search_redbook: Search Species Names in “The Red Book of Endemic Plants of...

In redbookperu: Access and Analyze Data from the Red Book of Endemic Plants of Peru

Search Species Names in “The Red Book of Endemic Plants of Peru”

Description

This function allows searching for plant taxa names listed in "The Red Book of Endemic Plants of Peru". It connects to the data listed in the catalog and validates if the species is present, removing orthographic errors in plant names.

Usage

search_redbook(
  splist,
  max_distance = 0.2,
  show_correct = FALSE,
  genus_fuzzy = FALSE,
  grammar_check = FALSE
)

Arguments

splist	A character vector specifying the input taxon, each element including genus and specific epithet and, potentially, infraspecific rank, infraspecific name, and author name. Only valid characters are allowed (see base::validEnc).
max_distance	An integer or fraction specifying the maximum distance allowed when comparing the submitted name with the closest name matches in the species listed in "The Red Book of Endemic Plants of Peru". The distance used is a generalized Levenshtein distance indicating the total number of insertions, deletions, and substitutions allowed to match the two names. For example, a name with a length of 10 and a max_distance = 0.1 allows only one change (insertion, deletion, or substitution). A max_distance = 2 allows two changes.
show_correct	If TRUE, a column is added to the final result indicating whether the binomial name was exactly matched (TRUE) or if it is misspelled (FALSE).
genus_fuzzy	If TRUE, allows fuzzy matching at the genus level.
grammar_check	If TRUE, performs a grammar check on the species names.

Details

The function tries to match names in "The Red Book of Endemic Plants of Peru", which has a corresponding accepted valid name (accepted_name). If the input name is a valid name, it will be duplicated in the accepted_name column.

The algorithm will first try to exactly match the binomial names provided in splist. If no match is found, it will try to find the closest name given the maximum distance defined in max_distance. Note that only binomial names with valid characters are allowed in this function.

Value

A data frame with the matched species names and additional information from the redbook catalog. If no match is found, a warning is issued suggesting to increase the max_distance argument.

References

León, Blanca, et.al. 2006. “The Red Book of Endemic Plants of Peru”. Revista Peruana De Biología 13 (2): 9s-22s. https://doi.org/10.15381/rpb.v13i2.1782.

redbookperu documentation built on July 2, 2024, 9:07 a.m.