Built site for AMR: 1.8.2.9014@dfae4c7

2026-10-01 04:13:33 +02:00 · 2022-10-11 09:00:04 +00:00
1 parent 4f02b97c70
commit a1d8ec7d4a
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -162,7 +162,7 @@
      <img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
                        <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
-            <h4 data-toc-skip class="date">10 October 2022</h4>
+            <h4 data-toc-skip class="date">11 October 2022</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>
@@ -170,7 +170,7 @@
-<p><strong>Note:</strong> values on this page will change with every 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 10 October 2022.</p>
+<p><strong>Note:</strong> values on this page will change with every 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 11 October 2022.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -201,21 +201,21 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2022-10-10</td>
+<td align="center">2022-10-11</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">2022-10-10</td>
+<td align="center">2022-10-11</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">2022-10-10</td>
+<td align="center">2022-10-11</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -325,52 +325,19 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2013-01-05</td>
+<td align="center">2015-02-02</td>
-<td align="center">B6</td>
+<td align="center">E3</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2012-10-29</td>
 <td align="center">N7</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
 <td align="center">2013-03-22</td>
 <td align="center">H6</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2012-10-06</td>
+<td align="center">2015-12-29</td>
-<td align="center">C7</td>
+<td align="center">W4</td>
 <td align="center">Hospital A</td>
 <td align="center">Escherichia coli</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="odd">
 <td align="center">2016-03-25</td>
 <td align="center">S8</td>
 <td align="center">Hospital D</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
@@ -379,17 +346,50 @@
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
-<tr class="even">
+<tr class="odd">
-<td align="center">2011-05-16</td>
+<td align="center">2013-03-05</td>
-<td align="center">I5</td>
+<td align="center">E4</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital C</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</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">2016-02-19</td>
 <td align="center">O7</td>
 <td align="center">Hospital C</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">F</td>
 </tr>
 <tr class="odd">
 <td align="center">2016-03-08</td>
 <td align="center">M10</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2016-12-01</td>
 <td align="center">U5</td>
 <td align="center">Hospital D</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">F</td>
 </tr>
 </tbody>
 </table>
 <p>Now, let’s start the cleaning and the analysis!</p>
@@ -422,16 +422,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,283</td>
+<td align="right">10,418</td>
-<td align="right">51.42%</td>
+<td align="right">52.09%</td>
-<td align="right">10,283</td>
+<td align="right">10,418</td>
-<td align="right">51.42%</td>
+<td align="right">52.09%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,717</td>
+<td align="right">9,582</td>
-<td align="right">48.59%</td>
+<td align="right">47.91%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -488,9 +488,9 @@ Longest: 1</p>
 <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 10,620 'phenotype-based' first isolates (53.1% of total where a</span></span>
+<span><span class="co"># =&gt; Found 10,684 'phenotype-based' first isolates (53.4% of total where a</span></span>
 <span><span class="co">#    microbial ID was available)</span></span></code></pre></div>
-<p>So only 53.1% 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>
+<p>So only 53.4% 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">
 <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="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@@ -499,7 +499,7 @@ Longest: 1</p>
 <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 10,620 isolates for analysis. Now our data looks like:</p>
+<p>So we end up with 10,684 isolates for analysis. Now our data looks like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
 <table class="table">
@@ -538,14 +538,14 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="left">1</td>
-<td align="center">2013-01-05</td>
+<td align="center">2015-02-02</td>
-<td align="center">B6</td>
+<td align="center">E3</td>
 <td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
@@ -553,77 +553,61 @@ Longest: 1</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">3</td>
 <td align="center">2013-03-22</td>
 <td align="center">H6</td>
 <td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">4</td>
-<td align="center">2012-10-06</td>
+<td align="center">2016-02-19</td>
-<td align="center">C7</td>
+<td align="center">O7</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital C</td>
 <td align="center">B_ESCHR_COLI</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>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">6</td>
 <td align="center">2011-05-16</td>
 <td align="center">I5</td>
 <td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">11</td>
 <td align="center">2014-02-18</td>
 <td align="center">K4</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">M</td>
+<td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
+<tr class="odd">
-<td align="left">12</td>
+<td align="left">6</td>
-<td align="center">2013-07-06</td>
+<td align="center">2016-12-01</td>
-<td align="center">Q5</td>
+<td align="center">U5</td>
 <td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">7</td>
 <td align="center">2017-10-01</td>
 <td align="center">K6</td>
 <td align="center">Hospital A</td>
 <td align="center">B_ESCHR_COLI</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>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">8</td>
 <td align="center">2015-04-05</td>
 <td align="center">R1</td>
 <td align="center">Hospital A</td>
 <td align="center">B_ESCHR_COLI</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>
@@ -632,6 +616,22 @@ Longest: 1</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">9</td>
 <td align="center">2010-02-04</td>
 <td align="center">B3</td>
 <td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
 <p>Time for the analysis!</p>
@@ -653,8 +653,8 @@ Longest: 1</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://rdrr.io/pkg/cleaner/man/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: 10,620<br>
+Length: 10,684<br>
-Available: 10,620 (100.0%, NA: 0 = 0.0%)<br>
+Available: 10,684 (100.0%, NA: 0 = 0.0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -671,33 +671,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,630</td>
+<td align="right">4,678</td>
-<td align="right">43.60%</td>
+<td align="right">43.79%</td>
-<td align="right">4,630</td>
+<td align="right">4,678</td>
-<td align="right">43.60%</td>
+<td align="right">43.79%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,705</td>
+<td align="right">2,715</td>
-<td align="right">25.47%</td>
+<td align="right">25.41%</td>
-<td align="right">7,335</td>
+<td align="right">7,393</td>
-<td align="right">69.07%</td>
