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@ -20,7 +20,7 @@
<script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
<script src="../extra.js"></script><meta property="og:title" content="How to conduct AMR analysis">
<meta property="og:description" content="AMR">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.svg">
<meta property="og:image" content="https://msberends.github.io/AMR/logo.png">
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@ -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">1.3.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.4.0</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">03 September 2020</h4>
<h4 class="date">30 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 03 September 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 30 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">2020-09-03</td>
<td align="center">2020-09-30</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">2020-09-03</td>
<td align="center">2020-09-30</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">2020-09-03</td>
<td align="center">2020-09-30</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -361,70 +361,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2014-05-29</td>
<td align="center">B4</td>
<td align="center">2016-08-26</td>
<td align="center">P9</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-09-24</td>
<td align="center">T6</td>
<td align="center">Hospital B</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">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-04-19</td>
<td align="center">S1</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<tr class="odd">
<td align="center">2017-04-02</td>
<td align="center">X1</td>
<td align="center">Hospital D</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>
</tr>
<tr class="odd">
<td align="center">2017-04-21</td>
<td align="center">L3</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="center">2016-12-13</td>
<td align="center">F1</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">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-01-19</td>
<td align="center">A7</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="center">2012-02-05</td>
<td align="center">O8</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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>
<td align="center">F</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">2017-06-17</td>
<td align="center">K1</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</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>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -459,16 +459,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</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>
<td align="right">10,232</td>
<td align="right">51.16%</td>
<td align="right">10,232</td>
<td align="right">51.16%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,591</td>
<td align="right">47.96%</td>
<td align="right">9,768</td>
<td align="right">48.84%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -489,6 +489,7 @@ Longest: 1</p>
<p>Because the amoxicillin (column <code>AMX</code>) and amoxicillin/clavulanic acid (column <code>AMC</code>) in our data were generated randomly, some rows will undoubtedly contain AMX = S and AMC = R, which is technically impossible. The <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> fixes this:</p>
<div class="sourceCode" id="cb13"><pre class="downlit">
<span class="kw">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/eucast_rules.html">eucast_rules</a></span>(<span class="kw">data</span>, col_mo = <span class="st">"bacteria"</span>, rules = <span class="st">"all"</span>)
<span class="co"># Set amoxicillin (AMX) = R where amoxicillin/clavulanic acid (AMC) = R</span>
</pre></div>
</div>
<div id="adding-new-variables" class="section level1">
@ -518,7 +519,7 @@ 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 28.6% 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>
<p>So only 28.5% 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 +533,7 @@ 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 M8, 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 Z5, sorted on date:</p>
<table class="table">
<thead><tr class="header">
<th align="center">isolate</th>
@ -548,76 +549,76 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-28</td>
<td align="center">M8</td>
<td align="center">2010-02-11</td>
<td align="center">Z5</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">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2</td>
<td align="center">2010-05-23</td>
<td align="center">M8</td>
<td align="center">2010-04-11</td>
<td align="center">Z5</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-11</td>
<td align="center">M8</td>
<td align="center">2010-05-31</td>
<td align="center">Z5</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">I</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">2010-10-01</td>
<td align="center">M8</td>
<td align="center">2011-03-29</td>
<td align="center">Z5</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">2010-12-02</td>
<td align="center">M8</td>
<td align="center">2011-04-23</td>
<td align="center">Z5</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">S</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">2010-12-23</td>
<td align="center">M8</td>
<td align="center">2011-05-06</td>
<td align="center">Z5</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-01-16</td>
<td align="center">M8</td>
<td align="center">2011-09-05</td>
