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 the taxonomy of microorganisms, since the package contains all microbial (sub)species from the \href{http://www.catalogueoflife.org}{Catalogue of Life}
\item Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
\item Determining first isolates to be used for AMR analysis
\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 therapies
\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, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)
\item Plotting antimicrobial resistance
\item Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code
\item Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code
\item Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
\item Principal component analysis for AMR
}
}
\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 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}.
}

\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 \cr
The Netherlands

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