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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9061</small>
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<li><a class="dropdown-item" href="../articles/AMR.html"><span class="fa fa-directions"></span> Conduct AMR Analysis</a></li>
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<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Conduct AMR data analysis</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/AMR.Rmd" class="external-link"><code>vignettes/AMR.Rmd</code></a></small>
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<div class="d-none name"><code>AMR.Rmd</code></div>
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</div>
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<p><strong>Note:</strong> values on this page will change with every
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 23 June 2026.</p>
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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<p>Conducting AMR data analysis unfortunately requires in-depth
|
||
knowledge from different scientific fields, which makes it hard to do
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right. At least, it requires:</p>
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<ul>
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<li>Good questions (always start with those!) and reliable data</li>
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<li>A thorough understanding of (clinical) epidemiology, to understand
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||
the clinical and epidemiological relevance and possible bias of
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||
results</li>
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<li>A thorough understanding of (clinical) microbiology/infectious
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diseases, to understand which microorganisms are causal to which
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infections and the implications of pharmaceutical treatment, as well as
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understanding intrinsic and acquired microbial resistance</li>
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||
<li>Experience with data analysis with microbiological tests and their
|
||
results, to understand the determination and limitations of MIC values
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||
and their interpretations to SIR values</li>
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||
<li>Availability of the biological taxonomy of microorganisms and
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||
probably normalisation factors for pharmaceuticals, such as defined
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||
daily doses (DDD)</li>
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<li>Available (inter-)national guidelines, and profound methods to apply
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them</li>
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</ul>
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<p>Of course, we cannot instantly provide you with knowledge and
|
||
experience. But with this <code>AMR</code> package, we aimed at
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providing (1) tools to simplify antimicrobial resistance data cleaning,
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transformation and analysis, (2) methods to easily incorporate
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international guidelines and (3) scientifically reliable reference data,
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including the requirements mentioned above.</p>
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<p>The <code>AMR</code> package enables standardised and reproducible
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AMR data analysis, with the application of evidence-based rules,
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determination of first isolates, translation of various codes for
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microorganisms and antimicrobial drugs, determination of (multi-drug)
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resistant microorganisms, and calculation of antimicrobial resistance,
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prevalence and future trends.</p>
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</div>
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<div class="section level2">
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<h2 id="preparation">Preparation<a class="anchor" aria-label="anchor" href="#preparation"></a>
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</h2>
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<p>For this tutorial, we will create fake demonstration data to work
|
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with.</p>
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<p>You can skip to <a href="#cleaning-the-data">Cleaning the data</a> if
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you already have your own data ready. If you start your analysis, try to
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make the structure of your data generally look like this:</p>
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||
<table class="table">
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||
<thead><tr class="header">
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<th align="center">date</th>
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<th align="center">patient_id</th>
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<th align="center">mo</th>
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<th align="center">AMX</th>
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<th align="center">CIP</th>
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</tr></thead>
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<tbody>
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<tr class="odd">
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<td align="center">2026-06-23</td>
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||
<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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||
<td align="center">S</td>
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</tr>
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<tr class="even">
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<td align="center">2026-06-23</td>
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||
<td align="center">abcd</td>
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||
<td align="center">Escherichia coli</td>
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||
<td align="center">S</td>
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||
<td align="center">R</td>
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</tr>
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<tr class="odd">
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<td align="center">2026-06-23</td>
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||
<td align="center">efgh</td>
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||
<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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||
<td align="center">S</td>
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||
</tr>
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||
</tbody>
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||
</table>
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<div class="section level3">
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<h3 id="needed-r-packages">Needed R packages<a class="anchor" aria-label="anchor" href="#needed-r-packages"></a>
|
||
</h3>
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||
<p>As with many uses in R, we need some additional packages for AMR data
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||
analysis. Our package works closely together with the <a href="https://www.tidyverse.org" class="external-link">tidyverse packages</a> <a href="https://dplyr.tidyverse.org/" class="external-link"><code>dplyr</code></a> and <a href="https://ggplot2.tidyverse.org" class="external-link"><code>ggplot2</code></a> by
|
||
RStudio. The tidyverse tremendously improves the way we conduct data
|
||
science - it allows for a very natural way of writing syntaxes and
|
||
creating beautiful plots in R.</p>
|
||
<p>We will also use the <code>cleaner</code> package, that can be used
|
||
for cleaning data and creating frequency tables.</p>
|
||
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><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://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</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://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</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://amr-for-r.org">AMR</a></span><span class="op">)</span></span>
|
||
<span></span>
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||
<span><span class="co"># (if not yet installed, install with:)</span></span>
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||
<span><span class="co"># install.packages(c("dplyr", "ggplot2", "AMR"))</span></span></code></pre></div>
|
||
<p>The <code>AMR</code> package contains a data set
|
||
<code>example_isolates_unclean</code>, which might look data that users
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||
have extracted from their laboratory systems:</p>
|
||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
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||
<code class="sourceCode R"><span><span class="va">example_isolates_unclean</span></span>
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||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 3,000 × 8</span></span></span>
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<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN </span></span>
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||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span></span></span>
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||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 E. coli R I S S </span></span>
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||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 K. pneumoniae R I S S </span></span>
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||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 E. coli R S S S </span></span>
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||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 E. coli S I S S </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 E. coli S S S S </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 S. aureus R S R S </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 E. coli R S S S </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 E. coli R S S S </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 E. coli S S S S </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 S. aureus S S S S </span></span>
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||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span>
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||
<span></span>
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||
<span><span class="co"># we will use 'our_data' as the data set name for this tutorial</span></span>
|
||
<span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">example_isolates_unclean</span></span></code></pre></div>
|
||
<p>For AMR data analysis, we would like the microorganism column to
|
||
contain valid, up-to-date taxonomy, and the antibiotic columns to be
|
||
cleaned as SIR values as well.</p>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="taxonomy-of-microorganisms">Taxonomy of microorganisms<a class="anchor" aria-label="anchor" href="#taxonomy-of-microorganisms"></a>
|
||
</h3>
|
||
<p>With <code><a href="../reference/as.mo.html">as.mo()</a></code>, users can transform arbitrary
|
||
microorganism names or codes to current taxonomy. The <code>AMR</code>
|
||
package contains up-to-date taxonomic data. To be specific, currently
|
||
included data were retrieved on 07 May 2026.</p>
|
||
