mirror of
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57 lines
3.1 KiB
R
57 lines
3.1 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/amr.R
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\name{AMR}
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\alias{AMR}
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\title{The \code{AMR} Package}
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\description{
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Welcome to the \code{AMR} package.
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}
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\details{
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\code{AMR} 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.
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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.
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This package can be used for:
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\itemize{
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\item{Reference for microorganisms, since it contains almost all 60,000 microbial (sub)species from the Catalogue of Life}
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\item{Calculating antimicrobial resistance}
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\item{Calculating empirical susceptibility of both mono therapy and combination therapy}
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\item{Predicting future antimicrobial resistance using regression models}
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\item{Getting properties for any microorganism (like Gram stain, species, genus or family)}
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\item{Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)}
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\item{Plotting antimicrobial resistance}
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\item{Determining first isolates to be used for AMR analysis}
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\item{Applying EUCAST expert rules (not the translation from MIC to RSI values)}
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\item{Determining multi-drug resistant organisms (MDRO)}
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\item{Descriptive statistics: frequency tables, kurtosis and skewness}
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}
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}
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\section{Authors}{
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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] \cr
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[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{rug.nl} \url{umcg.nl} \cr
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[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{certe.nl}
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}
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\section{Read more on our website!}{
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On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}.
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}
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\section{Contact us}{
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For suggestions, comments or questions, please contact us at:
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Matthijs S. Berends \cr
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m.s.berends [at] umcg [dot] nl \cr
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Department of Medical Microbiology, University of Groningen \cr
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University Medical Center Groningen \cr
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Post Office Box 30001 \cr
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9700 RB Groningen
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If you have found a bug, please file a new issue at: \cr
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\url{https://gitlab.com/msberends/AMR/issues}
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}
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