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@ -15,7 +15,7 @@
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<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">
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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="">1.8.2.9052</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9053</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">17 November 2022</h4>
<h4 data-toc-skip class="date">24 November 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
<div class="d-none name"><code>AMR.Rmd</code></div>
@ -180,7 +180,7 @@ Berends</h4>
website update since they are based on randomly created values and the
page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
Markdown</a>. However, the methodology remains unchanged. This page was
generated on 17 November 2022.</p>
generated on 24 November 2022.</p>
<div class="section level2">
<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h2>
@ -236,21 +236,21 @@ make the structure of your data generally look like this:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2022-11-17</td>
<td align="center">2022-11-24</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">2022-11-17</td>
<td align="center">2022-11-24</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">2022-11-17</td>
<td align="center">2022-11-24</td>
<td align="center">efgh</td>
<td align="center">Escherichia coli</td>
<td align="center">R</td>
@ -400,20 +400,9 @@ data set:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2015-12-23</td>
<td align="center">L8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2014-07-14</td>
<td align="center">M7</td>
<td align="center">Hospital B</td>
<td align="center">2015-01-29</td>
<td align="center">L10</td>
<td align="center">Hospital A</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">R</td>
@ -421,47 +410,58 @@ data set:</p>
<td align="center">S</td>
<td align="center">M</td>
</tr>
<tr class="even">
<td align="center">2011-01-24</td>
<td align="center">S8</td>
<td align="center">Hospital B</td>
<td align="center">Escherichia coli</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2010-06-02</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">Staphylococcus aureus</td>
<td align="center">2011-06-11</td>
<td align="center">U8</td>
<td align="center">Hospital D</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2012-05-12</td>
<td align="center">A5</td>
<td align="center">2013-08-22</td>
<td align="center">V5</td>
<td align="center">Hospital C</td>
<td align="center">Escherichia coli</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
</tr>
<tr class="odd">
<td align="center">2016-01-14</td>
<td align="center">Q3</td>
<td align="center">Hospital D</td>
<td align="center">2017-05-12</td>
<td align="center">V3</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
<tr class="even">
<td align="center">2013-02-21</td>
<td align="center">X1</td>
<td align="center">Hospital D</td>
<td align="center">2017-05-16</td>
<td align="center">X8</td>
<td align="center">Hospital C</td>
<td align="center">Streptococcus pneumoniae</td>
<td align="center">S</td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">F</td>
</tr>
@ -499,16 +499,16 @@ Longest: 1</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">M</td>
<td align="right">10,496</td>
<td align="right">52.48%</td>
<td align="right">10,496</td>
<td align="right">52.48%</td>
<td align="right">10,350</td>
<td align="right">51.75%</td>
<td align="right">10,350</td>
<td align="right">51.75%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">F</td>
<td align="right">9,504</td>
<td align="right">47.52%</td>
<td align="right">9,650</td>
<td align="right">48.25%</td>
<td align="right">20,000</td>
<td align="right">100.00%</td>
</tr>
@ -615,15 +615,15 @@ takes into account the antimicrobial susceptibility test results using
<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>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>first <span class="op">=</span> <span class="fu"><a href="../reference/first_isolate.html">first_isolate</a></span><span class="op">(</span>info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co"># Determining first isolates using an episode length of 365 days</span></span>
<span><span class="co"># ℹ Using column 'bacteria' as input for `col_mo`.</span></span>
<span><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></span>
<span><span class="co"># ℹ Using column 'patient_id' as input for `col_patient_id`.</span></span>
<span><span class="co"># ℹ Using column 'bacteria' as input for col_mo.</span></span>
<span><span class="co"># ℹ Using column 'date' as input for col_date.</span></span>
<span><span class="co"># ℹ Using column 'patient_id' as input for col_patient_id.</span></span>
<span><span class="co"># Basing inclusion on all antimicrobial results, using a points threshold of</span></span>
<span><span class="co"># 2</span></span>
<span><span class="co"># Including isolates from ICU.</span></span>
<span><span class="co"># =&gt; Found 10,612 'phenotype-based' first isolates (53.1% of total where a</span></span>
<span><span class="co"># =&gt; Found 10,691 'phenotype-based' first isolates (53.5% of total where a</span></span>
<span><span class="co"># microbial ID was available)</span></span></code></pre></div>
<p>So only 53.1% is suitable for resistance analysis! We can now filter
