Learn R Programming
phytools (version 0.3-72.1)

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(x) 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 $\sigma(1)^2$; sig2: starting value for $\sigma(2)^2$; a: starting value for a; sd1: standard deviation for the no

Value

  • A list with the following components:
  • mcmcresults from the MCMC run.
  • tipslist of stips in rate $\sigma(1)^2$ 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