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data analysis and to work with microbial and antimicrobial properties by
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using evidence-based methods, as described in <doi:10.18637/jss.v104.i03>.">
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9031</small>
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How to
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<a class="dropdown-item" href="articles/AMR.html">
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Conduct AMR analysis
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Predict antimicrobial resistance
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Conduct principal component analysis for AMR
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Determine multi-drug resistance (MDR)
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Work with WHONET data
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Import data from SPSS/SAS/Stata
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Apply EUCAST rules
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Get properties of a microorganism
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Get properties of an antibiotic
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<main id="main" class="col-md-9"><div class="section level1">
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<div class="page-header">
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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
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<a class="anchor" aria-label="anchor" href="#the-amr-package-for-r-"></a>
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</h1>
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<div class="section level3">
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<h3 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h3>
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<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.</p>
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<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>
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<p>After installing this package, R knows <a href="./reference/microorganisms.html"><strong>~49,000 distinct microbial species</strong></a> and all <a href="./reference/antibiotics.html"><strong>~570 antibiotic, antimycotic and antiviral drugs</strong></a> by name and code (including ATC, WHONET/EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net 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>, and is being <a href="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
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<div class="section level5">
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<h5 id="used-in-175-countries-translated-to-16-languages">Used in 175 countries, translated to 16 languages<a class="anchor" aria-label="anchor" href="#used-in-175-countries-translated-to-16-languages"></a>
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</h5>
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<p><a href="./countries_large.png"><img src="./countries.png" target="_blank" align="right" style="max-width: 300px;"></a></p>
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<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>
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<p>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_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_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_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_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>
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</div>
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</div>
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<div class="section level3">
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<h3 id="practical-examples">Practical examples<a class="anchor" aria-label="anchor" href="#practical-examples"></a>
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</h3>
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<div class="section level4">
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<h4 id="filtering-and-selecting-data">Filtering and selecting data<a class="anchor" aria-label="anchor" href="#filtering-and-selecting-data"></a>
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</h4>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span></span>
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<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>
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<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>
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<span></span>
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<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>
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<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">%>%</a></span></span>
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<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>
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<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">%>%</a></span></span>
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<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>
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<span> <span class="fu"><a href="reference/antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span>
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<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>
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<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>
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<table class="table">
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<thead><tr class="header">
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<th align="left">bacteria</th>
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<th align="center">GEN</th>
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<th align="center">TOB</th>
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<th align="center">AMK</th>
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<th align="center">KAN</th>
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<th align="center">IPM</th>
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<th align="center">MEM</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="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">I</td>
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<td align="center">S</td>
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<td align="center"></td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center"></td>
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</tr>
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<tr class="even">
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">I</td>
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<td align="center">S</td>
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<td align="center"></td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center"></td>
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</tr>
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<tr class="odd">
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">I</td>
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<td align="center">S</td>
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<td align="center"></td>
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<td align="center">R</td>
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<td align="center">S</td>
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<td align="center"></td>
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</tr>
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<tr class="even">
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center"></td>
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<td align="center">S</td>
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</tr>
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<tr class="odd">
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<td align="left"><em>Pseudomonas aeruginosa</em></td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</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="left"><em>Pseudomonas aeruginosa</em></td>
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<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="va">example_isolates</span><span class="op">$</span><span class="va">bacteria</span> <span class="op"><-</span> <span class="fu"><a href="reference/mo_property.html">mo_fullname</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">$</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">&</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 snippet will work in any version of R since April 2013 (R-3.0).</p>
|
||
</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>
|
||
<div class="sourceCode" id="cb3"><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"><-</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="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">%>%</a></span></span>
|
||
<span> <span class="co"># calculate AMR using resistance(), over all aminoglycosides</span></span>
|
||
<span> <span class="co"># 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">NA</td>
|
||
<td align="right">0.889</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<div class="sourceCode" id="cb4"><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">%>%</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">
|
||
<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">NA</td>
|
||
<td align="right">0.889</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
<div class="sourceCode" id="cb5"><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">%>%</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">
|
||
<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">NA</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 the latest CLSI or EUCAST guidelines (<a href="./reference/as.rsi.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 R/SI (<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="cb6"><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> > <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/R-code-check/badge.svg?branch=main" alt="R-code-check"></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="cb7"><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="cb8"><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> > <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:</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.png" 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.png" 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>Christian F. Luz <br><small class="roles"> Author, contributor </small> <a href="https://orcid.org/0000-0001-5809-5995" 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>
|
||
|
||
<div class="citation">
|
||
<h2 data-toc-skip>Citation</h2>
|
||
<ul class="list-unstyled">
|
||
<li><a href="authors.html#citation">Citing AMR</a></li>
|
||
</ul>
|
||
</div>
|
||
|
||
</aside>
|
||
</div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p>
|
||
<p><code>AMR</code> (for R). Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><a target="_blank" href="https://www.certe.nl" class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p></p>
|
||
<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></p>
|
||
</div>
|
||
|
||
</footer>
|
||
</div>
|
||
|
||
|
||
|
||
|
||
|
||
</body>
|
||
</html>
|