P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-06-29 20:16:22 +02:00
Code Releases Activity

(v3.0.1.9064) Documentation updates

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2026-06-24 18:32:08 +02:00
parent c7b17e5833
commit bd63794136
14 changed files with 148 additions and 62 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
README.Rmd
View File

@@ -21,7 +21,7 @@ Please visit our comprehensive package website <https://amr-for-r.org> to read m
Overview:
* Provides an **all-in-one solution** for antimicrobial resistance (AMR) data analysis in a One Health approach
* Peer-reviewed, used in over 175 countries, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
* **Peer-reviewed**, used in over 175 countries, available in `r length(AMR:::LANGUAGES_SUPPORTED)` languages
* Generates **antibiograms** - WISCA for empiric coverage estimates, or traditional/syndromic for AMR surveillance
* Provides the **full microbiological taxonomy** of `r AMR:::format_included_data_number(AMR::microorganisms)` distinct species and extensive info of `r AMR:::format_included_data_number(NROW(AMR::antimicrobials) + NROW(AMR::antivirals))` antimicrobial drugs
* Applies **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)))`** clinical and veterinary breakpoints, and ECOFFs, for MIC and disk zone interpretation