+<td align="right">69.20%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,115</td>
+<td align="right">2,108</td>
-<td align="right">19.92%</td>
+<td align="right">19.73%</td>
-<td align="right">9,450</td>
+<td align="right">9,501</td>
-<td align="right">88.98%</td>
+<td align="right">88.93%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,170</td>
+<td align="right">1,183</td>
-<td align="right">11.02%</td>
+<td align="right">11.07%</td>
-<td align="right">10,620</td>
+<td align="right">10,684</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -744,69 +744,54 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2013-01-05</td>
+<td align="center">2016-12-01</td>
-<td align="center">B6</td>
+<td align="center">U5</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">M</td>
+<td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2010-11-11</td>
+<td align="center">2012-09-03</td>
-<td align="center">D1</td>
+<td align="center">O8</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
-<td align="center">B_STRPT_PNMN</td>
+<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">M</td>
+<td align="center">F</td>
-<td align="center">Gram-positive</td>
+<td align="center">Gram-negative</td>
-<td align="center">Streptococcus</td>
+<td align="center">Escherichia</td>
-<td align="center">pneumoniae</td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2017-03-17</td>
+<td align="center">2015-04-26</td>
 <td align="center">C4</td>
 <td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2011-08-08</td>
 <td align="center">W2</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital B</td>
-<td align="center">B_STRPT_PNMN</td>
+<td align="center">B_ESCHR_COLI</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">Gram-negative</td>
-<td align="center">Streptococcus</td>
+<td align="center">Escherichia</td>
-<td align="center">pneumoniae</td>
+<td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
+<tr class="even">
-<td align="center">2017-12-12</td>
+<td align="center">2012-08-07</td>
-<td align="center">C9</td>
+<td align="center">I8</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
@@ -818,13 +803,13 @@ Longest: 24</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
+<tr class="odd">
-<td align="center">2013-06-02</td>
+<td align="center">2012-09-19</td>
-<td align="center">X9</td>
+<td align="center">Y3</td>
 <td align="center">Hospital A</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">I</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
@@ -833,6 +818,21 @@ Longest: 24</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2011-05-20</td>
 <td align="center">R9</td>
 <td align="center">Hospital D</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Klebsiella</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
 <p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@@ -854,50 +854,50 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2199</td>
+<td align="center">2191</td>
-<td align="center">136</td>
+<td align="center">130</td>
-<td align="center">2295</td>
+<td align="center">2357</td>
-<td align="center">4630</td>
+<td align="center">4678</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3430</td>
+<td align="center">3377</td>
-<td align="center">164</td>
+<td align="center">187</td>
-<td align="center">1036</td>
+<td align="center">1114</td>
-<td align="center">4630</td>
+<td align="center">4678</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3392</td>
+<td align="center">3413</td>
 <td align="center">0</td>
-<td align="center">1238</td>
+<td align="center">1265</td>
-<td align="center">4630</td>
+<td align="center">4678</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4003</td>
+<td align="center">4126</td>
 <td align="center">0</td>
-<td align="center">627</td>
+<td align="center">552</td>
-<td align="center">4630</td>
+<td align="center">4678</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">1170</td>
+<td align="center">1183</td>
-<td align="center">1170</td>
+<td align="center">1183</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">919</td>
+<td align="center">940</td>
-<td align="center">53</td>
+<td align="center">40</td>
-<td align="center">198</td>
+<td align="center">203</td>
-<td align="center">1170</td>
+<td align="center">1183</td>
 </tr>
 </tbody>
 </table>
@@ -920,34 +920,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4003</td>
+<td align="center">4126</td>
 <td align="center">0</td>
-<td align="center">627</td>
+<td align="center">552</td>
-<td align="center">4630</td>
+<td align="center">4678</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1058</td>
+<td align="center">1071</td>
 <td align="center">0</td>
 <td align="center">112</td>
-<td align="center">1170</td>
+<td align="center">1183</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2411</td>
+<td align="center">2406</td>
 <td align="center">0</td>
-<td align="center">294</td>
+<td align="center">309</td>
-<td align="center">2705</td>
+<td align="center">2715</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">2115</td>
+<td align="center">2108</td>
-<td align="center">2115</td>
+<td align="center">2108</td>
 </tr>
 </tbody>
 </table>
@@ -961,7 +961,7 @@ Longest: 24</p>
 <p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
 <div class="sourceCode" id="cb26"><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] 0.5410546</span></span></code></pre></div>
+<span><span class="co"># [1] 0.5446462</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="cb27"><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>
@@ -975,19 +975,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5427928</td>
+<td align="center">0.5423889</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5446957</td>
+<td align="center">0.5451578</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5358423</td>
+<td align="center">0.5370259</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5362524</td>
+<td align="center">0.5528979</td>
 </tr>
 </tbody>
 </table>
@@ -1008,23 +1008,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5427928</td>
+<td align="center">0.5423889</td>
-<td align="center">3108</td>
+<td align="center">3173</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5446957</td>
+<td align="center">0.5451578</td>
-<td align="center">3714</td>
+<td align="center">3676</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5358423</td>
+<td align="center">0.5370259</td>
-<td align="center">1674</td>
+<td align="center">1661</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5362524</td>
+<td align="center">0.5528979</td>
-<td align="center">2124</td>
+<td align="center">2174</td>
 </tr>
 </tbody>
 </table>
@@ -1047,27 +1047,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7762419</td>
+<td align="center">0.7618640</td>
-<td align="center">0.8645788</td>
+<td align="center">0.8820009</td>
-<td align="center">0.9792657</td>
+<td align="center">0.9764857</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8307692</td>
+<td align="center">0.8284024</td>
-<td align="center">0.9042735</td>
+<td align="center">0.9053254</td>
-<td align="center">0.9854701</td>
+<td align="center">0.9788673</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7940850</td>
+<td align="center">0.7893186</td>
-<td align="center">0.8913124</td>
+<td align="center">0.8861878</td>
-<td align="center">0.9818854</td>
