prepSpecies: Get Valid Plant Names

In LimaRAF/plantR: Managing Species Records from Biological Collections

Get Valid Plant Names

Description

Provides valid plant names or corrects typos and orthographic variants based on the Brazilian Flora 2020 project and on the The Plant List. It uses the functionalities of other R packages, namely flora (Carvalho 2019) and Taxonstand (Cayuela et al. 2017).

Usage

prepSpecies(
  x,
  tax.names = c("scientificName.new", "scientificNameAuthorship"),
  db = c("bfo"),
  sug.dist = 0.9,
  use.authors = TRUE,
  drop.cols = c("tmp.ordem", "family", "verbatimSpecies", "author", "full_sp",
    "authorship", "id")
)

Arguments

x	a data.frame containing the species scientific name without authors and their authorship, ideally already passed by the string check in fixSpecies. The authorship is only used for solving homonyms.
tax.names	character. Names of the columns containing the species names and authors. Defaults to 'scientificName.new' and 'scientificNameAuthorship'.
db	the list of database to be consulted for valid names, in their preferred order of priority. Only the results from Brazilian Flora 2020 ('bfo'), The Plant List ('tpl') or both are currently implemented.
sug.dist	a fraction expressing the maximum distance allowed between the original species name and the suggested species name, which is passed to the arguments suggestion.distance of function flora::get.taxa() and max.distance of function Taxonstand::TPL(). Defaults to 0.9.
use.authors	logical. Should all authors names be verified (takes longer)? Default to TRUE.
drop.cols	character. Name of columns that should be dropped from the results.

Details

The function currently uses packages flora and Taxonstand to provide suggested names. Not all information returned by those packages are returned here, but some of them can be controlled using the argument drop.cols.

The function does not provide the suggested names from the different databases/sources. It combines into the same column ('suggestedName') the suggestions from one or more databases. If more than one databases is used, the suggested names are combined following the same order of the database codes provided in the argument db. See examples for details.

Value

A data frame with the same columns provided by the user and some additional columns containing the suggested binomial ('suggestedName'), the corresponding scientific name ('scientific.name'), the notes and the sources used to retrieve the suggested binomial (columns 'notes' and 'source').

Author(s)

Renato A. Ferreira de Lima

References

Gustavo Carvalho (2019). flora: Tools for Interacting with the Brazilian Flora 2020. R package version 0.3.1. http://www.github.com/gustavobio/flora

Luis Cayuela, Anke Stein and Jari Oksanen (2017). Taxonstand: Taxonomic Standardization of Plant Species Names. R package version 2.1. https://CRAN.R-project.org/package=Taxonstand

See Also

Functions get.taxa and TPL.

Examples

sp.list <- c("Casearia sylvestris","Casearia sylvestirs",
  "Casearia sylvestris angustifolia", "Casearia attenuata",
  "Casearia celtidifolia", "Casearia celtidifolia","Casearia tropicana")
aut_list <- c("Sw.", "Sw.", "Uittien", "Rusby", "Kunth", "de Vriese","L.")

df <- data.frame(scientificName.new = sp.list,
  scientificNameAuthorship = aut_list)

prepSpecies(df)

LimaRAF/plantR documentation built on Jan. 1, 2023, 10:18 a.m.