fitBayes {phytools} | R Documentation |
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())
tree |
an object of class |
x |
a vector of phenotypic values for individuals; |
ngen |
a integer indicating the number of generations for the MCMC. |
model |
an evolutionary model: either |
method |
a method: either |
control |
a list of control parameters containing the following elements: |
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 liam.revell@umb.edu
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.
anc.Bayes
, brownie.lite
, evol.rate.mcmc