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(v2.1.1.9070) fix for mo_current mo (no-verify)

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dr. M.S. (Matthijs) Berends
2024-07-19 18:04:45 +02:00
parent 83907c9c65
commit 573c0346ed
6 changed files with 13 additions and 13 deletions
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14
R/mo.R
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@ -1258,14 +1258,14 @@ synonym_mo_to_accepted_mo <- function(x, fill_in_accepted = FALSE, dataset = AMR
# make sure to get the latest name, e.g. Fusarium pulicaris robiniae was first renamed to Fusarium roseum, then to Fusarium sambucinum
# we need the MO of Fusarium pulicaris robiniae to return the MO of Fusarium sambucinum
idx <- !is.na(is_still_synonym) & is_still_synonym
x_gbif <- dataset$gbif_renamed_to[match(out[idx], dataset$mo)]
x_mycobank <- dataset$mycobank_renamed_to[match(out[idx], dataset$mo)]
x_lpsn <- dataset$lpsn_renamed_to[match(out[idx], dataset$mo)]
must_be_corrected <- !is.na(is_still_synonym) & is_still_synonym
x_gbif <- dataset$gbif_renamed_to[match(out, dataset$mo)]
x_mycobank <- dataset$mycobank_renamed_to[match(out, dataset$mo)]
x_lpsn <- dataset$lpsn_renamed_to[match(out, dataset$mo)]
out[idx][!is.na(x_gbif)] <- dataset$mo[match(x_gbif[idx][!is.na(x_gbif)], dataset$gbif)]
out[idx][!is.na(x_mycobank)] <- dataset$mo[match(x_mycobank[idx][!is.na(x_mycobank)], dataset$mycobank)]
out[idx][!is.na(x_lpsn)] <- dataset$mo[match(x_lpsn[idx][!is.na(x_lpsn)], dataset$lpsn)]
out[must_be_corrected & !is.na(x_gbif)] <- dataset$mo[match(x_gbif[must_be_corrected & !is.na(x_gbif)], dataset$gbif)]
out[must_be_corrected & !is.na(x_mycobank)] <- dataset$mo[match(x_mycobank[must_be_corrected & !is.na(x_mycobank)], dataset$mycobank)]
out[must_be_corrected & !is.na(x_lpsn)] <- dataset$mo[match(x_lpsn[must_be_corrected & !is.na(x_lpsn)], dataset$lpsn)]
is_still_synonym <- dataset$status[match(out, dataset$mo)] == "synonym"
}

2
R/mo_property.R
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@ -928,7 +928,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), keep_synonyms =
# overwrite with LPSN:
u[!is.na(x.lpsn)] <- paste0(TAXONOMY_VERSION$LPSN$url, "/", x.rank[!is.na(x.lpsn)], "/", gsub(" ", "-", tolower(x.name[!is.na(x.lpsn)]), fixed = TRUE))
# overwrite with MycoBank (bacteria from LPSN will not be overwritten since MycoBank has no bacteria)
u[!is.na(x.mycobank)] <- paste0(TAXONOMY_VERSION$MycoBank$url, "/name/", gsub(" ", "%20", tolower(x.name[!is.na(x.mycobank)]), fixed = TRUE))
u[!is.na(x.mycobank)] <- paste0(TAXONOMY_VERSION$MycoBank$url, "/mb/", gsub(" ", "%20", tolower(x.mycobank[!is.na(x.mycobank)]), fixed = TRUE))
names(u) <- x.name