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fix coercing NA to custom codes, fixes #107

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dr. M.S. (Matthijs) Berends
2023-05-08 13:04:18 +02:00
parent 9de19fdc49
commit bf08d136a0
9 changed files with 19719 additions and 56 deletions
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8
R/mo.R
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@ -214,10 +214,10 @@ as.mo <- function(x,
# 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)]
# From SNOMED ----
if (any(is.na(out) & !is.na(x)) && any(is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed), na.rm = TRUE)) {
# found this extremely fast gem here: https://stackoverflow.com/a/11002456/4575331
out[is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed)] <- AMR_env$MO_lookup$mo[rep(seq_along(AMR_env$MO_lookup$snomed), vapply(FUN.VALUE = double(1), AMR_env$MO_lookup$snomed, length))[match(x[is.na(out) & x %in% unlist(AMR_env$MO_lookup$snomed)], unlist(AMR_env$MO_lookup$snomed))]]
}
# based on this extremely fast gem: https://stackoverflow.com/a/11002456/4575331
snomeds <- unlist(AMR_env$MO_lookup$snomed)
snomeds <- snomeds[!is.na(snomeds)]
out[is.na(out) & x %in% snomeds] <- AMR_env$MO_lookup$mo[rep(seq_along(AMR_env$MO_lookup$snomed), vapply(FUN.VALUE = double(1), AMR_env$MO_lookup$snomed, length))[match(x[is.na(out) & x %in% snomeds], snomeds)]]
# From other familiar output ----
# such as Salmonella groups, colloquial names, etc.
out[is.na(out)] <- convert_colloquial_input(x[is.na(out)])

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R/sysdata.rda
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