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dr. M.S. (Matthijs) Berends
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README.md
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# `AMR` (for R)
![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=master)
![R-code-check](https://github.com/msberends/AMR/workflows/R-code-check/badge.svg?branch=main)
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[![Codecov](https://codecov.io/gh/msberends/AMR/branch/master/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=master)
[![Codecov](https://codecov.io/gh/msberends/AMR/branch/main/graph/badge.svg)](https://codecov.io/gh/msberends/AMR?branch=main)
<img src="https://msberends.github.io/AMR/works_great_on.png" align="center" height="150px" />
The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/master/data-raw).
The latest built **source package** (`AMR_latest.tar.gz`) can be found in folder [/data-raw/](https://github.com/msberends/AMR/tree/main/data-raw).
`AMR` is a free, open-source and independent R package 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 antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. It is currently being used in over 150 countries.
After installing this package, R knows ~70,000 distinct microbial species and all ~550 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.
After installing this package, R knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic, and antiviral drugs by name and code (including ATC, EARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data. Antimicrobial names and group names are available in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish.
This package is fully independent of any other R package and works on Windows, macOS and Linux with all versions of R since R-3.0.0 (April 2013). 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 University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice Foundation and University Medical Center Groningen. 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.
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### Copyright
This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/master/LICENSE). In a nutshell, this means that this package:
This R package is licensed under the [GNU General Public License (GPL) v2.0](https://github.com/msberends/AMR/blob/main/LICENSE). In a nutshell, this means that this package:
- May be used for commercial purposes