Built site for AMR: 1.8.2.9078@a98d0d7

2024-12-26 08:46:11 +01:00 · 2023-01-05 13:53:59 +00:00 · 2023-01-05 13:53:59 +00:00 · d3e437e13a
commit d3e437e13a
parent ec8f871100
110 changed files with 687 additions and 535 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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/AMR.html
+++ b/articles/AMR.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
                        <h4 data-toc-skip class="author">Dr. Matthijs
 Berends</h4>
-            <h4 data-toc-skip class="date">30 December 2022</h4>
+            <h4 data-toc-skip class="date">05 January 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>
@ -180,7 +180,7 @@ 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 30 December 2022.</p>
+generated on 05 January 2023.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2022-12-30</td>
+<td align="center">2023-01-05</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">2022-12-30</td>
+<td align="center">2023-01-05</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">2022-12-30</td>
+<td align="center">2023-01-05</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -400,42 +400,31 @@ data set:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2014-10-07</td>
+<td align="center">2017-08-08</td>
-<td align="center">H2</td>
+<td align="center">G10</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Staphylococcus aureus</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2012-01-23</td>
+<td align="center">2013-01-20</td>
-<td align="center">S1</td>
+<td align="center">Y2</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Staphylococcus aureus</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2011-06-02</td>
+<td align="center">2010-03-18</td>
-<td align="center">B5</td>
+<td align="center">T1</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital B</td>
 <td align="center">Streptococcus pneumoniae</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2013-09-18</td>
 <td align="center">S10</td>
 <td align="center">Hospital D</td>
 <td align="center">Klebsiella pneumoniae</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -443,28 +432,39 @@ data set:</p>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
 <td align="center">2016-07-30</td>
 <td align="center">K5</td>
 <td align="center">Hospital A</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2015-07-25</td>
+<td align="center">2015-01-19</td>
-<td align="center">U6</td>
+<td align="center">A2</td>
 <td align="center">Hospital B</td>
 <td align="center">Streptococcus pneumoniae</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="odd">
 <td align="center">2017-11-10</td>
 <td align="center">S3</td>
 <td align="center">Hospital C</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 </tr>
 <tr class="even">
 <td align="center">2015-08-08</td>
 <td align="center">N3</td>
 <td align="center">Hospital A</td>
 <td align="center">Klebsiella pneumoniae</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 </tbody>
 </table>
 <p>Now, let’s start the cleaning and the analysis!</p>
@ -499,16 +499,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,393</td>
+<td align="right">10,351</td>
-<td align="right">51.97%</td>
+<td align="right">51.76%</td>
-<td align="right">10,393</td>
+<td align="right">10,351</td>
-<td align="right">51.97%</td>
+<td align="right">51.76%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,607</td>
+<td align="right">9,649</td>
-<td align="right">48.04%</td>
+<td align="right">48.25%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@ -621,9 +621,9 @@ 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 10,583 'phenotype-based' first isolates (52.9% of total where a</span></span>
+<span><span class="co"># =&gt; Found 10,772 'phenotype-based' first isolates (53.9% of total where a</span></span>
 <span><span class="co">#    microbial ID was available)</span></span></code></pre></div>
-<p>So only 52.9% is suitable for resistance analysis! We can now filter
+<p>So only 53.9% 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">
@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
 <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="co"># Including isolates from ICU.</span></span></code></pre></div>
-<p>So we end up with 10,583 isolates for analysis. Now our data looks
+<p>So we end up with 10,772 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>
@ -674,28 +674,60 @@ like:</p>
 <tbody>
 <tr class="odd">
 <td align="left">1</td>
-<td align="center">2014-10-07</td>
+<td align="center">2017-08-08</td>
-<td align="center">H2</td>
+<td align="center">G10</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</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">R</td>
 <td align="center">R</td>
 <td align="center">M</td>
-<td align="center">Gram-negative</td>
+<td align="center">Gram-positive</td>
-<td align="center">Escherichia</td>
+<td align="center">Staphylococcus</td>
-<td align="center">coli</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="center">2013-01-20</td>
 <td align="center">Y2</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">S</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-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
-<td align="center">2011-06-02</td>
+<td align="center">2010-03-18</td>
-<td align="center">B5</td>
+<td align="center">T1</td>
-<td align="center">Hospital C</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">S</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="even">
 <td align="left">4</td>
 <td align="center">2015-01-19</td>
 <td align="center">A2</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">I</td>
+<td align="center">S</td>
-<td align="center">I</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
@ -706,25 +738,25 @@ like:</p>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
-<td align="center">2016-07-30</td>
+<td align="center">2017-11-10</td>
-<td align="center">K5</td>
+<td align="center">S3</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital C</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">F</td>
 <td align="center">S</td>
 <td align="center">S</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="left">6</td>
+<td align="left">7</td>
-<td align="center">2015-07-25</td>
+<td align="center">2017-03-22</td>
-<td align="center">U6</td>
+<td align="center">P2</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -736,38 +768,6 @@ like:</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">7</td>
 <td align="center">2012-02-07</td>
 <td align="center">E10</td>
 <td align="center">Hospital B</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">S</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="left">8</td>
 <td align="center">2016-06-14</td>
 <td align="center">Y3</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">S</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-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>
@ -801,8 +801,8 @@ 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: 10,583<br>
+Length: 10,772<br>
-Available: 10,583 (100%, NA: 0 = 0%)<br>
+Available: 10,772 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,619</td>
+<td align="right">4,699</td>
-<td align="right">43.65%</td>
+<td align="right">43.62%</td>
-<td align="right">4,619</td>
+<td align="right">4,699</td>
-<td align="right">43.65%</td>
+<td align="right">43.62%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,672</td>
+<td align="right">2,732</td>
-<td align="right">25.25%</td>
+<td align="right">25.36%</td>
-<td align="right">7,291</td>
+<td align="right">7,431</td>
-<td align="right">68.89%</td>
+<td align="right">68.98%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,144</td>
+<td align="right">2,159</td>
-<td align="right">20.26%</td>
+<td align="right">20.04%</td>
-<td align="right">9,435</td>
+<td align="right">9,590</td>
-<td align="right">89.15%</td>
+<td align="right">89.03%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,148</td>
+<td align="right">1,182</td>
-<td align="right">10.85%</td>
+<td align="right">10.97%</td>
-<td align="right">10,583</td>
+<td align="right">10,772</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@ -902,58 +902,73 @@ antibiotic class they are in:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2011-06-02</td>
+<td align="center">2017-08-08</td>
-<td align="center">B5</td>
+<td align="center">G10</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital B</td>
-<td align="center">B_STRPT_PNMN</td>
+<td align="center">B_STPHY_AURS</td>
-<td align="center">I</td>
+<td align="center">R</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">Streptococcus</td>
+<td align="center">Staphylococcus</td>
-<td align="center">pneumoniae</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2015-07-25</td>
+<td align="center">2015-01-19</td>
-<td align="center">U6</td>
+<td align="center">A2</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</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">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2015-07-05</td>
+<td align="center">2017-11-10</td>
-<td align="center">C5</td>
+<td align="center">S3</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital C</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">S</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">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">2013-09-15</td>
+<td align="center">2017-03-22</td>
-<td align="center">E4</td>
+<td align="center">P2</td>
 <td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</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-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2015-09-11</td>
 <td align="center">L10</td>
 <td align="center">Hospital A</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">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
@ -961,34 +976,19 @@ antibiotic class they are in:</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2013-10-10</td>
 <td align="center">V1</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</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-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2012-01-02</td>
+<td align="center">2010-02-02</td>
-<td align="center">R4</td>
+<td align="center">P10</td>
 <td align="center">Hospital A</td>
-<td align="center">B_STPHY_AURS</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">R</td>
 <td align="center">F</td>
-<td align="center">Gram-positive</td>
+<td align="center">Gram-negative</td>
-<td align="center">Staphylococcus</td>
+<td align="center">Escherichia</td>
-<td align="center">aureus</td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2200</td>
+<td align="center">2231</td>
-<td align="center">131</td>
+<td align="center">147</td>
-<td align="center">2288</td>
+<td align="center">2321</td>
-<td align="center">4619</td>
+<td align="center">4699</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3389</td>
+<td align="center">3449</td>
-<td align="center">145</td>
+<td align="center">182</td>
-<td align="center">1085</td>
+<td align="center">1068</td>
-<td align="center">4619</td>
+<td align="center">4699</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3401</td>
+<td align="center">3429</td>
 <td align="center">0</td>
-<td align="center">1218</td>
+<td align="center">1270</td>
-<td align="center">4619</td>
+<td align="center">4699</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4069</td>
+<td align="center">4090</td>
 <td align="center">0</td>
-<td align="center">550</td>
+<td align="center">609</td>
-<td align="center">4619</td>
+<td align="center">4699</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1148</td>
+<td align="center">1182</td>
-<td align="center">1148</td>
+<td align="center">1182</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">901</td>
+<td align="center">935</td>
-<td align="center">44</td>
+<td align="center">39</td>
-<td align="center">203</td>
+<td align="center">208</td>
-<td align="center">1148</td>
+<td align="center">1182</td>
 </tr>
 </tbody>
 </table>
@ -1078,34 +1078,34 @@ 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">4069</td>
+<td align="center">4090</td>
 <td align="center">0</td>
-<td align="center">550</td>
+<td align="center">609</td>
-<td align="center">4619</td>
+<td align="center">4699</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1048</td>
+<td align="center">1071</td>
 <td align="center">0</td>
-<td align="center">100</td>
+<td align="center">111</td>
-<td align="center">1148</td>
+<td align="center">1182</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2381</td>
+<td align="center">2423</td>
 <td align="center">0</td>
-<td align="center">291</td>
+<td align="center">309</td>
-<td align="center">2672</td>
+<td align="center">2732</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">2144</td>
+<td align="center">2159</td>
-<td align="center">2144</td>
+<td align="center">2159</td>
 </tr>
 </tbody>
 </table>
@ -1137,7 +1137,7 @@ 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] 0.5408674</span></span></code></pre></div>
+<span><span class="co"># [1] 0.5386186</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">
@ -1152,19 +1152,19 @@ own:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5445669</td>
+<td align="center">0.5404491</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5366764</td>
+<td align="center">0.5344360</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5427167</td>
+<td align="center">0.5435294</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5413386</td>
+<td align="center">0.5391467</td>
 </tr>
 </tbody>
 </table>
@ -1189,23 +1189,23 @@ 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">0.5445669</td>
+<td align="center">0.5404491</td>
-<td align="center">3175</td>
+<td align="center">3251</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5366764</td>
+<td align="center">0.5344360</td>
-<td align="center">3749</td>
+<td align="center">3688</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5427167</td>
+<td align="center">0.5435294</td>
-<td align="center">1627</td>
+<td align="center">1700</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5413386</td>
+<td align="center">0.5391467</td>
-<td align="center">2032</td>
+<td align="center">2133</td>
 </tr>
 </tbody>
 </table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7651007</td>
+<td align="center">0.7727176</td>
-<td align="center">0.8809266</td>
+<td align="center">0.8703980</td>
-<td align="center">0.9742368</td>
+<td align="center">0.9765908</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8231707</td>
+<td align="center">0.8240271</td>
-<td align="center">0.9128920</td>
+<td align="center">0.9060914</td>
-<td align="center">0.9799652</td>
+<td align="center">0.9780034</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7911677</td>
+<td align="center">0.7986823</td>
-<td align="center">0.8910928</td>
+<td align="center">0.8868960</td>
-<td align="center">0.9805389</td>
+<td align="center">0.9795022</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5270522</td>
+<td align="center">0.5368226</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5270522</td>
+<td align="center">0.5368226</td>
 </tr>
 </tbody>
 </table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">54.5%</td>
+<td align="right">54.0%</td>
-<td align="right">27.0%</td>
+<td align="right">25.9%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">53.7%</td>
+<td align="right">53.4%</td>
-<td align="right">26.7%</td>
+<td align="right">25.6%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">54.3%</td>
+<td align="right">54.4%</td>
-<td align="right">27.8%</td>
+<td align="right">28.5%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">54.1%</td>
+<td align="right">53.9%</td>
-<td align="right">27.0%</td>
+<td align="right">26.0%</td>
 </tr>
 </tbody>
 </table>
@ -1410,18 +1410,16 @@ 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] 32      8       128     256     0.5     32      0.025   0.005   0.005  </span></span>
+<span><span class="co">#   [1] 1      0.5    16     0.5    0.01   0.25   128    0.025  0.005  0.005 </span></span>
-<span><span class="co">#  [10] 64      0.002   16      0.5     0.002   1       &lt;=0.001 256     0.125  </span></span>
+<span><span class="co">#  [11] 64     0.01   0.002  0.0625 1      4      0.002  0.025  0.125  0.5   </span></span>
-<span><span class="co">#  [19] 0.25    256     0.025   0.0625  8       0.0625  256     0.125   128    </span></span>
+<span><span class="co">#  [21] 32     0.25   0.125  4      0.002  8      32     0.002  1      1     </span></span>
-<span><span class="co">#  [28] 0.005   256     64      0.025   4       8       2       0.0625  8      </span></span>
+<span><span class="co">#  [31] 0.01   128    1      1      0.25   0.5    0.125  4      4      64    </span></span>
-<span><span class="co">#  [37] 32      1       16      0.5     0.01    16      8       0.025   16     </span></span>
+<span><span class="co">#  [41] &gt;=256  64     0.5    0.025  32     2      16     128    1      0.005 </span></span>
-<span><span class="co">#  [46] 0.005   &lt;=0.001 1       1       64      0.25    16      &lt;=0.001 0.025  </span></span>
+<span><span class="co">#  [51] 64     &gt;=256  8      0.002  64     0.005  0.125  0.0625 8      128   </span></span>
-<span><span class="co">#  [55] 256     0.002   0.25    0.01    2       1       0.5     0.5     4      </span></span>
+<span><span class="co">#  [61] 4      128    2      &gt;=256  64     0.005  0.01   8      0.002  0.5   </span></span>
-<span><span class="co">#  [64] 0.01    0.5     2       0.5     0.0625  16      16      0.025   64     </span></span>
+<span><span class="co">#  [71] 0.0625 64     1      0.001  8      0.0625 8      0.002  8      &gt;=256 </span></span>
-<span><span class="co">#  [73] 256     0.5     0.5     0.125   16      16      0.125   0.002   128    </span></span>
+<span><span class="co">#  [81] 1      0.01   &gt;=256  0.01   0.0625 0.0625 0.0625 0.0625 8      0.25  </span></span>
-<span><span class="co">#  [82] &lt;=0.001 64      64      64      0.005   0.25    64      0.5     256    </span></span>
+<span><span class="co">#  [91] 4      1      0.0625 8      2      1      0.25   0.5    0.25   4</span></span></code></pre></div>
 <span><span class="co">#  [91] 0.025   16      4       0.025   0.0625  &lt;=0.001 64      128     128    </span></span>
 <span><span class="co"># [100] 8</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>
@ -1455,10 +1453,10 @@ 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] 24 19 26 26 21 31 28 19 25 29 20 26 22 18 20 29 18 18 20 18 26 20 17 19 25</span></span>
+<span><span class="co">#   [1] 25 23 29 18 18 18 18 19 27 19 28 23 26 20 17 22 30 31 31 31 21 20 31 17 27</span></span>
-<span><span class="co">#  [26] 25 24 23 28 22 21 23 21 29 19 22 31 30 25 26 31 20 21 21 27 26 20 30 22 20</span></span>
+<span><span class="co">#  [26] 25 19 26 23 18 19 26 23 26 18 24 21 25 28 27 23 24 17 21 30 23 19 20 20 27</span></span>
-<span><span class="co">#  [51] 25 17 23 24 17 19 26 25 30 20 20 20 26 26 29 17 29 24 22 18 26 25 28 23 20</span></span>
+<span><span class="co">#  [51] 24 23 18 25 31 30 24 23 17 30 18 27 20 21 30 31 17 25 24 27 25 28 26 25 18</span></span>
-<span><span class="co">#  [76] 23 31 17 17 18 24 19 27 30 22 17 23 22 17 21 18 29 19 26 31 27 26 22 22 25</span></span></code></pre></div>
+<span><span class="co">#  [76] 18 29 26 28 21 18 24 27 29 17 26 20 17 23 22 29 23 24 19 31 30 20 29 25 31</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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/MDR.html
+++ b/articles/MDR.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,19 +375,19 @@ 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          S            S            S</span></span>
+<span><span class="co"># 1          I         S            S          R            I            R</span></span>
-<span><span class="co"># 2          R         I            S          S            R            I</span></span>
+<span><span class="co"># 2          R         S            S          R            R            R</span></span>
-<span><span class="co"># 3          S         S            R          S            S            R</span></span>
+<span><span class="co"># 3          R         S            I          S            S            S</span></span>
-<span><span class="co"># 4          R         R            I          S            S            I</span></span>
+<span><span class="co"># 4          I         S            I          I            R            R</span></span>
-<span><span class="co"># 5          I         S            I          I            I            S</span></span>
+<span><span class="co"># 5          I         S            S          I            S            S</span></span>
-<span><span class="co"># 6          R         R            S          R            I            I</span></span>
+<span><span class="co"># 6          S         I            R          I            R            S</span></span>
 <span><span class="co">#   kanamycin</span></span>
-<span><span class="co"># 1         I</span></span>
+<span><span class="co"># 1         S</span></span>
-<span><span class="co"># 2         S</span></span>
+<span><span class="co"># 2         R</span></span>
-<span><span class="co"># 3         I</span></span>
+<span><span class="co"># 3         R</span></span>
-<span><span class="co"># 4         R</span></span>
+<span><span class="co"># 4         I</span></span>
-<span><span class="co"># 5         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">
@ -428,40 +428,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3144</td>
+<td align="right">3261</td>
-<td align="right">62.88%</td>
+<td align="right">65.22%</td>
-<td align="right">3144</td>
+<td align="right">3261</td>
-<td align="right">62.88%</td>
+<td align="right">65.22%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">1012</td>
+<td align="right">959</td>
-<td align="right">20.24%</td>
+<td align="right">19.18%</td>
-<td align="right">4156</td>
+<td align="right">4220</td>
-<td align="right">83.12%</td>
+<td align="right">84.40%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">482</td>
+<td align="right">434</td>
-<td align="right">9.64%</td>
+<td align="right">8.68%</td>
-<td align="right">4638</td>
+<td align="right">4654</td>
-<td align="right">92.76%</td>
+<td align="right">93.08%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">261</td>
+<td align="right">243</td>
-<td align="right">5.22%</td>
+<td align="right">4.86%</td>
-<td align="right">4899</td>
+<td align="right">4897</td>
-<td align="right">97.98%</td>
+<td align="right">97.94%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">101</td>
+<td align="right">103</td>
-<td align="right">2.02%</td>
+<td align="right">2.06%</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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
                        <h4 data-toc-skip class="author">Dr. Matthijs
 Berends</h4>
-            <h4 data-toc-skip class="date">30 December 2022</h4>
+            <h4 data-toc-skip class="date">05 January 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>
@ -247,7 +247,7 @@ 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">475,704
+online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">476,194
 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
@ -306,7 +306,7 @@ didn’t even had a professional user interface until the last decade
 language itself <a href="https://www.tidyverse.org/packages/" class="external-link">has been
 restyled completely</a> by volunteers who are dedicated professionals in
 the field of data science. SPSS was great when there was nothing else
-that could compete. But now in 2022, I don’t see any reason why SPSS
+that could compete. But now in 2023, I don’t see any reason why SPSS
 would be of any better use than R.</p>
 </li>
 </ul>
--- 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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/datasets.html
+++ b/articles/datasets.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -166,7 +166,7 @@
  <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">30 December 2022</h4>
+            <h4 data-toc-skip class="date">05 January 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>
--- 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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/resistance_predict.html
+++ b/articles/resistance_predict.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -228,7 +228,7 @@ number of observations, the actual observed resistance, the estimated
 resistance and the standard error below and above the estimation:</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">predict_TZP</span></span>
-<span><span class="co"># <span style="color: #949494;"># A tibble: 31 × 7</span></span></span>
+<span><span class="co"># <span style="color: #949494;"># A tibble: 32 × 7</span></span></span>
 <span><span class="co">#     year  value se_min se_max observations observed estimated</span></span>
 <span><span class="co">#  <span style="color: #BCBCBC;">*</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;int&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>
 <span><span class="co"># <span style="color: #BCBCBC;"> 1</span>  <span style="text-decoration: underline;">2</span>002 0.2        <span style="color: #BB0000;">NA</span>     <span style="color: #BB0000;">NA</span>           15   0.2       0.056<span style="text-decoration: underline;">2</span></span></span>
@ -241,7 +241,7 @@ resistance and the standard error below and above the estimation:</p>
 <span><span class="co"># <span style="color: #BCBCBC;"> 8</span>  <span style="text-decoration: underline;">2</span>009 0.016<span style="text-decoration: underline;">4</span>     <span style="color: #BB0000;">NA</span>     <span style="color: #BB0000;">NA</span>           61   0.016<span style="text-decoration: underline;">4</span>    0.106 </span></span>
 <span><span class="co"># <span style="color: #BCBCBC;"> 9</span>  <span style="text-decoration: underline;">2</span>010 0.056<span style="text-decoration: underline;">6</span>     <span style="color: #BB0000;">NA</span>     <span style="color: #BB0000;">NA</span>           53   0.056<span style="text-decoration: underline;">6</span>    0.116 </span></span>
 <span><span class="co"># <span style="color: #BCBCBC;">10</span>  <span style="text-decoration: underline;">2</span>011 0.183      <span style="color: #BB0000;">NA</span>     <span style="color: #BB0000;">NA</span>           93   0.183     0.127 </span></span>
-<span><span class="co"># <span style="color: #949494;"># … with 21 more rows</span></span></span></code></pre></div>
+<span><span class="co"># <span style="color: #949494;"># … with 22 more rows</span></span></span></code></pre></div>
 <p>The function <code>plot</code> is available in base R, and can be
 extended by other packages to depend the output based on the type of
 input. We extended its function to cope with resistance predictions:</p>
--- a/articles/resistance_predict_files/figure-html/unnamed-chunk-4-1.png
+++ b/articles/resistance_predict_files/figure-html/unnamed-chunk-4-1.png
--- a/articles/resistance_predict_files/figure-html/unnamed-chunk-5-1.png
+++ b/articles/resistance_predict_files/figure-html/unnamed-chunk-5-1.png
--- a/articles/resistance_predict_files/figure-html/unnamed-chunk-5-2.png
+++ b/articles/resistance_predict_files/figure-html/unnamed-chunk-5-2.png
--- a/articles/resistance_predict_files/figure-html/unnamed-chunk-6-1.png
+++ b/articles/resistance_predict_files/figure-html/unnamed-chunk-6-1.png
--- a/articles/resistance_predict_files/figure-html/unnamed-chunk-7-1.png
+++ b/articles/resistance_predict_files/figure-html/unnamed-chunk-7-1.png
--- 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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/authors.html
+++ b/authors.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/index.html
+++ b/index.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -131,7 +131,134 @@
      <small>Source: <a href="https://github.com/msberends/AMR/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
    </div>
-  </main></div>
+    <div class="section level2">
 <h2 class="pkg-version" data-toc-text="1.8.2.9078" id="amr-1829078">AMR 1.8.2.9078<a class="anchor" aria-label="anchor" href="#amr-1829078"></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>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">rsi_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-1-8-2-9078">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9078"></a></h3>
 <div class="section level4">
 <h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9078">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9078"></a></h4>
 <p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.rsi.html">as.rsi()</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-1-8-2-9078">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9078"></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-1-8-2-9078">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9078"></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>
 <p>We also made the following changes regarding the included taxonomy or microorganisms functions:</p>
 <ul><li>Updated full microbiological taxonomy according to the latest daily LPSN data set (December 2022) and latest yearly GBIF taxonomy backbone (November 2022)</li>
 <li>Support for all 1,516 city-like serovars of <em>Salmonella</em>, such as <em>Salmonella</em> Goldcoast. Formally, these are serovars belonging to the <em>S. enterica</em> species, but they are reported with only the name of the genus and the city. For this reason, the serovars are in the <code>subspecies</code> column of the <code>microorganisms</code> data set and “enterica” is in the <code>species</code> column, but the full name does not contain the species name (<em>enterica</em>).</li>
 <li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus all <code>mo_*()</code> functions) while still following our original set-up as described in our recently published JSS paper (DOI <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">10.18637/jss.v104.i03</a>).
 <ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
 </li>
 <li>It has increased tremendously in speed and returns generally more consequent results</li>
 <li>Sequential coercion is now extremely fast as results are stored to the package environment, although coercion of unknown values must be run once per session. Previous results can be reset/removed with the new <code><a href="../reference/as.mo.html">mo_reset_session()</a></code> function.</li>
 <li>Support for microorganism codes of the ASIan Antimicrobial Resistance Surveillance Network (ASIARS-Net)</li>
 <li>The MO matching score algorithm (<code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code>) now counts deletions and substitutions as 2 instead of 1, which impacts the outcome of <code><a href="../reference/as.mo.html">as.mo()</a></code> and any <code>mo_*()</code> function</li>
 </ul></li>
 <li>
 <strong>Removed all species of the taxonomic kingdom Chromista</strong> from the package. This was done for multiple reasons:
 <ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
 <li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
 <li>Chromista are almost never clinically relevant, thus lacking the secondary scope of this package</li>
 </ul></li>
 <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-1-8-2-9078">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9078"></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>
 <li>Added some missing ATC codes</li>
 <li>Updated DDDs and PubChem Compound IDs</li>
 <li>Updated some antibiotic name spelling, now used by WHOCC (such as cephalexin -&gt; cefalexin, and phenethicillin -&gt; pheneticillin)</li>
 <li>Antibiotic code “CEI” for ceftolozane/tazobactam has been replaced with “CZT” to comply with EARS-Net and WHONET 2022. The old code will still work in all cases when using <code><a href="../reference/as.ab.html">as.ab()</a></code> or any of the <code>ab_*()</code> functions.</li>
 <li>Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code <code>B_ANAER</code> to the <code>microorganisms</code> data set and adding the breakpoints of anaerobics to the <code>rsi_interpretation</code> data set, which is used by <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for interpretion of MIC and disk diffusion values</li>
 </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-1-8-2-9078">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9078"></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-1-8-2-9078">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9078"></a></h4>
 <ul><li>Function <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">rsi_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.rsi.html">rsi_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.rsi.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.rsi.html">as.rsi()</a></code> was run.</li>
 <li>Function <code><a href="../reference/mo_property.html">mo_current()</a></code> to get the currently valid taxonomic name of a microorganism</li>
 <li>Function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> to add custom antimicrobial codes and names to the <code>AMR</code> package</li>
 </ul></div>
 </div>
 <div class="section level3">
 <h3 id="changes-1-8-2-9078">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9078"></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">rsi_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">rsi_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.rsi.html">as.rsi()</a></code>:
 <ul><li>Fixed certain EUCAST breakpoints for MIC values</li>
 <li>Allow <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
 <li>Fix for bug-drug combinations with multiple breakpoints for different body sites</li>
 <li>Interpretation from MIC and disk zones is now more informative about availability of breakpoints and more robust</li>
 </ul></li>
 <li>Removed the <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> method for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
 <li>Fixed determination of Gram stains (<code><a href="../reference/mo_property.html">mo_gramstain()</a></code>), since the taxonomic phyla Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes have been renamed to respectively Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota in 2021</li>
 <li>
 <code><a href="https://rdrr.io/r/base/droplevels.html" class="external-link">droplevels()</a></code> on MIC will now return a common <code>factor</code> at default and will lose the <code>mic</code> class. Use <code>droplevels(..., as.mic = TRUE)</code> to keep the <code>mic</code> class.</li>
 <li>Small fix for using <code><a href="../reference/ab_from_text.html">ab_from_text()</a></code>
 </li>
 <li>Fixes for reading in text files using <code><a href="../reference/mo_source.html">set_mo_source()</a></code>, which now also allows the source file to contain valid taxonomic names instead of only valid microorganism ID of this package</li>
 <li>Fixed a bug for <code><a href="../reference/mdro.html">mdro()</a></code> when using similar column names with the Magiorakos guideline</li>
 <li>Using any <code>random_*()</code> function (such as <code><a href="../reference/random.html">random_mic()</a></code>) is now possible by directly calling the package without loading it first: <code>AMR::random_mic(10)</code>
 </li>
 <li>Extended support for the <code>vctrs</code> package, used internally by the tidyverse. This allows to change values of class <code>mic</code>, <code>disk</code>, <code>rsi</code>, <code>mo</code> and <code>ab</code> in tibbles, and to use antibiotic selectors for selecting/filtering, e.g. <code>df[carbapenems() == "R", ]</code>
 </li>
 <li>Fix for using <code>info = FALSE</code> in <code><a href="../reference/mdro.html">mdro()</a></code>
 </li>
 <li>For all interpretation guidelines using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on amoxicillin, the rules for ampicillin will be used if amoxicillin rules are not available</li>
 <li>Fix for using <code><a href="../reference/ab_property.html">ab_atc()</a></code> on non-existing ATC codes</li>
 <li>Black and white message texts are now reversed in colour if using an RStudio dark theme</li>
 <li>
 <code><a href="../reference/mo_property.html">mo_snomed()</a></code> now returns class <code>character</code>, not <code>numeric</code> anymore (to make long SNOMED codes readable)</li>
 <li>Fix for using <code><a href="../reference/as.ab.html">as.ab()</a></code> on <code>NA</code> values</li>
 <li>Updated support for all WHONET 2022 microorganism codes</li>
 <li>Antimicrobial interpretation ‘SDD’ (susceptible dose-dependent, coined by CLSI) will be interpreted as ‘I’ to comply with EUCAST’s ‘I’ in <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
 </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.rsi.html">as.rsi()</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>
 </ul></div>
 <div class="section level3">
 <h3 id="other-1-8-2-9078">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9078"></a></h3>
 <ul><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>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
 <li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
 <li>Set scalar conditional expressions (<code>&amp;&amp;</code> and <code>||</code>) where possible to comply with the upcoming R 4.3</li>
 <li>An enormous lot of code cleaning, fixing some small bugs on the way</li>
 </ul><hr><p>This changelog only contains changes from AMR v2.0 and later. For prior versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our archive</a>.</p>
 </div>
 </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
    </nav></aside></div>
    <footer><div class="pkgdown-footer-left">
--- 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: 2022-12-30T12:06Z
+last_built: 2023-01-05T13:50Z
 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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/AMR.html
+++ b/reference/AMR.html
@ -62,7 +62,7 @@ Principal component analysis for AMR
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/Rplot002.png
+++ b/reference/Rplot002.png
--- a/reference/Rplot003.png
+++ b/reference/Rplot003.png
--- a/reference/Rplot004.png
+++ b/reference/Rplot004.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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/WHONET.html
+++ b/reference/WHONET.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ab_from_text.html
+++ b/reference/ab_from_text.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ab_property.html
+++ b/reference/ab_property.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -190,7 +190,7 @@
 <dt>...</dt>
-<dd><p>in case of <code>set_ab_names()</code> and <code>data</code> is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: variables to select (supports tidy selection such as <code>column1:column4</code>), otherwise other arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
+<dd><p>in case of <code>set_ab_names()</code> and <code>data</code> is a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>: columns to select (supports tidy selection such as <code>column1:column4</code>), otherwise other arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
 <dt>only_first</dt>
