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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="">1.8.2.9091</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9092</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">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">12 January 2023</h4>
<h4 data-toc-skip class="date">14 January 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>
@ -180,7 +180,7 @@ 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 12 January 2023.</p>
generated on 14 January 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-01-12</td>
<td align="center">2023-01-14</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">2023-01-12</td>
<td align="center">2023-01-14</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">2023-01-12</td>
<td align="center">2023-01-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -375,17 +375,17 @@ the <code><a href="https://rdrr.io/r/utils/head.html" class="external-link">head
data set:</p>
<div class="sourceCode" id="cb8"><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</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="8%">
<col width="14%">
<col width="14%">
<col width="14%">
<col width="21%">
<col width="6%">
<col width="6%">
<col width="6%">
<col width="6%">
<col width="9%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -400,32 +400,10 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-07-09</td>
<td align="center">W4</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="even">
<td align="center">2014-09-13</td>
<td align="center">W7</td>
<td align="center">2013-06-11</td>
<td align="center">R1</td>
<td align="center">Hospital A</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">2016-08-25</td>
<td align="center">N9</td>
<td align="center">Hospital B</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
@ -433,37 +411,59 @@ data set:</p>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-09-17</td>
<td align="center">K9</td>
<td align="center">2016-02-26</td>
<td align="center">G2</td>
<td align="center">Hospital C</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">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">2016-11-05</td>
<td align="center">M9</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">2014-06-18</td>
<td align="center">D2</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-10-09</td>
<td align="center">R5</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">2014-05-13</td>
<td align="center">L4</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia 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">F</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2010-05-08</td>
<td align="center">G4</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">2011-04-08</td>
<td align="center">G7</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>
</tbody>
</table>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,403</td>
<td align="right">52.02%</td>
<td align="right">10,403</td>
<td align="right">52.02%</td>
<td align="right">10,445</td>
<td align="right">52.23%</td>
<td align="right">10,445</td>
<td align="right">52.23%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,597</td>
<td align="right">47.99%</td>
<td align="right">9,555</td>
<td align="right">47.78%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -621,9 +621,9 @@ 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 10,702 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,661 'phenotype-based' first isolates (53.3% 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
<p>So only 53.3% 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">
@ -634,11 +634,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<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 10,702 isolates for analysis. Now our data looks
<p>So we end up with 10,661 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">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -651,7 +651,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -674,93 +674,93 @@ like:</p>
<tbody>
<tr class="odd">
<td align="left">4</td>
<td align="center">2011-09-17</td>
<td align="center">K9</td>
<td align="center">Hospital C</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">2014-05-13</td>
<td align="center">L4</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</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">5</td>
<td align="center">2016-11-05</td>
<td align="center">M9</td>
<td align="center">2010-05-08</td>
<td align="center">G4</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2011-04-08</td>
<td align="center">G7</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">7</td>
<td align="center">2015-06-18</td>
<td align="center">F7</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">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">9</td>
<td align="center">2013-04-22</td>
<td align="center">O4</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">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">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">2017-10-09</td>
<td align="center">R5</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">7</td>
<td align="center">2013-12-15</td>
<td align="center">T6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2017-04-06</td>
<td align="center">Q3</td>
<td align="left">13</td>
<td align="center">2014-07-04</td>
<td align="center">H10</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">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">9</td>
<td align="center">2014-02-24</td>
<td align="center">M10</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
