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add mo_current()
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9
R/mo.R
9
R/mo.R
@ -1094,14 +1094,19 @@ load_mo_uncertainties <- function(metadata) {
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AMR_env$mo_uncertainties <- metadata$uncertainties
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}
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synonym_mo_to_accepted_mo <- function(x) {
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synonym_mo_to_accepted_mo <- function(x, fill_in_accepted = FALSE) {
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x_gbif <- AMR::microorganisms$gbif_renamed_to[match(x, AMR::microorganisms$mo)]
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x_lpsn <- AMR::microorganisms$lpsn_renamed_to[match(x, AMR::microorganisms$mo)]
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x_gbif[!x_gbif %in% AMR::microorganisms$gbif] <- NA
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x_lpsn[!x_lpsn %in% AMR::microorganisms$lpsn] <- NA
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ifelse(is.na(x_lpsn),
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out <- ifelse(is.na(x_lpsn),
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AMR::microorganisms$mo[match(x_gbif, AMR::microorganisms$gbif)],
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AMR::microorganisms$mo[match(x_lpsn, AMR::microorganisms$lpsn)]
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)
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if (isTRUE(fill_in_accepted)) {
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x_accepted <- which(AMR::microorganisms$status[match(x, AMR::microorganisms$mo)] == "accepted")
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out[x_accepted] <- x[x_accepted]
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}
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out
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}
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