+<td align="center">0.9804788</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5390071</td>
+<td align="center">0.5398482</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5390071</td>
+<td align="center">0.5398482</td>
 </tr>
 </tbody>
 </table>
@@ -1092,23 +1092,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">54.3%</td>
+<td align="right">54.2%</td>
-<td align="right">26.1%</td>
+<td align="right">27.7%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
 <td align="right">54.5%</td>
-<td align="right">26.4%</td>
+<td align="right">25.9%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">53.6%</td>
+<td align="right">53.7%</td>
-<td align="right">25.1%</td>
+<td align="right">27.5%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">53.6%</td>
+<td align="right">55.3%</td>
-<td align="right">26.0%</td>
+<td align="right">26.3%</td>
 </tr>
 </tbody>
 </table>
@@ -1206,18 +1206,18 @@ Longest: 24</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 &lt;mic&gt;</span></span>
-<span><span class="co">#   [1] 0.005   2       1       0.0625  128     0.5     1       &gt;=256   64     </span></span>
+<span><span class="co">#   [1] 8       32      0.125   4       0.0625  32      0.5     0.01    8      </span></span>
-<span><span class="co">#  [10] 0.5     32      16      0.002   0.01    0.025   32      &gt;=256   2      </span></span>
+<span><span class="co">#  [10] 0.01    8       1       2       16      0.002   0.25    128     128    </span></span>
-<span><span class="co">#  [19] &lt;=0.001 0.01    2       0.25    0.5     0.5     32      0.005   0.5    </span></span>
+<span><span class="co">#  [19] 256     0.125   &lt;=0.001 0.125   &lt;=0.001 0.125   32      128     16     </span></span>
-<span><span class="co">#  [28] 0.125   2       1       0.025   128     0.125   0.002   0.125   16     </span></span>
+<span><span class="co">#  [28] 8       0.125   &lt;=0.001 128     0.005   0.5     1       2       0.25   </span></span>
-<span><span class="co">#  [37] &lt;=0.001 2       0.0625  8       1       0.125   0.002   &gt;=256   0.0625 </span></span>
+<span><span class="co">#  [37] 0.125   0.5     4       0.005   0.5     16      0.002   0.0625  2      </span></span>
-<span><span class="co">#  [46] 4       16      4       0.005   0.0625  4       0.002   0.0625  16     </span></span>
+<span><span class="co">#  [46] 0.01    256     &lt;=0.001 64      16      1       2       64      4      </span></span>
-<span><span class="co">#  [55] 2       4       1       0.5     16      0.5     64      128     0.005  </span></span>
+<span><span class="co">#  [55] 0.0625  128     0.002   0.25    8       1       0.005   0.5     16     </span></span>
-<span><span class="co">#  [64] 128     0.125   0.01    2       0.25    0.5     &lt;=0.001 16      32     </span></span>
+<span><span class="co">#  [64] 16      0.25    4       32      2       0.005   32      0.5     0.01   </span></span>
-<span><span class="co">#  [73] 2       8       &gt;=256   64      2       0.002   0.002   32      4      </span></span>
+<span><span class="co">#  [73] 0.01    4       256     256     &lt;=0.001 0.25    32      8       0.01   </span></span>
-<span><span class="co">#  [82] 0.005   64      32      32      128     0.002   0.002   0.025   &gt;=256  </span></span>
+<span><span class="co">#  [82] 0.0625  0.01    0.5     0.25    &lt;=0.001 64      1       0.5     16     </span></span>
-<span><span class="co">#  [91] 4       4       0.5     0.002   0.25    0.5     32      0.002   4      </span></span>
+<span><span class="co">#  [91] 0.0625  256     4       4       2       2       0.0625  0.125   0.5    </span></span>
-<span><span class="co"># [100] 8</span></span></code></pre></div>
+<span><span class="co"># [100] 4</span></span></code></pre></div>
 <div class="sourceCode" id="cb37"><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>
@@ -1244,10 +1244,10 @@ Longest: 24</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 &lt;disk&gt;</span></span>
-<span><span class="co">#   [1] 19 23 20 29 19 24 18 31 30 31 19 19 28 25 19 20 27 20 20 30 22 30 25 27 24</span></span>
+<span><span class="co">#   [1] 29 24 25 24 31 25 20 22 25 17 19 29 29 27 31 21 23 23 29 17 25 21 25 29 31</span></span>
-<span><span class="co">#  [26] 23 29 17 19 23 29 24 26 24 28 17 24 23 22 19 31 26 25 19 23 21 24 28 20 20</span></span>
+<span><span class="co">#  [26] 20 23 23 20 24 27 22 18 30 21 22 21 28 27 19 24 22 19 30 29 20 17 19 25 19</span></span>
-<span><span class="co">#  [51] 26 27 30 27 18 28 27 17 24 31 27 28 24 23 31 26 17 30 24 23 22 24 29 31 30</span></span>
+<span><span class="co">#  [51] 19 24 26 21 21 27 24 22 21 30 31 29 25 19 24 25 24 25 20 26 28 20 20 19 27</span></span>
-<span><span class="co">#  [76] 31 19 18 29 27 28 18 17 30 31 25 24 19 31 27 18 24 20 26 19 17 31 27 29 31</span></span></code></pre></div>
+<span><span class="co">#  [76] 22 22 24 31 24 22 28 22 22 23 26 17 28 18 28 23 22 26 26 21 25 31 22 31 31</span></span></code></pre></div>
 <div class="sourceCode" id="cb43"><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>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -314,19 +314,19 @@ Unique: 2</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          I         S            R          I            R            I</span></span>
+<span><span class="co"># 1          S         I            I          R            S            R</span></span>
-<span><span class="co"># 2          S         S            S          I            R            S</span></span>
+<span><span class="co"># 2          R         S            S          R            S            I</span></span>
-<span><span class="co"># 3          S         S            I          R            I            I</span></span>
+<span><span class="co"># 3          I         I            R          R            S            R</span></span>
-<span><span class="co"># 4          I         I            R          R            R            S</span></span>
+<span><span class="co"># 4          S         I            R          I            I            I</span></span>
-<span><span class="co"># 5          S         S            R          I            I            R</span></span>
+<span><span class="co"># 5          R         R            I          I            R            I</span></span>
-<span><span class="co"># 6          S         S            R          I            S            R</span></span>
+<span><span class="co"># 6          R         R            R          I            S            S</span></span>
 <span><span class="co">#   kanamycin</span></span>
 <span><span class="co"># 1         S</span></span>
-<span><span class="co"># 2         I</span></span>
+<span><span class="co"># 2         S</span></span>
-<span><span class="co"># 3         R</span></span>
+<span><span class="co"># 3         I</span></span>
 <span><span class="co"># 4         R</span></span>
-<span><span class="co"># 5         S</span></span>
+<span><span class="co"># 5         I</span></span>
-<span><span class="co"># 6         S</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">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@@ -357,40 +357,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3206</td>
+<td align="right">3261</td>
-<td align="right">64.12%</td>
+<td align="right">65.22%</td>
-<td align="right">3206</td>
+<td align="right">3261</td>
-<td align="right">64.12%</td>
