Built site for AMR: 1.8.2.9093@b94bc6c

2024-12-26 07:26:13 +01:00 · 2023-01-14 19:00:10 +00:00 · 2023-01-14 19:00:10 +00:00 · deed569722
commit deed569722
parent 805dcaf92e
100 changed files with 549 additions and 533 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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,16 +375,16 @@ the <code><a href="https://rdrr.io/r/utils/head.html" class="external-link">head
 data set:</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">data</span><span class="op">)</span></span></code></pre></div>
-<table style="width:100%;" class="table">
+<table class="table">
 <colgroup>
-<col width="14%">
+<col width="13%">
-<col width="14%">
+<col width="13%">
-<col width="14%">
+<col width="13%">
-<col width="21%">
+<col width="26%">
-<col width="6%">
+<col width="5%">
-<col width="6%">
+<col width="5%">
-<col width="6%">
+<col width="5%">
-<col width="6%">
+<col width="5%">
 <col width="9%">
 </colgroup>
 <thead><tr class="header">
@ -400,8 +400,19 @@ data set:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2013-06-11</td>
+<td align="center">2011-06-08</td>
-<td align="center">R1</td>
+<td align="center">B3</td>
 <td align="center">Hospital D</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2015-05-02</td>
 <td align="center">T1</td>
 <td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -410,22 +421,33 @@ data set:</p>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
-<tr class="even">
+<tr class="odd">
-<td align="center">2016-02-26</td>
+<td align="center">2015-10-18</td>
-<td align="center">G2</td>
+<td align="center">M10</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2016-05-15</td>
 <td align="center">B2</td>
 <td align="center">Hospital B</td>
 <td align="center">Staphylococcus aureus</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="odd">
-<td align="center">2014-06-18</td>
+<td align="center">2012-07-12</td>
-<td align="center">D2</td>
+<td align="center">B1</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Staphylococcus aureus</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -433,20 +455,9 @@ data set:</p>
 <td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2014-05-13</td>
+<td align="center">2013-06-19</td>
-<td align="center">L4</td>
+<td align="center">M2</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="odd">
 <td align="center">2010-05-08</td>
 <td align="center">G4</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -454,17 +465,6 @@ data set:</p>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 <tr class="even">
 <td align="center">2011-04-08</td>
 <td align="center">G7</td>
 <td align="center">Hospital A</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 </tr>
 </tbody>
 </table>
 <p>Now, let’s start the cleaning and the analysis!</p>
@ -499,16 +499,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,445</td>
+<td align="right">10,455</td>
-<td align="right">52.23%</td>
+<td align="right">52.28%</td>
-<td align="right">10,445</td>
+<td align="right">10,455</td>
-<td align="right">52.23%</td>
+<td align="right">52.28%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,555</td>
+<td align="right">9,545</td>
-<td align="right">47.78%</td>
+<td align="right">47.73%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@ -621,9 +621,9 @@ takes into account the antimicrobial susceptibility test results using
 <span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
 <span><span class="co"># 2</span></span>
 <span><span class="co"># Including isolates from ICU.</span></span>
-<span><span class="co"># =&gt; Found 10,661 'phenotype-based' first isolates (53.3% of total where a</span></span>
+<span><span class="co"># =&gt; Found 10,550 'phenotype-based' first isolates (52.8% of total where a</span></span>
 <span><span class="co">#    microbial ID was available)</span></span></code></pre></div>
-<p>So only 53.3% is suitable for resistance analysis! We can now filter
+<p>So only 52.8% is suitable for resistance analysis! We can now filter
 on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
 <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -634,7 +634,7 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
-<p>So we end up with 10,661 isolates for analysis. Now our data looks
+<p>So we end up with 10,550 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>
@ -651,8 +651,8 @@ like:</p>
 <col width="3%">
 <col width="6%">
 <col width="11%">
-<col width="11%">
+<col width="12%">
-<col width="9%">
+<col width="7%">
 <col width="5%">
 </colgroup>
 <thead><tr class="header">
@ -673,15 +673,15 @@ like:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">4</td>
+<td align="left">1</td>
-<td align="center">2014-05-13</td>
+<td align="center">2011-06-08</td>
-<td align="center">L4</td>
+<td align="center">B3</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">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>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
@ -689,10 +689,10 @@ like:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">5</td>
+<td align="left">6</td>
-<td align="center">2010-05-08</td>
+<td align="center">2013-06-19</td>
-<td align="center">G4</td>
+<td align="center">M2</td>
-<td align="center">Hospital B</td>
+<td align="center">Hospital D</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -705,67 +705,67 @@ like:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="left">6</td>
+<td align="left">7</td>
-<td align="center">2011-04-08</td>
+<td align="center">2017-08-21</td>
-<td align="center">G7</td>
+<td align="center">W8</td>
-<td align="center">Hospital A</td>
+<td align="center">Hospital B</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">M</td>
+<td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">7</td>
+<td align="left">8</td>
-<td align="center">2015-06-18</td>
+<td align="center">2011-06-07</td>
-<td align="center">F7</td>
+<td align="center">D4</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="center">B_STPHY_AURS</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
-<td align="center">Gram-negative</td>
+<td align="center">Gram-positive</td>
-<td align="center">Escherichia</td>
+<td align="center">Staphylococcus</td>
-<td align="center">coli</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="left">9</td>
-<td align="center">2013-04-22</td>
+<td align="center">2014-05-22</td>
-<td align="center">O4</td>
+<td align="center">G4</td>
 <td align="center">Hospital A</td>
-<td align="center">B_STRPT_PNMN</td>
+<td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
-<td align="center">F</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
+<td align="center">Staphylococcus</td>
-<td align="center">pneumoniae</td>
+<td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">13</td>
+<td align="left">10</td>
-<td align="center">2014-07-04</td>
+<td align="center">2017-10-08</td>
-<td align="center">H10</td>
+<td align="center">Y10</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital C</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">M</td>
+<td align="center">S</td>
-<td align="center">Gram-negative</td>
+<td align="center">F</td>
-<td align="center">Escherichia</td>
+<td align="center">Gram-positive</td>
-<td align="center">coli</td>
+<td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
@ -801,8 +801,8 @@ readable:</p>
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,661<br>
+Length: 10,550<br>
-Available: 10,661 (100%, NA: 0 = 0%)<br>
+Available: 10,550 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,638</td>
+<td align="right">4,580</td>
-<td align="right">43.50%</td>
+<td align="right">43.41%</td>
-<td align="right">4,638</td>
+<td align="right">4,580</td>
-<td align="right">43.50%</td>
+<td align="right">43.41%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,699</td>
+<td align="right">2,689</td>
-<td align="right">25.32%</td>
+<td align="right">25.49%</td>
-<td align="right">7,337</td>
+<td align="right">7,269</td>
-<td align="right">68.82%</td>
+<td align="right">68.90%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,127</td>
+<td align="right">2,098</td>
-<td align="right">19.95%</td>
+<td align="right">19.89%</td>
-<td align="right">9,464</td>
+<td align="right">9,367</td>
-<td align="right">88.77%</td>
+<td align="right">88.79%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,197</td>
+<td align="right">1,183</td>
-<td align="right">11.23%</td>
+<td align="right">11.21%</td>
-<td align="right">10,661</td>
+<td align="right">10,550</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@ -874,14 +874,14 @@ 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>
@ -902,8 +902,23 @@ antibiotic class they are in:</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2013-04-22</td>
+<td align="center">2014-02-15</td>
-<td align="center">O4</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="even">
 <td align="center">2013-04-24</td>
 <td align="center">U2</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
@ -916,10 +931,25 @@ antibiotic class they are in:</p>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
+<tr class="odd">
-<td align="center">2017-05-20</td>
+<td align="center">2016-10-17</td>
 <td align="center">J4</td>
-<td align="center">Hospital C</td>
+<td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">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">2016-08-24</td>
 <td align="center">B10</td>
 <td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -932,38 +962,8 @@ antibiotic class they are in:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2010-01-06</td>
+<td align="center">2014-02-03</td>
-<td align="center">Z7</td>
+<td align="center">F6</td>
 <td align="center">Hospital B</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2013-04-07</td>
 <td align="center">R8</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">R</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">2010-04-24</td>
 <td align="center">G2</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
