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(v2.1.1.9199) fix eucast

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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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9
R/mo.R
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@ -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)