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as.mo fix

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dr. M.S. (Matthijs) Berends
2023-05-26 19:20:21 +02:00
parent c6135d2082
commit 766db4e21f
5 changed files with 15 additions and 8 deletions
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17
R/mo.R
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@ -283,12 +283,19 @@ as.mo <- function(x,
# do a pre-match on first character (and if it contains a space, first chars of first two terms)
if (length(x_parts) %in% c(2, 3)) {
# for genus + species + subspecies
filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts[1], 1, 1) |
AMR_env$MO_lookup$species_first == substr(x_parts[2], 1, 1) |
AMR_env$MO_lookup$subspecies_first == substr(x_parts[2], 1, 1) |
AMR_env$MO_lookup$subspecies_first == substr(x_parts[3], 1, 1))
if (nchar(gsub("[^a-z]", "", x_parts[1], perl = TRUE)) <= 3) {
filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts[1], 1, 1) &
(AMR_env$MO_lookup$species_first == substr(x_parts[2], 1, 1) |
AMR_env$MO_lookup$subspecies_first == substr(x_parts[2], 1, 1) |
AMR_env$MO_lookup$subspecies_first == substr(x_parts[3], 1, 1)))
} else {
filtr <- which(AMR_env$MO_lookup$full_first == substr(x_parts[1], 1, 1) |
AMR_env$MO_lookup$species_first == substr(x_parts[2], 1, 1) |
AMR_env$MO_lookup$subspecies_first == substr(x_parts[2], 1, 1) |
AMR_env$MO_lookup$subspecies_first == substr(x_parts[3], 1, 1))
}
} else if (length(x_parts) > 3) {
first_chars <- paste0("(^| )", "[", paste(substr(x_parts, 1, 1), collapse = ""), "]")
first_chars <- paste0("(^| )[", paste(substr(x_parts, 1, 1), collapse = ""), "]")
filtr <- which(AMR_env$MO_lookup$full_first %like_case% first_chars)
} else if (nchar(x_out) == 4) {
# no space and 4 characters - probably a code such as STAU or ESCO

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R/sysdata.rda
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