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<p>The <code>AMR</code> package is a <ahref="#copyright">free and open-source</a> R package with <ahref="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>
<p>This work was published in the Journal of Statistical Software (Volume 104(3); <ahref="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 (<ahref="https://doi.org/10.33612/diss.177417131"class="external-link">DOI 10.33612/diss.177417131</a> and <ahref="https://doi.org/10.33612/diss.192486375"class="external-link">DOI 10.33612/diss.192486375</a>).</p>
<p>After installing this package, R knows <ahref="./reference/microorganisms.html"><strong>~49,000 distinct microbial species</strong></a> and all <ahref="./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 <ahref="https://www.rug.nl"class="external-link">University of Groningen</a>, in collaboration with non-profit organisations <ahref="https://www.certe.nl"class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <ahref="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a>, and is being <ahref="./news">actively and durably maintained</a> by two public healthcare organisations in the Netherlands.</p>
<h5id="used-in-175-countries-translated-to-16-languages">Used in 175 countries, translated to 16 languages<aclass="anchor"aria-label="anchor"href="#used-in-175-countries-translated-to-16-languages"></a>
<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 only having defined a row filter on Gram-negative bacteria with intrinsic resistance to cefotaxime (<code><ahref="reference/mo_property.html">mo_is_gram_negative()</a></code> and <code><ahref="reference/mo_property.html">mo_is_intrinsic_resistant()</a></code>) and a column selection on two antibiotic groups (<code><ahref="reference/antibiotic_class_selectors.html">aminoglycosides()</a></code> and <code><ahref="reference/antibiotic_class_selectors.html">carbapenems()</a></code>), the reference data about <ahref="./reference/microorganisms.html">all microorganisms</a> and <ahref="./reference/antibiotics.html">all antibiotics</a> in the <code>AMR</code> package make sure you get what you meant:</p>
<p>This base R snippet will work in any version of R since April 2013 (R-3.0).</p>
</div>
<divclass="section level4">
<h4id="calculating-resistance-per-group">Calculating resistance per group<aclass="anchor"aria-label="anchor"href="#calculating-resistance-per-group"></a>
<h3id="what-else-can-you-do-with-this-package">What else can you do with this package?<aclass="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>
<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 (<ahref="(https://lpsn.dsmz.de)"class="external-link">LPSN</a>) and the Global Biodiversity Information Facility (<ahref="https://www.gbif.org"class="external-link">GBIF</a>) (<ahref="./reference/mo_property.html">manual</a>)</li>
<li>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines (<ahref="./reference/as.rsi.html">manual</a>)</li>
<li>Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records (<ahref="./reference/ab_from_text.html">manual</a>)</li>
<li>Determining first isolates to be used for AMR data analysis (<ahref="./reference/first_isolate.html">manual</a>)</li>
<li>Calculating (empirical) susceptibility of both mono therapy and combination therapies (<ahref="./articles/AMR.html">tutorial</a>)</li>
<li>Predicting future antimicrobial resistance using regression models (<ahref="./articles/resistance_predict.html">tutorial</a>)</li>
<li>Getting properties for any microorganism (like Gram stain, species, genus or family) (<ahref="./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) (<ahref="./reference/ab_property.html">manual</a>)</li>
<li>Getting SNOMED codes of a microorganism, or getting properties of a microorganism based on a SNOMED code (<ahref="./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 (<ahref="./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 (<ahref="./articles/datasets.html">link</a>)</li>
<li>Principal component analysis for AMR (<ahref="./articles/PCA.html">tutorial</a>)</li>
</ul>
</div>
<divclass="section level3">
<h3id="get-this-package">Get this package<aclass="anchor"aria-label="anchor"href="#get-this-package"></a>
</h3>
<divclass="section level4">
<h4id="latest-official-version">Latest official version<aclass="anchor"aria-label="anchor"href="#latest-official-version"></a>
<p>This package is available <ahref="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>
<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>
<divclass="section level4">
<h4id="latest-development-version">Latest development version<aclass="anchor"aria-label="anchor"href="#latest-development-version"></a>
<codeclass="sourceCode R"><span><spanclass="fu"><ahref="https://rdrr.io/r/utils/install.packages.html"class="external-link">install.packages</a></span><spanclass="op">(</span><spanclass="st">"remotes"</span><spanclass="op">)</span><spanclass="co"># if you haven't already</span></span>
<p>Automatically, using the <ahref="https://ropensci.org/r-universe/"class="external-link">rOpenSci R-universe platform</a>, by adding <ahref="https://msberends.r-universe.dev"class="external-link">our R-universe address</a> to your list of repositories (‘repos’):</p>
<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>
<p>To find out how to conduct AMR data analysis, please <ahref="./articles/AMR.html">continue reading here to get started</a> or click a link in the <ahref="https://msberends.github.io/AMR/articles/">‘How to’ menu</a>.</p>
<divalign="center"><p><ahref="https://www.rug.nl"title="University of Groningen"class="external-link"><imgsrc="./logo_rug.svg"style="max-width: 200px;"></a><ahref="https://www.umcg.nl"title="University Medical Center Groningen"class="external-link"><imgsrc="./logo_umcg.png"style="max-width: 200px;"></a><ahref="https://www.certe.nl"title="Certe Medical Diagnostics and Advice Foundation"class="external-link"><imgsrc="./logo_certe.png"style="max-width: 200px;"></a><ahref="https://www.deutschland-nederland.eu"title="EurHealth-1-Health"class="external-link"><imgsrc="./logo_eh1h.png"style="max-width: 200px;"></a><ahref="https://www.deutschland-nederland.eu"title="INTERREG"class="external-link"><imgsrc="./logo_interreg.png"style="max-width: 200px;"></a></p></div>
<p>This R package is free, open-source software and licensed under the <ahref="./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>
<p><code>AMR</code> (for R). Developed at the <atarget="_blank"href="https://www.rug.nl"class="external-link">University of Groningen</a> in collaboration with non-profit organisations<br><atarget="_blank"href="https://www.certe.nl"class="external-link">Certe Medical Diagnostics and Advice Foundation</a> and <atarget="_blank"href="https://www.umcg.nl"class="external-link">University Medical Center Groningen</a>.</p>
