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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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Conduct AMR Analysis
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<img src="logo.svg" class="logo" alt=""><h1 id="the-amr-package-for-r-">The <code>AMR</code> Package for R
<a class="anchor" aria-label="anchor" href="#the-amr-package-for-r-"></a>
</h1>
</div>
<ul>
<li>Provides an <strong>all-in-one solution</strong> for AMR data analysis in a One Health approach</li>
<li>Generates <strong>antibiograms</strong> - traditional, combined, syndromic, and even WISCA</li>
<li>Provides the <strong>full microbiological taxonomy</strong> and data on <strong>all antimicrobial drugs</strong>
</li>
<li>Applies all recent <strong>CLSI and EUCAST clinical and veterinary breakpoints</strong> for MICs and disk zones</li>
<li>Corrects for duplicate isolates, <strong>calculates and predicts AMR</strong> per antibiotic class</li>
<li>Integrates with <strong>WHONET</strong>, ATC, <strong>EARS-Net</strong>, PubChem, <strong>LOINC</strong> and <strong>SNOMED CT</strong>
</li>
<li>Works on Windows, macOS and Linux with <strong>all versions of R</strong> since R-3.0 and is completely <strong>dependency-free</strong>, highly suitable for places with <strong>limited resources</strong>
</li>
</ul>
<div style="display: flex; font-size: 0.8em;">
<p style="text-align:left; width: 50%;">
<small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small>
</p>
<p style="text-align:right; width: 50%;">
<small><a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">https://doi.org/10.18637/jss.v104.i03</a></small>
</p>
</div>
<hr>
<div class="section level3">
<h3 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
</h3>
<p>The <code>AMR</code> package is a <a href="#copyright">free and open-source</a> R package with <a href="https://en.wikipedia.org/wiki/Dependency_hell" class="external-link">zero dependencies</a> to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. <strong>Our aim is to provide a standard</strong> for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. <a href="./authors.html">Many different researchers</a> from around the globe are continually helping us to make this a successful and durable project!</p>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <a href="https://doi.org/10.18637/jss.v104.i03" class="external-link">DOI 10.18637/jss.v104.i03</a>) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">DOI 10.33612/diss.177417131</a> and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">DOI 10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~52,000 distinct microbial species</strong></a> (updated December 2022) and all <a href="./reference/antibiotics.html"><strong>~600 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI and EUCAST are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <a href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
<div class="section level5">
<h5 id="used-in-over-175-countries-translated-into-20-languages">Used in over 175 countries, translated into 20 languages<a class="anchor" aria-label="anchor" href="#used-in-over-175-countries-translated-into-20-languages"></a>
</h5>
<p><a href="./countries_large.png"><img src="./countries.png" target="_blank" align="right" style="max-width: 300px;"></a></p>
<p>Since its first public release in early 2018, this R package has been used in almost all countries in the world. Click the map to enlarge and to see the country names.</p>
<p>With the help of contributors from all corners of the world, the <code>AMR</code> package is available in <img src="lang_en.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> English, <img src="lang_cs.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Czech, <img src="lang_zh.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Chinese, <img src="lang_da.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Dutch, <img src="lang_fi.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Finnish, <img src="lang_fr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> German, <img src="lang_el.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Greek, <img src="lang_it.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Italian, <img src="lang_ja.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Japanese, <img src="lang_no.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Norwegian, <img src="lang_pl.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Polish, <img src="lang_pt.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Portuguese, <img src="lang_ro.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Romanian, <img src="lang_ru.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Spanish, <img src="lang_sv.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Swedish, <img src="lang_tr.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Turkish, and <img src="lang_uk.svg" style="height: 13px !important; border: 1px solid #cccccc; vertical-align: initial !important;"> Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
