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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="">1.8.2.9111</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9114</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">08 February 2023</h4>
<h4 data-toc-skip class="date">10 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 08 February 2023.</p>
generated on 10 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">2023-02-08</td>
<td align="center">2023-02-10</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="center">2023-02-08</td>
<td align="center">2023-02-10</td>
<td align="center">abcd</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
</tr>
<tr class="odd">
<td align="center">2023-02-08</td>
<td align="center">2023-02-10</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -381,7 +381,7 @@ function.</p>
using the <code>patients_table</code> object we created earlier:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">data</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 class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate-joins.html" class="external-link">left_join</a></span><span class="op">(</span><span class="va">patients_table</span><span class="op">)</span></span></code></pre></div>
<p>The resulting data set contains 20,000 blood culture isolates. With
<p>The resulting data set contains 20 000 blood culture isolates. With
the <code><a href="https://rdrr.io/r/utils/head.html" class="external-link">head()</a></code> function we can preview the first 6 rows of this
data set:</p>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
@ -411,71 +411,71 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-11-01</td>
<td align="center">T4</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">2013-06-16</td>
<td align="center">R2</td>
<td align="center">Hospital C</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2011-08-07</td>
<td align="center">Q3</td>
<td align="center">2014-07-04</td>
<td align="center">Z4</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">S</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2015-04-08</td>
<td align="center">A9</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</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>
</tr>
<tr class="even">
<td align="center">2017-07-30</td>
<td align="center">I8</td>
<td align="center">Hospital D</td>
<td align="center">Klebsiella pneumoniae</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="odd">
<td align="center">2012-01-05</td>
<td align="center">M5</td>
<td align="center">Hospital B</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2017-06-03</td>
<td align="center">F5</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2015-02-21</td>
<td align="center">E9</td>
<td align="center">Hospital D</td>
<td align="center">2011-12-22</td>
<td align="center">H10</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">I</td>
<td align="center">R</td>
<td align="center">S</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">2017-01-25</td>
<td align="center">Y7</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2014-10-21</td>
<td align="center">Y1</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">R</td>
<td align="center">F</td>
</tr>
</tbody>
</table>
<p>Now, let’s start the cleaning and the analysis!</p>
@ -510,18 +510,18 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,359</td>
<td align="right">51.80%</td>
<td align="right">10,359</td>
<td align="right">51.8%</td>
<td align="right">10,343</td>
<td align="right">51.72%</td>
<td align="right">10,343</td>
<td align="right">51.72%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,641</td>
<td align="right">48.21%</td>
<td align="right">9,657</td>
<td align="right">48.29%</td>
<td align="right">20,000</td>
<td align="right">100.0%</td>
<td align="right">100.00%</td>
</tr>
</tbody>
</table>
@ -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 20,000 'phenotype-based' first isolates (100.0% of total where a</span></span>
<span><span class="co"># =&gt; Found 12,360 'phenotype-based' first isolates (61.8% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 100% is suitable for resistance analysis! We can now filter
<p>So only 61.8% 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">
@ -644,12 +644,13 @@ 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 20,000 isolates for analysis. Now our data looks
<p>So we end up with 12 360 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<table style="width:100%;" class="table">
<colgroup>
<col width="2%">
<col width="9%">
<col width="9%">
<col width="9%">
