# ==================================================================== # # 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 #' - Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records #' - 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 #' - Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code #' - Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code #' - Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI #' - Principal component analysis for AMR #' @section Read more on our website!: #' On our website you can find [a comprehensive 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 #' University of Groningen #' Department of Medical Microbiology #' 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 #' #' @name AMR #' @rdname AMR NULL