<p>So only 53.5% is suitable for resistance analysis! We can now filter
on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter()</a></code> function, also from the
<code>dplyr</code> package:</p>
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
@ -634,11 +634,11 @@ on it with the <code><a href="https://dplyr.tidyverse.org/reference/filter.html"
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op">&lt;-</span> <span class="va">data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="../reference/first_isolate.html">filter_first_isolate</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># Including isolates from ICU.</span></span></code></pre></div>
<p>So we end up with 10,612 isolates for analysis. Now our data looks
<p>So we end up with 10,691 isolates for analysis. Now our data looks
like:</p>
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span></span></code></pre></div>
<table style="width:100%;" class="table">
<table class="table">
<colgroup>
<col width="2%">
<col width="9%">
@ -651,7 +651,7 @@ like:</p>
<col width="3%">
<col width="6%">
<col width="11%">
<col width="12%">
<col width="11%">
<col width="9%">
<col width="5%">
</colgroup>
@ -673,42 +673,42 @@ like:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">1</td>
<td align="center">2015-01-29</td>
<td align="center">L10</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="center">2014-07-14</td>
<td align="center">M7</td>
<td align="center">2011-01-24</td>
<td align="center">S8</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">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">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">
<tr class="odd">
<td align="left">3</td>
<td align="center">2010-06-02</td>
<td align="center">F6</td>
<td align="center">Hospital A</td>
<td align="center">B_STPHY_AURS</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">Gram-positive</td>
<td align="center">Staphylococcus</td>
<td align="center">aureus</td>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="left">7</td>
<td align="center">2013-01-21</td>
<td align="center">Z7</td>
<td align="center">Hospital A</td>
<td align="center">2011-06-11</td>
<td align="center">U8</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
@ -721,30 +721,30 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">8</td>
<td align="center">2013-05-01</td>
<td align="center">S2</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="left">5</td>
<td align="center">2017-05-12</td>
<td align="center">V3</td>
<td align="center">Hospital B</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">F</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="left">12</td>
<td align="center">2016-06-06</td>
<td align="center">Q6</td>
<td align="center">Hospital D</td>
<td align="left">6</td>
<td align="center">2017-05-16</td>
<td align="center">X8</td>
<td align="center">Hospital C</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -753,16 +753,16 @@ like:</p>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="left">14</td>
<td align="center">2016-01-03</td>
<td align="center">N4</td>
<td align="center">Hospital A</td>
<td align="left">10</td>
<td align="center">2012-08-19</td>
<td align="center">N7</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">R</td>
<td align="center">S</td>
<td align="center">M</td>
<td align="center">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
@ -801,8 +801,8 @@ readable:</p>
<code class="sourceCode R"><span><span class="va">data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="va">genus</span>, <span class="va">species</span><span class="op">)</span></span></code></pre></div>
<p><strong>Frequency table</strong></p>
<p>Class: character<br>
Length: 10,612<br>
Available: 10,612 (100%, NA: 0 = 0%)<br>
Length: 10,691<br>
Available: 10,691 (100%, NA: 0 = 0%)<br>
Unique: 4</p>
<p>Shortest: 16<br>
Longest: 24</p>
@ -827,33 +827,33 @@ Longest: 24</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Escherichia coli</td>
<td align="right">4,601</td>
<td align="right">43.36%</td>
<td align="right">4,601</td>
<td align="right">43.36%</td>
<td align="right">4,607</td>
<td align="right">43.09%</td>
<td align="right">4,607</td>
<td align="right">43.09%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Staphylococcus aureus</td>
<td align="right">2,686</td>
<td align="right">25.31%</td>
<td align="right">7,287</td>
<td align="right">68.67%</td>
<td align="right">2,750</td>
<td align="right">25.72%</td>
<td align="right">7,357</td>
<td align="right">68.81%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Streptococcus pneumoniae</td>
<td align="right">2,115</td>
<td align="right">19.93%</td>
<td align="right">9,402</td>
<td align="right">88.60%</td>
<td align="right">2,124</td>
<td align="right">19.87%</td>
<td align="right">9,481</td>
<td align="right">88.68%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Klebsiella pneumoniae</td>
<td align="right">1,210</td>
<td align="right">11.40%</td>
<td align="right">10,612</td>
<td align="right">11.32%</td>
<td align="right">10,691</td>
<td align="right">100.00%</td>
</tr>
</tbody>
@ -868,20 +868,20 @@ antibiotic class they are in:</p>
<div class="sourceCode" id="cb20"><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>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<pre><code><span><span class="co"># ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)</span></span></code></pre>
<pre><code><span><span class="co"># ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span></code></pre>
<table class="table">
<colgroup>
<col width="9%">
<col width="9%">
<col width="9%">
<col width="11%">
<col width="10%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="3%">
<col width="6%">
<col width="11%">
<col width="11%">
<col width="12%">
<col width="9%">
<col width="5%">
</colgroup>
@ -902,28 +902,28 @@ antibiotic class they are in:</p>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">2013-05-01</td>
<td align="center">S2</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">2011-01-24</td>
<td align="center">S8</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">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">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">2016-06-06</td>
<td align="center">Q6</td>
<td align="center">Hospital D</td>
<td align="center">2017-05-16</td>
<td align="center">X8</td>
<td align="center">Hospital C</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">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
@ -932,63 +932,63 @@ antibiotic class they are in:</p>
<td align="center">TRUE</td>
</tr>
<tr class="odd">
<td align="center">2014-10-11</td>
<td align="center">K4</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">2016-09-23</td>
<td align="center">P4</td>
<td align="center">2011-11-29</td>
<td align="center">N9</td>
<td align="center">Hospital D</td>
<td align="center">B_ESCHR_COLI</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">F</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</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">2012-11-13</td>
<td align="center">A1</td>
<tr class="even">
<td align="center">2017-09-27</td>
<td align="center">I4</td>
<td align="center">Hospital A</td>
<td align="center">B_STRPT_PNMN</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="odd">
<td align="center">2010-01-03</td>
<td align="center">N7</td>
<td align="center">Hospital B</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
<tr class="even">
<td align="center">2013-02-15</td>
<td align="center">F3</td>
<td align="center">Hospital A</td>
<td align="center">B_ESCHR_COLI</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">2011-05-07</td>
<td align="center">W8</td>
<td align="center">Hospital D</td>
<td align="center">B_STRPT_PNMN</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">M</td>
<td align="center">Gram-negative</td>
<td align="center">Escherichia</td>
<td align="center">coli</td>
<td align="center">F</td>
<td align="center">Gram-positive</td>
<td align="center">Streptococcus</td>
<td align="center">pneumoniae</td>
<td align="center">TRUE</td>
</tr>
</tbody>
@ -1000,7 +1000,6 @@ different bug/drug combinations, you can use the
<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>
<span> <span class="fu"><a href="../reference/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</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="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>
<pre><code><span><span class="co"># ℹ Using column 'bacteria' as input for `col_mo`.</span></span></code></pre>
<table class="table">
<thead><tr class="header">
<th align="center">mo</th>
@ -1014,34 +1013,34 @@ 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">2181</td>
<td align="center">142</td>
<td align="center">2278</td>
<td align="center">4601</td>
<td align="center">2169</td>
<td align="center">130</td>
<td align="center">2308</td>
<td align="center">4607</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">AMC</td>
<td align="center">3411</td>
<td align="center">174</td>
<td align="center">1016</td>
<td align="center">4601</td>
<td align="center">3397</td>
<td align="center">171</td>
<td align="center">1039</td>
<td align="center">4607</td>
</tr>
<tr class="odd">
<td align="center">E. coli</td>
<td align="center">CIP</td>
<td align="center">3377</td>
<td align="center">3369</td>
<td align="center">0</td>
<td align="center">1224</td>
<td align="center">4601</td>
<td align="center">1238</td>
<td align="center">4607</td>
</tr>
<tr class="even">
<td align="center">E. coli</td>
<td align="center">GEN</td>
<td align="center">4021</td>
<td align="center">0</td>
<td align="center">580</td>
<td align="center">4601</td>
<td align="center">586</td>
<td align="center">4607</td>
</tr>
<tr class="odd">
<td align="center">K. pneumoniae</td>
@ -1054,19 +1053,18 @@ different bug/drug combinations, you can use the
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">AMC</td>
<td align="center">934</td>
<td align="center">38</td>
<td align="center">238</td>
<td align="center">941</td>
<td align="center">45</td>
<td align="center">224</td>
<td align="center">1210</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb23"><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>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">bacteria</span>, <span class="fu"><a href="../reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</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/bug_drug_combinations.html">bug_drug_combinations</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<pre><code><span><span class="co"># ℹ For `aminoglycosides()` using column 'GEN' (gentamicin)</span></span>
<span><span class="co"># ℹ Using column 'bacteria' as input for `col_mo`.</span></span></code></pre>