@ -665,6 +666,7 @@ like:</p>
<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>
@ -681,87 +683,61 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2012-11-01</td>
<td align="center">T4</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">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="center">2011-08-07</td>
<td align="center">Q3</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">I</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="center">2015-04-08</td>
<td align="center">A9</td>
<td align="center">Hospital D</td>
<td align="left">1</td>
<td align="center">2013-06-16</td>
<td align="center">R2</td>
<td align="center">Hospital C</td>
<td align="center">B_KLBSL_PNMN</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">M</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">2017-07-30</td>
<td align="center">I8</td>
<td align="center">Hospital D</td>
<td align="center">B_KLBSL_PNMN</td>
<td align="center">R</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-01-05</td>
<td align="center">M5</td>
<td align="center">Hospital B</td>
<td align="left">2</td>
<td align="center">2014-07-04</td>
<td align="center">Z4</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">S</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">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">2014-10-21</td>
<td align="center">Y1</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">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">2015-02-21</td>
<td align="left">7</td>
<td align="center">2017-08-18</td>
<td align="center">E9</td>
<td align="center">Hospital D</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">S</td>
<td align="center">R</td>
<td align="center">M</td>
@ -770,6 +746,38 @@ like:</p>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">8</td>
<td align="center">2017-10-08</td>
<td align="center">P4</td>
<td align="center">Hospital C</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">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">10</td>
<td align="center">2012-08-30</td>
<td align="center">C4</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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>Time for the analysis!</p>
@ -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: 20,000<br>
Available: 20,000 (100%, NA: 0 = 0%)<br>
Length: 12,360<br>
Available: 12,360 (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">9,956</td>
<td align="right">49.78%</td>
<td align="right">9,956</td>
<td align="right">49.78%</td>
<td align="right">5,976</td>
<td align="right">48.35%</td>
<td align="right">5,976</td>
<td align="right">48.35%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">4,995</td>
<td align="right">24.98%</td>
<td align="right">14,951</td>
<td align="right">74.76%</td>
<td align="right">3,242</td>
<td align="right">26.23%</td>
<td align="right">9,218</td>
<td align="right">74.58%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">3,001</td>
<td align="right">15.01%</td>
<td align="right">17,952</td>
<td align="right">89.76%</td>
<td align="right">1,860</td>
<td align="right">15.05%</td>
<td align="right">11,078</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">2,048</td>
<td align="right">10.24%</td>
<td align="right">20,000</td>
<td align="right">1,282</td>
<td align="right">10.37%</td>
<td align="right">12,360</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -904,95 +912,95 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-04-08</td>
<td align="center">A9</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">M</td>
<td align="center">Gram-negative</td>
<td align="center">Klebsiella</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2012-01-05</td>
<td align="center">M5</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">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="odd">
<td align="center">2015-02-21</td>
<td align="center">E9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-04-27</td>
<td align="center">C9</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">I</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">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2012-06-09</td>
<td align="center">C6</td>
<td align="center">2014-07-04</td>
<td align="center">Z4</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">I</td>
<td align="center">I</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">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2011-12-09</td>
<td align="center">W4</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">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="even">
<td align="center">2014-10-21</td>
<td align="center">Y1</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">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="odd">
<td align="center">2017-08-18</td>
<td align="center">E9</td>
<td align="center">Hospital B</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">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">TRUE</td>
</tr>
<tr class="even">
<td align="center">2017-10-08</td>
<td align="center">P4</td>
<td align="center">Hospital C</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">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">2012-08-30</td>
<td align="center">C4</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">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">2012-12-24</td>
<td align="center">Q5</td>
<td align="center">Hospital D</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">I</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>
</tbody>
</table>
<p>If you want to get a quick glance of the number of isolates in
@ -1004,6 +1012,7 @@ different bug/drug combinations, you can use the
<span> <span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show first 6 rows</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left"></th>
<th align="center">mo</th>
<th align="center">ab</th>
<th align="center">S</th>
@ -1013,52 +1022,58 @@ different bug/drug combinations, you can use the
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">2</td>
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">4463</td>
<td align="center">2199</td>
<td align="center">3294</td>
<td align="center">9956</td>
<td align="center">2812</td>
<td align="center">1160</td>
<td align="center">2004</td>
<td align="center">5976</td>
</tr>
<tr class="even">
<td align="left">1</td>
<td align="center">E. coli</td>
<td align="center">AMX</td>
<td align="center">2238</td>
<td align="center">2141</td>
<td align="center">5577</td>
<td align="center">9956</td>
<td align="center">1563</td>
<td align="center">1221</td>
<td align="center">3192</td>
<td align="center">5976</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3359</td>
<td align="center">3299</td>
<td align="center">3298</td>
<td align="center">9956</td>
<td align="center">2049</td>
<td align="center">1816</td>
<td align="center">2111</td>
<td align="center">5976</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">3360</td>
<td align="center">3332</td>
<td align="center">3264</td>
<td align="center">9956</td>
<td align="center">2047</td>
<td align="center">1864</td>
<td align="center">2065</td>
<td align="center">5976</td>
</tr>
<tr class="odd">
<td align="left">6</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">886</td>
<td align="center">555</td>
<td align="center">281</td>
<td align="center">446</td>
<td align="center">716</td>
<td align="center">2048</td>
<td align="center">1282</td>
</tr>
<tr class="even">
<td align="left">5</td>
<td align="center">K. pneumoniae</td>
<td align="center">AMX</td>
<td align="center">0</td>
<td align="center">0</td>
<td align="center">2048</td>
<td align="center">2048</td>
<td align="center">1282</td>
<td align="center">1282</td>
</tr>
</tbody>
</table>
@ -1080,34 +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">3360</td>
<td align="center">3332</td>
<td align="center">3264</td>
<td align="center">9956</td>
<td align="center">2047</td>
<td align="center">1864</td>
<td align="center">2065</td>
<td align="center">5976</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">682</td>
<td align="center">656</td>
<td align="center">710</td>
<td align="center">2048</td>
<td align="center">461</td>
<td align="center">406</td>
<td align="center">415</td>
<td align="center">1282</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">1668</td>
<td align="center">1653</td>
<td align="center">1674</td>
<td align="center">4995</td>
<td align="center">1122</td>
<td align="center">989</td>
<td align="center">1131</td>
<td align="center">3242</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">3001</td>
<td align="center">3001</td>
<td align="center">1860</td>
<td align="center">1860</td>
</tr>
</tbody>
</table>
@ -1139,7 +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] 0.60575</span></span></code></pre></div>
<span><span class="co"># [1] 0.5843042</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">
@ -1154,19 +1169,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.6017567</td>
<td align="center">0.5790487</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.6139130</td>
<td align="center">0.5752233</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.6064538</td>
<td align="center">0.5984384</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5972906</td>
<td align="center">0.5973469</td>
</tr>
</tbody>
</table>
@ -1191,23 +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">0.6017567</td>
<td align="center">6034</td>
<td align="center">0.5790487</td>
<td align="center">3637</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.6139130</td>
<td align="center">6900</td>
<td align="center">0.5752233</td>
<td align="center">4367</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.6064538</td>
<td align="center">3006</td>
<td align="center">0.5984384</td>
<td align="center">1793</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5972906</td>
<td align="center">4060</td>
<td align="center">0.5973469</td>
<td align="center">2563</td>
</tr>
</tbody>
</table>
@ -1232,27 +1247,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.6691442</td>
<td align="center">0.6721575</td>
<td align="center">0.8938329</td>
<td align="center">0.6646586</td>
<td align="center">0.6544511</td>
<td align="center">0.8840361</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.6503906</td>
<td align="center">0.6533203</td>
<td align="center">0.8803711</td>
<td align="center">0.6521061</td>
<td align="center">0.6762871</td>
<td align="center">0.8892356</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.6654655</td>
<td align="center">0.6648649</td>
<td align="center">0.8852853</td>
<td align="center">0.6748920</td>
<td align="center">0.6511413</td>
<td align="center">0.8834053</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.4325225</td>
<td align="center">0.4698925</td>
<td align="center">0.0000000</td>
<td align="center">0.4325225</td>
<td align="center">0.4698925</td>
</tr>
</tbody>
</table>
@ -1280,23 +1295,23 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">60.2%</td>
<td align="right">57.9%</td>
<td align="right">36.8%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">61.4%</td>
<td align="right">37.8%</td>
<td align="right">57.5%</td>
<td align="right">35.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">60.6%</td>
<td align="right">36.6%</td>
<td align="right">59.8%</td>
<td align="right">37.4%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">59.7%</td>
<td align="right">35.9%</td>
<td align="right">35.8%</td>
</tr>
</tbody>
</table>
@ -1412,18 +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] 0.025 8 0.25 32 0.005 4 32 128 &lt;=0.001</span></span>
<span><span class="co"># [10] 16 0.002 0.002 0.5 2 0.025 0.002 8 128 </span></span>
<span><span class="co"># [19] 0.0625 1 0.125 128 0.5 2 1 8 0.025 </span></span>
<span><span class="co"># [28] 0.01 0.5 0.0625 64 0.25 0.025 64 0.005 128 </span></span>
<span><span class="co"># [37] &lt;=0.001 &lt;=0.001 0.25 2 16 0.125 0.125 0.002 0.125 </span></span>
<span><span class="co"># [46] 32 16 0.005 0.0625 0.0625 32 16 16 8 </span></span>
<span><span class="co"># [55] 0.025 2 0.125 64 16 &lt;=0.001 64 &gt;=256 0.0625 </span></span>
<span><span class="co"># [64] &gt;=256 0.002 &gt;=256 0.125 &gt;=256 0.0625 1 0.0625 0.002 </span></span>
<span><span class="co"># [73] &lt;=0.001 0.005 32 0.25 128 64 32 0.25 0.125 </span></span>
<span><span class="co"># [82] &lt;=0.001 0.5 16 8 0.5 0.5 0.125 0.5 64 </span></span>
<span><span class="co"># [91] 1 0.0625 &gt;=256 0.005 128 &gt;=256 0.025 128 128 </span></span>
<span><span class="co"># [100] 0.01</span></span></code></pre></div>
<span><span class="co"># [1] 0.25 32 0.0625 1 0.125 16 0.0625 16 0.025 </span></span>
<span><span class="co"># [10] 0.25 &gt;=256 0.5 1 0.01 &gt;=256 2 0.5 8 </span></span>
<span><span class="co"># [19] 64 &gt;=256 1 2 0.005 0.002 0.5 0.01 0.0625 </span></span>
<span><span class="co"># [28] 0.125 0.002 0.002 &gt;=256 &gt;=256 0.025 4 1 2 </span></span>
<span><span class="co"># [37] 0.01 1 32 128 &gt;=256 &lt;=0.001 0.01 2 0.002 </span></span>
<span><span class="co"># [46] 2 4 0.002 0.25 &gt;=256 0.125 0.125 0.25 16 </span></span>
<span><span class="co"># [55] 128 0.25 0.0625 8 16 0.002 64 64 &gt;=256 </span></span>
<span><span class="co"># [64] 0.5 8 0.5 16 0.002 0.25 &lt;=0.001 &gt;=256 0.002 </span></span>
<span><span class="co"># [73] 4 0.005 128 2 8 32 1 1 2 </span></span>
<span><span class="co"># [82] 0.025 &lt;=0.001 &gt;=256 0.025 0.5 16 4 2 128 </span></span>
<span><span class="co"># [91] 64 0.002 0.002 1 &gt;=256 0.125 0.01 0.01 0.0625 </span></span>
<span><span class="co"># [100] 0.0625</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>
@ -1457,10 +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] 24 18 24 25 18 27 25 21 28 26 18 23 21 30 27 21 20 30 29 20 29 27 17 31 25</span></span>
<span><span class="co"># [26] 25 20 29 24 30 18 31 31 20 17 30 22 29 27 19 31 25 23 21 26 25 30 28 30 21</span></span>
<span><span class="co"># [51] 24 24 21 27 24 17 19 27 21 21 21 26 30 24 27 24 24 27 28 18 29 17 26 19 21</span></span>
<span><span class="co"># [76] 29 29 31 29 24 20 29 18 21 18 23 22 28 18 19 28 27 18 22 19 20 31 30 22 30</span></span></code></pre></div>
<span><span class="co"># [1] 31 22 24 20 23 20 22 27 19 20 20 23 28 30 23 21 17 17 25 19 21 31 18 31 19</span></span>
<span><span class="co"># [26] 26 28 31 17 21 31 20 30 26 22 24 30 18 31 25 17 29 29 18 26 27 24 21 22 18</span></span>
<span><span class="co"># [51] 17 19 22 27 19 23 24 20 30 30 19 17 31 31 17 25 24 31 22 22 19 27 17 19 19</span></span>
<span><span class="co"># [76] 31 22 22 23 26 29 20 17 29 31 27 30 18 17 31 26 17 27 22 20 19 23 24 28 20</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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@ -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="">1.8.2.9111</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9114</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">

60
articles/MDR.html
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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="">1.8.2.9111</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9114</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">
@ -385,19 +385,19 @@ 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 S I I S I</span></span>
<span><span class="co"># 2 S S S S I S</span></span>
<span><span class="co"># 3 R R I S I R</span></span>
<span><span class="co"># 4 I I R S S R</span></span>
<span><span class="co"># 5 R I S S I S</span></span>
<span><span class="co"># 6 R S R I R I</span></span>
<span><span class="co"># 1 R I S R R I</span></span>
<span><span class="co"># 2 I R S I R R</span></span>
<span><span class="co"># 3 I I R S I R</span></span>
<span><span class="co"># 4 R I R I R I</span></span>
<span><span class="co"># 5 R S I R R S</span></span>
<span><span class="co"># 6 S R R R R R</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 S</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 R</span></span>
<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 I</span></span></code></pre></div>
<span><span class="co"># 5 S</span></span>
<span><span class="co"># 6 R</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">
@ -438,40 +438,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3141</td>
<td align="right">62.82%</td>
<td align="right">3141</td>
<td align="right">62.82%</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
<td align="right">3194</td>
<td align="right">63.88%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1012</td>
<td align="right">20.24%</td>
<td align="right">4153</td>
<td align="right">83.06%</td>
<td align="right">998</td>
<td align="right">19.96%</td>
<td align="right">4192</td>
<td align="right">83.84%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">477</td>
<td align="right">9.54%</td>
<td align="right">4630</td>
<td align="right">92.60%</td>
<td align="right">468</td>
<td align="right">9.36%</td>
<td align="right">4660</td>
<td align="right">93.20%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">257</td>
<td align="right">5.14%</td>
<td align="right">4887</td>
<td align="right">97.74%</td>
<td align="right">232</td>
<td align="right">4.64%</td>
<td align="right">4892</td>
<td align="right">97.84%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">113</td>
<td align="right">2.26%</td>
<td align="right">108</td>
<td align="right">2.16%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

2
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@ -38,7 +38,7 @@
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@ -178,7 +178,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">08 February 2023</h4>
<h4 data-toc-skip class="date">10 February 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>
@ -257,7 +257,7 @@ data using a custom made website. The webdesign knowledge needed
<li>
<p><strong>R has a huge community.</strong></p>
<p>Many R users just ask questions on websites like <a href="https://stackoverflow.com" class="external-link">StackOverflow.com</a>, the largest
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">480,015
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">480 015
R-related questions</a> have already been asked on this platform (that
covers questions and answers for any programming language). In my own
experience, most questions are answered within a couple of

2
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@ -38,7 +38,7 @@
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@ -38,7 +38,7 @@
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@ -176,7 +176,7 @@
<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">08 February 2023</h4>
<h4 data-toc-skip class="date">10 February 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>
@ -197,7 +197,7 @@ of the data sets look like.</p>
<h2 id="microorganisms-full-microbial-taxonomy">
<code>microorganisms</code>: Full Microbial Taxonomy<a class="anchor" aria-label="anchor" href="#microorganisms-full-microbial-taxonomy"></a>
</h2>
<p>A data set with 52,142 rows and 22 columns, containing the following
<p>A data set with 52 142 rows and 22 columns, containing the following
column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</em>,
<em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>,
<em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>,
@ -275,23 +275,23 @@ Set Name ‘Microoganism’, OID 2.16.840.1.114222.4.11.1009 (v12). URL: <a href
</tr>
<tr class="even">
<td align="center">Animalia</td>
<td align="center">1,379</td>
<td align="center">1 379</td>
</tr>
<tr class="odd">
<td align="center">Archaea</td>
<td align="center">1,314</td>
<td align="center">1 314</td>
</tr>
<tr class="even">
<td align="center">Bacteria</td>
<td align="center">36,476</td>
<td align="center">36 476</td>
</tr>
<tr class="odd">
<td align="center">Fungi</td>
<td align="center">7,901</td>
<td align="center">7 901</td>
</tr>
<tr class="even">
<td align="center">Protozoa</td>
<td align="center">5,071</td>
<td align="center">5 071</td>
</tr>
</tbody>
</table>
@ -877,7 +877,7 @@ inhibitors</td>
<code>clinical_breakpoints</code>: Interpretation from MIC values
&amp; disk diameters to SIR<a class="anchor" aria-label="anchor" href="#clinical_breakpoints-interpretation-from-mic-values-disk-diameters-to-sir"></a>
</h2>
<p>A data set with 18,308 rows and 11 columns, containing the following
<p>A data set with 18 308 rows and 11 columns, containing the following
column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>,
<em>rank_index</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</em>,
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
@ -1052,7 +1052,7 @@ diffusion diameters. Included guidelines are CLSI (2013-2022) and EUCAST
<code>intrinsic_resistant</code>: Intrinsic Bacterial
Resistance<a class="anchor" aria-label="anchor" href="#intrinsic_resistant-intrinsic-bacterial-resistance"></a>
</h2>
<p>A data set with 134,634 rows and 2 columns, containing the following
<p>A data set with 134 634 rows and 2 columns, containing the following
column names:<br><em>mo</em> and <em>ab</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>,
after you load the <code>AMR</code> package.</p>
@ -1482,7 +1482,7 @@ Breakpoint Tables’ v12.0</a> (2022).</p>
<h2 id="example_isolates-example-data-for-practice">
<code>example_isolates</code>: Example Data for Practice<a class="anchor" aria-label="anchor" href="#example_isolates-example-data-for-practice"></a>
</h2>
<p>A data set with 2,000 rows and 46 columns, containing the following
<p>A data set with 2 000 rows and 46 columns, containing the following
column names:<br><em>date</em>, <em>patient</em>, <em>age</em>, <em>gender</em>,
<em>ward</em>, <em>mo</em>, <em>PEN</em>, <em>OXA</em>, <em>FLC</em>,
<em>AMX</em>, <em>AMC</em>, <em>AMP</em>, <em>TZP</em>, <em>CZO</em>,
@ -1901,7 +1901,7 @@ reality and can be used to practise AMR data analysis.</p>
<code>example_isolates_unclean</code>: Example Data for
Practice<a class="anchor" aria-label="anchor" href="#example_isolates_unclean-example-data-for-practice"></a>
</h2>
<p>A data set with 3,000 rows and 8 columns, containing the following
<p>A data set with 3 000 rows and 8 columns, containing the following
column names:<br><em>patient_id</em>, <em>hospital</em>, <em>date</em>,
<em>bacteria</em>, <em>AMX</em>, <em>AMC</em>, <em>CIP</em> and
<em>GEN</em>.</p>

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@ -202,7 +202,7 @@ treatment evaluation in any setting.</p>
10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI
10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI
10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows ~52,000 distinct microbial
<p>After installing this package, R knows ~52 000 distinct microbial
species and all ~600 antibiotic, antimycotic and antiviral drugs by name
and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
CT), and knows all about valid SIR and MIC values. The integral