<td align="center">Z5</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>
@ -625,19 +626,19 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">8</td>
<td align="center">2011-03-14</td>
<td align="center">M8</td>
<td align="center">2011-09-29</td>
<td align="center">Z5</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">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-04-02</td>
<td align="center">M8</td>
<td align="center">2011-11-16</td>
<td align="center">Z5</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -647,13 +648,13 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-05</td>
<td align="center">M8</td>
<td align="center">2011-11-26</td>
<td align="center">Z5</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">R</td>
<td align="center">FALSE</td>
</tr>
</tbody>
@ -686,35 +687,35 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="center">1</td>
<td align="center">2010-01-28</td>
<td align="center">M8</td>
<td align="center">2010-02-11</td>
<td align="center">Z5</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">S</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">2010-05-23</td>
<td align="center">M8</td>
<td align="center">2010-04-11</td>
<td align="center">Z5</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">3</td>
<td align="center">2010-07-11</td>
<td align="center">M8</td>
<td align="center">2010-05-31</td>
<td align="center">Z5</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">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">FALSE</td>
@ -722,97 +723,97 @@ Longest: 1</p>
</tr>
<tr class="even">
<td align="center">4</td>
<td align="center">2010-10-01</td>
<td align="center">M8</td>
<td align="center">2011-03-29</td>
<td align="center">Z5</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>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">5</td>
<td align="center">2010-12-02</td>
<td align="center">M8</td>
<td align="center">2011-04-23</td>
<td align="center">Z5</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">S</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">2010-12-23</td>
<td align="center">M8</td>
<td align="center">2011-05-06</td>
<td align="center">Z5</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">R</td>
<td align="center">S</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">7</td>
<td align="center">2011-01-16</td>
<td align="center">M8</td>
<td align="center">2011-09-05</td>
<td align="center">Z5</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="even">
<td align="center">8</td>
<td align="center">2011-03-14</td>
<td align="center">M8</td>
<td align="center">2011-09-29</td>
<td align="center">Z5</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">S</td>
<td align="center">S</td>
<td align="center">TRUE</td>
<td align="center">FALSE</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">9</td>
<td align="center">2011-04-02</td>
<td align="center">M8</td>
<td align="center">2011-11-16</td>
<td align="center">Z5</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>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">10</td>
<td align="center">2011-04-05</td>
<td align="center">M8</td>
<td align="center">2011-11-26</td>
<td align="center">Z5</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">R</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, 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>Instead of 2, now 10 isolates are flagged. In total, 78.6% 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>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 15,813 isolates for analysis.</p>
<p>So we end up with 15,718 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>
@ -857,32 +858,32 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2017-04-19</td>
<td align="center">S1</td>
<td align="left">1</td>
<td align="center">2016-08-26</td>
<td align="center">P9</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</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">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">2</td>
<td align="center">2016-09-24</td>
<td align="center">T6</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">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>
@ -890,27 +891,11 @@ Longest: 1</p>
</tr>
<tr class="odd">
<td align="left">4</td>
<td align="center">2011-01-19</td>
<td align="center">A7</td>
<td align="center">2016-12-13</td>
<td align="center">F1</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">S</td>
@ -920,31 +905,31 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<tr class="even">
<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">2017-06-17</td>
<td align="center">K1</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="even">
<td align="left">7</td>
<td align="center">2012-12-27</td>
<td align="center">Q9</td>
<td align="center">Hospital A</td>
<tr class="odd">
<td align="left">8</td>
<td align="center">2011-02-20</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">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">F</td>
<td align="center">Gram-negative</td>
@ -952,6 +937,22 @@ Longest: 1</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2016-09-22</td>
<td align="center">D3</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -975,8 +976,8 @@ Longest: 1</p>
</pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 15,813<br>
Available: 15,813 (100%, NA: 0 = 0%)<br>
Length: 15,718<br>
Available: 15,718 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -993,33 +994,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</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>
<td align="right">7,841</td>
<td align="right">49.89%</td>
<td align="right">7,841</td>
<td align="right">49.89%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</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>
<td align="right">3,956</td>
<td align="right">25.17%</td>
<td align="right">11,797</td>
<td align="right">75.05%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</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>
<td align="right">2,346</td>
<td align="right">14.93%</td>
<td align="right">14,143</td>
<td align="right">89.98%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,572</td>
<td align="right">9.94%</td>
<td align="right">15,813</td>
<td align="right">1,575</td>
<td align="right">10.02%</td>
<td align="right">15,718</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -1048,50 +1049,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">3774</td>
<td align="center">257</td>
<td align="center">3870</td>
<td align="center">7901</td>
<td align="center">3793</td>
<td align="center">242</td>
<td align="center">3806</td>
<td align="center">7841</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">6189</td>
<td align="center">306</td>
<td align="center">1406</td>
<td align="center">7901</td>
<td align="center">6205</td>
<td align="center">301</td>
<td align="center">1335</td>
<td align="center">7841</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">6042</td>
<td align="center">5980</td>
<td align="center">0</td>
<td align="center">1859</td>
<td align="center">7901</td>
<td align="center">1861</td>
<td align="center">7841</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">7094</td>
<td align="center">7075</td>
<td align="center">0</td>
<td align="center">807</td>
<td align="center">7901</td>
<td align="center">766</td>
<td align="center">7841</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">1572</td>
<td align="center">1572</td>
<td align="center">1575</td>
<td align="center">1575</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">1245</td>
<td align="center">56</td>
<td align="center">271</td>
<td align="center">1572</td>
<td align="center">1217</td>
<td align="center">77</td>
<td align="center">281</td>
<td align="center">1575</td>
</tr>
</tbody>
</table>
@ -1116,34 +1117,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">6042</td>
<td align="center">5980</td>
<td align="center">0</td>
<td align="center">1859</td>
<td align="center">7901</td>
<td align="center">1861</td>
<td align="center">7841</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1182</td>
<td align="center">1207</td>
<td align="center">0</td>
<td align="center">390</td>
<td align="center">1572</td>
<td align="center">368</td>
<td align="center">1575</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">CIP</td>
<td align="center">2966</td>
<td align="center">2971</td>
<td align="center">0</td>
<td align="center">980</td>
<td align="center">3946</td>
<td align="center">985</td>
<td align="center">3956</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">CIP</td>
<td align="center">1834</td>
<td align="center">1790</td>
<td align="center">0</td>
<td align="center">560</td>
<td align="center">2394</td>
<td align="center">556</td>
<td align="center">2346</td>
</tr>
</tbody>
</table>
@ -1156,7 +1157,7 @@ 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] 0.5330424</span>
<span class="co"># [1] 0.5318107</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 +1174,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5262478</td>
<td align="center">0.5401506</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5401022</td>
<td align="center">0.5244014</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5257556</td>
<td align="center">0.5256917</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5357938</td>
<td align="center">0.5363864</td>
</tr>
</tbody>
</table>
@ -1206,23 +1207,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5262478</td>
<td align="center">4648</td>
<td align="center">0.5401506</td>
<td align="center">4782</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5401022</td>
<td align="center">5673</td>
<td align="center">0.5244014</td>
<td align="center">5471</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5257556</td>
<td align="center">2349</td>
<td align="center">0.5256917</td>
<td align="center">2277</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5357938</td>
<td align="center">3143</td>
<td align="center">0.5363864</td>
<td align="center">3188</td>
</tr>
</tbody>
</table>
@ -1245,27 +1246,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.8220478</td>
<td align="center">0.8978610</td>
<td align="center">0.9860777</td>
<td align="center">0.8297411</td>
<td align="center">0.9023084</td>
<td align="center">0.9858436</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8276081</td>
<td align="center">0.9001272</td>
<td align="center">0.9860051</td>
<td align="center">0.8215873</td>
<td align="center">0.9060317</td>
<td align="center">0.9879365</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.8335023</td>
<td align="center">0.9206792</td>
<td align="center">0.9878358</td>
<td align="center">0.8276036</td>
<td align="center">0.9160768</td>
<td align="center">0.9848332</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5396825</td>
<td align="center">0.5392157</td>
<td align="center">0.0000000</td>
<td align="center">0.5396825</td>
<td align="center">0.5392157</td>
</tr>
</tbody>
</table>