+<td align="right">65.22%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">996</td>
+<td align="right">959</td>
-<td align="right">19.92%</td>
+<td align="right">19.18%</td>
-<td align="right">4202</td>
+<td align="right">4220</td>
-<td align="right">84.04%</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">441</td>
+<td align="right">452</td>
-<td align="right">8.82%</td>
+<td align="right">9.04%</td>
-<td align="right">4643</td>
+<td align="right">4672</td>
-<td align="right">92.86%</td>
+<td align="right">93.44%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">256</td>
+<td align="right">228</td>
-<td align="right">5.12%</td>
+<td align="right">4.56%</td>
-<td align="right">4899</td>
+<td align="right">4900</td>
-<td align="right">97.98%</td>
+<td align="right">98.00%</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">100</td>
-<td align="right">2.02%</td>
+<td align="right">2.00%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -162,7 +162,7 @@
      <img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1>
                        <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
-            <h4 data-toc-skip class="date">10 October 2022</h4>
+            <h4 data-toc-skip class="date">11 October 2022</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>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -161,7 +161,7 @@
  <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">10 October 2022</h4>
+            <h4 data-toc-skip class="date">11 October 2022</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>
@@ -177,7 +177,7 @@
 </h2>
 <p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 10 October 2022 19:40:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<p>It was last updated on 11 October 2022 08:55:02 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
@@ -449,7 +449,7 @@
 </h2>
 <p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 10 October 2022 19:40:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 11 October 2022 08:55:02 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@@ -622,7 +622,7 @@
 </h2>
 <p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 10 October 2022 19:40:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 11 October 2022 08:55:02 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@@ -754,7 +754,7 @@
 </h2>
 <p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 10 October 2022 19:40:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<p>It was last updated on 11 October 2022 08:55:02 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
@@ -913,7 +913,7 @@
 </h2>
 <p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 10 October 2022 19:40:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
+<p>It was last updated on 11 October 2022 08:55:02 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
@@ -1185,7 +1185,7 @@
 </h2>
 <p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 10 October 2022 19:40:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
+<p>It was last updated on 11 October 2022 08:55:02 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@@ -1302,7 +1302,7 @@
 </h2>
 <p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
 <p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 10 October 2022 19:40:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
+<p>It was last updated on 11 October 2022 08:55:02 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
 <div class="section level3">
 <h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
 </h3>
@@ -1707,7 +1707,7 @@
 </h2>
 <p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
 <p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 10 October 2022 19:40:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
+<p>It was last updated on 11 October 2022 08:55:02 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
 <div class="section level3">
 <h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
 </h3>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -42,7 +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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -127,10 +127,10 @@
    </div>
    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="1.8.2.9013" id="amr-1829013">AMR 1.8.2.9013<a class="anchor" aria-label="anchor" href="#amr-1829013"></a></h2>
+<h2 class="pkg-version" data-toc-text="1.8.2.9014" id="amr-1829014">AMR 1.8.2.9014<a class="anchor" aria-label="anchor" href="#amr-1829014"></a></h2>
 <p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
 <div class="section level4">
-<h4 id="breaking-1-8-2-9013">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9013"></a></h4>
+<h4 id="breaking-1-8-2-9014">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9014"></a></h4>
 <ul><li>Removed all species of the taxonomic kingdom Chromista 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>
@@ -140,7 +140,7 @@
 <li>The <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> now count 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></div>
 <div class="section level4">
-<h4 id="new-1-8-2-9013">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9013"></a></h4>
+<h4 id="new-1-8-2-9014">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9014"></a></h4>
 <ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
 <li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus internally all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).<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>
@@ -157,7 +157,7 @@
 <li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
 </ul></div>
 <div class="section level4">
-<h4 id="changed-1-8-2-9013">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9013"></a></h4>
+<h4 id="changed-1-8-2-9014">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9014"></a></h4>
 <ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
 <li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
 <li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> 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>
@@ -183,7 +183,7 @@
 <li>Fix for using <code><a href="../reference/as.ab.html">as.ab()</a></code> on <code>NA</code> values</li>
 </ul></div>
 <div class="section level4">
-<h4 id="other-1-8-2-9013">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9013"></a></h4>
+<h4 id="other-1-8-2-9014">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9014"></a></h4>
 <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 and Anton Mymrikov 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>
@@ -11,7 +11,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2022-10-10T19:43Z
+last_built: 2022-10-11T08:57Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -178,7 +178,7 @@
 <span class="r-in"><span>             <span class="co"># 'antibiotics' data set, such as 'group':</span></span></span>
 <span class="r-in"><span>             group <span class="op">=</span> <span class="st">"Test Group"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Added one record to internal `antibiotics` data set.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Added one record to the internal `antibiotics` data set.</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># "test" is now a new antibiotic:</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"test"</span><span class="op">)</span></span></span>
