search_redbook {redbookperu} | R Documentation |
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 |
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.