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Fix copyright link and add MycoBank in vignette

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uzumakienes authored and GitHub committed 2026-10-23 16:46:27 +03:00
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vignettes/welcome_to_AMR.Rmd
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@@ -26,7 +26,7 @@ Note: to keep the package size as small as possible, we only include this vignet
----
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.
@@ -36,7 +36,7 @@ The `AMR` package is available in `r AMR:::vector_and(vapply(FUN.VALUE = charact
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))