Built site for AMR: 1.8.2.9037@3d9faf8

2024-12-26 06:06:12 +01:00 · 2022-10-29 17:07:26 +00:00 · 2022-10-29 17:07:26 +00:00 · 0d936e8905
commit 0d936e8905
parent f988c3273a
94 changed files with 509 additions and 504 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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -395,66 +395,66 @@ data set:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2016-06-08</td>
+<td align="center">2012-02-21</td>
-<td align="center">H2</td>
+<td align="center">S5</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
-<td align="center">Staphylococcus aureus</td>
+<td align="center">Streptococcus pneumoniae</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">F</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2017-12-08</td>
+<td align="center">2011-05-13</td>
-<td align="center">T3</td>
+<td align="center">C3</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">F</td>
+<td align="center">M</td>
 </tr>
 <tr class="odd">
-<td align="center">2013-11-26</td>
+<td align="center">2012-04-05</td>
-<td align="center">C9</td>
+<td align="center">I6</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
-<td align="center">Staphylococcus aureus</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">R</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2011-09-18</td>
+<td align="center">2013-02-02</td>
-<td align="center">Y5</td>
+<td align="center">J7</td>
 <td align="center">Hospital B</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">R</td>
 <td align="center">M</td>
 </tr>
 <tr class="odd">
 <td align="center">2017-04-23</td>
 <td align="center">H1</td>
 <td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
 <td align="center">I</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
 <td align="center">2014-08-30</td>
 <td align="center">I4</td>
 <td align="center">Hospital A</td>
 <td align="center">Streptococcus pneumoniae</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2012-11-04</td>
+<td align="center">2013-08-13</td>
-<td align="center">T9</td>
+<td align="center">N9</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Staphylococcus aureus</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>
@ -494,16 +494,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,377</td>
+<td align="right">10,313</td>
-<td align="right">51.89%</td>
+<td align="right">51.57%</td>
-<td align="right">10,377</td>
+<td align="right">10,313</td>
-<td align="right">51.89%</td>
+<td align="right">51.57%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,623</td>
+<td align="right">9,687</td>
-<td align="right">48.12%</td>
+<td align="right">48.44%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@ -616,9 +616,9 @@ takes into account the antimicrobial susceptibility test results using
 <span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
 <span><span class="co"># 2</span></span>
 <span><span class="co"># Including isolates from ICU.</span></span>
-<span><span class="co"># =&gt; Found 10,687 'phenotype-based' first isolates (53.4% of total where a</span></span>
+<span><span class="co"># =&gt; Found 10,638 'phenotype-based' first isolates (53.2% 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
+<p>So only 53.2% 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">
@ -629,11 +629,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
-<p>So we end up with 10,687 isolates for analysis. Now our data looks
+<p>So we end up with 10,638 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%">
@ -647,7 +647,7 @@ like:</p>
 <col width="6%">
 <col width="11%">
 <col width="12%">
-<col width="7%">
+<col width="9%">
 <col width="5%">
 </colgroup>
 <thead><tr class="header">
@ -669,46 +669,78 @@ like:</p>
 <tbody>
 <tr class="odd">
 <td align="left">1</td>
-<td align="center">2016-06-08</td>
+<td align="center">2012-02-21</td>
-<td align="center">H2</td>
+<td align="center">S5</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
-<td align="center">B_STPHY_AURS</td>
+<td align="center">B_STRPT_PNMN</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">M</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">Streptococcus</td>
-<td align="center">aureus</td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
-<td align="center">2017-12-08</td>
+<td align="center">2011-05-13</td>
-<td align="center">T3</td>
+<td align="center">C3</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">F</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="left">3</td>
+<td align="left">6</td>
-<td align="center">2013-11-26</td>
+<td align="center">2013-08-13</td>
-<td align="center">C9</td>
+<td align="center">N9</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STPHY_AURS</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-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">7</td>
 <td align="center">2017-03-07</td>
 <td align="center">G5</td>
 <td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">10</td>
 <td align="center">2011-06-18</td>
 <td align="center">C3</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
@ -716,13 +748,13 @@ like:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">6</td>
+<td align="left">11</td>
-<td align="center">2012-11-04</td>
+<td align="center">2011-09-13</td>
-<td align="center">T9</td>
+<td align="center">U2</td>
 <td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
@ -731,38 +763,6 @@ like:</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">8</td>
 <td align="center">2011-09-02</td>
 <td align="center">U9</td>
 <td align="center">Hospital D</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">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="left">10</td>
 <td align="center">2015-12-26</td>
 <td align="center">Q6</td>
 <td align="center">Hospital D</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">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
 <p>Time for the analysis!</p>
@ -796,8 +796,8 @@ readable:</p>
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,687<br>
+Length: 10,638<br>
-Available: 10,687 (100%, NA: 0 = 0%)<br>
+Available: 10,638 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@ -822,33 +822,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,686</td>
+<td align="right">4,698</td>
-<td align="right">43.85%</td>
+<td align="right">44.16%</td>
-<td align="right">4,686</td>
+<td align="right">4,698</td>
-<td align="right">43.85%</td>
+<td align="right">44.16%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,764</td>
+<td align="right">2,683</td>
-<td align="right">25.86%</td>
+<td align="right">25.22%</td>
-<td align="right">7,450</td>
+<td align="right">7,381</td>
-<td align="right">69.71%</td>
+<td align="right">69.38%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,087</td>
+<td align="right">2,070</td>
-<td align="right">19.53%</td>
+<td align="right">19.46%</td>
-<td align="right">9,537</td>
+<td align="right">9,451</td>
-<td align="right">89.24%</td>
+<td align="right">88.84%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,150</td>
+<td align="right">1,187</td>
-<td align="right">10.76%</td>
+<td align="right">11.16%</td>
-<td align="right">10,687</td>
+<td align="right">10,638</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@ -869,14 +869,14 @@ antibiotic class they are in:</p>
 <col width="9%">
 <col width="9%">
 <col width="9%">
-<col width="10%">
+<col width="11%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="12%">
+<col width="11%">
