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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="">1.8.2.9123</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9124</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">13 February 2023</h4>
<h4 data-toc-skip class="date">14 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 13 February 2023.</p>
generated on 14 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">2023-02-13</td>
<td align="center">2023-02-14</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">2023-02-13</td>
<td align="center">2023-02-14</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">2023-02-13</td>
<td align="center">2023-02-14</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -391,12 +391,12 @@ data set:</p>
<col width="13%">
<col width="13%">
<col width="13%">
<col width="26%">
<col width="28%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="5%">
<col width="9%">
<col width="8%">
</colgroup>
<thead><tr class="header">
<th align="center">date</th>
@ -411,69 +411,69 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-09-28</td>
<td align="center">G4</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-08-23</td>
<td align="center">P4</td>
<td align="center">Hospital D</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">I</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-01-14</td>
<td align="center">C3</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">I</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-06-19</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-11-27</td>
<td align="center">N6</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia 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>
</tr>
<tr class="even">
<td align="center">2010-02-05</td>
<td align="center">U8</td>
<td align="center">2013-06-13</td>
<td align="center">O6</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</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>
</tr>
<tr class="even">
<td align="center">2013-01-19</td>
<td align="center">H7</td>
<td align="center">Hospital A</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-01-05</td>
<td align="center">O9</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">F</td>
</tr>
<tr class="even">
<td align="center">2010-08-24</td>
<td align="center">G4</td>
<td align="center">Hospital B</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2017-02-26</td>
<td align="center">D7</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2016-09-29</td>
<td align="center">R6</td>
<td align="center">Hospital D</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>
</tbody>
@ -510,16 +510,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,387</td>
<td align="right">51.94%</td>
<td align="right">10,387</td>
<td align="right">51.94%</td>
<td align="right">10,318</td>
<td align="right">51.59%</td>
<td align="right">10,318</td>
<td align="right">51.59%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,613</td>
<td align="right">48.07%</td>
<td align="right">9,682</td>
<td align="right">48.41%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -632,9 +632,9 @@ 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 12,362 'phenotype-based' first isolates (61.8% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,323 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.8% is suitable for resistance analysis! We can now filter
<p>So only 61.6% 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">
@ -644,27 +644,29 @@ 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 12 362 isolates for analysis. Now our data looks
<p>So we end up with 12 323 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">
<colgroup>
<col width="2%">
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="4%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="12%">
<col width="12%">
<col width="7%">
<col width="11%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
<thead><tr class="header">
<th align="left"></th>
<th align="center">date</th>
<th align="center">patient_id</th>
<th align="center">hospital</th>
@ -681,29 +683,31 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-09-28</td>
<td align="center">G4</td>
<td align="left">2</td>
<td align="center">2013-01-19</td>
<td align="center">H7</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">S</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-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2014-08-23</td>
<td align="center">P4</td>
<td align="center">Hospital D</td>
<td align="left">3</td>
<td align="center">2012-01-05</td>
<td align="center">O9</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -711,14 +715,15 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-01-14</td>
<td align="center">C3</td>
<td align="center">Hospital B</td>
<td align="left">5</td>
<td align="center">2017-02-26</td>
<td align="center">D7</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">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -726,14 +731,15 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-06-19</td>
<td align="center">V6</td>
<td align="center">Hospital B</td>
<td align="left">6</td>
<td align="center">2016-09-29</td>
<td align="center">R6</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
@ -741,27 +747,29 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-11-27</td>
<td align="center">N6</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">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">2010-02-05</td>
<td align="center">U8</td>
<td align="left">7</td>
<td align="center">2013-02-10</td>
<td align="center">R9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2011-04-23</td>
<td align="center">Q7</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">I</td>
<td align="center">F</td>
