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(v1.5.0.9028) Updated taxonomy until March 2021

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dr. M.S. (Matthijs) Berends
2021-03-04 23:28:32 +01:00
parent 41f94cde97
commit ddf88345f1
95 changed files with 25868 additions and 21574 deletions
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28
R/mo.R
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@@ -463,16 +463,22 @@ exec_as.mo <- function(x,
# translate 'unknown' names back to English
if (any(x %like% "unbekannt|onbekend|desconocid|sconosciut|iconnu|desconhecid", na.rm = TRUE)) {
trns <- subset(translations_file, pattern %like% "unknown" | affect_mo_name == TRUE)
lapply(seq_len(nrow(trns)),
function(i) x <<- gsub(pattern = trns$replacement[i],
replacement = trns$pattern[i],
x = x,
ignore.case = TRUE,
perl = TRUE))
langs <- LANGUAGES_SUPPORTED[LANGUAGES_SUPPORTED != "en"]
for (l in langs) {
for (i in seq_len(nrow(trns))) {
if (!is.na(trns[i, l, drop = TRUE])) {
x <- gsub(pattern = trns[i, l, drop = TRUE],
replacement = trns$pattern[i],
x = x,
ignore.case = TRUE,
perl = TRUE)
}
}
}
}
x_backup <- x
# from here on case-insensitive
x <- tolower(x)
@@ -1551,6 +1557,9 @@ exec_as.mo <- function(x,
if (property == "mo") {
x <- set_clean_class(x, new_class = c("mo", "character"))
}
# keep track of time
end_time <- Sys.time()
if (length(mo_renamed()) > 0) {
print(mo_renamed())
@@ -1571,10 +1580,9 @@ exec_as.mo <- function(x,
x <- structure(x, uncertainties = uncertainties)
} else {
# keep track of time - give some hints to improve speed if it takes a long time
end_time <- Sys.time()
delta_time <- difftime(end_time, start_time, units = "secs")
if (delta_time >= 30) {
message_("Using `as.mo()` took ", delta_time, " seconds, which is a long time. Some suggestions to improve speed include:")
message_("Using `as.mo()` took ", round(delta_time), " seconds, which is a long time. Some suggestions to improve speed include:")
message_(word_wrap("- Try to use as many valid taxonomic names as possible for your input.",
extra_indent = 2),
as_note = FALSE)
@@ -1922,7 +1930,7 @@ print.mo_renamed <- function(x, ...) {
"",
paste0(" (", gsub("et al.", font_italic("et al."), x$old_ref[i]), ")")),
" was renamed ",
ifelse(as.integer(gsub("[^0-9]", "", x$new_ref[i])) < as.integer(gsub("[^0-9]", "", x$old_ref[i])),
ifelse(!x$new_ref[i] %in% c("", NA) && as.integer(gsub("[^0-9]", "", x$new_ref[i])) < as.integer(gsub("[^0-9]", "", x$old_ref[i])),
font_bold("back to "),
""),
font_italic(x$new_name[i]),