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move object assignment to AMR_env

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-14 13:02:50 +02:00
parent dfae4c7e7d
commit 76bcd3528c
18 changed files with 116 additions and 127 deletions
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4
R/guess_ab_col.R
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@ -173,7 +173,7 @@ get_column_abx <- function(x,
# only check columns that are a valid AB code, ATC code, name, abbreviation or synonym,
# or already have the <rsi> class (as.rsi)
# and that they have no more than 50% invalid values
vectr_antibiotics <- unlist(AB_lookup$generalised_all)
vectr_antibiotics <- unlist(AMR_env$AB_lookup$generalised_all)
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
x_columns <- vapply(
FUN.VALUE = character(1),
@ -335,7 +335,7 @@ get_ab_from_namespace <- function(x, cols_ab) {
if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
# antibiotic group names, as defined in data-raw/_pre_commit_hook.R, such as `AB_CARBAPENEMS`
val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
} else if (val %in% AB_lookup$ab) {
} else if (val %in% AMR_env$AB_lookup$ab) {
# separate drugs, such as `AMX`
val <- as.ab(val)
} else {