(v1.3.0.9015) as.mo() speedup for valid taxonomic names

2025-07-09 03:22:00 +02:00 · 2020-09-03 20:59:21 +02:00
parent c4b87fe241
commit 68e9cb78e9
104 changed files with 542 additions and 529 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">1.3.0.9006</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
      </span>
    </div>

@ -79,7 +79,7 @@
      <a href="../articles/datasets.html">
        <span class="fa fa-database"></span>
         
-        Download our reference data sets for own use
+        Data sets for download / own use
      </a>
    </li>
    <li>
@ -193,7 +193,7 @@
      <h1 data-toc-skip>How to conduct AMR analysis</h1>
                        <h4 class="author">Matthijs S. Berends</h4>
            
-            <h4 class="date">21 August 2020</h4>
+            <h4 class="date">03 September 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 21 August 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 03 September 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">2020-08-21</td>
+<td align="center">2020-09-03</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">2020-08-21</td>
+<td align="center">2020-09-03</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">2020-08-21</td>
+<td align="center">2020-09-03</td>
 <td align="center">efgh</td>
 <td align="center">Escherichia coli</td>
 <td align="center">R</td>
@ -361,68 +361,68 @@
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="center">2011-03-20</td>
-<td align="center">W2</td>
-<td align="center">Hospital A</td>
-<td align="center">Streptococcus pneumoniae</td>
+<td align="center">2014-05-29</td>
+<td align="center">B4</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">R</td>
-<td align="center">F</td>
+<td align="center">S</td>
+<td align="center">M</td>
 </tr>
 <tr class="even">
-<td align="center">2011-12-03</td>
-<td align="center">X9</td>
-<td align="center">Hospital B</td>
-<td align="center">Klebsiella pneumoniae</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">2012-11-11</td>
-<td align="center">A5</td>
-<td align="center">Hospital D</td>
+<td align="center">2017-04-19</td>
+<td align="center">S1</td>
+<td align="center">Hospital C</td>
 <td align="center">Staphylococcus aureus</td>
 <td align="center">S</td>
-<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">M</td>
-</tr>
-<tr class="even">
-<td align="center">2012-09-03</td>
-<td align="center">Y3</td>
-<td align="center">Hospital C</td>
-<td align="center">Escherichia coli</td>
-<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
-<td align="center">R</td>
 <td align="center">F</td>
 </tr>
 <tr class="odd">
-<td align="center">2012-11-19</td>
-<td align="center">I3</td>
-<td align="center">Hospital C</td>
+<td align="center">2017-04-21</td>
+<td align="center">L3</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">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">2015-06-05</td>
-<td align="center">Q7</td>
+<td align="center">2011-01-19</td>
+<td align="center">A7</td>
+<td align="center">Hospital A</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="odd">
+<td align="center">2011-01-24</td>
+<td align="center">H10</td>
 <td align="center">Hospital B</td>
 <td align="center">Escherichia coli</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
+<td align="center">M</td>
+</tr>
+<tr class="even">
+<td align="center">2011-01-31</td>
+<td align="center">T9</td>
+<td align="center">Hospital C</td>
+<td align="center">Streptococcus pneumoniae</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>
@ -459,16 +459,16 @@ Longest: 1</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">M</td>
-<td align="right">10,358</td>
-<td align="right">51.79%</td>
-<td align="right">10,358</td>
-<td align="right">51.79%</td>
+<td align="right">10,409</td>
+<td align="right">52.05%</td>
+<td align="right">10,409</td>
+<td align="right">52.05%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">F</td>
-<td align="right">9,642</td>
-<td align="right">48.21%</td>
+<td align="right">9,591</td>
+<td align="right">47.96%</td>
 <td align="right">20,000</td>
 <td align="right">100.00%</td>
 </tr>
@ -518,7 +518,7 @@ Longest: 1</p>
 <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 28.3% 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>
+<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="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html">filter</a></span>(<span class="kw">first</span> <span class="op">==</span> <span class="fl">TRUE</span>)
@ -532,7 +532,7 @@ 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 C8, 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 M8, sorted on date:</p>
 <table class="table">
 <thead><tr class="header">
 <th align="center">isolate</th>
@ -548,21 +548,21 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-01-13</td>
-<td align="center">C8</td>
+<td align="center">2010-01-28</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-02-19</td>
-<td align="center">C8</td>
+<td align="center">2010-05-23</td>
+<td align="center">M8</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>
@ -570,10 +570,10 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-03-12</td>
-<td align="center">C8</td>
+<td align="center">2010-07-11</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -581,30 +581,30 @@ Longest: 1</p>
 </tr>
 <tr class="even">
 <td align="center">4</td>
-<td align="center">2010-03-25</td>
-<td align="center">C8</td>
+<td align="center">2010-10-01</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-04-28</td>
-<td align="center">C8</td>
+<td align="center">2010-12-02</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 </tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2010-07-22</td>
-<td align="center">C8</td>
+<td align="center">2010-12-23</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -614,8 +614,8 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2010-12-05</td>
-<td align="center">C8</td>
+<td align="center">2011-01-16</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -625,33 +625,33 @@ Longest: 1</p>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2011-01-18</td>
-<td align="center">C8</td>
+<td align="center">2011-03-14</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2011-05-24</td>
-<td align="center">C8</td>
+<td align="center">2011-04-02</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">I</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</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">2011-06-24</td>
-<td align="center">C8</td>
+<td align="center">2011-04-05</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
@ -686,34 +686,34 @@ Longest: 1</p>
 <tbody>
 <tr class="odd">
 <td align="center">1</td>
-<td align="center">2010-01-13</td>
-<td align="center">C8</td>
+<td align="center">2010-01-28</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">TRUE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">2</td>
-<td align="center">2010-02-19</td>
-<td align="center">C8</td>
+<td align="center">2010-05-23</td>
+<td align="center">M8</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>
 <td align="center">FALSE</td>
-<td align="center">FALSE</td>
+<td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">3</td>
-<td align="center">2010-03-12</td>
-<td align="center">C8</td>
+<td align="center">2010-07-11</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -722,32 +722,32 @@ Longest: 1</p>
 </tr>
 <tr class="even">
 <td align="center">4</td>
-<td align="center">2010-03-25</td>
-<td align="center">C8</td>
+<td align="center">2010-10-01</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="odd">
 <td align="center">5</td>
-<td align="center">2010-04-28</td>
-<td align="center">C8</td>
+<td align="center">2010-12-02</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
 <td align="center">6</td>
-<td align="center">2010-07-22</td>
-<td align="center">C8</td>
+<td align="center">2010-12-23</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -758,8 +758,8 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">7</td>
-<td align="center">2010-12-05</td>
-<td align="center">C8</td>
+<td align="center">2011-01-16</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">S</td>
 <td align="center">S</td>
@ -770,11 +770,11 @@ Longest: 1</p>
 </tr>
 <tr class="even">
 <td align="center">8</td>
-<td align="center">2011-01-18</td>
-<td align="center">C8</td>
+<td align="center">2011-03-14</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">TRUE</td>
@ -782,23 +782,23 @@ Longest: 1</p>
 </tr>
 <tr class="odd">
 <td align="center">9</td>
-<td align="center">2011-05-24</td>
-<td align="center">C8</td>
+<td align="center">2011-04-02</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">R</td>
-<td align="center">I</td>
-<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</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">10</td>
-<td align="center">2011-06-24</td>
-<td align="center">C8</td>
+<td align="center">2011-04-05</td>
+<td align="center">M8</td>
 <td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
 <td align="center">S</td>
 <td align="center">FALSE</td>
@ -806,13 +806,13 @@ Longest: 1</p>
 </tr>
 </tbody>
 </table>
-<p>Instead of 2, now 8 isolates are flagged. In total, 78.4% of all isolates are marked ‘first weighted’ - 50.1% 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 8 isolates are flagged. In total, 79.1% of all isolates are marked ‘first weighted’ - 50.5% 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="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data</span> <span class="op">%&gt;%</span> 
  <span class="fu"><a href="../reference/first_isolate.html">filter_first_weighted_isolate</a></span>()
 </pre></div>
-<p>So we end up with 15,686 isolates for analysis.</p>
+<p>So we end up with 15,813 isolates for analysis.</p>
 <p>We can remove unneeded columns:</p>
 <div class="sourceCode" id="cb20"><pre class="downlit">
 <span class="kw">data_1st</span> <span class="op">&lt;-</span> <span class="kw">data_1st</span> <span class="op">%&gt;%</span> 
@ -857,13 +857,77 @@ Longest: 1</p>
 </tr></thead>
 <tbody>
 <tr class="odd">
-<td align="left">1</td>
