AMR/man/AMR.Rd

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\name{AMR}
\alias{AMR}
\title{The \code{AMR} Package}
\description{
Welcome to the \code{AMR} package.
}
\details{
\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.

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.

This package can be used for:
\itemize{
  \item{Reference for microorganisms, since it contains all microbial (sub)species from the Catalogue of Life}
  \item{Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines}
  \item{Calculating antimicrobial resistance}
  \item{Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)}
  \item{Calculating empirical susceptibility of both mono therapy and combination therapy}
  \item{Predicting future antimicrobial resistance using regression models}
  \item{Getting properties for any microorganism (like Gram stain, species, genus or family)}
  \item{Getting properties for any antibiotic (like name, ATC code, defined daily dose or trade name)}
  \item{Plotting antimicrobial resistance}
  \item{Determining first isolates to be used for AMR analysis}
  \item{Applying EUCAST expert rules}
  \item{Descriptive statistics: frequency tables, kurtosis and skewness}
}
}
\section{Authors}{

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

[1] Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands - \url{https://www.rug.nl} \url{https://www.umcg.nl} \cr
[2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{https://www.certe.nl}
}

\section{Read more on our website!}{

On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a 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}.
}

\section{Contact us}{

For suggestions, comments or questions, please contact us at:

Matthijs S. Berends \cr
m.s.berends [at] umcg [dot] nl \cr
Department of Medical Microbiology, University of Groningen \cr
University Medical Center Groningen \cr
Post Office Box 30001 \cr
9700 RB Groningen

If you have found a bug, please file a new issue at: \cr
\url{https://gitlab.com/msberends/AMR/issues}
}