<p>The codes of the AMR packages that come from <code><a href="../reference/as.mo.html">as.mo()</a></code> are
|
||
short, but still human readable. More importantly, <code><a href="../reference/as.mo.html">as.mo()</a></code>
|
||
supports all kinds of input:</p>
|
||
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> Class <span style="color: #0000BB;"><mo></span></span></span>
|
||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span>
|
||
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> Class <span style="color: #0000BB;"><mo></span></span></span>
|
||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span>
|
||
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLEPNE"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> Class <span style="color: #0000BB;"><mo></span></span></span>
|
||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span>
|
||
<span><span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"KLPN"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> Class <span style="color: #0000BB;"><mo></span></span></span>
|
||
<span><span class="co">#> [1] B_KLBSL_PNMN</span></span></code></pre></div>
|
||
<p>The first character in above codes denote their taxonomic kingdom,
|
||
such as Bacteria (B), Fungi (F), and Protozoa (P).</p>
|
||
<p>The <code>AMR</code> package also contain functions to directly
|
||
retrieve taxonomic properties, such as the name, genus, species, family,
|
||
order, and even Gram-stain. They all start with <code>mo_</code> and
|
||
they use <code><a href="../reference/as.mo.html">as.mo()</a></code> internally, so that still any arbitrary
|
||
user input can be used:</p>
|
||
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/mo_property.html">mo_family</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> [1] "Enterobacteriaceae"</span></span>
|
||
<span><span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> [1] "Klebsiella"</span></span>
|
||
<span><span class="fu"><a href="../reference/mo_property.html">mo_species</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> [1] "pneumoniae"</span></span>
|
||
<span></span>
|
||
<span><span class="fu"><a href="../reference/mo_property.html">mo_gramstain</a></span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> [1] "Gram-negative"</span></span>
|
||
<span></span>
|
||
<span><span class="fu"><a href="../reference/mo_property.html">mo_ref</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> [1] "Trevisan, 1887"</span></span>
|
||
<span></span>
|
||
<span><span class="fu"><a href="../reference/mo_property.html">mo_snomed</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span></span>
|
||
<span><span class="co">#> [[1]]</span></span>
|
||
<span><span class="co">#> [1] "1098101000112102" "446870005" "1098201000112108" "409801009" </span></span>
|
||
<span><span class="co">#> [5] "56415008" "714315002" "713926009"</span></span></code></pre></div>
|
||
<p>Now we can thus clean our data:</p>
|
||
<div class="sourceCode" id="cb5"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span> <span class="op"><-</span> <span class="fu"><a href="../reference/as.mo.html">as.mo</a></span><span class="op">(</span><span class="va">our_data</span><span class="op">$</span><span class="va">bacteria</span>, info <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Retrieved values from the `microorganisms.codes` data set for <span style="color: #0000BB;">"ESCCOL"</span>,</span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">"KLEPNE"</span>, <span style="color: #0000BB;">"STAAUR"</span>, and <span style="color: #0000BB;">"STRPNE"</span>.</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Microorganism translation was uncertain for four microorganisms. Run</span></span>
|
||
<span><span class="co">#> `mo_uncertainties()` to review these uncertainties, or use</span></span>
|
||
<span><span class="co">#> `add_custom_microorganisms()` to add custom entries.</span></span></code></pre></div>
|
||
<p>Apparently, there was some uncertainty about the translation to
|
||
taxonomic codes. Let’s check this:</p>
|
||
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span>
|
||
<span><span class="co">#> Matching scores are based on the resemblance between the input and the full</span></span>
|
||
<span><span class="co">#> taxonomic name, and the pathogenicity in humans. See `mo_matching_score()`.</span></span>
|
||
<span><span class="co">#> Colour keys: <span style="color: #080808; background-color: #FF5F5F;"> 0.000-0.549 </span><span style="color: #080808; background-color: #FFD787;"> 0.550-0.649 </span><span style="color: #080808; background-color: #FFFF87;"> 0.650-0.749 </span><span style="color: #080808; background-color: #5FD7AF;"> 0.750-1.000 </span></span></span>
|
||
<span><span class="co">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">"E. coli"</span> -> <span style="font-weight: bold; font-style: italic;">Escherichia coli</span> (B_ESCHR_COLI, <span style="color: #080808; background-color: #FFFF87;">0.688</span>)</span></span>
|
||
<span><span class="co">#> Also matched: <span style="font-style: italic;">Enterococcus crotali</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.650</span>), <span style="font-style: italic;">Escherichia coli coli</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>),</span></span>
|
||
<span><span class="co">#> <span style="font-style: italic;">Escherichia coli expressing</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.611</span>), <span style="font-style: italic;">Enterobacter cowanii</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.600</span>), <span style="font-style: italic;">Enterococcus</span></span></span>
|
||
<span><span class="co">#> <span style="font-style: italic;">columbae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Enterococcus camelliae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.591</span>), <span style="font-style: italic;">Enterococcus casseliflavus</span></span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.577</span>), <span style="font-style: italic;">Enterobacter cloacae cloacae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), <span style="font-style: italic;">Enterobacter cloacae</span> complex</span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), and <span style="font-style: italic;">Enterobacter cloacae dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</span>)</span></span>
|
||
<span><span class="co">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">"K. pneumoniae"</span> -> <span style="font-weight: bold; font-style: italic;">Klebsiella pneumoniae</span> (B_KLBSL_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.786</span>)</span></span>
|
||
<span><span class="co">#> Also matched: <span style="font-style: italic;">Klebsiella pneumoniae</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae</span></span></span>
|
||
<span><span class="co">#> <span style="font-style: italic;">ozaenae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae pneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.688</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
|
||
<span><span class="co">#> <span style="font-style: italic;">pneumoniae rhinoscleromatis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.658</span>), <span style="font-style: italic;">Klebsiella pasteurii</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
|
||
<span><span class="co">#> <span style="font-style: italic;">planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Kosakonia pseudosacchari</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.471</span>), <span style="font-style: italic;">Kaistella palustris</span></span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.435</span>), <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.435</span>), and <span style="font-style: italic;">Kocuria palustris</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.435</span>)</span></span>
|
||
<span><span class="co">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">"S. aureus"</span> -> <span style="font-weight: bold; font-style: italic;">Staphylococcus aureus</span> (B_STPHY_AURS, <span style="color: #080808; background-color: #FFFF87;">0.690</span>)</span></span>
|
||
<span><span class="co">#> Also matched: <span style="font-style: italic;">Staphylococcus aureus aureus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>), <span style="font-style: italic;">Staphylococcus argenteus</span></span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.625</span>), <span style="font-style: italic;">Staphylococcus aureus anaerobius</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.625</span>), <span style="font-style: italic;">Streptomyces aureus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.618</span>),</span></span>
|
||
<span><span class="co">#> <span style="font-style: italic;">Staphylococcus auricularis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.615</span>), <span style="font-style: italic;">Streptomyces azureus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.609</span>), <span style="font-style: italic;">Salmonella</span></span></span>
|
||
<span><span class="co">#> Aurelianis<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.595</span>), <span style="font-style: italic;">Salmonella</span> Aarhus<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.588</span>), <span style="font-style: italic;">Salmonella</span> Amounderness<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>),</span></span>
|
||
<span><span class="co">#> and <span style="font-style: italic;">Staphylococcus argensis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.587</span>)</span></span>
|
||
<span><span class="co">#> <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">"S. pneumoniae"</span> -> <span style="font-weight: bold; font-style: italic;">Streptococcus pneumoniae</span> (B_STRPT_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.750</span>)</span></span>
|
||
<span><span class="co">#> Also matched: <span style="font-style: italic;">Streptococcus parapneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.714</span>), <span style="font-style: italic;">Streptococcus</span></span></span>
|
||
<span><span class="co">#> <span style="font-style: italic;">pseudopneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.700</span>), <span style="font-style: italic;">Serratia proteamaculans quinivorans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.557</span>),</span></span>
|
||
<span><span class="co">#> <span style="font-style: italic;">Streptococcus phocae salmonis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.552</span>), <span style="font-style: italic;">Serratia proteamaculans quinovora</span></span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.545</span>), <span style="font-style: italic;">Sphingomonas piscinae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.538</span>), <span style="font-style: italic;">Streptococcus pseudoporcinus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.536</span>),</span></span>
|
||
<span><span class="co">#> <span style="font-style: italic;">Staphylococcus piscifermentans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.533</span>), <span style="font-style: italic;">Staphylococcus pseudintermedius</span></span></span>
|
||
<span><span class="co">#> <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.532</span>), and <span style="font-style: italic;">Serratia proteamaculans proteamaculans</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.526</span>)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Only the first 10 other matches of each record are shown. Run ``</span></span>
|
||
<span><span class="co">#> `print(mo_uncertainties(), n = ...)` `` to view more entries, or save</span></span>
|
||
<span><span class="co">#> `mo_uncertainties()` to an object.</span></span></code></pre></div>
|
||
<p>That’s all good.</p>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="antibiotic-results">Antibiotic results<a class="anchor" aria-label="anchor" href="#antibiotic-results"></a>
|
||
</h3>
|
||
<p>The column with antibiotic test results must also be cleaned. The
|
||
<code>AMR</code> package comes with three new data types to work with
|
||
such test results: <code>mic</code> for minimal inhibitory
|
||
concentrations (MIC), <code>disk</code> for disk diffusion diameters,
|
||
and <code>sir</code> for SIR data that have been interpreted already.
