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AMR
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Update mo.R

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Dr. Matthijs Berends 2022-09-25 14:26:08 +02:00 committed by GitHub
parent 3a5e20c11a
commit aa66632934
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1 changed files with 11 additions and 4 deletions
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@ -989,8 +989,8 @@ repair_reference_df <- function(reference_df) {
}
convert_colloquial_input <- function(x) {
x.bak <- trimws(x)
x <- trimws(tolower(x))
x.bak <- trimws2(x)
x <- trimws2(tolower(x))
out <- rep(NA_character_, length(x))
# Streptococci, like GBS = Group B Streptococci (B_STRPT_GRPB)
@ -1019,13 +1019,20 @@ convert_colloquial_input <- function(x) {
out[x %like_case% "gram[ -]?neg.*|negatie?[vf]"] <- "B_GRAMN"
out[x %like_case% "gram[ -]?pos.*|positie?[vf]"] <- "B_GRAMP"
# Salmonella city names, starting with capital species name - they are all S. enterica
# yeasts and fungi
out[x %like_case% "^yeast?"] <- "F_YEAST"
out[x %like_case% "^fung(us|i)"] <- "F_FUNGUS"
# Salmonella city names, starting with capital species name - they are all S. enterica
out[x.bak %like_case% "[sS]almonella [A-Z][a-z]+ ?.*" & x %unlike% "typhi"] <- "B_SLMNL_ENTR"
# trivial names known to the field
out[x %like_case% "meningo[ck]o[ck]"] <- "B_NESSR_MNNG"
out[x %like_case% "gono[ck]o[ck]"] <- "B_NESSR_GNRR"
out[x %like_case% "pneumo[ck]o[ck]"] <- "B_STRPT_PNMN"
# unexisting names (xxx and con are WHONET codes)
out[x %in% c("xxx", "con", "other", "none", "unknown") | x %like_case% "virus"] <- "UNKNOWN"
out
}