addpart: Calculates additive partitioning of diversity

In stratigraph: Toolkit for the plotting and analysis of stratigraphic and palaeontological data

Description

Returns or writes to a file measures of the additive partitioning of diversity according to Lande (1996).

Usage

addpart(x = NULL, file = 'rawcounts.txt', outfile = NULL)

Arguments

x	an object of class strat.column or a counts matrix with species in rows and sites in columns
file	ignored unless x is NULL; otherwise a file from which to read the counts matrix. Must be in tab-delimited text format with column labels in the first, header row, which must be one entry shorter than the following data rows. Row labels in the first column. [check this]
outfile	a file to which to write the output. If NULL (the default) writes to standard output.

Details

Based on an Excel spreadsheet set up by Scott Wing.

Value

returns a data frame list with components $counttable, $Sstats, and $Saddpart.

$counttable is a data frame giving the original count matrix with row and column marginals added to the right and bottom.

$Sstats is a data frame giving species diversity (Sobs), Simpson's Diversity Index (SimpsonsD = 1 - sum of squares of proportional counts), and Hurlbert's PIE (PIE = SimpsonsD * (n/(n-1)), where n = total number of individuals found at a site) for each site.

$Saddpart is a data frame giving alpha and beta partitions of divisersity under three different weighting scenarios: with sites weighted by n = total number of individuals found at a site, natural log of n (ln n), and assuming that all sites have equal number of individuals.

Note

Currently no other notes.

Author(s)

Scott Wing, Walton Green

References

Hurlbert (1971)

Lande, R. (1996) ‘Statistics and Partitioning of Species Diversity, and Similarity among Multiple Communities’. Oikos. 76(1):5–13.

See Also

plot.strat.column, stratigraph

Examples

#none yet

stratigraph documentation built on May 30, 2017, 12:31 a.m.