mirror of
https://github.com/msberends/AMR.git
synced 2024-12-25 18:46:11 +01:00
64 lines
4.3 KiB
R
64 lines
4.3 KiB
R
# ==================================================================== #
|
|
# 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.gitlab.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{Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the 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{Applying EUCAST expert rules}
|
|
#' }
|
|
#' @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 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
|
|
#' The Netherlands
|
|
#'
|
|
#' If you have found a bug, please file a new issue at: \cr
|
|
#' \url{https://gitlab.com/msberends/AMR/issues}
|
|
#' @name AMR
|
|
#' @rdname AMR
|
|
#' @importFrom microbenchmark microbenchmark
|
|
#' @importFrom knitr kable
|
|
NULL
|