AMR/man/AMR.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/aa_amr-package.R
\docType{package}
\name{AMR}
\alias{AMR}
\alias{AMR-package}
\title{The \code{AMR} Package}
\source{
To cite AMR in publications use:

Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C (2022). "AMR: An R Package for Working with Antimicrobial Resistance Data." \emph{Journal of Statistical Software}, \emph{104}(3), 1-31. \doi{10.18637/jss.v104.i03}.

A BibTeX entry for LaTeX users is:

\preformatted{
@Article{,
  title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},
  author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},
  journal = {Journal of Statistical Software},
  year = {2022},
  volume = {104},
  number = {3},
  pages = {1--31},
  doi = {10.18637/jss.v104.i03},
}
}
}
\description{
Welcome to the \code{AMR} package.

The \code{AMR} package is a \href{https://msberends.github.io/AMR/#copyright}{free and open-source} R package with \href{https://en.wikipedia.org/wiki/Dependency_hell}{zero dependencies} to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. \strong{Our aim is to provide a standard} for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. \href{https://msberends.github.io/AMR/authors.html}{Many different researchers} from around the globe are continually helping us to make this a successful and durable project!

This work was published in the Journal of Statistical Software (Volume 104(3); \href{https://doi.org/10.18637/jss.v104.i03}{DOI 10.18637/jss.v104.i03}) and formed the basis of two PhD theses (\href{https://doi.org/10.33612/diss.177417131}{DOI 10.33612/diss.177417131} and \href{https://doi.org/10.33612/diss.192486375}{DOI 10.33612/diss.192486375}).

After installing this package, R knows \href{https://msberends.github.io/AMR/reference/microorganisms.html}{\strong{~52,000}} (updated December 2022) and all \href{https://msberends.github.io/AMR/reference/antibiotics.html}{\strong{~600 antibiotic, antimycotic and antiviral drugs}} by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral breakpoint guidelines from CLSI and EUCAST are included from the last 10 years. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). \strong{It was designed to work in any setting, including those with very limited resources}. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the \href{https://www.rug.nl}{University of Groningen}, in collaboration with non-profit organisations \href{https://www.certe.nl}{Certe Medical Diagnostics and Advice Foundation} and \href{https://www.umcg.nl}{University Medical Center Groningen}.

The \code{AMR} package is available in English, Chinese, Danish, Dutch, French, German, Greek, Italian, Japanese, Polish, Portuguese, Russian, Spanish, Swedish, Turkish and Ukrainian. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
}
\section{Reference Data Publicly Available}{

All data sets in this \code{AMR} package (about microorganisms, antibiotics, SIR interpretation, EUCAST rules, etc.) are publicly and freely available for download in the following formats: R, MS Excel, Apache Feather, Apache Parquet, SPSS, SAS, and Stata. We also provide tab-separated plain text files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please visit \href{https://msberends.github.io/AMR/articles/datasets.html}{our website for the download links}. The actual files are of course available on \href{https://github.com/msberends/AMR/tree/main/data-raw}{our GitHub repository}.
}

\seealso{
Useful links:
\itemize{
  \item \url{https://msberends.github.io/AMR/}
  \item \url{https://github.com/msberends/AMR}
  \item Report bugs at \url{https://github.com/msberends/AMR/issues}
}

}
\author{
\strong{Maintainer}: Matthijs S. Berends \email{m.berends@certe.nl} (\href{https://orcid.org/0000-0001-7620-1800}{ORCID})

Authors:
\itemize{
  \item Christian F. Luz (\href{https://orcid.org/0000-0001-5809-5995}{ORCID}) [contributor]
  \item Dennis Souverein (\href{https://orcid.org/0000-0003-0455-0336}{ORCID}) [contributor]
  \item Erwin E. A. Hassing [contributor]
}

Other contributors:
\itemize{
  \item Casper J. Albers (\href{https://orcid.org/0000-0002-9213-6743}{ORCID}) [thesis advisor]
  \item Peter Dutey-Magni (\href{https://orcid.org/0000-0002-8942-9836}{ORCID}) [contributor]
  \item Judith M. Fonville [contributor]
  \item Alex W. Friedrich (\href{https://orcid.org/0000-0003-4881-038X}{ORCID}) [thesis advisor]
  \item Corinna Glasner (\href{https://orcid.org/0000-0003-1241-1328}{ORCID}) [thesis advisor]
  \item Eric H. L. C. M. Hazenberg [contributor]
  \item Gwen Knight (\href{https://orcid.org/0000-0002-7263-9896}{ORCID}) [contributor]
  \item Annick Lenglet (\href{https://orcid.org/0000-0003-2013-8405}{ORCID}) [contributor]
  \item Bart C. Meijer [contributor]
  \item Dmytro Mykhailenko [contributor]
  \item Anton Mymrikov [contributor]
  \item Andrew P. Norgan (\href{https://orcid.org/0000-0002-2955-2066}{ORCID}) [contributor]
  \item Sofia Ny (\href{https://orcid.org/0000-0002-2017-1363}{ORCID}) [contributor]
  \item Jonas Salm [contributor]
  \item Rogier P. Schade [contributor]
  \item Bhanu N. M. Sinha (\href{https://orcid.org/0000-0003-1634-0010}{ORCID}) [thesis advisor]
  \item Anthony Underwood (\href{https://orcid.org/0000-0002-8547-4277}{ORCID}) [contributor]
}

}
\keyword{internal}