diff --git a/DESCRIPTION b/DESCRIPTION index 3b6e8db44..56d2e453d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ 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) diff --git a/NEWS.md b/NEWS.md index c80f102c1..aa58e146e 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,7 +1,8 @@ -# 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 diff --git a/vignettes/welcome_to_AMR.Rmd b/vignettes/welcome_to_AMR.Rmd index 58663554a..ab70aea82 100644 --- a/vignettes/welcome_to_AMR.Rmd +++ b/vignettes/welcome_to_AMR.Rmd @@ -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))