get_occurrence: Return occurrences for taxa within the PBDB/Neotoma.

In EarthLifeConsortium/earthlife: Biodiversity in space and time. A wrapper for the EarthLife Consortium API.

Description

A wrapper for the Composite API, returning all records from both datasets.

Usage

get_occurrence(x, occ_id, taxon_name, base_name, match_name, base_id, taxon_id,
  site_id, bbox, vocab)

Arguments

x	An optional value, either a numeric site ID or object of class download, download_list or site.
occ_id	A numeric Occurrence ID.
taxon_name	The taxon name as a character
base_name	The taxon name as a character
match_name	The taxon name as a character
base_id	The taxon name as a character
taxon_id	The taxon name as a character
site_id	The taxon name as a character
bbox	The taxon name as a character
vocab	The taxonomic vocabulary to use, either \'pbdb\' or \'neotoma\'.

Value

More details on the use of these parameters can be obtained from https://training.paleobiodb.org/comp1.0/.

A list of class 'occurrence' and 'list'. The list is composed of two elements:

records	The complete listing of taxon occurrences.
meta	Metadata for the search.

The records object is a data.frame

collection_name	Site or collection unit name for the record.
lng	Collection site longitude.
lat	Collection site latitude.
accepted_name	The taxon name.
max_age	The oldest of all sample ages (in calendar years before present) in the dataset.
min_age	The youngest of all sample ages (in calendar years before present) in the dataset.
age_unit	The units for age (by default "Mya").
database	The database from which the record was obtained.
occurrence_no	The numeric ID for the record within the parent database.
dataset_no	For records within Neotoma, the numeric ID of the dataset from which the sample was obtained.
accepted_no	The numeric identifier for the taxon name from the parent database.
collection_no	The numeric identifier for the collection within the parent database.
country	The country within which the sample is found (if known).
state	The state (when known) within the identified country.

Author(s)

Simon J. Goring [e-mail]

References

Neotoma Project Website: http://www.neotomadb.org API Reference: https://training.paleobiodb.org/comp1.0

Examples

## Not run: 
# Search for sites with "Thuja" pollen that are older than 8kyr BP and
# that are on the west coast of North America:
t8kyr.datasets <- get_dataset(taxonname='Thuja*', loc=c(-150, 20, -100, 60), ageyoung = 8000)

# Search for vertebrate fossils in Canada (gpid: 756) within the last 2kyr.
gpids <- get_table(table.name='GeoPoliticalUnits')
canID <- gpids[which(gpids$GeoPoliticalName == 'Canada'),1]

v2kyr.datasets <- get_dataset(datasettype='vertebrate fauna', gpid=canID, ageold = 2000)

## End(Not run)

EarthLifeConsortium/earthlife documentation built on May 6, 2019, 3:10 p.m.