phytools (version 0.2-50)

fitBayes: Evolutionary model fitting with intraspecific variability using Bayesian MCMC

Description

This function uses Bayesian MCMC to sample terminal states (species means) as well as evolutionary parameters.

Usage

fitBayes(tree, x, ngen=10000, model="BM", method="reduced", control=list())

Arguments

tree

an object of class "phylo".

x

a vector of phenotypic values for individuals; names(x) should contain the species names (not individual IDs).

ngen

a integer indicating the number of generations for the MCMC.

model

an evolutionary model: either "BM" or "lambda".

method

a method: either "reduced" or "full".

control

a list of control parameters containing the following elements: sig2: starting value for $\sigma^2$ (BM rate); lambda: starting value for the $\lambda$ parameter; a: starting for the state at the root node; xba

Value

• a matrix with number of rows ngen/control$sample+1 containing the posterior sample and likelihoods. Matrix columns are labeled by species (for species means and variances), or by the corresponding evolutionary parameter.

References

Revell, L. J. and R. G. Reynolds. (2012) A new Bayesian method for fitting evolutionary models to comparative data with intraspecific variation. Evolution, 66, 2697-2707.

See Also

anc.Bayes, brownie.lite, evol.rate.mcmc