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(v1.8.0.9002) as.rsi() cleanup, more informative warnings

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dr. M.S. (Matthijs) Berends
2022-03-02 15:38:55 +01:00
parent 18e8525d10
commit 3b2b2be5f8
35 changed files with 267 additions and 320 deletions
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10
R/key_antimicrobials.R
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@@ -150,7 +150,7 @@ key_antimicrobials <- function(x = NULL,
col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
}
if (is.null(col_mo)) {
warning_("No column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`", call = FALSE)
warning_("in `key_antimicrobials()`: no column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`")
gramstain <- NA_character_
kingdom <- NA_character_
} else {
@@ -172,11 +172,11 @@ key_antimicrobials <- function(x = NULL,
if (values_new_length < values_old_length &
any(filter, na.rm = TRUE) &
message_not_thrown_before("key_antimicrobials", name)) {
warning_(ifelse(values_new_length == 0,
warning_("in `key_antimicrobials()`: ",
ifelse(values_new_length == 0,
"No columns available ",
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
"as key antimicrobials for ", name, "s. See ?key_antimicrobials.",
call = FALSE)
"as key antimicrobials for ", name, "s. See ?key_antimicrobials.")
}
generate_antimcrobials_string(x[which(filter), c(universal, values), drop = FALSE])
@@ -217,7 +217,7 @@ key_antimicrobials <- function(x = NULL,
cols = cols)
if (length(unique(key_ab)) == 1) {
warning_("No distinct key antibiotics determined.", call = FALSE)
warning_("in `key_antimicrobials()`: no distinct key antibiotics determined.")
}
key_ab