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(v3.0.1.9064) Documentation updates

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dr. M.S. (Matthijs) Berends
2026-06-24 18:32:08 +02:00
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vignettes/welcome_to_AMR.Rmd
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@@ -30,7 +30,7 @@ The `AMR` package is a peer-reviewed, [free and open-source](https://amr-for-r.o
This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and 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)).
After installing this package, R knows [**`r AMR:::format_included_data_number(AMR::microorganisms)` distinct microbial species**](https://amr-for-r.org/reference/microorganisms.html) (updated June 2024) and all [**`r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial and antiviral drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))` and EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))` are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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) and the [University Medical Center Groningen](https://www.umcg.nl).
After installing this package, R knows [**`r AMR:::format_included_data_number(AMR::microorganisms)` distinct microbial species**](https://amr-for-r.org/reference/microorganisms.html) (updated `r format(AMR:::TAXONOMY_VERSION$GBIF$accessed_date, "%B %Y")`) and all [**`r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial and antiviral drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("CLSI", guideline))$guideline)))` and EUCAST `r min(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(AMR::clinical_breakpoints, grepl("EUCAST", guideline))$guideline)))` are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package 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) and the [University Medical Center Groningen](https://www.umcg.nl).
The `AMR` package is available in `r AMR:::vector_and(vapply(FUN.VALUE = character(1), AMR:::LANGUAGES_SUPPORTED_NAMES, function(x) x$exonym), quotes = FALSE, sort = FALSE)`. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.