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dr. M.S. (Matthijs) Berends
2023-01-06 19:21:04 +01:00
parent cf16bc7de1
commit 84ed8c32bb
12 changed files with 37 additions and 64 deletions
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R/aa_helper_functions.R
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@ -229,7 +229,7 @@ search_type_in_df <- function(x, type, info = TRUE) {
# take first 'mo' column
found <- colnames(x)[vapply(FUN.VALUE = logical(1), x, is.mo)]
} else if ("mo" %in% colnames_formatted &&
suppressWarnings(all(x$mo %in% c(NA, AMR::microorganisms$mo)))) {
suppressWarnings(all(x$mo %in% c(NA, AMR_env$MO_lookup$mo)))) {
found <- "mo"
} else if (any(colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$")) {
found <- sort(colnames(x)[colnames_formatted %like_case% "^(mo|microorganism|organism|bacteria|ba[ck]terie)s?$"])