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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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16
R/mo_property.R
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@ -660,10 +660,20 @@ mo_url <- function(x, open = FALSE, language = get_locale(), ...) {
pm_left_join(pm_select(microorganisms, mo, source, species_id), by = "mo")
df$url <- ifelse(df$source == "CoL",
paste0(catalogue_of_life$url_CoL, "details/species/id/", df$species_id, "/"),
ifelse(df$source == "DSMZ",
paste0(catalogue_of_life$url_DSMZ, "/advanced_search?adv[taxon-name]=", gsub(" ", "+", mo_names), "/"),
NA_character_))
NA_character_)
u <- df$url
u[mo_kingdom(mo) == "Bacteria"] <- paste0(catalogue_of_life$url_LPSN, "/species/", gsub(" ", "-", tolower(mo_names), fixed = TRUE))
u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"] <- gsub("/species/",
"/genus/",
u[mo_kingdom(mo) == "Bacteria" & mo_rank(mo) == "genus"],
fixed = TRUE)
u[mo_kingdom(mo) == "Bacteria" &
mo_rank(mo) %in% c("subsp.", "infraspecies")] <- gsub("/species/",
"/subspecies/",
u[mo_kingdom(mo) == "Bacteria" &
mo_rank(mo) %in% c("subsp.", "infraspecies")],
fixed = TRUE)
names(u) <- mo_names
if (open == TRUE) {