|
||
This package can also determine SIR values based on MIC or disk
|
||
diffusion values, read more about that on the <code><a href="../reference/as.sir.html">as.sir()</a></code>
|
||
page.</p>
|
||
<p>For now, we will just clean the SIR columns in our data using
|
||
dplyr:</p>
|
||
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="co"># method 1, be explicit about the columns:</span></span>
|
||
<span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_at</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/vars.html" class="external-link">vars</a></span><span class="op">(</span><span class="va">AMX</span><span class="op">:</span><span class="va">GEN</span><span class="op">)</span>, <span class="va">as.sir</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="co"># method 2, let the AMR package determine the eligible columns</span></span>
|
||
<span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate_all.html" class="external-link">mutate_if</a></span><span class="op">(</span><span class="va">is_sir_eligible</span>, <span class="va">as.sir</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="co"># result:</span></span>
|
||
<span><span class="va">our_data</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 3,000 × 8</span></span></span>
|
||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN </span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> J8 A 2016-06-14 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> M3 A 2015-10-25 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> J3 A 2019-06-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> G6 A 2015-04-27 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,990 more rows</span></span></span></code></pre></div>
|
||
<p>This is basically it for the cleaning, time to start the data
|
||
inclusion.</p>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="first-isolates">First isolates<a class="anchor" aria-label="anchor" href="#first-isolates"></a>
|
||
</h3>
|
||
<p>We need to know which isolates we can <em>actually</em> use for
|
||
analysis without repetition bias.</p>
|
||
<p>To conduct an analysis of antimicrobial resistance, you must <a href="https:/pubmed.ncbi.nlm.nih.gov/17304462/">only include the first
|
||
isolate of every patient per episode</a> (Hindler <em>et al.</em>, Clin
|
||
Infect Dis. 2007). If you would not do this, you could easily get an
|
||
overestimate or underestimate of the resistance of an antibiotic.
|
||
Imagine that a patient was admitted with an MRSA and that it was found
|
||
in 5 different blood cultures the following weeks (yes, some countries
|
||
like the Netherlands have these blood drawing policies). The resistance
|
||
percentage of oxacillin of all isolates would be overestimated, because
|
||
you included this MRSA more than once. It would clearly be <a href="https://en.wikipedia.org/wiki/Selection_bias" class="external-link">selection
|
||
bias</a>.</p>
|
||
<p>The Clinical and Laboratory Standards Institute (CLSI) appoints this
|
||
as follows:</p>
|
||
<blockquote>
|
||
<p><em>(…) When preparing a cumulative antibiogram to guide clinical
|
||
decisions about empirical antimicrobial therapy of initial infections,
|
||
<strong>only the first isolate of a given species per patient, per
|
||
analysis period (eg, one year) should be included, irrespective of body
|
||
site, antimicrobial susceptibility profile, or other phenotypical
|
||
characteristics (eg, biotype)</strong>. The first isolate is easily
|
||
identified, and cumulative antimicrobial susceptibility test data
|
||
prepared using the first isolate are generally comparable to cumulative
|
||
antimicrobial susceptibility test data calculated by other methods,
|
||
providing duplicate isolates are excluded.</em> <br><a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">M39-A4
|
||
Analysis and Presentation of Cumulative Antimicrobial Susceptibility
|
||
Test Data, 4th Edition. CLSI, 2014. Chapter 6.4</a></p>
|
||
</blockquote>
|
||
<p>This <code>AMR</code> package includes this methodology with the
|
||
<code><a href="../reference/first_isolate.html">first_isolate()</a></code> function and is able to apply the four
|
||
different methods as defined by <a href="https://academic.oup.com/cid/article/44/6/867/364325" class="external-link">Hindler
|
||
<em>et al.</em> in 2007</a>: phenotype-based, episode-based,
|
||
patient-based, isolate-based. The right method depends on your goals and
|
||
analysis, but the default phenotype-based method is in any case the
|
||
method to properly correct for most duplicate isolates. Read more about
|
||
the methods on the <code><a href="../reference/first_isolate.html">first_isolate()</a></code> page.</p>
|
||
<p>The outcome of the function can easily be added to our data:</p>
|
||
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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">#> <span style="color: #00BBBB;">ℹ</span> Determining first isolates using an episode length of <span style="font-weight: bold;">365 days</span></span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">bacteria</span> as input for `col_mo`.</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Column <span style="color: #00BB00; font-weight: bold;">first</span> is SIR eligible (despite only having empty values), since it</span></span>
|
||
<span><span class="co">#> seems to be cefozopran (ZOP)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">date</span> as input for `col_date`.</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Using column <span style="color: #00BB00; font-weight: bold;">patient_id</span> as input for `col_patient_id`.</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> Basing inclusion on all antimicrobial results, using a points threshold of 2</span></span>
|
||
<span><span class="co">#> => Found <span style="font-weight: bold;">2,724 'phenotype-based' first isolates</span> (90.8% of total where a</span></span>
|
||
<span><span class="co">#> microbial ID was available)</span></span></code></pre></div>
|
||
<p>So only 91% 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="cb9"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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="va">first</span> <span class="op">==</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
|
||
<p>For future use, the above two syntaxes can be shortened:</p>
|
||
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><-</span> <span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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 2 724 isolates for analysis. Now our data looks
|
||
like:</p>
|
||
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">our_data_1st</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 9</span></span></span>
|
||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J3 A 2012-11-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R7 A 2018-04-03 <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> P3 A 2014-09-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> P10 A 2015-12-10 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B7 A 2015-03-02 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> W3 A 2018-03-31 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> M3 A 2015-10-25 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> J3 A 2019-06-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> G6 A 2015-04-27 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> P4 A 2011-06-21 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span></code></pre></div>
|
||
<p>Time for the analysis.</p>
|
||
</div>
|
||
</div>
|
||
<div class="section level2">
|
||
<h2 id="analysing-the-data">Analysing the data<a class="anchor" aria-label="anchor" href="#analysing-the-data"></a>
|
||
</h2>
|
||
<p>The base R <code><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary()</a></code> function gives a good first
|
||
impression, as it comes with support for the new <code>mo</code> and
|
||
<code>sir</code> classes that we now have in our data set:</p>
|
||
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/summary.html" class="external-link">summary</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
|
||
<span><span class="co">#> patient_id hospital date bacteria </span></span>
|
||
<span><span class="co">#> Length :2724 Length :2724 Min. :2011-01-01 Class :mo </span></span>
|
||
<span><span class="co">#> N.unique : 260 N.unique : 3 1st Qu.:2013-04-07 <NA> :0 </span></span>
|
||
<span><span class="co">#> N.blank : 0 N.blank : 0 Median :2015-06-03 Unique:4 </span></span>
|
||
<span><span class="co">#> Min.nchar: 2 Min.nchar: 1 Mean :2015-06-09 #1 :B_ESCHR_COLI </span></span>
|
||
<span><span class="co">#> Max.nchar: 3 Max.nchar: 1 3rd Qu.:2017-08-11 #2 :B_STPHY_AURS </span></span>
|
||
<span><span class="co">#> Max. :2019-12-27 #3 :B_STRPT_PNMN </span></span>
|
||
<span><span class="co">#> AMX AMC CIP </span></span>
|
||
<span><span class="co">#> Class:sir Class:sir Class:sir </span></span>
|
||
<span><span class="co">#> %S :41.6% (n=1133) %S :52.6% (n=1432) %S :52.5% (n=1431) </span></span>
|
||
<span><span class="co">#> %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) %SDD : 0.0% (n=0) </span></span>
|
||
<span><span class="co">#> %I :16.4% (n=446) %I :12.2% (n=333) %I : 6.5% (n=176) </span></span>
|
||
<span><span class="co">#> %R :42.0% (n=1145) %R :35.2% (n=959) %R :41.0% (n=1117) </span></span>
|
||
<span><span class="co">#> %NI : 0.0% (n=0) %NI : 0.0% (n=0) %NI : 0.0% (n=0) </span></span>
|
||
<span><span class="co">#> GEN first </span></span>
|
||
<span><span class="co">#> Class:sir Mode:logical </span></span>
|
||
<span><span class="co">#> %S :61.0% (n=1661) TRUE:2724 </span></span>
|
||
<span><span class="co">#> %SDD : 0.0% (n=0) </span></span>
|
||
<span><span class="co">#> %I : 3.0% (n=82) </span></span>
|
||
<span><span class="co">#> %R :36.0% (n=981) </span></span>
|
||
<span><span class="co">#> %NI : 0.0% (n=0)</span></span>
|
||
<span></span>
|
||
<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">our_data_1st</span><span class="op">)</span></span>
|
||
<span><span class="co">#> Rows: 2,724</span></span>
|
||
<span><span class="co">#> Columns: 9</span></span>
|
||
<span><span class="co">#> $ patient_id <span style="color: #949494; font-style: italic;"><chr></span> "J3"<span style="color: #949494;">, </span>"R7"<span style="color: #949494;">, </span>"P3"<span style="color: #949494;">, </span>"P10"<span style="color: #949494;">, </span>"B7"<span style="color: #949494;">, </span>"W3"<span style="color: #949494;">, </span>"M3"<span style="color: #949494;">, </span>"J3"<span style="color: #949494;">, </span>"G6"<span style="color: #949494;">, </span>"P4"…</span></span>
|
||
<span><span class="co">#> $ hospital <span style="color: #949494; font-style: italic;"><chr></span> "A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">, </span>"A"<span style="color: #949494;">,</span>…</span></span>
|
||
<span><span class="co">#> $ date <span style="color: #949494; font-style: italic;"><date></span> 2012-11-21<span style="color: #949494;">, </span>2018-04-03<span style="color: #949494;">, </span>2014-09-19<span style="color: #949494;">, </span>2015-12-10<span style="color: #949494;">, </span>2015-03-02…</span></span>
|
||
<span><span class="co">#> $ bacteria <span style="color: #949494; font-style: italic;"><mo></span> "B_ESCHR_COLI"<span style="color: #949494;">, </span>"B_KLBSL_PNMN"<span style="color: #949494;">, </span>"B_ESCHR_COLI"<span style="color: #949494;">, </span>"B_ESCHR_COL…</span></span>
|
||
<span><span class="co">#> $ AMX <span style="color: #949494; font-style: italic;"><sir></span> R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">,</span>…</span></span>
|
||
<span><span class="co">#> $ AMC <span style="color: #949494; font-style: italic;"><sir></span> I<span style="color: #949494;">, </span>I<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>I<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">,</span>…</span></span>
|
||
<span><span class="co">#> $ CIP <span style="color: #949494; font-style: italic;"><sir></span> S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">,</span>…</span></span>
|
||
<span><span class="co">#> $ GEN <span style="color: #949494; font-style: italic;"><sir></span> S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>R<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">, </span>S<span style="color: #949494;">,</span>…</span></span>
|
||
<span><span class="co">#> $ first <span style="color: #949494; font-style: italic;"><lgl></span> TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">, </span>TRUE<span style="color: #949494;">,</span>…</span></span>
|
||
<span></span>
|
||
<span><span class="co"># number of unique values per column:</span></span>
|
||
<span><span class="fu"><a href="https://rdrr.io/r/base/lapply.html" class="external-link">sapply</a></span><span class="op">(</span><span class="va">our_data_1st</span>, <span class="va">n_distinct</span><span class="op">)</span></span>
|
||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP </span></span>
|
||
<span><span class="co">#> 260 3 1854 4 3 3 3 </span></span>
|
||
<span><span class="co">#> GEN first </span></span>
|
||
<span><span class="co">#> 3 1</span></span></code></pre></div>
|
||
<div class="section level3">
|
||
<h3 id="availability-of-species">Availability of species<a class="anchor" aria-label="anchor" href="#availability-of-species"></a>
|
||
</h3>
|
||
<p>To just get an idea how the species are distributed, create a
|
||
frequency table with <code><a href="../reference/count.html">count()</a></code> based on the name of the
|
||
microorganisms:</p>
|
||
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">our_data</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||
<span> <span class="fu"><a href="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
|
||
<span><span class="co">#> `mo_name(bacteria)` n</span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>518</span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 730</span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 426</span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 326</span></span>
|
||
<span></span>
|
||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||
<span> <span class="fu"><a href="../reference/count.html">count</a></span><span class="op">(</span><span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="va">bacteria</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 2</span></span></span>
|
||
<span><span class="co">#> `mo_name(bacteria)` n</span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> Escherichia coli <span style="text-decoration: underline;">1</span>321</span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> Staphylococcus aureus 682</span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> Streptococcus pneumoniae 402</span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 319</span></span></code></pre></div>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="select-and-filter-with-antibiotic-selectors">Select and filter with antibiotic selectors<a class="anchor" aria-label="anchor" href="#select-and-filter-with-antibiotic-selectors"></a>
|
||
</h3>
|
||
<p>Using so-called antibiotic class selectors, you can select or filter
|
||
columns based on the antibiotic class that your antibiotic results are
|
||
in:</p>
|
||
<div class="sourceCode" id="cb14"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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">date</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column <span style="color: #00BB00; font-weight: bold;">GEN</span></span></span>
|
||
<span><span class="co">#> (gentamicin)</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 2</span></span></span>
|
||
<span><span class="co">#> date GEN </span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 2012-11-21 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 2018-04-03 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2014-09-19 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2015-12-10 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2015-03-02 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2018-03-31 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2015-10-25 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2019-06-19 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2015-04-27 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2011-06-21 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||
<span></span>
|
||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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/antimicrobial_selectors.html">betalactams</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span>
|
||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 3</span></span></span>
|
||
<span><span class="co">#> bacteria AMX AMC </span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||
<span></span>
|
||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</span><span class="op">)</span><span class="op">)</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,724 × 5</span></span></span>
|
||
<span><span class="co">#> bacteria AMX AMC CIP GEN </span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>KLBSL<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #AFFFD7;"> I </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 2,714 more rows</span></span></span>
|
||
<span></span>
|
||
<span><span class="co"># filtering using AB selectors is also possible:</span></span>
|
||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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/antimicrobial_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>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using column <span style="color: #00BB00; font-weight: bold;">GEN</span></span></span>
|
||
<span><span class="co">#> (gentamicin)</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 981 × 9</span></span></span>
|
||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> J5 A 2017-12-25 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> X1 A 2017-07-04 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> B3 A 2016-07-24 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> V7 A 2012-04-03 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> C9 A 2017-03-23 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> R1 A 2018-06-10 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> S2 A 2013-07-19 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> P5 A 2019-03-09 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> Q8 A 2019-08-10 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> K5 A 2013-03-15 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 971 more rows</span></span></span>
|
||
<span></span>
|
||
<span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</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>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span>
|
||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> N3 A 2014-12-29 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 452 more rows</span></span></span>
|
||
<span></span>
|
||
<span><span class="co"># even works in base R (since R 3.0):</span></span>
|
||
<span><span class="va">our_data_1st</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">betalactams</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>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `betalactams()` using columns <span style="color: #00BB00; font-weight: bold;">AMX</span> (amoxicillin) and <span style="color: #00BB00; font-weight: bold;">AMC</span></span></span>
|
||
<span><span class="co">#> (amoxicillin/clavulanic acid)</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 462 × 9</span></span></span>
|
||
<span><span class="co">#> patient_id hospital date bacteria AMX AMC CIP GEN first</span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><lgl></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> M7 A 2013-07-22 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> R10 A 2013-12-20 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> R7 A 2015-10-25 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> R8 A 2019-10-25 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> B6 A 2016-11-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> I7 A 2015-08-19 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> N3 A 2014-12-29 <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> Q2 A 2019-09-22 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> X7 A 2011-03-20 <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> V1 A 2018-08-07 <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> TRUE </span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 452 more rows</span></span></span></code></pre></div>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="generate-antibiograms">Generate antibiograms<a class="anchor" aria-label="anchor" href="#generate-antibiograms"></a>
|
||
</h3>
|
||
<p>The <code>AMR</code> package supports 28 different languages for
|
||
antibiograms and provides four types, as proposed by Klinker <em>et
|
||
al.</em> (2021, <a href="https://doi.org/10.1177/20499361211011373" class="external-link">DOI
|
||
10.1177/20499361211011373</a>):</p>
|
||
<ol style="list-style-type: decimal">
|
||
<li>
|
||
<strong>Traditional Antibiogram (TA)</strong> – susceptibility of a
|
||
species to individual antibiotics</li>
|
||
<li>
|
||
<strong>Combination Antibiogram (CA)</strong> – susceptibility of a
|
||
species to combination regimens</li>
|
||
<li>
|
||
<strong>Syndromic Antibiogram (SA)</strong> – susceptibility of a
|
||
species, stratified by clinical syndrome or setting</li>
|
||
<li>
|
||
<strong>Weighted-Incidence Syndromic Combination Antibiogram
|
||
(WISCA)</strong> – estimated empirical coverage of a <em>regimen</em>
|
||
for a <em>syndrome</em>, weighted by pathogen incidence and with
|
||
quantified uncertainty</li>
|
||
</ol>
|
||
<p><strong>If your goal is to guide empirical therapy, WISCA should be
|
||
your default.</strong> The reason is simple: when you start empirical
|
||
treatment, you do not know which pathogen is causing the infection. Your
|
||
next patient will not present with a species label attached to them.