 <col width="9%">
 <col width="5%">
 </colgroup>
@ -897,39 +897,9 @@ antibiotic class they are in:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2017-01-02</td>
+<td align="center">2012-02-21</td>
-<td align="center">H1</td>
+<td align="center">S5</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2014-06-28</td>
 <td align="center">F2</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2013-11-15</td>
 <td align="center">R3</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
@ -942,9 +912,9 @@ antibiotic class they are in:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2016-09-25</td>
+<td align="center">2017-03-07</td>
-<td align="center">A7</td>
+<td align="center">G5</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -957,12 +927,12 @@ antibiotic class they are in:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2017-08-10</td>
+<td align="center">2011-03-18</td>
-<td align="center">D9</td>
+<td align="center">F8</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital C</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">R</td>
+<td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">M</td>
@ -972,18 +942,48 @@ antibiotic class they are in:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2010-12-30</td>
+<td align="center">2017-06-06</td>
-<td align="center">J6</td>
+<td align="center">M4</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital B</td>
-<td align="center">B_STPHY_AURS</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">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2012-12-07</td>
 <td align="center">C6</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
-<td align="center">Staphylococcus</td>
+<td align="center">Streptococcus</td>
-<td align="center">aureus</td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2012-02-15</td>
 <td align="center">M4</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">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@ -1009,50 +1009,50 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2208</td>
+<td align="center">2229</td>
-<td align="center">140</td>
+<td align="center">110</td>
-<td align="center">2338</td>
+<td align="center">2359</td>
-<td align="center">4686</td>
+<td align="center">4698</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
 <td align="center">3438</td>
-<td align="center">171</td>
+<td align="center">153</td>
-<td align="center">1077</td>
+<td align="center">1107</td>
-<td align="center">4686</td>
+<td align="center">4698</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3403</td>
+<td align="center">3430</td>
 <td align="center">0</td>
-<td align="center">1283</td>
+<td align="center">1268</td>
-<td align="center">4686</td>
+<td align="center">4698</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4139</td>
+<td align="center">4120</td>
 <td align="center">0</td>
-<td align="center">547</td>
+<td align="center">578</td>
-<td align="center">4686</td>
+<td align="center">4698</td>
 </tr>
 <tr class="odd">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMX</td>
 <td align="center">0</td>
 <td align="center">0</td>
-<td align="center">1150</td>
+<td align="center">1187</td>
-<td align="center">1150</td>
+<td align="center">1187</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">902</td>
+<td align="center">939</td>
-<td align="center">50</td>
+<td align="center">48</td>
-<td align="center">198</td>
+<td align="center">200</td>
-<td align="center">1150</td>
+<td align="center">1187</td>
 </tr>
 </tbody>
 </table>
@ -1075,34 +1075,34 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4139</td>
+<td align="center">4120</td>
 <td align="center">0</td>
-<td align="center">547</td>
+<td align="center">578</td>
-<td align="center">4686</td>
+<td align="center">4698</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1039</td>
+<td align="center">1081</td>
 <td align="center">0</td>
-<td align="center">111</td>
+<td align="center">106</td>
-<td align="center">1150</td>
+<td align="center">1187</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2463</td>
+<td align="center">2424</td>
 <td align="center">0</td>
-<td align="center">301</td>
+<td align="center">259</td>
-<td align="center">2764</td>
+<td align="center">2683</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">2087</td>
+<td align="center">2070</td>
-<td align="center">2087</td>
+<td align="center">2070</td>
 </tr>
 </tbody>
 </table>
@ -1134,7 +1134,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
 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] 0.5448676</span></span></code></pre></div>
+<span><span class="co"># [1] 0.5418312</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">
@ -1149,19 +1149,19 @@ own:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5442717</td>
+<td align="center">0.5577628</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5377861</td>
+<td align="center">0.5364725</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5453991</td>
+<td align="center">0.5250313</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5577913</td>
+<td align="center">0.5391595</td>
 </tr>
 </tbody>
 </table>
@ -1186,23 +1186,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5442717</td>
+<td align="center">0.5577628</td>
-<td align="center">3151</td>
+<td align="center">3272</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5377861</td>
+<td align="center">0.5364725</td>
-<td align="center">3758</td>
+<td align="center">3674</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5453991</td>
+<td align="center">0.5250313</td>
-<td align="center">1641</td>
+<td align="center">1598</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5577913</td>
+<td align="center">0.5391595</td>
-<td align="center">2137</td>
+<td align="center">2094</td>
 </tr>
 </tbody>
 </table>
@ -1227,27 +1227,27 @@ therapies very easily:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7701665</td>
+<td align="center">0.7643678</td>
-<td align="center">0.8832693</td>
+<td align="center">0.8769689</td>
-<td align="center">0.9812207</td>
+<td align="center">0.9753086</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8278261</td>
+<td align="center">0.8315080</td>
-<td align="center">0.9034783</td>
+<td align="center">0.9106992</td>
-<td align="center">0.9860870</td>
+<td align="center">0.9831508</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7948625</td>
+<td align="center">0.7935147</td>
-<td align="center">0.8910999</td>
+<td align="center">0.9034663</td>
-<td align="center">0.9851664</td>
+<td align="center">0.9836004</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5304264</td>
+<td align="center">0.5526570</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5304264</td>
+<td align="center">0.5526570</td>
 </tr>
 </tbody>
 </table>
@ -1275,23 +1275,23 @@ classes, use a antibiotic class selector such as
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">54.4%</td>
+<td align="right">55.8%</td>
-<td align="right">25.9%</td>
+<td align="right">26.8%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">53.8%</td>
+<td align="right">53.6%</td>
-<td align="right">26.2%</td>
+<td align="right">26.5%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">54.5%</td>
+<td align="right">52.5%</td>
-<td align="right">27.5%</td>
+<td align="right">25.1%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">55.8%</td>
+<td align="right">53.9%</td>
-<td align="right">26.6%</td>
