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add mo_current()

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-10 10:12:08 +02:00
parent b753b84128
commit 43c638d122
7 changed files with 37 additions and 8 deletions
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9
R/mo.R
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@ -1094,14 +1094,19 @@ load_mo_uncertainties <- function(metadata) {
AMR_env$mo_uncertainties <- metadata$uncertainties
}
synonym_mo_to_accepted_mo <- function(x) {
synonym_mo_to_accepted_mo <- function(x, fill_in_accepted = FALSE) {
x_gbif <- AMR::microorganisms$gbif_renamed_to[match(x, AMR::microorganisms$mo)]
x_lpsn <- AMR::microorganisms$lpsn_renamed_to[match(x, AMR::microorganisms$mo)]
x_gbif[!x_gbif %in% AMR::microorganisms$gbif] <- NA
x_lpsn[!x_lpsn %in% AMR::microorganisms$lpsn] <- NA
ifelse(is.na(x_lpsn),
out <- ifelse(is.na(x_lpsn),
AMR::microorganisms$mo[match(x_gbif, AMR::microorganisms$gbif)],
AMR::microorganisms$mo[match(x_lpsn, AMR::microorganisms$lpsn)]
)
if (isTRUE(fill_in_accepted)) {
x_accepted <- which(AMR::microorganisms$status[match(x, AMR::microorganisms$mo)] == "accepted")
out[x_accepted] <- x[x_accepted]
}
out
}