@@ -235,6 +235,34 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># Add Co-fluampicil, which is one of the many J01CR50 codes, see</span></span></span>
 <span class="r-in"><span><span class="co"># https://www.whocc.no/ddd/list_of_ddds_combined_products/</span></span></span>
 <span class="r-in"><span><span class="fu">add_custom_antimicrobials</span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"COFLU"</span>,</span></span>
 <span class="r-in"><span>             name <span class="op">=</span> <span class="st">"Co-fluampicil"</span>,</span></span>
 <span class="r-in"><span>             atc <span class="op">=</span> <span class="st">"J01CR50"</span>,</span></span>
 <span class="r-in"><span>             group <span class="op">=</span> <span class="st">"Beta-lactams/penicillines"</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 Added one record to the internal `antibiotics` data set.</span>
 <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"Co-fluampicil"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "J01CR50"</span>
 <span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"J01CR50"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Co-fluampicil"</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># even antibiotic selectors work</span></span></span>
 <span class="r-in"><span><span class="va">x</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>random_column <span class="op">=</span> <span class="st">"test"</span>,</span></span>
 <span class="r-in"><span>               coflu <span class="op">=</span> <span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"S"</span><span class="op">)</span>,</span></span>
 <span class="r-in"><span>               ampicillin <span class="op">=</span> <span class="fu"><a href="as.rsi.html">as.rsi</a></span><span class="op">(</span><span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">x</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   random_column coflu ampicillin</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1          test     S          R</span>
 <span class="r-in"><span><span class="va">x</span><span class="op">[</span>, <span class="fu"><a href="antibiotic_class_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For `betalactams()` using columns 'coflu' (co-fluampicil) and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   'ampicillin'</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   coflu ampicillin</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> 1     S          R</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -190,16 +190,16 @@
 <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  1997-02-21  25  25.63288          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1961-11-04  60  60.93425         38</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1981-01-28  41  41.69863         18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1959-05-25  63  63.38082         40</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1984-04-02  38  38.52329         15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1932-03-21  90  90.55890         67</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1945-03-25  77  77.54521         54</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1943-08-14  79  79.15890         56</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1964-10-04  58  58.01644         35</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1980-11-06  41  41.92877         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1955-05-14  67  67.40822         44</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1962-10-20  59  59.97534         37</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1942-02-07  80  80.67123         57</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-09-02  82  82.10685         59</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1970-05-17  52  52.40000         29</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1953-11-03  68  68.93699         46</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1972-05-11  50  50.41644         27</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1965-10-11  57  57.00000         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-03-11  36  36.58356         13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1979-06-17  43  43.31781         20</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -484,16 +484,16 @@ 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 × 13</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_input   ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</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> 2022-10-10 <span style="color: #949494;">19:43:35</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> 2022-10-11 <span style="color: #949494;">08:57:29</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> 2022-10-10 <span style="color: #949494;">19:43:35</span>     1 AMP        AMP         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-11 <span style="color: #949494;">08:57:29</span>     1 AMP        AMP         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-10 <span style="color: #949494;">19:43:35</span>     1 CIP        CIP         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-11 <span style="color: #949494;">08:57:29</span>     1 CIP        CIP         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-10 <span style="color: #949494;">19:43:36</span>     1 GEN        GEN         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-11 <span style="color: #949494;">08:57:29</span>     1 GEN        GEN         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-10 <span style="color: #949494;">19:43:36</span>     1 TOB        TOB         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-11 <span style="color: #949494;">08:57:29</span>     1 TOB        TOB         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-10 <span style="color: #949494;">19:43:36</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> 2022-10-11 <span style="color: #949494;">08:57:30</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> 2022-10-10 <span style="color: #949494;">19:43:37</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> 2022-10-11 <span style="color: #949494;">08:57:30</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> 2022-10-10 <span style="color: #949494;">19:43:37</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> 2022-10-11 <span style="color: #949494;">08:57:30</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> 2022-10-10 <span style="color: #949494;">19:43:37</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> 2022-10-11 <span style="color: #949494;">08:57:30</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> 2022-10-10 <span style="color: #949494;">19:43:37</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> 2022-10-11 <span style="color: #949494;">08:57:30</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, 6 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;">#   breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   and abbreviated variable names ¹ab_considered, ²mo_input, ³mo_considered,</span></span>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -177,39 +177,40 @@
