spocc (version 1.1.0)

occ_names: Search for species names across many data sources.

Description

Search for species names across many data sources.

Usage

occ_names(
  query = NULL,
  from = "gbif",
  limit = 100,
  rank = "species",
  callopts = list(),
  gbifopts = list(),
  bisonopts = list(),
  ecoengineopts = list()
)

Arguments

query

(character) One to many names. Either a scientific name or a common name. Only scientific names supported right now.

from

(character) Data source to get data from, any combination of gbif, bison, or ecoengine.

limit

(numeric) Number of records to return. This is passed across all sources. To specify different limits for each source, use the options for each source (gbifopts, bisonopts, ecoengineopts). See Details for more. This parameter is ignored for ecoengine.

rank

(character) Taxonomic rank to limit search space. Used in GBIF, but not used in BISON.

callopts

Options passed on to crul::HttpClient(), e.g., for debugging curl calls, setting timeouts, etc.

gbifopts

(list) List of named options to pass on to rgbif::name_lookup(). See also occ_names_options()

bisonopts

(list) List of named options to pass on to rbison::bison_tax(). See also occ_names_options()

ecoengineopts

(list) List of named options to pass on to ee_search. See also occ_names_options()

Details

Not all 7 data sources available from the occ() function are available here, as not all of those sources have functionality to search for names.

We strongly encourage you to use the taxize package if you want to search for taxonomic or common names, convert common to scientific names, etc. That package was built exactly for that purpose, and we only provide a bit of name searching here in this function.

See Also

Other queries: occ_names_options(), occ_options(), occ(), spocc_objects

Examples

# NOT RUN {
# Single data sources
## gbif
(res <- occ_names(query = 'Accipiter striatus', from = 'gbif'))
head(res$gbif$data[[1]])

## bison
(res <- occ_names(query = '*bear', from = 'bison'))
res$bison$data

## ecoengine
(res <- occ_names(query = 'genus:Lynx', from = 'ecoengine'))
head(res$ecoengine$data[[1]])
# }