get_by_taxon: 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_by_taxon(x, lower = TRUE, pattern = TRUE, ...)

Arguments

x	A taxon name, at any level, may use wildcards. Taxonomy follows either Neotoma (morpho-type based) or Paleobiology DB taxonomy.
lower	Include all taxa at an order below the focal taxon (default TRUE).
pattern	Is the search string a pattern match i.e. a partial or wildcard search (default TRUE)
...	Other parameters to be passed into the API, described at https://training.paleobiodb.org/comp1.0.

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

EarthLife Consortium: http://earthlifeconsortium.org/ API Reference: https://training.paleobiodb.org/comp1.0

Examples

## Not run: 
# Search for sites with "Canis" fossils.
canis <- get_by_taxon("Canis")

# Limit searches to North America (undocumented use of \code{bbox})
canis_na <- get_by_taxon("Canis", bbox = c(-180, 20, -20, 90))


## End(Not run)

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