phyloCovar: Calculation of Brownian (co)variance using independent...

In PuttickMacroevolution/motmot: Models of Trait Macroevolution on Trees

Description

Calculates the Brownian variance (single trait) or variance-covariance matrix (mutliple traits) using phylogenetically independent contrasts.

Usage

phyloCovar(x, phy, estimator = "unbiased")

Arguments

x	A continuous trait
phy	An object of class phylo (see ape).
estimator	Should Brownian variance (or covariance) be based on the unbiased ("unbiased" - default) or maximum likelihood ("ML") estimator.

Value

brownianVariance Brownian variance (or covariance for multiple traits) given the data and phylogeny

Author(s)

Gavin Thomas, Rob Freckleton

References

Felsenstein J. 1973. Maximum-likelihood estimation of evolutionary trees from continuous characters. Am. J. Hum. Genet. 25, 471-492.

Felsenstein J. 1985. Phylogenies and the comparative method. American Naturalist 125, 1-15.

Freckleton RP & Jetz W. 2009. Space versus phylogeny: disentangling phylogenetic and spatial signals in comparative data. Proc. Roy. Soc. B 276, 21-30.

Examples

data(anolis.tree)
data(anolis.data)
## calculate Brownian variance of female SVL
female.svl <- matrix(anolis.data[,"Female_SVL"], 
dimnames=list(rownames(anolis.data)))
input.data <- sortTraitData(phy=anolis.tree, y=female.svl, log.trait=TRUE)
phyloCovar(x=input.data$trait, phy = input.data$phy)

PuttickMacroevolution/motmot documentation built on June 5, 2020, 7 p.m.