<pre><code><span><span class="co"># ℹ For aminoglycosides() using column 'GEN' (gentamicin)</span></span></code></pre>
<table class="table">
<thead><tr class="header">
<th align="center">mo</th>
@ -1082,32 +1080,32 @@ different bug/drug combinations, you can use the
<td align="center">GEN</td>
<td align="center">4021</td>
<td align="center">0</td>
<td align="center">580</td>
<td align="center">4601</td>
<td align="center">586</td>
<td align="center">4607</td>
</tr>
<tr class="even">
<td align="center">K. pneumoniae</td>
<td align="center">GEN</td>
<td align="center">1098</td>
<td align="center">1081</td>
<td align="center">0</td>
<td align="center">112</td>
<td align="center">129</td>
<td align="center">1210</td>
</tr>
<tr class="odd">
<td align="center">S. aureus</td>
<td align="center">GEN</td>
<td align="center">2365</td>
<td align="center">2427</td>
<td align="center">0</td>
<td align="center">321</td>
<td align="center">2686</td>
<td align="center">323</td>
<td align="center">2750</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">2115</td>
<td align="center">2115</td>
<td align="center">2124</td>
<td align="center">2124</td>
</tr>
</tbody>
</table>
@ -1137,12 +1135,12 @@ proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a>
I (<code><a href="../reference/proportion.html">proportion_SI()</a></code>, equal to
<code><a href="../reference/proportion.html">susceptibility()</a></code>). These functions can be used on their
own:</p>
<div class="sourceCode" id="cb26"><pre class="downlit sourceCode r">
<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] 0.5434414</span></span></code></pre></div>
<span><span class="co"># [1] 0.5467215</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="cb27"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb26"><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>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital</span><span class="op">)</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="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span>amoxicillin <span class="op">=</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 class="op">)</span></span></code></pre></div>
@ -1154,19 +1152,19 @@ own:</p>
<tbody>
<tr class="odd">
<td align="center">Hospital A</td>
<td align="center">0.5427245</td>
<td align="center">0.5395156</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5589124</td>
<td align="center">0.5511053</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5351942</td>
<td align="center">0.5408886</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5241280</td>
<td align="center">0.5535963</td>
</tr>
</tbody>
</table>
@ -1175,7 +1173,7 @@ responsible for the percentages. For that purpose the
<code><a href="../reference/count.html">n_rsi()</a></code> can be used, which works exactly like
<code><a href="https://dplyr.tidyverse.org/reference/n_distinct.html" class="external-link">n_distinct()</a></code> from the <code>dplyr</code> package. It counts
all isolates available for every group (i.e. values S, I or R):</p>
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb27"><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>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital</span><span class="op">)</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="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span>
@ -1191,30 +1189,30 @@ 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">0.5427245</td>
<td align="center">3230</td>
<td align="center">0.5395156</td>
<td align="center">3138</td>
</tr>
<tr class="even">
<td align="center">Hospital B</td>
<td align="center">0.5589124</td>
<td align="center">3641</td>
<td align="center">0.5511053</td>
<td align="center">3845</td>
</tr>
<tr class="odd">
<td align="center">Hospital C</td>
<td align="center">0.5351942</td>
<td align="center">1648</td>
<td align="center">0.5408886</td>
<td align="center">1553</td>
</tr>
<tr class="even">
<td align="center">Hospital D</td>
<td align="center">0.5241280</td>
<td align="center">2093</td>
<td align="center">0.5535963</td>
<td align="center">2155</td>
</tr>
</tbody>
</table>
<p>These functions can also be used to get the proportion of multiple
antibiotics, to calculate empiric susceptibility of combination
therapies very easily:</p>
<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb28"><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>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</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="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span>
@ -1232,27 +1230,27 @@ therapies very easily:</p>
<tbody>
<tr class="odd">
<td align="center">Escherichia</td>
<td align="center">0.7791784</td>
<td align="center">0.8739404</td>
<td align="center">0.9819604</td>
<td align="center">0.7744736</td>
<td align="center">0.8728023</td>
<td align="center">0.9791621</td>
</tr>
<tr class="even">
<td align="center">Klebsiella</td>
<td align="center">0.8033058</td>
<td align="center">0.9074380</td>
<td align="center">0.9826446</td>
<td align="center">0.8148760</td>
<td align="center">0.8933884</td>
<td align="center">0.9809917</td>
</tr>
<tr class="odd">
<td align="center">Staphylococcus</td>
<td align="center">0.7915115</td>
<td align="center">0.8804914</td>
<td align="center">0.9791512</td>
<td align="center">0.7949091</td>
<td align="center">0.8825455</td>
<td align="center">0.9800000</td>
</tr>
<tr class="even">
<td align="center">Streptococcus</td>
<td align="center">0.5295508</td>
<td align="center">0.5343691</td>
<td align="center">0.0000000</td>
<td align="center">0.5295508</td>
<td align="center">0.5343691</td>
</tr>
</tbody>
</table>
@ -1260,7 +1258,7 @@ therapies very easily:</p>
classes, use a antibiotic class selector such as
<code><a href="../reference/antibiotic_class_selectors.html">penicillins()</a></code>, which automatically will include the columns
<code>AMX</code> and <code>AMC</code> of our data:</p>
<div class="sourceCode" id="cb30"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb29"><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>
<span> <span class="co"># group by hospital</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">hospital</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
@ -1280,29 +1278,29 @@ classes, use a antibiotic class selector such as
<tbody>
<tr class="odd">
<td align="left">Hospital A</td>
<td align="right">54.3%</td>
<td align="right">26.9%</td>
<td align="right">54.0%</td>
<td align="right">25.7%</td>
</tr>
<tr class="even">
<td align="left">Hospital B</td>
<td align="right">55.9%</td>
<td align="right">55.1%</td>
<td align="right">26.8%</td>
</tr>
<tr class="odd">
<td align="left">Hospital C</td>
<td align="right">53.5%</td>
<td align="right">25.5%</td>
<td align="right">54.1%</td>
<td align="right">26.3%</td>
</tr>
<tr class="even">
<td align="left">Hospital D</td>
<td align="right">52.4%</td>
<td align="right">25.9%</td>
<td align="right">55.4%</td>
<td align="right">26.4%</td>
</tr>
</tbody>
</table>
<p>To make a transition to the next part, let’s see how differences in
the previously calculated combination therapies could be plotted:</p>
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb30"><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>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</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="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span></span>
@ -1327,7 +1325,7 @@ the previously calculated combination therapies could be plotted:</p>
<code>ggplot2</code> package. This package lets you create plots in
layers. You can read more about it <a href="https://ggplot2.tidyverse.org/" class="external-link">on their website</a>. A quick
example would look like these syntaxes:</p>
<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span></span>
<span> data <span class="op">=</span> <span class="va">a_data_set</span>,</span>
<span> mapping <span class="op">=</span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span></span>
@ -1351,7 +1349,7 @@ example would look like these syntaxes:</p>
automatically transforms data with <code><a href="../reference/count.html">count_df()</a></code> or
<code><a href="../reference/proportion.html">proportion_df()</a></code> and show results in stacked bars. Its
simplest and shortest example:</p>
<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb32"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</span><span class="va">data_1st</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="fu"><a href="../reference/ggplot_rsi.html">geom_rsi</a></span><span class="op">(</span>translate_ab <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_files/figure-html/plot%203-1.png" width="720"></p>
@ -1361,7 +1359,7 @@ codes (AMX, AMC, CIP, GEN) translated to official WHO names
gentamicin).</p>
<p>If we group on e.g. the <code>genus</code> column and add some
additional functions from our package, we can create this:</p>
<div class="sourceCode" id="cb34"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb33"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># group the data on `genus`</span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/ggplot.html" class="external-link">ggplot</a></span><span class="op">(</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://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</span><span class="op">)</span> <span class="op">+</span></span>
<span> <span class="co"># create bars with genus on x axis</span></span>
@ -1387,7 +1385,7 @@ additional functions from our package, we can create this:</p>
<p><img src="AMR_files/figure-html/plot%204-1.png" width="720"></p>
<p>To simplify this, we also created the <code><a href="../reference/ggplot_rsi.html">ggplot_rsi()</a></code>
function, which combines almost all above functions:</p>
<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb34"><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>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/group_by.html" class="external-link">group_by</a></span><span class="op">(</span><span class="va">genus</span><span class="op">)</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/ggplot_rsi.html">ggplot_rsi</a></span><span class="op">(</span></span>
@ -1408,31 +1406,31 @@ disk diffusion diameters (created with <code><a href="../reference/as.disk.html"
<p>With the <code><a href="../reference/random.html">random_mic()</a></code> and <code><a href="../reference/random.html">random_disk()</a></code>
functions, we can generate sampled values for the new data types (S3
classes) <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code>:</p>
<div class="sourceCode" id="cb36"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb35"><pre class="downlit sourceCode r">
