Built site for AMR: 1.8.2.9016@76bcd35

2024-12-26 18:46:13 +01:00 · 2022-10-14 11:08:40 +00:00 · 2022-10-14 11:08:40 +00:00 · 1a10d0f4ee
commit 1a10d0f4ee
parent a1d8ec7d4a
94 changed files with 497 additions and 493 deletions
--- a/404.html
+++ b/404.html
@ -36,7 +36,7 @@
    <a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/AMR.html
+++ b/articles/AMR.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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">11 October 2022</h4>
+            <h4 data-toc-skip class="date">14 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 11 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 14 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">2022-10-11</td>
+<td align="center">2022-10-14</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">2022-10-11</td>
+<td align="center">2022-10-14</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">2022-10-11</td>
+<td align="center">2022-10-14</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -325,69 +325,69 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2015-02-02</td>
+<td align="center">2015-11-18</td>
-<td align="center">E3</td>
+<td align="center">X2</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Klebsiella pneumoniae</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>
 </tr>
 <tr class="even">
 <td align="center">2015-12-29</td>
 <td align="center">W4</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">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
-<tr class="odd">
+<tr class="even">
-<td align="center">2013-03-05</td>
+<td align="center">2014-12-18</td>
-<td align="center">E4</td>
+<td align="center">I9</td>
 <td align="center">Hospital C</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">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
-<tr class="even">
+<tr class="odd">
-<td align="center">2016-02-19</td>
+<td align="center">2015-09-24</td>
-<td align="center">O7</td>
+<td align="center">V4</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital A</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
-<tr class="odd">
+<tr class="even">
-<td align="center">2016-03-08</td>
+<td align="center">2012-11-26</td>
-<td align="center">M10</td>
+<td align="center">E7</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="odd">
 <td align="center">2010-08-28</td>
 <td align="center">A7</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="even">
-<td align="center">2016-12-01</td>
+<td align="center">2016-05-06</td>
-<td align="center">U5</td>
+<td align="center">V5</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">I</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">F</td>
 </tr>
 </tbody>
@ -422,16 +422,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,418</td>
+<td align="right">10,324</td>
-<td align="right">52.09%</td>
+<td align="right">51.62%</td>
-<td align="right">10,418</td>
+<td align="right">10,324</td>
-<td align="right">52.09%</td>
+<td align="right">51.62%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,582</td>
+<td align="right">9,676</td>
-<td align="right">47.91%</td>
+<td align="right">48.38%</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 10,684 'phenotype-based' first isolates (53.4% of total where a</span></span>
+<span><span class="co"># =&gt; Found 10,765 'phenotype-based' first isolates (53.8% of total where a</span></span>
 <span><span class="co">#    microbial ID was available)</span></span></code></pre></div>
-<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>
+<p>So only 53.8% 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>
@ -499,10 +499,10 @@ 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 10,684 isolates for analysis. Now our data looks like:</p>
+<p>So we end up with 10,765 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">
+<table style="width:100%;" class="table">
 <colgroup>
 <col width="2%">
 <col width="9%">
@ -516,7 +516,7 @@ Longest: 1</p>
 <col width="6%">
 <col width="11%">
 <col width="12%">
-<col width="7%">
+<col width="9%">
 <col width="5%">
 </colgroup>
 <thead><tr class="header">
@ -538,9 +538,25 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="left">1</td>
-<td align="center">2015-02-02</td>
+<td align="center">2015-11-18</td>
-<td align="center">E3</td>
+<td align="center">X2</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital A</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Klebsiella</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="center">2014-12-18</td>
 <td align="center">I9</td>
 <td align="center">Hospital C</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -552,14 +568,14 @@ Longest: 1</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
+<tr class="odd">
-<td align="left">4</td>
+<td align="left">3</td>
-<td align="center">2016-02-19</td>
+<td align="center">2015-09-24</td>
-<td align="center">O7</td>
+<td align="center">V4</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital A</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
@ -568,30 +584,14 @@ Longest: 1</p>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
+<tr class="even">
-<td align="left">6</td>
+<td align="left">4</td>
-<td align="center">2016-12-01</td>
+<td align="center">2012-11-26</td>
-<td align="center">U5</td>
+<td align="center">E7</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">I</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>
@ -601,14 +601,14 @@ Longest: 1</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="left">8</td>
+<td align="left">6</td>
-<td align="center">2015-04-05</td>
+<td align="center">2016-05-06</td>
-<td align="center">R1</td>
+<td align="center">V5</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">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
@ -617,14 +617,14 @@ Longest: 1</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">9</td>
+<td align="left">7</td>
-<td align="center">2010-02-04</td>
+<td align="center">2011-03-21</td>
-<td align="center">B3</td>
+<td align="center">N1</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</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">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
@ -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: 10,684<br>
+Length: 10,765<br>
-Available: 10,684 (100.0%, NA: 0 = 0.0%)<br>
+Available: 10,765 (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">4,678</td>
+<td align="right">4,655</td>
-<td align="right">43.79%</td>
