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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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47
R/mo.R
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@ -1489,9 +1489,8 @@ exec_as.mo <- function(x,
"You can also use your own reference data with set_mo_source() or directly, e.g.:\n",
' as.mo("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n',
' mo_name("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n')
warning_(paste0("\n", msg),
warning_(paste0("\nin `as.mo()`: ", msg),
add_fn = font_red,
call = FALSE,
immediate = TRUE) # thus will always be shown, even if >= warnings
}
# handling uncertainties ----
@ -1531,12 +1530,11 @@ exec_as.mo <- function(x,
# comment below code if all staphylococcal species are categorised as CoNS/CoPS
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
if (message_not_thrown_before("as.mo", "becker")) {
warning_("Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
font_italic(paste("S.",
sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
collapse = ", ")),
". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
call = FALSE,
immediate = TRUE)
}
}
@ -1709,8 +1707,7 @@ pillar_shaft.mo <- function(x, ...) {
col <- "The data"
}
warning_(col, " contains old MO codes (from a previous AMR package version). ",
"Please update your MO codes with `as.mo()`.",
call = FALSE)
"Please update your MO codes with `as.mo()`.")
}
# make it always fit exactly
@ -1784,8 +1781,7 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
names(x) <- x_names
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
warning_("Some MO codes are from a previous AMR package version. ",
"Please update these MO codes with `as.mo()`.",
call = FALSE)
"Please update the MO codes with `as.mo()`.")
}
print.default(x, quote = FALSE)
}
@ -1814,8 +1810,7 @@ summary.mo <- function(object, ...) {
as.data.frame.mo <- function(x, ...) {
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
warning_("The data contains old MO codes (from a previous AMR package version). ",
"Please update your MO codes with `as.mo()`.",
call = FALSE)
"Please update your MO codes with `as.mo()`.")
}
nm <- deparse1(substitute(x))
if (!"nm" %in% names(list(...))) {
@ -2119,24 +2114,22 @@ replace_old_mo_codes <- function(x, property) {
n_unique <- ""
}
if (property != "mo") {
warning_(paste0("The input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
"Please update your MO codes with `as.mo()` to increase speed."),
call = FALSE)
warning_("in `mo_", property, "()`: the input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
"Please update your MO codes with `as.mo()` to increase speed.")
} else {
warning_(paste0("The input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),
ifelse(n_solved == 1, " was", " were"),
ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
"to ", ifelse(n_solved == 1, "a ", ""),
"currently used MO code", ifelse(n_solved == 1, "", "s"),
ifelse(n_unsolved > 0,
paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
".")),
call = FALSE)
warning_("in `as.mo()`: the input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),
ifelse(n_solved == 1, " was", " were"),
ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
"to ", ifelse(n_solved == 1, "a ", ""),
"currently used MO code", ifelse(n_solved == 1, "", "s"),
ifelse(n_unsolved > 0,
paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
"."))
}
}
x