 <td align="center">S</td>
@ -977,17 +977,17 @@ antibiotic class they are in:</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2017-10-15</td>
+<td align="center">2010-06-12</td>
-<td align="center">U1</td>
+<td align="center">J7</td>
 <td align="center">Hospital B</td>
-<td align="center">B_STRPT_PNMN</td>
+<td align="center">B_KLBSL_PNMN</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">F</td>
+<td align="center">M</td>
-<td align="center">Gram-positive</td>
+<td align="center">Gram-negative</td>
-<td align="center">Streptococcus</td>
+<td align="center">Klebsiella</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2172</td>
+<td align="center">2132</td>
-<td align="center">141</td>
+<td align="center">111</td>
-<td align="center">2325</td>
+<td align="center">2337</td>
-<td align="center">4638</td>
+<td align="center">4580</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3409</td>
+<td align="center">3342</td>
-<td align="center">162</td>
+<td align="center">182</td>
-<td align="center">1067</td>
+<td align="center">1056</td>
-<td align="center">4638</td>
+<td align="center">4580</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3344</td>
+<td align="center">3363</td>
 <td align="center">0</td>
-<td align="center">1294</td>
+<td align="center">1217</td>
-<td align="center">4638</td>
+<td align="center">4580</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4074</td>
+<td align="center">4007</td>
 <td align="center">0</td>
-<td align="center">564</td>
+<td align="center">573</td>
-<td align="center">4638</td>
+<td align="center">4580</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">1197</td>
+<td align="center">1183</td>
-<td align="center">1197</td>
+<td align="center">1183</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">926</td>
+<td align="center">909</td>
-<td align="center">62</td>
+<td align="center">59</td>
-<td align="center">209</td>
+<td align="center">215</td>
-<td align="center">1197</td>
+<td align="center">1183</td>
 </tr>
 </tbody>
 </table>
@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4074</td>
+<td align="center">4007</td>
 <td align="center">0</td>
-<td align="center">564</td>
+<td align="center">573</td>
-<td align="center">4638</td>
+<td align="center">4580</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1080</td>
+<td align="center">1071</td>
 <td align="center">0</td>
-<td align="center">117</td>
+<td align="center">112</td>
-<td align="center">1197</td>
+<td align="center">1183</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2419</td>
+<td align="center">2383</td>
 <td align="center">0</td>
-<td align="center">280</td>
+<td align="center">306</td>
-<td align="center">2699</td>
+<td align="center">2689</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">2127</td>
+<td align="center">2098</td>
-<td align="center">2127</td>
+<td align="center">2098</td>
 </tr>
 </tbody>
 </table>
@ -1137,7 +1137,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
 own:</p>
 <div class="sourceCode" id="cb25"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
-<span><span class="co"># [1] 0.5433824</span></span></code></pre></div>
+<span><span class="co"># [1] 0.5512796</span></span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and
 <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
@ -1152,19 +1152,19 @@ own:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5447360</td>
+<td align="center">0.5525129</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5379915</td>
+<td align="center">0.5444295</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5309842</td>
+<td align="center">0.5600751</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5608238</td>
+<td align="center">0.5548752</td>
 </tr>
 </tbody>
 </table>
@ -1189,23 +1189,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5447360</td>
+<td align="center">0.5525129</td>
-<td align="center">3163</td>
+<td align="center">3104</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5379915</td>
+<td align="center">0.5444295</td>
-<td align="center">3764</td>
+<td align="center">3725</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5309842</td>
+<td align="center">0.5600751</td>
-<td align="center">1646</td>
+<td align="center">1598</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5608238</td>
+<td align="center">0.5548752</td>
-<td align="center">2088</td>
+<td align="center">2123</td>
 </tr>
 </tbody>
 </table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7699439</td>
+<td align="center">0.7694323</td>
-<td align="center">0.8783959</td>
+<td align="center">0.8748908</td>
-<td align="center">0.9762829</td>
+<td align="center">0.9772926</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8253968</td>
+<td align="center">0.8182587</td>
-<td align="center">0.9022556</td>
+<td align="center">0.9053254</td>
-<td align="center">0.9841270</td>
+<td align="center">0.9822485</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7899222</td>
+<td align="center">0.7746374</td>
-<td align="center">0.8962579</td>
+<td align="center">0.8862030</td>
-<td align="center">0.9818451</td>
+<td align="center">0.9750837</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5514810</td>
+<td align="center">0.5424214</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5514810</td>
+<td align="center">0.5424214</td>
 </tr>
 </tbody>
 </table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">54.5%</td>
+<td align="right">55.3%</td>
-<td align="right">26.8%</td>
+<td align="right">26.3%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">53.8%</td>
+<td align="right">54.4%</td>
-<td align="right">25.7%</td>
+<td align="right">26.6%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">53.1%</td>
+<td align="right">56.0%</td>
-<td align="right">26.5%</td>
+<td align="right">27.7%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">56.1%</td>
+<td align="right">55.5%</td>
-<td align="right">26.0%</td>
+<td align="right">27.7%</td>
 </tr>
 </tbody>
 </table>
@ -1410,17 +1410,17 @@ 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] 8       1       8       128     0.125   0.025   0.125   0.25    0.01   </span></span>
+<span><span class="co">#   [1] 128     4       8       0.002   0.005   0.25    0.002   1       2      </span></span>
-<span><span class="co">#  [10] 0.002   0.025   0.125   &lt;=0.001 0.125   0.01    32      0.025   64     </span></span>
+<span><span class="co">#  [10] 128     0.025   64      0.5     2       1       0.025   0.025   64     </span></span>
-<span><span class="co">#  [19] 0.025   16      0.125   0.5     8       0.005   256     256     256    </span></span>
+<span><span class="co">#  [19] 8       0.025   0.005   128     0.002   64      32      0.002   &gt;=256  </span></span>
-<span><span class="co">#  [28] 8       0.5     0.005   32      256     0.01    &lt;=0.001 0.01    0.002  </span></span>
+<span><span class="co">#  [28] 0.5     0.5     1       4       0.005   0.005   0.005   16      &lt;=0.001</span></span>
-<span><span class="co">#  [37] 64      64      0.0625  2       256     2       0.005   0.005   8      </span></span>
+<span><span class="co">#  [37] 16      0.01    64      2       128     0.25    2       &gt;=256   16     </span></span>
-<span><span class="co">#  [46] &lt;=0.001 4       64      0.025   128     256     0.0625  &lt;=0.001 8      </span></span>
+<span><span class="co">#  [46] 0.002   0.25    0.0625  0.5     16      128     0.125   32      0.005  </span></span>
-<span><span class="co">#  [55] 0.5     0.002   1       &lt;=0.001 4       0.5     32      2       256    </span></span>
+<span><span class="co">#  [55] 128     32      32      8       0.002   16      0.002   128     2      </span></span>
-<span><span class="co">#  [64] 0.01    0.002   0.25    4       8       128     128     0.0625  16     </span></span>
+<span><span class="co">#  [64] 0.0625  2       4       0.005   0.25    16      1       8       0.025  </span></span>
-<span><span class="co">#  [73] 2       0.01    0.002   4       0.5     0.5     256     0.005   64     </span></span>
+<span><span class="co">#  [73] 16      8       0.01    32      0.125   8       1       0.01    0.0625 </span></span>
-<span><span class="co">#  [82] 16      0.125   128     0.005   4       1       1       256     0.01   </span></span>
+<span><span class="co">#  [82] &gt;=256   0.01    0.005   0.002   2       0.125   128     64      0.5    </span></span>
-<span><span class="co">#  [91] 0.002   4       1       0.0625  0.125   32      256     2       0.002  </span></span>
+<span><span class="co">#  [91] 0.01    8       64      64      1       0.025   &gt;=256   8       4      </span></span>
 <span><span class="co"># [100] 2</span></span></code></pre></div>
 <div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># base R:</span></span>
@ -1455,10 +1455,10 @@ 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] 30 31 18 26 29 17 30 31 18 18 19 25 28 22 22 24 26 31 30 29 27 25 26 30 19</span></span>
+<span><span class="co">#   [1] 31 25 30 30 21 26 27 26 22 21 30 31 22 29 22 30 30 28 21 19 31 31 30 20 25</span></span>
-<span><span class="co">#  [26] 23 17 17 25 21 21 28 27 29 17 28 30 29 28 29 28 31 29 28 28 29 19 30 29 27</span></span>
+<span><span class="co">#  [26] 24 17 20 27 24 20 22 28 31 20 25 30 25 21 31 21 22 29 18 23 19 23 19 19 19</span></span>
-<span><span class="co">#  [51] 24 29 17 27 28 18 21 17 26 17 23 31 27 17 18 29 26 22 20 20 21 21 28 19 17</span></span>
+<span><span class="co">#  [51] 25 22 22 29 22 17 21 19 21 26 17 27 23 28 27 20 18 24 29 26 23 27 27 19 20</span></span>
-<span><span class="co">#  [76] 31 27 24 28 21 24 23 30 25 22 19 28 25 27 25 28 25 18 26 30 19 27 28 20 17</span></span></code></pre></div>
+<span><span class="co">#  [76] 28 24 22 31 22 28 22 27 31 30 25 27 18 22 18 17 25 20 20 25 22 24 20 23 22</span></span></code></pre></div>
 <div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># base R:</span></span>
