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@@ -36,7 +36,7 @@
     
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
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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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -162,7 +162,7 @@
       <img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
                         <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
             
-            <h4 data-toc-skip class="date">15 October 2022</h4>
+            <h4 data-toc-skip class="date">18 October 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
       <div class="d-none name"><code>AMR.Rmd</code></div>
@@ -170,7 +170,7 @@
 
     
     
-<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 15 October 2022.</p>
+<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 18 October 2022.</p>
 <div class="section level2">
 <h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
 </h2>
@@ -201,21 +201,21 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2022-10-15</td>
+<td align="center">2022-10-18</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 </tr>
 <tr class="even">
-<td align="center">2022-10-15</td>
+<td align="center">2022-10-18</td>
 <td align="center">abcd</td>
 <td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">R</td>
 </tr>
 <tr class="odd">
-<td align="center">2022-10-15</td>
+<td align="center">2022-10-18</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@@ -325,54 +325,54 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2013-11-03</td>
+<td align="center">2015-11-08</td>
-<td align="center">S4</td>
+<td align="center">S1</td>
 <td align="center">Hospital D</td>
+<td align="center">Streptococcus pneumoniae</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+</tr>
+<tr class="even">
+<td align="center">2013-09-07</td>
+<td align="center">B1</td>
+<td align="center">Hospital C</td>
 <td align="center">Klebsiella pneumoniae</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">F</td>
+<td align="center">M</td>
+</tr>
+<tr class="odd">
+<td align="center">2014-08-17</td>
+<td align="center">K1</td>
+<td align="center">Hospital C</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2010-09-09</td>
+<td align="center">2015-03-30</td>
-<td align="center">P3</td>
+<td align="center">O4</td>
 <td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Staphylococcus aureus</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2011-01-31</td>
+<td align="center">2015-11-12</td>
-<td align="center">E10</td>
+<td align="center">T8</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Staphylococcus aureus</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="even">
-<td align="center">2012-02-03</td>
-<td align="center">D6</td>
-<td align="center">Hospital D</td>
-<td align="center">Escherichia coli</td>
-<td align="center">S</td>
-<td align="center">I</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="odd">
-<td align="center">2015-06-15</td>
-<td align="center">V10</td>
-<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@@ -380,15 +380,15 @@
 <td align="center">F</td>
 </tr>
 <tr class="even">
-<td align="center">2010-03-18</td>
+<td align="center">2011-12-03</td>
-<td align="center">U8</td>
+<td align="center">I9</td>
 <td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
+<td align="center">Staphylococcus aureus</td>
-<td align="center">R</td>
-<td align="center">I</td>
 <td align="center">S</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>
 </tr>
 </tbody>
 </table>
@@ -422,16 +422,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,447</td>
+<td align="right">10,419</td>
-<td align="right">52.24%</td>
+<td align="right">52.10%</td>
-<td align="right">10,447</td>
+<td align="right">10,419</td>
-<td align="right">52.24%</td>
+<td align="right">52.10%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,553</td>
+<td align="right">9,581</td>
-<td align="right">47.77%</td>
+<td align="right">47.91%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@@ -488,9 +488,9 @@ Longest: 1</p>
 <span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
 <span><span class="co"># 2</span></span>
 <span><span class="co"># Including isolates from ICU.</span></span>
-<span><span class="co"># =&gt; Found 10,641 'phenotype-based' first isolates (53.2% of total where a</span></span>
+<span><span class="co"># =&gt; Found 10,701 'phenotype-based' first isolates (53.5% of total where a</span></span>
 <span><span class="co">#    microbial ID was available)</span></span></code></pre></div>
-<p>So only 53.2% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
+<p>So only 53.5% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@@ -499,7 +499,7 @@ Longest: 1</p>
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
 <span>  <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
 <span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
-<p>So we end up with 10,641 isolates for analysis. Now our data looks like:</p>
+<p>So we end up with 10,701 isolates for analysis. Now our data looks like:</p>
 <div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
 <table style="width:100%;" class="table">
@@ -537,78 +537,94 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
+<td align="left">2</td>
-<td align="center">2013-11-03</td>
+<td align="center">2013-09-07</td>
-<td align="center">S4</td>
+<td align="center">B1</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital C</td>
 <td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Klebsiella</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="left">9</td>
-<td align="center">2016-10-09</td>
-<td align="center">U9</td>
-<td align="center">Hospital B</td>
-<td align="center">B_KLBSL_PNMN</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Klebsiella</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="left">10</td>
-<td align="center">2016-12-03</td>
-<td align="center">D2</td>
-<td align="center">Hospital A</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
+<td align="center">Klebsiella</td>
-<td align="center">coli</td>
+<td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">12</td>
+<td align="left">7</td>
-<td align="center">2017-12-08</td>
+<td align="center">2014-10-09</td>
-<td align="center">C5</td>
+<td align="center">X9</td>
 <td align="center">Hospital A</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">M</td>
+<td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="left">13</td>
+<td align="left">8</td>
-<td align="center">2015-07-26</td>
+<td align="center">2016-01-09</td>
-<td align="center">W6</td>
+<td align="center">V8</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">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="left">10</td>
+<td align="center">2013-10-07</td>
+<td align="center">X9</td>
 <td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
+<td align="center">F</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td align="left">11</td>
+<td align="center">2017-09-13</td>
+<td align="center">G8</td>
+<td align="center">Hospital B</td>
+<td align="center">B_KLBSL_PNMN</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+<td align="center">Gram-negative</td>
+<td align="center">Klebsiella</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="left">13</td>
+<td align="center">2014-10-23</td>
+<td align="center">Y3</td>
+<td align="center">Hospital D</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-negative</td>
@@ -616,22 +632,6 @@ Longest: 1</p>
 <td align="center">coli</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="left">14</td>
-<td align="center">2014-06-06</td>
-<td align="center">I9</td>
-<td align="center">Hospital D</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">I</td>
-<td align="center">I</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>
 </tbody>
 </table>
 <p>Time for the analysis!</p>
@@ -653,8 +653,8 @@ Longest: 1</p>
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 10,641<br>
+Length: 10,701<br>
-Available: 10,641 (100.0%, NA: 0 = 0.0%)<br>
+Available: 10,701 (100.0%, NA: 0 = 0.0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@@ -671,33 +671,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">4,650</td>
+<td align="right">4,606</td>
-<td align="right">43.70%</td>
+<td align="right">43.04%</td>
-<td align="right">4,650</td>
+<td align="right">4,606</td>
-<td align="right">43.70%</td>
+<td align="right">43.04%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">2,752</td>
+<td align="right">2,751</td>
-<td align="right">25.86%</td>
+<td align="right">25.71%</td>
-<td align="right">7,402</td>
+<td align="right">7,357</td>
-<td align="right">69.56%</td>
+<td align="right">68.75%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,109</td>
+<td align="right">2,166</td>
-<td align="right">19.82%</td>
+<td align="right">20.24%</td>
-<td align="right">9,511</td>
+<td align="right">9,523</td>
-<td align="right">89.38%</td>
+<td align="right">88.99%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,130</td>
+<td align="right">1,178</td>
-<td align="right">10.62%</td>
+<td align="right">11.01%</td>
-<td align="right">10,641</td>
+<td align="right">10,701</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@@ -716,14 +716,14 @@ Longest: 24</p>
 <col width="9%">
 <col width="9%">
 <col width="9%">
-<col width="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>
@@ -744,14 +744,44 @@ Longest: 24</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2014-06-06</td>
+<td align="center">2016-01-09</td>
-<td align="center">I9</td>
+<td align="center">V8</td>
-<td align="center">Hospital D</td>
+<td align="center">Hospital A</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">I</td>
+<td align="center">R</td>
-<td align="center">I</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
+<td align="center">F</td>
+<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">2013-10-07</td>
+<td align="center">X9</td>
+<td align="center">Hospital B</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">F</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td align="center">2012-07-31</td>
+<td align="center">E10</td>
+<td align="center">Hospital A</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
@@ -759,75 +789,45 @@ Longest: 24</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="center">2012-11-06</td>
+<td align="center">2017-01-14</td>
-<td align="center">S6</td>
+<td align="center">L10</td>
-<td align="center">Hospital C</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">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
-<td align="center">2013-06-12</td>
+<td align="center">2013-01-17</td>
-<td align="center">X6</td>
+<td align="center">B3</td>
+<td align="center">Hospital B</td>
+<td align="center">B_STRPT_PNMN</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center">Streptococcus</td>
+<td align="center">pneumoniae</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="center">2012-09-05</td>
+<td align="center">A8</td>
 <td align="center">Hospital D</td>
 <td align="center">B_STRPT_PNMN</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">F</td>
-<td align="center">Gram-positive</td>
-<td align="center">Streptococcus</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="center">2012-05-27</td>
-<td align="center">U4</td>
-<td align="center">Hospital B</td>
-<td align="center">B_STPHY_AURS</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">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">2011-05-24</td>
-<td align="center">T10</td>
-<td align="center">Hospital B</td>
-<td align="center">B_KLBSL_PNMN</td>
 <td align="center">R</td>
 <td align="center">R</td>
-<td align="center">S</td>
 <td align="center">R</td>
-<td align="center">F</td>
-<td align="center">Gram-negative</td>
-<td align="center">Klebsiella</td>
-<td align="center">pneumoniae</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="center">2016-12-19</td>
-<td align="center">T6</td>
-<td align="center">Hospital B</td>
-<td align="center">B_STRPT_PNMN</td>
-<td align="center">I</td>
-<td align="center">I</td>
-<td align="center">S</td>
 <td align="center">R</td>
-<td align="center">F</td>
+<td align="center">M</td>
 <td align="center">Gram-positive</td>
 <td align="center">Streptococcus</td>
 <td align="center">pneumoniae</td>
@@ -854,50 +854,50 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">2161</td>
+<td align="center">2177</td>
-<td align="center">117</td>
+<td align="center">144</td>
-<td align="center">2372</td>
+<td align="center">2285</td>
-<td align="center">4650</td>
+<td align="center">4606</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">3443</td>
+<td align="center">3399</td>
-<td align="center">155</td>
+<td align="center">161</td>
-<td align="center">1052</td>
+<td align="center">1046</td>
-<td align="center">4650</td>
+<td align="center">4606</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">3401</td>
+<td align="center">3382</td>
 <td align="center">0</td>
-<td align="center">1249</td>
+<td align="center">1224</td>
-<td align="center">4650</td>
+<td align="center">4606</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4070</td>
+<td align="center">4032</td>
 <td align="center">0</td>
-<td align="center">580</td>
+<td align="center">574</td>
-<td align="center">4650</td>
+<td align="center">4606</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">1130</td>
+<td align="center">1178</td>
-<td align="center">1130</td>
+<td align="center">1178</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">902</td>
+<td align="center">927</td>
-<td align="center">47</td>
+<td align="center">40</td>
-<td align="center">181</td>
+<td align="center">211</td>
-<td align="center">1130</td>
+<td align="center">1178</td>
 </tr>
 </tbody>
 </table>
@@ -920,34 +920,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">4070</td>
+<td align="center">4032</td>
 <td align="center">0</td>
-<td align="center">580</td>
+<td align="center">574</td>
-<td align="center">4650</td>
+<td align="center">4606</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">GEN</td>
-<td align="center">1013</td>
+<td align="center">1059</td>
 <td align="center">0</td>
-<td align="center">117</td>
+<td align="center">119</td>
-<td align="center">1130</td>
+<td align="center">1178</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">GEN</td>
-<td align="center">2450</td>
+<td align="center">2442</td>
 <td align="center">0</td>
-<td align="center">302</td>
+<td align="center">309</td>
-<td align="center">2752</td>
+<td align="center">2751</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">2109</td>
+<td align="center">2166</td>
-<td align="center">2109</td>
+<td align="center">2166</td>
 </tr>
 </tbody>
 </table>
@@ -961,7 +961,7 @@ Longest: 24</p>
 <p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
 <div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
-<span><span class="co"># [1] 0.5466591</span></span></code></pre></div>
+<span><span class="co"># [1] 0.5415382</span></span></code></pre></div>
 <p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@@ -975,19 +975,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5511962</td>
+<td align="center">0.5472908</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5518367</td>
+<td align="center">0.5424089</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5463475</td>
+<td align="center">0.5286935</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5317893</td>
+<td align="center">0.5414567</td>
 </tr>
 </tbody>
 </table>
@@ -1008,23 +1008,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5511962</td>
+<td align="center">0.5472908</td>
-<td align="center">3135</td>
+<td align="center">3119</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5518367</td>
+<td align="center">0.5424089</td>
-<td align="center">3675</td>
+<td align="center">3761</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5463475</td>
+<td align="center">0.5286935</td>
-<td align="center">1629</td>
+<td align="center">1638</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5317893</td>
+<td align="center">0.5414567</td>
-<td align="center">2202</td>
+<td align="center">2183</td>
 </tr>
 </tbody>
 </table>
@@ -1047,27 +1047,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.7737634</td>
+<td align="center">0.7729049</td>
-<td align="center">0.8752688</td>
+<td align="center">0.8753799</td>
-<td align="center">0.9750538</td>
+<td align="center">0.9780721</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8398230</td>
+<td align="center">0.8208829</td>
-<td align="center">0.8964602</td>
+<td align="center">0.8989813</td>
-<td align="center">0.9787611</td>
+<td align="center">0.9813243</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.7914244</td>
+<td align="center">0.7931661</td>
-<td align="center">0.8902616</td>
+<td align="center">0.8876772</td>
-<td align="center">0.9792878</td>
+<td align="center">0.9756452</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5400664</td>
+<td align="center">0.5420129</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5400664</td>
+<td align="center">0.5420129</td>
 </tr>
 </tbody>
 </table>
@@ -1092,23 +1092,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="left">Hospital A</td>
-<td align="right">55.1%</td>
+<td align="right">54.7%</td>
-<td align="right">26.5%</td>
+<td align="right">26.4%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital B</td>
-<td align="right">55.2%</td>
+<td align="right">54.2%</td>
-<td align="right">26.7%</td>
+<td align="right">26.5%</td>
 </tr>
 <tr class="odd">
 <td align="left">Hospital C</td>
-<td align="right">54.6%</td>
+<td align="right">52.9%</td>
-<td align="right">25.0%</td>
+<td align="right">25.6%</td>
 </tr>
 <tr class="even">
 <td align="left">Hospital D</td>
-<td align="right">53.2%</td>
+<td align="right">54.1%</td>
-<td align="right">25.3%</td>
+<td align="right">26.4%</td>
 </tr>
 </tbody>
 </table>
@@ -1206,16 +1206,18 @@ Longest: 24</p>
 <code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
 <span><span class="va">mic_values</span></span>
 <span><span class="co"># Class &lt;mic&gt;</span></span>
-<span><span class="co">#   [1] 128    64     128    0.001  4      0.25   64     0.5    32     0.25  </span></span>
+<span><span class="co">#   [1] 0.025   &lt;=0.001 &lt;=0.001 128     4       0.0625  0.0625  2       64     </span></span>
-<span><span class="co">#  [11] 0.025  0.002  1      16     0.005  0.025  0.25   0.005  0.001  64    </span></span>
+<span><span class="co">#  [10] 4       8       0.25    16      0.002   0.5     0.125   64      0.0625 </span></span>
-<span><span class="co">#  [21] 0.025  1      16     &gt;=256  16     1      16     0.001  0.125  64    </span></span>
+<span><span class="co">#  [19] 16      2       0.25    0.01    0.25    32      &lt;=0.001 32      64     </span></span>
-<span><span class="co">#  [31] 8      0.002  0.5    0.005  0.005  4      8      0.002  0.025  32    </span></span>
+<span><span class="co">#  [28] 0.0625  &lt;=0.001 0.005   2       0.5     0.01    0.25    1       &lt;=0.001</span></span>
-<span><span class="co">#  [41] 0.0625 0.001  0.125  2      8      16     0.25   1      128    4     </span></span>
+<span><span class="co">#  [37] 0.125   0.25    4       128     64      0.25    2       16      256    </span></span>
-<span><span class="co">#  [51] 0.001  0.125  0.005  0.25   0.5    0.0625 0.0625 0.005  0.5    1     </span></span>
+<span><span class="co">#  [46] 4       0.005   8       0.25    16      0.005   0.125   0.005   1      </span></span>
-<span><span class="co">#  [61] 0.005  16     4      0.025  32     16     128    0.5    16     4     </span></span>
+<span><span class="co">#  [55] &lt;=0.001 32      1       0.25    256     1       16      128     0.002  </span></span>
-<span><span class="co">#  [71] 0.002  1      0.5    0.5    0.025  8      32     16     64     32    </span></span>
+<span><span class="co">#  [64] 64      8       16      0.005   0.5     1       0.025   &lt;=0.001 &lt;=0.001</span></span>
-<span><span class="co">#  [81] 4      32     2      &gt;=256  0.125  0.025  &gt;=256  16     2      0.01  </span></span>
+<span><span class="co">#  [73] 0.005   0.002   0.0625  64      64      2       0.125   0.002   0.125  </span></span>
-<span><span class="co">#  [91] 0.5    128    0.01   0.0625 128    32     0.125  1      0.125  0.025</span></span></code></pre></div>
+<span><span class="co">#  [82] 1       0.025   1       2       8       0.0625  1       256     256    </span></span>
+<span><span class="co">#  [91] &lt;=0.001 32      0.002   2       0.002   &lt;=0.001 1       0.01    2      </span></span>
+<span><span class="co"># [100] 0.01</span></span></code></pre></div>
 <div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># base R:</span></span>
 <span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@@ -1242,10 +1244,10 @@ Longest: 24</p>
 <code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
 <span><span class="va">disk_values</span></span>
 <span><span class="co"># Class &lt;disk&gt;</span></span>
-<span><span class="co">#   [1] 28 21 23 24 17 19 17 17 29 20 28 20 31 17 24 25 21 29 19 18 30 21 22 29 19</span></span>
+<span><span class="co">#   [1] 19 20 26 23 18 29 19 26 26 18 19 29 31 31 18 25 23 19 25 26 19 24 17 25 26</span></span>
-<span><span class="co">#  [26] 24 27 18 19 28 20 19 21 30 17 29 28 26 23 19 20 30 25 19 19 28 19 25 23 19</span></span>
+<span><span class="co">#  [26] 30 23 19 17 31 19 25 26 22 24 26 24 31 21 20 29 23 19 21 18 31 24 18 29 22</span></span>
-<span><span class="co">#  [51] 20 18 23 27 28 28 17 30 22 24 30 27 18 24 25 22 30 21 29 30 29 31 23 28 31</span></span>
+<span><span class="co">#  [51] 22 19 29 17 30 27 26 24 23 21 19 27 22 22 27 17 22 18 28 27 23 19 20 25 18</span></span>
-<span><span class="co">#  [76] 19 17 22 25 25 21 17 31 31 24 30 30 26 20 19 20 25 25 23 17 24 21 20 18 18</span></span></code></pre></div>
+<span><span class="co">#  [76] 31 31 27 30 29 29 24 27 30 28 24 23 26 18 29 21 27 27 25 25 18 21 28 19 19</span></span></code></pre></div>
 <div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="co"># base R:</span></span>
 <span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -314,19 +314,19 @@ Unique: 2</p>
 <div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
 <span><span class="co">#   rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
-<span><span class="co"># 1          R         S            R          S            I            R</span></span>
+<span><span class="co"># 1          I         R            I          I            R            S</span></span>
-<span><span class="co"># 2          I         S            R          R            R            S</span></span>
+<span><span class="co"># 2          R         R            I          S            S            R</span></span>
-<span><span class="co"># 3          S         I            I          S            I            I</span></span>
+<span><span class="co"># 3          R         R            R          R            I            R</span></span>
-<span><span class="co"># 4          I         I            S          S            R            R</span></span>
+<span><span class="co"># 4          R         R            I          S            R            S</span></span>
-<span><span class="co"># 5          R         I            R          S            I            I</span></span>
+<span><span class="co"># 5          R         R            I          R            S            I</span></span>
-<span><span class="co"># 6          I         I            S          S            I            S</span></span>
+<span><span class="co"># 6          S         S            I          S            S            I</span></span>
 <span><span class="co">#   kanamycin</span></span>
-<span><span class="co"># 1         S</span></span>
+<span><span class="co"># 1         I</span></span>
-<span><span class="co"># 2         I</span></span>
+<span><span class="co"># 2         R</span></span>
 <span><span class="co"># 3         R</span></span>
-<span><span class="co"># 4         R</span></span>
+<span><span class="co"># 4         S</span></span>
 <span><span class="co"># 5         S</span></span>
-<span><span class="co"># 6         S</span></span></code></pre></div>
+<span><span class="co"># 6         R</span></span></code></pre></div>
 <p>We can now add the interpretation of MDR-TB to our data set. You can use:</p>
 <div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu"><a href="../reference/mdro.html">mdro</a></span><span class="op">(</span><span class="va">my_TB_data</span>, guideline <span class="op">=</span> <span class="st">"TB"</span><span class="op">)</span></span></code></pre></div>
@@ -357,40 +357,40 @@ Unique: 5</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Mono-resistant</td>
-<td align="right">3196</td>
+<td align="right">3246</td>
-<td align="right">63.92%</td>
+<td align="right">64.92%</td>
-<td align="right">3196</td>
+<td align="right">3246</td>
-<td align="right">63.92%</td>
+<td align="right">64.92%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Negative</td>
-<td align="right">989</td>
+<td align="right">982</td>
-<td align="right">19.78%</td>
+<td align="right">19.64%</td>
-<td align="right">4185</td>
+<td align="right">4228</td>
-<td align="right">83.70%</td>
+<td align="right">84.56%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Multi-drug-resistant</td>
-<td align="right">455</td>
+<td align="right">407</td>
-<td align="right">9.10%</td>
+<td align="right">8.14%</td>
-<td align="right">4640</td>
+<td align="right">4635</td>
-<td align="right">92.80%</td>
+<td align="right">92.70%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Poly-resistant</td>
-<td align="right">249</td>
+<td align="right">248</td>
-<td align="right">4.98%</td>
+<td align="right">4.96%</td>
-<td align="right">4889</td>
+<td align="right">4883</td>
-<td align="right">97.78%</td>
+<td align="right">97.66%</td>
 </tr>
 <tr class="odd">
 <td align="left">5</td>
 <td align="left">Extensively drug-resistant</td>
-<td align="right">111</td>
+<td align="right">117</td>
-<td align="right">2.22%</td>
+<td align="right">2.34%</td>
 <td align="right">5000</td>
 <td align="right">100.00%</td>
 </tr>

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
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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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
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@@ -162,7 +162,7 @@
       <img src="../logo.svg" class="logo" alt=""><h1>How to import data from SPSS / SAS / Stata</h1>
                         <h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
             
-            <h4 data-toc-skip class="date">15 October 2022</h4>
+            <h4 data-toc-skip class="date">18 October 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
       <div class="d-none name"><code>SPSS.Rmd</code></div>
@@ -196,7 +196,7 @@
 </li>
 <li>
 <p><strong>R has a huge community.</strong></p>
-<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">466,054 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
+<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">466,988 R-related questions</a> have already been asked on this platform (that covers questions and answers for any programming language). In my own experience, most questions are answered within a couple of minutes.</p>
 </li>
 <li>
 <p><strong>R understands any data type, including SPSS/SAS/Stata.</strong></p>

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="">1.8.2.9018</small>
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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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
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@@ -161,7 +161,7 @@
   <main id="main" class="col-md-9"><div class="page-header">
       <img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
             
-            <h4 data-toc-skip class="date">15 October 2022</h4>
+            <h4 data-toc-skip class="date">18 October 2022</h4>
       
       <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
       <div class="d-none name"><code>datasets.Rmd</code></div>
@@ -177,7 +177,7 @@
 </h2>
 <p>A data set with 48,787 rows and 22 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>source</em>, <em>lpsn</em>, <em>lpsn_parent</em>, <em>lpsn_renamed_to</em>, <em>gbif</em>, <em>gbif_parent</em>, <em>gbif_renamed_to</em>, <em>prevalence</em> and <em>snomed</em>.</p>
 <p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 15 October 2022 13:21:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
+<p>It was last updated on 18 October 2022 20:55:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds" class="external-link">original R Data Structure (RDS) file</a> (1.1 MB)<br>
@@ -449,7 +449,7 @@
 </h2>
 <p>A data set with 464 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
 <p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 15 October 2022 13:21:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 18 October 2022 20:55:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds" class="external-link">original R Data Structure (RDS) file</a> (36 kB)<br>
@@ -622,7 +622,7 @@
 </h2>
 <p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
 <p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 15 October 2022 13:21:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
+<p>It was last updated on 18 October 2022 20:55:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds" class="external-link">original R Data Structure (RDS) file</a> (4 kB)<br>
@@ -754,7 +754,7 @@
 </h2>
 <p>A data set with 20,369 rows and 11 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>, <em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
 <p>This data set is in R available as <code>rsi_translation</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 15 October 2022 13:21:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
+<p>It was last updated on 18 October 2022 20:55:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">original R Data Structure (RDS) file</a> (49 kB)<br>
@@ -913,7 +913,7 @@
 </h2>
 <p>A data set with 134,659 rows and 2 columns, containing the following column names:<br><em>mo</em> and <em>ab</em>.</p>
 <p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 15 October 2022 13:21:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
+<p>It was last updated on 18 October 2022 20:55:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds" class="external-link">original R Data Structure (RDS) file</a> (78 kB)<br>
@@ -1185,7 +1185,7 @@
 </h2>
 <p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
 <p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 15 October 2022 13:21:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
+<p>It was last updated on 18 October 2022 20:55:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.html">here</a>.</p>
 <p><strong>Direct download links:</strong></p>
 <ul>
 <li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds" class="external-link">original R Data Structure (RDS) file</a> (3 kB)<br>
@@ -1302,7 +1302,7 @@
 </h2>
 <p>A data set with 2,000 rows and 46 columns, containing the following column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>, <em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>, <em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>, <em>FEP</em>, <em>CXM</em>, <em>FOX</em>, <em>CTX</em>, <em>CAZ</em>, <em>CRO</em>, <em>GEN</em>, <em>TOB</em>, <em>AMK</em>, <em>KAN</em>, <em>TMP</em>, <em>SXT</em>, <em>NIT</em>, <em>FOS</em>, <em>LNZ</em>, <em>CIP</em>, <em>MFX</em>, <em>VAN</em>, <em>TEC</em>, <em>TCY</em>, <em>TGC</em>, <em>DOX</em>, <em>ERY</em>, <em>CLI</em>, <em>AZM</em>, <em>IPM</em>, <em>MEM</em>, <em>MTR</em>, <em>CHL</em>, <em>COL</em>, <em>MUP</em> and <em>RIF</em>.</p>
 <p>This data set is in R available as <code>example_isolates</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 15 October 2022 13:21:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
+<p>It was last updated on 18 October 2022 20:55:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates.html">here</a>.</p>
 <div class="section level3">
 <h3 id="source-6">Source<a class="anchor" aria-label="anchor" href="#source-6"></a>
 </h3>
@@ -1707,7 +1707,7 @@
 </h2>
 <p>A data set with 3,000 rows and 8 columns, containing the following column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>, <em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and <em>GEN</em>.</p>
 <p>This data set is in R available as <code>example_isolates_unclean</code>, after you load the <code>AMR</code> package.</p>
-<p>It was last updated on 15 October 2022 13:21:31 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
+<p>It was last updated on 18 October 2022 20:55:18 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/example_isolates_unclean.html">here</a>.</p>
 <div class="section level3">
 <h3 id="source-7">Source<a class="anchor" aria-label="anchor" href="#source-7"></a>
 </h3>

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="">1.8.2.9018</small>
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@@ -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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
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articles/welcome_to_AMR.html

@@ -38,7 +38,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
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@@ -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="">1.8.2.9018</small>
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@@ -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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
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@@ -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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
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@@ -127,10 +127,10 @@
     </div>
 
     <div class="section level2">
-<h2 class="pkg-version" data-toc-text="1.8.2.9018" id="amr-1829018">AMR 1.8.2.9018<a class="anchor" aria-label="anchor" href="#amr-1829018"></a></h2>
+<h2 class="pkg-version" data-toc-text="1.8.2.9019" id="amr-1829019">AMR 1.8.2.9019<a class="anchor" aria-label="anchor" href="#amr-1829019"></a></h2>
 <p>This version will eventually become v2.0! We’re happy to reach a new major milestone soon!</p>
 <div class="section level4">
-<h4 id="breaking-1-8-2-9018">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9018"></a></h4>
+<h4 id="breaking-1-8-2-9019">Breaking<a class="anchor" aria-label="anchor" href="#breaking-1-8-2-9019"></a></h4>
 <ul><li>Removed all species of the taxonomic kingdom Chromista from the package. This was done for multiple reasons:<ul><li>CRAN allows packages to be around 5 MB maximum, some packages are exempted but this package is not one of them</li>
 <li>Chromista are not relevant when it comes to antimicrobial resistance, thus lacking the primary scope of this package</li>
 <li>Chromista are almost never clinically relevant, thus lacking the secondary scope of this package</li>
@@ -140,7 +140,7 @@
 <li>The <code><a href="../reference/mo_matching_score.html">mo_matching_score()</a></code> now count deletions and substitutions as 2 instead of 1, which impacts the outcome of <code><a href="../reference/as.mo.html">as.mo()</a></code> and any <code>mo_*()</code> function</li>
 </ul></div>
 <div class="section level4">
-<h4 id="new-1-8-2-9018">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9018"></a></h4>
+<h4 id="new-1-8-2-9019">New<a class="anchor" aria-label="anchor" href="#new-1-8-2-9019"></a></h4>
 <ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
 <li>All new algorithm for <code><a href="../reference/as.mo.html">as.mo()</a></code> (and thus internally all <code>mo_*()</code> functions) while still following our original set-up as described in our paper (DOI 10.18637/jss.v104.i03).<ul><li>A new argument <code>keep_synonyms</code> allows to <em>not</em> correct for updated taxonomy, in favour of the now deleted argument <code>allow_uncertain</code>
 </li>
@@ -157,7 +157,7 @@
 <li>Our data sets are now also continually exported to Apache Feather and Apache Parquet formats. You can find more info <a href="https://msberends.github.io/AMR/articles/datasets.html">in this article on our website</a>.</li>
 </ul></div>
 <div class="section level4">
-<h4 id="changed-1-8-2-9018">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9018"></a></h4>
+<h4 id="changed-1-8-2-9019">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-2-9019"></a></h4>
 <ul><li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
 <li>Fix for using <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on <code>NA</code> values (e.g. <code>as.rsi(as.disk(NA), ...)</code>)</li>
 <li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
@@ -183,7 +183,7 @@
 <li>Fix for using <code><a href="../reference/as.ab.html">as.ab()</a></code> on <code>NA</code> values</li>
 </ul></div>
 <div class="section level4">
-<h4 id="other-1-8-2-9018">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9018"></a></h4>
+<h4 id="other-1-8-2-9019">Other<a class="anchor" aria-label="anchor" href="#other-1-8-2-9019"></a></h4>
 <ul><li>New website to make use of the new Bootstrap 5 and pkgdown 2.0. The website now contains results for all examples and will be automatically regenerated with every change to our repository, using GitHub Actions</li>
 <li>Added Peter Dutey-Magni, Dmytro Mykhailenko and Anton Mymrikov as contributors, to thank them for their valuable input</li>
 <li>All R and Rmd files in this project are now styled using the <code>styler</code> package</li>

pkgdown.yml

@@ -11,7 +11,7 @@ articles:
   datasets: datasets.html
   resistance_predict: resistance_predict.html
   welcome_to_AMR: welcome_to_AMR.html
-last_built: 2022-10-15T13:24Z
+last_built: 2022-10-18T20:58Z
 urls:
   reference: https://msberends.github.io/AMR/reference
   article: https://msberends.github.io/AMR/articles

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

reference/add_custom_antimicrobials.html

@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -190,16 +190,16 @@
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="va">df</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    birth_date age age_exact age_at_y2k</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1959-12-08  62  62.85205         40</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1947-04-12  75  75.51781         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1953-03-16  69  69.58356         46</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1956-07-27  66  66.22740         43</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1945-02-19  77  77.65205         54</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1960-01-24  62  62.73151         39</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1995-02-12  27  27.67123          4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1981-02-05  41  41.69863         18</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1971-01-22  51  51.72877         28</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1948-10-08  74  74.02740         51</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1933-09-12  89  89.09041         66</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1979-06-06  43  43.36712         20</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1953-10-17  68  68.99452         46</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1967-09-29  55  55.05205         32</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1972-06-19  50  50.32329         27</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1933-04-01  89  89.54795         66</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1964-01-10  58  58.76164         35</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-04-08  25  25.52877          2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1985-08-26  37  37.13699         14</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1938-06-11  84  84.35342         61</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -484,16 +484,16 @@ A microorganism is categorised as <em>Susceptible, Increased exposure</em> when
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 50 × 13</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    datetime            index ab_input   ab_consid…¹ mo_in…² mo_conside…³ guide…⁴</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span>        <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-15 <span style="color: #949494;">13:24:55</span>     1 ampicillin AMP         Strep … B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2022-10-18 <span style="color: #949494;">20:58:54</span>     1 ampicillin AMP         Strep … B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-15 <span style="color: #949494;">13:24:56</span>     1 AMP        AMP         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2022-10-18 <span style="color: #949494;">20:58:54</span>     1 AMP        AMP         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-15 <span style="color: #949494;">13:24:56</span>     1 CIP        CIP         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2022-10-18 <span style="color: #949494;">20:58:54</span>     1 CIP        CIP         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-15 <span style="color: #949494;">13:24:56</span>     1 GEN        GEN         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2022-10-18 <span style="color: #949494;">20:58:55</span>     1 GEN        GEN         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-15 <span style="color: #949494;">13:24:56</span>     1 TOB        TOB         Escher… B_ESCHR_COLI EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2022-10-18 <span style="color: #949494;">20:58:55</span>     1 TOB        TOB         Escher… B_ESCHR_COLI EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-15 <span style="color: #949494;">13:24:57</span>     1 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2022-10-18 <span style="color: #949494;">20:58:55</span>     1 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-15 <span style="color: #949494;">13:24:57</span>     1 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2022-10-18 <span style="color: #949494;">20:58:56</span>     1 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-15 <span style="color: #949494;">13:24:57</span>     2 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2022-10-18 <span style="color: #949494;">20:58:56</span>     2 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-15 <span style="color: #949494;">13:24:57</span>     3 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2022-10-18 <span style="color: #949494;">20:58:56</span>     3 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-15 <span style="color: #949494;">13:24:57</span>     4 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2022-10-18 <span style="color: #949494;">20:58:56</span>     4 AMX        AMX         B_STRP… B_STRPT_PNMN EUCAST…</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 40 more rows, 6 more variables: ref_table &lt;chr&gt;, method &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;, input &lt;dbl&gt;, interpretation &lt;rsi&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   and abbreviated variable names ¹​ab_considered, ²​mo_input, ³​mo_considered,</span></span>

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -177,40 +177,42 @@
 <span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/sample.html" class="external-link">sample</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq_len</a></span><span class="op">(</span><span class="fl">2000</span><span class="op">)</span>, size <span class="op">=</span> <span class="fl">200</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># indices</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 14 30 51 63 66  3 25 25 10 50 17 32 20 64 19 41 45 62 25 18 24 26 28  6 63</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] 10 47 31 55 58 16 64 14 50 14 64 21 49 13 25 53 66 26 22 63 59 25 57 49 27</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 47 32 10 16 28 23  2  4 66 62  8 41 13 15 56  9 22 34 51 15 65 45  1 53 57</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [26] 13 23 17 10  6 58 12 63 18 55 65 33 36 38 13 50 56  2  5 66 10 17  9 45 35</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 29 39 12 52 12 33 58 57 48 51 40 27 30 18 36 43 13  7 65 60 13 25 16 21 62</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [51] 68 45 47  3 43 42 36 60  1 20 43 19 41 33  8 37 67 25 63 29 24 66 40 66 57</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 66 39 22 39  7  8 24 60 19 27 27 58  5 49  6 62 23 15 39 10 66 63  7 50  5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [76] 60 35 50  3  8 66 64  3 51 63 58 58 58 36 14 23 45  8 51  2  2 35 67 36 32</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [101] 60 29 67 51 52 57 34 48 60 18 65 55 48 51 66 12 20 49 41 65 41 67 53 39 11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [101]  6 12 29 19 11 34 68 61 28 41 28 20 45 44  1 47 41 10 61 55  4 15 67 40  8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 55 65 66 68 13 27 43 34 46 51  3 13 11 23 31 65 34 11 37 10 54 16 66 24 50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [126] 58 12 51 58 59 40 37 39 54 11 65 11 19  5  7 45 48 42 14 68 15 22 19 60 19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 38 10  5  8 59 30 49 63 59  9 36 44 38 28 30 65  5  6 66 10 30  5 26  1 42</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [151] 58 30 31 49  3 10 17 52 63 29 63 62 10 22  4 33 46 23 26 43 56  7 21 12  7</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 18 63 66 14 60 64 35 55 47 13 43 21 66 61  8 61 54 41 64 12 65 16 40 10 52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [176] 36 45 34  1 53 24 57 14 54 45 61  8 60 11 12 14 27 33 65 36 21  1 24 53 66</span>
 <span class="r-in"><span><span class="fu">is_new_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, episode_days <span class="op">=</span> <span class="fl">60</span><span class="op">)</span> <span class="co"># TRUE/FALSE</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>   [1]  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>   [1] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [13] FALSE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [13] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [25] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [25]  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE  TRUE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [37] FALSE FALSE FALSE  TRUE FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [37]  TRUE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [49]  TRUE FALSE  TRUE  TRUE FALSE  TRUE  TRUE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [49] FALSE FALSE  TRUE  TRUE FALSE  TRUE  TRUE FALSE FALSE FALSE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [61] FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE  TRUE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [73] FALSE  TRUE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [85] FALSE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [97] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE  TRUE  TRUE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [109] FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE  TRUE  TRUE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [121] FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [133] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE FALSE FALSE FALSE  TRUE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [133]  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [145]  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [145] FALSE  TRUE  TRUE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [157]  TRUE  TRUE  TRUE  TRUE  TRUE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [157] FALSE  TRUE FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE  TRUE FALSE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [169] FALSE FALSE FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE  TRUE FALSE  TRUE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE  TRUE FALSE  TRUE FALSE FALSE FALSE FALSE FALSE FALSE  TRUE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [181] FALSE FALSE FALSE  TRUE FALSE FALSE  TRUE  TRUE FALSE FALSE  TRUE FALSE</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE FALSE  TRUE  TRUE FALSE FALSE</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [193] FALSE FALSE FALSE  TRUE FALSE  TRUE FALSE FALSE</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># filter on results from the third 60-day episode only, using base R</span></span></span>
 <span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu">get_episode</span><span class="op">(</span><span class="va">df</span><span class="op">$</span><span class="va">date</span>, <span class="fl">60</span><span class="op">)</span> <span class="op">==</span> <span class="fl">3</span><span class="op">)</span>, <span class="op">]</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 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> 2002-10-20 F35553     51 M      ICU      B_STPHY_AURS S     NA    S     NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2002-06-23 798871     82 M      Clinical  B_ENTRC_FCLS NA    NA    NA    NA   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-11-18 956065     89 F      Clinical B_ESCHR_COLI R     NA    NA    NA   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2002-07-16 241328     78 M      Outpatie… B_STPHY_CONS R     NA    S     R    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2002-08-14 785317     51 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;">4</span> 2002-07-15 426426     67 F      ICU       B_ESCHR_COLI R     NA    NA    NA   </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 36 more variables: AMC &lt;rsi&gt;, AMP &lt;rsi&gt;, TZP &lt;rsi&gt;, CZO &lt;rsi&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   FEP &lt;rsi&gt;, CXM &lt;rsi&gt;, FOX &lt;rsi&gt;, CTX &lt;rsi&gt;, CAZ &lt;rsi&gt;, CRO &lt;rsi&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   GEN &lt;rsi&gt;, TOB &lt;rsi&gt;, AMK &lt;rsi&gt;, KAN &lt;rsi&gt;, TMP &lt;rsi&gt;, SXT &lt;rsi&gt;,</span></span>
@@ -246,16 +248,16 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   condition [3]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient date       condition new_episode</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 219024  2005-02-17 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 89F578  2004-02-28 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A31059  2008-12-04 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 175532  2012-10-11 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> D53062  2014-07-28 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 380628  2009-01-18 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 305134  2016-10-28 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 4F9406  2015-01-23 B         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> D80438  2017-07-03 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 097186  2015-10-28 A         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F35553  2002-10-20 C         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> FB50D6  2005-04-24 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ED4982  2007-07-13 B         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 716939  2017-01-05 B         TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 122506  2007-08-11 A         FALSE      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 400169  2004-12-24 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 05B00F  2004-05-11 A         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 512FFD  2013-06-19 C         FALSE      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 8F77B2  2014-01-14 C         TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B27238  2004-12-24 C         FALSE      </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -267,19 +269,19 @@
 <span class="r-in"><span>    <span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 5</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [180]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   ward, patient [188]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    ward     date       patient new_index new_logical</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;date&gt;</span>     <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2005-02-17 219024          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Clinical 2004-02-28 89F578          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2008-12-04 A31059          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Clinical 2012-10-11 175532          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2014-07-28 D53062          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Clinical 2009-01-18 380628          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> ICU      2016-10-28 305134          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Clinical 2015-01-23 4F9406          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2017-07-03 D80438          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Clinical 2015-10-28 097186          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2002-10-20 F35553          2 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> ICU      2005-04-24 FB50D6          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU      2007-07-13 ED4982          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ICU      2017-01-05 716939          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Clinical 2007-08-11 122506          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> ICU      2004-12-24 400169          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> ICU      2004-05-11 05B00F          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Clinical 2013-06-19 512FFD          1 TRUE       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2014-01-14 8F77B2          1 TRUE       </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Clinical 2004-12-24 B27238          1 TRUE       </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 190 more rows</span></span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span>  <span class="va">df</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
@@ -294,9 +296,9 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 3 × 5</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   ward       n_patients n_episodes_365 n_episodes_60 n_episodes_30</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>           <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>          <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          112             14            55            73</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> Clinical          124             15            57            80</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                56             12            36            46</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> ICU                57             13            34            43</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient         12              8            11            12</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> Outpatient          7              6             7             7</span>
 <span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span>  <span class="co"># grouping on patients and microorganisms leads to the same</span></span></span>
@@ -326,19 +328,19 @@
 <span class="r-in"><span>    <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_data.html" class="external-link">group_vars</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span>, <span class="va">flag_episode</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="op">}</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 200 × 4</span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [188]</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># Groups:   patient, mo, ward [195]</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    patient mo           ward     flag_episode</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>         <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;lgl&gt;</span>       </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 219024  B_ESCHR_COLI Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 89F578  B_STPHY_CONS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> A31059  B_STRPT_MTNS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 175532  B_ESCHR_COLI Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> D53062  B_HMPHL_INFL Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 380628  B_ESCHR_COLI Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 305134  B_PROTS_VLGR ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 4F9406  B_KLBSL_PNMN Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> D80438  B_STPHY_AURS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 097186  B_STPHY_EPDR Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> F35553  B_STPHY_AURS ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> FB50D6  B_STRPT_MITS ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> ED4982  B_ESCHR_COLI ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 716939  B_STPHY_HMNS ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 122506  B_STPHY_AURS Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 400169  B_STPHY_EPDR ICU      TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 05B00F  F_CANDD_ALBC ICU      TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 512FFD  B_STPHY_HMNS Clinical TRUE        </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 8F77B2  B_ENTRC_FACM Clinical TRUE        </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> B27238  B_STRPT_MITS 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>

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -167,9 +167,9 @@
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">kurtosis</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">10000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 3.023296</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 2.997868</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] 0.1095747</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] -0.06572697</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -195,11 +195,10 @@
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">x</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.25    32      0.01    32      0.01    1       0.125   &gt;=256   &lt;=0.002</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.25  0.001 0.005 0.025 0.01  0.005 0.25  256   0.005 256  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 128    </span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.28698184  0.84500052 -1.03794802  0.84500052 -1.03794802  0.03644169</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.1992569 -1.0346858 -0.6750067 -0.3153276 -0.5201013 -0.6750067</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.44869360  1.33013581 -1.41343111  1.16842405</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.1992569  1.7483105 -0.6750067  1.7483105</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>
@@ -210,37 +209,37 @@
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">y</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox    cipr gent tobr</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    4 &lt;=0.125    2    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A   32       2  &lt;=1 0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   16     0.5 0.25  &gt;=4</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   64       2    4    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C   16     &gt;=1   16  0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    4    0.25  &lt;=1  0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D   16 &lt;=0.125   16    1</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    8       2    2    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4     0.5    8    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E   16       2    8 0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F   32     0.5 0.25  0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    8     0.5  &lt;=1    1</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G  &lt;=2 &lt;=0.125  0.5    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G   64     0.5  &lt;=1    8</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H   32 &lt;=0.125    8  0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H   16 &lt;=0.125    8  0.5</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16 &lt;=0.125   16    2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16    0.25    2 0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J   16     &gt;=1  0.5  0.5</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    4     &gt;=4    8    4</span>
 <span class="r-in"><span><span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent",</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "id" and "tobr"</span>
 <span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>NAs introduced by coercion</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.55656226  0.35659439  0.44544165  0.10294421  0.24387145 -0.14027373</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.1221358  0.9889067 -0.9671616  0.2844407  0.2660982 -0.5349017</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.70751904 -0.03633100  0.33011266 -0.03827833</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.3214630 -0.2081835 -0.5481505  0.5196245</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span> <span class="op">&lt;-</span> <span class="fu">mean_amr_distance</span><span class="op">(</span><span class="va">y</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.mic</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
 <span class="r-in"><span><span class="va">y</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/order.html" class="external-link">order</a></span><span class="op">(</span><span class="va">y</span><span class="op">$</span><span class="va">amr_distance</span><span class="op">)</span>, <span class="op">]</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox    cipr gent tobr amr_distance</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G  &lt;=2 &lt;=0.125  0.5    2  -0.70751904</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C    4    0.25  &lt;=1  0.5   -0.9671616</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A    4 &lt;=0.125    2    1  -0.55656226</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16    0.25    2 0.25   -0.5481505</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F   32     0.5 0.25  0.5  -0.14027373</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   F    8     0.5  &lt;=1    1   -0.5349017</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J   16     &gt;=1  0.5  0.5  -0.03827833</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H   16 &lt;=0.125    8  0.5   -0.2081835</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   H   32 &lt;=0.125    8  0.5  -0.03633100</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   A   32       2  &lt;=1 0.25   -0.1221358</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D   16 &lt;=0.125   16    1   0.10294421</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E   16       2    8 0.25    0.2660982</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   E    4     0.5    8    2   0.24387145</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   D    8       2    2    8    0.2844407</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   I   16 &lt;=0.125   16    2   0.33011266</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   G   64     0.5  &lt;=1    8    0.3214630</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   16     0.5 0.25  &gt;=4   0.35659439</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  J    4     &gt;=4    8    4    0.5196245</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   C   16     &gt;=1   16  0.5   0.44544165</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   64       2    4    8    0.9889067</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>
@@ -253,16 +252,16 @@
 <span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Calculating mean AMR distance based on columns "amox", "cipr", "gent" and</span>
 <span class="r-msg co"><span class="r-pr">#&gt;</span>   "tobr"</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    id amox    cipr gent tobr amr_distance check_id_C</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C   16     &gt;=1   16  0.5   0.44544165 0.00000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1   C    4    0.25  &lt;=1  0.5   -0.9671616  0.0000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2   B   16     0.5 0.25  &gt;=4   0.35659439 0.08884727</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2   I   16    0.25    2 0.25   -0.5481505  0.4190111</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3   I   16 &lt;=0.125   16    2   0.33011266 0.11532899</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3   F    8     0.5  &lt;=1    1   -0.5349017  0.4322599</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4   E    4     0.5    8    2   0.24387145 0.20157020</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4   H   16 &lt;=0.125    8  0.5   -0.2081835  0.7589781</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5   D   16 &lt;=0.125   16    1   0.10294421 0.34249744</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5   A   32       2  &lt;=1 0.25   -0.1221358  0.8450258</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6   H   32 &lt;=0.125    8  0.5  -0.03633100 0.48177265</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6   E   16       2    8 0.25    0.2660982  1.2332598</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7   J   16     &gt;=1  0.5  0.5  -0.03827833 0.48371999</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7   D    8       2    2    8    0.2844407  1.2516023</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8   F   32     0.5 0.25  0.5  -0.14027373 0.58571538</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8   G   64     0.5  &lt;=1    8    0.3214630  1.2886246</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9   A    4 &lt;=0.125    2    1  -0.55656226 1.00200391</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9   J    4     &gt;=4    8    4    0.5196245  1.4867861</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10  G  &lt;=2 &lt;=0.125  0.5    2  -0.70751904 1.15296069</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10  B   64       2    4    8    0.9889067  1.9560683</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>

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -178,43 +178,43 @@
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 32     1      0.001  0.25   1      16     0.0625 64     0.25   2     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 64      2       0.002   128     2       2       0.005   0.005   256    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 4      0.01   0.125  8      128    0.0625 &gt;=256  0.025  &gt;=256  0.125 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 2       0.025   128     256     0.5     1       256     &lt;=0.001 0.025  </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 64     32     0.0625 1      4     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.002   0.0625  8       2       128     32      0.5    </span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 15 46 30 46 39 44 18 22  8 28 24 30 14 20 47 46 10 41 46 21 23 47 13 25 49</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 41 50 44 50 41 22  8 38 35 50 20 13  9  6 17 45 34 12 45 39 44 39 15 35 12</span>
 <span class="r-in"><span><span class="fu">random_rsi</span><span class="op">(</span><span class="fl">25</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;rsi&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] R R R I S S S S S R R R I R S S S I R S I R S I I</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] R R S I R I S I S I I S R S S I R S S I I S S I R</span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># \donttest{</span></span></span>
 <span class="r-in"><span><span class="co"># make the random generation more realistic by setting a bug and/or drug:</span></span></span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 0.0625-64</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.5   64    0.005 32    4     0.005 128   0.25  64    0.025 0.5   2    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.002   32      &lt;=0.001 1       0.125   0.0625  0.002   0.002   0.01   </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.025 0.025 2     0.125 64    8     2     1     0.125 64    32    32   </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10] 0.002   64      32      0.5     0.5     2       4       32      0.0625 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 0.5  </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [19] 0.005   0.025   0.002   32      &gt;=128   0.005   16     </span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-16</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 8      4      8      8      2      8      1      0.5    16     2     </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 8      1      16     32     &lt;=0.25 &lt;=0.25 0.5    16     2      &lt;=0.25</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 8      16     &lt;=0.25 0.5    8      8      1      2      2      &lt;=0.25</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [11] 4      &lt;=0.25 32     4      1      &lt;=0.25 32     4      16     16    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 8      8      2      2      16    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [21] 1      1      8      1      8     </span>
 <span class="r-in"><span><span class="fu">random_mic</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"meropenem"</span><span class="op">)</span> <span class="co"># range 0.0625-4</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;mic&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.25  8     0.125 8     16    4     8     0.025 8     4     8     4    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 2     8     8     1     0.125 8     4     0.5   0.125 &gt;=16  0.025 &gt;=16 </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 0.125 0.125 0.25  1     0.025 8     0.025 1     2     4     4     0.25 </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [13] 2     &gt;=16  0.5   0.025 1     8     4     0.125 8     1     2     4    </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [25] 4    </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [25] &gt;=16 </span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span> <span class="co"># range 8-50</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 35 48 23 48 32 44 49 43 11 18 41 37 30 22 19 26 40 50 15 30 41 41 42 21 15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 43 45 38 25 41 41 36 22 23 44 50 50 10 33 43 40 23 46 19 23 39 14  8 43 27</span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Klebsiella pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 11-17</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 15 16 13 12 16 11 12 16 17 15 14 13 12 13 15 16 15 13 16 14 16 16 17 16 15</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 17 13 13 12 17 13 17 11 13 17 14 11 14 15 11 16 13 17 11 16 11 12 14 15 15</span>
 <span class="r-in"><span><span class="fu">random_disk</span><span class="op">(</span><span class="fl">25</span>, <span class="st">"Streptococcus pneumoniae"</span>, <span class="st">"ampicillin"</span><span class="op">)</span> <span class="co"># range 12-27</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> Class &lt;disk&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 25 18 18 18 24 15 20 19 20 21 26 22 18 15 23 21 19 22 26 25 21 23 20 16 23</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 15 17 20 25 19 17 25 18 23 20 17 17 19 26 19 21 26 16 20 18 16 15 18 15 18</span>
 <span class="r-in"><span><span class="co"># }</span></span></span>
 </code></pre></div>
     </div>

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

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="">1.8.2.9018</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9019</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -166,7 +166,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
     <div class="section level2">
     <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">skewness</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Uniform.html" class="external-link">runif</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.02786978</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.04873666</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>

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="">1.8.2.9018</small>
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search.json

@@ -1 +1 @@
-[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(   patient_id = patients,   gender = c(     rep(\"M\", 135),     rep(\"F\", 125)   ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(   \"Escherichia coli\", \"Staphylococcus aureus\",   \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated
+[{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"introduction","dir":"Articles","previous_headings":"","what":"Introduction","title":"How to conduct AMR data analysis","text":"Conducting AMR data analysis unfortunately requires -depth knowledge different scientific fields, makes hard right. least, requires: Good questions (always start !) thorough understanding (clinical) epidemiology, understand clinical epidemiological relevance possible bias results thorough understanding (clinical) microbiology/infectious diseases, understand microorganisms causal infections implications pharmaceutical treatment, well understanding intrinsic acquired microbial resistance Experience data analysis microbiological tests results, understand determination limitations MIC values interpretations RSI values Availability biological taxonomy microorganisms probably normalisation factors pharmaceuticals, defined daily doses (DDD) Available (inter-)national guidelines, profound methods apply course, instantly provide knowledge experience. AMR package, aimed providing (1) tools simplify antimicrobial resistance data cleaning, transformation analysis, (2) methods easily incorporate international guidelines (3) scientifically reliable reference data, including requirements mentioned . AMR package enables standardised reproducible AMR data analysis, application evidence-based rules, determination first isolates, translation various codes microorganisms antimicrobial agents, determination (multi-drug) resistant microorganisms, calculation antimicrobial resistance, prevalence future trends.","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"preparation","dir":"Articles","previous_headings":"","what":"Preparation","title":"How to conduct AMR data analysis","text":"tutorial, create fake demonstration data work . can skip Cleaning data already data ready. start analysis, try make structure data generally look like :","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"needed-r-packages","dir":"Articles","previous_headings":"Preparation","what":"Needed R packages","title":"How to conduct AMR data analysis","text":"many uses R, need additional packages AMR data analysis. package works closely together tidyverse packages dplyr ggplot2 RStudio. tidyverse tremendously improves way conduct data science - allows natural way writing syntaxes creating beautiful plots R. also use cleaner package, can used cleaning data creating frequency tables.","code":"library(dplyr) library(ggplot2) library(AMR) library(cleaner)  # (if not yet installed, install with:) # install.packages(c(\"dplyr\", \"ggplot2\", \"AMR\", \"cleaner\"))"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"creation-of-data","dir":"Articles","previous_headings":"","what":"Creation of data","title":"How to conduct AMR data analysis","text":"create fake example data use analysis. AMR data analysis, need least: patient ID, name code microorganism, date antimicrobial results (antibiogram). also include specimen type (e.g. filter blood urine), ward type (e.g. filter ICUs). additional columns (like hospital name, patients gender even [well-defined] clinical properties) can comparative analysis, tutorial demonstrate .","code":""},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"patients","dir":"Articles","previous_headings":"Creation of data","what":"Patients","title":"How to conduct AMR data analysis","text":"start patients, need unique list patients. LETTERS object available R - ’s vector 26 characters: Z. patients object just created now vector length 260, values (patient IDs) varying A1 Z10. Now also set gender patients, putting ID gender table: first 135 patient IDs now male, 125 female.","code":"patients <- unlist(lapply(LETTERS, paste0, 1:10)) patients_table <- data.frame(   patient_id = patients,   gender = c(     rep(\"M\", 135),     rep(\"F\", 125)   ) )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"dates","dir":"Articles","previous_headings":"Creation of data","what":"Dates","title":"How to conduct AMR data analysis","text":"Let’s pretend data consists blood cultures isolates 1 January 2010 1 January 2018. dates object now contains days date range.","code":"dates <- seq(as.Date(\"2010-01-01\"), as.Date(\"2018-01-01\"), by = \"day\")"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"microorganisms","dir":"Articles","previous_headings":"Creation of data > Dates","what":"Microorganisms","title":"How to conduct AMR data analysis","text":"tutorial, uses four different microorganisms: Escherichia coli, Staphylococcus aureus, Streptococcus pneumoniae, Klebsiella pneumoniae:","code":"bacteria <- c(   \"Escherichia coli\", \"Staphylococcus aureus\",   \"Streptococcus pneumoniae\", \"Klebsiella pneumoniae\" )"},{"path":"https://msberends.github.io/AMR/articles/AMR.html","id":"put-everything-together","dir":"Articles","previous_headings":"CreatLine truncated