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(v1.3.0.9029) eucast rules fix, unique()

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dr. M.S. (Matthijs) Berends
2020-09-25 14:44:50 +02:00
parent 1d982a82b4
commit 9667c2994f
32 changed files with 234 additions and 160 deletions
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4
R/zzz.R
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@ -90,10 +90,10 @@ create_MO_lookup <- function() {
MO_lookup$subspecies)))
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname)
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"])
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower))
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
# add a column with only "e coli" like combinations
MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower)
MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
# so arrange data on prevalence first, then kingdom, then full name
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ]