fitBayes: Evolutionary model fitting with intraspecific variability...

Description Usage Arguments Value Author(s) References See Also

View source: R/fitBayes.R

Description

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

Usage

1
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 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.

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 [email protected]

References

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


liamrevell/phytools documentation built on June 30, 2018, 8:15 a.m.