<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] 0.001 &gt;=256 &gt;=256 0.25 0.25 0.25 0.0625 &gt;=256 0.025 0.25 </span></span>
<span><span class="co"># [11] 64 0.001 4 &gt;=256 0.005 128 0.5 0.005 &gt;=256 64 </span></span>
<span><span class="co"># [21] 0.025 &gt;=256 0.01 &gt;=256 64 8 &gt;=256 4 0.01 4 </span></span>
<span><span class="co"># [31] 0.001 64 0.125 2 0.002 0.002 2 0.125 128 0.5 </span></span>
<span><span class="co"># [41] 16 0.001 1 32 0.125 0.25 0.025 0.025 0.005 128 </span></span>
<span><span class="co"># [51] 0.01 0.125 0.01 128 2 &gt;=256 0.001 &gt;=256 0.25 0.125 </span></span>
<span><span class="co"># [61] 0.125 32 0.25 0.5 8 0.01 4 0.001 1 0.002 </span></span>
<span><span class="co"># [71] 0.002 0.025 0.025 1 4 0.5 0.5 2 64 0.025 </span></span>
<span><span class="co"># [81] 0.025 0.005 0.005 0.5 &gt;=256 64 0.0625 0.5 0.005 1 </span></span>
<span><span class="co"># [91] 4 0.002 0.5 0.01 0.001 0.5 4 16 32 128</span></span></code></pre></div>
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<span><span class="co"># [1] 128 0.002 4 64 64 0.125 1 256 32 0.001 </span></span>
<span><span class="co"># [11] 32 0.5 1 4 0.25 8 4 0.005 16 256 </span></span>
<span><span class="co"># [21] 16 16 128 0.125 0.125 16 0.25 4 0.005 2 </span></span>
<span><span class="co"># [31] 0.25 1 2 0.01 0.5 256 8 0.025 0.125 0.125 </span></span>
<span><span class="co"># [41] 8 0.5 8 0.5 0.25 1 0.001 256 1 64 </span></span>
<span><span class="co"># [51] 0.01 0.001 1 0.25 0.125 32 4 16 8 0.001 </span></span>
<span><span class="co"># [61] 256 0.025 16 0.01 0.25 64 64 128 0.25 1 </span></span>
<span><span class="co"># [71] 0.025 256 0.001 0.5 0.001 64 0.5 64 32 0.025 </span></span>
<span><span class="co"># [81] 0.125 0.002 0.005 2 8 256 16 8 16 0.002 </span></span>
<span><span class="co"># [91] 128 0.0625 256 256 0.005 0.25 0.005 0.125 64 0.5</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>
<p><img src="AMR_files/figure-html/mic_plots-1.png" width="720"></p>
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb37"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># ggplot2:</span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
<p><img src="AMR_files/figure-html/mic_plots-2.png" width="720"></p>
<p>But we could also be more specific, by generating MICs that are
likely to be found in <em>E. coli</em> for ciprofloxacin:</p>
<div class="sourceCode" id="cb39"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb38"><pre class="downlit sourceCode r">
<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>, 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>
<p>For the <code><a href="../reference/plot.html">plot()</a></code> and <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> function, we
can define the microorganism and an antimicrobial agent the same way.
@ -1441,32 +1439,32 @@ guidelines (defaults to the latest EUCAST guideline).</p>
<p>Default colours are colour-blind friendly, while maintaining the
convention that e.g. ‘susceptible’ should be green and ‘resistant’
should be red:</p>
<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb39"><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>, 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>
<p><img src="AMR_files/figure-html/mic_plots_mo_ab-1.png" width="720"></p>
<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb40"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># ggplot2:</span></span>
<span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span><span class="va">mic_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>
<p><img src="AMR_files/figure-html/mic_plots_mo_ab-2.png" width="720"></p>
<p>For disk diffusion values, there is not much of a difference in
plotting:</p>
<div class="sourceCode" id="cb42"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb41"><pre class="downlit sourceCode r">
<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] 30 31 31 26 17 19 19 22 23 25 19 21 29 29 19 19 23 22 28 28 22 28 25 22 21</span></span>
<span><span class="co"># [26] 22 25 24 29 24 19 29 21 25 27 28 20 31 19 21 25 30 22 30 29 23 19 26 23 20</span></span>
<span><span class="co"># [51] 28 24 31 31 22 22 30 30 29 25 24 29 27 24 29 21 17 18 30 19 26 21 18 30 19</span></span>
<span><span class="co"># [76] 28 29 21 25 30 28 31 22 22 27 31 23 30 20 29 23 29 28 31 28 20 26 20 20 25</span></span></code></pre></div>
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<span><span class="co"># [1] 29 30 18 31 18 23 29 17 27 28 31 18 17 21 20 18 30 17 17 21 20 31 24 19 23</span></span>
<span><span class="co"># [26] 20 24 28 23 30 26 24 19 21 17 21 21 21 25 25 29 19 25 29 21 17 21 28 18 26</span></span>
<span><span class="co"># [51] 30 27 19 27 19 17 21 24 25 21 21 19 23 31 25 22 24 22 28 23 29 28 24 19 28</span></span>
<span><span class="co"># [76] 21 22 17 31 26 24 26 20 18 26 30 17 18 22 30 28 30 23 18 28 29 30 26 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>
<p><img src="AMR_files/figure-html/disk_plots-1.png" width="720"></p>
<p>And when using the <code>ggplot2</code> package, but now choosing the
latest implemented CLSI guideline (notice that the EUCAST-specific term
“Susceptible, incr. exp.” has changed to “Intermediate”):</p>
<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb43"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span></span>
