get_dataset: Obtain dataset information from the Neotoma Paleoecological...

In neotoma: Access to the Neotoma Paleoecological Database Through R

Description

A function to access the Neotoma API and return datasets corresponding to the parameters defined by the user.

Usage

get_dataset(x, datasettype, piid, altmin, altmax, loc, gpid, taxonids,
  taxonname, ageold, ageyoung, ageof, subdate)

Arguments

x	An optional value, either a numeric site ID or object of class download, download_list or site.
datasettype	A character string corresponding to one of the allowed dataset types in the Neotoma Database. Allowed types include: "geochronologic", "loss-on-ignition", "pollen", "plant macrofossils", "vertebrate fauna", "mollusks", and "pollen surface sample".
piid	Numeric value for the Principle Investigator's ID number.
altmin	Numeric value indicating the minimum altitude for the site (can be used alone or with altmax).
altmax	Numeric value indicating the maximum altitude for the site (can be used alone or with altmin).
loc	A numeric vector c(lonW, latS, lonE, latN) representing the bounding box within which to search for sites. The convention here is to use negative values for longitudes west of Greenwich or longitudes south of the equator
gpid	A character string or numeric value, must correspond to a valid geopolitical identity in the Neotoma Database. Use get.tables('GeoPoliticalUnits') for a list of acceptable values, or link here: http://api.neotomadb.org/apdx/geopol.htm
taxonids	A numeric identifier for the taxon. See get_table and use get_tables('Taxa') for a list of acceptable values.
taxonname	A character string corresponding to a valid taxon identity in the Neotoma Database. See get_table and use get_table('Taxa') for a list of acceptable values.
ageold	The oldest date acceptable for the search (in years before present).
ageyoung	The youngest date acceptable for the search.
ageof	If a taxon ID or taxon name is defined this parameter must be set to "taxon", otherwise it may refer to "sample", in which case the age bounds are for any samples within datasets or "dataset" if you want only datasets that are within the bounds of ageold and ageyoung.
subdate	Date of dataset submission, either YYYY-MM-DD or MM-DD-YYYY.

Value

More details on the use of these parameters can be obtained from http://api.neotomadb.org/doc/resources/datasets.

A list of class 'dataset_list', with each item corresponding to an individual record. Searches that return no items will result in a NULL value being returned. Otherwise each list item (each dataset record) includes the following components:

dataset.id	Unique database record identifier for the dataset.
dataset.name	Name of the dataset; not commonly used.
CollUnitHandle	Code name of the Collection Unit with which the dataset is associated. This code may be up to 10 characters. Data are frequently distributed by Collection Unit, and the Handle is used for file names.
CollUnitID	Unique database record identifier for the collection unit.
CollType	The collection type. Types include cores, sections, excavations, and animal middens.
DatasetType	The dataset type, such as: geochronologic, loss-on-ignition, pollen, plant macrofossils, vertebrate fauna, etc.
AgeOldest	The oldest of all sample ages (in calendar years before present) in the dataset.
AgeYoungest	The youngest of all sample ages (in calendar years before present) in the dataset.
SubDates	An array of objects that describe dataset submission events. If multiple submissions occurred then this is a table.
DatasetPIs	An array of objects that describe Principal Investigators associated with a dataset.
Site	An object describing the site where the dataset samples were taken.

Author(s)

Simon J. Goring [e-mail]

References

Neotoma Project Website: http://www.neotomadb.org API Reference: http://api.neotomadb.org/doc/resources/contacts

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)

neotoma documentation built on May 2, 2019, 1:10 p.m.