</div>
</div>
<div class="section level3">
<h3 id="practical-examples">Practical examples<a class="anchor" aria-label="anchor" href="#practical-examples"></a>
</h3>
<div class="section level4">
<h4 id="filtering-and-selecting-data">Filtering and selecting data<a class="anchor" aria-label="anchor" href="#filtering-and-selecting-data"></a>
</h4>
<p>One of the most powerful functions of this package, aside from calculating and plotting AMR, is selecting and filtering based on antibiotic columns. This can be done using the so-called <a href="https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html">antibiotic class selectors</a> that work in base R, <code>dplyr</code> and <code>data.table</code>:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># AMR works great with dplyr, but it's not required or neccesary</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://msberends.github.io/AMR/">AMR</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://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span></span>
<span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span>bacteria <span class="op">=</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># filtering functions for microorganisms:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># antibiotic selectors:</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>
<span> <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p>With only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><a href="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><a href="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><a href="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><a href="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <a href="./reference/microorganisms.html">all microorganisms</a> and <a href="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<table class="table">
<thead><tr class="header">
<th align="left">bacteria</th>
<th align="center">GEN</th>
<th align="center">TOB</th>
<th align="center">AMK</th>
<th align="center">KAN</th>
<th align="center">IPM</th>
<th align="center">MEM</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="odd">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">I</td>
<td align="center">S</td>
<td align="center"></td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center"></td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left"><em>Stenotrophomonas maltophilia</em></td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
<td align="center">R</td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="odd">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center"></td>
<td align="center">S</td>
</tr>
<tr class="even">
<td align="left"><em>Pseudomonas aeruginosa</em></td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">S</td>
<td align="center">R</td>
<td align="center">S</td>
<td align="center">S</td>
</tr>
</tbody>
</table>
<p>A base R equivalent would be:</p>
<div class="sourceCode" id="cb2"><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://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
<span><span class="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op">&lt;-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</span><span class="va">mo</span><span class="op">)</span></span>
<span><span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="reference/mo_property.html">mo_is_gram_negative</a></span><span class="op">(</span><span class="op">)</span> <span class="op">&amp;</span></span>
<span> <span class="fu"><a href="reference/mo_property.html">mo_is_intrinsic_resistant</a></span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"cefotax"</span><span class="op">)</span><span class="op">)</span>,</span>
<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">"bacteria"</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></code></pre></div>
<p>This base R code will work in any version of R since April 2013 (R-3.0). Moreover, this code works identically with the <code>data.table</code> package, only by starting with:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op">&lt;-</span> <span class="fu">data.table</span><span class="fu">::</span><span class="fu"><a href="https://rdatatable.gitlab.io/data.table/reference/as.data.table.html" class="external-link">as.data.table</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level4">
<h4 id="generating-antibiograms">Generating antibiograms<a class="anchor" aria-label="anchor" href="#generating-antibiograms"></a>
</h4>
<p>The <code>AMR</code> package supports generating traditional, combined, syndromic, and even weighted-incidence syndromic combination antibiograms (WISCA).</p>
<p>If used inside R Markdown or Quarto, the table will be printed in the right output format automatically (such as markdown, LaTeX, HTML, etc.).</p>
