fitBayes {phytools}R Documentation

Evolutionary model fitting with intraspecific variability using Bayesian MCMC


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


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



an object of class "phylo".


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


a integer indicating the number of generations for the MCMC.


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


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


a list of control parameters containing the following elements: sig2: starting value for σ^2 (BM rate); lambda: starting value for the λ parameter; a: starting for the state at the root node; xbar: starting values for the states at the tips; intV: starting value for the intraspecific variance (reduced method); or v: starting value for the vector of intraspecific variances for all species (full method); pr.mean: means for the prior distributions in the following order - sig2, lambda (if applicable), a, xbar, intV or v (if applicable), note that the prior probability distribution is exponential for sig2 and normal for a and y; pr.var: variances on the prior distributions, same order as pr.mean.


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.


Liam Revell


Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

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

[Package phytools version 0.4-60 Index]