mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 16:46:13 +01:00
55 lines
3.2 KiB
R
55 lines
3.2 KiB
R
% Generated by roxygen2: do not edit by hand
|
|
% Please edit documentation in R/amr.R
|
|
\name{AMR}
|
|
\alias{AMR}
|
|
\title{The \code{AMR} Package}
|
|
\description{
|
|
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 \href{http://www.catalogueoflife.org}{Catalogue of Life}
|
|
\item Interpreting raw MIC and disk diffusion values, based on the latest CLSI or EUCAST guidelines
|
|
\item Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records
|
|
\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 Getting SNOMED codes of a microorganism, or get its name associated with a SNOMED code
|
|
\item Getting LOINC codes of an antibiotic, or get its name associated with a LOINC code
|
|
\item Machine reading the EUCAST and CLSI guidelines from 2011-2020 to translate MIC values and disk diffusion diameters to R/SI
|
|
\item Principal component analysis for AMR
|
|
}
|
|
}
|
|
\section{Read more on our website!}{
|
|
|
|
On our website \url{https://msberends.github.io/AMR} you can find \href{https://msberends.github.io/AMR/articles/AMR.html}{a comprehensive tutorial} about how to conduct AMR analysis, the \href{https://msberends.github.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.github.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
|
|
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
|
|
\url{https://github.com/msberends/AMR/issues}
|
|
}
|
|
|