name_usage: Lookup details for specific names in all taxonomies in GBIF.

In rgbif: Interface to the Global Biodiversity Information Facility API

Lookup details for specific names in all taxonomies in GBIF.

Description

Lookup details for specific names in all taxonomies in GBIF.

Usage

name_usage(
  key = NULL,
  name = NULL,
  data = "all",
  language = NULL,
  datasetKey = NULL,
  uuid = NULL,
  rank = NULL,
  shortname = NULL,
  start = 0,
  limit = 100,
  return = NULL,
  curlopts = list()
)

Arguments

key	(numeric or character) A GBIF key for a taxon
name	(character) Filters by a case insensitive, canonical namestring, e.g. 'Puma concolor'
data	(character) Specify an option to select what data is returned. See Description below.
language	(character) Language, default is english
datasetKey	(character) Filters by the dataset's key (a uuid). Must be length=1
uuid	(character) A dataset key
rank	(character) Taxonomic rank. Filters by taxonomic rank as one of: CLASS, CULTIVAR, CULTIVAR_GROUP, DOMAIN, FAMILY, FORM, GENUS, INFORMAL, INFRAGENERIC_NAME, INFRAORDER, INFRASPECIFIC_NAME, INFRASUBSPECIFIC_NAME, KINGDOM, ORDER, PHYLUM, SECTION, SERIES, SPECIES, STRAIN, SUBCLASS, SUBFAMILY, SUBFORM, SUBGENUS, SUBKINGDOM, SUBORDER, SUBPHYLUM, SUBSECTION, SUBSERIES, SUBSPECIES, SUBTRIBE, SUBVARIETY, SUPERCLASS, SUPERFAMILY, SUPERORDER, SUPERPHYLUM, SUPRAGENERIC_NAME, TRIBE, UNRANKED, VARIETY
shortname	(character) A short name for a dataset - it may not do anything
start	Record number to start at. Default: 0.
limit	Number of records to return. Default: 100.
return	Defunct. All components are returned; index to the one(s) you want
curlopts	list of named curl options passed on to HttpClient. see curl::curl_options for curl options

Details

This service uses fuzzy lookup so that you can put in partial names and you should get back those things that match. See examples below.

This function is different from name_lookup() in that that function searches for names. This function encompasses a bunch of API endpoints, most of which require that you already have a taxon key, but there is one endpoint that allows name searches (see examples below).

Note that data="verbatim" hasn't been working.

Options for the data parameter are: 'all', 'verbatim', 'name', 'parents', 'children', 'related', 'synonyms', 'descriptions','distributions', 'media', 'references', 'speciesProfiles', 'vernacularNames', 'typeSpecimens', 'root', 'iucnRedListCategory'

This function used to be vectorized with respect to the data parameter, where you could pass in multiple values and the function internally loops over each option making separate requests. This has been removed. You can still loop over many options for the data parameter, just use an lapply family function, or a for loop, etc.

See name_issues() for more information about issues in issues column.

Value

An object of class gbif, which is a S3 class list, with slots for metadata (meta) and the data itself (data). In addition, the object has attributes listing the user supplied arguments and type of search, which is, differently from occurrence data, always equals to 'single' even if multiple values for some parameters are given. meta is a list of length four with offset, limit, endOfRecords and count fields. data is a tibble (aka data.frame) containing all information about the found taxa.

Repeat parameter inputs

These parameters used to accept many inputs, but no longer do:

• rank

• name

• langugae

• datasetKey

References

https://www.gbif.org/developer/species#nameUsages

Examples

## Not run: 
# A single name usage
name_usage(key=1)

# Name usage for a taxonomic name
name_usage(name='Puma', rank="GENUS")

# Name usage for all taxa in a dataset
# (set sufficient high limit, but less than 100000)
# name_usage(datasetKey = "9ff7d317-609b-4c08-bd86-3bc404b77c42", 
#  limit = 10000)
# All name usages
name_usage()

# References for a name usage
name_usage(key=2435099, data='references')

# Species profiles, descriptions
name_usage(key=3119195, data='speciesProfiles')
name_usage(key=3119195, data='descriptions')
name_usage(key=2435099, data='children')

# Vernacular names for a name usage
name_usage(key=3119195, data='vernacularNames')

# Limit number of results returned
name_usage(key=3119195, data='vernacularNames', limit=3)

# Search for names by dataset with datasetKey parameter
name_usage(datasetKey="d7dddbf4-2cf0-4f39-9b2a-bb099caae36c")

# Search for a particular language
name_usage(key=3119195, language="FRENCH", data='vernacularNames')

# get root usage with a uuid
name_usage(data = "root", uuid = "73605f3a-af85-4ade-bbc5-522bfb90d847")

# search by language
name_usage(language = "spanish")

# Pass on curl options
name_usage(name='Puma concolor', limit=300, curlopts = list(verbose=TRUE))

# look up iucn red list category 
name_usage(key = 7707728, data = 'iucnRedListCategory') 

## End(Not run)

rgbif documentation built on Sept. 27, 2024, 5:07 p.m.