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(v1.7.1.9067) Support for Swedish and Russian

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dr. M.S. (Matthijs) Berends
2021-12-12 09:42:03 +01:00
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# `AMR` (for R) <img src="./logo.png" align="right" height="120px" />
> Update: The latest [EUCAST guideline for intrinsic resistance](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) (v3.3, October 2021) is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).
> Update: The latest [EUCAST guideline for intrinsic resistance](https://www.eucast.org/expert_rules_and_intrinsic_resistance/) (v3.3, October 2021) is now supported, and our taxonomy tables have been updated as well (LPSN, 5 October 2021).
>
> **A new version will be released after the [EUCAST guideline for clinical breakpoints](https://www.eucast.org/clinical_breakpoints/) (v12.0, likely January 2022) are implemented, to be expected shortly after the official guideline release.**
### What is `AMR` (for R)?
`AMR` is a free, open-source and independent [R package](https://www.r-project.org) (see [Copyright](#copyright)) 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.
After installing this package, R knows [**~71,000 distinct microbial species**](./reference/microorganisms.html) and all [**~560 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) 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.
After installing this package, R knows [**~71,000 distinct microbial species**](./reference/microorganisms.html) and all [**~560 antibiotic, antimycotic and antiviral drugs**](./reference/antibiotics.html) 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.
The `AMR` package is available in <img src="lang_da.svg" style="height: 11px !important; vertical-align: initial !important;"> Danish, <img src="lang_nl.svg" style="height: 11px !important; vertical-align: initial !important;"> Dutch, <img src="lang_en.svg" style="height: 11px !important; vertical-align: initial !important;"> English, <img src="lang_fr.svg" style="height: 11px !important; vertical-align: initial !important;"> French, <img src="lang_de.svg" style="height: 11px !important; vertical-align: initial !important;"> German, <img src="lang_it.svg" style="height: 11px !important; vertical-align: initial !important;"> Italian, <img src="lang_pt.svg" style="height: 11px !important; vertical-align: initial !important;"> Portuguese, <img src="lang_ru.svg" style="height: 11px !important; vertical-align: initial !important;"> Russian, <img src="lang_es.svg" style="height: 11px !important; vertical-align: initial !important;"> Spanish and <img src="lang_sv.svg" style="height: 11px !important; vertical-align: initial !important;"> Swedish. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.
This package is [fully independent of any other R package](https://en.wikipedia.org/wiki/Dependency_hell) 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**. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the [University of Groningen](https://www.rug.nl), in collaboration with non-profit organisations [Certe Medical Diagnostics and Advice Foundation](https://www.certe.nl) and [University Medical Center Groningen](https://www.umcg.nl). This R package formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)) but is [actively and durably maintained](./news) by two public healthcare organisations in the Netherlands.