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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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24
R/mo.R
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@ -1481,14 +1481,22 @@ exec_as.mo <- function(x,
if (NROW(uncertainties) > 0 & initial_search == TRUE) {
uncertainties <- as.list(pm_distinct(uncertainties, input, .keep_all = TRUE))
pkg_env$mo_uncertainties <- uncertainties
plural <- c("", "it", "was")
if (length(uncertainties$input) > 1) {
plural <- c("s", "them", "were")
if (message_not_thrown_before("as.mo", "uncertainties", uncertainties$input)) {
plural <- c("", "this", "uncertainty")
if (length(uncertainties$input) > 1) {
plural <- c("s", "these", "uncertainties")
}
if (length(uncertainties$input) <= 3) {
examples <- vector_and(paste0('"', uncertainties$input,
'" (assuming ', font_italic(uncertainties$fullname, collapse = NULL), ")"),
quotes = FALSE)
} else {
examples <- paste0(nr2char(length(uncertainties$input)), " microorganism", plural[1])
}
msg <- paste0("Function `as.mo()` is uncertain about ", examples,
". Run `mo_uncertainties()` to review ", plural[2], " ", plural[3], ".")
message_(msg)
}
msg <- paste0("Translation is uncertain of ", nr2char(length(uncertainties$input)), " microorganism", plural[1],
". Use `mo_uncertainties()` to review ", plural[2], ".")
message_(msg)
}
x[already_known] <- x_known
}
@ -1505,7 +1513,7 @@ exec_as.mo <- function(x,
# nolint start
# comment below code if all staphylococcal species are categorised as CoNS/CoPS
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
if (message_not_thrown_before("as.mo_becker")) {
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: ",
font_italic(paste("S.",
sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),