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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="">1.8.2.9007</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9008</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">06 October 2022</h4>
<h4 data-toc-skip class="date">10 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 06 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 10 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">2022-10-06</td>
<td align="center">2022-10-10</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">2022-10-06</td>
<td align="center">2022-10-10</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">2022-10-06</td>
<td align="center">2022-10-10</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -325,70 +325,70 @@
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-11-17</td>
<td align="center">Y8</td>
<td align="center">Hospital B</td>
<td align="center">2017-08-15</td>
<td align="center">V8</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2015-02-26</td>
<td align="center">V8</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">2013-01-31</td>
<td align="center">L3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-03-22</td>
<td align="center">Y6</td>
<td align="center">Hospital D</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">2011-11-24</td>
<td align="center">I6</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<tr class="even">
<td align="center">2012-02-11</td>
<td align="center">I1</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">M</td>
</tr>
<tr class="even">
<td align="center">2013-06-23</td>
<td align="center">O2</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">F</td>
</tr>
<tr class="odd">
<td align="center">2010-10-16</td>
<td align="center">X2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-03-22</td>
<td align="center">U10</td>
<td align="center">2012-09-29</td>
<td align="center">F5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-03-01</td>
<td align="center">H10</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">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -422,16 +422,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
<td align="right">10,361</td>
<td align="right">51.81%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,625</td>
<td align="right">48.13%</td>
<td align="right">9,639</td>
<td align="right">48.20%</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 10,694 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,672 '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 53.5% 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 10,694 isolates for analysis. Now our data looks like:</p>
<p>So we end up with 10,672 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 style="width:100%;" class="table">
@ -538,13 +538,13 @@ Longest: 1</p>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2017-11-17</td>
<td align="center">Y8</td>
<td align="center">Hospital B</td>
<td align="center">2017-08-15</td>
<td align="center">V8</td>
<td align="center">Hospital C</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">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -553,30 +553,46 @@ Longest: 1</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2015-02-26</td>
<td align="center">V8</td>
<td align="left">3</td>
<td align="center">2012-03-22</td>
<td align="center">Y6</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">9</td>
<td align="center">2013-06-02</td>
<td align="center">G6</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">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">2011-11-24</td>
<td align="center">I6</td>
<td align="center">Hospital D</td>
<tr class="even">
<td align="left">10</td>
<td align="center">2014-03-13</td>
<td align="center">C9</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -584,49 +600,33 @@ Longest: 1</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2017-08-17</td>
<td align="center">U7</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">I</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>
<tr class="odd">
<td align="left">8</td>
<td align="center">2013-09-19</td>
<td align="center">X2</td>
<td align="left">11</td>
<td align="center">2016-12-02</td>
<td align="center">S9</td>
<td align="center">Hospital B</td>
<td align="center">B_KLBSL_PNMN</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">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">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2012-04-26</td>
<td align="center">L7</td>
<td align="center">Hospital C</td>
<td align="left">13</td>
<td align="center">2017-06-05</td>
<td align="center">U8</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">R</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-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -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: 10,694<br>
Available: 10,694 (100.0%, NA: 0 = 0.0%)<br>
Length: 10,672<br>
Available: 10,672 (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">4,609</td>
<td align="right">43.10%</td>
<td align="right">4,609</td>
<td align="right">43.10%</td>
<td align="right">4,684</td>
<td align="right">43.89%</td>
<td align="right">4,684</td>
<td align="right">43.89%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,749</td>
<td align="right">25.71%</td>
<td align="right">7,358</td>
<td align="right">68.80%</td>
<td align="right">2,763</td>
<td align="right">25.89%</td>
<td align="right">7,447</td>
<td align="right">69.78%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,179</td>
<td align="right">20.38%</td>
<td align="right">9,537</td>
<td align="right">89.18%</td>
<td align="right">2,092</td>
<td align="right">19.60%</td>
<td align="right">9,539</td>
<td align="right">89.38%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,157</td>
<td align="right">10.82%</td>
<td align="right">10,694</td>
<td align="right">1,133</td>
<td align="right">10.62%</td>
<td align="right">10,672</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -744,12 +744,42 @@ Longest: 24</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-11-17</td>
<td align="center">Y8</td>
<td align="center">Hospital B</td>
<td align="center">2017-08-15</td>
<td align="center">V8</td>
<td align="center">Hospital C</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">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">2010-05-16</td>
<td align="center">G10</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="odd">
<td align="center">2017-11-18</td>
<td align="center">Z3</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">F</td>
@ -759,80 +789,50 @@ Longest: 24</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-08-17</td>
<td align="center">U7</td>
<td align="center">2010-06-25</td>
<td align="center">W9</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">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">2014-12-03</td>
<td align="center">A1</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">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">2014-11-26</td>
<td align="center">A3</td>
<td align="center">Hospital A</td>
<td align="center">B_KLBSL_PNMN</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">F</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="center">2016-01-02</td>
<td align="center">E9</td>
<td align="center">Hospital C</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">2015-02-13</td>
<td align="center">D10</td>
<td align="center">Hospital A</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">2016-05-02</td>
<td align="center">E2</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="even">
<td align="center">2014-04-15</td>
<td align="center">W8</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>
</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">2165</td>
<td align="center">105</td>
<td align="center">2339</td>
<td align="center">4609</td>
<td align="center">2201</td>
<td align="center">138</td>
<td align="center">2345</td>
<td align="center">4684</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3396</td>
<td align="center">157</td>
<td align="center">1056</td>
<td align="center">4609</td>
<td align="center">3471</td>
<td align="center">156</td>
<td align="center">1057</td>
<td align="center">4684</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3357</td>
<td align="center">3422</td>
<td align="center">0</td>
<td align="center">1252</td>
<td align="center">4609</td>
<td align="center">1262</td>
<td align="center">4684</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4052</td>
<td align="center">4073</td>
<td align="center">0</td>
<td align="center">557</td>
<td align="center">4609</td>
<td align="center">611</td>
<td align="center">4684</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">1157</td>
<td align="center">1157</td>
<td align="center">1133</td>
<td align="center">1133</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">899</td>
<td align="center">49</td>
<td align="center">209</td>
<td align="center">1157</td>
<td align="center">898</td>
<td align="center">43</td>
<td align="center">192</td>
<td align="center">1133</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">4052</td>
<td align="center">4073</td>
<td align="center">0</td>
<td align="center">557</td>
<td align="center">4609</td>
<td align="center">611</td>
<td align="center">4684</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1054</td>
<td align="center">1009</td>
<td align="center">0</td>
<td align="center">103</td>
<td align="center">1157</td>
<td align="center">124</td>
<td align="center">1133</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2418</td>
<td align="center">2462</td>
<td align="center">0</td>
<td align="center">331</td>
<td align="center">2749</td>
<td align="center">301</td>
<td align="center">2763</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">2179</td>
<td align="center">2179</td>
<td align="center">2092</td>
<td align="center">2092</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] 0.5487189</span></span></code></pre></div>
<span><span class="co"># [1] 0.5403861</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">0.5417823</td>
<td align="center">0.5367144</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5486465</td>
<td align="center">0.5420436</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5634971</td>
<td align="center">0.5339252</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5485369</td>
<td align="center">0.5478097</td>
</tr>
</tbody>
</table>
@ -1008,23 +1008,23 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5417823</td>
<td align="center">3243</td>
<td align="center">0.5367144</td>
<td align="center">3214</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5486465</td>
<td align="center">3731</td>
<td align="center">0.5420436</td>
<td align="center">3758</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5634971</td>
<td align="center">1567</td>
<td align="center">0.5339252</td>
<td align="center">1577</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5485369</td>
<td align="center">2153</td>
<td align="center">0.5478097</td>
<td align="center">2123</td>
</tr>
</tbody>
</table>
@ -1047,27 +1047,27 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7708831</td>
<td align="center">0.8791495</td>
<td align="center">0.9791712</td>
<td align="center">0.7743382</td>
<td align="center">0.8695559</td>
<td align="center">0.9739539</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8193604</td>
<td align="center">0.9109767</td>
<td align="center">0.9783924</td>
<td align="center">0.8305384</td>
<td align="center">0.8905560</td>
<td align="center">0.9841130</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7871953</td>
<td align="center">0.8795926</td>
<td align="center">0.9770826</td>
<td align="center">0.7853782</td>
<td align="center">0.8910604</td>
<td align="center">0.9768368</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5268472</td>
<td align="center">0.5363289</td>
<td align="center">0.0000000</td>
<td align="center">0.5268472</td>
<td align="center">0.5363289</td>
</tr>
</tbody>
</table>
@ -1092,22 +1092,22 @@ Longest: 24</p>
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.2%</td>
<td align="right">26.2%</td>
<td align="right">53.7%</td>
<td align="right">26.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.9%</td>
<td align="right">27.0%</td>
<td align="right">54.2%</td>
<td align="right">26.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">56.3%</td>
<td align="right">28.1%</td>
<td align="right">53.4%</td>
<td align="right">25.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">54.9%</td>
<td align="right">54.8%</td>
<td align="right">27.1%</td>
</tr>
</tbody>
@ -1206,16 +1206,16 @@ 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] 2 0.0625 0.25 128 64 256 0.01 0.01 0.0625 0.5 </span></span>
<span><span class="co"># [11] 0.002 0.001 0.125 0.025 128 0.002 0.01 256 1 1 </span></span>
<span><span class="co"># [21] 0.025 32 0.125 1 0.0625 1 2 1 0.25 32 </span></span>
<span><span class="co"># [31] 0.0625 0.5 0.002 0.25 0.001 0.002 0.025 0.01 32 0.5 </span></span>
<span><span class="co"># [41] 128 16 16 0.0625 4 256 256 16 64 0.125 </span></span>
<span><span class="co"># [51] 0.01 0.01 8 0.01 2 256 64 1 0.5 32 </span></span>
<span><span class="co"># [61] 0.025 2 16 0.005 0.025 16 2 64 8 4 </span></span>
<span><span class="co"># [71] 16 0.5 0.01 16 8 0.0625 0.01 128 128 0.005 </span></span>
<span><span class="co"># [81] 64 0.25 0.25 0.001 0.001 256 8 0.0625 0.125 0.01 </span></span>
<span><span class="co"># [91] 0.5 8 64 0.5 0.002 0.002 32 128 4 128</span></span></code></pre></div>
<span><span class="co"># [1] 0.125 64 256 0.005 0.001 0.025 2 256 16 256 </span></span>
<span><span class="co"># [11] 0.002 0.25 0.002 4 64 256 16 0.01 0.025 0.025 </span></span>
<span><span class="co"># [21] 8 8 4 0.005 32 1 0.0625 0.125 0.125 0.025 </span></span>
<span><span class="co"># [31] 4 0.025 0.005 16 0.001 256 8 0.002 0.0625 0.0625</span></span>
<span><span class="co"># [41] 256 0.25 4 0.005 0.5 16 64 0.002 0.125 4 </span></span>
<span><span class="co"># [51] 128 32 8 0.125 0.005 128 0.01 0.5 128 0.025 </span></span>
<span><span class="co"># [61] 0.125 0.002 64 0.005 0.001 0.01 64 0.01 0.01 16 </span></span>
<span><span class="co"># [71] 32 64 16 1 64 0.002 8 0.0625 0.125 0.01 </span></span>
<span><span class="co"># [81] 32 2 0.125 8 128 0.005 0.01 0.002 0.5 0.25 </span></span>
<span><span class="co"># [91] 0.01 1 64 0.025 0.25 2 256 0.0625 0.001 0.002</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>
@ -1242,10 +1242,10 @@ 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] 18 31 31 29 22 20 28 21 23 17 27 23 24 21 23 28 27 27 28 29 23 20 30 17 31</span></span>
<span><span class="co"># [26] 21 25 21 30 31 31 26 26 19 31 23 26 18 23 24 29 27 23 23 20 29 23 24 26 18</span></span>
<span><span class="co"># [51] 21 25 31 22 31 22 30 25 31 21 27 28 26 29 28 17 18 31 27 27 20 26 23 27 18</span></span>
<span><span class="co"># [76] 28 20 29 30 27 23 26 24 22 27 26 20 22 29 21 19 26 22 24 23 29 22 20 27 24</span></span></code></pre></div>
<span><span class="co"># [1] 26 20 31 29 17 23 21 22 28 21 30 24 28 29 31 26 21 29 27 18 18 24 18 20 26</span></span>
<span><span class="co"># [26] 19 23 21 29 25 25 18 21 22 28 29 30 20 20 23 23 30 23 26 23 30 31 30 29 25</span></span>
<span><span class="co"># [51] 19 25 31 18 30 31 25 27 28 29 27 22 26 29 23 18 24 20 20 17 21 19 21 23 28</span></span>
<span><span class="co"># [76] 21 30 23 31 17 19 17 31 17 29 17 26 17 23 26 27 18 21 24 19 22 20 22 31 18</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>