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(v3.0.1.9060) WISCA fix

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dr. M.S. (Matthijs) Berends
2026-06-23 19:27:40 +02:00
parent 9898b5df4b
commit fd90b2c250
11 changed files with 170 additions and 315 deletions
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README.Rmd
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@@ -22,7 +22,7 @@ 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
* Generates **antibiograms** - traditional, combined, syndromic, and even WISCA
* 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
* Corrects for duplicate isolates, **calculates** and **predicts** AMR per antimicrobial class