 <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] 48 59 29 38 17 25 17 65  4 35  7  6 23 10 54 12 27 58 52 44 11 61 29 42  8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 47 52 21 26 19 32 19  8 51 55 23 43 55  7  6 20 57 21 45 24 53 34  5 16 15</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 12 45 30 11 21 14 60 27 28 14 54 17 30 61 39  8 53 34 65  1  5 45 47 51 18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 11 39 26 10  3 13 23 41 29 18 60  4 57 37 63 38 42 15  7 13 60 32 14 50 24</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 41 36 59 59 59 47  4 11  1 59 42  2 30 38 67 46 18 34  8 63 40  6 22 60 25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 10  1 21 52  1  9 27 49 43 40  4 26 43 56 16 28 19 36 20 13 59 54 51 43 64</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 68 11 23 30 16 37 40 31 43 23 21 27 21 57 46 54 35 60 44  1 43 45  2 37 59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 52 57 49 46 61 29 13 38 55 16 60 15 26 30 57 21 14 44 28 22 61 56 19 28 25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 67 67 68 32 26  1 36 13 57 51 49 45 38 19 62  6 69 40  9 66 14 55 40 61  4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 51 34 37  5 37 31 16  2  6  2 55 46  5  6 23 55 10 61 13 20  1 16 58 64 30</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 28 15 58 63 65 39 49 31 11 26 65 27 13 21 68 50 14  3  4 42 24 20 22 59 61</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 43 26 10  1 30 21 62 12 14 10 55 16 64 46  6  8 53 48 57 43 35 33 27 52 56</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 64 16 60 48 51 29  7 25 41 16 48 33 66 67 61 63 43 18 59  2 39 49 64 14 51</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 57 56 33 32 13 20 26 11 24  6  8 61  5 25 37 42  7 19 58 32 28  9 17 63 62</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 52 10 40  4 61  6 30  4 56 10 59 68 31 62 65 60  1 24 65 31  2 22 15  5 53</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 58 22 18 39 34 34 64  5 42 63 24 52 13 43  3 24  1 34 56 20 62 14 16 32 56</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 FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE FALSE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61]  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [109]  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [121]  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [133]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [145]  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [169]  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [193]  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE  TRUE  TRUE FALSE  TRUE  TRUE 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: 1 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 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>   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: #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> 2002-06-22 FD8039     75 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;">1</span> 2002-11-04 304347     62 M      Clinical  B_STRPT_PNMN S     NA    NA    S    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-11-11 D80753     74 F      Outpatie… B_STPHY_CONS 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>
@@ -245,16 +246,16 @@
 <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> 660761  2013-03-05 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B43936  2013-05-16 A         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 992282  2015-11-17 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> AC8303  2014-10-20 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 445249  2008-06-10 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E19253  2006-08-22 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 566040  2010-12-14 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D81577  2008-05-12 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 425433  2005-07-11 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> FD439C  2006-03-18 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 92F410  2007-03-26 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B26404  2010-01-08 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B338BC  2005-07-02 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D99170  2006-03-13 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 423709  2017-01-30 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 955371  2003-12-12 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 390178  2002-08-28 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C40150  2014-03-05 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 16F0F7  2010-01-17 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 557266  2015-10-12 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>
@@ -266,19 +267,19 @@
 <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 [185]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [186]</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>    <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 2013-03-05 660761          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU      2013-05-16 B43936          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU      2015-11-17 992282          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2014-10-20 AC8303          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2008-06-10 445249          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2006-08-22 E19253          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU      2010-12-14 566040          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2008-05-12 D81577          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2005-07-11 425433          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2006-03-18 FD439C          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2007-03-26 92F410          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical 2010-01-08 B26404          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2005-07-02 B338BC          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU      2006-03-13 D99170          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2017-01-30 423709          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU      2003-12-12 955371          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2002-08-28 390178          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2014-03-05 C40150          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2010-01-17 16F0F7          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2015-10-12 557266          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>
@@ -293,9 +294,9 @@
 <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          111             14            55            71</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          110             15            55            73</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                56             12            34            41</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                59             14            33            42</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         18              7            14            17</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         17             10            15            15</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>
@@ -326,18 +327,18 @@
