mirror of https://github.com/msberends/AMR.git
71 lines
4.4 KiB
R
Executable File
71 lines
4.4 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
#' The \code{AMR} Package
|
|
#'
|
|
#' 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{Calculating antimicrobial resistance}
|
|
#' \item{Predicting 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 rules}
|
|
#' \item{Determining multi-drug resistance organisms (MDRO)}
|
|
#' \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{rug.nl} \url{umcg.nl} \cr
|
|
#' [2] Certe Medical Diagnostics & Advice, Groningen, the Netherlands - \url{certe.nl}
|
|
|
|
#' @section Read more on our website!:
|
|
#' \if{html}{\figure{logo.png}{options: height=40px style=margin-bottom:5px} \cr}
|
|
#' 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
|
|
#'
|
|
#' If you have found a bug, please file a new issue at: \cr
|
|
#' \url{https://gitlab.com/msberends/AMR/issues}
|
|
#' @name AMR
|
|
#' @rdname AMR
|
|
NULL
|
|
|
|
.onLoad <- function(libname, pkgname) {
|
|
backports::import(pkgname)
|
|
}
|