rgbif (version 0.9.6)

occ_count: Get number of occurrence records.

Description

Get number of occurrence records.

Usage

occ_count(taxonKey = NULL, georeferenced = NULL, basisOfRecord = NULL, datasetKey = NULL, date = NULL, typeStatus = NULL, catalogNumber = NULL, country = NULL, hostCountry = NULL, year = NULL, from = 2000, to = 2012, type = "count", publishingCountry = "US", nubKey = NULL, protocol = NULL, ...)

Arguments

taxonKey

Species key

georeferenced

Return only occurence records with lat/long data (TRUE) or all records (FALSE, default).

basisOfRecord

Basis of record

datasetKey

Dataset key

date

Collection date

typeStatus

A type status. See typestatus dataset for options

catalogNumber

Catalog number. PARAMETER GONE.

country

Country data was collected in, two letter abbreviation. See http://countrycode.org/ for abbreviations.

hostCountry

Country that hosted the data. PARAMETER GONE.

year

Year data were collected in

from

Year to start at

to

Year to end at

type

One of count (default), schema, basis_of_record, countries, or year.

publishingCountry

Publishing country, two letter ISO country code

nubKey

Species key. PARAMETER NAME CHANGED TO taxonKey.

protocol

Protocol. E.g., 'DWC_ARCHIVE'

...

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

Value

A single numeric value, or a list of numerics.

Supported dimensions

That is, there are only a certain set of supported query parameter combinations that GBIF allows on this API route. They can be found with the call occ_count(type='schema'). They are also presented below:

• basisOfRecord
• basisOfRecord, country
• basisOfRecord, country, isGeoreferenced
• basisOfRecord, country, isGeoreferenced, taxonKey
• basisOfRecord, country, taxonKey
• basisOfRecord, datasetKey
• basisOfRecord, datasetKey, isGeoreferenced
• basisOfRecord, datasetKey, isGeoreferenced, taxonKey
• basisOfRecord, datasetKey, taxonKey
• basisOfRecord, isGeoreferenced, taxonKey
• basisOfRecord, isGeoreferenced, publishingCountry
• basisOfRecord, isGeoreferenced, publishingCountry, taxonKey
• basisOfRecord, publishingCountry
• basisOfRecord, publishingCountry, taxonKey
• basisOfRecord, taxonKey
• country
• country, datasetKey, isGeoreferenced
• country, isGeoreferenced
• country, isGeoreferenced, publishingCountry
• country, isGeoreferenced, taxonKey
• country, publishingCountry
• country, taxonKey
• country, typeStatus
• datasetKey
• datasetKey, isGeoreferenced
• datasetKey, isGeoreferenced, taxonKey
• datasetKey, issue
• datasetKey, taxonKey
• datasetKey, typeStatus
• isGeoreferenced
• isGeoreferenced, publishingCountry
• isGeoreferenced, publishingCountry, taxonKey
• isGeoreferenced, taxonKey
• issue
• publishingCountry
• publishingCountry, taxonKey
• publishingCountry, typeStatus
• taxonKey
• taxonKey, typeStatus
• typeStatus
• protocol
• year

Details

There is a slight difference in the way records are counted here vs. results from occ_search. For equivalent outcomes, in the occ_search function use hasCoordinate=TRUE, and hasGeospatialIssue=FALSE to have the same outcome for this function using georeferenced=TRUE.

References

http://www.gbif.org/developer/occurrence#metrics

Examples

## Not run: 
# occ_count(basisOfRecord='OBSERVATION')
# occ_count(georeferenced=TRUE)
# occ_count(country='DE')
# occ_count(country='CA', georeferenced=TRUE, basisOfRecord='OBSERVATION')
# occ_count(datasetKey='9e7ea106-0bf8-4087-bb61-dfe4f29e0f17')
# occ_count(year=2012)
# occ_count(taxonKey=2435099)
# occ_count(taxonKey=2435099, georeferenced=TRUE)
# occ_count(protocol='DWC_ARCHIVE')
# 
# # Just schema
# occ_count(type='schema')
# 
# # Counts by basisOfRecord types
# occ_count(type='basisOfRecord')
# 
# # Counts by basisOfRecord types
# occ_count(typeStatus='ALLOTYPE')
# occ_count(typeStatus='HOLOTYPE')
# 
# # Counts by countries. publishingCountry must be supplied (default to US)
# occ_count(type='countries')
# 
# # Counts by year. from and to years have to be supplied, default to 2000 and 2012
# occ_count(type='year', from=2000, to=2012)
# 
# # Counts by publishingCountry, must supply a country (default to US)
# occ_count(type='publishingCountry')
# occ_count(type='publishingCountry', country='BZ')
# 
# # Pass on options to httr
# library('httr')
# # res <- occ_count(type='year', from=2000, to=2012, config=progress())
# # res
# ## End(Not run)