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@ -44,7 +44,7 @@
</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">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
</span>
</div>
@ -185,13 +185,13 @@
</header><script src="AMR_files/header-attrs-2.9/header-attrs.js"></script><div class="row">
</header><script src="AMR_files/header-attrs-2.11/header-attrs.js"></script><div class="row">
<div class="col-md-9 contents">
<div class="page-header toc-ignore">
<h1 data-toc-skip>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Matthijs S. Berends</h4>
<h4 data-toc-skip class="date">29 August 2021</h4>
<h4 data-toc-skip class="date">29 September 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="hidden name"><code>AMR.Rmd</code></div>
@ -200,7 +200,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 August 2021.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 29 September 2021.</p>
<div id="introduction" class="section level1">
<h1 class="hasAnchor">
<a href="#introduction" class="anchor" aria-hidden="true"></a>Introduction</h1>
@ -231,21 +231,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2021-08-29</td>
<td align="center">2021-09-29</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">2021-08-29</td>
<td align="center">2021-09-29</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">2021-08-29</td>
<td align="center">2021-09-29</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -342,8 +342,30 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-06-29</td>
<td align="center">E6</td>
<td align="center">2017-08-27</td>
<td align="center">L5</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="even">
<td align="center">2017-02-15</td>
<td align="center">L4</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-01-01</td>
<td align="center">H4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -353,57 +375,35 @@
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-08-25</td>
<td align="center">D8</td>
<td align="center">Hospital D</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">M</td>
</tr>
<tr class="odd">
<td align="center">2017-01-14</td>
<td align="center">V1</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2010-10-15</td>
<td align="center">X2</td>
<td align="center">2014-12-09</td>
<td align="center">C5</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</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>
</tr>
<tr class="odd">
<td align="center">2011-04-05</td>
<td align="center">H6</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus 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">M</td>
</tr>
<tr class="even">
<td align="center">2012-01-10</td>
<td align="center">Y7</td>
<tr class="odd">
<td align="center">2010-02-19</td>
<td align="center">W1</td>
<td align="center">Hospital D</td>
<td align="center">Streptococcus pneumoniae</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">F</td>
</tr>
<tr class="even">
<td align="center">2010-11-16</td>
<td align="center">X9</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">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
@ -439,16 +439,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,326</td>
<td align="right">51.63%</td>
<td align="right">10,326</td>
<td align="right">51.63%</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>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,674</td>
<td align="right">48.37%</td>
<td align="right">9,588</td>
<td align="right">47.94%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -465,7 +465,6 @@ Longest: 1</p>
<span class="co"># [1] FALSE FALSE FALSE FALSE TRUE TRUE TRUE TRUE FALSE</span>
<span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span><span class="op">[</span><span class="fu"><a href="../reference/as.rsi.html">is.rsi.eligible</a></span><span class="op">(</span><span class="va">data</span><span class="op">)</span><span class="op">]</span>
<span class="co"># [1] "AMX" "AMC" "CIP" "GEN"</span>
<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" class="external-link">mutate</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.rsi.eligible</span><span class="op">)</span>, <span class="va">as.rsi</span><span class="op">)</span><span class="op">)</span></code></pre></div>
<p>Finally, we will apply <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> on our antimicrobial results. In Europe, most medical microbiological laboratories already apply these rules. Our package features their latest insights on intrinsic resistance and exceptional phenotypes. Moreover, the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function can also apply additional rules, like forcing <help title="ATC: J01CA01">ampicillin</help> = R when <help title="ATC: J01CR02">amoxicillin/clavulanic acid</help> = R.</p>
@ -496,16 +495,15 @@ Longest: 1</p>
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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" class="external-link">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>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span>
<span class="co"># Determining first isolates using the 'phenotype-based' method and an</span>
<span class="co"># episode length of 365 days</span>
<span class="co"># Determining first isolates using an episode length of 365 days</span>
<span class="co"># ℹ Using column 'bacteria' as input for `col_mo`.</span>
<span class="co"># ℹ Using column 'date' as input for `col_date`.</span>
<span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span>
<span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span>
<span class="co"># 2</span>
<span class="co"># =&gt; Found 10,571 first weighted isolates (phenotype-based, 52.9% of total</span>
<span class="co"># where a microbial ID was available)</span></code></pre></div>
<p>So only 52.9% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<span class="co"># =&gt; Found 10,617 'phenotype-based' first isolates (53.1% of total where a</span>
<span class="co"># microbial ID was available)</span></code></pre></div>
<p>So only 53.1% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span 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" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></code></pre></div>
@ -513,10 +511,10 @@ Longest: 1</p>
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
<code class="sourceCode R"><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_isolate</a></span><span class="op">(</span><span class="op">)</span></code></pre></div>
<p>So we end up with 10,571 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,617 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -530,7 +528,7 @@ Longest: 1</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -551,9 +549,9 @@ Longest: 1</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2012-06-29</td>
<td align="center">E6</td>
<td align="left">3</td>
<td align="center">2010-01-01</td>
<td align="center">H4</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
@ -567,83 +565,83 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-08-25</td>
<td align="center">D8</td>
<td align="left">4</td>
<td align="center">2014-12-09</td>
<td align="center">C5</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">6</td>
<td align="center">2010-11-16</td>
<td align="center">X9</td>
<td align="center">Hospital A</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">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">2011-07-04</td>
<td align="center">T1</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</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">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="odd">
<td align="left">10</td>
<td align="center">2012-05-19</td>
<td align="center">M7</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">14</td>
<td align="center">2016-05-14</td>
<td align="center">C2</td>
<td align="center">Hospital D</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">R</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="odd">
<td align="left">4</td>
<td align="center">2010-10-15</td>
<td align="center">X2</td>
<td align="center">Hospital B</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">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2012-01-10</td>
<td align="center">Y7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2016-02-07</td>
<td align="center">V2</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2016-11-08</td>
<td align="center">D4</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">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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -667,8 +665,8 @@ Longest: 1</p>
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,571<br>
Available: 10,571 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,617<br>
Available: 10,617 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -685,33 +683,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,507</td>
<td align="right">42.64%</td>
<td align="right">4,507</td>
<td align="right">42.64%</td>
<td align="right">4,569</td>
<td align="right">43.03%</td>
<td align="right">4,569</td>
<td align="right">43.03%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,799</td>
<td align="right">26.48%</td>
<td align="right">7,306</td>
<td align="right">69.11%</td>
<td align="right">2,718</td>
<td align="right">25.60%</td>
<td align="right">7,287</td>
<td align="right">68.64%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,087</td>
<td align="right">19.74%</td>
<td align="right">9,393</td>
<td align="right">88.86%</td>
<td align="right">2,158</td>
<td align="right">20.33%</td>
<td align="right">9,445</td>
<td align="right">88.96%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,178</td>
<td align="right">11.14%</td>
<td align="right">10,571</td>
<td align="right">1,172</td>
<td align="right">11.04%</td>
<td align="right">10,617</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -758,90 +756,90 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-10-15</td>
