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phytools (version 0.0-8)

posterior.evolrate: Analysis of the posterior sample from evol.rate.mcmc

Description

This fucntion takes a phylogenetic tree, an average split position, and a raw MCMC output from evol.rate.mcmc and returns a posterior sample of evolutionary rates rootward (sig(1)^2) and tipward (sig(2)^2) or the average split.

Usage

posterior.evolrate(tree,ave.shift,mcmc,tips,showTree=FALSE)

Arguments

tree
a phylogenetic tree in "phylo" format.
ave.shift
mean or median shift-point from the posterior sample (see minSplit.
mcmc
matrix $mcmc from evol.rate.mcmc (probably with burnin excluded).
tips
list of stips in state sig(1)^2 for each sampled generation of MCMC.
showTree
optional logical value indicating whether or not to plot the stretched and shrunken tree generated by the pre-processing algorithm implemented in this function (default is FALSE).

Value

  • a matrix containing the posterior sample of evolutionary rates and shift-points between rates.

References

Revell, L. J., D. L. Mahler, P. Peres-Neto, and B. D. Redelings. In review. A new method for identifying exceptional phenotypic diversification.

See Also

evol.rate.mcmc, minSplit