+<td align="right">25.5%</td>
 </tr>
 </tbody>
 </table>
@ -1407,18 +1407,18 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
 <code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
 <span><span class="va">mic_values</span></span>
 <span><span class="co"># Class 'mic'</span></span>
-<span><span class="co">#   [1] 128     8       0.5     0.01    4       0.025   0.002   256     &lt;=0.001</span></span>
+<span><span class="co">#   [1] 8       &lt;=0.001 64      128     8       0.01    16      0.0625  0.5    </span></span>
-<span><span class="co">#  [10] 0.002   2       4       0.5     32      0.025   0.002   0.5     16     </span></span>
+<span><span class="co">#  [10] 0.01    128     8       0.125   1       0.25    8       0.01    32     </span></span>
-<span><span class="co">#  [19] 0.005   0.025   2       4       4       16      256     4       2      </span></span>
+<span><span class="co">#  [19] 4       0.5     1       0.002   0.25    1       4       0.025   0.005  </span></span>
-<span><span class="co">#  [28] 0.002   2       256     0.025   0.01    0.01    0.01    0.125   &lt;=0.001</span></span>
+<span><span class="co">#  [28] 0.01    128     0.005   0.125   0.125   2       32      16      16     </span></span>
-<span><span class="co">#  [37] &lt;=0.001 128     32      0.25    2       0.125   32      32      0.002  </span></span>
+<span><span class="co">#  [37] &lt;=0.001 0.01    0.125   0.5     &lt;=0.001 4       0.25    8       8      </span></span>
-<span><span class="co">#  [46] 0.002   128     0.002   4       64      0.005   1       8       0.01   </span></span>
+<span><span class="co">#  [46] 0.025   4       1       128     0.0625  0.025   1       0.125   1      </span></span>
-<span><span class="co">#  [55] &lt;=0.001 0.005   0.005   0.25    0.5     0.0625  0.25    0.0625  0.0625 </span></span>
+<span><span class="co">#  [55] 0.025   &lt;=0.001 8       0.002   0.25    2       &gt;=256   32      0.005  </span></span>
-<span><span class="co">#  [64] 0.01    0.002   256     0.5     0.25    0.0625  0.025   0.005   16     </span></span>
+<span><span class="co">#  [64] 2       0.0625  4       0.5     128     0.002   0.01    1       0.005  </span></span>
-<span><span class="co">#  [73] 32      0.0625  256     128     128     128     2       256     4      </span></span>
+<span><span class="co">#  [73] 0.125   0.125   0.25    &lt;=0.001 8       128     0.125   128     4      </span></span>
-<span><span class="co">#  [82] 2       0.005   16      0.005   64      1       0.5     8       0.025  </span></span>
+<span><span class="co">#  [82] &gt;=256   16      8       16      64      8       &lt;=0.001 4       0.002  </span></span>
-<span><span class="co">#  [91] 0.005   0.5     64      0.0625  0.025   0.01    32      128     0.002  </span></span>
+<span><span class="co">#  [91] 64      0.005   128     1       0.5     32      1       0.0625  0.01   </span></span>
-<span><span class="co"># [100] 128</span></span></code></pre></div>
+<span><span class="co"># [100] 0.0625</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>
@ -1452,10 +1452,10 @@ plotting:</p>
 <code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
 <span><span class="va">disk_values</span></span>
 <span><span class="co"># Class 'disk'</span></span>
-<span><span class="co">#   [1] 19 31 30 19 20 26 24 22 22 19 18 20 19 23 20 28 23 28 20 20 21 22 18 17 24</span></span>
+<span><span class="co">#   [1] 22 30 22 24 23 21 30 20 25 25 31 26 21 31 20 24 18 31 28 28 27 28 20 18 29</span></span>
-<span><span class="co">#  [26] 18 22 31 23 22 31 28 29 24 22 26 23 19 18 26 30 23 31 17 27 26 17 17 28 26</span></span>
+<span><span class="co">#  [26] 27 31 26 19 28 28 17 29 30 23 22 31 24 31 17 18 24 26 21 26 17 21 26 19 27</span></span>
-<span><span class="co">#  [51] 17 31 23 30 31 23 17 26 17 23 23 28 23 20 30 17 30 18 23 31 25 31 21 28 19</span></span>
+<span><span class="co">#  [51] 22 19 19 21 23 24 27 20 31 18 23 22 30 24 31 26 25 22 22 24 23 30 19 28 18</span></span>
-<span><span class="co">#  [76] 23 26 29 17 23 29 25 18 25 21 25 22 31 28 24 31 28 19 23 22 17 19 25 23 30</span></span></code></pre></div>
+<span><span class="co">#  [76] 28 29 25 22 25 23 27 20 23 20 19 23 18 22 28 21 23 26 17 17 18 27 26 28 30</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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -370,19 +370,19 @@ names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
 <span><span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
-<span><span class="co"># 1          I         S            S          R            I            I</span></span>
+<span><span class="co"># 1          S         R            S          R            R            I</span></span>
-<span><span class="co"># 2          S         S            R          R            I            I</span></span>
+<span><span class="co"># 2          R         S            I          I            S            I</span></span>
-<span><span class="co"># 3          I         I            S          I            R            R</span></span>
+<span><span class="co"># 3          I         S            I          I            S            I</span></span>
-<span><span class="co"># 4          S         R            S          S            I            R</span></span>
+<span><span class="co"># 4          I         I            S          R            S            R</span></span>
-<span><span class="co"># 5          R         R            S          R            R            S</span></span>
+<span><span class="co"># 5          S         I            S          S            R            I</span></span>
-<span><span class="co"># 6          R         S            R          I            R            R</span></span>
+<span><span class="co"># 6          R         S            I          R            S            R</span></span>
 <span><span class="co">#   kanamycin</span></span>
-<span><span class="co"># 1         S</span></span>
+<span><span class="co"># 1         I</span></span>
-<span><span class="co"># 2         S</span></span>
+<span><span class="co"># 2         I</span></span>
-<span><span class="co"># 3         I</span></span>
+<span><span class="co"># 3         R</span></span>
-<span><span class="co"># 4         S</span></span>
+<span><span class="co"># 4         I</span></span>
-<span><span class="co"># 5         S</span></span>
+<span><span class="co"># 5         I</span></span>
-<span><span class="co"># 6         R</span></span></code></pre></div>
+<span><span class="co"># 6         S</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">
@ -423,32 +423,32 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3255</td>
+<td align="right">3190</td>
-<td align="right">65.10%</td>
+<td align="right">63.80%</td>
-<td align="right">3255</td>
+<td align="right">3190</td>
-<td align="right">65.10%</td>
+<td align="right">63.80%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">989</td>
+<td align="right">978</td>
-<td align="right">19.78%</td>
+<td align="right">19.56%</td>
-<td align="right">4244</td>
+<td align="right">4168</td>
-<td align="right">84.88%</td>
+<td align="right">83.36%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">427</td>
+<td align="right">498</td>
-<td align="right">8.54%</td>
+<td align="right">9.96%</td>
-<td align="right">4671</td>
+<td align="right">4666</td>
-<td align="right">93.42%</td>
+<td align="right">93.32%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">237</td>