 <span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>
--- a/articles/AMR_files/figure-html/disk_plots-1.png
+++ b/articles/AMR_files/figure-html/disk_plots-1.png
--- a/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
+++ b/articles/AMR_files/figure-html/disk_plots_mo_ab-1.png
--- a/articles/AMR_files/figure-html/mic_plots-1.png
+++ b/articles/AMR_files/figure-html/mic_plots-1.png
--- a/articles/AMR_files/figure-html/mic_plots-2.png
+++ b/articles/AMR_files/figure-html/mic_plots-2.png
--- a/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
+++ b/articles/AMR_files/figure-html/mic_plots_mo_ab-1.png
--- a/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
+++ b/articles/AMR_files/figure-html/mic_plots_mo_ab-2.png
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/AMR_files/figure-html/plot
+++ b/articles/AMR_files/figure-html/plot
--- a/articles/EUCAST.html
+++ b/articles/EUCAST.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -375,19 +375,19 @@ names or codes, this would have worked exactly the same way:</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
 <span><span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
-<span><span class="co"># 1          R         S            S          S            S            R</span></span>
+<span><span class="co"># 1          S         S            S          R            R            S</span></span>
-<span><span class="co"># 2          I         R            I          R            I            I</span></span>
+<span><span class="co"># 2          R         R            I          R            S            I</span></span>
-<span><span class="co"># 3          R         S            I          S            S            R</span></span>
+<span><span class="co"># 3          I         R            I          S            R            I</span></span>
-<span><span class="co"># 4          R         S            I          S            I            S</span></span>
+<span><span class="co"># 4          R         I            R          S            R            S</span></span>
-<span><span class="co"># 5          R         R            R          I            I            R</span></span>
+<span><span class="co"># 5          I         I            I          S            I            R</span></span>
-<span><span class="co"># 6          S         R            R          S            S            S</span></span>
+<span><span class="co"># 6          S         S            R          S            I            I</span></span>
 <span><span class="co">#   kanamycin</span></span>
 <span><span class="co"># 1         I</span></span>
 <span><span class="co"># 2         R</span></span>
-<span><span class="co"># 3         S</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         R</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">
@ -428,40 +428,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3163</td>
+<td align="right">3198</td>
-<td align="right">63.26%</td>
+<td align="right">63.96%</td>
-<td align="right">3163</td>
+<td align="right">3198</td>
-<td align="right">63.26%</td>
+<td align="right">63.96%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">976</td>
+<td align="right">1027</td>
-<td align="right">19.52%</td>
+<td align="right">20.54%</td>
-<td align="right">4139</td>
+<td align="right">4225</td>
-<td align="right">82.78%</td>
+<td align="right">84.50%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">504</td>
+<td align="right">423</td>
-<td align="right">10.08%</td>
+<td align="right">8.46%</td>
-<td align="right">4643</td>
+<td align="right">4648</td>
-<td align="right">92.86%</td>
+<td align="right">92.96%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">259</td>
+<td align="right">243</td>
-<td align="right">5.18%</td>
+<td align="right">4.86%</td>
-<td align="right">4902</td>
+<td align="right">4891</td>
-<td align="right">98.04%</td>
+<td align="right">97.82%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">98</td>
+<td align="right">109</td>
-<td align="right">1.96%</td>
+<td align="right">2.18%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>
--- a/articles/PCA.html
+++ b/articles/PCA.html
@ -38,7 +38,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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/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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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/extra.css
+++ b/extra.css
@ -78,6 +78,11 @@ pre .co, .co {
  color: #999999 !important;
  font-style: italic !important;
 }
 pre code .r-out,
 pre code .r-msg {
  /* output of functions */
  color: #555555 !important;
 }
 code a[href],
 a[href] code,
 pre a[href],
--- a/extra.js
+++ b/extra.js
@ -33,15 +33,14 @@ $(document).ready(function() {
  // Replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
  $(".developers h2").text("Maintainers");
-  $(".citation h2:first").text("All contributors");
+  $(".citation h2:nth(0)").text("All contributors");
-  $(".citation h2:second").text("How to Cite");
+  $(".citation h2:nth(1)").text("How to Cite");
  // remove \donttest and \dontrun texts in Examples
  if ($("#ref-examples ~ div pre").length > 0) {
-    const regex1 = /# \\dont(test|run)\{(\n|<br>)*/ig;
+    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\donttest{", ""));
-    const regex2 = /(\n|<br>)*# \}/ig;
+    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# \\dontrun{", ""));
-    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll(regex1, ""));
+    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
    $("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll(regex2, ""));
  }
  // remove leading newline in code examples on changelog
--- 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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -132,7 +132,7 @@
    </div>
    <div class="section level2">
-<h2 class="pkg-version" data-toc-text="1.8.2.9092" id="amr-1829092">AMR 1.8.2.9092<a class="anchor" aria-label="anchor" href="#amr-1829092"></a></h2>
+<h2 class="pkg-version" data-toc-text="1.8.2.9093" id="amr-1829093">AMR 1.8.2.9093<a class="anchor" aria-label="anchor" href="#amr-1829093"></a></h2>
 <p><em>(this beta version will eventually become v2.0! We’re happy to reach a new major milestone soon!)</em></p>
 <p>This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.</p>
 <p><strong><a href="https://en.wikipedia.org/wiki/TL;DR" class="external-link">TL;DR</a></strong></p>
@ -145,19 +145,19 @@
 <li>Many new interesting functions, such as <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> and <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code>, and <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add custom microorganisms to this package</li>
 <li>Many small bug fixes</li>
 </ul><div class="section level3">
-<h3 id="new-1-8-2-9092">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9092"></a></h3>
+<h3 id="new-1-8-2-9093">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9093"></a></h3>
 <div class="section level4">
-<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9092">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9092"></a></h4>
+<h4 id="interpretation-of-mic-and-disk-diffusion-values-1-8-2-9093">Interpretation of MIC and disk diffusion values<a class="anchor" aria-label="anchor" href="#interpretation-of-mic-and-disk-diffusion-values-1-8-2-9093"></a></h4>
 <p>The clinical breakpoints and intrinsic resistance of EUCAST 2022 and CLSI 2022 have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 (v12.0) is now the new default guideline for all MIC and disks diffusion interpretations, and for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> to apply EUCAST Expert Rules. The default guideline (EUCAST) can now be changed with the new <code>AMR_guideline</code> option, such as: <code>options(AMR_guideline = "CLSI 2020")</code>.</p>
 <p>Interpretation guidelines older than 10 years were removed, the oldest now included guidelines of EUCAST and CLSI are from 2013.</p>
 </div>
 <div class="section level4">
-<h4 id="supported-languages-1-8-2-9092">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9092"></a></h4>
+<h4 id="supported-languages-1-8-2-9093">Supported languages<a class="anchor" aria-label="anchor" href="#supported-languages-1-8-2-9093"></a></h4>
 <p>We added support for the following languages: Chinese, Greek, Japanese, Polish, Turkish and Ukrainian. All antibiotic names are now available in these languages, and the AMR package will automatically determine a supported language based on the user system language.</p>
 <p>We are very grateful for the valuable input by our colleagues from other countries. The <code>AMR</code> package is now available in 16 languages and according to download stats used in almost all countries in the world!</p>
 </div>
 <div class="section level4">
-<h4 id="microbiological-taxonomy-1-8-2-9092">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9092"></a></h4>
+<h4 id="microbiological-taxonomy-1-8-2-9093">Microbiological taxonomy<a class="anchor" aria-label="anchor" href="#microbiological-taxonomy-1-8-2-9093"></a></h4>
 <p>The <code>microorganisms</code> data set no longer relies on the Catalogue of Life, but on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and is supplemented with the ‘backbone taxonomy’ from the Global Biodiversity Information Facility (GBIF). The structure of this data set has changed to include separate LPSN and GBIF identifiers. Almost all previous MO codes were retained. It contains over 1,400 taxonomic names from 2022.</p>
 <p>We previously relied on our own experience to categorise species into pathogenic groups, but we were very happy to encounter the very recent work of Bartlett <em>et al.</em> (2022, DOI <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">10.1099/mic.0.001269</a>) who extensively studied medical-scientific literature to categorise all bacterial species into groups. See <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> on how their work was incorporated into the <code>prevalence</code> column of the <code>microorganisms</code> data set. Using their results, the <code><a href="../reference/as.mo.html">as.mo()</a></code> and all <code>mo_*()</code> functions are now much better capable of converting user input to valid taxonomic records.</p>
