(v1.4.0.9033) documentation update

2025-07-09 19:01:51 +02:00 · 2020-12-08 12:37:25 +01:00
parent 1bdb136b3a
commit 2145f1d1ba
110 changed files with 839 additions and 576 deletions
--- a/docs/articles/AMR.html
+++ b/docs/articles/AMR.html
@ -39,7 +39,7 @@
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">AMR (for R)</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9000</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0.9032</span>
      </span>
    </div>

@ -193,7 +193,7 @@
      <h1 data-toc-skip>How to conduct AMR analysis</h1>
                        <h4 class="author">Matthijs S. Berends</h4>
            
-            <h4 class="date">15 October 2020</h4>
+            <h4 class="date">08 December 2020</h4>
      
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd"><code>vignettes/AMR.Rmd</code></a></small>
      <div class="hidden name"><code>AMR.Rmd</code></div>
@ -202,7 +202,7 @@

    
    
-<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/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 15 October 2020.</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/">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 08 December 2020.</p>
 <div id="introduction" class="section level1">
 <h1 class="hasAnchor">
 <a href="#introduction" class="anchor"></a>Introduction</h1>
@ -233,21 +233,21 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2020-10-15</td>
+<td align="center">2020-12-08</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">2020-10-15</td>
+<td align="center">2020-12-08</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">2020-10-15</td>
+<td align="center">2020-12-08</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -352,70 +352,70 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2011-04-04</td>
-<td align="center">A3</td>
+<td align="center">2015-10-08</td>
+<td align="center">Y10</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">R</td>
+<td align="center">S</td>
+<td align="center">F</td>
+</tr>
+<tr class="even">
+<td align="center">2014-04-05</td>
+<td align="center">O10</td>
+<td align="center">Hospital C</td>
+<td align="center">Escherichia coli</td>
+<td align="center">R</td>
+<td align="center">I</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">F</td>
+</tr>
+<tr class="odd">
+<td align="center">2012-07-06</td>
+<td align="center">H9</td>
+<td align="center">Hospital A</td>
+<td align="center">Escherichia coli</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+</tr>
+<tr class="even">
+<td align="center">2016-09-05</td>
+<td align="center">U3</td>
 <td align="center">Hospital C</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">M</td>
-</tr>
-<tr class="even">
-<td align="center">2011-10-13</td>
-<td align="center">I4</td>
-<td align="center">Hospital B</td>
-<td align="center">Escherichia coli</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="odd">
-<td align="center">2015-11-20</td>
-<td align="center">J6</td>
-<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
-<td align="center">I</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="even">
-<td align="center">2017-02-04</td>
-<td align="center">X3</td>
-<td align="center">Hospital B</td>
-<td align="center">Klebsiella pneumoniae</td>
-<td align="center">S</td>
-<td align="center">I</td>
-<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2010-10-17</td>
-<td align="center">N9</td>
-<td align="center">Hospital D</td>
-<td align="center">Staphylococcus aureus</td>
+<td align="center">2017-05-23</td>
+<td align="center">S5</td>
+<td align="center">Hospital C</td>
+<td align="center">Escherichia coli</td>
+<td align="center">I</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>
 </tr>
 <tr class="even">
-<td align="center">2014-06-04</td>
-<td align="center">X3</td>
-<td align="center">Hospital A</td>
-<td align="center">Escherichia coli</td>
+<td align="center">2013-11-30</td>
+<td align="center">J2</td>
+<td align="center">Hospital C</td>
+<td align="center">Streptococcus pneumoniae</td>
 <td align="center">S</td>
 <td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">S</td>
-<td align="center">F</td>
+<td align="center">M</td>
 </tr>
 </tbody>
 </table>
@ -449,16 +449,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,412</td>
-<td align="right">52.06%</td>
-<td align="right">10,412</td>
-<td align="right">52.06%</td>
+<td align="right">10,384</td>
+<td align="right">51.92%</td>
+<td align="right">10,384</td>
+<td align="right">51.92%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,588</td>
-<td align="right">47.94%</td>
+<td align="right">9,616</td>
+<td align="right">48.08%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@ -501,10 +501,10 @@ Longest: 1</p>
 <div class="sourceCode" id="cb15"><pre class="downlit">
 <span class="va">data</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span>
-<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