+<td align="right">242</td>
-<td align="right">4.74%</td>
+<td align="right">4.84%</td>
 <td align="right">4908</td>
 <td align="right">98.16%</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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/articles/WHONET.html
+++ b/articles/WHONET.html
@ -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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -191,7 +191,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
 <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after
 you load the <code>AMR</code> package.</p>
-<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
+<p>It was last updated on 29 October 2022 17:02:33 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>
@ -219,12 +219,12 @@ SPSS Statistics data file</a> (15.8 MB)<br>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata
 DTA file</a> (43.8 MB)</li>
 </ul>
-<p><strong>NOTE: The exported files for Excel, SAS, SPSS and Stata
+<p><strong>NOTE: The exported files for SAS, SPSS and Stata contain only
-contain only the first 50 SNOMED codes per record, as their file size
+the first 50 SNOMED codes per record, as their file size would otherwise
-would otherwise exceed 100 MB; the file size limit of GitHub.</strong>
+exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R
-Advice? Use R instead.</p>
+instead.</p>
-<p>The tab-separated text file contains all SNOMED codes as comma
+<p>The tab-separated text file and Microsoft Excel workbook both contain
-separated values.</p>
+all SNOMED codes as comma separated values.</p>
 <div class="section level3">
 <h3 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a>
 </h3>
@ -490,7 +490,7 @@ column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>a
 <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 29 October 2022 14:10:26 UTC. Find more info
+<p>It was last updated on 29 October 2022 17:02:33 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>
@ -498,10 +498,10 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
 R Data Structure (RDS) file</a> (36 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">tab-separated
-text file</a> (0.2 kB)<br>
+text file</a> (0.1 MB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Microsoft
-Excel workbook</a> (66 kB)<br>
+Excel workbook</a> (63 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.feather" class="external-link">Apache
 Feather file</a> (97 kB)<br>
@ -518,6 +518,9 @@ SPSS Statistics data file</a> (0.3 MB)<br>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata
 DTA file</a> (0.3 MB)</li>
 </ul>
 <p>The tab-separated text file and Microsoft Excel workbook, and SAS,
 SPSS and Stata files all contain the ATC codes, common abbreviations,
 trade names and LOINC codes as comma separated values.</p>
 <div class="section level3">
 <h3 id="source-1">Source<a class="anchor" aria-label="anchor" href="#source-1"></a>
 </h3>
@ -684,7 +687,7 @@ column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</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 29 October 2022 14:10:26 UTC. Find more info
+<p>It was last updated on 29 October 2022 17:02:33 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>
@ -692,10 +695,10 @@ about the structure of this data set <a href="https://msberends.github.io/AMR/re
 R Data Structure (RDS) file</a> (4 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">tab-separated
-text file</a> (16 kB)<br>
+text file</a> (14 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Microsoft
-Excel workbook</a> (14 kB)<br>
+Excel workbook</a> (13 kB)<br>
 </li>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.feather" class="external-link">Apache
 Feather file</a> (12 kB)<br>
@ -712,6 +715,9 @@ SPSS Statistics data file</a> (27 kB)<br>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata
 DTA file</a> (67 kB)</li>
 </ul>
 <p>The tab-separated text file and Microsoft Excel workbook, and SAS,
 SPSS and Stata files all contain the trade names as comma separated
 values.</p>
 <div class="section level3">
 <h3 id="source-2">Source<a class="anchor" aria-label="anchor" href="#source-2"></a>
 </h3>
@ -841,7 +847,7 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</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 29 October 2022 14:10:26 UTC. Find more info
+<p>It was last updated on 29 October 2022 17:02:33 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>
@ -1014,7 +1020,7 @@ Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intri
 column names:<br><em>mo</em> and <em>ab</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
+<p>It was last updated on 29 October 2022 17:02:33 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>
@ -1302,7 +1308,7 @@ column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>,
 <em>original_txt</em> and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you
 load the <code>AMR</code> package.</p>
-<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
+<p>It was last updated on 29 October 2022 17:02:33 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>
@ -1452,7 +1458,7 @@ column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
 <em>MUP</em> and <em>RIF</em>.</p>
 <p>This data set is in R available as <code>example_isolates</code>,
 after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
+<p>It was last updated on 29 October 2022 17:02:33 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>
@ -1865,7 +1871,7 @@ column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
 <p>This data set is in R available as
 <code>example_isolates_unclean</code>, after you load the
 <code>AMR</code> package.</p>
-<p>It was last updated on 29 October 2022 14:10:26 UTC. Find more info
+<p>It was last updated on 29 October 2022 17:02:33 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>
--- 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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="1.8.2.9035" id="amr-1829035">AMR 1.8.2.9035<a class="anchor" aria-label="anchor" href="#amr-1829035"></a></h2>
+<h2 class="pkg-version" data-toc-text="1.8.2.9037" id="amr-1829037">AMR 1.8.2.9037<a class="anchor" aria-label="anchor" href="#amr-1829037"></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-1-8-2-9035">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9035"></a></h4>
+<h4 id="breaking-1-8-2-9037">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9037"></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>
@ -143,7 +143,7 @@
 <li>Removal of interpretation guidelines older than 10 years, the oldest now included guidelines of EUCAST and CLSI are from 2013</li>
 </ul></div>
 <div class="section level4">
-<h4 id="new-1-8-2-9035">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9035"></a></h4>
+<h4 id="new-1-8-2-9037">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9037"></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 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>
@ -167,7 +167,7 @@
 <li>Support for antimicrobial interpretation of anaerobic bacteria, by adding a ‘placeholder’ code <code>B_ANAER</code> to the <code>microorganisms</code> data set and add the breakpoints of anaerobics to the <code>rsi_interpretation</code> data set, which is used by <code><a href="../reference/as.rsi.html">as.rsi()</a></code> when interpreting MIC and disk diffusion values</li>
 </ul></div>
 <div class="section level4">
-<h4 id="changed-1-8-2-9035">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9035"></a></h4>