--- 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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/add_custom_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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/age.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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -195,16 +195,16 @@
 <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  1981-01-25  41  41.92877         18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1968-01-10  54  54.98630         31</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-07-25  42  42.43288         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1991-02-27  31  31.85479          8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1991-10-10  31  31.22192          8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1948-01-05  75  75.00000         51</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1967-05-14  55  55.63014         32</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1985-02-05  37  37.91507         14</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1999-10-10  23  23.22192          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1932-08-26  90  90.36164         67</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1970-08-21  52  52.35890         29</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1949-08-28  73  73.35616         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1967-02-25  55  55.84384         32</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1985-11-10  37  37.15342         14</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1963-10-06  59  59.23288         36</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1947-09-21  75  75.29041         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1964-12-12  58  58.04932         35</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1992-05-26  30  30.61370          7</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1958-12-04  64  64.07123         41</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1955-09-09  67  67.32329         44</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- 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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -918,7 +918,21 @@
 <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/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="fu">ab_class</span><span class="op">(</span><span class="st">"mycobact"</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-err co"><span class="r-pr">#&gt;</span> <span class="error">Error in select(., mo, ab_class("mycobact")):</span> Problem while evaluating `ab_class("mycobact")`.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For ab_class("mycobact") using column 'RIF' (rifampicin)</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    mo           RIF  </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;rsi&gt;</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ESCHR_COLI R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_ESCHR_COLI R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_STPHY_EPDR NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_STPHY_EPDR NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_STPHY_EPDR NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_STPHY_EPDR NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_STPHY_AURS NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_STPHY_AURS NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA   </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="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></span>
 <span class="r-in"><span>  <span class="co"># get bug/drug combinations for only glycopeptides in Gram-positives:</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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.av.html
+++ b/reference/as.av.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.disk.html
+++ b/reference/as.disk.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.mic.html
+++ b/reference/as.mic.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.mo.html
+++ b/reference/as.mo.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.rsi.html
+++ b/reference/as.rsi.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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -506,16 +506,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 <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_gu…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> 2022-12-30 <span style="color: #949494;">12:07:24</span>     1 ampicillin AMP     Strep … B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-01-05 <span style="color: #949494;">13:50:52</span>     1 ampicillin AMP     Strep … B_STRPT_PNMN     EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-12-30 <span style="color: #949494;">12:07:25</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;"> 2</span> 2023-01-05 <span style="color: #949494;">13:50:53</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;"> 3</span> 2022-12-30 <span style="color: #949494;">12:07:25</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> 2023-01-05 <span style="color: #949494;">13:50:53</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> 2022-12-30 <span style="color: #949494;">12:07:26</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;"> 4</span> 2023-01-05 <span style="color: #949494;">13:50:53</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;"> 5</span> 2022-12-30 <span style="color: #949494;">12:07:26</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;"> 5</span> 2023-01-05 <span style="color: #949494;">13:50:54</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;"> 6</span> 2022-12-30 <span style="color: #949494;">12:07:27</span>     1 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-01-05 <span style="color: #949494;">13:50:55</span>     1 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-12-30 <span style="color: #949494;">12:07:28</span>     1 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-01-05 <span style="color: #949494;">13:50:55</span>     1 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-12-30 <span style="color: #949494;">12:07:28</span>     2 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-01-05 <span style="color: #949494;">13:50:55</span>     2 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-12-30 <span style="color: #949494;">12:07:28</span>     3 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-01-05 <span style="color: #949494;">13:50:55</span>     3 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-12-30 <span style="color: #949494;">12:07:28</span>     4 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-01-05 <span style="color: #949494;">13:50:55</span>     4 AMX        AMX     B_STRP… B_STRPT_PNMN     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;rsi&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>
--- 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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/av_from_text.html
+++ b/reference/av_from_text.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/av_property.html
+++ b/reference/av_property.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/availability.html
+++ b/reference/availability.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/bug_drug_combinations.html
+++ b/reference/bug_drug_combinations.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/count.html
+++ b/reference/count.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -197,7 +197,7 @@
 <h3 id="using-taxonomic-properties-in-rules">Using taxonomic properties in rules<a class="anchor" aria-label="anchor" href="#using-taxonomic-properties-in-rules"></a></h3>
-<p>There is one exception in variables used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "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" and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
+<p>There is one exception in columns used for the rules: all column names of the <a href="microorganisms.html">microorganisms</a> data set can also be used, but do not have to exist in the data set. These column names are: "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" and "snomed". Thus, this next example will work as well, despite the fact that the <code>df</code> data set does not contain a column <code>genus</code>:</p>
 <p></p><div class="sourceCode r"><pre><code><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/custom_eucast_rules.html">custom_eucast_rules</a></span><span class="op">(</span><span class="va">TZP</span> <span class="op">==</span> <span class="st">"S"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"S"</span>,</span>
 <span>                         <span class="va">TZP</span> <span class="op">==</span> <span class="st">"R"</span> <span class="op">&amp;</span> <span class="va">genus</span> <span class="op">==</span> <span class="st">"Klebsiella"</span> <span class="op">~</span> <span class="va">aminopenicillins</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span></span>
 <span></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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/eucast_rules.html
+++ b/reference/eucast_rules.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/example_isolates.html
+++ b/reference/example_isolates.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/example_isolates_unclean.html
+++ b/reference/example_isolates_unclean.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/first_isolate.html
+++ b/reference/first_isolate.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/get_episode.html
+++ b/reference/get_episode.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -182,42 +182,39 @@
