search_names: Lookup of taxonomic names

In AtlasOfLivingAustralia/ALA4R: Atlas of Living Australia (ALA) Data and Resources in R

Description

Provides GUID, taxonomic classification, and other information for a list of names. Case-insensitive but otherwise exact matches are used.

Usage

search_names(
  taxa = c(),
  vernacular = FALSE,
  guids_only = FALSE,
  occurrence_count = FALSE,
  output_format = "simple"
)

Arguments

taxa	string: a single name or vector of names
vernacular	logical: if TRUE, match on common names as well as scientific names, otherwise match only on scientific names
guids_only	logical: if TRUE, a named list of GUIDs will be returned. Otherwise, a data frame with more comprehensive information for each name will be returned.
occurrence_count	logical: if TRUE (and if guids_only is FALSE) then also return the number of occurrences of each matched name. Note that this requires one extra web call for each name, and so may be slow. Only applicable if guids_only is FALSE.
output_format	string: controls the print method for the returned object (only has an effect when guids_only is FALSE). Either "complete" (the complete data structure is displayed), or "simple" (a simplified version is displayed). Note that the complete data structure exists in both cases: this option only controls what is displayed when the object is printed to the console. The default output format is "simple"

Value

A data frame of results, or named list of GUIDs if guids_only is TRUE. The results should include one entry (i.e. one data.frame row or one list element) per input name. The columns in the data.frame output may vary depending on the results returned by the ALA server, but should include searchTerm, name, rank, and guid.

References

The associated ALA web service: https://api.ala.org.au/#ws87

Examples

## Not run: 
search_names(c("Grevillea humilis", "Grevillea humilis subsp. maritima",
  "Heleioporus", "Thisisnot aname"))

search_names(c("Grevillea humilis", "Grevillea humilis subsp. maritima",
  "Heleioporus", "Thisisnot aname"), guids_only = TRUE)

search_names("kookaburra", vernacular = FALSE)

search_names("kookaburra", vernacular = TRUE)

## occurrence counts for matched names
search_names(c("Grevillea humilis", "Grevillea humilis subsp. maritima",
  "Heleioporus", "Thisisnot aname"), occurrence_count = TRUE)

## no occurrence counts because guids_only is TRUE
search_names(c("Grevillea humilis", "Grevillea humilis subsp. maritima",
  "Heleioporus", "Thisisnot aname"), occurrence_count = TRUE,
  guids_only = TRUE)

## End(Not run)

AtlasOfLivingAustralia/ALA4R documentation built on Sept. 16, 2021, 4:33 a.m.