Note: to keep the package size as small as possible, we only include this vignette on CRAN. You can read more vignettes on our website about how to conduct AMR data analysis, determine MDROs, find explanation of EUCAST and CLSI breakpoints, and much more: https://msberends.github.io/AMR/articles/.
AMR package is a free and
open-source R package with 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.
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. 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); DOI 10.18637/jss.v104.i03) and formed the basis of two PhD theses (DOI 10.33612/diss.177417131 and DOI 10.33612/diss.192486375).
After installing this package, R knows ~52 000 distinct microbial species and all ~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.
With the help of contributors from all corners of the world, the
AMR package is available in English, Czech, Chinese,
Danish, Dutch, Finnish, French, German, Greek, Italian, Japanese,
Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swedish,
Turkish, and Ukrainian. Antimicrobial drug (group) names and colloquial
microorganism names are provided in these languages.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. Since its first public release in early 2018, this package has been downloaded from more than 175 countries.
This package can be used for:
All reference data sets (about microorganisms, antibiotics, SIR
interpretation, EUCAST rules, etc.) in this
AMR package are
publicly and freely available. We continually export our data sets to
formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat
files that are machine-readable and suitable for input in any software
program, such as laboratory information systems. Please find all
download links on our website, which is automatically updated with
every code change.
This R package was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen, and is being actively and durably maintained by two public healthcare organisations in the Netherlands.
This AMR package for R is free, open-source software and licensed under the GNU General Public License v2.0 (GPL-2). These requirements are consequently legally binding: modifications must be released under the same license when distributing the package, changes made to the code must be documented, source code must be made available when the package is distributed, and a copy of the license and copyright notice must be included with the package.