 <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 [193]</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> 660761  B_STRPT_DYSG Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> B43936  B_CRYNB       ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 992282  B_STRPT_PNMN ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> AC8303  B_STPHY_HMLY  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 445249  B_STPHY_CONS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E19253  B_STPHY_CONS  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 566040  B_STPHY_CONS ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> D81577  B_HMPHL_INFL  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 425433  B_ESCHR_COLI Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> FD439C  B_STPHY_CONS  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 92F410  B_PROTS_MRBL Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> B26404  B_STPHY_EPDR  Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> B338BC  B_ENTRC      Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D99170  B_STPHY_EPDR  ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 423709  B_ESCHR_COLI Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 955371  B_STPHY_AURS  ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 390178  B_STRPT_SLVR Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> C40150  B_CTBCTR_ACNS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 16F0F7  B_STPHY_AURS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 557266  B_STPHY_HMLY  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>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -167,9 +167,9 @@
    <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] 3.019693</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.043154</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] 0.00504598</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.0150379</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -195,10 +195,10 @@
    <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>
 <span class="r-in"><span><span class="va">x</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16    0.5   32    &gt;=128 64    16    4     1     0.25  0.025</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] &lt;=0.01 0.025  4      0.0625 1      4      16     0.5    0.025  8     </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]  0.514153850 -0.750868464  0.767158312  1.273167238  1.020162775</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.4081939 -1.0706595  0.7988846 -0.7331250  0.2882147  0.7988846</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6]  0.514153850  0.008144924 -0.497864001 -1.003872926 -1.844335559</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  1.3095545  0.0328798 -1.0706595  1.0542196</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>
@@ -208,38 +208,38 @@
 <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   64      1    8     4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    4 &lt;=0.025  &lt;=1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B  &lt;=1   0.25    4     4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    2   0.125    2    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C  &lt;=1      2    8     8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C   32 &lt;=0.025   16    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    8   0.25    8     1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    2       2  &lt;=1    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    2    &gt;=4    2     1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E   32       1    8  0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F   64      1    2     1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    1   0.125    2    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G   64 0.0625  &lt;=1     4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    4     0.5   16    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H   64   0.25    8     4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    2       1  &lt;=1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16      1    2 &lt;=0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    8   0.125  &lt;=1    4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    4   0.25    4     4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    1     &gt;=4    4   16</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]  0.78252639 -0.31251848  0.52307535 -0.17070133 -0.26327320 -0.05158778</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.77937382 -0.36771977  0.74573282 -0.12706157  0.43836890 -0.50465041</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.45702796  0.50350189 -0.43776038 -0.11623450</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.41987005 -0.39451457 -0.07597364  0.64532202</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-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> 7   G   64 0.0625  &lt;=1     4  -0.45702796</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    4 &lt;=0.025  &lt;=1    1  -0.77937382</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16      1    2 &lt;=0.5  -0.43776038</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    1   0.125    2    2  -0.50465041</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B  &lt;=1   0.25    4     4  -0.31251848</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    2       1  &lt;=1    1  -0.39451457</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    2    &gt;=4    2     1  -0.26327320</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    2   0.125    2    2  -0.36771977</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    8   0.25    8     1  -0.17070133</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    2       2  &lt;=1    2  -0.12706157</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    4   0.25    4     4  -0.11623450</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    8   0.125  &lt;=1    4  -0.07597364</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F   64      1    2     1  -0.05158778</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    4     0.5   16    2   0.41987005</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H   64   0.25    8     4   0.50350189</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E   32       1    8  0.5   0.43836890</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C  &lt;=1      2    8     8   0.52307535</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    1     &gt;=4    4   16   0.64532202</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A   64      1    8     4   0.78252639</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C   32 &lt;=0.025   16    8   0.74573282</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>
@@ -251,17 +251,17 @@
