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@ -15,7 +15,7 @@
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
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<!-- bootstrap-toc --><script src="https://cdn.jsdelivr.net/gh/afeld/bootstrap-toc@v1.0.1/dist/bootstrap-toc.min.js" integrity="sha256-4veVQbu7//Lk5TSmc7YV48MxtMy98e26cf5MrgZYnwo=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- search --><script src="https://cdnjs.cloudflare.com/ajax/libs/fuse.js/6.4.6/fuse.js" integrity="sha512-zv6Ywkjyktsohkbp9bb45V6tEMoWhzFzXis+LrMehmJZZSys19Yxf1dopHx7WzIKxr5tK2dVcYmaCk2uqdjF4A==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/autocomplete.js/0.38.0/autocomplete.jquery.min.js" integrity="sha512-GU9ayf+66Xx2TmpxqJpliWbT5PiGYxpaG8rfnBEk1LL8l1KGkRShhngwdXK1UgqhAzWpZHSiYPc09/NwDQIGyg==" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/mark.min.js" integrity="sha512-5CYOlHXGh6QpOFA/TeTylKLWfB3ftPsde7AnmhuitiTX4K5SqCLBeKro6sPS8ilsz1Q4NRx3v8Ko2IBiszzdww==" crossorigin="anonymous"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet">
@ -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="">1.8.2.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9100</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">
@ -173,7 +173,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">23 January 2023</h4>
<h4 data-toc-skip class="date">24 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>
@ -185,7 +185,7 @@ 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 23 January 2023.</p>
generated on 24 January 2023.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -241,21 +241,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2023-01-23</td>
<td align="center">2023-01-24</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">2023-01-23</td>
<td align="center">2023-01-24</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">2023-01-23</td>
<td align="center">2023-01-24</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -406,70 +406,70 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2010-08-18</td>
<td align="center">D8</td>
<td align="center">2016-07-10</td>
<td align="center">S7</td>
<td align="center">Hospital D</td>
<td align="center">Staphylococcus aureus</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>
<tr class="even">
<td align="center">2016-11-08</td>
<td align="center">W2</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">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-03-28</td>
<td align="center">H7</td>
<td align="center">Hospital D</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">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2016-12-20</td>
<td align="center">M9</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2012-11-13</td>
<td align="center">Y5</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">S</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2013-06-06</td>
<td align="center">Q7</td>
<td align="center">2011-05-09</td>
<td align="center">W10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-02-21</td>
<td align="center">R6</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</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">R</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2017-05-04</td>
<td align="center">U8</td>
<tr class="odd">
<td align="center">2014-12-12</td>
<td align="center">H2</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2017-03-14</td>
<td align="center">I10</td>
<td align="center">Hospital C</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">S</td>
<td align="center">M</td>
</tr>
</tbody>
</table>
@ -505,16 +505,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
<td align="right">10,375</td>
<td align="right">51.88%</td>
<td align="right">10,398</td>
<td align="right">51.99%</td>
<td align="right">10,398</td>
<td align="right">51.99%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,625</td>
<td align="right">48.13%</td>
<td align="right">9,602</td>
<td align="right">48.01%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -627,9 +627,9 @@ 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 12,316 'phenotype-based' first isolates (61.6% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,181 'phenotype-based' first isolates (60.9% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 61.6% is suitable for resistance analysis! We can now filter
<p>So only 60.9% 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">
@ -640,11 +640,11 @@ 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 12,316 isolates for analysis. Now our data looks
<p>So we end up with 12,181 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%">
@ -658,7 +658,7 @@ like:</p>
<col width="6%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="7%">
<col width="5%">
</colgroup>
<thead><tr class="header">
@ -679,101 +679,101 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">2011-03-28</td>
<td align="center">H7</td>
<td align="left">1</td>
<td align="center">2016-07-10</td>
<td align="center">S7</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">6</td>
<td align="center">2017-05-04</td>
<td align="center">U8</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">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="left">7</td>
<td align="center">2015-09-03</td>
<td align="center">S1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_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>
<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">2010-01-29</td>
<td align="center">D7</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">M</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="odd">
<td align="left">9</td>
<td align="center">2016-12-13</td>
<td align="center">D1</td>
<tr class="even">
<td align="left">4</td>
<td align="center">2014-02-21</td>
<td align="center">R6</td>
<td align="center">Hospital C</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">I</td>
<td align="center">M</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">11</td>
<td align="center">2017-08-05</td>
<td align="center">Z10</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">S</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">10</td>
<td align="center">2014-01-28</td>
<td align="center">E1</td>
<td align="left">15</td>
<td align="center">2017-10-24</td>
<td align="center">W2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">R</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="left">16</td>
<td align="center">2017-01-01</td>
<td align="center">Y9</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</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="even">
<td align="left">17</td>
<td align="center">2011-09-19</td>
<td align="center">K10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
</tbody>
</table>
<p>Time for the analysis!</p>
@ -807,8 +807,8 @@ 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: 12,316<br>
Available: 12,316 (100%, NA: 0 = 0%)<br>
Length: 12,181<br>
Available: 12,181 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -833,33 +833,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">5,959</td>
<td align="right">48.38%</td>
<td align="right">5,959</td>
<td align="right">48.38%</td>
<td align="right">5,814</td>
<td align="right">47.73%</td>
<td align="right">5,814</td>
<td align="right">47.73%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">3,259</td>
<td align="right">26.46%</td>
<td align="right">9,218</td>
<td align="right">74.85%</td>
<td align="right">3,254</td>
<td align="right">26.71%</td>
<td align="right">9,068</td>
<td align="right">74.44%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">1,827</td>
<td align="right">14.83%</td>
<td align="right">11,045</td>
<td align="right">89.68%</td>
<td align="right">1,814</td>
<td align="right">14.89%</td>
<td align="right">10,882</td>
<td align="right">89.34%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,271</td>
<td align="right">10.32%</td>
<td align="right">12,316</td>
<td align="right">1,299</td>
<td align="right">10.66%</td>
<td align="right">12,181</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -908,95 +908,95 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2017-05-04</td>
<td align="center">U8</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">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">2015-09-03</td>
<td align="center">S1</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_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>
<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">2010-01-29</td>
<td align="center">D7</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">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">2012-05-22</td>
<td align="center">G6</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">I</td>
<td align="center">I</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="odd">
<td align="center">2010-01-09</td>
<td align="center">L8</td>
<td align="center">Hospital A</td>
<td align="center">2016-07-10</td>
<td align="center">S7</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<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="even">
<td align="center">2015-03-09</td>
<td align="center">S9</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">2017-10-24</td>
<td align="center">W2</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</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>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2011-09-19</td>
<td align="center">K10</td>
<td align="center">Hospital C</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2016-11-01</td>
<td align="center">X5</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">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">2015-10-12</td>
<td align="center">Q10</td>
<td align="center">Hospital B</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="even">
<td align="center">2016-06-03</td>
<td align="center">G1</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">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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1019,50 +1019,50 @@ 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">1510</td>
<td align="center">1283</td>
<td align="center">3166</td>
<td align="center">5959</td>
<td align="center">1429</td>
<td align="center">1211</td>
<td align="center">3174</td>
<td align="center">5814</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">2778</td>
<td align="center">1154</td>
<td align="center">2027</td>
<td align="center">5959</td>
<td align="center">2674</td>
<td align="center">1190</td>
<td align="center">1950</td>
<td align="center">5814</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">2112</td>
<td align="center">1820</td>
<td align="center">2027</td>
<td align="center">5959</td>
<td align="center">2013</td>
<td align="center">1796</td>
<td align="center">2005</td>
<td align="center">5814</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">2063</td>
<td align="center">1825</td>
<td align="center">2071</td>
<td align="center">5959</td>
<td align="center">1931</td>
<td align="center">1816</td>
<td align="center">2067</td>
<td align="center">5814</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">1271</td>
<td align="center">1271</td>
<td align="center">1299</td>
<td align="center">1299</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">579</td>
<td align="center">266</td>
<td align="center">426</td>
<td align="center">1271</td>
<td align="center">589</td>
<td align="center">258</td>
<td align="center">452</td>
<td align="center">1299</td>
</tr>
</tbody>
</table>
@ -1084,34 +1084,34 @@ 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">2063</td>
<td align="center">1825</td>
<td align="center">2071</td>
<td align="center">5959</td>
<td align="center">1931</td>
<td align="center">1816</td>
<td align="center">2067</td>
<td align="center">5814</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">402</td>
<td align="center">443</td>
<td align="center">411</td>
<td align="center">458</td>
<td align="center">1271</td>
<td align="center">445</td>
<td align="center">1299</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1171</td>
<td align="center">1032</td>
<td align="center">1056</td>
<td align="center">3259</td>
<td align="center">1156</td>
<td align="center">1009</td>
<td align="center">1089</td>
<td align="center">3254</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">1827</td>
<td align="center">1827</td>
<td align="center">1814</td>
<td align="center">1814</td>
</tr>
</tbody>
</table>
@ -1143,7 +1143,7 @@ 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] 0.5802209</span></span></code></pre></div>
<span><span class="co"># [1] 0.5895247</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">
@ -1158,19 +1158,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5650667</td>
<td align="center">0.5991561</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5838028</td>
<td align="center">0.5865273</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5864369</td>
<td align="center">0.5910560</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5923414</td>
<td align="center">0.5797160</td>
</tr>
</tbody>
</table>
@ -1195,23 +1195,23 @@ 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">0.5650667</td>
<td align="center">3750</td>
<td align="center">0.5991561</td>
<td align="center">3555</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5838028</td>
<td align="center">4260</td>
<td align="center">0.5865273</td>
<td align="center">4305</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5864369</td>
<td align="center">1799</td>
<td align="center">0.5910560</td>
<td align="center">1856</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5923414</td>
<td align="center">2507</td>
<td align="center">0.5797160</td>
<td align="center">2465</td>
</tr>
</tbody>
</table>
@ -1236,27 +1236,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6598423</td>
<td align="center">0.6524585</td>
<td align="center">0.8848800</td>
<td align="center">0.6646027</td>
<td align="center">0.6444788</td>
<td align="center">0.8778810</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6648308</td>
<td align="center">0.6396538</td>
<td align="center">0.8686074</td>
<td align="center">0.6520400</td>
<td align="center">0.6574288</td>
<td align="center">0.8760585</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6738263</td>
<td align="center">0.6759742</td>
<td align="center">0.8922983</td>
<td align="center">0.6681008</td>
<td align="center">0.6653350</td>
<td align="center">0.8899816</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4564860</td>
<td align="center">0.4751929</td>
<td align="center">0.0000000</td>
<td align="center">0.4564860</td>
<td align="center">0.4751929</td>
</tr>
</tbody>
</table>
@ -1284,23 +1284,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">56.5%</td>
<td align="right">34.9%</td>
<td align="right">59.9%</td>
<td align="right">35.9%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">58.4%</td>
<td align="right">37.2%</td>
<td align="right">58.7%</td>
<td align="right">36.4%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">58.6%</td>
<td align="right">59.1%</td>
<td align="right">37.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">59.2%</td>
<td align="right">37.7%</td>
<td align="right">58.0%</td>
<td align="right">36.4%</td>
</tr>
</tbody>
</table>
@ -1416,18 +1416,18 @@ 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] &lt;=0.001 0.025 128 0.125 0.0625 8 0.025 32 &gt;=256 </span></span>
<span><span class="co"># [10] 4 32 0.005 4 2 32 0.5 0.0625 128 </span></span>
<span><span class="co"># [19] 0.01 16 1 0.01 64 0.0625 8 &gt;=256 0.005 </span></span>
<span><span class="co"># [28] 128 &lt;=0.001 8 1 0.025 1 64 128 0.0625 </span></span>
<span><span class="co"># [37] 2 0.125 4 4 4 16 0.0625 16 0.0625 </span></span>
<span><span class="co"># [46] 0.5 0.5 &lt;=0.001 64 8 128 1 64 2 </span></span>
<span><span class="co"># [55] 1 &gt;=256 &lt;=0.001 0.002 0.5 4 4 32 &lt;=0.001</span></span>
<span><span class="co"># [64] 16 0.002 128 128 4 0.002 8 8 0.0625 </span></span>
<span><span class="co"># [73] 0.002 0.0625 8 16 0.125 0.005 8 &gt;=256 8 </span></span>
<span><span class="co"># [82] 0.01 0.025 0.005 64 1 0.025 0.002 16 32 </span></span>
<span><span class="co"># [91] 0.005 32 0.002 &lt;=0.001 0.25 4 &lt;=0.001 0.25 16 </span></span>
<span><span class="co"># [100] 0.025</span></span></code></pre></div>
<span><span class="co"># [1] 0.025 &lt;=0.001 &lt;=0.001 32 0.01 4 0.002 0.125 0.01 </span></span>
<span><span class="co"># [10] 32 0.002 0.125 0.005 0.5 1 2 16 4 </span></span>
<span><span class="co"># [19] &lt;=0.001 0.25 0.125 128 &lt;=0.001 0.005 &gt;=256 64 16 </span></span>
<span><span class="co"># [28] 32 0.025 8 0.125 1 0.25 64 0.0625 0.25 </span></span>
<span><span class="co"># [37] 0.5 0.5 16 0.002 0.002 0.5 0.005 16 0.25 </span></span>
<span><span class="co"># [46] 0.125 8 &lt;=0.001 1 0.025 &lt;=0.001 0.5 8 16 </span></span>
<span><span class="co"># [55] 1 16 8 0.002 0.5 0.5 128 16 &gt;=256 </span></span>
<span><span class="co"># [64] 2 0.005 0.01 4 8 0.0625 0.125 0.125 0.125 </span></span>
<span><span class="co"># [73] 16 0.002 0.01 8 1 8 0.125 2 32 </span></span>
<span><span class="co"># [82] 0.0625 &gt;=256 4 0.005 128 0.025 1 128 0.005 </span></span>
<span><span class="co"># [91] &gt;=256 0.025 32 8 &lt;=0.001 &lt;=0.001 &lt;=0.001 1 0.025 </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>
@ -1461,10 +1461,10 @@ 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 26 20 20 26 31 29 17 28 21 27 17 30 23 21 19 23 23 20 23 19 27 23 20 23</span></span>
<span><span class="co"># [26] 25 22 25 28 31 19 31 20 31 19 19 28 31 20 29 23 25 28 27 18 24 26 21 30 23</span></span>
<span><span class="co"># [51] 22 31 27 26 27 26 23 22 17 19 18 24 31 25 29 21 29 19 27 20 31 23 23 25 18</span></span>
<span><span class="co"># [76] 31 18 27 31 20 21 23 25 22 31 26 28 21 30 17 31 29 19 25 24 17 19 19 21 21</span></span></code></pre></div>
<span><span class="co"># [1] 22 28 30 21 25 20 18 28 17 29 29 23 17 17 21 18 17 17 23 20 21 21 23 28 29</span></span>
<span><span class="co"># [26] 18 19 31 17 20 26 29 27 29 18 30 21 30 28 20 26 28 30 30 23 31 20 22 25 30</span></span>
<span><span class="co"># [51] 22 19 25 25 26 21 22 23 22 24 24 27 23 29 30 26 18 24 31 29 30 31 19 25 22</span></span>
<span><span class="co"># [76] 28 20 18 31 17 18 23 27 23 26 28 22 28 18 25 22 28 24 31 26 25 18 30 18 21</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>

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@ -15,7 +15,7 @@
<link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png">
<script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<link href="../deps/bootstrap-5.2.2/bootstrap.min.css" rel="stylesheet">
<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/font.css" rel="stylesheet">
<script src="../deps/bootstrap-5.2.2/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.5/font.css" rel="stylesheet">
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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="">1.8.2.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9100</small>
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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="">1.8.2.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9100</small>
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@ -380,19 +380,19 @@ names or codes, this would have worked exactly the same way:</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">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># rifampicin isoniazid gatifloxacin ethambutol pyrazinamide moxifloxacin</span></span>
<span><span class="co"># 1 I R R R S R</span></span>
<span><span class="co"># 2 R I R S R S</span></span>
<span><span class="co"># 3 R R R I I R</span></span>
<span><span class="co"># 4 I S R R S I</span></span>
<span><span class="co"># 5 S R R S R R</span></span>
<span><span class="co"># 6 S I R I S R</span></span>
<span><span class="co"># 1 R S I R I I</span></span>
<span><span class="co"># 2 I R R S I I</span></span>
<span><span class="co"># 3 I S R S I R</span></span>
<span><span class="co"># 4 S S R R R I</span></span>
<span><span class="co"># 5 R I R S S I</span></span>
<span><span class="co"># 6 S R S I I I</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 S</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 R</span></span>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 I</span></span></code></pre></div>
<span><span class="co"># 3 I</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 5 R</span></span>
<span><span class="co"># 6 S</span></span></code></pre></div>
<p>We can now add the interpretation of MDR-TB to our data set. You can
use:</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
@ -433,40 +433,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3227</td>
<td align="right">64.54%</td>
<td align="right">3237</td>
<td align="right">64.74%</td>
<td align="right">3237</td>
<td align="right">64.74%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">976</td>
<td align="right">19.52%</td>
<td align="right">4203</td>
<td align="right">84.06%</td>
<td align="right">975</td>
<td align="right">19.50%</td>
<td align="right">4212</td>
<td align="right">84.24%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">442</td>
<td align="right">8.84%</td>
<td align="right">4645</td>
<td align="right">92.90%</td>
<td align="right">458</td>
<td align="right">9.16%</td>
<td align="right">4670</td>
<td align="right">93.40%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">247</td>
<td align="right">4.94%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
<td align="right">234</td>
<td align="right">4.68%</td>
<td align="right">4904</td>
<td align="right">98.08%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">96</td>
<td align="right">1.92%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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@ -15,7 +15,7 @@
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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="">1.8.2.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9100</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">

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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="">1.8.2.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9100</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">
@ -173,7 +173,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">23 January 2023</h4>
<h4 data-toc-skip class="date">24 January 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/SPSS.Rmd" class="external-link"><code>vignettes/SPSS.Rmd</code></a></small>
<div class="d-none name"><code>SPSS.Rmd</code></div>

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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="">1.8.2.9099</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9100</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">

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<main id="main" class="col-md-9"><div class="page-header">
<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">23 January 2023</h4>
<h4 data-toc-skip class="date">24 January 2023</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="d-none name"><code>datasets.Rmd</code></div>

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