@ -801,8 +801,8 @@ 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: 10,702<br>
Available: 10,702 (100%, NA: 0 = 0%)<br>
Length: 10,661<br>
Available: 10,661 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,654</td>
<td align="right">43.49%</td>
<td align="right">4,654</td>
<td align="right">43.49%</td>
<td align="right">4,638</td>
<td align="right">43.50%</td>
<td align="right">4,638</td>
<td align="right">43.50%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,733</td>
<td align="right">25.54%</td>
<td align="right">7,387</td>
<td align="right">69.02%</td>
<td align="right">2,699</td>
<td align="right">25.32%</td>
<td align="right">7,337</td>
<td align="right">68.82%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,084</td>
<td align="right">19.47%</td>
<td align="right">9,471</td>
<td align="right">88.50%</td>
<td align="right">2,127</td>
<td align="right">19.95%</td>
<td align="right">9,464</td>
<td align="right">88.77%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,231</td>
<td align="right">11.50%</td>
<td align="right">10,702</td>
<td align="right">1,197</td>
<td align="right">11.23%</td>
<td align="right">10,661</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -902,9 +902,24 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2016-11-05</td>
<td align="center">M9</td>
<td align="center">Hospital B</td>
<td align="center">2013-04-22</td>
<td align="center">O4</td>
<td align="center">Hospital A</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">2017-05-20</td>
<td align="center">J4</td>
<td align="center">Hospital C</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
@ -916,69 +931,39 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-01-06</td>
<td align="center">Z7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">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">2013-01-10</td>
<td align="center">M6</td>
<td align="center">Hospital D</td>
<td align="center">2013-04-07</td>
<td align="center">R8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</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">2013-01-04</td>
<td align="center">O3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-03-19</td>
<td align="center">X10</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>
<tr class="odd">
<td align="center">2012-12-30</td>
<td align="center">D6</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">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">2015-06-21</td>
<td align="center">L7</td>
<td align="center">2010-04-24</td>
<td align="center">G2</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
@ -991,6 +976,21 @@ antibiotic class they are in:</p>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-10-15</td>
<td align="center">U1</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
@ -1013,50 +1013,50 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2199</td>
<td align="center">122</td>
<td align="center">2333</td>
<td align="center">4654</td>
<td align="center">2172</td>
<td align="center">141</td>
<td align="center">2325</td>
<td align="center">4638</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3424</td>
<td align="center">171</td>
<td align="center">1059</td>
<td align="center">4654</td>
<td align="center">3409</td>
<td align="center">162</td>
<td align="center">1067</td>
<td align="center">4638</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3437</td>
<td align="center">3344</td>
<td align="center">0</td>
<td align="center">1217</td>
<td align="center">4654</td>
<td align="center">1294</td>
<td align="center">4638</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4071</td>
<td align="center">4074</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4654</td>
<td align="center">564</td>
<td align="center">4638</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">1231</td>
<td align="center">1231</td>
<td align="center">1197</td>
<td align="center">1197</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">954</td>
<td align="center">44</td>
<td align="center">233</td>
<td align="center">1231</td>
<td align="center">926</td>
<td align="center">62</td>
<td align="center">209</td>
<td align="center">1197</td>
</tr>
</tbody>
</table>
@ -1078,34 +1078,34 @@ different bug/drug combinations, you can use the
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4071</td>
<td align="center">4074</td>
<td align="center">0</td>
<td align="center">583</td>
<td align="center">4654</td>
<td align="center">564</td>
<td align="center">4638</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1102</td>
<td align="center">1080</td>
<td align="center">0</td>
<td align="center">129</td>
<td align="center">1231</td>
<td align="center">117</td>
<td align="center">1197</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2410</td>
<td align="center">2419</td>
<td align="center">0</td>
<td align="center">323</td>
<td align="center">2733</td>
<td align="center">280</td>
<td align="center">2699</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">2084</td>
<td align="center">2084</td>
<td align="center">2127</td>
<td align="center">2127</td>
</tr>
</tbody>
</table>
@ -1137,7 +1137,7 @@ 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] 0.5480284</span></span></code></pre></div>
<span><span class="co"># [1] 0.5433824</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">
@ -1152,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5506410</td>
<td align="center">0.5447360</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5437995</td>
<td align="center">0.5379915</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5497288</td>