|
||
What matters is the probability that the <em>regimen</em> you choose
|
||
will cover <em>whatever pathogen turns out to be the cause</em>, given
|
||
the local epidemiology of the syndrome. Traditional antibiograms do not
|
||
answer that question. They fragment information by species, ignore how
|
||
frequently each species causes the syndrome, do not evaluate combination
|
||
regimens, and provide no measure of uncertainty. WISCA addresses all of
|
||
these limitations using a Bayesian framework (Hebert <em>et al.</em>,
|
||
2012; Bielicki <em>et al.</em>, 2016). See the <a href="https://amr-for-r.org/articles/WISCA.html">WISCA vignette</a> for
|
||
the full explanation.</p>
|
||
<p>Traditional, combination, and syndromic antibiograms remain useful
|
||
for <strong>surveillance</strong> purposes, i.e., tracking resistance
|
||
trends per species over time. But if you care about clinical impact,
|
||
about choosing the right empirical regimen for your patient, use
|
||
WISCA.</p>
|
||
<p>For starters, this is what the included <code>example_isolates</code>
|
||
data set looks like:</p>
|
||
<div class="sourceCode" id="cb15"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">example_isolates</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span></span>
|
||
<span><span class="co">#> date patient age gender ward mo PEN OXA FLC AMX </span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> <span style="color: #949494;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FF5F5F;"> R </span> <span style="color: #949494;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #949494;"> NA</span> </span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 1,990 more rows</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span></span></code></pre></div>
|
||
<div class="section level4">
|
||
<h4 id="wisca-recommended-for-empirical-therapy-guidance">WISCA (recommended for empirical therapy guidance)<a class="anchor" aria-label="anchor" href="#wisca-recommended-for-empirical-therapy-guidance"></a>
|
||
</h4>
|
||
<p>Use the <code><a href="../reference/antibiogram.html">wisca()</a></code> function, or equivalently
|
||
<code>antibiogram(..., wisca = TRUE)</code>. WISCA produces a single
|
||
coverage estimate per regimen for the entire syndrome, weighted by
|
||
pathogen incidence, with a 95% credible interval from Bayesian Monte
|
||
Carlo simulation:</p>
|
||
<div class="sourceCode" id="cb16"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">wisca_result</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||
<span> <span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span></span>
|
||
<span> antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
|
||
<span> minimum <span class="op">=</span> <span class="fl">10</span></span>
|
||
<span> <span class="op">)</span> <span class="co"># Recommended threshold: ≥30</span></span>
|
||
<span><span class="va">wisca_result</span></span></code></pre></div>
|
||
<table style="width:100%;" class="table">
|
||
<colgroup>
|
||
<col width="24%">
|
||
<col width="37%">
|
||
<col width="37%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="left">Piperacillin/tazobactam</th>
|
||
<th align="left">Piperacillin/tazobactam + Gentamicin</th>
|
||
<th align="left">Piperacillin/tazobactam + Tobramycin</th>
|
||
</tr></thead>
|
||
<tbody><tr class="odd">
|
||
<td align="left">70.2% (64.8-75.2%)</td>
|
||
<td align="left">93.6% (92.2-95%)</td>
|
||
<td align="left">89.9% (87-92.3%)</td>
|
||
</tr></tbody>
|
||
</table>
|
||
<p>The output tells you: <em>“given the species distribution in your
|
||
data, there is an estimated X% probability that this regimen covers the
|
||
infection, with 95% credible interval [lower, upper]”</em>. That is the
|
||
clinically relevant question.</p>
|
||
<p>For <strong>syndrome-specific</strong> or <strong>patient-specific
|
||
WISCA</strong>, use the <code>syndromic_group</code> argument or group
|
||
your data first. You can stratify by anything: ward, age group, risk
|
||
profile, acquisition type. The <code>syndromic_group</code> argument
|
||
accepts any column or expression:</p>
|
||
<div class="sourceCode" id="cb17"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">wisca_out</span> <span class="op"><-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||
<span> <span class="fu"><a href="../reference/top_n_microorganisms.html">top_n_microorganisms</a></span><span class="op">(</span>n <span class="op">=</span> <span class="fl">10</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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>
|
||
<span> age_group <span class="op">=</span> <span class="fu"><a href="../reference/age_groups.html">age_groups</a></span><span class="op">(</span><span class="va">age</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fl">25</span>, <span class="fl">50</span>, <span class="fl">75</span><span class="op">)</span><span class="op">)</span>,</span>
|
||
<span> <span class="va">gender</span></span>
|
||
<span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span>
|
||
<span> <span class="fu"><a href="../reference/antibiogram.html">wisca</a></span><span class="op">(</span>antimicrobials <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="va">wisca_out</span></span></code></pre></div>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="8%">
|
||
<col width="6%">
|
||
<col width="20%">
|
||
<col width="32%">
|
||
<col width="32%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="left">age_group</th>
|
||
<th align="left">gender</th>
|
||
<th align="left">Piperacillin/tazobactam</th>
|
||
<th align="left">Piperacillin/tazobactam + Gentamicin</th>
|
||
<th align="left">Piperacillin/tazobactam + Tobramycin</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="left">0-24</td>
|
||
<td align="left">F</td>
|
||
<td align="left">56.8% (29.9-81.3%)</td>
|
||
<td align="left">70.7% (45.2-89%)</td>
|
||
<td align="left">65.9% (42.3-86.6%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">0-24</td>
|
||
<td align="left">M</td>
|
||
<td align="left">59.5% (31.2-85.5%)</td>
|
||
<td align="left">76.1% (56.5-92%)</td>
|
||
<td align="left">59.6% (31.7-85.1%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">25-49</td>
|
||
<td align="left">F</td>
|
||
<td align="left">67.7% (43.9-89.7%)</td>
|
||
<td align="left">93.8% (87.4-98.1%)</td>
|
||
<td align="left">87% (70.1-97%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">25-49</td>
|
||
<td align="left">M</td>
|
||
<td align="left">56.9% (26.6-86.2%)</td>
|
||
<td align="left">91% (82-97.2%)</td>
|
||
<td align="left">76.6% (51.4-93.5%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">50-74</td>
|
||
<td align="left">F</td>
|
||
<td align="left">68% (54.1-81.8%)</td>
|
||
<td align="left">96.9% (94.6-98.5%)</td>
|
||
<td align="left">90.2% (82-96.2%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">50-74</td>
|
||
<td align="left">M</td>
|
||
<td align="left">67% (56-78.5%)</td>
|
||
<td align="left">96.7% (94.1-98.5%)</td>
|
||
<td align="left">86.7% (77.3-94.4%)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">75+</td>
|
||
<td align="left">F</td>
|
||
<td align="left">73.1% (61.8-84.1%)</td>
|
||
<td align="left">97.7% (95.9-99%)</td>
|
||
<td align="left">92.8% (85.7-97.2%)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">75+</td>
|
||
<td align="left">M</td>
|
||
<td align="left">74% (63.6-82.6%)</td>
|
||
<td align="left">97.9% (96-99%)</td>
|
||
<td align="left">94.7% (89.3-97.9%)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>Keep in mind that more granular stratification produces more relevant
|
||
estimates for each subgroup, but with wider credible intervals due to
|
||
smaller sample sizes. There is always a trade-off between granularity
|
||
and precision. If local numbers are small, consider pooling data from
|
||
multiple sites (Bielicki <em>et al.</em>, 2016).</p>
|
||
<p>For reliable WISCA results, ensure your data includes <strong>only
|
||
first isolates</strong> (use <code><a href="../reference/first_isolate.html">first_isolate()</a></code>) and consider
|
||
filtering for <strong>the top <em>n</em> species</strong> (use
|
||
<code><a href="../reference/top_n_microorganisms.html">top_n_microorganisms()</a></code>), since rare contaminants can
|
||
distort coverage estimates.</p>
|
||
<p>After creating the WISCA model, assessments can be done on the
|
||
distributions of the Monte Carlo simulations that WISCA carried out:</p>
|
||
<div class="sourceCode" id="cb18"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca_plot</a></span><span class="op">(</span><span class="va">wisca_out</span><span class="op">)</span></span></code></pre></div>
|
||
<p><img src="AMR_files/figure-html/wisca_plots-1.png" class="r-plt" alt="" width="720"></p>
|
||
<div class="sourceCode" id="cb19"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">wisca_plot</a></span><span class="op">(</span><span class="va">wisca_out</span>, wisca_plot_type <span class="op">=</span> <span class="st">"posterior_coverage"</span><span class="op">)</span></span></code></pre></div>
|
||
<p><img src="AMR_files/figure-html/wisca_plots-2.png" class="r-plt" alt="" width="720"></p>
|
||
<div class="sourceCode" id="cb20"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span></span>
