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(v2.1.1.9199) fix eucast

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2025-03-14 13:43:22 +01:00
parent e134e01418
commit 58d7aa8790
57 changed files with 143 additions and 122 deletions
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7
R/aa_helper_functions.R
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@ -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
View File

@ -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)