@ -803,8 +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: 12,362<br>
Available: 12,362 (100%, NA: 0 = 0%)<br>
Length: 12,323<br>
Available: 12,323 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -829,33 +837,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,901</td>
<td align="right">47.73%</td>
<td align="right">5,901</td>
<td align="right">47.73%</td>
<td align="right">5,914</td>
<td align="right">47.99%</td>
<td align="right">5,914</td>
<td align="right">47.99%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,281</td>
<td align="right">26.54%</td>
<td align="right">9,182</td>
<td align="right">74.28%</td>
<td align="right">3,290</td>
<td align="right">26.70%</td>
<td align="right">9,204</td>
<td align="right">74.69%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,852</td>
<td align="right">14.98%</td>
<td align="right">11,034</td>
<td align="right">89.26%</td>
<td align="right">1,841</td>
<td align="right">14.94%</td>
<td align="right">11,045</td>
<td align="right">89.63%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,328</td>
<td align="right">10.74%</td>
<td align="right">12,362</td>
<td align="right">1,278</td>
<td align="right">10.37%</td>
<td align="right">12,323</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -904,24 +912,24 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-06-19</td>
<td align="center">V6</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">2013-01-19</td>
<td align="center">H7</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</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">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">2017-11-27</td>
<td align="center">N6</td>
<td align="center">Hospital D</td>
<td align="center">2013-02-10</td>
<td align="center">R9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
@ -934,28 +942,13 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2010-05-19</td>
<td align="center">L4</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">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">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-05-08</td>
<td align="center">P1</td>
<td align="center">Hospital B</td>
<td align="center">2010-06-09</td>
<td align="center">N8</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -963,31 +956,46 @@ antibiotic class they are in:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2017-02-17</td>
<td align="center">D3</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<tr class="even">
<td align="center">2016-05-28</td>
<td align="center">I1</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2016-03-09</td>
<td align="center">F9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">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">2012-12-04</td>
<td align="center">N7</td>
<td align="center">2010-01-17</td>
<td align="center">E9</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
@ -1017,46 +1025,46 @@ different bug/drug combinations, you can use the
<td align="left">2</td>
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2771</td>
<td align="center">1155</td>
<td align="center">1975</td>
<td align="center">5901</td>
<td align="center">2766</td>
<td align="center">1160</td>
<td align="center">1988</td>
<td align="center">5914</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">1531</td>
<td align="center">1205</td>
<td align="center">3165</td>
<td align="center">5901</td>
<td align="center">1479</td>
<td align="center">1276</td>
<td align="center">3159</td>
<td align="center">5914</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2061</td>
<td align="center">1749</td>
<td align="center">2091</td>
<td align="center">5901</td>
<td align="center">2052</td>
<td align="center">1848</td>
<td align="center">2014</td>
<td align="center">5914</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2045</td>
<td align="center">1817</td>
<td align="center">2039</td>
<td align="center">5901</td>
<td align="center">2093</td>
<td align="center">1804</td>
<td align="center">2017</td>
<td align="center">5914</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">583</td>
<td align="center">278</td>
<td align="center">467</td>
<td align="center">1328</td>
<td align="center">561</td>
<td align="center">265</td>
<td align="center">452</td>
<td align="center">1278</td>
</tr>
<tr class="even">
<td align="left">5</td>
@ -1064,8 +1072,8 @@ different bug/drug combinations, you can use the
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">1328</td>
<td align="center">1328</td>
<td align="center">1278</td>
<td align="center">1278</td>
</tr>
</tbody>
</table>
@ -1087,34 +1095,34 @@ 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">2045</td>
<td align="center">1817</td>
<td align="center">2039</td>
<td align="center">5901</td>
<td align="center">2093</td>
<td align="center">1804</td>
<td align="center">2017</td>
<td align="center">5914</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">458</td>
<td align="center">417</td>
<td align="center">453</td>
<td align="center">1328</td>
<td align="center">425</td>
<td align="center">436</td>
<td align="center">1278</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1126</td>
<td align="center">1065</td>
<td align="center">1090</td>
<td align="center">3281</td>
<td align="center">1174</td>
<td align="center">980</td>
<td align="center">1136</td>
<td align="center">3290</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">1852</td>
<td align="center">1852</td>
<td align="center">1841</td>
<td align="center">1841</td>
</tr>
</tbody>
</table>
@ -1146,7 +1154,7 @@ 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] 0.5856657</span></span></code></pre></div>
<span><span class="co"># [1] 0.5826503</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">
@ -1161,19 +1169,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5945799</td>
