0.38884763 -0.31701792</span>
-<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</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="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in .subset(x, j):</span> invalid subscript type 'list'</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr gent tobr amr_distance</span>
+<span class="r-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in order(y$amr_distance):</span> argument 1 is not a vector</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    I   28  0.5    8  -0.27108669</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    S   19    2    2  -0.20035843</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   26    8  0.5  -0.12963016</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    I   25   16 0.25  -0.09426603</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    I   30   16 0.25  -0.09426603</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    I   26   16 0.25  -0.09426603</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    R   21   16 0.25  -0.09426603</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    I   27    8    1   0.14377582</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   19    8    1   0.14377582</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   28    8    4   0.69058778</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://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -272,16 +267,16 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr  gent   tobr amr_distance  check_id_C</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    I   28  0.5    8  -0.09209741 0.00000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    R   22     1    0.5   0.30459906 0.000000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   D    I   26   16 0.25  -0.13188752 0.03979011</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    I   20  &gt;=16      2   0.31310698 0.008507921</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   E    S   26    8  0.5  -0.14956959 0.05747218</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   I    R   25     1 &lt;=0.25   0.38884763 0.084248568</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   A    I   25   16 0.25  -0.19598774 0.10389034</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   H    S   21     8    0.5  -0.02905708 0.333656139</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   H    I   27    8    1   0.05123363 0.14333103</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   A    S   26 &lt;=0.5    0.5  -0.08308833 0.387687383</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   I    R   19    8    1   0.05598101 0.14807842</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   E    I   18  &gt;=16    0.5  -0.15475222 0.459351276</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   F    R   21   16 0.25   0.06516053 0.15725794</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   J    S   25 &lt;=0.5 &lt;=0.25  -0.31701792 0.621616981</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   B    I   30   16 0.25   0.12451337 0.21661078</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   D    S   25  &gt;=16    &gt;=8   1.01959980 0.715000742</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   G    S   19    2    2  -0.63363528 0.54153787</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   G    S   19     2 &lt;=0.25  -0.56840820 0.873007255</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   28    8    4   0.90628900 0.99838641</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  F    S   18 &lt;=0.5 &lt;=0.25  -0.87382971 1.178428772</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://dplyr.tidyverse.org" class="external-link">"dplyr"</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 groups</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.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"><meta name="description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><title>Data Set with 5,910 Common Microorganism Codes — microorganisms.codes • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 5,910 Common Microorganism Codes — microorganisms.codes"><meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- 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"><meta name="description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><title>Data Set with 5 910 Common Microorganism Codes — microorganisms.codes • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 5 910 Common Microorganism Codes — microorganisms.codes"><meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -132,7 +137,7 @@
 </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 Set with 5,910 Common Microorganism Codes</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Data Set with 5 910 Common Microorganism Codes</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
      <div class="d-none name"><code>microorganisms.codes.Rd</code></div>
    </div>
@@ -148,7 +153,7 @@
    <div class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 5,910 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 5 910 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism</p></li>
 <li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
 </ul></div>
    <div class="section level2">
--- a/reference/microorganisms.html
+++ b/reference/microorganisms.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
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+<!-- 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"><meta name="description" content="A data set containing the full microbial taxonomy (last updated: 11 December, 2022) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this AMR package. MO codes can be looked up using as.mo()."><title>Data Set with 52 142 Microorganisms — microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 52 142 Microorganisms — microorganisms"><meta property="og:description" content="A data set containing the full microbial taxonomy (last updated: 11 December, 2022) of five kingdoms from the List of Prokaryotic names with Standing in Nomenclature (LPSN) and the Global Biodiversity Information Facility (GBIF). This data set is the backbone of this AMR package. MO codes can be looked up using as.mo()."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -132,7 +137,7 @@
 </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 Set with 52,141 Microorganisms</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Data Set with 52 142 Microorganisms</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/data.R" class="external-link"><code>R/data.R</code></a></small>
      <div class="d-none name"><code>microorganisms.Rd</code></div>
    </div>
@@ -148,7 +153,7 @@
    <div class="section level2">
    <h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
-    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 52,141 observations and 22 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 52 142 observations and 22 variables:</p><ul><li><p><code>mo</code><br> ID of microorganism as used by this package</p></li>
 <li><p><code>fullname</code><br> Full name, like <code>"Escherichia coli"</code>. For the taxonomic ranks genus, species and subspecies, this is the 'pasted' text of genus, species, and subspecies. For all taxonomic ranks higher than genus, this is the name of the taxon.</p></li>
 <li><p><code>status</code> <br> Status of the taxon, either "accepted" or "synonym"</p></li>
 <li><p><code>kingdom</code>, <code>phylum</code>, <code>class</code>, <code>order</code>, <code>family</code>, <code>genus</code>, <code>species</code>, <code>subspecies</code><br> Taxonomic rank of the microorganism</p></li>
@@ -231,20 +236,20 @@
    <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">microorganisms</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 52,141 × 22</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 52,142 × 22</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    mo               fullname      status kingdom phylum class order family genus</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>             <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;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> B_ANAER          (unknown ana… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_GRAMN          (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> F_FUNGUS         (unknown fun… accep… Fungi   (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_GRAMP          (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_GRAMN          (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_ANAER          (unknown ana… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_GRAMP          (unknown Gra… accep… Bacter… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F_FUNGUS         (unknown fun… accep… Fungi   (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span>   UNKNOWN        (unknown nam… accep… (unkno… (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F_YEAST          (unknown yea… accep… Fungi   (unkn… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(un… <span style="color: #949494;">"</span>(unk… <span style="color: #949494;">"</span>(un…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_[FAM]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abdi… <span style="color: #949494;">""</span>   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_[ORD]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span>     <span style="color: #949494;">""</span>   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_[CLS]_ADTBCTRA Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">"</span>Abd… <span style="color: #949494;">""</span>    <span style="color: #949494;">""</span>     <span style="color: #949494;">""</span>   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_[PHL]_ABDTBCTR Abditibacter… accep… Bacter… Abdit… <span style="color: #949494;">""</span>    <span style="color: #949494;">""</span>    <span style="color: #949494;">""</span>     <span style="color: #949494;">""</span>   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 52,131 more rows, and 13 more variables: species &lt;chr&gt;,</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 52,132 more rows, and 13 more variables: species &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   subspecies &lt;chr&gt;, rank &lt;chr&gt;, ref &lt;chr&gt;, source &lt;chr&gt;, lpsn &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   lpsn_parent &lt;chr&gt;, lpsn_renamed_to &lt;chr&gt;, gbif &lt;chr&gt;, gbif_parent &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   gbif_renamed_to &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;</span></span>
