Computes the moments of the Phylogenetic Diversity measure

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Description

Calculates the mean and standard deviation of the unrooted Phylogenetic Diversity (PD) for a tree and a vector of tip set sizes.

Usage

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pd.moments(tree, sample.sizes, comp.expectation = TRUE, 
           comp.deviation = TRUE)

Arguments

tree

A phylo tree object

sample.sizes

A vector of non-negative integers specifying the tip set sizes for which to calculate moments

comp.expectation

Specifies whether the function should compute the mean (default = TRUE)

comp.deviation

Specifies whether the function should compute the standard deviation (default = TRUE)

Value

If both comp.expectation and comp.deviation are TRUE, the function returns a two-column matrix with one row per element in sample.sizes, where the first column stores the mean PD and the second column stores the standard deviation for this sample size. If only one of comp.expectation or comp.deviation are TRUE, the function returns a vector with the corresponding values instead.

Author(s)

Constantinos Tsirogiannis (constant@madalgo.au.dk)

References

Faith, D.P. 1992. Conservation evaluation and phylogenetic diversity. Biological Conservation 61: 1-10.

Tsirogiannis, C., B. Sandel and D. Cheliotis. 2012. Efficient computation of popular phylogenetic tree measures. Algorithms in Bioinformatics, LNCS 7534: 30-43.

Tsirogiannis, C., B. Sandel and A. Kalvisa. 2014. New algorithms for computing phylogenetic biodiversity. Algorithms in Bioinformatics, LNCS 8701: 187-203.

See Also

pd.query

Examples

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#Load phylogenetic tree of bird families from package "ape"
data(bird.families, package = "ape")

pd.moments(bird.families,1:100)