phytools (version 0.2-1)

evol.rate.mcmc: Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny

Description

This function takes a phylogenetic tree and data for a single continuously valued character and uses a Bayesian MCMC approach to identify the phylogenetic location of a shift in the evolutionary rate through time.

Usage

evol.rate.mcmc(tree, x, ngen=10000, control=list())

Arguments

tree

a phylogenetic tree in "phylo" format.

x

a vector of tip values for species; names(dat) should be the species names.

ngen

an optional integer value indicating the number of generations for the MCMC.

control

a list of control parameters containing the following elements: sig1: starting value for sig(1)^2; sig2: starting value for sig(2)^2; a: starting value for a; sd1: standard deviation for the normal propo

Value

• a list with the following components:
• mcmc
  results from the MCMC run.
• tips
  list of stips in state sig(1)^2 for each sampled generation of MCMC (to polarize the rate shift).

Details

Default values of control are given in Revell et al. (2012).

References

Revell, L. J., D. L. Mahler, P. Peres-Neto, and B. D. Redelings. 2012. A new method for identifying exceptional phenotypic diversification. Evolution, 66, 135-146.

See Also

anc.Bayes, brownie.lite, evol.vcv, minSplit, posterior.evolrate