+<h4 id="changed-1-8-2-9037">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9037"></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>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on drug-drug combinations with multiple breakpoints for different body sites</li>
@ -195,9 +195,10 @@
 <li>Antimicrobial interpretation ‘SDD’ (susceptible dose-dependent, coined by CLSI) will be interpreted as ‘I’ to comply with EUCAST’s ‘I’ in <code><a href="../reference/as.rsi.html">as.rsi()</a></code>
 </li>
 <li>Fix for <code><a href="../reference/mo_property.html">mo_shortname()</a></code> in case of higher taxonomic ranks (order, class, phylum)</li>
 <li>Updated DDDs and ATCs for the <code>antibiotics</code> data set - ATC codes J04AB06 (enviomycin) and D06AX14 (ozenoxacin) were added</li>
 </ul></div>
 <div class="section level4">
-<h4 id="other-1-8-2-9035">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9035"></a></h4>
+<h4 id="other-1-8-2-9037">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9037"></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, Anton Mymrikov, and Jonas Salm as contributors, to thank them for their valuable input</li>
 <li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
--- 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: 2022-10-29T14:13Z
+last_built: 2022-10-29T17:04Z
 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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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  1980-09-03  42  42.15342         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1933-11-08  88  88.97260         66</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1980-05-29  42  42.41918         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1932-04-27  90  90.50685         67</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1945-03-05  77  77.65205         54</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1969-07-28  53  53.25479         30</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1934-07-09  88  88.30685         65</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1977-03-14  45  45.62740         22</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1975-06-07  47  47.39452         24</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1998-05-31  24  24.41370          1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1959-02-26  63  63.67123         40</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1990-01-02  32  32.82192          9</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1998-08-19  24  24.19452          1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1999-06-09  23  23.38904          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1993-03-30  29  29.58356          6</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1939-10-15  83  83.03836         60</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1941-06-18  81  81.36438         58</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1995-01-21  27  27.76986          4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1984-07-05  38  38.31781         15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1936-03-11  86  86.63562         63</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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -153,7 +153,7 @@
 <li><p><code>atc_group2</code><br> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
 <li><p><code>abbr</code><br> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
 <li><p><code>synonyms</code><br> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
-<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
+<li><p><code>oral_ddd</code><br> Defined Daily Dose (DDD), oral treatment, currently available for 171 drugs</p></li>
 <li><p><code>oral_units</code><br> Units of <code>oral_ddd</code></p></li>
 <li><p><code>iv_ddd</code><br> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
 <li><p><code>iv_units</code><br> Units of <code>iv_ddd</code></p></li>
--- 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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -496,16 +496,16 @@ 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> 2022-10-29 <span style="color: #949494;">14:13:20</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> 2022-10-29 <span style="color: #949494;">17:04:55</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> 2022-10-29 <span style="color: #949494;">14:13:20</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> 2022-10-29 <span style="color: #949494;">17:04:55</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> 2022-10-29 <span style="color: #949494;">14:13:21</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> 2022-10-29 <span style="color: #949494;">17:04:55</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> 2022-10-29 <span style="color: #949494;">14:13:21</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> 2022-10-29 <span style="color: #949494;">17:04:56</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> 2022-10-29 <span style="color: #949494;">14:13:21</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> 2022-10-29 <span style="color: #949494;">17:04:56</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> 2022-10-29 <span style="color: #949494;">14:13:22</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> 2022-10-29 <span style="color: #949494;">17:04:56</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> 2022-10-29 <span style="color: #949494;">14:13:22</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> 2022-10-29 <span style="color: #949494;">17:04:57</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> 2022-10-29 <span style="color: #949494;">14:13:22</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> 2022-10-29 <span style="color: #949494;">17:04:57</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> 2022-10-29 <span style="color: #949494;">14:13:22</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> 2022-10-29 <span style="color: #949494;">17:04:57</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> 2022-10-29 <span style="color: #949494;">14:13:22</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> 2022-10-29 <span style="color: #949494;">17:04:57</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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -177,41 +177,40 @@
