evol.rate.mcmc {phytools}R Documentation

Bayesian MCMC method for identifying exceptional phenotypic diversification in a phylogeny


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.


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



a phylogenetic tree in "phylo" format.


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


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


a list of control parameters containing the following elements: sig1: starting value for σ(1)^2; sig2: starting value for σ(2)^2; a: starting value for a; sd1: standard deviation for the normal proposal distribution for σ(1)^2; sd2: standard deviation for the normal proposal distribution for σ(2)^2; kloc: scaling parameter for tree move proposals - 1/λ for the reflected exponential distribution; sdlnr: standard deviation on the log-normal prior on σ(1)^2/σ(2)^2; rand.shift: probability of proposing a random shift in the tree (improves mixing); print: print frequency for the MCMC; sample: sample frequency.


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


A list with the following components:


results from the MCMC run.


list of stips in rate σ(1)^2 for each sampled generation of MCMC (to polarize the rate shift).


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., 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

[Package phytools version 0.4-60 Index]