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(v1.2.0.9011) mo_domain(), improved error handling

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dr. M.S. (Matthijs) Berends
2020-06-22 11:18:40 +02:00
parent e88d7853f5
commit 93a158aebd
49 changed files with 523 additions and 590 deletions
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10
R/zzz.R
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@ -23,11 +23,11 @@
assign(x = "MO_lookup",
value = create_MO_lookup(),
envir = asNamespace("AMR"))
assign(x = "MO.old_lookup",
value = create_MO.old_lookup(),
envir = asNamespace("AMR"))
assign(x = "mo_codes_v0.5.0",
value = make_trans_tbl(),
envir = asNamespace("AMR"))
@ -47,10 +47,10 @@ create_MO_lookup <- function() {
# use this paste instead of `fullname` to
# work with Viridans Group Streptococci, etc.
MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
MO_lookup$species,
MO_lookup$subspecies)))
MO_lookup$species,
MO_lookup$subspecies)))
MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname), "fullname_lower"] <- tolower(trimws(MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname),
"fullname"]))
"fullname"]))
MO_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower)
# add a column with only "e coli" like combinations