rgbif (version 0.7.0)

name_lookup: Lookup names in all taxonomies in GBIF.

Description

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.

Faceting: If facet=FALSE or left to the default (NULL), no faceting is done. And therefore, all parameters with facet in their name are ignored (facet_only, facet_mincount, facet_multiselect).

Usage

name_lookup(query = NULL, rank = NULL, highertaxon_key = NULL,
  status = NULL, extinct = NULL, habitat = NULL, name_type = NULL,
  dataset_key = NULL, nomenclatural_status = NULL, limit = 20,
  facet = NULL, facetMincount = NULL, facetMultiselect = NULL,
  type = NULL, callopts = list(), verbose = FALSE, return = "all")

Arguments

query

Query term(s) for full text search.

rank

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,

highertaxon_key

Filters by any of the higher Linnean rank keys. Note this is within the respective checklist and not searching nub keys across all checklists.

status

Filters by the taxonomic status as one of:

• ACCEPTED
• DETERMINATION_SYNONYM Used for unknown child taxa referred to via spec, ssp, ...
• DOUBTFUL Treated as accepted, but doubtful whether this is correct.
• HETEROTYPIC_SYNONYM Mo

extinct

Filters by extinction status (a boolean, e.g. extinct=true)

habitat

Filters by the habitat, though currently only as boolean marine or not-marine (i.e. habitat=true means marine, false means not-marine)

name_type

Filters by the name type as one of:

• BLACKLISTED surely not a scientific name.
• CANDIDATUS Candidatus is a component of the taxonomic name for a bacterium that cannot be maintained in a Bacteriology Culture Collection.
• CULTIVAR a cu

dataset_key

Filters by the dataset's key (a uuid)

nomenclatural_status

Not yet implemented, but will eventually allow for filtering by a nomenclatural status enum

facet

A list of facet names used to retrieve the 100 most frequent values for a field. Allowed facets are: dataset_key, highertaxon_key, rank, status, extinct, habitat, and name_type. Additionally threat and nomenclatural_status are legal values but not yet imp

facetMincount

Used in combination with the facet parameter. Set facet_mincount={#} to exclude facets with a count less than {#}, e.g. http://bit.ly/1bMdByP only shows the type value 'ACCEPTED' because the other statuses have counts less than 7,000,000

facetMultiselect

Used in combination with the facet parameter. Set facet_multiselect=TRUE to still return counts for values that are not currently filtered, e.g. http://bit.ly/19YLXPO still shows all status values even though status is being filtered by

type

Type of name.

limit

Number of records to return

callopts

Further arguments passed on to the GET request.

verbose

If TRUE, all data is returned as a list for each element. If FALSE (default) a subset of the data that is thought to be most essential is organized into a data.frame.

return

One of data, meta, facets, names, or all. If data, a data.frame with the data. facets returns the facets, if facets=TRUE, or empy list if facets=FALSE. meta returns the metadata for the entire call. names returns the vernacular (common) names for each tax

Value

• A list of length three. The first element is metadata. The second is either a data.frame (verbose=FALSE, default) or a list (verbose=TRUE), and the third element is the facet data.

References

http://www.gbif.org/developer/summary

Examples

# Look up names like mammalia
name_lookup(query='mammalia')

# Get all data and parse it, removing descriptions which can be quite long
out <- name_lookup('Helianthus annuus', rank="species", verbose=TRUE)
library("plyr")
llply(out$data, function(x) x[!names(x) %in% c("descriptions","descriptionsSerialized")])

# Search for a genus, returning just data
name_lookup(query='Cnaemidophorus', rank="genus", return="data")

# Just metadata
name_lookup(query='Cnaemidophorus', rank="genus", return="meta")

# Just hierarchies
name_lookup(query='Cnaemidophorus', rank="genus", return="hierarchy")

# Just vernacular (common) names
name_lookup(query='Cnaemidophorus', rank="genus", return="names")

# Fuzzy searching
name_lookup(query='Cnaemidophor', rank="genus")

# Get more data from the API call
library("httr")
name_lookup(query='Cnaemidophorus', rank="genus", callopts=verbose())

# Limit records to certain number
name_lookup('Helianthus annuus', rank="species", limit=2)

# Using faceting
name_lookup(facet='status', limit=0, facetMincount='70000')
name_lookup(facet=c('status','highertaxon_key'), limit=0, facetMincount='700000')

name_lookup(facet='name_type', limit=0)
name_lookup(facet='habitat', limit=0)
name_lookup(facet='dataset_key')
name_lookup(facet='rank', limit=0)
name_lookup(facet='extinct', limit=0)