Normalize a source taxon name for an authority lookup — clean_taxon

Strips the open-nomenclature and qualifier noise that source spreadsheets carry in their column headers and species lists, so the name reaches WoRMS in a form it can match. "Bathophilus sp." becomes "Bathophilus" (WoRMS holds the genus, never the sp. form), "Phaeocystis cf pouchetti" becomes "Phaeocystis pouchetti", "indistinguished Pterosperma spp." becomes "Pterosperma".

Usage

clean_taxon_name(x)

Arguments

x: character vector of source names

Value

character vector of cleaned names (NA in, NA out)

Details

Use the result as the lookup query only — never as ds_taxa_code. For sio_mesopelagic-fish the local code is the verbatim column header and is the join key from obs; rewriting it would silently orphan every observation.

This generalizes the hand-maintained name_query column that metadata/calcofi/phytoplankton/taxon_worms.csv already carries for one dataset.

Examples

clean_taxon_name(c("Bathophilus sp.", "Phaeocystis cf pouchetti",
                   "indistinguished Pterosperma spp.", "Uria aalge"))
#> [1] "Bathophilus"           "Phaeocystis pouchetti" "Pterosperma"          
#> [4] "Uria aalge"