 <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  &lt;=1      2    8     8   0.52307535 0.00000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C   32 &lt;=0.025   16    8   0.74573282  0.0000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   H   64   0.25    8     4   0.50350189 0.01957347</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   J    1     &gt;=4    4   16   0.64532202  0.1004108</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   A   64      1    8     4   0.78252639 0.25945103</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   E   32       1    8  0.5   0.43836890  0.3073639</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   F   64      1    2     1  -0.05158778 0.57466313</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   G    4     0.5   16    2   0.41987005  0.3258628</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   J    4   0.25    4     4  -0.11623450 0.63930986</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   I    8   0.125  &lt;=1    4  -0.07597364  0.8217065</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   D    8   0.25    8     1  -0.17070133 0.69377669</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   D    2       2  &lt;=1    2  -0.12706157  0.8727944</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   E    2    &gt;=4    2     1  -0.26327320 0.78634856</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   B    2   0.125    2    2  -0.36771977  1.1134526</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   B  &lt;=1   0.25    4     4  -0.31251848 0.83559383</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    2       1  &lt;=1    1  -0.39451457  1.1402474</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16      1    2 &lt;=0.5  -0.43776038 0.96083573</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   F    1   0.125    2    2  -0.50465041  1.2503832</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  G   64 0.0625  &lt;=1     4  -0.45702796 0.98010332</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  A    4 &lt;=0.025  &lt;=1    1  -0.77937382  1.5251066</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>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -178,42 +178,42 @@
    <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">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.0625  8       0.005   1       &lt;=0.002 0.25    2       2       0.005  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 32     8      0.001  0.01   0.002  0.01   4      64     0.001  1     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.0625  0.025   128     32      128     4       0.25    &lt;=0.002 0.005  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [11] &gt;=256  0.0625 64     32     2      0.01   128    0.002  0.125  4     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 128     &lt;=0.002 2       &lt;=0.002 0.025   0.0625  256    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 4      2      128    128    128   </span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 30 36 49 27 28 21 45 21 47 48 20  6 47 11 47 33 26 11 48 36 23 46  8 47 33</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 17  8 25 21 29 42 27 20 13 48 11 35 32 36 30 34 12 19 43 42 15 46 46 34 48</span>
 <span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;rsi&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] S R S S S S S I S S R R S S S S I R I S I R R S I</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] I S R S I S R I S R S S R R I I R R I R S I S S I</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.25   0.0625 4      8      4      0.5    64     0.002  64     2     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 64      16      &lt;=0.001 &lt;=0.001 0.002   &gt;=256   &gt;=256   0.01    0.125  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 0.01   &gt;=128  64     0.25   16     0.002  0.025  0.125  64     0.01  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25    &gt;=256   0.005   0.5     0.01    0.5     2       16      64     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.002  16     1      4      1     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 64      0.125   1       128     0.025   32      128    </span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16   16   &gt;=32 2    16   8    &gt;=32 8    4    &gt;=32 2    8    2    4    8   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] &lt;=1 8   16  4   &lt;=1 2   16  8   8   16  &lt;=1 8   &lt;=1 &lt;=1 4   2   4   2   2  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [16] 1    8    2    1    4    16   &gt;=32 &gt;=32 16   4   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [20] 2   4   4   8   &lt;=1 2  </span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 1       &lt;=0.125 &gt;=8     2       1       1       4       &lt;=0.125 1      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.25  0.25  16    8     4     4     1     2     8     0.125 1     4    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25    &lt;=0.125 0.25    4       0.5     0.25    0.5     0.5     2      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 4     0.25  1     4     0.125 0.125 1     4     16    2     0.5   8    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [19] &lt;=0.125 &gt;=8     &lt;=0.125 4       2       &gt;=8     0.5    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 4    </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 43 23 12 45 35 12 16 32 44 17 18 47 48 25 48 17 50 22 29 35 46 50 49 24 40</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 17 40 22 46 19 41 16 27 42 10 39 25 10 26 12 36 50 20 33 11 49 43 21  8 20</span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 14 13 16 11 13 12 16 13 16 11 14 17 16 14 13 17 13 14 16 13 15 15 15 14 11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16 12 13 17 17 15 17 12 15 16 17 15 17 14 14 17 15 14 13 13 15 14 14 12 14</span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 19 21 19 26 17 25 19 27 19 23 23 22 17 23 25 19 19 25 21 18 27 18 15 18 18</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16 21 15 19 21 19 15 18 15 19 24 16 25 16 23 17 15 21 19 19 21 23 27 21 16</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
    </div>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -12,7 +12,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <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 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
    <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">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.02401056</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04641902</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -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="">1.8.2.9013</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -1 +1 @@
-[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(   patient_id = patients,   gender = c(     rep(\"M\", 135),     rep(\"F\", 125)   ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(   \"Escherichia coli\", \"Staphylococcus aureus\",   \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated
+[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(   patient_id = patients,   gender = c(     rep(\"M\", 135),     rep(\"F\", 125)   ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(   \"Escherichia coli\", \"Staphylococcus aureus\",   \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated
		`@@ -1 +1 @@`
			[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated				[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner) # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame( patient_id = patients, gender = c( rep(\"M\", 135), rep(\"F\", 125) ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c( \"Escherichia coli\", \"Staphylococcus aureus\", \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated