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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="">1.8.2.9115</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9118</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">
@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">10 February 2023</h4>
<h4 data-toc-skip class="date">11 February 2023</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>
@ -190,7 +190,7 @@ Berends</h4>
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 February 2023.</p>
generated on 11 February 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -246,21 +246,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-02-10</td>
<td align="center">2023-02-11</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">2023-02-10</td>
<td align="center">2023-02-11</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">2023-02-10</td>
<td align="center">2023-02-11</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -411,71 +411,71 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-12-30</td>
<td align="center">O7</td>
<td align="center">2012-01-10</td>
<td align="center">X7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia 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">F</td>
</tr>
<tr class="even">
<td align="center">2017-01-11</td>
<td align="center">D6</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2013-10-15</td>
<td align="center">Y7</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-09-08</td>
<td align="center">K1</td>
<td align="center">2014-07-13</td>
<td align="center">B3</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">R</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">M</td>
</tr>
<tr class="odd">
<td align="center">2010-07-19</td>
<td align="center">W2</td>
<td align="center">2017-10-17</td>
<td align="center">C2</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2010-11-25</td>
<td align="center">H4</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2016-09-29</td>
<td align="center">O10</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia 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">S</td>
<td align="center">I</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-11-01</td>
<td align="center">M1</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">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2013-03-20</td>
<td align="center">T1</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</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>
@ -510,18 +510,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,479</td>
<td align="right">52.40%</td>
<td align="right">10,479</td>
<td align="right">52.4%</td>
<td align="right">10,273</td>
<td align="right">51.37%</td>
<td align="right">10,273</td>
<td align="right">51.37%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,521</td>
<td align="right">47.61%</td>
<td align="right">9,727</td>
<td align="right">48.64%</td>
<td align="right">20,000</td>
<td align="right">100.0%</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>
@ -632,7 +632,7 @@ takes into account the antimicrobial susceptibility test results using
<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 12,291 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,300 'phenotype-based' first isolates (61.5% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.5% 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
@ -644,11 +644,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<div class="sourceCode" id="cb16"><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="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>So we end up with 12 291 isolates for analysis. Now our data looks
<p>So we end up with 12 300 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">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -661,7 +661,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -683,48 +683,48 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">4</td>
<td align="center">2016-09-29</td>
<td align="center">O10</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="left">2</td>
<td align="center">2017-01-11</td>
<td align="center">D6</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">I</td>
<td align="center">S</td>
<td align="center">I</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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">2015-11-01</td>
<td align="center">M1</td>
<td align="center">Hospital B</td>
<td align="left">10</td>
<td align="center">2011-03-19</td>
<td align="center">U9</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">S</td>
<td align="center">I</td>
<td align="center">M</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">2011-03-28</td>
<td align="center">W6</td>
<td align="left">11</td>
<td align="center">2010-12-27</td>
<td align="center">A2</td>
<td align="center">Hospital C</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">R</td>
<td align="center">F</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>
@ -732,14 +732,14 @@ like:</p>
</tr>
<tr class="even">
<td align="left">12</td>
<td align="center">2016-01-01</td>
<td align="center">J2</td>
<td align="center">2012-12-11</td>
<td align="center">I9</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">I</td>
<td align="center">R</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>
@ -747,35 +747,35 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">14</td>
<td align="center">2013-09-11</td>
<td align="center">C2</td>
<td align="left">13</td>
<td align="center">2015-07-02</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</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">S</td>
<td align="center">I</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">16</td>
<td align="center">2017-06-17</td>
<td align="center">W2</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">I</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">15</td>
<td align="center">2015-08-12</td>
<td align="center">V4</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">I</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>
</tbody>
@ -811,8 +811,8 @@ readable:</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://msberends.github.io/cleaner/reference/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: 12,291<br>
Available: 12,291 (100%, NA: 0 = 0%)<br>
Length: 12,300<br>
Available: 12,300 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -837,33 +837,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,932</td>
<td align="right">48.26%</td>
<td align="right">5,932</td>
<td align="right">48.26%</td>
<td align="right">5,826</td>
<td align="right">47.37%</td>
<td align="right">5,826</td>
<td align="right">47.37%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,234</td>
<td align="right">26.31%</td>
<td align="right">9,166</td>
<td align="right">74.57%</td>
<td align="right">3,233</td>
<td align="right">26.28%</td>
<td align="right">9,059</td>
<td align="right">73.65%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,831</td>
<td align="right">14.90%</td>
<td align="right">10,997</td>
<td align="right">89.47%</td>
<td align="right">1,875</td>
<td align="right">15.24%</td>
<td align="right">10,934</td>
<td align="right">88.89%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,294</td>
<td align="right">10.53%</td>
<td align="right">12,291</td>
<td align="right">1,366</td>
<td align="right">11.11%</td>
<td align="right">12,300</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -884,14 +884,14 @@ antibiotic class they are in:</p>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -912,86 +912,71 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2011-03-28</td>
<td align="center">W6</td>
<td align="center">Hospital C</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">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">2017-06-17</td>
<td align="center">W2</td>
<td align="center">2012-12-11</td>
<td align="center">I9</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">I</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">2015-08-02</td>
<td align="center">T7</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">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">2012-04-29</td>
<td align="center">Q6</td>
<td align="center">Hospital D</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">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">2014-12-09</td>
<td align="center">E7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">B_KLBSL_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">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</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="center">2010-08-29</td>
<td align="center">N8</td>
<td align="center">2015-07-02</td>
<td align="center">Y10</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">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="odd">
<td align="center">2012-09-28</td>
<td align="center">N1</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">I</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">2011-07-31</td>
<td align="center">K9</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">I</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-06-02</td>
<td align="center">V9</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">I</td>
<td align="center">R</td>
@ -1001,6 +986,21 @@ antibiotic class they are in:</p>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-02-06</td>
<td align="center">M7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1012,7 +1012,6 @@ different bug/drug combinations, you can use the
<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="op">)</span> <span class="co"># show first 6 rows</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="center">mo</th>
<th align="center">ab</th>
<th align="center">S</th>
@ -1022,58 +1021,52 @@ different bug/drug combinations, you can use the
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2766</td>
<td align="center">1182</td>
<td align="center">1984</td>
<td align="center">5932</td>
<td align="center">S</td>
<td align="center">1489</td>
<td align="center">1236</td>
<td align="center">3101</td>
<td align="center">5826</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1503</td>
<td align="center">1271</td>
<td align="center">3158</td>
<td align="center">5932</td>
<td align="center">S1</td>
<td align="center">2720</td>
<td align="center">1160</td>
<td align="center">1946</td>
<td align="center">5826</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2090</td>
<td align="center">1798</td>
<td align="center">2044</td>
<td align="center">5932</td>
<td align="center">S2</td>
<td align="center">1974</td>
<td align="center">1845</td>
<td align="center">2007</td>
<td align="center">5826</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2053</td>
<td align="center">1791</td>
<td align="center">2088</td>
<td align="center">5932</td>
<td align="center">S3</td>
<td align="center">2027</td>
<td align="center">1830</td>
<td align="center">1969</td>
<td align="center">5826</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">590</td>
<td align="center">264</td>
<td align="center">440</td>
<td align="center">1294</td>
<td align="center">S</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1366</td>
<td align="center">1366</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1294</td>
<td align="center">1294</td>
<td align="center">S1</td>
<td align="center">570</td>
<td align="center">310</td>
<td align="center">486</td>
<td align="center">1366</td>
</tr>
</tbody>
</table>
@ -1094,35 +1087,35 @@ different bug/drug combinations, you can use the
<tbody>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2053</td>
<td align="center">1791</td>
<td align="center">2088</td>
<td align="center">5932</td>
<td align="center">S</td>
<td align="center">2027</td>
<td align="center">1830</td>
<td align="center">1969</td>
<td align="center">5826</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">443</td>
<td align="center">418</td>
<td align="center">433</td>
<td align="center">1294</td>
<td align="center">S</td>
<td align="center">501</td>
<td align="center">402</td>
<td align="center">463</td>
<td align="center">1366</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1084</td>
<td align="center">1013</td>
<td align="center">1137</td>
<td align="center">3234</td>
<td align="center">S</td>
<td align="center">1155</td>
<td align="center">992</td>
<td align="center">1086</td>
<td align="center">3233</td>
</tr>
<tr class="even">
<td align="center">S. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">S</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1831</td>
<td align="center">1831</td>
<td align="center">1875</td>
<td align="center">1875</td>
</tr>
</tbody>
</table>
@ -1154,7 +1147,7 @@ I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equa
own:</p>
<div class="sourceCode" id="cb25"><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] 0.5826214</span></span></code></pre></div>
<span><span class="co"># [1] 0.59</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="cb26"><pre class="downlit sourceCode r">
@ -1169,19 +1162,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5758659</td>
<td align="center">0.5931973</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5828610</td>
<td align="center">0.5891020</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5882029</td>
<td align="center">0.5969416</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5881384</td>
<td align="center">0.5818110</td>
</tr>
</tbody>
</table>
@ -1206,23 +1199,23 @@ all isolates available for every group (i.e. values S, I or R):</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5758659</td>
<td align="center">3638</td>
<td align="center">0.5931973</td>
<td align="center">3675</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5828610</td>
<td align="center">4411</td>
<td align="center">0.5891020</td>
<td align="center">4276</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5882029</td>
<td align="center">1814</td>
<td align="center">0.5969416</td>
<td align="center">1831</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5881384</td>
<td align="center">2428</td>
<td align="center">0.5818110</td>
<td align="center">2518</td>
</tr>
</tbody>
</table>
@ -1247,27 +1240,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6655428</td>
