get_geochron: Function to return geochronological data from records.

In ropensci/neotoma: Access to the Neotoma Paleoecological Database Through R

Function to return geochronological data from records.

Description

Using the dataset ID, return all geochronological data associated with the dataID. At present, only returns the dataset in an unparsed format, not as a data table. This function will only download one dataset at a time.

Usage

get_geochron(x, verbose = TRUE)

Arguments

x	A numeric dataset ID or a vector of numeric dataset IDs, or an object of class of class site, dataset, dataset_list, download or download_list for which geochrons are required.
verbose	logical; should messages on API call be printed?

Value

This command returns either an object of class "try-error"' (see try) defined by the error returned from the Neotoma API call, or a geochronologic object, which is a list with two components, a dataset and a geochronology table, a data.frame with the following components:

sample.id	A unique identifier for the geochronological unit.
age.type	String. The age type, one of calendar years, radiocarbon years, etc.
age	Dated age of the material.
e.older	The older error limit of the age value. Commonly 1 standard deviation.
e.young	The younger error limit of the age value.
delta13C	The measured or assumed delta13C value for radiocarbon dates, if provided.
material.dated	A table describing the collection, including dataset information, PI data compatible with get_contact and site data compatable with get_site.
geo.chron.type	Text string, type of geochronological analysis, i.e., Radiocarbon dating, luminesence.
notes	Text string
infinite	Boolean, does the dated material return an "infinite" date?

A full data object containing all the relevant geochronological data available for a dataset.

Author(s)

Simon J. Goring [e-mail]

References

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

Examples

## Not run: 
#  Search for the sites around Marion Lake, BC.  I want to find sites within 
#  about 1km.

marion <- get_site(sitename = "Marion Lake*")

marion_close <- get_closest(marion, n = 10, buffer = 1)

#  Returns 116 records (as of 13/07/2015).  These are the pollen records though, 
#  we want the sites:
geochron.records <- get_geochron(marion_close)

#  We want to extract all the radiocarbon ages from the records:

get_ages <- function(x){
  any.ages <- try(x[[2]]$age[x[[2]]$age.type == 'Radiocarbon years BP'])
  if(is(any.ages, 'try-error')) output <- NA
  if(!is(any.ages, 'try-error')) output <- unlist(any.ages)
  output
}

radio.chron <- unlist(sapply(geochron.records, get_ages))

hist(radio.chron[radio.chron<40000], breaks=seq(0, 25000, by = 1000),
     main = 'Radiocarbon dates for Pseudotsuga records',
     xlab = 'Radiocarbon date (14C years before 1950)')

## End(Not run)

ropensci/neotoma documentation built on Dec. 6, 2022, 6:26 p.m.