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

Description Usage Arguments Value Author(s) References Examples

View source: R/get_dataset.R

Description

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

Usage

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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 Grewnwich 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 occured 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 [email protected]

References

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

Examples

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## 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 June 23, 2017, 4:44 a.m.