mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 17:26:12 +01:00
63 lines
4.2 KiB
R
63 lines
4.2 KiB
R
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2018-2020 Berends MS, Luz CF et al. #
|
|
# #
|
|
# 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. #
|
|
# #
|
|
# We created this package for both routine data analysis and academic #
|
|
# research and it 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 `AMR` Package
|
|
#'
|
|
#' Welcome to the `AMR` package.
|
|
#' @details
|
|
#' `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:
|
|
#' - Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the [Catalogue of Life](http://www.catalogueoflife.org)
|
|
#' - Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
|
|
#' - Determining first isolates to be used for AMR analysis
|
|
#' - Calculating antimicrobial resistance
|
|
#' - Determining multi-drug resistance (MDR) / multi-drug resistant organisms (MDRO)
|
|
#' - Calculating (empirical) susceptibility of both mono therapy and combination therapies
|
|
#' - Predicting future antimicrobial resistance using regression models
|
|
#' - Getting properties for any microorganism (like Gram stain, species, genus or family)
|
|
#' - Getting properties for any antibiotic (like name, EARS-Net code, ATC code, PubChem code, defined daily dose or trade name)
|
|
#' - Plotting antimicrobial resistance
|
|
#' - Applying EUCAST expert rules
|
|
|
|
#' @section Read more on our website!:
|
|
#' On our website <https://msberends.gitlab.io/AMR> you can find [a tutorial](https://msberends.gitlab.io/AMR/articles/AMR.html) about how to conduct AMR analysis, the [complete documentation of all functions](https://msberends.gitlab.io/AMR/reference) (which reads a lot easier than here in R) and [an example analysis using WHONET data](https://msberends.gitlab.io/AMR/articles/WHONET.html).
|
|
#' @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 \cr
|
|
#' The Netherlands
|
|
#'
|
|
#' If you have found a bug, please file a new issue at: \cr
|
|
#' <https://gitlab.com/msberends/AMR/issues>
|
|
#' @name AMR
|
|
#' @rdname AMR
|
|
#' @importFrom microbenchmark microbenchmark
|
|
#' @importFrom knitr kable
|
|
NULL
|