 <p>The new function <code><a href="../reference/add_custom_microorganisms.html">add_custom_microorganisms()</a></code> allows users to add custom microorganisms to the <code>AMR</code> package.</p>
@ -181,7 +181,7 @@
 <li>The <code>microorganisms.old</code> data set was removed, and all previously accepted names are now included in the <code>microorganisms</code> data set. A new column <code>status</code> contains <code>"accepted"</code> for currently accepted names and <code>"synonym"</code> for taxonomic synonyms; currently invalid names. All previously accepted names now have a microorganisms ID and - if available - an LPSN, GBIF and SNOMED CT identifier.</li>
 </ul></div>
 <div class="section level4">
-<h4 id="antibiotic-agents-and-selectors-1-8-2-9092">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9092"></a></h4>
+<h4 id="antibiotic-agents-and-selectors-1-8-2-9093">Antibiotic agents and selectors<a class="anchor" aria-label="anchor" href="#antibiotic-agents-and-selectors-1-8-2-9093"></a></h4>
 <p>The new function <code><a href="../reference/add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> allows users to add custom antimicrobial codes and names to the <code>AMR</code> package.</p>
 <p>The <code>antibiotics</code> data set was greatly updated:</p>
 <ul><li>The following 20 antibiotics have been added (also includes the <a href="https://www.whocc.no/atc_ddd_index/?code=J01RA&amp;showdescription=no" class="external-link">new J01RA ATC group</a>): azithromycin/fluconazole/secnidazole (AFC), cefepime/amikacin (CFA), cefixime/ornidazole (CEO), ceftriaxone/beta-lactamase inhibitor (CEB), ciprofloxacin/metronidazole (CIM), ciprofloxacin/ornidazole (CIO), ciprofloxacin/tinidazole (CIT), furazidin (FUR), isoniazid/sulfamethoxazole/trimethoprim/pyridoxine (IST), lascufloxacin (LSC), levofloxacin/ornidazole (LEO), nemonoxacin (NEM), norfloxacin/metronidazole (NME), norfloxacin/tinidazole (NTI), ofloxacin/ornidazole (OOR), oteseconazole (OTE), rifampicin/ethambutol/isoniazid (REI), sarecycline (SRC), tetracycline/oleandomycin (TOL), and thioacetazone (TAT)</li>
@ -193,14 +193,14 @@
 </ul><p>Also, we added support for using antibiotic selectors in scoped <code>dplyr</code> verbs (with or without using <code><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars()</a></code>), such as in: <code>... %&gt;% summarise_at(aminoglycosides(), resistance)</code>, please see <code><a href="../reference/proportion.html">resistance()</a></code> for examples.</p>
 </div>
 <div class="section level4">
-<h4 id="antiviral-agents-1-8-2-9092">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9092"></a></h4>
+<h4 id="antiviral-agents-1-8-2-9093">Antiviral agents<a class="anchor" aria-label="anchor" href="#antiviral-agents-1-8-2-9093"></a></h4>
 <p>We now added extensive support for antiviral agents! For the first time, the <code>AMR</code> package has extensive support for antiviral drugs and to work with their names, codes and other data in any way.</p>
 <ul><li>The <code>antivirals</code> data set has been extended with 18 new drugs (also from the <a href="https://www.whocc.no/atc_ddd_index/?code=J05AJ&amp;showdescription=no" class="external-link">new J05AJ ATC group</a>) and now also contains antiviral identifiers and LOINC codes</li>
 <li>A new data type <code>av</code> (<em>antivirals</em>) has been added, which is functionally similar to <code>ab</code> for antibiotics</li>
 <li>Functions <code><a href="../reference/as.av.html">as.av()</a></code>, <code><a href="../reference/av_property.html">av_name()</a></code>, <code><a href="../reference/av_property.html">av_atc()</a></code>, <code><a href="../reference/av_property.html">av_synonyms()</a></code>, <code><a href="../reference/av_from_text.html">av_from_text()</a></code> have all been added as siblings to their <code>ab_*()</code> equivalents</li>
 </ul></div>
 <div class="section level4">
-<h4 id="other-new-functions-1-8-2-9092">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9092"></a></h4>
+<h4 id="other-new-functions-1-8-2-9093">Other new functions<a class="anchor" aria-label="anchor" href="#other-new-functions-1-8-2-9093"></a></h4>
 <ul><li>Function <code><a href="../reference/proportion.html">rsi_confidence_interval()</a></code> to add confidence intervals in AMR calculation. This is now also included in <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/proportion.html">proportion_df()</a></code>.</li>
 <li>Function <code><a href="../reference/mean_amr_distance.html">mean_amr_distance()</a></code> to calculate the mean AMR distance. The mean AMR distance is a normalised numeric value to compare AMR test results and can help to identify similar isolates, without comparing antibiograms by hand.</li>
 <li>Function <code><a href="../reference/as.rsi.html">rsi_interpretation_history()</a></code> to view the history of previous runs of <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. This returns a ‘logbook’ with the selected guideline, reference table and specific interpretation of each row in a data set on which <code><a href="../reference/as.rsi.html">as.rsi()</a></code> was run.</li>
@ -209,7 +209,7 @@
 </ul></div>
 </div>
 <div class="section level3">
-<h3 id="changes-1-8-2-9092">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9092"></a></h3>
+<h3 id="changes-1-8-2-9093">Changes<a class="anchor" aria-label="anchor" href="#changes-1-8-2-9093"></a></h3>
 <ul><li>Argument <code>combine_IR</code> has been removed from this package (affecting functions <code><a href="../reference/count.html">count_df()</a></code>, <code><a href="../reference/proportion.html">proportion_df()</a></code>, and <code><a href="../reference/proportion.html">rsi_df()</a></code> and some plotting functions), since it was replaced with <code>combine_SI</code> three years ago</li>
 <li>Using <code>units</code> in <code>ab_ddd(..., units = "...")</code> had been deprecated for some time and is now not supported anymore. Use <code><a href="../reference/ab_property.html">ab_ddd_units()</a></code> instead.</li>
 <li>Support for <code>data.frame</code>-enhancing R packages, more specifically: <code><a href="https://Rdatatable.gitlab.io/data.table/reference/data.table.html" class="external-link">data.table::data.table</a></code>, <code><a href="https://rdrr.io/pkg/janitor/man/tabyl.html" class="external-link">janitor::tabyl</a></code>, <code><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble::tibble</a></code>, and <code><a href="https://tsibble.tidyverts.org/reference/tsibble.html" class="external-link">tsibble::tsibble</a></code>. AMR package functions that have a data set as output (such as <code><a href="../reference/proportion.html">rsi_df()</a></code> and <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code>), will now return the same data type as the input.</li>
@ -248,7 +248,7 @@
 <li>Cleaning columns with <code><a href="../reference/as.rsi.html">as.rsi()</a></code>, <code><a href="../reference/as.mic.html">as.mic()</a></code>, or <code><a href="../reference/as.disk.html">as.disk()</a></code> will now show the column name in the warning for invalid results</li>
 </ul></div>
 <div class="section level3">
-<h3 id="other-1-8-2-9092">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9092"></a></h3>
+<h3 id="other-1-8-2-9093">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9093"></a></h3>
 <ul><li>Added Peter Dutey-Magni, Dmytro Mykhailenko, Anton Mymrikov, Andrew Norgan, and Jonas Salm as contributors, to thank them for their valuable input</li>
 <li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
 <li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>
--- a/pkgdown.yml
+++ b/pkgdown.yml
@ -11,7 +11,7 @@ articles:
  datasets: datasets.html
  resistance_predict: resistance_predict.html
  welcome_to_AMR: welcome_to_AMR.html
-last_built: 2023-01-14T16:17Z
+last_built: 2023-01-14T18:56Z
 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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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
@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="With add_custom_antimicrobials() you can add your own custom antimicrobial drug codes to the AMR package."><title>Add Custom Antimicrobials to This Package — add_custom_antimicrobials • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Add Custom Antimicrobials to This Package — add_custom_antimicrobials"><meta property="og:description" content="With add_custom_antimicrobials() you can add your own custom antimicrobial drug codes to the AMR package."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="With add_custom_antimicrobials() you can add your own custom antimicrobial drug names and codes."><title>Add Custom Antimicrobials — add_custom_antimicrobials • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Add Custom Antimicrobials — add_custom_antimicrobials"><meta property="og:description" content="With add_custom_antimicrobials() you can add your own custom antimicrobial drug names and codes."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -127,13 +127,13 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>Add Custom Antimicrobials to This Package</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Add Custom Antimicrobials</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/custom_antimicrobials.R" class="external-link"><code>R/custom_antimicrobials.R</code></a></small>
      <div class="d-none name"><code>add_custom_antimicrobials.Rd</code></div>
    </div>
    <div class="ref-description section level2">
-    <p>With <code>add_custom_antimicrobials()</code> you can add your own custom antimicrobial drug codes to the <code>AMR</code> package.</p>