-<span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
-<span class="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span></pre></div>
-<p>So only 28.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
+<span class="co"># NOTE: Using column 'bacteria' as input for `col_mo`.</span>
+<span class="co"># NOTE: Using column 'date' as input for `col_date`.</span>
+<span class="co"># NOTE: Using column 'patient_id' as input for `col_patient_id`.</span></pre></div>
+<p>So only 28.6% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb16"><pre class="downlit">
 <span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">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></pre></div>
@ -516,7 +516,7 @@ Longest: 1</p>
 <div id="first-weighted-isolates" class="section level2">
 <h2 class="hasAnchor">
 <a href="#first-weighted-isolates" class="anchor"></a>First <em>weighted</em> isolates</h2>
-<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient Z7, sorted on date:</p>
+<p>We made a slight twist to the CLSI algorithm, to take into account the antimicrobial susceptibility profile. Have a look at all isolates of patient A3, sorted on date:</p>
 <table class="table">
 <thead><tr class="header">
 <th align="center">isolate</th>
@ -532,21 +532,21 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-03-27</td>
-<td align="center">Z7</td>
+<td align="center">2010-01-04</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
 <td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-06-10</td>
-<td align="center">Z7</td>
+<td align="center">2010-01-05</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -554,30 +554,30 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-06-25</td>
-<td align="center">Z7</td>
+<td align="center">2010-02-07</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">I</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">FALSE</td>
-</tr>
-<tr class="even">
-<td align="center">4</td>
-<td align="center">2010-11-05</td>
-<td align="center">Z7</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
+<tr class="even">
+<td align="center">4</td>
+<td align="center">2010-06-17</td>
+<td align="center">A3</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">FALSE</td>
+</tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-11-22</td>
-<td align="center">Z7</td>
+<td align="center">2010-07-23</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -587,8 +587,8 @@ Longest: 1</p>
 </tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2011-02-06</td>
-<td align="center">Z7</td>
+<td align="center">2010-11-16</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -598,45 +598,45 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2011-03-19</td>
-<td align="center">Z7</td>
+<td align="center">2010-12-05</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
+<td align="center">I</td>
+<td align="center">I</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2011-07-19</td>
-<td align="center">Z7</td>
+<td align="center">2011-01-17</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
+<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2011-08-15</td>
-<td align="center">Z7</td>
+<td align="center">2011-01-26</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">10</td>
-<td align="center">2011-09-22</td>
-<td align="center">Z7</td>
+<td align="center">2011-02-12</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
@ -648,11 +648,12 @@ Longest: 1</p>
 <span class="va">data</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>keyab <span class="op">=</span> <span class="fu"><a href="../reference/key_antibiotics.html">key_antibiotics</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html">mutate</a></span><span class="op">(</span>first_weighted <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span><span class="va">.</span><span class="op">)</span><span class="op">)</span>
-<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
-<span class="co"># NOTE: Using column `bacteria` as input for `col_mo`.</span>
-<span class="co"># NOTE: Using column `date` as input for `col_date`.</span>
-<span class="co"># NOTE: Using column `patient_id` as input for `col_patient_id`.</span>
-<span class="co"># NOTE: Using column `keyab` as input for `col_keyantibiotics`. Use col_keyantibiotics = FALSE to prevent this.</span></pre></div>
+<span class="co"># NOTE: Using column 'bacteria' as input for `col_mo`.</span>
+<span class="co"># NOTE: Using column 'bacteria' as input for `col_mo`.</span>
+<span class="co"># NOTE: Using column 'date' as input for `col_date`.</span>
+<span class="co"># NOTE: Using column 'patient_id' as input for `col_patient_id`.</span>
+<span class="co"># NOTE: Using column 'keyab' as input for `col_keyantibiotics`. Use</span>
+<span class="co">#       col_keyantibiotics = FALSE to prevent this.</span></pre></div>
 <table class="table">