+<td align="right">43.24%</td>
-<td align="right">4,678</td>
+<td align="right">4,655</td>
-<td align="right">43.79%</td>
+<td align="right">43.24%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,715</td>
+<td align="right">2,771</td>
-<td align="right">25.41%</td>
+<td align="right">25.74%</td>
-<td align="right">7,393</td>
+<td align="right">7,426</td>
-<td align="right">69.20%</td>
+<td align="right">68.98%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,108</td>
+<td align="right">2,156</td>
-<td align="right">19.73%</td>
+<td align="right">20.03%</td>
-<td align="right">9,501</td>
+<td align="right">9,582</td>
-<td align="right">88.93%</td>
+<td align="right">89.01%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
 <td align="right">1,183</td>
-<td align="right">11.07%</td>
+<td align="right">10.99%</td>
-<td align="right">10,684</td>
+<td align="right">10,765</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@ -716,14 +716,14 @@ Longest: 24</p>
 <col width="9%">
 <col width="9%">
 <col width="9%">
-<col width="11%">
+<col width="10%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="11%">
+<col width="12%">
 <col width="9%">
 <col width="5%">
 </colgroup>
@ -744,57 +744,42 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2016-12-01</td>
+<td align="center">2016-02-22</td>
-<td align="center">U5</td>
+<td align="center">Y6</td>
 <td align="center">Hospital D</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="center">B_STPHY_AURS</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
-<td align="center">Gram-negative</td>
+<td align="center">Gram-positive</td>
-<td align="center">Escherichia</td>
+<td align="center">Staphylococcus</td>
-<td align="center">coli</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2012-09-03</td>
+<td align="center">2012-04-22</td>
-<td align="center">O8</td>
+<td align="center">E8</td>
 <td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</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">F</td>
+<td align="center">R</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="center">2015-04-26</td>
+<td align="center">2010-08-20</td>
-<td align="center">W2</td>
+<td align="center">F1</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">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">2012-08-07</td>
 <td align="center">I8</td>
 <td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">R</td>
+<td align="center">I</td>
-<td align="center">R</td>
+<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
@ -803,13 +788,43 @@ Longest: 24</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
+<tr class="even">
-<td align="center">2012-09-19</td>
+<td align="center">2016-05-20</td>
-<td align="center">Y3</td>
+<td align="center">X2</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2017-02-25</td>
 <td align="center">Y7</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2016-01-31</td>
 <td align="center">Y4</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">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
@ -818,21 +833,6 @@ 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>
@ -854,34 +854,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2191</td>
+<td align="center">2244</td>
-<td align="center">130</td>
+<td align="center">103</td>
-<td align="center">2357</td>
+<td align="center">2308</td>
-<td align="center">4678</td>
+<td align="center">4655</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3377</td>
+<td align="center">3412</td>
-<td align="center">187</td>
+<td align="center">156</td>
-<td align="center">1114</td>
+<td align="center">1087</td>
-<td align="center">4678</td>
+<td align="center">4655</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3413</td>
+<td align="center">3414</td>
 <td align="center">0</td>
-<td align="center">1265</td>
+<td align="center">1241</td>
-<td align="center">4678</td>
+<td align="center">4655</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4126</td>
+<td align="center">4073</td>
 <td align="center">0</td>
-<td align="center">552</td>
+<td align="center">582</td>
-<td align="center">4678</td>
+<td align="center">4655</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
@ -894,9 +894,9 @@ Longest: 24</p>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">940</td>
+<td align="center">960</td>
-<td align="center">40</td>
+<td align="center">38</td>
-<td align="center">203</td>
+<td align="center">185</td>
 <td align="center">1183</td>
 </tr>
 </tbody>
@ -920,34 +920,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4126</td>
+<td align="center">4073</td>
 <td align="center">0</td>
-<td align="center">552</td>
+<td align="center">582</td>
-<td align="center">4678</td>
+<td align="center">4655</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1071</td>
+<td align="center">1070</td>
 <td align="center">0</td>
-<td align="center">112</td>
+<td align="center">113</td>
 <td align="center">1183</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2406</td>
+<td align="center">2442</td>
 <td align="center">0</td>
-<td align="center">309</td>
+<td align="center">329</td>
-<td align="center">2715</td>
+<td align="center">2771</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">2108</td>
+<td align="center">2156</td>
-<td align="center">2108</td>
+<td align="center">2156</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] 0.5446462</span></span></code></pre></div>
+<span><span class="co"># [1] 0.5452856</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">0.5423889</td>
+<td align="center">0.5467334</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5451578</td>
+<td align="center">0.5472356</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5370259</td>
+<td align="center">0.5282083</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5528979</td>
+<td align="center">0.5523125</td>
 </tr>
 </tbody>
 </table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5423889</td>
+<td align="center">0.5467334</td>
-<td align="center">3173</td>
+<td align="center">3199</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5451578</td>
+<td align="center">0.5472356</td>
-<td align="center">3676</td>
+<td align="center">3726</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5370259</td>
+<td align="center">0.5282083</td>
-<td align="center">1661</td>
+<td align="center">1613</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5528979</td>
+<td align="center">0.5523125</td>