+    <p>With <code>add_custom_antimicrobials()</code> you can add your own custom antimicrobial drug names and codes.</p>
    </div>
    <div class="section level2">
@ -171,14 +171,14 @@
    </div>
    <div class="section level2">
    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add custom microorganisms to this package.</p></div>
+    <div class="dont-index"><p><code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code> to add custom microorganisms.</p></div>
    </div>
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span></span></span>
-<span class="r-in"><span><span class="co"># returns NA and throws a warning (which is now suppressed):</span></span></span>
+<span class="r-in"><span><span class="co"># returns NA and throws a warning (which is suppressed here):</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/warning.html" class="external-link">suppressWarnings</a></span><span class="op">(</span></span></span>
 <span class="r-in"><span>  <span class="fu"><a href="as.ab.html">as.ab</a></span><span class="op">(</span><span class="st">"testab"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
--- a/reference/add_custom_microorganisms.html
+++ b/reference/add_custom_microorganisms.html
@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="With add_custom_microorganisms() you can add your own custom microorganisms to the AMR package, such the non-taxonomic outcome of laboratory analysis."><title>Add Custom Microorganisms to This Package — add_custom_microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Add Custom Microorganisms to This Package — add_custom_microorganisms"><meta property="og:description" content="With add_custom_microorganisms() you can add your own custom microorganisms to the AMR package, such the non-taxonomic outcome of laboratory analysis."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><meta name="description" content="With add_custom_microorganisms() you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis."><title>Add Custom Microorganisms — add_custom_microorganisms • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/font.css" rel="stylesheet"><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Add Custom Microorganisms — add_custom_microorganisms"><meta property="og:description" content="With add_custom_microorganisms() you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@msberends"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
 <script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
 <script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
 <![endif]--></head><body>
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -127,13 +127,13 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>Add Custom Microorganisms to This Package</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Add Custom Microorganisms</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/custom_microorganisms.R" class="external-link"><code>R/custom_microorganisms.R</code></a></small>
      <div class="d-none name"><code>add_custom_microorganisms.Rd</code></div>
    </div>
    <div class="ref-description section level2">
-    <p>With <code>add_custom_microorganisms()</code> you can add your own custom microorganisms to the <code>AMR</code> package, such the non-taxonomic outcome of laboratory analysis.</p>
+    <p>With <code>add_custom_microorganisms()</code> you can add your own custom microorganisms, such the non-taxonomic outcome of laboratory analysis.</p>
    </div>
    <div class="section level2">
@ -171,7 +171,7 @@
    </div>
    <div class="section level2">
    <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"></a></h2>
-    <div class="dont-index"><p><code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> to add custom antimicrobials to this package.</p></div>
+    <div class="dont-index"><p><code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> to add custom antimicrobials.</p></div>
    </div>
    <div class="section level2">
@ -263,22 +263,32 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># the function tries to be forgiving:</span></span></span>
 <span class="r-in"><span><span class="fu">add_custom_microorganisms</span><span class="op">(</span></span></span>
-<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>GENUS <span class="op">=</span> <span class="st">"ESCHERICHIA / KLEBSIELLA"</span>,</span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>GENUS <span class="op">=</span> <span class="st">"ESCHERICHIA / KLEBSIELLA SLASHLINE"</span>,</span></span>
-<span class="r-in"><span>             SPECIES <span class="op">=</span> <span class="st">"SPECIES"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span>             SPECIES <span class="op">=</span> <span class="st">"SPECIES"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Added Escherichia/Klebsiella to the internal microorganisms data set.</span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"ESCHERICHIA / KLEBSIELLA"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Escherichia/Klebsiella"</span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_rank</a></span><span class="op">(</span><span class="st">"ESCHERICHIA / KLEBSIELLA"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "genus"</span>
 <span class="r-in"><span><span class="co"># taxonomy still works, although a slashline genus was given as input:</span></span></span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"Escherichia/Klebsiella"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Enterobacteriaceae"</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># for groups and complexes, set them as species or subspecies:</span></span></span>
 <span class="r-in"><span><span class="fu">add_custom_microorganisms</span><span class="op">(</span></span></span>
-<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="st">"Citrobacter"</span>, species <span class="op">=</span> <span class="st">"freundii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span>  <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>genus <span class="op">=</span> <span class="st">"Citrobacter"</span>, </span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Added Citrobacter freundii Complex to the internal microorganisms data</span>
+<span class="r-in"><span>             species <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"freundii"</span>, <span class="st">"braakii complex"</span><span class="op">)</span>,</span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span>   set.</span>
+<span class="r-in"><span>             subspecies <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"complex"</span>, <span class="st">""</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"C. freundii complex"</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> [1] "Citrobacter freundii Complex"</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Added Citrobacter braakii complex and Citrobacter freundii complex to the</span>
-<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"C. freundii complex"</span><span class="op">)</span></span></span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span>   internal microorganisms data set.</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative"</span>
+<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Citrobacter freundii complex" "Citrobacter braakii complex" </span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_species</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "freundii complex" "braakii complex" </span>
 <span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [1] "Gram-negative" "Gram-negative"</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
    </div>
--- 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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -195,16 +195,16 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    birth_date age age_exact age_at_y2k</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1952-10-25  70  70.22192         47</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1935-04-03  87  87.78356         64</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1969-05-11  53  53.67945         30</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1962-12-21  60  60.06575         37</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1979-02-19  43  43.90137         20</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1948-03-12  74  74.84384         51</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1974-03-24  48  48.81096         25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1952-05-19  70  70.65753         47</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1932-09-05  90  90.35890         67</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1962-03-08  60  60.85479         37</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1953-11-17  69  69.15890         46</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-04-28  75  75.71507         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1936-10-22  86  86.23014         63</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1986-06-29  36  36.54521         13</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1961-02-11  61  61.92329         38</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1953-09-21  69  69.31507         46</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1933-09-12  89  89.33973         66</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1932-04-11  90  90.76164         67</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1937-08-10  85  85.43014         62</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1994-02-16  28  28.90959          5</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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.ab.html
+++ b/reference/as.ab.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/as.av.html
