Clean taxonomic names

A utility to sanitize taxonomic names to increase probability of resolving names.

Usage

clean_names(
  names,
  fix_delim = TRUE,
  binomial_only = TRUE,
  remove_sp = TRUE,
  ascii_only = TRUE,
  lowercase = TRUE,
  remove_punc = FALSE
)

Arguments

names

a character vector of taxonomic names (usually species names)

fix_delim

Should we replace separators ., _, - with spaces? e.g. 'Homo.sapiens' becomes 'Homo sapiens'. logical, default TRUE.

binomial_only

Attempt to prune name to a binomial name, e.g. Genus and species (specific epithet), e.g. Homo sapiens sapiens becomes Homo sapiens. logical, default TRUE.

remove_sp

Should we drop unspecified species epithet designations? e.g. Homo sp. becomes Homo (thus only matching against genus level ids). logical, default TRUE.

ascii_only

should we coerce strings to ascii characters? (see stringi::stri_trans_general())

lowercase

should names be coerced to lower-case to provide case-insensitive matching?

remove_punc

replace all punctuation but apostrophes with a space, remove apostrophes

Details

Current implementation is limited to handling a few common cases. Additional extensions may be added later. A goal of the clean_names function is that any modification rule of the name strings be precise, atomic, and toggle-able, rather than relying on clever but more opaque rules and arbitrary scores. This utility should always be used with care, as indiscriminate modification of names may result in successful but inaccurate name matching. A good pattern is to only apply this function to the subset of names that cannot be directly matched.

Examples

clean_names(c("Homo sapiens sapiens", "Homo.sapiens", "Homo sp."))
#> [1] "homo sapiens" "homo sapiens" "homo"