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(v1.7.1.9054) mdro() update - fixes #49, first_isolate() speedup

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dr. M.S. (Matthijs) Berends
2021-11-28 23:01:26 +01:00
parent 9a2c431e16
commit 694cf5ba77
72 changed files with 780 additions and 669 deletions
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22
R/guess_ab_col.R
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@ -293,6 +293,28 @@ get_column_abx <- function(x,
out
}
get_ab_from_namespace <- function(x, cols_ab) {
# cols_ab comes from get_column_abx()
x <- trimws(unique(toupper(unlist(strsplit(x, ",")))))
x_new <- character()
for (val in x) {
if (paste0("AB_", val) %in% ls(envir = asNamespace("AMR"))) {
# antibiotic group names, as defined in data-raw/_internals.R, such as `AB_CARBAPENEMS`
val <- eval(parse(text = paste0("AB_", val)), envir = asNamespace("AMR"))
} else if (val %in% AB_lookup$ab) {
# separate drugs, such as `AMX`
val <- as.ab(val)
} else {
stop_("unknown antimicrobial agent (group): ", val, call = FALSE)
}
x_new <- c(x_new, val)
}
x_new <- unique(x_new)
out <- cols_ab[match(x_new, names(cols_ab))]
out[!is.na(out)]
}
generate_warning_abs_missing <- function(missing, any = FALSE) {
missing <- paste0(missing, " (", ab_name(missing, tolower = TRUE, language = NULL), ")")
if (any == TRUE) {