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