rgbif (version 0.9.2)

name_lookup: Lookup names in all taxonomies in GBIF.

Description

Lookup names in all taxonomies in GBIF.

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 (facetOnly, facetMincount, facetMultiselect).

Usage

name_lookup(query = NULL, rank = NULL, higherTaxonKey = NULL,
  status = NULL, isExtinct = NULL, habitat = NULL, nameType = NULL,
  datasetKey = NULL, nomenclaturalStatus = NULL, limit = 100,
  start = NULL, facet = NULL, facetMincount = NULL,
  facetMultiselect = NULL, type = NULL, hl = NULL, 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,

higherTaxonKey

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

isExtinct

(logical) Filters by extinction status (e.g. isExtinct=TRUE)

habitat

(character) Filters by habitat. One of: marine, freshwater, or terrestrial

nameType

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

datasetKey

Filters by the dataset's key (a uuid)

nomenclaturalStatus

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

limit

Number of records to return. Maximum: 1000.

start

Record number to start at.

facet

A list of facet names used to retrieve the 100 most frequent values for a field. Allowed facets are: datasetKey, higherTaxonKey, rank, status, isExtinct, habitat, and nameType. Additionally threat and nomenclaturalStatus are legal values but not yet imple

facetMincount

Used in combination with the facet parameter. Set facetMincount={#} 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

(logical) Used in combination with the facet parameter. Set facetMultiselect=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

type

Type of name. One of occurrence, checklist, or metadata.

hl

(logical) Set hl=TRUE to highlight terms matching the query when in fulltext search fields. The highlight will be an emphasis tag of class 'gbifH1' e.g. query='plant', hl=TRUE. Fulltext search fields include: title, keyword, coun

verbose

(logical) 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

...

Further named parameters, such as query, path, etc, passed on to modify_url within GET call. Unnamed parameters will be comb

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/species#searching

Examples

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

# Paging
name_lookup(query='mammalia', limit=1)
name_lookup(query='mammalia', limit=1, start=2)

# large requests, use start parameter
first <- name_lookup(query='mammalia', limit=1000)
second <- name_lookup(query='mammalia', limit=1000, start=1000)
tail(first$data)
head(second$data)
first$meta
second$meta

# Get all data and parse it, removing descriptions which can be quite long
out <- name_lookup('Helianthus annuus', rank="species", verbose=TRUE)
lapply(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")

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

# Query by habitat
name_lookup(habitat = "terrestrial", limit=2)
name_lookup(habitat = "marine", limit=2)
name_lookup(habitat = "freshwater", limit=2)

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

name_lookup(facet='nameType', limit=0)
name_lookup(facet='habitat', limit=0)
name_lookup(facet='datasetKey', limit=0)
name_lookup(facet='rank', limit=0)
name_lookup(facet='isExtinct', limit=0)

name_lookup(isExtinct=TRUE, limit=0)

# text highlighting
## turn on highlighting
res <- name_lookup(query='canada', hl=TRUE, limit=5)
res$data
name_lookup(query='canada', hl=TRUE, limit=45, return='data')
## and you can pass the output to gbif_names() function
res <- name_lookup(query='canada', hl=TRUE, limit=5)
gbif_names(res)

# Lookup by datasetKey
name_lookup(datasetKey='3f8a1297-3259-4700-91fc-acc4170b27ce')

# Pass on httr options
library('httr')
name_lookup(query='Cnaemidophorus', rank="genus", config=verbose())