 <span class="r-in"><span><span class="va">df</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/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</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="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 67  8 32 43 12 22 22 31  7 57 67 15 29 40 20  1 43 49  7 45 64  1 31 67  1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 60 59 40 62 19 23 22  5 49 47  2 53 35 32 20 62 40 56 17 42 59 57 38 15 61</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 65 20 55 41  2  9 20 31 60 61 36 24 41 34 41 62 34 20  5 11 63 49 41 61 46</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 14 26 13  6  9 27 28 59 34 36 44  9  7 47 17  5 16  5 14 13 24 48  9 62  5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 16 33 28 29 51 50 29 61 14  7 18 10 60 18 47 59 22 16 55 33 64 33 48  3 58</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 56  1 57  6 26 52 22 13 16 51 42 19 30 13 15  2 38 63  4  9 13 34 13  1 24</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 57  6 31 40 21 36 24 61 14 57 26  2 24 27 12 12 22 17  9 18 66 34 14  3  5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 29 44 19 11 58  1 61 21 37 61 64 41 26 39 40 19 31 21  1 43  1 23 52 27  5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 53 67 38  1 18 65 33 46 46 51  4 17  5  1 55 40 44 20 51 38 50 38 18 47 62</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 31 31 23 43 57  3  6 59 55 22 58 29 33 12 32 63 25 11 61 29 37 62 26 21 57</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 12 14 18 51 25 31 35 30 40 14 61 54 47 16 67 36 14 39 23 55  7 56 39 13 21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 61 25 26 34 54  7 10 13 11 18 56 33 23  2 34 45 24 20 64 24 30 57 50 39 16</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 12 44 25 35 50 27 51  2  1 58 49 20 60 52 66 63 17 31 19 47 15 52 64 31 17</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 60  8 56 62 45 43 61 53  8  4  9 51 56 15 49 11 10 10 41 26 49 36 63 13 26</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 25 30  8 54 36 39 21 51 23 64  3 66 19 38  3 27 26 44  6 48 11 42 61  5 37</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 46 13 13 38 54 14 27 10 58 55 29 25 39 27 22 60 32  8 59 25  8 23 56 57 24</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49]  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85]  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85]  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [109]  TRUE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [157]  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [169]  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
 <span class="r-in"><span><span class="va">df</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">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 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;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-07-21 955940     82 F      Clinical B_PSDMN_AERG R     NA    NA    R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-15 426426     67 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;">3</span> 2002-06-06 24D393     20 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;">4</span> 2002-07-15 C42193     84 M      ICU      B_STPHY_HMNS R     NA    R     R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@ -253,16 +250,16 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   condition [3]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient date       condition new_episode</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;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 5DB1C8  2017-12-28 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 671620  2016-12-04 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 4DD722  2003-06-02 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> BF4515  2016-09-25 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C7C641  2008-12-27 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 116866  2011-11-07 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 704554  2012-01-01 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 422833  2017-05-26 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 304508  2004-05-09 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 344184  2006-08-01 A         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E27874  2006-12-19 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 92F410  2007-09-03 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 418311  2006-11-10 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 534816  2007-04-16 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 501361  2008-11-01 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 088256  2003-01-25 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 6BC362  2003-04-02 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 959835  2013-11-16 A         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> D40405  2015-06-03 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 255339  2013-07-22 B         FALSE      </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</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">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -274,19 +271,19 @@
 <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-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [177]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [182]</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    ward       date       patient new_index new_logical</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    ward     date       patient new_index new_logical</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;dbl&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: #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;dbl&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   2017-12-28 5DB1C8          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2016-12-04 671620          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU        2003-06-02 4DD722          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2016-09-25 BF4515          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Outpatient 2008-12-27 C7C641          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2011-11-07 116866          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU        2012-01-01 704554          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2017-05-26 422833          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical   2004-05-09 304508          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2006-08-01 344184          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical   2006-12-19 E27874          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2007-09-03 92F410          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU        2006-11-10 418311          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2007-04-16 534816          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical   2008-11-01 501361          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU      2003-01-25 088256          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU        2003-04-02 6BC362          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2013-11-16 959835          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU        2015-06-03 D40405          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2013-07-22 255339          1 TRUE       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</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">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -301,9 +298,9 @@
 <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       n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>          <span 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> Clinical          115             14            50            71</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          127             15            55            79</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                56             13            37            43</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                44             11            31            34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          6              4             5             5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         11              6             9            10</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></span>
 <span class="r-in"><span>  <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@ -333,19 +330,19 @@
 <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="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</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: 200 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [191]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [194]</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo           ward       flag_episode</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo            ward     flag_episode</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;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&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: #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 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> 5DB1C8  B_STPHY_CPTS Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 671620  B_ESCHR_COLI  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 4DD722  B_ESCHR_COLI ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> BF4515  B_STPHY_EPDR  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> C7C641  B_STPHY_CONS Outpatient TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 116866  B_STPHY_CONS  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 704554  B_STPHY_CONS ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 422833  B_ENTRC_FCLS  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 304508  B_STRPT_PNMN Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 344184  B_STPHY_CONS  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E27874  B_STRPT_PNMN Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 92F410  B_ENTRBC_CLOC Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 418311  B_STPHY_EPDR ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 534816  B_ENTRC_FCLS  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 501361  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 088256  B_STPHY_HMNS  ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 6BC362  B_STRPT_PNMN ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 959835  B_STPHY_CONS  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> D40405  B_ENTRC_FCLS ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 255339  B_ESCHR_COLI  Clinical TRUE        </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