 <thead><tr class="header">
 <th align="center">isolate</th>
@ -669,22 +670,22 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-03-27</td>
-<td align="center">Z7</td>
+<td align="center">2010-01-04</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
-<td align="center">S</td>
-<td align="center">S</td>
 <td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">TRUE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-06-10</td>
-<td align="center">Z7</td>
+<td align="center">2010-01-05</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -693,32 +694,20 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-06-25</td>
-<td align="center">Z7</td>
+<td align="center">2010-02-07</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">I</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">FALSE</td>
-<td align="center">FALSE</td>
-</tr>
-<tr class="even">
-<td align="center">4</td>
-<td align="center">2010-11-05</td>
-<td align="center">Z7</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="odd">
-<td align="center">5</td>
-<td align="center">2010-11-22</td>
-<td align="center">Z7</td>
+<tr class="even">
+<td align="center">4</td>
+<td align="center">2010-06-17</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -727,10 +716,22 @@ Longest: 1</p>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
+<tr class="odd">
+<td align="center">5</td>
+<td align="center">2010-07-23</td>
+<td align="center">A3</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">FALSE</td>
+<td align="center">FALSE</td>
+</tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2011-02-06</td>
-<td align="center">Z7</td>
+<td align="center">2010-11-16</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -741,60 +742,60 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2011-03-19</td>
-<td align="center">Z7</td>
+<td align="center">2010-12-05</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
+<td align="center">I</td>
+<td align="center">I</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
-<td align="center">TRUE</td>
+<td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2011-07-19</td>
-<td align="center">Z7</td>
+<td align="center">2011-01-17</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">I</td>
 <td align="center">S</td>
 <td align="center">S</td>
+<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">TRUE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2011-08-15</td>
-<td align="center">Z7</td>
+<td align="center">2011-01-26</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">10</td>
-<td align="center">2011-09-22</td>
-<td align="center">Z7</td>
+<td align="center">2011-02-12</td>
+<td align="center">A3</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 </tbody>
 </table>
-<p>Instead of 2, now 8 isolates are flagged. In total, 78.6% of all isolates are marked ‘first weighted’ - 50.2% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
+<p>Instead of 2, now 7 isolates are flagged. In total, 79.1% of all isolates are marked ‘first weighted’ - 50.6% more than when using the CLSI guideline. In real life, this novel algorithm will yield 5-10% more isolates than the classic CLSI guideline.</p>
 <p>As with <code><a href="../reference/first_isolate.html">filter_first_isolate()</a></code>, there’s a shortcut for this new algorithm too:</p>
 <div class="sourceCode" id="cb19"><pre class="downlit">
 <span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span><span class="op">(</span><span class="op">)</span></pre></div>
-<p>So we end up with 15,713 isolates for analysis.</p>
+<p>So we end up with 15,822 isolates for analysis.</p>
 <p>We can remove unneeded columns:</p>
 <div class="sourceCode" id="cb20"><pre class="downlit">
 <span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data_1st</span> <span class="op">%&gt;%</span> 
@ -837,47 +838,15 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
-<td align="center">2011-04-04</td>
-<td align="center">A3</td>
-<td align="center">Hospital C</td>
-<td align="center">B_STPHY_AURS</td>
-<td align="center">R</td>
-<td align="center">I</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-<td align="center">Gram-positive</td>
-<td align="center">Staphylococcus</td>
-<td align="center">aureus</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="even">
-<td align="left">2</td>
-<td align="center">2011-10-13</td>
-<td align="center">I4</td>
-<td align="center">Hospital B</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">M</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
 <td align="left">3</td>
-<td align="center">2015-11-20</td>
-<td align="center">J6</td>
+<td align="center">2012-07-06</td>
+<td align="center">H9</td>
 <td align="center">Hospital A</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">I</td>
-<td align="center">S</td>
 <td align="center">R</td>
 <td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">M</td>
 <td align="center">Gram-negative</td>
 <td align="center">Escherichia</td>
@ -886,45 +855,77 @@ Longest: 1</p>
 </tr>
 <tr class="even">
 <td align="left">4</td>
-<td align="center">2017-02-04</td>
-<td align="center">X3</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">5</td>
-<td align="center">2010-10-17</td>
-<td align="center">N9</td>
-<td align="center">Hospital D</td>
+<td align="center">2016-09-05</td>
+<td align="center">U3</td>
+<td align="center">Hospital C</td>
 <td align="center">B_STPHY_AURS</td>
 <td align="center">R</td>
-<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">F</td>
 <td align="center">Gram-positive</td>
 <td align="center">Staphylococcus</td>
 <td align="center">aureus</td>
 <td align="center">TRUE</td>
 </tr>
-<tr class="even">
-<td align="left">7</td>
-<td align="center">2011-06-10</td>
-<td align="center">P2</td>
-<td align="center">Hospital B</td>
-<td align="center">B_STRPT_PNMN</td>
+<tr class="odd">
+<td align="left">5</td>
+<td align="center">2017-05-23</td>
+<td align="center">S5</td>
+<td align="center">Hospital C</td>
+<td align="center">B_ESCHR_COLI</td>
 <td align="center">I</td>
 <td align="center">I</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">F</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="left">8</td>
+<td align="center">2016-07-20</td>
+<td align="center">D2</td>
+<td align="center">Hospital B</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">R</td>
+<td align="center">I</td>
 <td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+<td align="center">Gram-negative</td>
+<td align="center">Escherichia</td>
+<td align="center">coli</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="odd">
+<td align="left">9</td>
+<td align="center">2010-09-20</td>
+<td align="center">H10</td>
+<td align="center">Hospital D</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">M</td>
+<td align="center">Gram-positive</td>
+<td align="center">Staphylococcus</td>
+<td align="center">aureus</td>
+<td align="center">TRUE</td>
+</tr>
+<tr class="even">
+<td align="left">10</td>
+<td align="center">2012-03-30</td>
+<td align="center">Y4</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">F</td>
 <td align="center">Gram-positive</td>
@ -953,8 +954,8 @@ Longest: 1</p>
 <span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 15,713<br>
-Available: 15,713 (100%, NA: 0 = 0%)<br>
+Length: 15,822<br>
+Available: 15,822 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@ -971,33 +972,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">7,867</td>
-<td align="right">50.07%</td>
-<td align="right">7,867</td>
-<td align="right">50.07%</td>
+<td align="right">7,935</td>
+<td align="right">50.15%</td>
+<td align="right">7,935</td>
+<td align="right">50.15%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">3,842</td>
-<td align="right">24.45%</td>
-<td align="right">11,709</td>
-<td align="right">74.52%</td>
+<td align="right">3,933</td>
+<td align="right">24.86%</td>
+<td align="right">11,868</td>
+<td align="right">75.01%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,346</td>
-<td align="right">14.93%</td>
-<td align="right">14,055</td>
-<td align="right">89.45%</td>
+<td align="right">2,376</td>
+<td align="right">15.02%</td>
+<td align="right">14,244</td>
+<td align="right">90.03%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,658</td>
-<td align="right">10.55%</td>
-<td align="right">15,713</td>
+<td align="right">1,578</td>
+<td align="right">9.97%</td>
+<td align="right">15,822</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@ -1011,7 +1012,7 @@ Longest: 24</p>
 <span class="va">data_1st</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://rdrr.io/r/utils/head.html">head</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show first 6 rows</span></pre></div>
-<pre><code># NOTE: Using column `bacteria` as input for `col_mo`.</code></pre>
+<pre><code># NOTE: Using column 'bacteria' as input for `col_mo`.</code></pre>
 <table class="table">
 <thead><tr class="header">
 <th align="center">mo</th>
@ -1025,50 +1026,50 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">3806</td>
-<td align="center">262</td>
-<td align="center">3799</td>
-<td align="center">7867</td>
+<td align="center">3811</td>
+<td align="center">259</td>
+<td align="center">3865</td>
+<td align="center">7935</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">6223</td>
-<td align="center">321</td>
-<td align="center">1323</td>
-<td align="center">7867</td>
+<td align="center">6278</td>
+<td align="center">298</td>
+<td align="center">1359</td>
+<td align="center">7935</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">6006</td>
+<td align="center">6070</td>
 <td align="center">0</td>
-<td align="center">1861</td>
-<td align="center">7867</td>
+<td align="center">1865</td>
+<td align="center">7935</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">7072</td>
+<td align="center">7138</td>
 <td align="center">0</td>
-<td align="center">795</td>
-<td align="center">7867</td>
+<td align="center">797</td>
+<td align="center">7935</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">1658</td>
-<td align="center">1658</td>
+<td align="center">1578</td>
+<td align="center">1578</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">1298</td>
-<td align="center">56</td>
-<td align="center">304</td>
-<td align="center">1658</td>
+<td align="center">1248</td>
+<td align="center">57</td>
+<td align="center">273</td>
+<td align="center">1578</td>
 </tr>
 </tbody>
 </table>
@ -1077,8 +1078,8 @@ Longest: 24</p>
 <span class="va">data_1st</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">fluoroquinolones</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</span></pre></div>
-<pre><code># Selecting fluoroquinolones: `CIP` (ciprofloxacin)
-# NOTE: Using column `bacteria` as input for `col_mo`.</code></pre>
+<pre><code># Selecting fluoroquinolones: 'CIP' (ciprofloxacin)
+# NOTE: Using column 'bacteria' as input for `col_mo`.</code></pre>
 <table class="table">
 <thead><tr class="header">
 <th align="center">mo</th>
@ -1092,34 +1093,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">6006</td>
+<td align="center">6070</td>
 <td align="center">0</td>
-<td align="center">1861</td>
-<td align="center">7867</td>
+<td align="center">1865</td>
+<td align="center">7935</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">CIP</td>
-<td align="center">1257</td>
+<td align="center">1219</td>
 <td align="center">0</td>
-<td align="center">401</td>
-<td align="center">1658</td>
+<td align="center">359</td>
+<td align="center">1578</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">CIP</td>
-<td align="center">2963</td>
+<td align="center">3015</td>
 <td align="center">0</td>
-<td align="center">879</td>
-<td align="center">3842</td>
+<td align="center">918</td>
+<td align="center">3933</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">CIP</td>
-<td align="center">1785</td>
+<td align="center">1798</td>
 <td align="center">0</td>
-<td align="center">561</td>
-<td align="center">2346</td>
+<td align="center">578</td>
+<td align="center">2376</td>
 </tr>
 </tbody>
 </table>
@ -1132,7 +1133,7 @@ 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="cb28"><pre class="downlit">
 <span class="va">data_1st</span> <span class="op">%&gt;%</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 class="co"># [1] 0.5382168</span></pre></div>
+<span class="co"># [1] 0.535457</span></pre></div>
 <p>Or can be used in conjuction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
 <div class="sourceCode" id="cb29"><pre class="downlit">
 <span class="va">data_1st</span> <span class="op">%&gt;%</span> 
@ -1147,19 +1148,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5459117</td>
+<td align="center">0.5309604</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5280457</td>
+<td align="center">0.5345539</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5268007</td>
+<td align="center">0.5403226</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5537583</td>
+<td align="center">0.5401970</td>
 </tr>
 </tbody>
 </table>
@ -1179,23 +1180,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5459117</td>
-<td align="center">4574</td>
+<td align="center">0.5309604</td>
+<td align="center">4748</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5280457</td>
-<td align="center">5598</td>
+<td align="center">0.5345539</td>
+<td align="center">5571</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5268007</td>
-<td align="center">2388</td>
+<td align="center">0.5403226</td>
+<td align="center">2356</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5537583</td>
-<td align="center">3153</td>
+<td align="center">0.5401970</td>
+<td align="center">3147</td>
 </tr>
 </tbody>
 </table>
@ -1217,27 +1218,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.8318292</td>
-<td align="center">0.8989450</td>
-<td align="center">0.9853820</td>
+<td align="center">0.8287335</td>
+<td align="center">0.8995589</td>
+<td align="center">0.9863894</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8166466</td>
-<td align="center">0.8908323</td>
-<td align="center">0.9782871</td>
+<td align="center">0.8269962</td>
+<td align="center">0.8941698</td>
+<td align="center">0.9828897</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.8232691</td>
-<td align="center">0.9190526</td>
-<td align="center">0.9880271</td>
+<td align="center">0.8245614</td>
+<td align="center">0.9211798</td>
+<td align="center">0.9839817</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5264280</td>
+<td align="center">0.5366162</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5264280</td>
+<td align="center">0.5366162</td>
 </tr>
 </tbody>
 </table>