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(v1.6.0.9008) unlike, bugfix for col_mo naming

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-04-23 09:59:36 +02:00
parent c6289c3fc3
commit 70b803dbb6
33 changed files with 269 additions and 137 deletions
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12
R/mo.R
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@ -708,7 +708,7 @@ exec_as.mo <- function(x,
# check for very small input, but ignore the O antigens of E. coli
if (nchar(gsub("[^a-zA-Z]", "", x_trimmed[i])) < 3
& !toupper(x_backup_without_spp[i]) %like_case% "O?(26|103|104|104|111|121|145|157)") {
& toupper(x_backup_without_spp[i]) %unlike_case% "O?(26|103|104|104|111|121|145|157)") {
# fewer than 3 chars and not looked for species, add as failure
x[i] <- lookup(mo == "UNKNOWN")
if (initial_search == TRUE) {
@ -860,7 +860,7 @@ exec_as.mo <- function(x,
x[i] <- lookup(genus == "Salmonella", uncertainty = -1)
next
} else if (x_backup[i] %like_case% "[sS]almonella [A-Z][a-z]+ ?.*" &
!x_backup[i] %like% "t[iy](ph|f)[iy]") {
x_backup[i] %unlike% "t[iy](ph|f)[iy]") {
# Salmonella with capital letter species like "Salmonella Goettingen" - they're all S. enterica
# except for S. typhi, S. paratyphi, S. typhimurium
x[i] <- lookup(fullname == "Salmonella enterica", uncertainty = -1)
@ -916,7 +916,7 @@ exec_as.mo <- function(x,
# FIRST TRY FULLNAMES AND CODES ----
# if only genus is available, return only genus
if (all(!c(x[i], b.x_trimmed) %like_case% " ")) {
if (all(c(x[i], b.x_trimmed) %unlike_case% " ")) {
found <- lookup(fullname_lower %in% c(h.x_species, i.x_trimmed_species),
haystack = data_to_check)
if (!is.na(found)) {
@ -1123,8 +1123,8 @@ exec_as.mo <- function(x,
if (isTRUE(debug)) {
cat(font_bold("\n[ UNCERTAINTY LEVEL", now_checks_for_uncertainty_level, "] (3) look for genus only, part of name\n"))
}
if (nchar(g.x_backup_without_spp) > 4 & !b.x_trimmed %like_case% " ") {
if (!b.x_trimmed %like_case% "^[A-Z][a-z]+") {
if (nchar(g.x_backup_without_spp) > 4 & b.x_trimmed %unlike_case% " ") {
if (b.x_trimmed %unlike_case% "^[A-Z][a-z]+") {
if (isTRUE(debug)) {
message("Running '", paste(b.x_trimmed, "species"), "'")
}
@ -1268,7 +1268,7 @@ exec_as.mo <- function(x,
stringsAsFactors = FALSE)
return(found)
}
if (b.x_trimmed %like_case% "(fungus|fungi)" & !b.x_trimmed %like_case% "fungiphrya") {
if (b.x_trimmed %like_case% "(fungus|fungi)" & b.x_trimmed %unlike_case% "fungiphrya") {
found <- "F_FUNGUS"
found_result <- found
found <- lookup(mo == found)