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 \(\sigma(1)^2\); sig2: starting value for \(\sigma(2)^2\); a: starting value for a; sd1: standard deviation for the normal proposal distribution for \(\sigma(1)^2\); sd2: standard deviation for the normal proposal distribution for \(\sigma(2)^2\); kloc: scaling parameter for tree move proposals - \(1/\lambda\) for the reflected exponential distribution; sdlnr: standard deviation on the log-normal prior on \(\sigma(1)^2/\sigma(2)^2\); rand.shift: probability of proposing a random shift in the tree (improves mixing); print: print frequency for the MCMC; sample: sample frequency.
other optional arguments.
An object of class "evol.rate.mcmc" consisting of at least the following elements:
results from the MCMC run.
list of stips in rate \(\sigma(1)^2\) for each sampled generation of MCMC (to polarize the rate shift).
Default values of control are given in Revell et al. (2012).
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.
anc.Bayes, brownie.lite, evol.vcv, minSplit, posterior.evolrate