stratigraph (version 0.66)

addpart: Calculates additive partitioning of diversity

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.

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.

Details

Based on an Excel spreadsheet set up by Scott Wing.

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

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