|
||
<span><span class="co"># a ggplot2 extension for WISCAs and other antibiograms:</span></span>
|
||
<span><span class="fu">ggplot2</span><span class="fu">::</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">wisca_out</span><span class="op">)</span></span></code></pre></div>
|
||
<p><img src="AMR_files/figure-html/wisca_plots-3.png" class="r-plt" alt="" width="720"></p>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="traditional-antibiogram">Traditional Antibiogram<a class="anchor" aria-label="anchor" href="#traditional-antibiogram"></a>
|
||
</h4>
|
||
<p>If you need per-species susceptibility rates, e.g., for AMR
|
||
surveillance reports, the traditional antibiogram remains the right
|
||
tool. It reports the proportion of susceptible isolates per species per
|
||
antibiotic:</p>
|
||
<div class="sourceCode" id="cb21"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
|
||
<span><span class="op">)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
|
||
<span><span class="co">#> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="12%">
|
||
<col width="15%">
|
||
<col width="14%">
|
||
<col width="15%">
|
||
<col width="11%">
|
||
<col width="15%">
|
||
<col width="14%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="left">Pathogen</th>
|
||
<th align="left">Amikacin</th>
|
||
<th align="left">Gentamicin</th>
|
||
<th align="left">Imipenem</th>
|
||
<th align="left">Kanamycin</th>
|
||
<th align="left">Meropenem</th>
|
||
<th align="left">Tobramycin</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="left">CoNS</td>
|
||
<td align="left">0% (0-8%,N=43)</td>
|
||
<td align="left">86% (82-90%,N=309)</td>
|
||
<td align="left">52% (37-67%,N=48)</td>
|
||
<td align="left">0% (0-8%,N=43)</td>
|
||
<td align="left">52% (37-67%,N=48)</td>
|
||
<td align="left">22% (12-35%,N=55)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>E. coli</em></td>
|
||
<td align="left">100% (98-100%,N=171)</td>
|
||
<td align="left">98% (96-99%,N=460)</td>
|
||
<td align="left">100% (99-100%,N=422)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (99-100%,N=418)</td>
|
||
<td align="left">97% (96-99%,N=462)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>E. faecalis</em></td>
|
||
<td align="left">0% (0-9%,N=39)</td>
|
||
<td align="left">0% (0-9%,N=39)</td>
|
||
<td align="left">100% (91-100%,N=38)</td>
|
||
<td align="left">0% (0-9%,N=39)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">0% (0-9%,N=39)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>K. pneumoniae</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">90% (79-96%,N=58)</td>
|
||
<td align="left">100% (93-100%,N=51)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (93-100%,N=53)</td>
|
||
<td align="left">90% (79-96%,N=58)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>P. aeruginosa</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (88-100%,N=30)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">0% (0-12%,N=30)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (88-100%,N=30)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>P. mirabilis</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">94% (80-99%,N=34)</td>
|
||
<td align="left">94% (79-99%,N=32)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">94% (80-99%,N=34)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>S. aureus</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">99% (97-100%,N=233)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">98% (92-100%,N=86)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>S. epidermidis</em></td>
|
||
<td align="left">0% (0-8%,N=44)</td>
|
||
<td align="left">79% (71-85%,N=163)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">0% (0-8%,N=44)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">51% (40-61%,N=89)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>S. hominis</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">92% (84-97%,N=80)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">85% (74-93%,N=62)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>S. pneumoniae</em></td>
|
||
<td align="left">0% (0-3%,N=117)</td>
|
||
<td align="left">0% (0-3%,N=117)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">0% (0-3%,N=117)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">0% (0-3%,N=117)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<p>Notice that the <code><a href="../reference/antibiogram.html">antibiogram()</a></code> function automatically
|
||
prints in the right format when using Quarto or R Markdown (such as this
|
||
page), and even applies italics for taxonomic names (by using
|
||
<code><a href="../reference/italicise_taxonomy.html">italicise_taxonomy()</a></code> internally).</p>
|
||
<p>It also uses the language of your OS if this is either English,
|
||
Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German,
|
||
Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish,
|
||
Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish,
|
||
Ukrainian, Urdu, or Vietnamese. In this next example, we force the
|
||
language to be Spanish using the <code>language</code> argument:</p>
|
||
<div class="sourceCode" id="cb22"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
|
||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
|
||
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
|
||
<span> language <span class="op">=</span> <span class="st">"es"</span></span>
|
||
<span><span class="op">)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
|
||
<span><span class="co">#> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span></code></pre></div>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="15%">
|
||
<col width="21%">
|
||
<col width="22%">
|
||
<col width="18%">
|
||
<col width="21%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="left">Patógeno</th>
|
||
<th align="left">Amikacina</th>
|
||
<th align="left">Gentamicina</th>
|
||
<th align="left">Kanamicina</th>
|
||
<th align="left">Tobramicina</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="left">Gram negativo</td>
|
||
<td align="left">98% (96-99%,N=256)</td>
|
||
<td align="left">96% (95-98%,N=684)</td>
|
||
<td align="left">0% (0-10%,N=35)</td>
|
||
<td align="left">96% (94-97%,N=686)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">Gram positivo</td>
|
||
<td align="left">0% (0-1%,N=436)</td>
|
||
<td align="left">63% (60-66%,N=1170)</td>
|
||
<td align="left">0% (0-1%,N=436)</td>
|
||
<td align="left">34% (31-38%,N=665)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="combination-antibiogram">Combination Antibiogram<a class="anchor" aria-label="anchor" href="#combination-antibiogram"></a>
|
||
</h4>
|
||
<p>A combination antibiogram shows how much additional susceptibility a
|
||
second agent adds for a given species. This is useful for surveillance
|
||
of combination regimens, but note that it is still species-stratified
|
||
and does not account for pathogen incidence in the syndrome:</p>
|
||
<div class="sourceCode" id="cb23"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="va">combined_ab</span> <span class="op"><-</span> <span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
|
||
<span> ab_transform <span class="op">=</span> <span class="cn">NULL</span></span>
|
||
<span><span class="op">)</span></span>
|
||
<span><span class="va">combined_ab</span></span></code></pre></div>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="21%">
|
||
<col width="26%">
|
||
<col width="26%">
|
||
<col width="26%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="left">Pathogen</th>
|
||
<th align="left">TZP</th>
|
||
<th align="left">TZP + GEN</th>
|
||
<th align="left">TZP + TOB</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="left">CoNS</td>
|
||
<td align="left">30% (16-49%,N=33)</td>
|
||
<td align="left">97% (95-99%,N=274)</td>
|
||
<td align="left">NA</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>E. coli</em></td>
|
||
<td align="left">94% (92-96%,N=416)</td>
|
||
<td align="left">100% (98-100%,N=459)</td>
|
||
<td align="left">99% (97-100%,N=461)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>K. pneumoniae</em></td>
|
||
<td align="left">89% (77-96%,N=53)</td>
|
||
<td align="left">93% (83-98%,N=58)</td>
|
||
<td align="left">93% (83-98%,N=58)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>P. aeruginosa</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (88-100%,N=30)</td>
|
||
<td align="left">100% (88-100%,N=30)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>P. mirabilis</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (90-100%,N=34)</td>
|
||
<td align="left">100% (90-100%,N=34)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>S. aureus</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (98-100%,N=231)</td>
|
||
<td align="left">100% (96-100%,N=91)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>S. epidermidis</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (97-100%,N=128)</td>
|
||
<td align="left">100% (92-100%,N=46)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left"><em>S. hominis</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (95-100%,N=74)</td>
|
||
<td align="left">100% (93-100%,N=53)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left"><em>S. pneumoniae</em></td>
|
||
