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(v2.1.1.9081) HUGE microorganisms update for fungi!

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dr. M.S. (Matthijs) Berends
2024-09-29 22:17:56 +02:00
parent a558f4c121
commit ac1c40d8bb
119 changed files with 36445 additions and 67400 deletions
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15
R/mo.R
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@ -315,12 +315,15 @@ as.mo <- function(x,
# take out the parts, split by space
x_parts <- strsplit(gsub("-", " ", x_out, fixed = TRUE), " ", fixed = TRUE)[[1]]
# 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
if (paste(x_parts[1:2], collapse = " ") %in% MO_lookup_current$fullname_lower) {
filtr <- which(MO_lookup_current$fullname_lower %like% paste(x_parts[1:2], collapse = " "))
} else if (x_parts[1] %in% MO_lookup_current$genus_lower && !paste(x_parts[1:2], collapse = " ") %in% MO_lookup_current$fullname_lower) {
# for a known genus, but unknown (sub)species
filtr <- which(MO_lookup_current$genus_lower == x_parts[1])
minimum_matching_score <- 0.05
} else if (nchar(gsub("[^a-z]", "", x_parts[1], perl = TRUE)) <= 3) {
filtr <- which(MO_lookup_current$full_first == substr(x_parts[1], 1, 1) &
(MO_lookup_current$species_first == substr(x_parts[2], 1, 1) |
@ -953,11 +956,15 @@ print.mo_uncertainties <- function(x, n = 10, ...) {
),
collapse = "\n"
),
# Add note if result was coerced to accepted taxonomic name
ifelse(x[i, ]$keep_synonyms == FALSE & x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
ifelse(x[i, ]$mo %in% AMR_env$MO_lookup$mo[which(AMR_env$MO_lookup$status == "synonym")],
paste0(
strrep(" ", nchar(x[i, ]$original_input) + 6),
font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL)
ifelse(x[i, ]$keep_synonyms == FALSE,
# Add note if result was coerced to accepted taxonomic name
font_red(paste0("This outdated taxonomic name was converted to ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", synonym_mo_to_accepted_mo(x[i, ]$mo), ")."), collapse = NULL),
# Or add note if result is currently another taxonomic name
font_red(paste0(font_bold("Note: "), "The current name is ", font_italic(AMR_env$MO_lookup$fullname[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], collapse = NULL), " (", AMR_env$MO_lookup$ref[match(synonym_mo_to_accepted_mo(x[i, ]$mo), AMR_env$MO_lookup$mo)], ")."), collapse = NULL)
)
),
""
),