<td align="center">0.5309842</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5503985</td>
<td align="center">0.5608238</td>
</tr>
</tbody>
</table>
@ -1189,23 +1189,23 @@ 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">0.5506410</td>
<td align="center">3120</td>
<td align="center">0.5447360</td>
<td align="center">3163</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5437995</td>
<td align="center">3790</td>
<td align="center">0.5379915</td>
<td align="center">3764</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5497288</td>
<td align="center">1659</td>
<td align="center">0.5309842</td>
<td align="center">1646</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5503985</td>
<td align="center">2133</td>
<td align="center">0.5608238</td>
<td align="center">2088</td>
</tr>
</tbody>
</table>
@ -1230,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7724538</td>
<td align="center">0.8747314</td>
<td align="center">0.9774388</td>
<td align="center">0.7699439</td>
<td align="center">0.8783959</td>
<td align="center">0.9762829</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8107230</td>
<td align="center">0.8952071</td>
<td align="center">0.9764419</td>
<td align="center">0.8253968</td>
<td align="center">0.9022556</td>
<td align="center">0.9841270</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7896085</td>
<td align="center">0.8818149</td>
<td align="center">0.9806074</td>
<td align="center">0.7899222</td>
<td align="center">0.8962579</td>
<td align="center">0.9818451</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5465451</td>
<td align="center">0.5514810</td>
<td align="center">0.0000000</td>
<td align="center">0.5465451</td>
<td align="center">0.5514810</td>
</tr>
</tbody>
</table>
@ -1278,23 +1278,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">55.1%</td>
<td align="right">25.8%</td>
<td align="right">54.5%</td>
<td align="right">26.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">54.4%</td>
<td align="right">26.2%</td>
<td align="right">53.8%</td>
<td align="right">25.7%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">55.0%</td>
<td align="right">26.4%</td>
<td align="right">53.1%</td>
<td align="right">26.5%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">55.0%</td>
<td align="right">27.0%</td>
<td align="right">56.1%</td>
<td align="right">26.0%</td>
</tr>
</tbody>
</table>
@ -1410,18 +1410,18 @@ 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] 0.125 0.01 32 0.125 &lt;=0.001 2 32 0.125 1 </span></span>
<span><span class="co"># [10] &gt;=256 32 0.0625 0.002 0.01 &lt;=0.001 &lt;=0.001 32 128 </span></span>
<span><span class="co"># [19] 0.125 0.0625 0.025 0.125 0.005 1 32 32 32 </span></span>
<span><span class="co"># [28] &lt;=0.001 0.01 0.125 4 0.25 0.025 4 &lt;=0.001 0.125 </span></span>
<span><span class="co"># [37] 128 0.125 32 1 0.002 32 &lt;=0.001 32 0.125 </span></span>
<span><span class="co"># [46] 64 0.25 1 16 16 &gt;=256 &gt;=256 128 1 </span></span>
<span><span class="co"># [55] 64 0.005 0.01 16 128 64 8 0.0625 0.025 </span></span>
<span><span class="co"># [64] 0.0625 8 0.25 0.25 0.01 0.0625 0.01 &gt;=256 0.01 </span></span>
<span><span class="co"># [73] 0.125 128 0.125 128 128 4 0.0625 0.125 2 </span></span>
<span><span class="co"># [82] 0.5 2 64 4 0.0625 0.5 0.5 64 8 </span></span>
<span><span class="co"># [91] 0.125 1 8 0.0625 0.0625 0.01 0.25 32 8 </span></span>
<span><span class="co"># [100] 0.5</span></span></code></pre></div>
<span><span class="co"># [1] 8 1 8 128 0.125 0.025 0.125 0.25 0.01 </span></span>
<span><span class="co"># [10] 0.002 0.025 0.125 &lt;=0.001 0.125 0.01 32 0.025 64 </span></span>
<span><span class="co"># [19] 0.025 16 0.125 0.5 8 0.005 256 256 256 </span></span>
<span><span class="co"># [28] 8 0.5 0.005 32 256 0.01 &lt;=0.001 0.01 0.002 </span></span>
<span><span class="co"># [37] 64 64 0.0625 2 256 2 0.005 0.005 8 </span></span>
<span><span class="co"># [46] &lt;=0.001 4 64 0.025 128 256 0.0625 &lt;=0.001 8 </span></span>
<span><span class="co"># [55] 0.5 0.002 1 &lt;=0.001 4 0.5 32 2 256 </span></span>
<span><span class="co"># [64] 0.01 0.002 0.25 4 8 128 128 0.0625 16 </span></span>
<span><span class="co"># [73] 2 0.01 0.002 4 0.5 0.5 256 0.005 64 </span></span>
<span><span class="co"># [82] 16 0.125 128 0.005 4 1 1 256 0.01 </span></span>
<span><span class="co"># [91] 0.002 4 1 0.0625 0.125 32 256 2 0.002 </span></span>
<span><span class="co"># [100] 2</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>
@ -1455,10 +1455,10 @@ 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] 29 27 17 22 31 31 31 23 25 23 29 20 19 29 17 29 26 20 28 19 27 25 28 24 24</span></span>
<span><span class="co"># [26] 27 21 29 24 20 18 30 28 17 30 29 25 18 22 25 20 26 29 22 27 17 21 17 25 31</span></span>
<span><span class="co"># [51] 30 26 25 23 26 28 30 29 28 21 17 20 25 23 20 30 20 25 30 30 24 20 30 23 18</span></span>
<span><span class="co"># [76] 23 27 26 22 28 28 28 24 24 23 18 19 31 23 31 17 27 18 21 31 31 23 26 20 22</span></span></code></pre></div>
<span><span class="co"># [1] 30 31 18 26 29 17 30 31 18 18 19 25 28 22 22 24 26 31 30 29 27 25 26 30 19</span></span>
<span><span class="co"># [26] 23 17 17 25 21 21 28 27 29 17 28 30 29 28 29 28 31 29 28 28 29 19 30 29 27</span></span>
<span><span class="co"># [51] 24 29 17 27 28 18 21 17 26 17 23 31 27 17 18 29 26 22 20 20 21 21 28 19 17</span></span>
<span><span class="co"># [76] 31 27 24 28 21 24 23 30 25 22 19 28 25 27 25 28 25 18 26 30 19 27 28 20 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>