<div class="sourceCode" id="cb4"><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/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">Pathogen (N min-max)</th>
<th align="right">AMK</th>
<th align="right">GEN</th>
<th align="right">IPM</th>
<th align="right">KAN</th>
<th align="right">MEM</th>
<th align="right">TOB</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">CoNS (43-309)</td>
<td align="right">0</td>
<td align="right">86</td>
<td align="right">52</td>
<td align="right">0</td>
<td align="right">52</td>
<td align="right">22</td>
</tr>
<tr class="even">
<td align="left">
<em>E. coli</em> (0-462)</td>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">97</td>
</tr>
<tr class="odd">
<td align="left">
<em>E. faecalis</em> (0-39)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">100</td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">
<em>K. pneumoniae</em> (0-58)</td>
<td align="right"></td>
<td align="right">90</td>
<td align="right">100</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">90</td>
</tr>
<tr class="odd">
<td align="left">
<em>P. aeruginosa</em> (17-30)</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">
<em>P. mirabilis</em> (0-34)</td>
<td align="right"></td>
<td align="right">94</td>
<td align="right">94</td>
<td align="right"></td>
<td align="right"></td>
<td align="right">94</td>
</tr>
<tr class="odd">
<td align="left">
<em>S. aureus</em> (2-233)</td>
<td align="right"></td>
<td align="right">99</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">98</td>
</tr>
<tr class="even">
<td align="left">
<em>S. epidermidis</em> (8-163)</td>
<td align="right">0</td>
<td align="right">79</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">51</td>
</tr>
<tr class="odd">
<td align="left">
<em>S. hominis</em> (3-80)</td>
<td align="right"></td>
<td align="right">92</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">85</td>
</tr>
<tr class="even">
<td align="left">
<em>S. pneumoniae</em> (11-117)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right"></td>
<td align="right">0</td>
</tr>
</tbody>
</table>
<p>In combination antibiograms, it is clear that combined antibiotics yield higher empiric coverage:</p>
<div class="sourceCode" id="cb5"><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="st">"TZP"</span>, <span class="st">"TZP+TOB"</span>, <span class="st">"TZP+GEN"</span><span class="op">)</span>,</span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">Pathogen (N min-max)</th>
<th align="right">TZP</th>
<th align="right">TZP + GEN</th>
<th align="right">TZP + TOB</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Gram-negative (641-693)</td>
<td align="right">88</td>
<td align="right">99</td>
<td align="right">98</td>
</tr>
<tr class="even">
<td align="left">Gram-positive (345-1044)</td>
<td align="right">86</td>
<td align="right">98</td>
<td align="right">95</td>
</tr>
</tbody>
</table>
<p>Like many other functions in this package, <code><a href="reference/antibiogram.html">antibiogram()</a></code> comes with support for 20 languages that are often detected automatically based on system language:</p>
<div class="sourceCode" id="cb6"><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="st">"cipro"</span>, <span class="st">"tobra"</span>, <span class="st">"genta"</span><span class="op">)</span>, <span class="co"># any arbitrary name or code will work</span></span>
<span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span>,</span>
<span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span>
<span> language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">Збудник (N min-max)</th>
<th align="right">Гентаміцин</th>
<th align="right">Тобраміцин</th>
<th align="right">Ципрофлоксацин</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Грамнегативні (684-686)</td>
<td align="right">96</td>
<td align="right">96</td>
<td align="right">91</td>
</tr>
<tr class="even">
<td align="left">Грампозитивні (665-1170)</td>
<td align="right">63</td>
<td align="right">34</td>
<td align="right">77</td>
</tr>
</tbody>
</table>
</div>
<div class="section level4">
<h4 id="calculating-resistance-per-group">Calculating resistance per group<a class="anchor" aria-label="anchor" href="#calculating-resistance-per-group"></a>
</h4>
<p>For a manual approach, you can use the <code>resistance</code> or <code><a href="reference/proportion.html">susceptibility()</a></code> function:</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># group by ward:</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">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># calculate AMR using resistance() for gentamicin and tobramycin</span></span>
<span> <span class="co"># and get their 95% confidence intervals using sir_confidence_interval():</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</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="va">GEN</span>, <span class="va">TOB</span><span class="op">)</span>,</span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>total_R <span class="op">=</span> <span class="va">resistance</span>,</span>
