Obtain dataset information from the Neotoma Paleoecological Database or an existing object.

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". See note in Details delow.
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://wnapi.neotomadb.org/apdx/geopol.htm
taxonids: A numeric identifier for the taxon. See get_table and use get_table('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://wnapi.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.

Details

With regards to datasettypes, because Neotoma is a "living" database, and new dataset types are being added in an ongoing manner as new research disciplines use the database, you can use get_table("datasettypes") to see the full list of available dataset types in the database.

References

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

Author

Simon J. Goring simon.j.goring@gmail.com

Examples

if (FALSE) {
# 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)
}