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 54 11 30 29 30 50  7 45  9  6 24 33 46 62 13 31 11 14 11 56 60 40 56  6 16</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  3 26 59 49 10 61  4  8 14 45  1  4 46 38 48 56 20 27  8 51 63 12  8 37 35</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26]  8 61 60 64 40  9 62 60 49 58 55  2 33  3 57 11 22 20  4 56  9 44 13 15 54</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 26 35  6  8  9 40 40 25 43 34 19 40  1 17 26 10 40 14 33 12  9 55  3 40 29</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 59 62 41 48 56 20 15 57 24 21 45  4  9 42 45 29 35 60 64 11 11 19  8 37 45</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 61 29 36 21 53 13 32  6  6 51 49 50 24 17 61 41 48 49 20 41 27 60 23 40 17</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 63 41 48 49 31  7 58  6  3 43 12 54 59  4 63  1 38 35 36 62 20  5 43 24 60</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 43 57 36 30 31  9 20 54 39 35  9  8 40 63  6 12 49 32 41 52  6 24 51 30 46</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 10 47 12 59 57 50 44 59 16 61 51 38  4 18  8 10 64 12 42 37 16 47  1 50 37</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 58 19 19 21 24 27 26 55 55 23  1 16 32  9 26 43 32 12 57 26 36 56 15  9 30</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 12 34  8 54 61 22 52 32 28 26 34 53 46 27 48 37 31 40 37 17 61 55 25 25 62</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 59 34 47 51  4 26 60 55 51 42 48 35 51  8 63 47 63 54 44 41 50 14  9 17 12</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 27 51 25 18 16 39  9  8 21 33 45 57 26 59  6 10 23 22 64 58 45 16 34  3 62</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 60  8 62 16 58 29 30 26 22 61 10  7 17  6 38  2 19  9 50 21 23  7 40  5 57</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 54 20 55 47  9 29 31 23 59 40 58 63 61 18 49 29 34 57 42 53  4 63 28 23 61</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 26 28 47 15  9 62 61 41 39 11 11 38 53 48 21  8 32  7 55 16 61 44 18 42  5</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13]  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37]  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37]  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49]  TRUE  TRUE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97]  TRUE  TRUE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [133]  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [145]  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [169]  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [181]  TRUE FALSE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [193]  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
 <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward      mo           PEN   OXA   FLC   AMX  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward     mo           PEN   OXA   FLC   AMX  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span> <span style="color: #949494; font-style: italic;">&lt;rsi&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-10-11 974319     78 M      Outpatie… B_STPHY_EPDR S     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-23 798871     82 M      Clinical B_ENTRC_FCLS NA    NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-08-19 A49852     70 M      Clinical  B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-06-06 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> 2002-10-11 871360     78 M      Clinical  B_STPHY_EPDR R     NA    S     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>
@ -247,16 +246,16 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   condition [3]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient date       condition new_episode</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 324415  2015-10-03 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 798871  2002-06-23 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 895298  2004-06-10 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 800264  2008-04-10 A         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 380628  2009-01-18 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 620753  2016-10-15 C         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 501361  2008-11-01 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 997433  2014-01-30 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 380628  2009-01-18 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 05B00F  2004-05-11 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 454595  2014-12-20 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 422833  2017-05-26 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D63414  2003-09-09 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> F35553  2002-09-23 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 545388  2013-07-29 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 739C43  2003-09-26 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 288260  2004-02-01 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 848254  2005-03-29 A         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 328792  2003-05-27 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 210954  2012-11-01 B         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>
@ -268,19 +267,19 @@
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [181]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [172]</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        2015-10-03 324415          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical   2002-06-23 798871          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> ICU        2004-06-10 895298          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Outpatient 2008-04-10 800264          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical   2009-01-18 380628          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical   2016-10-15 620753          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical   2008-11-01 501361          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical   2014-01-30 997433          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical   2009-01-18 380628          1 FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> ICU        2004-05-11 05B00F          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Outpatient 2014-12-20 454595          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Clinical   2017-05-26 422833          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical   2003-09-09 D63414          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU        2002-09-23 F35553          2 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical   2013-07-29 545388          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical   2003-09-26 739C43          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU        2004-02-01 288260          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU        2005-03-29 848254          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical   2003-05-27 328792          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical   2012-11-01 210954          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>
@ -295,9 +294,9 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          116             15            56            72</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          110             15            54            74</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                54             12            35            43</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                50             12            36            43</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         11              7             9             9</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         12              7            11            11</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>
@ -316,7 +315,7 @@
 <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] FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</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>
@ -327,19 +326,19 @@