<td align="left">100% (97-100%,N=112)</td>
|
||
<td align="left">100% (97-100%,N=112)</td>
|
||
<td align="left">100% (97-100%,N=112)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="syndromic-antibiogram">Syndromic Antibiogram<a class="anchor" aria-label="anchor" href="#syndromic-antibiogram"></a>
|
||
</h4>
|
||
<p>A syndromic antibiogram stratifies per-species susceptibility by
|
||
clinical context (ward, specimen type, etc.). It adds clinical context
|
||
to the traditional antibiogram but is still species-level, without
|
||
incidence weighting or uncertainty quantification. For surveillance by
|
||
setting this is fine; for empirical therapy guidance, WISCA is
|
||
preferred:</p>
|
||
<div class="sourceCode" id="cb24"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="../reference/antibiogram.html">antibiogram</a></span><span class="op">(</span><span class="va">example_isolates</span>,</span>
|
||
<span> antibiotics <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu"><a href="../reference/antimicrobial_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="../reference/antimicrobial_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
|
||
<span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span>
|
||
<span><span class="op">)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `aminoglycosides()` using columns <span style="color: #00BB00; font-weight: bold;">GEN</span> (gentamicin), <span style="color: #00BB00; font-weight: bold;">TOB</span> (tobramycin), <span style="color: #00BB00; font-weight: bold;">AMK</span></span></span>
|
||
<span><span class="co">#> (amikacin), and <span style="color: #00BB00; font-weight: bold;">KAN</span> (kanamycin)</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> For `carbapenems()` using columns <span style="color: #00BB00; font-weight: bold;">IPM</span> (imipenem) and <span style="color: #00BB00; font-weight: bold;">MEM</span> (meropenem)</span></span></code></pre></div>
|
||
<table class="table">
|
||
<colgroup>
|
||
<col width="10%">
|
||
<col width="11%">
|
||
<col width="13%">
|
||
<col width="13%">
|
||
<col width="13%">
|
||
<col width="10%">
|
||
<col width="13%">
|
||
<col width="13%">
|
||
</colgroup>
|
||
<thead><tr class="header">
|
||
<th align="left">Syndromic Group</th>
|
||
<th align="left">Pathogen</th>
|
||
<th align="left">Amikacin</th>
|
||
<th align="left">Gentamicin</th>
|
||
<th align="left">Imipenem</th>
|
||
<th align="left">Kanamycin</th>
|
||
<th align="left">Meropenem</th>
|
||
<th align="left">Tobramycin</th>
|
||
</tr></thead>
|
||
<tbody>
|
||
<tr class="odd">
|
||
<td align="left">Clinical</td>
|
||
<td align="left">CoNS</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">89% (84-93%,N=205)</td>
|
||
<td align="left">57% (39-74%,N=35)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">57% (39-74%,N=35)</td>
|
||
<td align="left">26% (12-45%,N=31)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">ICU</td>
|
||
<td align="left">CoNS</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">79% (68-88%,N=73)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">Outpatient</td>
|
||
<td align="left">CoNS</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">84% (66-95%,N=31)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">Clinical</td>
|
||
<td align="left"><em>E. coli</em></td>
|
||
<td align="left">100% (97-100%,N=104)</td>
|
||
<td align="left">98% (96-99%,N=297)</td>
|
||
<td align="left">100% (99-100%,N=266)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (99-100%,N=276)</td>
|
||
<td align="left">98% (96-99%,N=299)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">ICU</td>
|
||
<td align="left"><em>E. coli</em></td>
|
||
<td align="left">100% (93-100%,N=52)</td>
|
||
<td align="left">99% (95-100%,N=137)</td>
|
||
<td align="left">100% (97-100%,N=133)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (97-100%,N=118)</td>
|
||
<td align="left">96% (92-99%,N=137)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">Clinical</td>
|
||
<td align="left"><em>K. pneumoniae</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">92% (81-98%,N=51)</td>
|
||
<td align="left">100% (92-100%,N=44)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (92-100%,N=46)</td>
|
||
<td align="left">92% (81-98%,N=51)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">Clinical</td>
|
||
<td align="left"><em>P. mirabilis</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (88-100%,N=30)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (88-100%,N=30)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">Clinical</td>
|
||
<td align="left"><em>S. aureus</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">99% (95-100%,N=150)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">97% (89-100%,N=63)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">ICU</td>
|
||
<td align="left"><em>S. aureus</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">100% (95-100%,N=66)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">Clinical</td>
|
||
<td align="left"><em>S. epidermidis</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">82% (72-90%,N=79)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">55% (39-70%,N=44)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">ICU</td>
|
||
<td align="left"><em>S. epidermidis</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">72% (60-82%,N=75)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">41% (26-58%,N=41)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">Clinical</td>
|
||
<td align="left"><em>S. hominis</em></td>
|
||
<td align="left">NA</td>
|
||
<td align="left">96% (85-99%,N=45)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">94% (79-99%,N=31)</td>
|
||
</tr>
|
||
<tr class="odd">
|
||
<td align="left">Clinical</td>
|
||
<td align="left"><em>S. pneumoniae</em></td>
|
||
<td align="left">0% (0-5%,N=78)</td>
|
||
<td align="left">0% (0-5%,N=78)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">0% (0-5%,N=78)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">0% (0-5%,N=78)</td>
|
||
</tr>
|
||
<tr class="even">
|
||
<td align="left">ICU</td>
|
||
<td align="left"><em>S. pneumoniae</em></td>
|
||
<td align="left">0% (0-12%,N=30)</td>
|
||
<td align="left">0% (0-12%,N=30)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">0% (0-12%,N=30)</td>
|
||
<td align="left">NA</td>
|
||
<td align="left">0% (0-12%,N=30)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</div>
|
||
<div class="section level4">
|
||
<h4 id="plotting-antibiograms">Plotting antibiograms<a class="anchor" aria-label="anchor" href="#plotting-antibiograms"></a>
|
||
</h4>
|
||
<p>All antibiogram types, including WISCA, can be plotted using
|
||
<code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> from the <code>ggplot2</code> package, since
|
||
this <code>AMR</code> package provides an extension to that
|
||
function:</p>
|
||
<div class="sourceCode" id="cb25"><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 class="va">wisca_result</span><span class="op">)</span></span></code></pre></div>
|
||
<p><img src="AMR_files/figure-html/unnamed-chunk-10-1.png" class="r-plt" alt="" width="720"></p>
|
||
<p>To calculate antimicrobial resistance in a more sensible way, also by
|
||
correcting for too few results, we use the <code><a href="../reference/proportion.html">resistance()</a></code> and
|
||
<code><a href="../reference/proportion.html">susceptibility()</a></code> functions.</p>
|
||
</div>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="resistance-percentages">Resistance percentages<a class="anchor" aria-label="anchor" href="#resistance-percentages"></a>
|
||
</h3>
|
||
<p>The functions <code><a href="../reference/proportion.html">resistance()</a></code> and
|
||
<code><a href="../reference/proportion.html">susceptibility()</a></code> can be used to calculate antimicrobial
|
||
resistance or susceptibility. For more specific analyses, the functions
|
||
<code><a href="../reference/proportion.html">proportion_S()</a></code>, <code><a href="../reference/proportion.html">proportion_SI()</a></code>,
|
||
<code><a href="../reference/proportion.html">proportion_I()</a></code>, <code><a href="../reference/proportion.html">proportion_IR()</a></code> and
|
||
<code><a href="../reference/proportion.html">proportion_R()</a></code> can be used to determine the proportion of a
|
||
specific antimicrobial outcome.</p>
|
||
<p>All these functions contain a <code>minimum</code> argument, denoting
|
||
the minimum required number of test results for returning a value. These
|
||
functions will otherwise return <code>NA</code>. The default is
|
||
<code>minimum = 30</code>, following the <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">CLSI
|
||
M39-A4 guideline</a> for applying microbial epidemiology.</p>
|
||
<p>As per the EUCAST guideline of 2019, we calculate resistance as the
|
||
proportion of R (<code><a href="../reference/proportion.html">proportion_R()</a></code>, equal to
|
||
<code><a href="../reference/proportion.html">resistance()</a></code>) and susceptibility as the proportion of S and
|
||
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">
|
||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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">#> <span style="color: #00BBBB;">ℹ</span> `resistance()` assumes the EUCAST guideline and thus considers the 'I'</span></span>
