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# The `AMR` Package
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Welcome to the `AMR` package.
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The `AMR` package is a peer-reviewed, [free and
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open-source](https://amr-for-r.org/#copyright) R package with [zero
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dependencies](https://en.wikipedia.org/wiki/Dependency_hell) to simplify
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the analysis and prediction of Antimicrobial Resistance (AMR) and to
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work with microbial and antimicrobial data and properties, by using
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evidence-based methods. **Our aim is to provide a standard** for clean
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and reproducible AMR data analysis, that can therefore empower
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epidemiological analyses to continuously enable surveillance and
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treatment evaluation in any setting. We are a team of [many different
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researchers](https://amr-for-r.org/authors.html) from around the globe
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to make this a successful and durable project!
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This work was published in the Journal of Statistical Software (Volume
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104(3);
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[doi:10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03) ) and
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formed the basis of two PhD theses
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([doi:10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131)
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and
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[doi:10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)
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).
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After installing this package, R knows [**~79 000 distinct microbial
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species**](https://amr-for-r.org/reference/microorganisms.html) (updated
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June 2024) and all [**~620 antimicrobial and antiviral
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drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name
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and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
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CT), and knows all about valid SIR and MIC values. The integral clinical
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breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are
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included, even with epidemiological cut-off (ECOFF) values. It supports
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and can read any data format, including WHONET data. This package works
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on Windows, macOS and Linux with all versions of R since R-3.0 (April
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2013). **It was designed to work in any setting, including those with
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very limited resources**. It was created for both routine data analysis
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and academic research at the Faculty of Medical Sciences of the
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[University of Groningen](https://www.rug.nl) and the [University
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Medical Center Groningen](https://www.umcg.nl).
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The `AMR` package is available in English, Arabic, Bengali, Chinese,
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Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian,
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Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian,
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Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and
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Vietnamese. Antimicrobial drug (group) names and colloquial
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microorganism names are provided in these languages.
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## Source
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To cite AMR in publications use:
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Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C
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(2022). "AMR: An R Package for Working with Antimicrobial Resistance
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Data." *Journal of Statistical Software*, *104*(3), 1-31.
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[doi:10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)
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A BibTeX entry for LaTeX users is:
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@Article{,
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title = {{AMR}: An {R} Package for Working with Antimicrobial Resistance Data},
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author = {Matthijs S. Berends and Christian F. Luz and Alexander W. Friedrich and Bhanu N. M. Sinha and Casper J. Albers and Corinna Glasner},
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journal = {Journal of Statistical Software},
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year = {2022},
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volume = {104},
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number = {3},
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pages = {1--31},
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doi = {10.18637/jss.v104.i03},
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}
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## Download Our Reference Data
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All reference data sets in the AMR package - including information on
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microorganisms, antimicrobials, and clinical breakpoints - are freely
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available for download in multiple formats: R, MS Excel, Apache Feather,
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Apache Parquet, SPSS, and Stata.
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For maximum compatibility, we also provide machine-readable,
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tab-separated plain text files suitable for use in any software,
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including laboratory information systems.
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Visit [our website for direct download
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links](https://amr-for-r.org/articles/datasets.html), or explore the
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actual files in [our GitHub
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repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
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## See also
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Useful links:
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- <https://amr-for-r.org>
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- <https://github.com/msberends/AMR>
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- Report bugs at <https://github.com/msberends/AMR/issues>
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## Author
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**Maintainer**: Matthijs S. Berends <m.s.berends@umcg.nl>
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([ORCID](https://orcid.org/0000-0001-7620-1800))
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Authors:
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- Dennis Souverein ([ORCID](https://orcid.org/0000-0003-0455-0336))
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\[contributor\]
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- Erwin E. A. Hassing \[contributor\]
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Other contributors:
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- Aislinn Cook ([ORCID](https://orcid.org/0000-0002-9189-7815))
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\[contributor\]
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- Andrew P. Norgan ([ORCID](https://orcid.org/0000-0002-2955-2066))
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\[contributor\]
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- Anita Williams ([ORCID](https://orcid.org/0000-0002-5295-8451))
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\[contributor\]
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- Annick Lenglet ([ORCID](https://orcid.org/0000-0003-2013-8405))
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\[contributor\]
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- Anthony Underwood ([ORCID](https://orcid.org/0000-0002-8547-4277))
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\[contributor\]
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- Anton Mymrikov \[contributor\]
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- Bart C. Meijer \[contributor\]
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- Christian F. Luz ([ORCID](https://orcid.org/0000-0001-5809-5995))
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\[contributor\]
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- Dmytro Mykhailenko \[contributor\]
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- Eric H. L. C. M. Hazenberg \[contributor\]
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- Gwen Knight ([ORCID](https://orcid.org/0000-0002-7263-9896))
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\[contributor\]
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- Jane Hawkey ([ORCID](https://orcid.org/0000-0001-9661-5293))
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\[contributor\]
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- Jason Stull ([ORCID](https://orcid.org/0000-0002-9028-8153))
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\[contributor\]
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- Javier Sanchez ([ORCID](https://orcid.org/0000-0003-2605-8094))
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\[contributor\]
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- Jonas Salm \[contributor\]
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- Judith M. Fonville \[contributor\]
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- Kathryn Holt ([ORCID](https://orcid.org/0000-0003-3949-2471))
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\[contributor\]
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- Larisse Bolton ([ORCID](https://orcid.org/0000-0001-7879-2173))
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\[contributor\]
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- Matthew Saab ([ORCID](https://orcid.org/0009-0008-6626-7919))
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\[contributor\]
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- Natacha Couto ([ORCID](https://orcid.org/0000-0002-9152-5464))
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\[contributor\]
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- Peter Dutey-Magni ([ORCID](https://orcid.org/0000-0002-8942-9836))
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\[contributor\]
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- Rogier P. Schade ([ORCID](https://orcid.org/0000-0002-9487-4467))
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\[contributor\]
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- Sofia Ny ([ORCID](https://orcid.org/0000-0002-2017-1363))
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\[contributor\]
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- Alex W. Friedrich ([ORCID](https://orcid.org/0000-0003-4881-038X))
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\[thesis advisor\]
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- Bhanu N. M. Sinha ([ORCID](https://orcid.org/0000-0003-1634-0010))
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\[thesis advisor\]
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- Casper J. Albers ([ORCID](https://orcid.org/0000-0002-9213-6743))
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\[thesis advisor\]
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- Corinna Glasner ([ORCID](https://orcid.org/0000-0003-1241-1328))
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\[thesis advisor\]
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