 <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 [189]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [182]</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> 324415  B_PROTS_MRBL ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 798871  B_ENTRC_FCLS Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 895298  B_STPHY_CONS ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 800264  B_ESCHR_COLI Outpatient TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 380628  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 620753  B_ESCHR_COLI Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 501361  B_ESCHR_COLI Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 997433  B_STPHY_HMNS Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 380628  B_ESCHR_COLI Clinical   FALSE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 05B00F  F_CANDD_ALBC ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 454595  B_STPHY_HMNS Outpatient TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 422833  B_ENTRC_FCLS Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> D63414  B_PROTS_MRBL Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> F35553  B_STPHY_AURS ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 545388  B_KLBSL_PNMN Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 739C43  B_ESCHR_COLI Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 288260  B_STPHY_EPDR ICU        TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 848254  B_STPHY_EPDR ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 328792  B_STRPT_MITS Clinical   TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 210954  B_STPHY_AURS Clinical   TRUE        </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
--- a/reference/ggplot_pca.html
+++ b/reference/ggplot_pca.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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] 2.912495</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.943874</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] -0.01024742</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.05253874</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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -195,10 +195,10 @@
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">x</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 64     0.002  32     8      4      0.0625 16     16     &gt;=128  2     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 4     0.5   2     1     0.125 64    0.5   0.125 128   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]  0.83591041 -2.21787096  0.63185954  0.22375779  0.01970691 -1.20459833</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.4169169 -0.4169169  0.1389723 -0.1389723 -0.9728062  1.5286955</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.42780866  0.42780866  1.03996128 -0.18434396</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.4169169 -0.9728062  1.8066401 -0.9728062</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">y</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  id <span class="op">=</span> <span class="va">LETTERS</span><span class="op">[</span><span class="fl">1</span><span class="op">:</span><span class="fl">10</span><span class="op">]</span>,</span></span>
@ -208,38 +208,38 @@
 <span class="r-in"><span>  tobr <span class="op">=</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span>, ab <span class="op">=</span> <span class="st">"tobr"</span>, mo <span class="op">=</span> <span class="st">"Escherichia coli"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">y</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox    cipr gent  tobr</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox  cipr gent  tobr</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    8       2  0.5     4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A &gt;=64 0.125    1     2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    2    0.25  &gt;=8     8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    1   &gt;=2    1     1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C   16 &lt;=0.125    4     8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    8   0.5    4     2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    4     0.5    4     2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    8 0.125    1     2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4    0.25  0.5     2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4   0.5 0.25     4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    4    0.25    4     4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    4   0.5    1     4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    8       4    4     1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G &gt;=64   &gt;=2    4   &gt;=8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H   16       2    4 &lt;=0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H &gt;=64     1    1 &lt;=0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16 &lt;=0.125    2     4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I &gt;=64   0.5    1 &lt;=0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    8     0.5  0.5     4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    2   0.5    1     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]  0.08585104  0.02969570  0.45008891 -0.14447995 -0.77838010 -0.08925698</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.119951582 -0.226246173  0.362260603 -0.443032753 -0.436374819</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.32583189  0.22919702  0.08907477 -0.19762231</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6]  0.004040346  1.429997229  0.047588443 -0.134850653 -0.483430641</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox    cipr gent  tobr amr_distance</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox  cipr gent  tobr amr_distance</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4    0.25  0.5     2  -0.77838010</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    2   0.5    1     1 -0.483430641</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    8     0.5  0.5     4  -0.19762231</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    8 0.125    1     2 -0.443032753</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    4     0.5    4     2  -0.14447995</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4   0.5 0.25     4 -0.436374819</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    4    0.25    4     4  -0.08925698</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    1   &gt;=2    1     1 -0.226246173</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    2    0.25  &gt;=8     8   0.02969570</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I &gt;=64   0.5    1 &lt;=0.5 -0.134850653</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    8       2  0.5     4   0.08585104</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A &gt;=64 0.125    1     2 -0.119951582</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16 &lt;=0.125    2     4   0.08907477</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    4   0.5    1     4  0.004040346</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H   16       2    4 &lt;=0.5   0.22919702</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H &gt;=64     1    1 &lt;=0.5  0.047588443</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    8       4    4     1   0.32583189</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    8   0.5    4     2  0.362260603</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C   16 &lt;=0.125    4     8   0.45008891</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G &gt;=64   &gt;=2    4   &gt;=8  1.429997229</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">y</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -251,17 +251,17 @@
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox    cipr gent  tobr amr_distance check_id_C</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox  cipr gent  tobr amr_distance check_id_C</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C   16 &lt;=0.125    4     8   0.45008891  0.0000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    8   0.5    4     2  0.362260603  0.0000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   G    8       4    4     1   0.32583189  0.1242570</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   H &gt;=64     1    1 &lt;=0.5  0.047588443  0.3146722</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   H   16       2    4 &lt;=0.5   0.22919702  0.2208919</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   F    4   0.5    1     4  0.004040346  0.3582203</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   I   16 &lt;=0.125    2     4   0.08907477  0.3610141</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   A &gt;=64 0.125    1     2 -0.119951582  0.4822122</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   A    8       2  0.5     4   0.08585104  0.3642379</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   I &gt;=64   0.5    1 &lt;=0.5 -0.134850653  0.4971113</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   B    2    0.25  &gt;=8     8   0.02969570  0.4203932</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   B    1   &gt;=2    1     1 -0.226246173  0.5885068</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   F    4    0.25    4     4  -0.08925698  0.5393459</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   E    4   0.5 0.25     4 -0.436374819  0.7986354</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   D    4     0.5    4     2  -0.14447995  0.5945689</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   D    8 0.125    1     2 -0.443032753  0.8052934</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   J    8     0.5  0.5     4  -0.19762231  0.6477112</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   J    2   0.5    1     1 -0.483430641  0.8456912</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  E    4    0.25  0.5     2  -0.77838010  1.2284690</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  G &gt;=64   &gt;=2    4   &gt;=8  1.429997229  1.0677366</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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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 +178,41 @@
    <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 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16      8       8       &lt;=0.001 0.5     16      &lt;=0.001 32      32     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 128    2      0.001  0.01   0.125  0.25   0.125  4      0.125  64    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002   0.25    16      0.5     16      8       0.125   32      4      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [11] &gt;=256  0.0625 2      32     16     0.01   0.001  64     1      32    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.025   0.0625  0.01    4       4       0.125   16     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 1      &gt;=256  0.5    64     0.5   </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 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 47 47 41 21  6  7  6 11  8 33 32 33 31 32 10 12 19 21 48 13 42 35 42 18 25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 18 44 40 45 12 48 17 46 17 35 12  9 26 16 42 15 40 44 25 32 49 42 27 40 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 'rsi'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] I R S R I I S I S I S S S S I I I I R R S S R S I</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] R R I I S I I R S I R S S I S R R I R I I S I S S</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 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] &lt;=0.001 0.125   0.125   0.01    32      0.005   128     8       0.01   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 64      &gt;=256   2       0.01    0.025   0.0625  &lt;=0.001 0.125   16     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.125   32      0.01    0.5     32      0.002   16      2       0.01   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.005   0.01    &lt;=0.001 &lt;=0.001 0.5     &lt;=0.001 8       0.125   &lt;=0.001</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.5     0.125   32      2       0.5     0.25    0.002  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 64      0.005   &lt;=0.001 0.005   &lt;=0.001 0.5     0.125  </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 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 1   8   1   0.5 1   1   16  16  4   16  16  16  32  2   1   2   2   16  1  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 2  1  64 8  4  8  8  8  1  64 1  1  8  4  64 2  8  2  2  1  64 1  2  4  1 </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [20] 0.5 1   8   4   0.5 16 </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 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 2      2      0.25   1      0.5    0.5    &gt;=4    0.125  2      0.0625</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 1       &lt;=0.025 0.125   0.25    0.25    2       0.125   &gt;=8     &lt;=0.025</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 2      0.0625 2      0.0625 0.5    0.25   0.125  0.5    1      &gt;=4   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.25    &gt;=8     2       &gt;=8     1       2       &gt;=8     4       0.5    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.25   0.125  2      0.125  0.125 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 1       0.25    2       0.0625  &gt;=8     0.25    1      </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 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 26 43 41 44 48 48 40 10 44 13 38 34 15 49 37 12 42 40 39 29 23 23 41 35 44</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 32 45 50 29 50 27 46 34 15 47  9 34 47 22 36 34 23 34 33 13 46 11 32  9 24</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 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 17 12 16 13 13 13 11 15 15 17 17 13 16 16 12 16 11 15 14 14 14 11 16 16 13</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 14 16 15 13 12 14 12 14 14 12 16 12 12 15 16 12 12 12 16 17 13 17 11 16 15</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 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16 24 26 24 27 18 16 16 25 27 25 24 27 18 21 25 27 26 25 22 16 22 15 23 21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 15 19 27 21 22 26 20 24 24 23 22 26 19 18 15 19 22 26 26 26 25 21 20 17 23</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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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] -0.05491494</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.03580118</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="">1.8.2.9035</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9037</small>
    <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