<td align="center">0.5831750</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5890156</td>
<td align="center">0.5843303</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5738308</td>
<td align="center">0.5608604</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5756472</td>
<td align="center">0.5957878</td>
</tr>
</tbody>
</table>
@ -1198,23 +1206,23 @@ 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">0.5945799</td>
<td align="center">3690</td>
<td align="center">0.5831750</td>
<td align="center">3685</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5890156</td>
<td align="center">4297</td>
<td align="center">0.5843303</td>
<td align="center">4263</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5738308</td>
<td align="center">1903</td>
<td align="center">0.5608604</td>
<td align="center">1906</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5756472</td>
<td align="center">2472</td>
<td align="center">0.5957878</td>
<td align="center">2469</td>
</tr>
</tbody>
</table>
@ -1239,27 +1247,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6653110</td>
<td align="center">0.6544653</td>
<td align="center">0.8818844</td>
<td align="center">0.6638485</td>
<td align="center">0.6589449</td>
<td align="center">0.8887386</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6483434</td>
<td align="center">0.6588855</td>
<td align="center">0.8734940</td>
<td align="center">0.6463224</td>
<td align="center">0.6588419</td>
<td align="center">0.8740219</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6638220</td>
<td align="center">0.6677842</td>
<td align="center">0.8857056</td>
<td align="center">0.6620061</td>
<td align="center">0.6547112</td>
<td align="center">0.8854103</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4649028</td>
<td align="center">0.4627920</td>
<td align="center">0.0000000</td>
<td align="center">0.4649028</td>
<td align="center">0.4627920</td>
</tr>
</tbody>
</table>
@ -1287,22 +1295,22 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">59.5%</td>
<td align="right">36.3%</td>
<td align="right">58.3%</td>
<td align="right">37.1%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.9%</td>
<td align="right">36.9%</td>
<td align="right">58.4%</td>
<td align="right">36.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">57.4%</td>
<td align="right">36.6%</td>
<td align="right">56.1%</td>
<td align="right">36.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">57.6%</td>
<td align="right">59.6%</td>
<td align="right">37.0%</td>
</tr>
</tbody>
@ -1419,18 +1427,18 @@ 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] 1 0.0625 2 8 0.025 64 1 &gt;=256 0.125 </span></span>
<span><span class="co"># [10] 1 1 &lt;=0.001 2 32 0.01 0.005 &gt;=256 0.25 </span></span>
<span><span class="co"># [19] &lt;=0.001 0.25 0.0625 8 16 0.125 128 128 32 </span></span>
<span><span class="co"># [28] 128 2 &lt;=0.001 &lt;=0.001 0.0625 &gt;=256 4 4 1 </span></span>
<span><span class="co"># [37] 8 0.025 &lt;=0.001 64 4 64 32 0.025 &lt;=0.001</span></span>
<span><span class="co"># [46] 128 0.5 16 64 32 64 1 0.002 &gt;=256 </span></span>
<span><span class="co"># [55] 32 4 0.0625 2 &lt;=0.001 0.005 0.125 0.0625 &lt;=0.001</span></span>
<span><span class="co"># [64] &lt;=0.001 0.025 32 4 64 128 0.25 &gt;=256 0.0625 </span></span>
<span><span class="co"># [73] 0.0625 32 8 32 8 &lt;=0.001 0.01 32 8 </span></span>
<span><span class="co"># [82] 64 128 32 8 0.005 0.0625 0.005 4 16 </span></span>
<span><span class="co"># [91] 1 8 &lt;=0.001 2 0.125 0.002 0.025 1 0.002 </span></span>
<span><span class="co"># [100] 0.125</span></span></code></pre></div>
<span><span class="co"># [1] 0.125 0.01 4 0.005 0.01 0.125 128 1 0.5 </span></span>
<span><span class="co"># [10] 0.01 0.01 0.002 &lt;=0.001 16 2 1 64 0.005 </span></span>
<span><span class="co"># [19] 16 16 2 0.0625 0.5 0.01 &gt;=256 &lt;=0.001 64 </span></span>
<span><span class="co"># [28] 8 0.125 0.025 16 0.002 &lt;=0.001 0.0625 0.005 0.25 </span></span>
<span><span class="co"># [37] 0.01 32 1 8 0.025 2 0.01 0.002 0.125 </span></span>
<span><span class="co"># [46] 64 32 32 &gt;=256 0.025 8 0.025 0.002 0.125 </span></span>
<span><span class="co"># [55] 16 0.0625 0.125 1 0.01 0.25 2 0.01 16 </span></span>
<span><span class="co"># [64] 64 0.005 &gt;=256 128 &lt;=0.001 2 0.0625 0.5 0.005 </span></span>
<span><span class="co"># [73] 0.01 0.5 32 16 1 8 0.01 64 0.0625 </span></span>
<span><span class="co"># [82] &lt;=0.001 0.0625 2 2 4 32 0.01 128 &lt;=0.001</span></span>
<span><span class="co"># [91] 0.002 64 0.0625 0.002 4 8 128 0.002 &lt;=0.001</span></span>
<span><span class="co"># [100] 0.01</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>
@ -1464,10 +1472,10 @@ 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] 20 20 24 24 20 31 20 26 27 29 20 19 17 20 19 23 22 21 20 24 31 21 22 30 18</span></span>
<span><span class="co"># [26] 22 22 22 25 19 24 26 17 26 24 27 31 20 29 19 18 22 19 31 28 26 31 27 25 28</span></span>
<span><span class="co"># [51] 17 18 19 25 27 27 17 17 30 24 26 23 19 26 24 22 27 24 29 24 27 23 27 17 21</span></span>
<span><span class="co"># [76] 21 25 30 25 19 22 25 18 27 31 27 26 28 21 31 19 18 28 18 23 30 28 24 31 27</span></span></code></pre></div>
<span><span class="co"># [1] 27 22 26 27 24 20 25 22 22 27 24 22 18 28 20 22 18 19 26 31 17 23 29 18 25</span></span>
<span><span class="co"># [26] 21 22 26 21 31 17 30 22 18 29 23 18 30 25 27 20 19 19 31 20 25 28 30 19 21</span></span>
<span><span class="co"># [51] 21 20 21 29 20 23 18 30 20 27 21 27 28 25 30 18 18 21 25 23 21 31 19 22 19</span></span>
<span><span class="co"># [76] 25 25 31 26 20 24 24 27 24 27 30 22 30 23 27 25 25 17 19 23 30 22 27 18 27</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>