cbl.moments: Computes the moments of the Common Branch Length measure under the uniform null model

Description

Calculates the mean and standard deviation of the Common Branch Length (CBL) on a given tree for several pairs of tip set sizes. These calculations consider equal (uniform) probability among all possible tip samples of the same richness.

Usage

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

Arguments

tree

A phylo tree object

sample.sizes

A two-column matrix of non-negative integers indicating the tip set sizes for which the moments should be calculated. The moments are calculated for each row of the matrix. Let x and y be the values that are stored in the i-th row of sample.sizes. For this row, the CBL moments are calculated considering all pairs of tip sets that can be extracted from the input tree such that one set has x elements and the other set has y elements.

comp.expectation

Specifies whether the function computes the mean of the CBL (default = TRUE)

comp.deviation

Specifies whether the function computes the standard deviation of the CBL (default = TRUE)

Value

References

Graham, C.H. and P.V.A. Fine. 2008. Phylogenetic beta diversity: linking ecological and evolutionary processes across space and time. Ecology Letters 11: 1265:1277.

Swenson, N.G. 2011. Phylogenetic beta diversity metrics, trait evolution and inferring functional beta diversity of communities. PLoS ONE: 6: e21264.

Tsirogiannis, C. and B. Sandel. In prep. Fast computation of measures of phylogenetic beta diversity.

Examples

Run this code

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

cbl.moments(bird.families,sample.sizes = expand.grid(1:10,1:10))