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72 lines
4.7 KiB
R
72 lines
4.7 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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#' The \code{AMR} Package
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#'
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#' Welcome to the \code{AMR} package.
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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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#'
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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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#'
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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 all microbial (sub)species from the 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{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 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}
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#' \item{Descriptive statistics: frequency tables, kurtosis and skewness}
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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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#'
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#' [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
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#' [2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{https://www.certe.nl}
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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 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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#' @section Contact us:
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#' For suggestions, comments or questions, please contact us at:
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#'
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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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#'
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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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#' @name AMR
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#' @rdname AMR
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# # prevent NOTE on R >= 3.6
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#' @importFrom microbenchmark microbenchmark
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#' @importFrom scales percent
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NULL
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