--- 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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ggplot_rsi.html
+++ b/reference/ggplot_rsi.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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/index.html
+++ b/reference/index.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/italicise_taxonomy.html
+++ b/reference/italicise_taxonomy.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/join.html
+++ b/reference/join.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/key_antimicrobials.html
+++ b/reference/key_antimicrobials.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/kurtosis.html
+++ b/reference/kurtosis.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -172,9 +172,9 @@
    <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] 2.979693</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.923487</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] 0.0343079</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.01643722</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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -152,7 +152,7 @@
    <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 vector of class <a href="as.rsi.html">rsi</a>, <a href="as.rsi.html">rsi</a> or <a href="as.rsi.html">rsi</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
+<dd><p>a vector of class <a href="as.rsi.html">rsi</a>, <a href="as.mic.html">mic</a> or <a href="as.disk.html">disk</a>, or a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> containing columns of any of these classes</p></dd>
 <dt>...</dt>
@ -173,10 +173,10 @@
 </dl></div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>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. For common numeric data this distance is equal to <a href="https://en.wikipedia.org/wiki/Standard_score" class="external-link">Z scores</a> (the number of standard deviations from the mean).</p>
+    <p>The mean AMR distance is effectively <a href="https://en.wikipedia.org/wiki/Standard_score" class="external-link">the Z-score</a>; a normalised numeric value to compare AMR test results which can help to identify similar isolates, without comparing antibiograms by hand.</p>
-<p>MIC values (see <code><a href="as.mic.html">as.mic()</a></code>) are transformed with <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code> first; their distance is calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
+<p>MIC values (see <code><a href="as.mic.html">as.mic()</a></code>) are transformed with <code><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2()</a></code> first; their distance is thus calculated as <code>(log2(x) - mean(log2(x))) / sd(log2(x))</code>.</p>
 <p>R/SI values (see <code><a href="as.rsi.html">as.rsi()</a></code>) are transformed using <code>"S"</code> = 1, <code>"I"</code> = 2, and <code>"R"</code> = 3. If <code>combine_SI</code> is <code>TRUE</code> (default), the <code>"I"</code> will be considered to be 1.</p>
-<p>For data sets, the mean AMR distance will be calculated per variable, after which the mean of all columns will returned per row (using <code><a href="https://rdrr.io/r/base/colSums.html" class="external-link">rowMeans()</a></code>), see <em>Examples</em>.</p>
+<p>For data sets, the mean AMR distance will be calculated per column, after which the mean per row will be returned, see <em>Examples</em>.</p>
 <p>Use <code>amr_distance_from_row()</code> to subtract distances from the distance of one row, see <em>Examples</em>.</p>
    </div>
    <div class="section level2">
@ -188,104 +188,121 @@
    <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">x</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>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_rsi</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">x</span></span></span>
+<span class="r-in"><span><span class="va">rsi</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [1] S I S S R S S S I R</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">rsi</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.4743416 -0.4743416 -0.4743416 -0.4743416  1.8973666 -0.4743416</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.4743416 -0.4743416 -0.4743416  1.8973666</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] 0.01    0.002   &gt;=256   1       &lt;=0.001 0.01    64      0.005   64     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] &gt;=64  0.25  16    0.001 0.125 32    0.125 0.001 0.002 8    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] &gt;=256  </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-in"><span><span class="fu">mean_amr_distance</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>  [1]  1.26281480 -0.01764874  0.94269891 -1.29263579 -0.17770669  1.10275686</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.7233354 -1.0310806  1.2175417  0.1572324 -1.1636193 -0.7233354</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.17770669 -1.29263579 -1.13257785  0.78264097</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.9524644 -0.8558740  0.9524644  1.2175417</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]  1.26281480 -0.01764874  0.94269891 -1.29263579 -0.17770669  1.10275686</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.17770669 -1.29263579 -1.13257785  0.78264097</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] 17 29 32 37 48 40 28 37 40 49</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] -1.9401430 -0.6951315 -0.3838786  0.1348763  1.2761369  0.4461291</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.7988824  0.1348763  0.4461291  1.3798878</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>
-<span class="r-in"><span>  amox <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"amox"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  amox <span class="op">=</span> <span class="fu"><a href="random.html">random_rsi</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"amox"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
-<span class="r-in"><span>  cipr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"cipr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
+<span class="r-in"><span>  cipr <span class="op">=</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"cipr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  gent <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"gent"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>  tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</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="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>    id amox cipr gent tobr</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    8     1    2    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    R   23 &gt;=16    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   32   &gt;=4    1  &gt;=8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    I   24    1    4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    4  0.25    4    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    S   24    8 0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D   16   &gt;=4    2    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    R   18    2    4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4   &gt;=4    1    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   17    4    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F   16     1    4    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    S   22    8    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    4   0.5    1  &gt;=8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    R   29    2 0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    4  0.25    1    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    S   28 &gt;=16    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16   0.5    1  0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    I   31    4    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    8 0.125  &gt;=8  0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    S   20 &gt;=16  0.5</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",</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "id" and "tobr"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.0410109  0.8951387 -0.4091718  0.5415853 -0.1399200  0.6721245</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.1964756 -0.6867320 -0.4492455 -0.2683146</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-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]  0.76502575 -0.22559420 -0.39112580  0.14405101 -0.59747772  0.01884049</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.04569124  0.34391737  0.15560237 -0.25893050</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</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-out co"><span class="r-pr">#&gt;</span>    id amox cipr gent tobr