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(v1.7.1.9064) eucast 3.3 for mdro(), major change to repeated calling

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dr. M.S. (Matthijs) Berends
2021-12-11 13:41:31 +01:00
parent e18c49ed93
commit 77ba4318ea
64 changed files with 51141 additions and 9840 deletions
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7
R/key_antimicrobials.R
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@@ -142,7 +142,7 @@ key_antimicrobials <- function(x = NULL,
# force regular data.frame, not a tibble or data.table
x <- as.data.frame(x, stringsAsFactors = FALSE)
cols <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns)
cols <- get_column_abx(x, info = FALSE, only_rsi_columns = only_rsi_columns, fn = "key_antimicrobials")
# try to find columns based on type
# -- mo
@@ -171,7 +171,7 @@ key_antimicrobials <- function(x = NULL,
if (values_new_length < values_old_length &
any(filter, na.rm = TRUE) &
message_not_thrown_before(paste0("key_antimicrobials.", name))) {
message_not_thrown_before("key_antimicrobials", name)) {
warning_(ifelse(values_new_length == 0,
"No columns available ",
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
@@ -238,7 +238,8 @@ all_antimicrobials <- function(x = NULL,
# force regular data.frame, not a tibble or data.table
x <- as.data.frame(x, stringsAsFactors = FALSE)
cols <- get_column_abx(x, only_rsi_columns = only_rsi_columns, info = FALSE, sort = FALSE)
cols <- get_column_abx(x, only_rsi_columns = only_rsi_columns, info = FALSE,
sort = FALSE, fn = "all_antimicrobials")
generate_antimcrobials_string(x[ , cols, drop = FALSE])
}