<td align="center">X2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">2016-05-14</td>
<td align="center">C2</td>
<td align="center">Hospital D</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">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="even">
<td align="center">2013-08-08</td>
<td align="center">C10</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-08-12</td>
<td align="center">H8</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-09-19</td>
<td align="center">S7</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-01-10</td>
<td align="center">Y7</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-02-02</td>
<td align="center">K7</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">2016-07-27</td>
<td align="center">I10</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">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="center">2011-08-05</td>
<td align="center">V3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-06-16</td>
<td align="center">Z8</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-08-23</td>
<td align="center">J10</td>
<td align="center">2013-11-25</td>
<td align="center">P4</td>
<td align="center">Hospital D</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">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@ -868,50 +866,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2196</td>
<td align="center">119</td>
<td align="center">2192</td>
<td align="center">4507</td>
<td align="center">2159</td>
<td align="center">142</td>
<td align="center">2268</td>
<td align="center">4569</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3378</td>
<td align="center">151</td>
<td align="center">978</td>
<td align="center">4507</td>
<td align="center">3349</td>
<td align="center">169</td>
<td align="center">1051</td>
<td align="center">4569</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3282</td>
<td align="center">3375</td>
<td align="center">0</td>
<td align="center">1225</td>
<td align="center">4507</td>
<td align="center">1194</td>
<td align="center">4569</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3929</td>
<td align="center">3985</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4507</td>
<td align="center">584</td>
<td align="center">4569</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">1178</td>
<td align="center">1178</td>
<td align="center">1172</td>
<td align="center">1172</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">930</td>
<td align="center">45</td>
<td align="center">203</td>
<td align="center">1178</td>
<td align="center">35</td>
<td align="center">207</td>
<td align="center">1172</td>
</tr>
</tbody>
</table>
@ -934,34 +932,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3929</td>
<td align="center">3985</td>
<td align="center">0</td>
<td align="center">578</td>
<td align="center">4507</td>
<td align="center">584</td>
<td align="center">4569</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1052</td>
<td align="center">1073</td>
<td align="center">0</td>
<td align="center">126</td>
<td align="center">1178</td>
<td align="center">99</td>
<td align="center">1172</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2473</td>
<td align="center">2409</td>
<td align="center">0</td>
<td align="center">326</td>
<td align="center">2799</td>
<td align="center">309</td>
<td align="center">2718</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2087</td>
<td align="center">2087</td>
<td align="center">2158</td>
<td align="center">2158</td>
</tr>
</tbody>
</table>
@ -975,7 +973,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span 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] 0.5403462</span></code></pre></div>
<span class="co"># [1] 0.5429029</span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="va">data_1st</span> <span class="op">%&gt;%</span>
@ -989,19 +987,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5487147</td>
<td align="center">0.5478773</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5436519</td>
<td align="center">0.5516767</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5257549</td>
<td align="center">0.5306768</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5338095</td>
<td align="center">0.5297098</td>
</tr>
</tbody>
</table>
@ -1020,23 +1018,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5487147</td>
<td align="center">3151</td>
<td align="center">0.5478773</td>
<td align="center">3227</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5436519</td>
<td align="center">3631</td>
<td align="center">0.5516767</td>
<td align="center">3638</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5257549</td>
<td align="center">1689</td>
<td align="center">0.5306768</td>
<td align="center">1581</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5338095</td>
<td align="center">2100</td>
<td align="center">0.5297098</td>
<td align="center">2171</td>
</tr>
</tbody>
</table>