--- a/reference/mo_matching_score.html
+++ b/reference/mo_matching_score.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/mo_property.html
+++ b/reference/mo_property.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -400,7 +405,7 @@
 <dt>property</dt>
-<dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" or "snomed", or must be <code>"shortname"</code></p></dd>
+<dd><p>one of the column names of the <a href="microorganisms.html">microorganisms</a> data set: "mo", "fullname", "status", "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "source", "lpsn", "lpsn_parent", "lpsn_renamed_to", "gbif", "gbif_parent", "gbif_renamed_to", "prevalence" or "snomed"</p></dd>
 </dl></div>
    <div class="section level2">
@@ -506,8 +511,10 @@
 <span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
 <span class="r-in"><span><span class="fu">mo_snomed</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1098101000112102" "1098201000112108" "409801009"        "446870005"       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [[1]]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "56415008"         "713926009"        "714315002"       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1098101000112102" "446870005"        "1098201000112108" "409801009"       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [5] "56415008"         "714315002"        "713926009"       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Bacteria"</span>
 <span class="r-in"><span><span class="fu">mo_rank</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
@@ -748,8 +755,8 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Trevisan, 1887"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> $snomed</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1098101000112102" "1098201000112108" "409801009"        "446870005"       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "1098101000112102" "446870005"        "1098201000112108" "409801009"       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "56415008"         "713926009"        "714315002"       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [5] "56415008"         "714315002"        "713926009"       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
--- a/reference/mo_source.html
+++ b/reference/mo_source.html
@@ -12,7 +12,7 @@ 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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -44,6 +44,11 @@ This is the fastest way to have your organisation (or analysis) specific codes p
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
--- a/reference/pca.html
+++ b/reference/pca.html
@@ -10,7 +10,7 @@
    <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="">1.8.2.9103</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9111</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,6 +42,11 @@
      Conduct AMR Analysis
    </a>
    <a class="dropdown-item" href="../reference/antibiogram.html">
      <span class="fa fa-file-prescription"></span>
      Generate Antibiogram (Trad./Syndromic/WISCA)
    </a>
    <a class="dropdown-item" href="../articles/resistance_predict.html">
      <span class="fa fa-dice"></span>
@@ -251,152 +256,15 @@
 <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">"Title here"</span><span class="op">)</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-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 14 results available for PEN in group: order =</span>
+<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 73 warnings in `summarise()`.</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `PEN = (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 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" (minimum = 30).</span>
-<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: order =</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-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 13 results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 15 results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for OXA in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 13 results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FLC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 26 results available for AMX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 26 results available for AMP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for TZP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 12 results available for CZO in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 5 results available for CZO in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for FEP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for FEP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 29 results available for FOX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 26 results available for AMK in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 6 results available for AMK in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 17 results available for AMK in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for KAN in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 6 results available for NIT in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 17 results available for NIT in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 8 results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for FOS in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 7 results available for LNZ in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 5 results available for CIP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 23 results available for CIP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 7 results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MFX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 6 results available for TEC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 3 results available for TCY in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for TCY in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 18 results available for TGC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 7 results available for TGC in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for DOX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for DOX in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 27 results available for IPM in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 25 results available for MEM in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 26 results available for MEM in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Caryophanales", genus = "Staphylococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 2 results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MTR in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for CHL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: only 9 results available for COL in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Escherichia" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Klebsiella" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Enterobacterales", genus = "Proteus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for MUP in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Pseudomonadales", genus = "Pseudomonas" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for RIF in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Enterococcus" (minimum = 30).</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Introducing NA: no results available for RIF in group: order =</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> "Lactobacillales", genus = "Streptococcus" (minimum = 30).</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Columns selected for PCA: "AMC", "CAZ", "CTX", "CXM", "GEN", "SXT", "TMP"</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   and "TOB". Total observations available: 7.</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Groups (n=4, named as 'order'):</span>
--- a/reference/plot-1.png
+++ b/reference/plot-1.png
--- a/reference/plot-2.png
+++ b/reference/plot-2.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/Show More
+++ b/Show More