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(v2.1.1.9186) replace antibiotics
with antimicrobials
!
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@ -266,7 +266,7 @@ search_type_in_df <- function(x, type, info = TRUE, add_col_prefix = TRUE) {
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found <- sort(colnames(x)[colnames_formatted %like_case% "species"])
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}
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}
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# -- key antibiotics
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# -- key antimicrobials
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if (type %in% c("keyantibiotics", "keyantimicrobials")) {
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if (any(colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)")) {
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found <- sort(colnames(x)[colnames_formatted %like_case% "^key.*(ab|antibiotics|antimicrobials)"])
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@ -712,7 +712,7 @@ create_eucast_ab_documentation <- function() {
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ab <- character()
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for (val in x) {
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if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
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# antibiotic group names, as defined in data-raw/_pre_commit_checks.R, such as `CARBAPENEMS`
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# antimicrobial group names, as defined in data-raw/_pre_commit_checks.R, such as `CARBAPENEMS`
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val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
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} else if (val %in% AMR_env$AB_lookup$ab) {
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# separate drugs, such as `AMX`
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