P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-10 17:01:52 +02:00
Code Releases Activity

fix coercing NA to custom codes, fixes #107

Browse Source
This commit is contained in:
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
Download Patch File Download Diff File Expand all files Collapse all files

8
R/mo.R
View File

@ -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)])

BIN
R/sysdata.rda
View File

Binary file not shown.