-<td align="center">2174</td>
+<td align="center">2227</td>
 </tr>
 </tbody>
 </table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7618640</td>
+<td align="center">0.7664876</td>
-<td align="center">0.8820009</td>
+<td align="center">0.8749731</td>
-<td align="center">0.9764857</td>
+<td align="center">0.9735768</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8284024</td>
+<td align="center">0.8436179</td>
-<td align="center">0.9053254</td>
+<td align="center">0.9044801</td>
-<td align="center">0.9788673</td>
+<td align="center">0.9873204</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7893186</td>
+<td align="center">0.7971851</td>
-<td align="center">0.8861878</td>
+<td align="center">0.8812703</td>
-<td align="center">0.9804788</td>
+<td align="center">0.9765428</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5398482</td>
+<td align="center">0.5343228</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5398482</td>
+<td align="center">0.5343228</td>
 </tr>
 </tbody>
 </table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">54.2%</td>
+<td align="right">54.7%</td>
-<td align="right">27.7%</td>
+<td align="right">27.4%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">54.5%</td>
+<td align="right">54.7%</td>
-<td align="right">25.9%</td>
+<td align="right">26.0%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">53.7%</td>
+<td align="right">52.8%</td>
-<td align="right">27.5%</td>
+<td align="right">24.9%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">55.3%</td>
+<td align="right">55.2%</td>
-<td align="right">26.3%</td>
+<td align="right">26.5%</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] 8       32      0.125   4       0.0625  32      0.5     0.01    8      </span></span>
+<span><span class="co">#   [1] 32      &lt;=0.001 0.025   &lt;=0.001 4       0.125   0.01    0.002   32     </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">#  [10] 16      64      4       &lt;=0.001 0.01    16      0.01    64      64     </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">#  [19] 256     0.0625  0.002   0.005   0.125   0.025   32      128     0.5    </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">#  [28] 16      0.5     32      0.005   32      0.01    2       0.125   128    </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">#  [37] 64      8       0.002   0.01    2       &lt;=0.001 0.005   64      0.0625 </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">#  [46] &lt;=0.001 8       0.5     64      32      0.5     0.005   0.01    &lt;=0.001</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">#  [55] 16      0.5     8       0.0625  0.125   128     16      0.5     0.002  </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">#  [64] 16      8       128     128     4       256     0.5     8       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">#  [73] 16      0.025   2       1       16      0.005   0.01    16      1      </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">#  [82] 0.25    0.01    0.002   0.0625  0.005   128     64      128     8      </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">#  [91] 0.002   1       8       8       0.25    0.125   16      2       0.5    </span></span>
-<span><span class="co"># [100] 4</span></span></code></pre></div>
+<span><span class="co"># [100] 256</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] 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">#   [1] 29 31 21 24 20 24 29 22 21 20 19 25 17 30 30 28 25 27 23 20 18 22 31 25 24</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">#  [26] 29 25 21 29 20 22 23 27 30 23 22 30 22 18 20 23 27 25 23 21 21 24 21 29 26</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">#  [51] 21 26 26 24 30 24 30 25 23 30 20 29 22 17 20 18 21 22 27 29 30 30 30 21 30</span></span>
-<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>
+<span><span class="co">#  [76] 26 19 28 26 22 25 19 21 23 29 17 23 23 24 26 28 17 17 30 23 29 31 19 19 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>
--- a/articles/AMR_files/figure-html/disk_plots-1.png
+++ b/articles/AMR_files/figure-html/disk_plots-1.png
--- a/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
+++ b/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
--- a/articles/AMR_files/figure-html/mic_plots-1.png
+++ b/articles/AMR_files/figure-html/mic_plots-1.png
--- a/articles/AMR_files/figure-html/mic_plots-2.png
+++ b/articles/AMR_files/figure-html/mic_plots-2.png
--- a/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
+++ b/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
--- a/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
+++ b/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/MDR.html
+++ b/articles/MDR.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -314,18 +314,18 @@ 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          S         I            I          R            S            R</span></span>
+<span><span class="co"># 1          S         I            I          R            R            S</span></span>
-<span><span class="co"># 2          R         S            S          R            S            I</span></span>
+<span><span class="co"># 2          R         I            R          I            S            R</span></span>
-<span><span class="co"># 3          I         I            R          R            S            R</span></span>
+<span><span class="co"># 3          R         S            R          S            I            S</span></span>
-<span><span class="co"># 4          S         I            R          I            I            I</span></span>
+<span><span class="co"># 4          S         I            I          S            R            I</span></span>
-<span><span class="co"># 5          R         R            I          I            R            I</span></span>
+<span><span class="co"># 5          S         S            I          I            I            R</span></span>
-<span><span class="co"># 6          R         R            R          I            S            S</span></span>
+<span><span class="co"># 6          R         I            R          R            I            I</span></span>
 <span><span class="co">#   kanamycin</span></span>
-<span><span class="co"># 1         S</span></span>
+<span><span class="co"># 1         R</span></span>
 <span><span class="co"># 2         S</span></span>
 <span><span class="co"># 3         I</span></span>
-<span><span class="co"># 4         R</span></span>
+<span><span class="co"># 4         S</span></span>
-<span><span class="co"># 5         I</span></span>
+<span><span class="co"># 5         R</span></span>
 <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">
@ -357,40 +357,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3261</td>
+<td align="right">3186</td>
-<td align="right">65.22%</td>
+<td align="right">63.72%</td>
-<td align="right">3261</td>
+<td align="right">3186</td>
-<td align="right">65.22%</td>
+<td align="right">63.72%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">959</td>
+<td align="right">1014</td>
-<td align="right">19.18%</td>
+<td align="right">20.28%</td>
-<td align="right">4220</td>
+<td align="right">4200</td>
-<td align="right">84.40%</td>
+<td align="right">84.00%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">452</td>
+<td align="right">475</td>
-<td align="right">9.04%</td>
+<td align="right">9.50%</td>
-<td align="right">4672</td>
+<td align="right">4675</td>
-<td align="right">93.44%</td>
+<td align="right">93.50%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">228</td>
+<td align="right">233</td>
-<td align="right">4.56%</td>
+<td align="right">4.66%</td>
-<td align="right">4900</td>
+<td align="right">4908</td>
-<td align="right">98.00%</td>
+<td align="right">98.16%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">100</td>
+<td align="right">92</td>
-<td align="right">2.00%</td>
+<td align="right">1.84%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
--- a/articles/PCA.html
+++ b/articles/PCA.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/SPSS.html
+++ b/articles/SPSS.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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">11 October 2022</h4>
+            <h4 data-toc-skip class="date">14 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>
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/datasets.html
+++ b/articles/datasets.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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">11 October 2022</h4>
+            <h4 data-toc-skip class="date">14 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 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>It was last updated on 14 October 2022 11:03:47 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 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>It was last updated on 14 October 2022 11:03:47 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 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>It was last updated on 14 October 2022 11:03:47 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 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>It was last updated on 14 October 2022 11:03:47 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 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>It was last updated on 14 October 2022 11:03:47 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 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>It was last updated on 14 October 2022 11:03:47 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 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>
+<p>It was last updated on 14 October 2022 11:03:47 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 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>
+<p>It was last updated on 14 October 2022 11:03:47 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>
--- a/articles/index.html
+++ b/articles/index.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/resistance_predict.html
+++ b/articles/resistance_predict.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/welcome_to_AMR.html
+++ b/articles/welcome_to_AMR.html
@ -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="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/authors.html
+++ b/authors.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/index.html
+++ b/index.html
@ -42,7 +42,7 @@
    <a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/news/index.html
+++ b/news/index.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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="1.8.2.9014" id="amr-1829014">AMR 1.8.2.9014<a class="anchor" aria-label="anchor" href="#amr-1829014"></a></h2>
+<h2 class="pkg-version" data-toc-text="1.8.2.9016" id="amr-1829016">AMR 1.8.2.9016<a class="anchor" aria-label="anchor" href="#amr-1829016"></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-1-8-2-9014">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9014"></a></h4>
+<h4 id="breaking-1-8-2-9016">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9016"></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-1-8-2-9014">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9014"></a></h4>
+<h4 id="new-1-8-2-9016">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9016"></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-1-8-2-9014">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9014"></a></h4>
+<h4 id="changed-1-8-2-9016">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9016"></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-1-8-2-9014">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9014"></a></h4>
+<h4 id="other-1-8-2-9016">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9016"></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>
--- a/pkgdown.yml
+++ b/pkgdown.yml
@ -11,7 +11,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2022-10-11T08:57Z
+last_built: 2022-10-14T11:06Z
 urls:
  reference: https://msberends.github.io/AMR/reference
  article: https://msberends.github.io/AMR/articles
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/AMR.html
+++ b/reference/AMR.html
@ -62,7 +62,7 @@ Principal component analysis for AMR
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/Rplot005.png
+++ b/reference/Rplot005.png
--- a/reference/Rplot006.png
+++ b/reference/Rplot006.png
--- a/reference/Rplot007.png
+++ b/reference/Rplot007.png
--- a/reference/Rplot008.png
+++ b/reference/Rplot008.png
--- a/reference/Rplot009.png
+++ b/reference/Rplot009.png
--- a/reference/WHOCC.html
+++ b/reference/WHOCC.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/WHONET.html
+++ b/reference/WHONET.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ab_from_text.html
+++ b/reference/ab_from_text.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ab_property.html
+++ b/reference/ab_property.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.html
@ -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="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/age.html
+++ b/reference/age.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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  1961-11-04  60  60.93425         38</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1963-02-15  59  59.66027         36</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> 2  1979-08-05  43  43.19178         20</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> 3  1962-10-01  60  60.03562         37</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> 4  1990-03-08  32  32.60274          9</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> 5  1982-01-26  40  40.71507         17</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> 6  1954-02-09  68  68.67671         45</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> 7  1964-08-19  58  58.15342         35</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> 8  1938-04-08  84  84.51781         61</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> 9  1985-07-19  37  37.23836         14</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1979-06-17  43  43.31781         20</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1945-03-20  77  77.56986         54</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/age_groups.html
+++ b/reference/age_groups.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/antibiotic_class_selectors.html
+++ b/reference/antibiotic_class_selectors.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/antibiotics.html
+++ b/reference/antibiotics.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.ab.html
+++ b/reference/as.ab.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.disk.html
+++ b/reference/as.disk.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.mic.html
+++ b/reference/as.mic.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.mo.html
+++ b/reference/as.mo.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.rsi.html
+++ b/reference/as.rsi.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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> 2022-10-11 <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;"> 1</span> 2022-10-14 <span style="color: #949494;">11:06:17</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> 2022-10-11 <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;"> 2</span> 2022-10-14 <span style="color: #949494;">11:06:18</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> 2022-10-11 <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;"> 3</span> 2022-10-14 <span style="color: #949494;">11:06:18</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> 2022-10-11 <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;"> 4</span> 2022-10-14 <span style="color: #949494;">11:06:18</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> 2022-10-11 <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;"> 5</span> 2022-10-14 <span style="color: #949494;">11:06:18</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> 2022-10-11 <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;"> 6</span> 2022-10-14 <span style="color: #949494;">11:06:18</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;"> 7</span> 2022-10-14 <span style="color: #949494;">11:06:19</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> 2022-10-11 <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;"> 8</span> 2022-10-14 <span style="color: #949494;">11:06:19</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> 2022-10-11 <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;"> 9</span> 2022-10-14 <span style="color: #949494;">11:06:19</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> 2022-10-11 <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: #BCBCBC;">10</span> 2022-10-14 <span style="color: #949494;">11:06:19</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>
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/availability.html
+++ b/reference/availability.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/bug_drug_combinations.html
+++ b/reference/bug_drug_combinations.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/count.html
+++ b/reference/count.html
@ -12,7 +12,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/custom_eucast_rules.html
+++ b/reference/custom_eucast_rules.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/dosage.html
+++ b/reference/dosage.html
@ -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="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/eucast_rules.html
+++ b/reference/eucast_rules.html
@ -12,7 +12,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/example_isolates.html
+++ b/reference/example_isolates.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/example_isolates_unclean.html
+++ b/reference/example_isolates_unclean.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/first_isolate.html
+++ b/reference/first_isolate.html
@ -12,7 +12,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/g.test.html
+++ b/reference/g.test.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/get_episode.html
+++ b/reference/get_episode.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -177,40 +177,42 @@
 <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] 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>   [1] 18 63 33  7  6 44 11 62 32 15  4  7 35 59 25 42 38 20  2 49 36 21 14 59 32</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>  [26] 14 19  3 31 38 11 55 64 14 50 38 60  4  7 51 27 12  4 53  8 21 60  8  2 14</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>  [51]  6 31  9 58 27  1 63 23 10  7 23 61  4 56  9 60 19 56 44 48 14 23 33 28 54</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>  [76] 26 19 61  6 60 28 28 28 59  3 58 30  5 34 60 18 46 42 18  6 62 38 39 17  7</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> [101] 40 43  5 49 31 33 51 54 56 34 31 52  3 43 45 31 40 38  5 62  8  3 13 16 46</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> [126] 35 48 65 19 28 48 48 60 54 14 32 60 52 27  1 57 14 53 64 34 28 33 19  9 13</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> [151] 51 52  4  6 64 27 14 56 63 20 47  8 37 37 56 10 32 11 25  6 27 17 52 26 34</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-out co"><span class="r-pr">#&gt;</span> [176] 12 22 18 29 64 40 24 62 48 16 58 41 30 36 43 32 58 14 58 32 61 26 24  1 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]  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE 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>  [13] FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE  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>  [25] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE  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>  [37]  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE</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>  [49] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE 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>  [61] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE 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>  [73] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</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>  [85]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE</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>  [97] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</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> [109] FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE  TRUE 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> [121] FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE 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> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE 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> [145] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE</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> [157] FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE</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> [169] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE 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> [181] FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE 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-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE</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: 2 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-11-04 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;">1</span> 2002-07-23 F35553     51 M      ICU      B_STPHY_AURS R     NA    S     R    </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: #BCBCBC;">2</span> 2002-06-06 24D393     20 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-07-23 F35553     51 M      ICU      B_STPHY_AURS R     NA    S     R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2002-06-06 24D393     20 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #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>
@ -246,16 +248,16 @@
 <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> B43936  2013-05-16 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E67091  2006-01-25 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;"> 2</span> D80438  2017-06-28 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;"> 3</span> B26404  2010-01-04 A         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;"> 4</span> A73011  2003-08-13 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;"> 5</span> 53F0B8  2003-06-25 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;"> 6</span> 23C701  2012-07-27 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;"> 7</span> 022060  2004-05-04 C         TRUE       </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;"> 8</span> 976997  2017-03-02 A         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;"> 9</span> 22B987  2009-10-19 C         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: #BCBCBC;">10</span> FB50D6  2005-04-24 C         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>
@ -267,19 +269,19 @@
 <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 [186]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [177]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    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> ICU      2013-05-16 B43936          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2006-01-25 E67091          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;"> 2</span> ICU      2017-06-28 D80438          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;"> 3</span> Clinical 2010-01-04 B26404          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;"> 4</span> Clinical 2003-08-13 A73011          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;"> 5</span> Clinical 2003-06-25 53F0B8          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;"> 6</span> Clinical 2012-07-27 23C701          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;"> 7</span> ICU      2004-05-04 022060          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;"> 8</span> Clinical 2017-03-02 976997          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;"> 9</span> Clinical 2009-10-19 22B987          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: #BCBCBC;">10</span> ICU      2005-04-24 FB50D6          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>
@ -294,9 +296,9 @@
 <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          110             15            55            73</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          108             14            50            67</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;">2</span> ICU                55             13            36            42</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-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         14              8            12            12</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>
@ -315,7 +317,7 @@
 <span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/identical.html" class="external-link">identical</a></span><span class="op">(</span><span class="va">x</span>, <span class="va">y</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> Including isolates from ICU.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</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"># but is_new_episode() has a lot more flexibility than first_isolate(),</span></span></span>
