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(v0.7.1.9095) get_column_abx() fix

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dr. M.S. (Matthijs) Berends
2019-10-06 22:19:26 +02:00
parent 3d5692219e
commit 1e260d85c8
10 changed files with 20 additions and 15 deletions
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11
R/guess_ab_col.R
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@ -129,9 +129,14 @@ get_column_abx <- function(x,
x <- as.character(df_trans$colnames)
names(x) <- df_trans$abcode
# remove the ones that do not already have the rsi class (as.rsi) and that have >50% invalid values
x <- sapply(x, function(col = x, df = x_bak) {
ifelse(is.rsi(as.data.frame(df)[, col]) |
# remove the ones that are not a valid AB code, ATC code, name, abbreviation or synonym,
# and do not already have the rsi class (as.rsi)
# and that have >50% invalid values
vectr_antibiotics <- unique(toupper(unlist(AMR::antibiotics[,c("ab", "atc", "name", "abbreviations", "synonyms")])))
vectr_antibiotics <- vectr_antibiotics[!is.na(vectr_antibiotics) & nchar(vectr_antibiotics) >= 3]
x <- sapply(x, function(col = x, df = x_bak) {
ifelse(toupper(col) %in% vectr_antibiotics |
is.rsi(as.data.frame(df)[, col]) |
is.rsi.eligible(as.data.frame(df)[, col], threshold = 0.5),
col,
NA)