mirror of https://github.com/msberends/AMR.git
71 lines
3.4 KiB
R
Executable File
71 lines
3.4 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This program is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This program is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License for more details. #
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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. This page gives some additional contact information about the authors.
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#' @details
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#' This package was intended to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and work with antibiotic properties by using evidence-based methods.
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#'
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#' This package was created for academic research by PhD students of 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).
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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 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{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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#' @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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NULL
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.onLoad <- function(libname, pkgname) {
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backports::import(pkgname)
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}
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.onAttach <- function(libname, pkgname) {
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# save data.tables to improve speed of as.mo:
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MOs <- data.table::as.data.table(AMR::microorganisms)
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data.table::setkey(MOs, prevalence, tsn)
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base::assign(x = "MOs",
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value = MOs,
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envir = base::as.environment("package:AMR"))
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base::assign(x = "MOs_mostprevalent",
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value = MOs[prevalence != 9999,],
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envir = base::as.environment("package:AMR"))
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base::assign(x = "MOs_allothers",
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value = MOs[prevalence == 9999,],
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envir = base::as.environment("package:AMR"))
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base::assign(x = "MOs_old",
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value = data.table::as.data.table(AMR::microorganisms.old),
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envir = base::as.environment("package:AMR"))
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}
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