-<td align="center">2011-03-20</td>
-<td align="center">W2</td>
+<td align="left">2</td>
+<td align="center">2017-04-19</td>
+<td align="center">S1</td>
+<td align="center">Hospital C</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">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">3</td>
+<td align="center">2017-04-21</td>
+<td align="center">L3</td>
+<td align="center">Hospital B</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+<td align="center">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">4</td>
+<td align="center">2011-01-19</td>
+<td align="center">A7</td>
 <td align="center">Hospital A</td>
+<td align="center">B_STPHY_AURS</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">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">5</td>
+<td align="center">2011-01-24</td>
+<td align="center">H10</td>
+<td align="center">Hospital B</td>
+<td align="center">B_ESCHR_COLI</td>
+<td align="center">R</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">S</td>
+<td align="center">M</td>
+<td align="center">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">6</td>
+<td align="center">2011-01-31</td>
+<td align="center">T9</td>
+<td align="center">Hospital C</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">S</td>
 <td align="center">R</td>
 <td align="center">F</td>
@ -873,85 +937,21 @@ Longest: 1</p>
 <td align="center">TRUE</td>
 </tr>
 <tr class="even">
-<td align="left">3</td>
-<td align="center">2012-11-11</td>
-<td align="center">A5</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">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="odd">
-<td align="left">4</td>
-<td align="center">2012-09-03</td>
-<td align="center">Y3</td>
-<td align="center">Hospital C</td>
+<td align="left">7</td>
+<td align="center">2012-12-27</td>
+<td align="center">Q9</td>
+<td align="center">Hospital A</td>
 <td align="center">B_ESCHR_COLI</td>
 <td align="center">R</td>
+<td align="center">R</td>
+<td align="center">R</td>
 <td align="center">S</td>
-<td align="center">R</td>
-<td align="center">R</td>
 <td align="center">F</td>
 <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">5</td>
-<td align="center">2012-11-19</td>
-<td align="center">I3</td>
-<td align="center">Hospital C</td>
-<td align="center">B_ESCHR_COLI</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">S</td>
-<td align="center">R</td>
-<td align="center">M</td>
-<td align="center">Gram-negative</td>
-<td align="center">Escherichia</td>
-<td align="center">coli</td>
-<td align="center">TRUE</td>
-</tr>
-<tr class="odd">
-<td align="left">8</td>
-<td align="center">2013-11-06</td>
-<td align="center">B1</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">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">9</td>
-<td align="center">2017-01-21</td>
-<td align="center">U3</td>
-<td align="center">Hospital D</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>
 </tbody>
 </table>
 <p>Time for the analysis!</p>
@ -975,8 +975,8 @@ Longest: 1</p>
 </pre></div>
 <p><strong>Frequency table</strong></p>
 <p>Class: character<br>
-Length: 15,686<br>
-Available: 15,686 (100%, NA: 0 = 0%)<br>
+Length: 15,813<br>
+Available: 15,813 (100%, NA: 0 = 0%)<br>
 Unique: 4</p>
 <p>Shortest: 16<br>
 Longest: 24</p>
@ -993,33 +993,33 @@ Longest: 24</p>
 <tr class="odd">
 <td align="left">1</td>
 <td align="left">Escherichia coli</td>
-<td align="right">7,774</td>
-<td align="right">49.56%</td>
-<td align="right">7,774</td>
-<td align="right">49.56%</td>
+<td align="right">7,901</td>
+<td align="right">49.97%</td>
+<td align="right">7,901</td>
+<td align="right">49.97%</td>
 </tr>
 <tr class="even">
 <td align="left">2</td>
 <td align="left">Staphylococcus aureus</td>
-<td align="right">3,952</td>
-<td align="right">25.19%</td>
-<td align="right">11,726</td>
-<td align="right">74.75%</td>
+<td align="right">3,946</td>
+<td align="right">24.95%</td>
+<td align="right">11,847</td>
+<td align="right">74.92%</td>
 </tr>
 <tr class="odd">
 <td align="left">3</td>
 <td align="left">Streptococcus pneumoniae</td>
-<td align="right">2,367</td>
-<td align="right">15.09%</td>
-<td align="right">14,093</td>
-<td align="right">89.84%</td>
+<td align="right">2,394</td>
+<td align="right">15.14%</td>
+<td align="right">14,241</td>
+<td align="right">90.06%</td>
 </tr>
 <tr class="even">
 <td align="left">4</td>
 <td align="left">Klebsiella pneumoniae</td>
-<td align="right">1,593</td>
-<td align="right">10.16%</td>
-<td align="right">15,686</td>
+<td align="right">1,572</td>
+<td align="right">9.94%</td>
+<td align="right">15,813</td>
 <td align="right">100.00%</td>
 </tr>
 </tbody>
@ -1048,50 +1048,50 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">AMX</td>
-<td align="center">3685</td>
+<td align="center">3774</td>
 <td align="center">257</td>
-<td align="center">3832</td>
-<td align="center">7774</td>
+<td align="center">3870</td>
+<td align="center">7901</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">AMC</td>
-<td align="center">6104</td>
-<td align="center">275</td>
-<td align="center">1395</td>
