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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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4
R/aa_helper_functions.R
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@ -266,7 +266,7 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
found <- sort(colnames(x)[colnames_formatted %like_case% "species"])
}
}
# -- key antibiotics
# -- key antimicrobials
if (type %in% c("keyantibiotics", "keyantimicrobials")) {
if (any(colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)")) {
found <- sort(colnames(x)[colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)"])
@ -712,7 +712,7 @@ create_eucast_ab_documentation <- function() {
ab <- character()
for (val in x) {
if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
# antibiotic group names, as defined in data-raw/_pre_commit_checks.R, such as `CARBAPENEMS`
# antimicrobial group names, as defined in data-raw/_pre_commit_checks.R, such as `CARBAPENEMS`
val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
} else if (val %in% AMR_env$AB_lookup$ab) {
# separate drugs, such as `AMX`