fitBayes: Evolutionary model fitting with intraspecific variability...

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Evolutionary model fitting with intraspecific variability using Bayesian MCMC

Description

fitBayes uses Bayesian MCMC to sample terminal states (species means) as well as the parameters of an evolutionary model from their joint posterior distribution, following Revell & Reynolds (2012).

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; 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.

Value

An object of class "fitBayes" that includes a matrix (mcmc) with a 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.

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

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

phytools documentation built on June 22, 2024, 10:39 a.m.