<span> conf_int <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="reference/proportion.html">sir_confidence_interval</a></span><span class="op">(</span><span class="va">x</span>, collapse <span class="op">=</span> <span class="st">"-"</span><span class="op">)</span><span class="op">)</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="center">ward</th>
<th align="center">GEN_total_R</th>
<th align="center">GEN_conf_int</th>
<th align="center">TOB_total_R</th>
<th align="center">TOB_conf_int</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="center">Clinical</td>
<td align="center">0.229</td>
<td align="center">0.205-0.254</td>
<td align="center">0.315</td>
<td align="center">0.284-0.347</td>
</tr>
<tr class="even">
<td align="center">ICU</td>
<td align="center">0.290</td>
<td align="center">0.253-0.330</td>
<td align="center">0.400</td>
<td align="center">0.353-0.449</td>
</tr>
<tr class="odd">
<td align="center">Outpatient</td>
<td align="center">0.200</td>
<td align="center">0.131-0.285</td>
<td align="center">0.368</td>
<td align="center">0.254-0.493</td>
</tr>
</tbody>
</table>
<p>Or use <a href="https://msberends.github.io/AMR/reference/antibiotic_class_selectors.html">antibiotic class selectors</a> to select a series of antibiotic columns:</p>
<div class="sourceCode" id="cb8"><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://msberends.github.io/AMR/">AMR</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://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
<span></span>
<span><span class="va">out</span> <span class="op">&lt;-</span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># group by ward:</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">ward</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span>
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides and polymyxins:</span></span>
<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise.html" class="external-link">summarise</a></span><span class="op">(</span><span class="fu"><a href="https://dplyr.tidyverse.org/reference/across.html" class="external-link">across</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="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="reference/antibiotic_class_selectors.html">polymyxins</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span>
<span> <span class="va">resistance</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="va">out</span></span></code></pre></div>
<table class="table">
<thead><tr class="header">
<th align="left">ward</th>
<th align="right">GEN</th>
<th align="right">TOB</th>
<th align="right">AMK</th>
<th align="right">KAN</th>
<th align="right">COL</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Clinical</td>
<td align="right">0.229</td>
<td align="right">0.315</td>
<td align="right">0.626</td>
<td align="right">1</td>
<td align="right">0.780</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="right">0.290</td>
<td align="right">0.400</td>
<td align="right">0.662</td>
<td align="right">1</td>
<td align="right">0.857</td>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="right">0.200</td>
<td align="right">0.368</td>
<td align="right">0.605</td>
<td align="right"></td>
<td align="right">0.889</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic columns to names:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="17%">
<col width="17%">
<col width="17%">
<col width="14%">
<col width="16%">
<col width="16%">
</colgroup>
<thead><tr class="header">
<th align="left">ward</th>
<th align="right">gentamicin</th>
<th align="right">tobramycin</th>
<th>amikacin</th>
<th align="right">kanamycin</th>
<th align="right">colistin</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Clinical</td>
<td align="right">0.229</td>
<td align="right">0.315</td>
<td>0.626</td>
<td align="right">1</td>
<td align="right">0.780</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="right">0.290</td>
<td align="right">0.400</td>
<td>0.662</td>
<td align="right">1</td>
<td align="right">0.857</td>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="right">0.200</td>
<td align="right">0.368</td>
<td>0.605</td>
<td align="right"></td>
<td align="right">0.889</td>
</tr>
</tbody>
</table>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># transform the antibiotic column to ATC codes:</span></span>
<span><span class="va">out</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> <span class="fu"><a href="reference/ab_property.html">set_ab_names</a></span><span class="op">(</span>property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></code></pre></div>
<table class="table">
<colgroup>
<col width="17%">
<col width="17%">
<col width="17%">
<col width="14%">
<col width="16%">
<col width="16%">
</colgroup>
<thead><tr class="header">
