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76 lines
3.1 KiB
Markdown
Executable File
76 lines
3.1 KiB
Markdown
Executable File
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<!-- README.md is generated from README.Rmd; please edit that file. -->
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# The `AMR` Package for R
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Please visit our comprehensive package website <https://amr-for-r.org>
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to read more about this package, including many examples and tutorials.
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Overview:
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- Provides an **all-in-one solution** for antimicrobial resistance (AMR)
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data analysis in a One Health approach
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- Peer-reviewed, used in over 175 countries, available in 20 languages
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- Generates **antibiograms** - traditional, combined, syndromic, and
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even WISCA
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- Provides the **full microbiological taxonomy** of ~79 000 distinct
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species and extensive info of ~620 antimicrobial drugs
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- Applies **CLSI 2011-2025** and **EUCAST 2011-2025** clinical and
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veterinary breakpoints, and ECOFFs, for MIC and disk zone
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interpretation
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- Corrects for duplicate isolates, **calculates** and **predicts** AMR
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per antimicrobial class
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- Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**,
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**SNOMED CT**, and **NCBI**
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- 100% free of costs and dependencies, highly suitable for places with
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**limited resources**
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------------------------------------------------------------------------
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The `AMR` package is a peer-reviewed, free and open-source R package
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with zero dependencies to simplify the analysis and prediction of
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Antimicrobial Resistance (AMR) and to work with microbial and
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antimicrobial data and properties, by using evidence-based methods.
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**Our aim is to provide a standard** for clean and reproducible AMR data
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analysis, that can therefore empower epidemiological analyses to
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continuously enable surveillance and treatment evaluation in any
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setting.
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The `AMR` package supports and can read any data format, including
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WHONET data. This package works on Windows, macOS and Linux with all
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versions of R since R-3.0 (April 2013). **It was designed to work in any
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setting, including those with very limited resources**. It was created
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for both routine data analysis and academic research at the Faculty of
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Medical Sciences of the [University of Groningen](https://www.rug.nl)
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and the [University Medical Center Groningen](https://www.umcg.nl).
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------------------------------------------------------------------------
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### How to get this package
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To install the latest ‘release’ version from CRAN:
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``` r
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install.packages("AMR")
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```
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To install the latest ‘beta’ version:
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``` r
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install.packages("AMR", repos = "beta.amr-for-r.org")
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# if this does not work, try to install directly from GitHub using the 'remotes' package:
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remotes::install_github("msberends/AMR")
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```
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------------------------------------------------------------------------
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<small> This AMR package for R is free, open-source software and
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licensed under the [GNU General Public License v2.0
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(GPL-2)](https://amr-for-r.org/LICENSE-text.html). These requirements
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are consequently legally binding: modifications must be released under
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the same license when distributing the package, changes made to the code
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must be documented, source code must be made available when the package
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is distributed, and a copy of the license and copyright notice must be
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included with the package. </small>
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