AMR/README.md

# The `AMR` Package for R

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The `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.

Overview:

* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
* Used in over 175 countries, available in 20 languages
* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
* Provides the **full microbiological taxonomy** and extensive info on **all antimicrobial drugs**
* Applies all recent **CLSI** and **EUCAST** clinical and veterinary breakpoints for MICs, disk zones and ECOFFs
* Corrects for duplicate isolates, **calculates** and **predicts** AMR per antimicrobial class
* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC**, **SNOMED CT**, and **NCBI**
* 100% free of costs and dependencies, highly suitable for places with **limited resources**

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Please visit our extensive website [https://msberends.github.io/AMR/](https://msberends.github.io/AMR/) to read more about this package, including many examples and tutorials.

### How to get this package

To install the latest 'release' version from CRAN:

```r
install.packages("AMR")
```

To install the latest 'beta' version from GitHub:

```r
remotes::install_github("msberends/AMR")
```

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<small>
This AMR package for R is free, open-source software and licensed under the [GNU General Public License v2.0 (GPL-2)](https://msberends.github.io/AMR/LICENSE-text.html). 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.
</small>