<span> <span class="va">disk_values</span>,</span>
<span> mo <span class="op">=</span> <span class="st">"E. coli"</span>,</span>
@ -1487,7 +1485,7 @@ can be used to practise AMR data analysis.</p>
<code>FOS</code>) between an ICU and other clinical wards. The input for
the <code><a href="https://rdrr.io/r/stats/fisher.test.html" class="external-link">fisher.test()</a></code> can be retrieved with a transformation
like this:</p>
<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb44"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># use package 'tidyr' to pivot data:</span></span>
<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://tidyr.tidyverse.org" class="external-link">tidyr</a></span><span class="op">)</span></span>
<span></span>
@ -1508,7 +1506,7 @@ like this:</p>
<span><span class="co"># [1,] 396 942</span></span>
<span><span class="co"># [2,] 184 240</span></span></code></pre></div>
<p>We can apply the test now with:</p>
<div class="sourceCode" id="cb46"><pre class="downlit sourceCode r">
<div class="sourceCode" id="cb45"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># do Fisher's Exact Test</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/stats/fisher.test.html" class="external-link">fisher.test</a></span><span class="op">(</span><span class="va">check_FOS</span><span class="op">)</span></span>
<span><span class="co"># </span></span>

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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-5.1.3/bootstrap.min.css" rel="stylesheet">
<script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet">
<script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/font.css" rel="stylesheet">
<!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous">
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous">
<!-- bootstrap-toc --><script src="https://cdn.rawgit.com/afeld/bootstrap-toc/v1.0.1/dist/bootstrap-toc.min.js"></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="">1.8.2.9052</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9053</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">

66
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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-5.1.3/bootstrap.min.css" rel="stylesheet">
<script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.2/font.css" rel="stylesheet">
<script src="../deps/bootstrap-5.1.3/bootstrap.bundle.min.js"></script><link href="../deps/Fira_Code-0.4.4/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="">1.8.2.9052</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9053</small>
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@ -299,8 +299,8 @@ on this data set, we get:</p>
<code class="sourceCode R"><span><span class="va">example_isolates</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/mdro.html">mdro</a></span><span class="op">(</span><span class="op">)</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="https://msberends.github.io/cleaner/reference/freq.html" class="external-link">freq</a></span><span class="op">(</span><span class="op">)</span> <span class="co"># show frequency table of the result</span></span>
<span><span class="co"># Warning: in `mdro()`: NA introduced for isolates where the available percentage of</span></span>
<span><span class="co"># antimicrobial classes was below 50% (set with `pct_required_classes`)</span></span></code></pre></div>
<span><span class="co"># Warning: in mdro(): NA introduced for isolates where the available percentage of</span></span>
<span><span class="co"># antimicrobial classes was below 50% (set with pct_required_classes)</span></span></code></pre></div>
<p>(16 isolates had no test results)</p>
<p><strong>Frequency table</strong></p>
<p>Class: factor &gt; ordered (numeric)<br>
@ -375,17 +375,17 @@ 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 S R S I S R</span></span>
<span><span class="co"># 2 R I R S R I</span></span>
<span><span class="co"># 3 S I S R S I</span></span>
<span><span class="co"># 4 I I I I R R</span></span>
<span><span class="co"># 5 S I R S I I</span></span>
<span><span class="co"># 6 R R S S R I</span></span>
<span><span class="co"># 1 S I S I R R</span></span>
<span><span class="co"># 2 S R I S R S</span></span>
<span><span class="co"># 3 I S R I R R</span></span>
<span><span class="co"># 4 S S S S I R</span></span>
<span><span class="co"># 5 R S I R R S</span></span>
<span><span class="co"># 6 R R R I R S</span></span>
<span><span class="co"># kanamycin</span></span>
<span><span class="co"># 1 R</span></span>
<span><span class="co"># 2 I</span></span>
<span><span class="co"># 3 R</span></span>
<span><span class="co"># 4 S</span></span>
<span><span class="co"># 1 I</span></span>
<span><span class="co"># 2 R</span></span>
<span><span class="co"># 3 S</span></span>
<span><span class="co"># 4 I</span></span>
<span><span class="co"># 5 R</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
@ -395,7 +395,7 @@ use:</p>
<p>or its shortcut <code><a href="../reference/mdro.html">mdr_tb()</a></code>:</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">my_TB_data</span><span class="op">$</span><span class="va">mdr</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/mdro.html">mdr_tb</a></span><span class="op">(</span><span class="va">my_TB_data</span><span class="op">)</span></span>
<span><span class="co"># ℹ No column found as input for `col_mo`, assuming all rows contain</span></span>
<span><span class="co"># ℹ No column found as input for col_mo, assuming all rows contain</span></span>
<span><span class="co"># Mycobacterium tuberculosis.</span></span></code></pre></div>
<p>Create a frequency table of the results:</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
@ -428,40 +428,40 @@ Unique: 5</p>
<tr class="odd">
<td align="left">1</td>
<td align="left">Mono-resistant</td>
<td align="right">3220</td>
<td align="right">64.40%</td>
<td align="right">3220</td>
<td align="right">64.40%</td>
<td align="right">3125</td>
<td align="right">62.50%</td>
<td align="right">3125</td>
<td align="right">62.50%</td>
</tr>
<tr class="even">
<td align="left">2</td>
<td align="left">Negative</td>
<td align="right">1018</td>
<td align="right">20.36%</td>
<td align="right">4238</td>
<td align="right">84.76%</td>
<td align="right">1008</td>
<td align="right">20.16%</td>
<td align="right">4133</td>
<td align="right">82.66%</td>
</tr>
<tr class="odd">
<td align="left">3</td>
<td align="left">Multi-drug-resistant</td>
<td align="right">403</td>
<td align="right">8.06%</td>
<td align="right">4641</td>
<td align="right">92.82%</td>
<td align="right">506</td>
<td align="right">10.12%</td>
<td align="right">4639</td>
<td align="right">92.78%</td>
</tr>
<tr class="even">
<td align="left">4</td>
<td align="left">Poly-resistant</td>
<td align="right">258</td>
<td align="right">5.16%</td>
<td align="right">4899</td>
<td align="right">97.98%</td>
<td align="right">259</td>
<td align="right">5.18%</td>
<td align="right">4898</td>
<td align="right">97.96%</td>
</tr>
<tr class="odd">
<td align="left">5</td>
<td align="left">Extensively drug-resistant</td>
<td align="right">101</td>
<td align="right">2.02%</td>
<td align="right">102</td>
<td align="right">2.04%</td>
<td align="right">5000</td>
<td align="right">100.00%</td>
</tr>

4
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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="">1.8.2.9052</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9053</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="">1.8.2.9052</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9053</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -168,7 +168,7 @@
<h4 data-toc-skip class="author">Dr. Matthijs
Berends</h4>
<h4 data-toc-skip class="date">17 November 2022</h4>
<h4 data-toc-skip class="date">24 November 2022</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>
@ -247,7 +247,7 @@ 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">470,620
online community for programmers. At the time of writing, <a href="https://stackoverflow.com/questions/tagged/r?sort=votes" class="external-link">471,510
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

4
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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9053</small>
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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">17 November 2022</h4>
<h4 data-toc-skip class="date">24 November 2022</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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@ -38,7 +38,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9052</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9053</small>
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@ -272,8 +272,7 @@ is enormous:</p>
<code class="sourceCode R"><span><span class="va">example_isolates</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="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</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/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"binomial"</span><span class="op">)</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/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></span></code></pre></div>
<span> <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-6-1.png" width="720"></p>
<p>Vancomycin resistance could be 100% in ten years, but might remain
very low.</p>
@ -325,8 +324,7 @@ model might be more appropriate:</p>
<code class="sourceCode R"><span><span class="va">example_isolates</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="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="va">mo</span>, language <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Gram-positive"</span><span class="op">)</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/resistance_predict.html">resistance_predict</a></span><span class="op">(</span>col_ab <span class="op">=</span> <span class="st">"VAN"</span>, year_min <span class="op">=</span> <span class="fl">2010</span>, info <span class="op">=</span> <span class="cn">FALSE</span>, model <span class="op">=</span> <span class="st">"linear"</span><span class="op">)</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/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co"># ℹ Using column 'date' as input for `col_date`.</span></span></code></pre></div>
<span> <span class="fu"><a href="../reference/resistance_predict.html">ggplot_rsi_predict</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p><img src="resistance_predict_files/figure-html/unnamed-chunk-7-1.png" width="720"></p>
<p>The model itself is also available from the object, as an
<code>attribute</code>:</p>

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