search_pt {perutimber}R Documentation

Search plant names according to the Catalogue of the timber forest species of the Amazon and the Peruvian Yunga.

Description

Allow plant search plant taxa names listed in the "Catalogue of the timber forest species of the Amazon and the Peruvian Yunga". Connects to the data listed in the catalog and validates if species its present, removing orthographic errors in plant names.

Usage

search_pt(
  splist,
  max_distance = 0.2,
  show_correct = FALSE,
  genus_fuzzy = FALSE,
  grammar_check = FALSE,
  progress_bar = 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

match when comparing the submitted name with the closest name matches in the species listed in the "Catalogue of the timber forest species of the Amazon and the Peruvian Yunga". The distance used is a generalized Levenshtein distance that indicates the total number of insertions, deletions, and substitutions allowed to match the two names. It can be expressed as an integer or as the fraction of the binomial name. For example, a name with length 10, and a max_distance = 0.1, allow 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).

Details

The function tries to match a names in the "Catalogue of the timber forest species of the Amazon and the Peruvian Yunga", which has a corresponding accepted valid name (accepted_name). If the input name is a valid name, it will be the duplicated in 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 See perutimber::tab_perutimber for more details.

References

Vásquez Martínez and Rojas Gonzáles (2022) titled "Catálogo de las especies forestales maderables de la Amazonía y la Yunga Peruana" in Revista Forestal del Perú 37(3, Número Especial): 5-138 https://revistas.lamolina.edu.pe/index.php/rfp/article/view/1956.


[Package perutimber version 0.1.0 Index]