<th align="left">ward</th>
<th align="right">J01GB03</th>
<th align="right">J01GB01</th>
<th>J01GB06</th>
<th align="right">J01GB04</th>
<th align="right">J01XB01</th>
</tr></thead>
<tbody>
<tr class="odd">
<td align="left">Clinical</td>
<td align="right">0.229</td>
<td align="right">0.315</td>
<td>0.626</td>
<td align="right">1</td>
<td align="right">0.780</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="right">0.290</td>
<td align="right">0.400</td>
<td>0.662</td>
<td align="right">1</td>
<td align="right">0.857</td>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="right">0.200</td>
<td align="right">0.368</td>
<td>0.605</td>
<td align="right"></td>
<td align="right">0.889</td>
</tr>
</tbody>
</table>
</div>
</div>
<div class="section level3">
<h3 id="what-else-can-you-do-with-this-package">What else can you do with this package?<a class="anchor" aria-label="anchor" href="#what-else-can-you-do-with-this-package"></a>
</h3>
<p>This package was intended as a comprehensive toolbox for integrated AMR data analysis. This package can be used for:</p>
<ul>
<li>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature (<a href="(https://lpsn.dsmz.de)" class="external-link">LPSN</a>) and the Global Biodiversity Information Facility (<a href="https://www.gbif.org" class="external-link">GBIF</a>) (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline (<a href="./reference/as.sir.html">manual</a>)</li>
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<a href="./reference/ab_from_text.html">manual</a>)</li>
<li>Determining first isolates to be used for AMR data analysis (<a href="./reference/first_isolate.html">manual</a>)</li>
<li>Calculating antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO) (<a href="./articles/MDR.html">tutorial</a>)</li>
<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Predicting future antimicrobial resistance using regression models (<a href="./articles/resistance_predict.html">tutorial</a>)</li>
<li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Getting properties for any antibiotic (like name, code of EARS-Net/ATC/LOINC/PubChem, defined daily dose or trade name) (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Plotting antimicrobial resistance (<a href="./articles/AMR.html">tutorial</a>)</li>
<li>Applying EUCAST expert rules (<a href="./reference/eucast_rules.html">manual</a>)</li>
<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<a href="./reference/mo_property.html">manual</a>)</li>
<li>Getting LOINC codes of an antibiotic, or getting properties of an antibiotic based on a LOINC code (<a href="./reference/ab_property.html">manual</a>)</li>
<li>Machine reading the EUCAST and CLSI guidelines from 2011-2021 to translate MIC values and disk diffusion diameters to SIR (<a href="./articles/datasets.html">link</a>)</li>
<li>Principal component analysis for AMR (<a href="./articles/PCA.html">tutorial</a>)</li>
</ul>
</div>
<div class="section level3">
<h3 id="get-this-package">Get this package<a class="anchor" aria-label="anchor" href="#get-this-package"></a>
</h3>
<div class="section level4">
<h4 id="latest-official-version">Latest official version<a class="anchor" aria-label="anchor" href="#latest-official-version"></a>
</h4>
<p><a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://www.r-pkg.org/badges/version-ago/AMR" alt="CRAN"></a> <a href="https://cran.r-project.org/package=AMR" class="external-link"><img src="https://cranlogs.r-pkg.org/badges/grand-total/AMR" alt="CRANlogs"></a></p>
<p>This package is available <a href="https://cran.r-project.org/package=AMR" class="external-link">here on the official R network (CRAN)</a>. Install this package in R from CRAN by using the command:</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"AMR"</span><span class="op">)</span></span></code></pre></div>
<p>It will be downloaded and installed automatically. For RStudio, click on the menu <em>Tools</em> &gt; <em>Install Packages…</em> and then type in “AMR” and press <kbd>Install</kbd>.</p>
<p><strong>Note:</strong> Not all functions on this website may be available in this latest release. To use all functions and data sets mentioned on this website, install the latest development version.</p>
</div>
<div class="section level4">
<h4 id="latest-development-version">Latest development version<a class="anchor" aria-label="anchor" href="#latest-development-version"></a>
</h4>
<p><a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/check-old/badge.svg?branch=main" alt="check-recent"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://github.com/msberends/AMR/workflows/check-recent/badge.svg?branch=main" alt="check-recent"></a> <a href="https://www.codefactor.io/repository/github/msberends/amr" class="external-link"><img src="https://www.codefactor.io/repository/github/msberends/amr/badge" alt="CodeFactor"></a> <a href="https://codecov.io/gh/msberends/AMR?branch=main" class="external-link"><img src="https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg" alt="Codecov"></a></p>