+++ b/reference/as.av.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -506,16 +506,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 12</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_input   ab_gu…¹ mo_in…² mo_guideline     guide…³</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>             <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-01-14 <span style="color: #949494;">16:18:00</span>     1 ampicillin AMP     Strep … B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2023-01-14 <span style="color: #949494;">18:56:49</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> 2023-01-14 <span style="color: #949494;">16:18:00</span>     1 AMP        AMP     Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2023-01-14 <span style="color: #949494;">18:56:50</span>     1 AMP        AMP     Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-01-14 <span style="color: #949494;">16:18:00</span>     1 CIP        CIP     Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2023-01-14 <span style="color: #949494;">18:56:50</span>     1 CIP        CIP     Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-01-14 <span style="color: #949494;">16:18:01</span>     1 GEN        GEN     Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2023-01-14 <span style="color: #949494;">18:56:50</span>     1 GEN        GEN     Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-01-14 <span style="color: #949494;">16:18:01</span>     1 TOB        TOB     Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2023-01-14 <span style="color: #949494;">18:56:51</span>     1 TOB        TOB     Escher… B_[ORD]_ENTRBCTR EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-01-14 <span style="color: #949494;">16:18:01</span>     1 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2023-01-14 <span style="color: #949494;">18:56:52</span>     1 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-01-14 <span style="color: #949494;">16:18:02</span>     1 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2023-01-14 <span style="color: #949494;">18:56:52</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> 2023-01-14 <span style="color: #949494;">16:18:02</span>     2 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2023-01-14 <span style="color: #949494;">18:56:52</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> 2023-01-14 <span style="color: #949494;">16:18:02</span>     3 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2023-01-14 <span style="color: #949494;">18:56:52</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> 2023-01-14 <span style="color: #949494;">16:18:02</span>     4 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2023-01-14 <span style="color: #949494;">18:56:52</span>     4 AMX        AMX     B_STRP… B_STRPT_PNMN     EUCAST…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 5 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   input &lt;dbl&gt;, outcome &lt;rsi&gt;, breakpoint_S_R &lt;chr&gt;, and abbreviated variable</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   names ¹ab_guideline, ²mo_input, ³guideline</span></span>
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/av_from_text.html
+++ b/reference/av_from_text.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
--- a/reference/av_property.html
+++ b/reference/av_property.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -182,40 +182,42 @@
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 36 10 11 17 57 60 18  7  5 18  8 60 31 28 16 41  3 43 48 61  2 46 35 51  2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 26 38 48  5  5  4 36 61 56  6 56 45 10 48 13 11 49 55 54 24  4 25 44 62 54</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 28 44 45  3 49 25 56 44 31 16  1  4 32 57  6 57 62 19 50 14 55 38 55 24 35</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 55 16 26 28 11  4 32 57  7 55 21 56 49 16  6  6 35  1 55 50 26 54 17 39  8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51]  5 15  7 36 38 28 20  5 24 12 63 39 17 13 35 20 30 20 13 44 13 23 21 36 45</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 36  6 41 59 47 18  8 47 13 24 18 24  3 59 49 24 32 34 59 20 60  2 25 17  4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 43 52 53 50 35 24 32  5 23 40 16 63 44 17 63 13 16 51 36 60 12  1  8 10 26</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 12 36 48 29  4 22  2 19 34 61 33 15 44  9 60  7 32 20 27 16 45 42 42 56 19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 25 56 55 60  1 37 23 30 20 58 11 25  8 21 29 27 10 54 59 59 17 12 11 44 33</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 60 43  3 36 13 30  8 16 12 22 27 14 22 36 25  4  8 29 14 45 43 12 20 52  3</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 48 54 18 39  8 52 26 40 58 33  7 16  8 16 49 12 15 61  1 28 48 18  1  4 19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 61 30 19 29 28 48 21 57 36 52 47 40 12 37 37 51 53 50 24 57 43 60 45 51 19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [151]  2 38 37 36  9 58 35 37 57 42 16 14 29 30 34 35  5 62 48 12 11 55 26 57 35</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 19 12 26 43 23 50 27 63 40 57 55  7  8 46 32 20 31 22 57 26 45 61 25 29 39</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 47 31 24 60 37 31 56 52 41 61 33 26 47 11  8 55 13 59 62 35 34 11 22 38  8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [176]  9  3 31 38  5 22 26 42 31 18 10 58 33 51 41 31 39 31 61 30 25 32 44 35  6</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13] FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73]  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85]  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [133]  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [169]  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE  TRUE FALSE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE  TRUE  TRUE  TRUE FALSE  TRUE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
 <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 2 × 46</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 46</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   date       patient   age gender ward  mo           PEN   OXA   FLC   AMX  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   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> 2002-07-23 F35553     51 M      ICU   B_STPHY_AURS R     NA    S     R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-12-13 285137     78 F      ICU      B_ESCHR_COLI R     NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-24 F35553     51 M      ICU   B_STPHY_AURS R     NA    S     R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2003-01-27 F35553     51 M      ICU      B_STPHY_EPDR R     NA    S     NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2003-01-25 088256     73 F      ICU      B_STPHY_CONS R     NA    R     R    </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2003-01-08 783073     83 M      Clinical B_STPHY_CONS 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>
@ -251,16 +253,16 @@
 <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> 207325  2011-05-08 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> A42180  2008-04-21 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 304508  2004-05-09 B         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 116866  2011-11-07 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 619705  2004-07-29 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 786327  2014-06-02 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 3CF3C4  2006-06-26 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F71508  2003-08-14 A         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> A79917  2016-05-21 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 900485  2003-07-17 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F5F794  2017-02-18 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 4DD722  2003-06-02 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 698578  2006-11-13 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E31724  2011-07-05 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 438785  2003-10-03 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 650215  2017-05-27 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> A26548  2003-04-13 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F61180  2016-02-15 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 418311  2006-11-10 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1B0933  2003-09-28 C         FALSE      </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@ -272,19 +274,19 @@
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [186]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [189]</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    ward     date       patient new_index new_logical</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    ward       date       patient new_index new_logical</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> ICU      2011-05-08 207325          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical   2008-04-21 A42180          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2004-05-09 304508          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical   2011-11-07 116866          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> ICU      2004-07-29 619705          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Outpatient 2014-06-02 786327          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2006-06-26 3CF3C4          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical   2003-08-14 F71508          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2016-05-21 A79917          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical   2003-07-17 900485          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2017-02-18 F5F794          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU        2003-06-02 4DD722          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Clinical 2006-11-13 698578          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU        2011-07-05 E31724          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU      2003-10-03 438785          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU        2017-05-27 650215          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU      2003-04-13 A26548          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU        2016-02-15 F61180          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> ICU      2006-11-10 418311          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical   2003-09-28 1B0933          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>
@ -299,9 +301,9 @@
 <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          126             14            52            77</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          112             15            52            73</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                47             12            30            35</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                65             13            36            50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         13              7            12            12</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         12              7            10            12</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@ -331,19 +333,19 @@
 <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 [192]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [197]</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo           ward     flag_episode</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo           ward       flag_episode</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 207325    UNKNOWN    ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> A42180  B_ENTRC_AVIM Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 304508  B_STRPT_PNMN Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 116866  B_STPHY_CONS Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 619705  B_STRPT_ANGN ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 786327  B_STRPT_EQUI Outpatient TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 3CF3C4  B_STPHY_CONS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> F71508  B_STRPT_GRPB Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> A79917  B_ESCHR_COLI Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 900485  B_STPHY_CONS Clinical   TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F5F794  B_STPHY_AURS ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 4DD722  B_ESCHR_COLI ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 698578  B_ESCHR_COLI Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E31724  B_STPHY_CONS ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 438785  B_STPHY_EPDR ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 650215  B_STRPT_INFN ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> A26548  B_STPHY_CONS ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> F61180  B_ESCHR_COLI ICU        TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 418311  B_STPHY_CONS ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1B0933  B_ENTRC      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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -155,7 +155,7 @@
          <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code> <code><a href="add_custom_microorganisms.html">clear_custom_microorganisms()</a></code> 
        </dt>
-        <dd>Add Custom Microorganisms to This Package</dd>
+        <dd>Add Custom Microorganisms</dd>
      </dl><dl><dt>
          <code><a href="mo_source.html">set_mo_source()</a></code> <code><a href="mo_source.html">get_mo_source()</a></code> 
@ -196,7 +196,7 @@
          <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code> <code><a href="add_custom_antimicrobials.html">clear_custom_antimicrobials()</a></code> 
        </dt>
-        <dd>Add Custom Antimicrobials to This Package</dd>
+        <dd>Add Custom Antimicrobials</dd>
      </dl></div><div class="section level2">
      <h2 id="preparing-data-antimicrobial-resistance">Preparing data: antimicrobial resistance<a class="anchor" aria-label="anchor" href="#preparing-data-antimicrobial-resistance"></a></h2>
--- 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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -172,9 +172,9 @@
    <div class="section level2">
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.080028</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.945639</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] -0.02298422</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04391036</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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -191,31 +191,30 @@
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">rsi</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_rsi</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">rsi</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'rsi'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] S S R S R I S R I S</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] I I I R S I I I I I</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">rsi</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.621059 -0.621059  1.449138 -0.621059  1.449138 -0.621059 -0.621059</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.3162278 -0.3162278 -0.3162278  2.8460499 -0.3162278 -0.3162278</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8]  1.449138 -0.621059 -0.621059</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.3162278 -0.3162278 -0.3162278 -0.3162278</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">mic</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">mic</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 64      0.5     &lt;=0.025 128     4       0.0625  256     2       128    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 4      &gt;=64   0.001  1      0.0625 0.0625 0.25   0.0625 4      4     </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.125  </span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">mic</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.84443028 -0.55224804 -1.41458279  1.04395575  0.04632838 -1.15082446</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.7050535  1.5873138 -1.9341805  0.2639234 -0.6183369 -0.6183369</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  1.24348122 -0.15319709  1.04395575 -0.95129899</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.1772067 -0.6183369  0.7050535  0.7050535</span>
 <span class="r-in"><span><span class="co"># equal to the Z-score of their log2:</span></span></span>
 <span class="r-in"><span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span> <span class="op">-</span> <span class="fu"><a href="https://rdrr.io/r/base/mean.html" class="external-link">mean</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span><span class="op">)</span> <span class="op">/</span> <span class="fu"><a href="https://rdrr.io/r/stats/sd.html" class="external-link">sd</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/Log.html" class="external-link">log2</a></span><span class="op">(</span><span class="va">mic</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.84443028 -0.55224804 -1.41458279  1.04395575  0.04632838 -1.15082446</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.7050535  1.5873138 -1.9341805  0.2639234 -0.6183369 -0.6183369</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  1.24348122 -0.15319709  1.04395575 -0.95129899</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.1772067 -0.6183369  0.7050535  0.7050535</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">disk</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_disk</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">disk</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'disk'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 31 19 25 45 43 45 10 42 38 47</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 38 50 21 40 26 10 16 45 24 19</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">disk</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.2747505 -1.2167523 -0.7457514  0.8242516  0.6672513  0.8242516</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.6768341  1.5693625 -0.5875812  0.8255888 -0.2156944 -1.4057323</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -1.9232536  0.5887511  0.2747505  0.9812518</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.9594681  1.1974757 -0.3644491 -0.7363360</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>
@ -225,36 +224,36 @@
 <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    S   20 &lt;=0.25    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    I   30    8    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    R   25      1    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    S   17    4  &gt;=4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    I   24    0.5    4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    R   19    8  &gt;=4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    S   17      2  &gt;=8</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    R   29    2  &gt;=4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   25 &lt;=0.25    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    I   19    8  &lt;=1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    R   28    &gt;=4 0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    R   28    8    2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    I   29      2    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    R   26    8  &gt;=4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    I   22      1  0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    I   25    1  &gt;=4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    I   18      2 0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   27    4  &gt;=4</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    I   21    0.5    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   21  0.5  &lt;=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" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.39633734  0.72619085  0.03532415  0.11086821 -0.37841945  0.83757068</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.09446764 -0.47291812  0.29008010  0.47684186 -0.78696988  0.47223165</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.41812023 -0.34726311 -0.56085146 -0.44520275</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.66233628 -0.39251526  0.54299934 -0.88655361</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "gent" and "tobr"</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr   gent tobr amr_distance</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>    id amox cipr gent tobr amr_distance</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   25 &lt;=0.25    1  -0.78135160</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   21  0.5  &lt;=1  -1.83069295</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    I   21    0.5    1  -0.41647341</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    I   19    8  &lt;=1  -0.45056183</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    I   22      1  0.5  -0.34520532</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H    I   25    1  &gt;=4  -0.29980604</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    I   18      2 0.25  -0.27393724</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    R   29    2  &gt;=4   0.04522674</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    S   20 &lt;=0.25    4  -0.19413138</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    I   30    8    2   0.14236523</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    R   28    &gt;=4 0.25   0.09094095</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    R   28    8    2   0.14236523</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    I   24    0.5    4   0.17074681</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    S   17    4  &gt;=4   0.39025951</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B    R   25      1    2   0.24201490</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I    R   27    4  &gt;=4   0.39025951</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    I   29      2    1   0.31328298</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    R   19    8  &gt;=4   0.73529229</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    S   17      2  &gt;=8   1.19411331</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G    R   26    8  &gt;=4   0.73529229</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>
@ -266,17 +265,17 @@
 <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    I   24    0.5    4   0.03532415 0.00000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    R   19    8  &gt;=4   0.29008010  0.0000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   D    S   17      2  &gt;=8   0.11086821 0.07554406</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   F    R   28    8    2   0.47223165  0.1821516</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   H    I   22      1  0.5  -0.34726311 0.38258727</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   D    R   29    2  &gt;=4   0.47684186  0.1867618</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   G    I   29      2    1   0.41812023 0.38279607</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   A    I   30    8    2   0.09446764  0.1956125</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    S   25 &lt;=0.25    1  -0.37841945 0.41374361</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   I    R   27    4  &gt;=4   0.54299934  0.2529192</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   A    S   20 &lt;=0.25    4  -0.39633734 0.43166149</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   G    R   26    8  &gt;=4   0.66233628  0.3722562</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   J    I   21    0.5    1  -0.44520275 0.48052690</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   H    I   25    1  &gt;=4  -0.39251526  0.6825954</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   I    I   18      2 0.25  -0.56085146 0.59617562</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   B    S   17    4  &gt;=4  -0.47291812  0.7629982</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   B    R   25      1    2   0.72619085 0.69086670</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   E    I   19    8  &lt;=1  -0.78696988  1.0770500</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  F    R   28    &gt;=4 0.25   0.83757068 0.80224652</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    R   21  0.5  &lt;=1  -0.88655361  1.1766337</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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -195,7 +195,7 @@
    <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"><a href="as.mo.html">mo_reset_session</a></span><span class="op">(</span><span class="op">)</span></span></span>
-<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Reset 16 previously matched input values.</span>
+<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Reset 17 previously matched input values.</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mo'</span>
--- a/reference/mo_property.html
+++ b/reference/mo_property.html
@ -10,7 +10,7 @@
    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -183,41 +183,42 @@
    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.002  0.005  32     32     &gt;=256  0.025  8      0.001  64     0.0625</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.5    0.25   8      0.025  0.01   2      0.025  8      64     256   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [11] &gt;=256  8      1      64     0.025  128    0.01   64     0.025  0.5   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 256    0.0625 128    0.005  64     1      256    4      16     8     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 4      0.002  0.5    0.001  0.5   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 256    8      0.001  4      32    </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] 32 43 22 35 41 40 26  6 34 37 42 11 50 10 41  8  7 44 31 19 44 26 16 46 33</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 41 32 18 50 41 40 44 26 32 22 48 24 42 49  7 16 19 15 39  9 50 46 27 41 19</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] R S S S I R S R S R R R R R S R S S R R I R I R S</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] R R I I S I R I I R I I S I R S R S R R I R I I 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] 0.01    0.125   2       &lt;=0.001 0.025   0.125   0.5     0.5     1      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] &lt;=0.005 8       0.0625  1       0.125   0.025   0.125   0.025   0.025  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 16      2       0.25    1       64      0.0625  0.5     0.002   0.01   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.01    0.5     0.125   16      2       64      16      0.0625  0.5    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.5     0.01    0.5     0.025   0.0625  1       0.025  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 32      0.0625  4       64      0.0625  &gt;=128   &lt;=0.005</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] 2  4  8  4  16 2  8  16 16 2  1  1  4  8  1  16 8  1  2  2  4  1  8  1  8 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.25 4    4    8    4    0.5  32   8    32   8    64   4    2    8    64  </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> [16] 16   0.25 4    0.5  2    8    2    16   4    4   </span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class 'mic'</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 8      0.0625 4      4      0.0625 8      8      0.25   0.25   0.125 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.125 0.5   4     8     1     1     0.5   8     0.25  0.25  0.125 2    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 4      0.25   0.125  0.125  8      4      2      0.0625 1      4     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.5   8     0.5   0.125 0.125 2     0.25  8     4     2     0.125 0.25 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 0.0625 1      0.5    16     1     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 8    </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] 44 19 39 43 28 43 13 43 29  8 33 45 19 20 10 32  9 30 35 37 23 40 18 27 22</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 33 38 45 45 16 20 31 36 34 30 44 26 18 37 31 48  8 38 50 35  9 22 49 46 23</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] 14 12 11 16 16 13 15 14 15 13 16 15 13 15 12 16 13 11 17 17 14 15 12 13 15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 16 13 12 16 14 17 16 17 11 12 14 17 12 12 14 13 16 15 13 12 12 12 16 15 17</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] 15 15 27 18 26 16 23 18 18 27 23 15 21 26 15 16 23 25 18 18 18 17 24 25 21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 26 15 18 19 17 15 26 25 18 19 23 16 16 15 24 15 21 22 26 25 24 22 24 21 25</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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -171,7 +171,7 @@ 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] -0.02838807</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.04475973</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="">1.8.2.9092</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9093</small>
    <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