clean_names: Clean taxonomic names

In boettiger-lab/taxadb-cache: Backend for generating taxadb cache

Clean taxonomic names

Description

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

Usage

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

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."))

boettiger-lab/taxadb-cache documentation built on March 20, 2023, 10:09 p.m.