@ -1057,27 +1055,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7830042</td>
<td align="center">0.8717550</td>
<td align="center">0.9764810</td>
<td align="center">0.7699715</td>
<td align="center">0.8721821</td>
<td align="center">0.9748304</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8276740</td>
<td align="center">0.8930390</td>
<td align="center">0.9787776</td>
<td align="center">0.8233788</td>
<td align="center">0.9155290</td>
<td align="center">0.9872014</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7874241</td>
<td align="center">0.8835298</td>
<td align="center">0.9828510</td>
<td align="center">0.7969095</td>
<td align="center">0.8863135</td>
<td align="center">0.9790287</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5318639</td>
<td align="center">0.5338276</td>
<td align="center">0.0000000</td>
<td align="center">0.5318639</td>
<td align="center">0.5338276</td>
</tr>
</tbody>
</table>
@ -1102,23 +1100,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.9%</td>
<td align="right">25.8%</td>
<td align="right">54.8%</td>
<td align="right">26.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.4%</td>
<td align="right">27.8%</td>
<td align="right">55.2%</td>
<td align="right">26.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">52.6%</td>
<td align="right">25.0%</td>
<td align="right">53.1%</td>
<td align="right">26.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.4%</td>
<td align="right">24.3%</td>
<td align="right">53.0%</td>
<td align="right">25.4%</td>
</tr>
</tbody>
</table>
@ -1202,16 +1200,18 @@ Longest: 24</p>
<code class="sourceCode R"><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span>
<span class="va">mic_values</span>
<span class="co"># Class &lt;mic&gt;</span>
<span class="co"># [1] 1 128 0.01 0.25 0.01 16 0.001 0.125 0.25 0.01 </span>
<span class="co"># [11] 0.005 16 0.0625 64 &gt;=256 0.5 0.01 16 0.5 0.0625</span>
<span class="co"># [21] 0.001 0.5 0.0625 4 2 8 0.5 0.0625 0.125 128 </span>
<span class="co"># [31] 0.002 0.25 2 8 0.125 0.0625 0.125 16 128 0.002 </span>
<span class="co"># [41] 1 0.005 2 32 0.01 0.0625 &gt;=256 64 16 0.005 </span>
<span class="co"># [51] 2 0.001 &gt;=256 32 64 &gt;=256 128 0.01 0.005 0.001 </span>
<span class="co"># [61] 0.01 0.125 2 0.125 &gt;=256 32 64 0.01 2 0.25 </span>
<span class="co"># [71] 0.01 64 0.5 128 0.001 64 128 0.002 &gt;=256 64 </span>
<span class="co"># [81] 0.01 8 0.5 4 16 0.025 0.025 0.001 0.125 0.025 </span>
<span class="co"># [91] 2 64 64 128 32 128 0.001 32 2 0.005</span></code></pre></div>
<span class="co"># [1] 0.005 0.125 32 0.0625 0.5 0.125 16 0.25 0.025 </span>
<span class="co"># [10] &lt;=0.001 &lt;=0.001 0.0625 0.01 1 2 32 0.01 8 </span>
<span class="co"># [19] 0.005 32 0.005 32 128 0.125 0.125 2 &lt;=0.001</span>
<span class="co"># [28] 4 8 0.005 0.002 0.5 0.002 0.5 64 0.125 </span>
<span class="co"># [37] 0.01 0.002 0.0625 128 0.5 1 0.125 0.0625 0.002 </span>
<span class="co"># [46] 32 0.025 0.005 8 0.002 &lt;=0.001 8 1 16 </span>
<span class="co"># [55] &lt;=0.001 0.25 0.125 0.025 4 8 0.0625 16 4 </span>
<span class="co"># [64] 64 &lt;=0.001 128 0.125 0.5 4 32 &lt;=0.001 128 </span>
<span class="co"># [73] 16 64 16 0.125 4 2 0.002 0.025 8 </span>
<span class="co"># [82] 4 2 0.01 4 0.125 &lt;=0.001 0.002 0.01 0.5 </span>
<span class="co"># [91] 32 128 0.01 1 0.125 4 0.002 0.25 0.25 </span>
<span class="co"># [100] 16</span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></code></pre></div>
@ -1240,10 +1240,10 @@ Longest: 24</p>
<span class="co"># to review it.</span>
<span class="va">disk_values</span>
<span class="co"># Class &lt;disk&gt;</span>
<span class="co"># [1] 30 29 25 23 27 18 23 21 31 26 17 30 18 31 30 25 22 19 18 26 31 19 21 25 29</span>
<span class="co"># [26] 22 26 30 20 20 18 19 18 29 22 17 27 21 24 18 17 23 27 18 19 31 18 29 30 25</span>
<span class="co"># [51] 27 23 21 20 31 19 19 25 25 23 23 19 17 25 21 30 20 31 26 23 29 27 30 29 24</span>
<span class="co"># [76] 20 23 23 27 20 24 19 28 24 31 29 26 23 20 29 23 18 17 27 21 28 28 17 23 17</span></code></pre></div>
<span class="co"># [1] 26 27 19 22 20 17 23 26 26 17 21 21 22 18 19 25 18 20 17 20 20 22 17 31 24</span>
<span class="co"># [26] 28 22 20 31 18 19 26 25 19 22 19 26 26 24 18 18 19 31 25 31 21 28 23 22 21</span>
<span class="co"># [51] 22 18 22 18 29 25 29 29 29 24 22 19 23 23 23 22 17 24 17 26 23 25 30 26 17</span>
<span class="co"># [76] 17 20 31 17 30 25 18 18 22 29 25 24 29 27 26 30 29 18 21 18 24 25 26 31 25</span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># base R:</span>
<span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></code></pre></div>
@ -1312,7 +1312,7 @@ Longest: 24</p>
<footer><div class="copyright">
<p></p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link external-link">Corinna Glasner</a>.</p>
<p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link external-link">Matthijs S. Berends</a>, Christian F. Luz.</p>
</div>
<div class="pkgdown">