<td align="center">0.6480108</td>
<td align="center">0.8833446</td>
<td align="center">0.6659801</td>
<td align="center">0.6620323</td>
<td align="center">0.8884312</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6599691</td>
<td align="center">0.6653787</td>
<td align="center">0.8802164</td>
<td align="center">0.6442167</td>
<td align="center">0.6610542</td>
<td align="center">0.8755490</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6719233</td>
<td align="center">0.6484230</td>
<td align="center">0.8862090</td>
<td align="center">0.6523353</td>
<td align="center">0.6640891</td>
<td align="center">0.8892669</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4729656</td>
<td align="center">0.4650667</td>
<td align="center">0.0000000</td>
<td align="center">0.4729656</td>
<td align="center">0.4650667</td>
</tr>
</tbody>
</table>
@ -1295,23 +1288,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">57.6%</td>
<td align="right">36.5%</td>
<td align="right">59.3%</td>
<td align="right">37.6%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.3%</td>
<td align="right">36.2%</td>
<td align="right">58.9%</td>
<td align="right">37.3%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">58.8%</td>
<td align="right">36.3%</td>
<td align="right">59.7%</td>
<td align="right">36.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">58.8%</td>
<td align="right">35.7%</td>
<td align="right">58.2%</td>
<td align="right">36.3%</td>
</tr>
</tbody>
</table>
@ -1427,18 +1420,16 @@ classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</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 'mic'</span></span>
<span><span class="co"># [1] 0.005 2 2 128 8 0.01 0.005 0.25 2 </span></span>
<span><span class="co"># [10] 8 256 0.125 256 0.002 0.0625 0.025 8 16 </span></span>
<span><span class="co"># [19] 0.002 0.5 0.25 256 16 2 0.002 0.01 0.01 </span></span>
<span><span class="co"># [28] 1 256 2 64 0.002 128 8 2 128 </span></span>
<span><span class="co"># [37] 0.002 4 0.025 32 8 0.125 32 0.5 8 </span></span>
<span><span class="co"># [46] 0.125 0.5 128 0.005 0.005 0.5 2 &lt;=0.001 0.025 </span></span>
<span><span class="co"># [55] 0.002 0.0625 1 32 0.125 64 0.002 0.025 0.01 </span></span>
<span><span class="co"># [64] 32 8 0.01 4 0.125 0.125 64 0.5 0.0625 </span></span>
<span><span class="co"># [73] 1 256 1 32 16 0.0625 1 16 64 </span></span>
<span><span class="co"># [82] 0.125 0.002 16 0.0625 128 32 64 0.0625 64 </span></span>
<span><span class="co"># [91] 2 2 0.005 256 0.25 0.0625 0.01 4 &lt;=0.001</span></span>
<span><span class="co"># [100] 1</span></span></code></pre></div>
<span><span class="co"># [1] 4 0.5 0.0625 0.25 64 0.025 0.002 128 0.25 16 </span></span>
<span><span class="co"># [11] 0.0625 0.002 32 32 64 &gt;=256 0.005 0.25 32 2 </span></span>
<span><span class="co"># [21] 4 0.002 0.01 128 &gt;=256 0.0625 2 0.002 4 0.001 </span></span>
<span><span class="co"># [31] 4 8 128 0.001 0.0625 32 0.01 0.002 64 16 </span></span>
<span><span class="co"># [41] 8 16 0.25 0.25 0.001 64 128 0.025 0.01 2 </span></span>
<span><span class="co"># [51] 0.01 1 0.0625 8 4 8 0.25 128 0.002 0.001 </span></span>
<span><span class="co"># [61] 1 2 0.25 0.5 128 0.125 0.125 1 0.5 0.001 </span></span>
<span><span class="co"># [71] 0.002 0.002 16 64 0.0625 2 0.0625 0.025 0.5 0.002 </span></span>
<span><span class="co"># [81] 4 &gt;=256 0.01 32 0.025 0.002 0.125 128 8 4 </span></span>
<span><span class="co"># [91] 0.005 4 1 4 128 &gt;=256 0.01 8 128 32</span></span></code></pre></div>
<div class="sourceCode" id="cb36"><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>
@ -1472,10 +1463,10 @@ plotting:</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 'disk'</span></span>
<span><span class="co"># [1] 17 30 22 31 20 25 23 17 24 17 30 26 21 20 28 19 28 29 24 17 29 30 31 27 25</span></span>
<span><span class="co"># [26] 29 21 21 18 25 19 25 22 26 28 18 25 19 24 30 23 22 24 22 22 22 18 24 19 19</span></span>
<span><span class="co"># [51] 17 17 28 29 28 24 20 23 25 29 31 21 31 18 18 18 28 22 18 25 29 24 27 29 23</span></span>
<span><span class="co"># [76] 21 31 17 29 30 24 29 21 29 24 17 28 18 19 31 27 25 26 18 27 27 29 28 25 26</span></span></code></pre></div>
<span><span class="co"># [1] 31 21 27 24 29 23 31 18 22 25 23 27 28 21 26 20 18 30 29 28 25 25 22 17 27</span></span>
<span><span class="co"># [26] 22 26 30 24 25 27 18 28 20 25 30 28 22 22 31 30 27 25 22 26 21 30 31 20 27</span></span>
<span><span class="co"># [51] 31 21 22 19 21 19 29 29 19 31 30 18 18 19 27 18 18 27 29 28 21 23 18 29 20</span></span>
<span><span class="co"># [76] 17 20 18 22 25 21 20 28 26 27 22 19 30 19 18 29 28 29 23 19 21 18 25 19 17</span></span></code></pre></div>
<div class="sourceCode" id="cb42"><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>