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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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8
R/mdro.R
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@ -240,7 +240,7 @@ mdro <- function(x = NULL,
}
if (!is.null(list(...)$country)) {
warning_("Using `country` is deprecated, use `guideline` instead. See ?mdro.", call = FALSE)
warning_("in `mdro()`: using `country` is deprecated, use `guideline` instead. See ?mdro")
guideline <- list(...)$country
}
@ -1550,8 +1550,8 @@ mdro <- function(x = NULL,
if (guideline$code == "cmi2012") {
if (any(x$MDRO == -1, na.rm = TRUE)) {
if (message_not_thrown_before("mdro", "availability")) {
warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
warning_("in `mdro()`: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes), " (set with `pct_required_classes`)")
}
# set these -1s to NA
x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
@ -1709,7 +1709,7 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
return("error")
})
if (identical(qry, "error")) {
warning_("in custom_mdro_guideline(): rule ", i,
warning_("in `custom_mdro_guideline()`: rule ", i,
" (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
pkg_env$err_msg,
call = FALSE,