<p>Please read our <a href="https://github.com/msberends/AMR/wiki/Developer-Guideline" class="external-link">Developer Guideline here</a>.</p>
<p>The latest and unpublished development version can be installed from GitHub in two ways:</p>
<ol style="list-style-type: decimal">
<li>
<p>Manually, using:</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/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span> <span class="co"># if you haven't already</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"msberends/AMR"</span><span class="op">)</span></span></code></pre></div>
</li>
<li>
<p>Automatically, using the <a href="https://ropensci.org/r-universe/" class="external-link">rOpenSci R-universe platform</a>, by adding <a href="https://msberends.r-universe.dev" class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">options</a></span><span class="op">(</span>repos <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="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"repos"</span><span class="op">)</span>,</span>
<span> msberends <span class="op">=</span> <span class="st">"https://msberends.r-universe.dev"</span><span class="op">)</span><span class="op">)</span></span></code></pre></div>
<p>After this, you can install and update this <code>AMR</code> package like any official release (e.g., using <code>install.packages("AMR")</code> or in RStudio via <em>Tools</em> &gt; <em>Check for Package Updates…</em>).</p>
</li>
</ol>
</div>
</div>
<div class="section level3">
<h3 id="get-started">Get started<a class="anchor" aria-label="anchor" href="#get-started"></a>
</h3>
<p>To find out how to conduct AMR data analysis, please <a href="./articles/AMR.html">continue reading here to get started</a> or click a link in the <a href="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
</div>
<div class="section level3">
<h3 id="partners">Partners<a class="anchor" aria-label="anchor" href="#partners"></a>
</h3>
<p>The development of this package is part of, related to, or made possible by the following non-profit organisations and initiatives:</p>
<div align="center">
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.svg" style="max-width: 200px;"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.svg" style="max-width: 200px;"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.svg" style="max-width: 200px;"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" style="max-width: 200px;"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" style="max-width: 200px;"></a></p>
</div>
</div>
<div class="section level3">
<h3 id="copyright">Copyright<a class="anchor" aria-label="anchor" href="#copyright"></a>
</h3>
<p>This R package is free, open-source software and licensed under the <a href="./LICENSE-text.html">GNU General Public License v2.0 (GPL-2)</a>. In a nutshell, this means that this package:</p>
<ul>
<li><p>May be used for commercial purposes</p></li>
<li><p>May be used for private purposes</p></li>
<li><p>May <strong>not</strong> be used for patent purposes</p></li>
<li>
<p>May be modified, although:</p>
<ul>
<li>Modifications <strong>must</strong> be released under the same license when distributing the package</li>
<li>Changes made to the code <strong>must</strong> be documented</li>
</ul>
</li>
<li>
<p>May be distributed, although:</p>
<ul>
<li>Source code <strong>must</strong> be made available when the package is distributed</li>
<li>A copy of the license and copyright notice <strong>must</strong> be included with the package.</li>
</ul>
</li>
<li><p>Comes with a LIMITATION of liability</p></li>
<li><p>Comes with NO warranty</p></li>
</ul>
</div>
</div>
</main><aside class="col-md-3"><div class="table-of-contents">
<h2 data-toc-skip>Table of contents</h2>
<ul class="list-unstyled">
<li><nav id="toc"></nav></li>
</ul>
</div>
<div class="links">
<h2 data-toc-skip>Links</h2>
<ul class="list-unstyled">
<li><a href="https://cloud.r-project.org/package=AMR" class="external-link">View on CRAN</a></li>
<li><a href="https://github.com/msberends/AMR/" class="external-link">Browse source code</a></li>
<li><a href="https://github.com/msberends/AMR/issues" class="external-link">Report a bug</a></li>
</ul>
</div>
<div class="developers">
<h2 data-toc-skip>Developers</h2>
<ul class="list-unstyled">
<li>Matthijs S. Berends <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0001-7620-1800" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>Dennis Souverein <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0003-0455-0336" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
<li>Erwin E. A. Hassing <br><small class="roles"> Author, contributor </small> </li>
<li><a href="authors.html">More about authors...</a></li>
</ul>
</div>
</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://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
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