|
||
<span><span class="co">#> category susceptible. Set the `guideline` argument or the `AMR_guideline`</span></span>
|
||
<span><span class="co">#> option to either "CLSI" or "EUCAST", see `?AMR-options`.</span></span>
|
||
<span><span class="co">#> <span style="color: #00BBBB;">ℹ</span> This message will be shown once per session.</span></span>
|
||
<span><span class="co">#> [1] 0.4203377</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">
|
||
<code class="sourceCode R"><span><span class="va">our_data_1st</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</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">%>%</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>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 3 × 2</span></span></span>
|
||
<span><span class="co">#> hospital amoxicillin</span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">1</span> A 0.340</span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">2</span> B 0.551</span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">3</span> C 0.370</span></span></code></pre></div>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="interpreting-mic-and-disk-diffusion-values">Interpreting MIC and Disk Diffusion Values<a class="anchor" aria-label="anchor" href="#interpreting-mic-and-disk-diffusion-values"></a>
|
||
</h3>
|
||
<p>Minimal inhibitory concentration (MIC) values and disk diffusion
|
||
diameters can be interpreted into clinical breakpoints (SIR) using
|
||
<code><a href="../reference/as.sir.html">as.sir()</a></code>. Here’s an example with randomly generated MIC
|
||
values for <em>Klebsiella pneumoniae</em> and ciprofloxacin:</p>
|
||
<div class="sourceCode" id="cb28"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Random.html" class="external-link">set.seed</a></span><span class="op">(</span><span class="fl">123</span><span class="op">)</span></span>
|
||
<span><span class="va">mic_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span></span>
|
||
<span><span class="va">sir_values</span> <span class="op"><-</span> <span class="fu"><a href="../reference/as.sir.html">as.sir</a></span><span class="op">(</span><span class="va">mic_values</span>, mo <span class="op">=</span> <span class="st">"K. pneumoniae"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, guideline <span class="op">=</span> <span class="st">"EUCAST 2024"</span><span class="op">)</span></span>
|
||
<span></span>
|
||
<span><span class="va">my_data</span> <span class="op"><-</span> <span class="fu"><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a></span><span class="op">(</span>MIC <span class="op">=</span> <span class="va">mic_values</span>, SIR <span class="op">=</span> <span class="va">sir_values</span><span class="op">)</span></span>
|
||
<span><span class="va">my_data</span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># A tibble: 100 × 2</span></span></span>
|
||
<span><span class="co">#> MIC SIR </span></span>
|
||
<span><span class="co">#> <span style="color: #949494; font-style: italic;"><mic></span> <span style="color: #949494; font-style: italic;"><sir></span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;"><=</span>0.0001 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 0.016<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">>=</span>8<span style="color: #949494;">.0000</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 0.032<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 0.008<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 64<span style="color: #949494;">.0000</span> <span style="color: #080808; background-color: #FF5F5F;"> R </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 0.008<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 0.125<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 0.032<span style="color: #949494;">0</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #BCBCBC;">10</span> 0.0002 <span style="color: #080808; background-color: #5FD7AF;"> S </span></span></span>
|
||
<span><span class="co">#> <span style="color: #949494;"># ℹ 90 more rows</span></span></span></code></pre></div>
|
||
<p>This allows direct interpretation according to EUCAST or CLSI
|
||
breakpoints, facilitating automated AMR data processing.</p>
|
||
</div>
|
||
<div class="section level3">
|
||
<h3 id="plotting-mic-and-sir-interpretations">Plotting MIC and SIR Interpretations<a class="anchor" aria-label="anchor" href="#plotting-mic-and-sir-interpretations"></a>
|
||
</h3>
|
||
<p>We can visualise MIC distributions and their SIR interpretations
|
||
using <code>ggplot2</code>, using the new <code><a href="../reference/plot.html">scale_y_mic()</a></code> for
|
||
the y-axis and <code><a href="../reference/plot.html">scale_colour_sir()</a></code> to colour-code SIR
|
||
categories.</p>
|
||
<div class="sourceCode" id="cb29"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span><span class="co"># add a group</span></span>
|
||
<span><span class="va">my_data</span><span class="op">$</span><span class="va">group</span> <span class="op"><-</span> <span class="fu"><a href="https://rdrr.io/r/base/rep.html" class="external-link">rep</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"A"</span>, <span class="st">"B"</span>, <span class="st">"C"</span>, <span class="st">"D"</span><span class="op">)</span>, each <span class="op">=</span> <span class="fl">25</span><span class="op">)</span></span>
|
||
<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>
|
||
<span> <span class="va">my_data</span>,</span>
|
||
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/aes.html" class="external-link">aes</a></span><span class="op">(</span>x <span class="op">=</span> <span class="va">group</span>, y <span class="op">=</span> <span class="va">MIC</span>, colour <span class="op">=</span> <span class="va">SIR</span><span class="op">)</span></span>
|
||
<span><span class="op">)</span> <span class="op">+</span></span>
|
||
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_jitter.html" class="external-link">geom_jitter</a></span><span class="op">(</span>width <span class="op">=</span> <span class="fl">0.2</span>, size <span class="op">=</span> <span class="fl">2</span><span class="op">)</span> <span class="op">+</span></span>
|
||
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/geom_boxplot.html" class="external-link">geom_boxplot</a></span><span class="op">(</span>fill <span class="op">=</span> <span class="cn">NA</span>, colour <span class="op">=</span> <span class="st">"grey40"</span><span class="op">)</span> <span class="op">+</span></span>
|
||
<span> <span class="fu"><a href="../reference/plot.html">scale_y_mic</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
|
||
<span> <span class="fu"><a href="../reference/plot.html">scale_colour_sir</a></span><span class="op">(</span><span class="op">)</span> <span class="op">+</span></span>
|
||
<span> <span class="fu"><a href="https://ggplot2.tidyverse.org/reference/labs.html" class="external-link">labs</a></span><span class="op">(</span></span>
|
||
<span> title <span class="op">=</span> <span class="st">"MIC Distribution and SIR Interpretation"</span>,</span>
|
||
<span> x <span class="op">=</span> <span class="st">"Sample Groups"</span>,</span>
|
||
<span> y <span class="op">=</span> <span class="st">"MIC (mg/L)"</span></span>
|
||
<span> <span class="op">)</span></span></code></pre></div>
|
||
<p><img src="AMR_files/figure-html/mic_plot-1.png" class="r-plt" alt="" width="720"></p>
|
||
<p>This plot provides an intuitive way to assess susceptibility patterns
|
||
across different groups while incorporating clinical breakpoints.</p>
|
||
<p>For a more straightforward and less manual approach,
|
||
<code>ggplot2</code>’s function <code><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot()</a></code> has been
|
||
extended by this package to directly plot MIC and disk diffusion
|
||
values:</p>
|
||
<div class="sourceCode" id="cb30"><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 class="va">mic_values</span><span class="op">)</span></span></code></pre></div>
|
||
<p><img src="AMR_files/figure-html/autoplot-1.png" class="r-plt" alt="" width="720"></p>
|
||
<div class="sourceCode" id="cb31"><pre class="downlit sourceCode r">
|
||
<code class="sourceCode R"><span></span>
|
||
<span><span class="co"># by providing `mo` and `ab`, colours will indicate the SIR interpretation:</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">"K. pneumoniae"</span>, ab <span class="op">=</span> <span class="st">"cipro"</span>, guideline <span class="op">=</span> <span class="st">"EUCAST 2024"</span><span class="op">)</span></span></code></pre></div>
|
||
<p><img src="AMR_files/figure-html/autoplot-2.png" class="r-plt" alt="" width="720"></p>
|
||
<hr>
|
||
<p><em>Author: Dr. Matthijs Berends, 23rd June 2026</em></p>
|
||
</div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||
</nav></aside>
|
||
</div>
|
||
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://amr-for-r.org/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://amr-for-r.org/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
||
</div>
|
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