Standardises taxon names by performing a series of text substitutions to remove common inconsistencies in taxonomic nomenclature.
The function takes a character vector of taxon names as input and returns a character vector of taxon names using standardised taxonomic syntax as output.
Details
It removes stray punctuation at the start and end of a character string.
It standardises unusual characters and symbols to ASCII equivalents.
It standardises taxon rank abbreviations and qualifiers (subsp., var., f.), as people use many variants of these terms.
It standardises or removes a few additional filler words used within taxon names (affinis becomes aff.; s.l. and s.s. are removed).
affinis is only treated as an affinity qualifier where it cannot be a
species epithet: it is left alone at the end of a name
(Acacia affinis) and before a rank marker
(Gomphrena affinis subsp. pilbarensis).
Examples
standardise_names(c("Quercus suber",
"Eucalyptus sp.",
"Eucalyptus spp.",
"Agave americana var. marginata",
"Agave americana v marginata",
"Notelaea longifolia forma longifolia",
"Notelaea longifolia f longifolia",
"Acacia affinis dealbata",
"Gomphrena affinis subsp. pilbarensis"))
#> [1] "Quercus suber"
#> [2] "Eucalyptus sp."
#> [3] "Eucalyptus sp."
#> [4] "Agave americana var. marginata"
#> [5] "Agave americana var. marginata"
#> [6] "Notelaea longifolia f. longifolia"
#> [7] "Notelaea longifolia f. longifolia"
#> [8] "Acacia aff. dealbata"
#> [9] "Gomphrena affinis subsp. pilbarensis"