likTraitPhylo: Log-likelihood rate estimation for traits and phylogenies

Description Usage Arguments Details Value Author(s) References

View source: R/likTraitPhylo.R

Description

This function calculates the log-likelihood and Brownian (co)variance for a trait(s) and a phylogeny using phylogenetically independent contrasts.

Usage

1
likTraitPhylo(y, phy, meserr=NULL)

Arguments

y

A matrix of trait data. Rownames must be included and match the taxon names in the phylogeny. Can accept single traits (calculates variance) or multiple traits (calculates variance-covariance matrix).

phy

An object of class "phylo" (see ape package).

meserr

A vector (or matrix) of measurement error for each tip. This is only applicable to univariate analyses.

Details

The "phylo" object must be rooted and fully dichotomous.

Value

brownianVariance

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

logLikelihood

The log-likelihood of the model and data

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.


ghthomas/motmot documentation built on July 31, 2018, 12:11 a.m.