@ -326,19 +328,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [193]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [186]</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>    <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> B43936  B_CRYNB       ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E67091  B_ENTRC_FCLS  Clinical 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;"> 2</span> D80438  B_CRYNB_STRT  ICU      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;"> 3</span> B26404  B_STPHY_CONS  Clinical 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;"> 4</span> A73011  B_STPHY_CONS  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;"> 5</span> 53F0B8  B_STPHY_CONS  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;"> 6</span> 23C701  B_PROTS_MRBL  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;"> 7</span> 022060  B_ENTRBC_CLOC ICU      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;"> 8</span> 976997  B_STRPT_PYGN  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;"> 9</span> 22B987  B_PSDMN_AERG  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: #BCBCBC;">10</span> FB50D6  B_STPHY_EPDR  ICU      TRUE        </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
--- a/reference/ggplot_pca.html
+++ b/reference/ggplot_pca.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/ggplot_rsi.html
+++ b/reference/ggplot_rsi.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/guess_ab_col.html
+++ b/reference/guess_ab_col.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/index.html
+++ b/reference/index.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/intrinsic_resistant.html
+++ b/reference/intrinsic_resistant.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/italicise_taxonomy.html
+++ b/reference/italicise_taxonomy.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/join.html
+++ b/reference/join.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/key_antimicrobials.html
+++ b/reference/key_antimicrobials.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/kurtosis.html
+++ b/reference/kurtosis.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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] 3.043154</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.921036</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] 0.0150379</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.001477015</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/like.html
+++ b/reference/like.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mdro.html
+++ b/reference/mdro.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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 +195,11 @@
    <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] &lt;=0.01 0.025  4      0.0625 1      4      16     0.5    0.025  8     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.125   &lt;=0.002 0.01    &gt;=64    0.01    0.25    0.5     0.025   2      </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.125  </span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -1.4081939 -1.0706595  0.7988846 -0.7331250  0.2882147  0.7988846</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.009782872 -1.384392080 -0.849383842  2.063956687 -0.849383842</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-out co"><span class="r-pr">#&gt;</span>  [6]  0.220632635  0.451048141 -0.544791110  0.911879154 -0.009782872</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>
@ -209,37 +210,37 @@
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">y</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox   cipr  gent tobr</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    4 &lt;=0.025  &lt;=1    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A   32      2     1 &gt;=16</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> 2   B &gt;=64   0.25     4 &gt;=16</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> 3   C   16 0.0625 &lt;=0.5    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> 4   D   16    0.5 &lt;=0.5    4</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> 5   E  &lt;=2      2    16    8</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> 6   F &gt;=64   0.25     8    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> 7   G   16 0.0625     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> 8   H    4      1     4    4</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> 9   I  &lt;=2      4    16    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    1     &gt;=4    4   16</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J   32      2    16    1</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] -0.77937382 -0.36771977  0.74573282 -0.12706157  0.43836890 -0.50465041</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.4639259  0.4984972 -1.0321239 -0.3551673  0.2661953  0.2953882</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-out co"><span class="r-pr">#&gt;</span>  [7] -0.2040150 -0.1307227 -0.1096856  0.3077079</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> 1   A    4 &lt;=0.025  &lt;=1    1  -0.77937382</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C   16 0.0625 &lt;=0.5    1   -1.0321239</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> 4   D   16    0.5 &lt;=0.5    4   -0.3551673</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> 7   G   16 0.0625     8    4   -0.2040150</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> 8   H    4      1     4    4   -0.1307227</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> 9   I  &lt;=2      4    16    1   -0.1096856</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> 5   E  &lt;=2      2    16    8    0.2661953</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> 6   F &gt;=64   0.25     8    4    0.2953882</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> 10  J   32      2    16    1    0.3077079</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   32      2     1 &gt;=16    0.4639259</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-out co"><span class="r-pr">#&gt;</span> 2   B &gt;=64   0.25     4 &gt;=16    0.4984972</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>