-<td align="center">7774</td>
+<td align="center">6189</td>
+<td align="center">306</td>
+<td align="center">1406</td>
+<td align="center">7901</td>
 </tr>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">5979</td>
+<td align="center">6042</td>
 <td align="center">0</td>
-<td align="center">1795</td>
-<td align="center">7774</td>
+<td align="center">1859</td>
+<td align="center">7901</td>
 </tr>
 <tr class="even">
 <td align="center">E. coli</td>
 <td align="center">GEN</td>
-<td align="center">6986</td>
+<td align="center">7094</td>
 <td align="center">0</td>
-<td align="center">788</td>
-<td align="center">7774</td>
+<td align="center">807</td>
+<td align="center">7901</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">1593</td>
-<td align="center">1593</td>
+<td align="center">1572</td>
+<td align="center">1572</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">AMC</td>
-<td align="center">1269</td>
-<td align="center">57</td>
-<td align="center">267</td>
-<td align="center">1593</td>
+<td align="center">1245</td>
+<td align="center">56</td>
+<td align="center">271</td>
+<td align="center">1572</td>
 </tr>
 </tbody>
 </table>
@ -1116,34 +1116,34 @@ Longest: 24</p>
 <tr class="odd">
 <td align="center">E. coli</td>
 <td align="center">CIP</td>
-<td align="center">5979</td>
+<td align="center">6042</td>
 <td align="center">0</td>
-<td align="center">1795</td>
-<td align="center">7774</td>
+<td align="center">1859</td>
+<td align="center">7901</td>
 </tr>
 <tr class="even">
 <td align="center">K. pneumoniae</td>
 <td align="center">CIP</td>
-<td align="center">1213</td>
+<td align="center">1182</td>
 <td align="center">0</td>
-<td align="center">380</td>
-<td align="center">1593</td>
+<td align="center">390</td>
+<td align="center">1572</td>
 </tr>
 <tr class="odd">
 <td align="center">S. aureus</td>
 <td align="center">CIP</td>
-<td align="center">3003</td>
+<td align="center">2966</td>
 <td align="center">0</td>
-<td align="center">949</td>
-<td align="center">3952</td>
+<td align="center">980</td>
+<td align="center">3946</td>
 </tr>
 <tr class="even">
 <td align="center">S. pneumoniae</td>
 <td align="center">CIP</td>
-<td align="center">1820</td>
+<td align="center">1834</td>
 <td align="center">0</td>
-<td align="center">547</td>
-<td align="center">2367</td>
+<td align="center">560</td>
+<td align="center">2394</td>
 </tr>
 </tbody>
 </table>
@ -1156,7 +1156,7 @@ 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="kw">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span>(<span class="kw">AMX</span>)
-<span class="co"># [1] 0.5350631</span>
+<span class="co"># [1] 0.5330424</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">
@ -1173,19 +1173,19 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5338783</td>
+<td align="center">0.5262478</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5368875</td>
+<td align="center">0.5401022</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5367068</td>
+<td align="center">0.5257556</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5322422</td>
+<td align="center">0.5357938</td>
 </tr>
 </tbody>
 </table>
@ -1206,23 +1206,23 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Hospital A</td>
-<td align="center">0.5338783</td>
-<td align="center">4649</td>
+<td align="center">0.5262478</td>
+<td align="center">4648</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital B</td>
-<td align="center">0.5368875</td>
-<td align="center">5571</td>
+<td align="center">0.5401022</td>
+<td align="center">5673</td>
 </tr>
 <tr class="odd">
 <td align="center">Hospital C</td>
-<td align="center">0.5367068</td>
-<td align="center">2411</td>
+<td align="center">0.5257556</td>
+<td align="center">2349</td>
 </tr>
 <tr class="even">
 <td align="center">Hospital D</td>
-<td align="center">0.5322422</td>
-<td align="center">3055</td>
+<td align="center">0.5357938</td>
+<td align="center">3143</td>
 </tr>
 </tbody>
 </table>
@ -1245,27 +1245,27 @@ Longest: 24</p>
 <tbody>
 <tr class="odd">
 <td align="center">Escherichia</td>
-<td align="center">0.8205557</td>
-<td align="center">0.8986365</td>
-<td align="center">0.9855930</td>
+<td align="center">0.8220478</td>
+<td align="center">0.8978610</td>
+<td align="center">0.9860777</td>
 </tr>
 <tr class="even">
 <td align="center">Klebsiella</td>
-<td align="center">0.8323917</td>
-<td align="center">0.8901444</td>
-<td align="center">0.9855618</td>
+<td align="center">0.8276081</td>
+<td align="center">0.9001272</td>
+<td align="center">0.9860051</td>
 </tr>
 <tr class="odd">
 <td align="center">Staphylococcus</td>
-<td align="center">0.8276822</td>
-<td align="center">0.9210526</td>
-<td align="center">0.9868421</td>
+<td align="center">0.8335023</td>
+<td align="center">0.9206792</td>
+<td align="center">0.9878358</td>
 </tr>
 <tr class="even">
 <td align="center">Streptococcus</td>
-<td align="center">0.5504858</td>
+<td align="center">0.5396825</td>
 <td align="center">0.0000000</td>
-<td align="center">0.5504858</td>
+<td align="center">0.5396825</td>
 </tr>
 </tbody>
 </table>