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<h1>The <code>AMR</code> Package</h1>
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<div class="hidden name"><code>AMR.Rd</code></div>
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<p>Welcome to the <code>AMR</code> package.</p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p><code>AMR</code> is a free and open-source R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial properties by using evidence-based methods. It supports any table format, including WHONET/EARS-Net data.</p>
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<p>We created this package for both academic research and routine analysis at the Faculty of Medical Sciences of the University of Groningen and the Medical Microbiology & Infection Prevention (MMBI) department of the University Medical Center Groningen (UMCG). This R package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
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<p>This package can be used for:</p><ul>
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<li><p>Reference for microorganisms, since it contains all microbial (sub)species from the Catalogue of Life</p></li>
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<li><p>Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines</p></li>
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<li><p>Calculating antimicrobial resistance</p></li>
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<li><p>Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)</p></li>
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<li><p>Calculating empirical susceptibility of both mono therapy and combination therapy</p></li>
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<li><p>Predicting future antimicrobial resistance using regression models</p></li>
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<li><p>Getting properties for any microorganism (like Gram stain, species, genus or family)</p></li>
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<li><p>Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)</p></li>
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<li><p>Plotting antimicrobial resistance</p></li>
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<li><p>Determining first isolates to be used for AMR analysis</p></li>
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<li><p>Applying EUCAST expert rules</p></li>
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<li><p>Descriptive statistics: frequency tables, kurtosis and skewness</p></li>
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</ul>
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<h2 class="hasAnchor" id="authors"><a class="anchor" href="#authors"></a>Authors</h2>
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<p>Matthijs S. Berends[1,2] Christian F. Luz[1], Erwin E.A. Hassing[2], Corinna Glasner[1], Alex W. Friedrich[1], Bhanu N.M. Sinha[1] <br /></p>
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<p>[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - <a href='https://www.rug.nl'>https://www.rug.nl</a> <a href='https://www.umcg.nl'>https://www.umcg.nl</a> <br />
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[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - <a href='https://www.certe.nl'>https://www.certe.nl</a></p>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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<p>On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a tutorial</a> about how to conduct AMR analysis, the <a href='https://msberends.gitlab.io/AMR/reference'>complete documentation of all functions</a> (which reads a lot easier than here in R) and <a href='https://msberends.gitlab.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
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<h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact us</h2>
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<p>For suggestions, comments or questions, please contact us at:</p>
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<p>Matthijs S. Berends <br />
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m.s.berends [at] umcg [dot] nl <br />
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Department of Medical Microbiology, University of Groningen <br />
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University Medical Center Groningen <br />
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Post Office Box 30001 <br />
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9700 RB Groningen</p>
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<p>If you have found a bug, please file a new issue at: <br />
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<a href='https://gitlab.com/msberends/AMR/issues'>https://gitlab.com/msberends/AMR/issues</a></p>
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<h2>Contents</h2>
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<li><a href="#details">Details</a></li>
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<li><a href="#authors">Authors</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<li><a href="#contact-us">Contact us</a></li>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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