@ -252,16 +253,16 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox   cipr  gent tobr amr_distance check_id_C</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C   32 &lt;=0.025   16    8   0.74573282  0.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C   16 0.0625 &lt;=0.5    1   -1.0321239  0.0000000</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> 2   D   16    0.5 &lt;=0.5    4   -0.3551673  0.6769567</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> 3   G   16 0.0625     8    4   -0.2040150  0.8281090</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> 4   H    4      1     4    4   -0.1307227  0.9014012</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> 5   I  &lt;=2      4    16    1   -0.1096856  0.9224383</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> 6   E  &lt;=2      2    16    8    0.2661953  1.2983192</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> 7   F &gt;=64   0.25     8    4    0.2953882  1.3275121</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> 8   J   32      2    16    1    0.3077079  1.3398318</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> 9   A   32      2     1 &gt;=16    0.4639259  1.4960498</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-out co"><span class="r-pr">#&gt;</span> 10  B &gt;=64   0.25     4 &gt;=16    0.4984972  1.5306211</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="co"># support for groups</span></span></span>
 <span class="r-in"><span>  <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@ -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="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/microorganisms.html
+++ b/reference/microorganisms.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_matching_score.html
+++ b/reference/mo_matching_score.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_property.html
+++ b/reference/mo_property.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/mo_source.html
+++ b/reference/mo_source.html
@ -12,7 +12,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/pca.html
+++ b/reference/pca.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/plot-1.png
+++ b/reference/plot-1.png
--- a/reference/plot-2.png
+++ b/reference/plot-2.png
--- a/reference/plot-3.png
+++ b/reference/plot-3.png
--- a/reference/plot-4.png
+++ b/reference/plot-4.png
--- a/reference/plot-5.png
+++ b/reference/plot-5.png
--- a/reference/plot-6.png
+++ b/reference/plot-6.png
--- a/reference/plot-7.png
+++ b/reference/plot-7.png
--- a/reference/plot-8.png
+++ b/reference/plot-8.png
--- a/reference/plot-9.png
+++ b/reference/plot-9.png
--- a/reference/plot.html
+++ b/reference/plot.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/proportion.html
+++ b/reference/proportion.html
@ -12,7 +12,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/random.html
+++ b/reference/random.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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 +178,43 @@
    <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] 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>  [1] 0.25    0.025   2       32      128     32      0.5     2       32     </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> [10] 0.002   0.005   &lt;=0.001 &gt;=256   2       128     0.5     &lt;=0.001 8      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 4      2      128    128    128   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 128     0.125   0.125   2       8       1       8      </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] 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-out co"><span class="r-pr">#&gt;</span>  [1] 45 21 42 40 33 36 34 29  9 20 43 34 40 49 28 43 44 37 43 20 35 16 11 47 15</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] 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-out co"><span class="r-pr">#&gt;</span>  [1] R R S S I I S R R S R S S R R I I S S R I I S I 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] 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>  [1] 2      2      0.0625 0.005  &gt;=128  0.005  2      0.005  0.0625 1     </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> [11] 0.001  0.01   0.5    0.001  8      0.001  16     16     16     0.01  </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-out co"><span class="r-pr">#&gt;</span> [21] 8      1      32     64     8     </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] &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>  [1] 1      0.5    2      &lt;=0.25 1      8      8      0.5    2      1     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [20] 2   4   4   8   &lt;=1 2  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 2      2      8      4      &gt;=16   &gt;=16   1      &lt;=0.25 4      0.5   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [21] 8      0.5    &gt;=16   8      4     </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] 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>  [1] 0.0625 1      0.125  0.125  0.125  &gt;=4    0.5    0.125  1      0.125 </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> [11] 2      2      &gt;=4    &gt;=4    0.25   2      &gt;=4    0.0625 1      2     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 4    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.0625 1      0.5    1      0.5   </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] 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-out co"><span class="r-pr">#&gt;</span>  [1] 23 14 32 50 15 38 35 50 21 34 41 36 46 49 43 41  9 20 20 27 31 21 13 46 22</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] 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-out co"><span class="r-pr">#&gt;</span>  [1] 15 13 11 14 12 14 15 15 17 14 17 13 11 16 17 12 14 17 17 17 12 14 13 15 16</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] 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-out co"><span class="r-pr">#&gt;</span>  [1] 22 23 20 22 18 23 21 16 20 23 23 19 15 26 27 20 22 19 22 16 21 20 15 19 26</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
    </div>
--- a/reference/resistance_predict.html
+++ b/reference/resistance_predict.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/rsi_translation.html
+++ b/reference/rsi_translation.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/skewness.html
+++ b/reference/skewness.html
@ -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="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <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] -0.04641902</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.02662042</span>
 </code></pre></div>
    </div>
  </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
--- a/reference/translate.html
+++ b/reference/translate.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9016</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/search.json
+++ b/search.json