amr_distance</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    4  0.25    1    2   -0.6867320</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    R   29    2 0.25   -1.2141339</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16   0.5    1  0.5   -0.4492455</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    S   24    8 0.25   -0.5147553</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    4  0.25    4    1   -0.4091718</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    I   24    1    4   -0.1836920</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    8 0.125  &gt;=8  0.5   -0.2683146</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   17    4    1   -0.1743790</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    4   0.5    1  &gt;=8   -0.1964756</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    I   31    4    1   -0.1743790</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4   &gt;=4    1    2   -0.1399200</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    R   18    2    4    0.1659973</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    8     1    2    2    0.0410109</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    S   20 &gt;=16  0.5    0.1799668</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D   16   &gt;=4    2    2    0.5415853</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    S   22    8    2    0.5203431</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F   16     1    4    4    0.6721245</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    S   28 &gt;=16    1    0.5249996</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   32   &gt;=4    1  &gt;=8    0.8951387</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    R   23 &gt;=16    2    0.8700324</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>
 <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></span></span>
-<span class="r-in"><span>      amr_distance <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</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>      amr_distance <span class="op">=</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-in"><span>      check_id_C <span class="op">=</span> <span class="fu">amr_distance_from_row</span><span class="op">(</span><span class="va">amr_distance</span>, <span class="va">id</span> <span class="op">==</span> <span class="st">"C"</span><span class="op">)</span></span></span>
 <span class="r-in"><span>    <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">check_id_C</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> 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>    id amox cipr gent tobr amr_distance check_id_C</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    4  0.25    4    1   -0.4091718  0.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    S   24    8 0.25  -0.39112580  0.0000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   I   16   0.5    1  0.5   -0.4492455  0.0400737</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   J    S   20 &gt;=16  0.5  -0.25893050  0.1321953</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   J    8 0.125  &gt;=8  0.5   -0.2683146  0.1408572</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   B    I   24    1    4  -0.22559420  0.1655316</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   G    4   0.5    1  &gt;=8   -0.1964756  0.2126962</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   E    S   17    4    1  -0.59747772  0.2063519</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4   &gt;=4    1    2   -0.1399200  0.2692518</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   F    S   22    8    2   0.01884049  0.4099663</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   H    4  0.25    1    2   -0.6867320  0.2775602</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   G    R   29    2 0.25   0.04569124  0.4368170</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   A    8     1    2    2    0.0410109  0.4501827</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   D    R   18    2    4   0.14405101  0.5351768</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   D   16   &gt;=4    2    2    0.5415853  0.9507571</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   I    I   31    4    1   0.15560237  0.5467282</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   F   16     1    4    4    0.6721245  1.0812963</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   H    S   28 &gt;=16    1   0.34391737  0.7350432</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  B   32   &gt;=4    1  &gt;=8    0.8951387  1.3043105</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  A    R   23 &gt;=16    2   0.76502575  1.1561516</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>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Enterococcus"</span> <span class="op">&amp;</span> <span class="fu"><a href="mo_property.html">mo_species</a></span><span class="op">(</span><span class="op">)</span> <span class="op">!=</span> <span class="st">""</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">TCY</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>d <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</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>dist <span class="op">=</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
-<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">d</span><span class="op">)</span></span></span>
+<span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/arrange.html" class="external-link">arrange</a></span><span class="op">(</span><span class="va">mo</span>, <span class="va">dist</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_genus()</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for mo_species()</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 Calculating mean AMR distance based on columns "IPM", "MEM" and "TCY"</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "TCY", "IPM" and "MEM"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 63 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   mo [4]</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    mo           TCY   IPM   MEM         d</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    mo           TCY   IPM   MEM     dist</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;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&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: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&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> B_ENTRC_AVIM S     S     NA    <span style="color: #BB0000;">NaN</span>    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B_ENTRC_AVIM S     S     NA     0    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S     S     NA    <span style="color: #BB0000;">NaN</span>    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> B_ENTRC_AVIM S     S     NA     0    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA    S     NA     <span style="color: #BB0000;">NA</span>    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> B_ENTRC_CSSL NA    S     NA    <span style="color: #BB0000;">NA</span>    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S     S     NA     -<span style="color: #BB0000;">2.66</span> </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> B_ENTRC_FACM S     S     NA    -<span style="color: #BB0000;">2.66</span> </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S     R     R      -<span style="color: #BB0000;">0.423</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> B_ENTRC_FACM S     R     R     -<span style="color: #BB0000;">0.423</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S     R     R      -<span style="color: #BB0000;">0.423</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B_ENTRC_FACM S     R     R     -<span style="color: #BB0000;">0.423</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA    R     R       0.224</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B_ENTRC_FACM NA    R     R      0.224</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA    R     R       0.224</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> B_ENTRC_FACM NA    R     R      0.224</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA    R     R       0.224</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> B_ENTRC_FACM NA    R     R      0.224</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ENTRC_FACM NA    R     R       0.224</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B_ENTRC_FACM NA    R     R      0.224</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 53 more rows</span></span>
 </code></pre></div>
    </div>
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/microorganisms.html
+++ b/reference/microorganisms.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_matching_score.html
+++ b/reference/mo_matching_score.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_property.html
+++ b/reference/mo_property.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_source.html
+++ b/reference/mo_source.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/pca.html
+++ b/reference/pca.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/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/reference/plot-7.png
+++ b/reference/plot-7.png
--- a/reference/plot-8.png
+++ b/reference/plot-8.png
--- a/reference/plot-9.png
+++ b/reference/plot-9.png
--- a/reference/plot.html
+++ b/reference/plot.html
@ -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="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/proportion.html
+++ b/reference/proportion.html
@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9076</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9078</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/Show More
+++ b/Show More