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auto-remove missing ABs in antibiogram()

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dr. M.S. (Matthijs) Berends
2023-02-22 16:00:52 +01:00
parent c2cfc5ef84
commit 551aaf6517
4 changed files with 15 additions and 11 deletions
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20
R/antibiogram.R
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@ -313,15 +313,19 @@ antibiogram <- function(x,
df_ab <- get_column_abx(x, verbose = FALSE, info = FALSE)
# get antibiotics from user
user_ab <- suppressMessages(suppressWarnings(lapply(antibiotics, as.ab, flag_multiple_results = FALSE, info = FALSE)))
user_ab <- lapply(user_ab, function(x) unname(df_ab[match(x, names(df_ab))]))
# remove non-existing columns
# non_existing <- unlist(antibiotics)[is.na(unlist(abx_ab))]
# if (length(non_existing) > 0) {
# warning_("The following antibiotics were not available and ignored: ", vector_and(non_existing, sort = FALSE))
# abx_user <- Map(antibiotics, abx_user, f = function(input, ab) input[!is.na(ab)])
# }
non_existing <- character(0)
user_ab <- lapply(user_ab, function(x) {
out <- unname(df_ab[match(x, names(df_ab))])
non_existing <<- c(non_existing, x[is.na(out) & !is.na(x)])
# remove non-existing columns
out[!is.na(out)]
})
user_ab <- user_ab[unlist(lapply(user_ab, length)) > 0]
if (length(non_existing) > 0) {
warning_("The following antibiotics were not available and ignored: ", vector_and(ab_name(non_existing, language = NULL, tolower = TRUE), quotes = FALSE))
}
# make list unique
antibiotics <- unique(user_ab)
# go through list to set AMR in combinations