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@ -38,7 +38,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9013</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9014</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -162,7 +162,7 @@
<img src="../logo.svg" class="logo" alt=""><h1>How to conduct AMR data analysis</h1>
<h4 data-toc-skip class="author">Dr. Matthijs Berends</h4>
<h4 data-toc-skip class="date">10 October 2022</h4>
<h4 data-toc-skip class="date">11 October 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -170,7 +170,7 @@
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 10 October 2022.</p>
<p><strong>Note:</strong> values on this page will change with every website update since they are based on randomly created values and the page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R Markdown</a>. However, the methodology remains unchanged. This page was generated on 11 October 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -201,21 +201,21 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-10-10</td>
<td align="center">2022-10-11</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2022-10-10</td>
<td align="center">2022-10-11</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2022-10-10</td>
<td align="center">2022-10-11</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -325,52 +325,19 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-01-05</td>
<td align="center">B6</td>
<td align="center">2015-02-02</td>
<td align="center">E3</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">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-10-29</td>
<td align="center">N7</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">F</td>
</tr>
<tr class="odd">
<td align="center">2013-03-22</td>
<td align="center">H6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia 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">M</td>
</tr>
<tr class="even">
<td align="center">2012-10-06</td>
<td align="center">C7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-03-25</td>
<td align="center">S8</td>
<td align="center">2015-12-29</td>
<td align="center">W4</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
@ -379,17 +346,50 @@
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-05-16</td>
<td align="center">I5</td>
<td align="center">Hospital B</td>
<tr class="odd">
<td align="center">2013-03-05</td>
<td align="center">E4</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia 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">M</td>
</tr>
<tr class="even">
<td align="center">2016-02-19</td>
<td align="center">O7</td>
<td align="center">Hospital C</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-03-08</td>
<td align="center">M10</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">2016-12-01</td>
<td align="center">U5</td>
<td align="center">Hospital D</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">R</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,283</td>
<td align="right">51.42%</td>
<td align="right">10,283</td>
<td align="right">51.42%</td>
<td align="right">10,418</td>
<td align="right">52.09%</td>
<td align="right">10,418</td>
<td align="right">52.09%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,717</td>
<td align="right">48.59%</td>
<td align="right">9,582</td>
<td align="right">47.91%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -488,9 +488,9 @@ Longest: 1</p>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,620 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,684 'phenotype-based' first isolates (53.4% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></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>
<p>So only 53.4% is suitable for resistance analysis! We can now filter on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
@ -499,7 +499,7 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,620 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,684 isolates for analysis. Now our data looks like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table class="table">
@ -538,14 +538,14 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2013-01-05</td>
<td align="center">B6</td>
<td align="center">2015-02-02</td>
<td align="center">E3</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -553,77 +553,61 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">3</td>
<td align="center">2013-03-22</td>
<td align="center">H6</td>
<td align="center">Hospital B</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">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">2012-10-06</td>
<td align="center">C7</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">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="left">6</td>
<td align="center">2011-05-16</td>
<td align="center">I5</td>
<td align="center">Hospital B</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">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">11</td>
<td align="center">2014-02-18</td>
<td align="center">K4</td>
<td align="center">Hospital B</td>
<td align="center">2016-02-19</td>
<td align="center">O7</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</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">12</td>
<td align="center">2013-07-06</td>
<td align="center">Q5</td>
<tr class="odd">
<td align="left">6</td>
<td align="center">2016-12-01</td>
<td align="center">U5</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">7</td>
<td align="center">2017-10-01</td>
<td align="center">K6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2015-04-05</td>
<td align="center">R1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
@ -632,6 +616,22 @@ 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">2010-02-04</td>
<td align="center">B3</td>
<td align="center">Hospital B</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -653,8 +653,8 @@ Longest: 1</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://rdrr.io/pkg/cleaner/man/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,620<br>
Available: 10,620 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,684<br>
Available: 10,684 (100.0%, NA: 0 = 0.0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -671,33 +671,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,630</td>
<td align="right">43.60%</td>
<td align="right">4,630</td>
<td align="right">43.60%</td>
<td align="right">4,678</td>
<td align="right">43.79%</td>
<td align="right">4,678</td>
<td align="right">43.79%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,705</td>
<td align="right">25.47%</td>
<td align="right">7,335</td>
<td align="right">69.07%</td>
<td align="right">2,715</td>
<td align="right">25.41%</td>
<td align="right">7,393</td>
<td align="right">69.20%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,115</td>
<td align="right">19.92%</td>
<td align="right">9,450</td>
<td align="right">88.98%</td>
<td align="right">2,108</td>
<td align="right">19.73%</td>
<td align="right">9,501</td>
<td align="right">88.93%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,170</td>
<td align="right">11.02%</td>
<td align="right">10,620</td>
<td align="right">1,183</td>
<td align="right">11.07%</td>
<td align="right">10,684</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -744,69 +744,54 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-01-05</td>
<td align="center">B6</td>
<td align="center">Hospital B</td>
<td align="center">2016-12-01</td>
<td align="center">U5</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</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="center">2010-11-11</td>
<td align="center">D1</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">2012-09-03</td>
<td align="center">O8</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">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">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="center">2017-03-17</td>
<td align="center">C4</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">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">2011-08-08</td>
<td align="center">2015-04-26</td>
<td align="center">W2</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</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">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">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-12-12</td>
<td align="center">C9</td>
<td align="center">Hospital B</td>
<tr class="even">
<td align="center">2012-08-07</td>
<td align="center">I8</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
@ -818,13 +803,13 @@ Longest: 24</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-06-02</td>
<td align="center">X9</td>
<tr class="odd">
<td align="center">2012-09-19</td>
<td align="center">Y3</td>
<td align="center">Hospital A</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">R</td>
<td align="center">F</td>
@ -833,6 +818,21 @@ Longest: 24</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-05-20</td>
<td align="center">R9</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in different bug/drug combinations, you can use the <code><a href="../reference/bug_drug_combinations.html">bug_drug_combinations()</a></code> function:</p>
@ -854,50 +854,50 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2199</td>
<td align="center">136</td>
<td align="center">2295</td>
<td align="center">4630</td>
<td align="center">2191</td>
<td align="center">130</td>
<td align="center">2357</td>
<td align="center">4678</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3430</td>
<td align="center">164</td>
<td align="center">1036</td>
<td align="center">4630</td>
<td align="center">3377</td>
<td align="center">187</td>
<td align="center">1114</td>
<td align="center">4678</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3392</td>
<td align="center">3413</td>
<td align="center">0</td>
<td align="center">1238</td>
<td align="center">4630</td>
<td align="center">1265</td>
<td align="center">4678</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4003</td>
<td align="center">4126</td>
<td align="center">0</td>
<td align="center">627</td>
<td align="center">4630</td>
<td align="center">552</td>
<td align="center">4678</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">1170</td>
<td align="center">1170</td>
<td align="center">1183</td>
<td align="center">1183</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">919</td>
<td align="center">53</td>
<td align="center">198</td>
<td align="center">1170</td>
<td align="center">940</td>
<td align="center">40</td>
<td align="center">203</td>
<td align="center">1183</td>
</tr>
</tbody>
</table>
@ -920,34 +920,34 @@ Longest: 24</p>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4003</td>
<td align="center">4126</td>
<td align="center">0</td>
<td align="center">627</td>
<td align="center">4630</td>
<td align="center">552</td>
<td align="center">4678</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1058</td>
<td align="center">1071</td>
<td align="center">0</td>
<td align="center">112</td>
<td align="center">1170</td>
<td align="center">1183</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2411</td>
<td align="center">2406</td>
<td align="center">0</td>
<td align="center">294</td>
<td align="center">2705</td>
<td align="center">309</td>
<td align="center">2715</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">2115</td>
<td align="center">2115</td>
<td align="center">2108</td>
<td align="center">2108</td>
</tr>
</tbody>
</table>
@ -961,7 +961,7 @@ Longest: 24</p>
<p>As per the EUCAST guideline of 2019, we calculate resistance as the proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to <code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to <code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="../reference/proportion.html">resistance</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">)</span></span>
<span><span class="co"># [1] 0.5410546</span></span></code></pre></div>
<span><span class="co"># [1] 0.5446462</span></span></code></pre></div>
<p>Or can be used in conjunction with <code><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by()</a></code> and <code><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise()</a></code>, both from the <code>dplyr</code> package:</p>
<div class="sourceCode" id="cb27"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -975,19 +975,19 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5427928</td>
<td align="center">0.5423889</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5446957</td>
<td align="center">0.5451578</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5358423</td>
<td align="center">0.5370259</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5362524</td>
<td align="center">0.5528979</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5427928</td>
<td align="center">3108</td>
<td align="center">0.5423889</td>
<td align="center">3173</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5446957</td>
<td align="center">3714</td>
<td align="center">0.5451578</td>
<td align="center">3676</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5358423</td>
<td align="center">1674</td>
<td align="center">0.5370259</td>
<td align="center">1661</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5362524</td>
<td align="center">2124</td>
<td align="center">0.5528979</td>
<td align="center">2174</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7762419</td>
<td align="center">0.8645788</td>
<td align="center">0.9792657</td>
<td align="center">0.7618640</td>
<td align="center">0.8820009</td>
<td align="center">0.9764857</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8307692</td>
<td align="center">0.9042735</td>
<td align="center">0.9854701</td>
<td align="center">0.8284024</td>
<td align="center">0.9053254</td>
<td align="center">0.9788673</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7940850</td>
<td align="center">0.8913124</td>
<td align="center">0.9818854</td>
<td align="center">0.7893186</td>
<td align="center">0.8861878</td>
<td align="center">0.9804788</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5390071</td>
<td align="center">0.5398482</td>
<td align="center">0.0000000</td>
<td align="center">0.5390071</td>
<td align="center">0.5398482</td>
</tr>
</tbody>
</table>
@ -1092,23 +1092,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.3%</td>
<td align="right">26.1%</td>
<td align="right">54.2%</td>
<td align="right">27.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.5%</td>
<td align="right">26.4%</td>
<td align="right">25.9%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.6%</td>
<td align="right">25.1%</td>
<td align="right">53.7%</td>
<td align="right">27.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">53.6%</td>
<td align="right">26.0%</td>
<td align="right">55.3%</td>
<td align="right">26.3%</td>
</tr>
</tbody>
</table>
@ -1206,18 +1206,18 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">mic_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span><span class="op">)</span></span>
<span><span class="va">mic_values</span></span>
<span><span class="co"># Class &lt;mic&gt;</span></span>
<span><span class="co"># [1] 0.005 2 1 0.0625 128 0.5 1 &gt;=256 64 </span></span>
<span><span class="co"># [10] 0.5 32 16 0.002 0.01 0.025 32 &gt;=256 2 </span></span>
<span><span class="co"># [19] &lt;=0.001 0.01 2 0.25 0.5 0.5 32 0.005 0.5 </span></span>
<span><span class="co"># [28] 0.125 2 1 0.025 128 0.125 0.002 0.125 16 </span></span>
<span><span class="co"># [37] &lt;=0.001 2 0.0625 8 1 0.125 0.002 &gt;=256 0.0625 </span></span>
<span><span class="co"># [46] 4 16 4 0.005 0.0625 4 0.002 0.0625 16 </span></span>
<span><span class="co"># [55] 2 4 1 0.5 16 0.5 64 128 0.005 </span></span>
<span><span class="co"># [64] 128 0.125 0.01 2 0.25 0.5 &lt;=0.001 16 32 </span></span>
<span><span class="co"># [73] 2 8 &gt;=256 64 2 0.002 0.002 32 4 </span></span>
<span><span class="co"># [82] 0.005 64 32 32 128 0.002 0.002 0.025 &gt;=256 </span></span>
<span><span class="co"># [91] 4 4 0.5 0.002 0.25 0.5 32 0.002 4 </span></span>
<span><span class="co"># [100] 8</span></span></code></pre></div>
<span><span class="co"># [1] 8 32 0.125 4 0.0625 32 0.5 0.01 8 </span></span>
<span><span class="co"># [10] 0.01 8 1 2 16 0.002 0.25 128 128 </span></span>
<span><span class="co"># [19] 256 0.125 &lt;=0.001 0.125 &lt;=0.001 0.125 32 128 16 </span></span>
<span><span class="co"># [28] 8 0.125 &lt;=0.001 128 0.005 0.5 1 2 0.25 </span></span>
<span><span class="co"># [37] 0.125 0.5 4 0.005 0.5 16 0.002 0.0625 2 </span></span>
<span><span class="co"># [46] 0.01 256 &lt;=0.001 64 16 1 2 64 4 </span></span>
<span><span class="co"># [55] 0.0625 128 0.002 0.25 8 1 0.005 0.5 16 </span></span>
<span><span class="co"># [64] 16 0.25 4 32 2 0.005 32 0.5 0.01 </span></span>
<span><span class="co"># [73] 0.01 4 256 256 &lt;=0.001 0.25 32 8 0.01 </span></span>
<span><span class="co"># [82] 0.0625 0.01 0.5 0.25 &lt;=0.001 64 1 0.5 16 </span></span>
<span><span class="co"># [91] 0.0625 256 4 4 2 2 0.0625 0.125 0.5 </span></span>
<span><span class="co"># [100] 4</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
@ -1244,10 +1244,10 @@ Longest: 24</p>
<code class="sourceCode R"><span><span class="va">disk_values</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_disk</a></span><span class="op">(</span>size <span class="op">=</span> <span class="fl">100</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span>
<span><span class="va">disk_values</span></span>
<span><span class="co"># Class &lt;disk&gt;</span></span>
<span><span class="co"># [1] 19 23 20 29 19 24 18 31 30 31 19 19 28 25 19 20 27 20 20 30 22 30 25 27 24</span></span>
<span><span class="co"># [26] 23 29 17 19 23 29 24 26 24 28 17 24 23 22 19 31 26 25 19 23 21 24 28 20 20</span></span>
<span><span class="co"># [51] 26 27 30 27 18 28 27 17 24 31 27 28 24 23 31 26 17 30 24 23 22 24 29 31 30</span></span>
<span><span class="co"># [76] 31 19 18 29 27 28 18 17 30 31 25 24 19 31 27 18 24 20 26 19 17 31 27 29 31</span></span></code></pre></div>
<span><span class="co"># [1] 29 24 25 24 31 25 20 22 25 17 19 29 29 27 31 21 23 23 29 17 25 21 25 29 31</span></span>
<span><span class="co"># [26] 20 23 23 20 24 27 22 18 30 21 22 21 28 27 19 24 22 19 30 29 20 17 19 25 19</span></span>
<span><span class="co"># [51] 19 24 26 21 21 27 24 22 21 30 31 29 25 19 24 25 24 25 20 26 28 20 20 19 27</span></span>
<span><span class="co"># [76] 22 22 24 31 24 22 28 22 22 23 26 17 28 18 28 23 22 26 26 21 25 31 22 31 31</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># base R:</span></span>
<span><span class="fu"><a href="../reference/plot.html">plot</a></span><span class="op">(</span><span class="va">disk_values</span>, mo <span class="op">=</span> <span class="st">"E. coli"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span><span class="op">)</span></span></code></pre></div>