get_download: Function to return full dataset records.

In neotoma: A Package to access the Neotoma Paleoecological Database using an API.

Description

Using the dataset ID, return all records associated with the data. 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_download(datasetid, verbose = TRUE)

Arguments

datasetid	A single numeric dataset ID or a vector of numeric dataset IDs as returned by get_datasets.
verbose	logical; should messages on API call be printed?

Value

This command returns either a 'try-error' definined by the error returned from the Neotoma API call, or a list comprising the following items:

• metadataA table describing the collection, including dataset information, PI data compatable with get_contacts and site data compatable with get_sites.

• sample.metaDataset information for the core, primarily the age-depth model and chronology.

• taxon.listThe list of taxa contained within the dataset, unordered, including information that can be used in get_taxa

• countsThe assemblage data for the dataset, arranged with each successive depth in rows and the taxa as columns. All taxa are described in taxon.list, the chronology is in sample.data

• lab.dataA data frame of laboratory data, such as exotic pollen spike, amount of sample counted, etc.

A full data object containing all the relevant assemblage information and metadata neccessary to understand a site. The data object is a list of lists and data.frames that describe an assemblage, the constituent taxa, the chronology, site and PIs who contributed the data.

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_datasets(taxonname='Thuja*', loc=c(-150, 20, -100, 60), ageyoung = 8000)

#  Returns 3 records (as of 04/04/2013), get dataset for the first record, Gold Lake Bog.
GOLDKBG <- get_download(t8kyr.datasets[[1]]$DatasetID)

taxa.no <- nrow(GOLDKBG$taxon.list)

#  Of the 60 taxa in the record, plot the pollen curve for Abies over time:

##pollen <- GOLDKBG$taxon.list$VariableElement == 'pollen'
pol.curve <- data.frame(age = GOLDKBG$sample.meta$Age,
                        Abies = GOLDKBG$counts[,'Abies'] / rowSums(GOLDKBG$counts, na.rm = TRUE))
plot(Abies * 100 ~ age, data = pol.curve, type='b',
     ylab = '% Abies', xlab='Calibrated Years BP', pch=19)


## End(Not run)

neotoma documentation built on May 2, 2019, 5:55 p.m.