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Merge pull request #333 from uzumakienes/uzumakienes-patch-1

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Fix copyright link and add MycoBank to the welcome vignette
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Matthijs Berends authored and GitHub committed 2026-10-23 19:42:19 +02:00
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DESCRIPTION
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Package: AMR
Version: 3.1.0.9005
Version: 3.1.0.9006
Date: 2026-10-23
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
NEWS.md
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# AMR 3.1.0.9005
# AMR 3.1.0.9006
### Other
* The manual index on the website was rewritten to improve findability, with sections ordered by task and a filter field
* Fixed the link to the copyright section and added MycoBank as a taxonomy source in the *Welcome to AMR* vignette (#325)
# AMR 3.1.0
vignettes/welcome_to_AMR.Rmd
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----
The `AMR` package is a peer-reviewed, [free and open-source](#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) 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.
The `AMR` package is a peer-reviewed, [free and open-source](https://amr-for-r.org/#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) 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 has always been 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. We are a team of [many different researchers](https://amr-for-r.org/authors.html) from around the globe to make this a successful and durable project! The `AMR` package was already cited [over 100 times](https://scholar.google.com/citations?view_op=view_citation&hl=en&citation_for_view=sAoHvIgAAAAJ:0EnyYjriUFMC) in scientific research.
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This package was intended as a comprehensive toolbox for integrated AMR data analysis. This package can be used for:
* Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature ([LPSN](https://lpsn.dsmz.de)) and the Global Biodiversity Information Facility ([GBIF](https://www.gbif.org)) ([manual](https://amr-for-r.org/reference/mo_property.html))
* Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the List of Prokaryotic names with Standing in Nomenclature ([LPSN](https://lpsn.dsmz.de)), [MycoBank](https://www.mycobank.org) and the Global Biodiversity Information Facility ([GBIF](https://www.gbif.org)) ([manual](https://amr-for-r.org/reference/mo_property.html))
* Interpreting raw MIC and disk diffusion values, based on any CLSI or EUCAST guideline ([manual](https://amr-for-r.org/reference/as.sir.html))
* Retrieving antimicrobial drug names, doses and forms of administration from clinical health care records ([manual](https://amr-for-r.org/reference/ab_from_text.html))
* Determining first isolates to be used for AMR data analysis ([manual](https://amr-for-r.org/reference/first_isolate.html))