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dr. M.S. (Matthijs) Berends
2019-02-21 18:55:52 +01:00
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docs/reference/AMR.html
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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>
<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 &amp; 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>
<p>This package can be used for:</p><ul>
<li><p>Reference for microorganisms, since it contains almost all 60,000 microbial (sub)species from the Catalogue of Life</p></li>
<li><p>Calculating antimicrobial resistance</p></li>
<li><p>Predicting antimicrobial resistance using regression models</p></li>
<li><p>Calculating empirical susceptibility of both mono therapy and combination therapy</p></li>
<li><p>Predicting future antimicrobial resistance using regression models</p></li>
<li><p>Getting properties for any microorganism (like Gram stain, species, genus or family)</p></li>
<li><p>Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)</p></li>
<li><p>Plotting antimicrobial resistance</p></li>
<li><p>Determining first isolates to be used for AMR analysis</p></li>
<li><p>Applying EUCAST rules</p></li>
<li><p>Determining multi-drug resistance organisms (MDRO)</p></li>
<li><p>Applying EUCAST expert rules (not the translation from MIC to RSI values)</p></li>
<li><p>Determining multi-drug resistant organisms (MDRO)</p></li>
<li><p>Descriptive statistics: frequency tables, kurtosis and skewness</p></li>
</ul>
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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>
<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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 comprehensive 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>
<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 comprehensive 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>
<h2 class="hasAnchor" id="contact-us"><a class="anchor" href="#contact-us"></a>Contact us</h2>