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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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16
R/eucast_rules.R
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@ -181,8 +181,7 @@ eucast_rules <- function(x,
meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
if ("custom" %in% rules & is.null(custom_rules)) {
warning_("No custom rules were set with the `custom_rules` argument",
call = FALSE,
warning_("in `eucast_rules()`: no custom rules were set with the `custom_rules` argument",
immediate = TRUE)
rules <- rules[rules != "custom"]
if (length(rules) == 0) {
@ -915,13 +914,12 @@ eucast_rules <- function(x,
# take order from original data set
warn_lacking_rsi_class <- warn_lacking_rsi_class[order(colnames(x.bak))]
warn_lacking_rsi_class <- warn_lacking_rsi_class[!is.na(warn_lacking_rsi_class)]
warning_("Not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
warning_("in `eucast_rules()`: not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
" - ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1,
warn_lacking_rsi_class,
paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)])), ")\n",
" - ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n",
" - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))",
call = FALSE)
" - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))")
}
# Return data set ---------------------------------------------------------
@ -986,14 +984,14 @@ edit_rsi <- function(x,
TRUE
})
suppressWarnings(new_edits[rows, cols] <<- to)
warning_("Value \"", to, "\" added to the factor levels of column", ifelse(length(cols) == 1, "", "s"),
warning_("in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
ifelse(length(cols) == 1, "", "s"),
" ", vector_and(cols, quotes = "`", sort = FALSE),
" because this value was not an existing factor level.",
call = FALSE)
" because this value was not an existing factor level.")
txt_warning()
warned <- FALSE
} else {
warning_(w$message, call = FALSE)
warning_("in `eucast_rules()`: ", w$message)
txt_warning()
}
},