compile_list: Function to convert assemblage taxa to standardized lists.

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

Description

From the assemblage data for the core return assemblage data with the assemblage taxa

Usage

  compile_list(object, list.name, verbose = TRUE)

Arguments

object	A pollen object returned by get_download.
list.name	The taxon compilation list, one of a set of lists from the literature (e.g., P25, Whitmore). More detail in the Description.

Value

This command returns a list object containing count and taxon.list objects, similar to those associated with the get_download object. Any pollen taxon not included in the major taxa defined in the pollen gets returned as 'Other'.

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

• counts The 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

The data object uses the smaller pollen subset. As this package develops we will add the capacity to summarize data output from the translation. Currently we can return only subsets that have been defined in the literature. These lists include:

• P25 This list is derived from Gavin et al., (2003), and includes 25 pollen taxa.

• WS64 This list is derived from Williams and Shuman (2008).

• WhitmoreFull This is the full list associated with the Whitmore et al., (2008) North American Modern Pollen Database.

• Whitmore As above, but taxa for which both fully resolved and undifferentiated exist these taxa are summed.

Author(s)

Simon J. Goring [e-mail]

References

Neotoma Project Website: http://www.neotomadb.org Williams J, Shuman B. 2008. Obtaining accurate and precise environmental reconstructions from the modern analog technique and North American surface pollen dataset. Quaternary Science Reviews. 27:669-687. http://dx.doi.org/10.1016/j.quascirev.2008.01.004

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)

gold.p25 <- compile_list(GOLDKBG, 'P25')




## End(Not run)

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