rgbif (version 1.3.0)

name_usage: 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 = "all", 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

One of data, meta, or all. If data, a data.frame with the data. meta returns the metadata for the entire call. all gives all data back in a list.

curlopts

list of named curl options passed on to HttpClient. see curl_options for curl options

Value

If return="all", a list of length two, with metadata and data, each as data.frame's. If return="meta" only the metadata data.frame, and if return="data" only the data data.frame

Repeat parameter inputs

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

• rank

• name

• langugae

• datasetKey

see also many-values

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'

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 information on name usage issues related to the issues column in output from this function

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))
# }