mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 23:41:51 +02:00
(v2.1.1.9199) fix eucast
This commit is contained in:
@ -532,9 +532,14 @@ word_wrap <- function(...,
|
||||
url = paste0("ide:run:AMR::", parts[cmds & parts %unlike% "[.]"]),
|
||||
txt = parts[cmds & parts %unlike% "[.]"]
|
||||
)
|
||||
# datasets should give help page as well
|
||||
parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")] <- font_url(
|
||||
url = paste0("ide:help:AMR::", gsub("()", "", parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")], fixed = TRUE)),
|
||||
txt = parts[parts %in% c("antimicrobials", "microorganisms", "microorganisms.codes", "microorganisms.groups")]
|
||||
)
|
||||
# text starting with `?` must also lead to the help page
|
||||
parts[parts %like% "^[?]"] <- font_url(
|
||||
url = paste0("ide:help:AMR::", gsub("()", "", gsub("^[?]", "", parts[parts %like% "^[?]"]), fixed = TRUE)),
|
||||
url = paste0("ide:help:AMR::", parts[parts %like% "^[?]"]),
|
||||
txt = parts[parts %like% "^[?]"]
|
||||
)
|
||||
msg <- paste0(parts, collapse = "`")
|
||||
|
9
R/mo.R
9
R/mo.R
@ -242,7 +242,14 @@ as.mo <- function(x,
|
||||
# one exception: "Fungi" matches the kingdom, but instead it should return the 'unknown' code for fungi
|
||||
out[out == "F_[KNG]_FUNGI"] <- "F_FUNGUS"
|
||||
# From known codes ----
|
||||
out[is.na(out) & toupper(x) %in% AMR::microorganisms.codes$code] <- AMR::microorganisms.codes$mo[match(toupper(x)[is.na(out) & toupper(x) %in% AMR::microorganisms.codes$code], AMR::microorganisms.codes$code)]
|
||||
ind <- is.na(out) & toupper(x) %in% AMR::microorganisms.codes$code
|
||||
out[ind] <- AMR::microorganisms.codes$mo[match(toupper(x)[ind], AMR::microorganisms.codes$code)]
|
||||
if (length(which(ind)) > 0 && isTRUE(info) && message_not_thrown_before("as.mo_microorganisms.codes", is.na(out), toupper(x))) {
|
||||
message_(
|
||||
"Retrieved value", ifelse(sum(ind) > 1, "s", ""),
|
||||
" from the `microorganisms.codes` data set for ", vector_and(toupper(x)[ind]), "."
|
||||
)
|
||||
}
|
||||
# From SNOMED ----
|
||||
# based on this extremely fast gem: https://stackoverflow.com/a/11002456/4575331
|
||||
snomeds <- unlist(AMR_env$MO_lookup$snomed)
|
||||
|
Reference in New Issue
Block a user