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

Description Usage Arguments Value Author(s) References See Also

View source: R/evol.rate.mcmc.R

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 (σ(1)^2) and tipward (σ(2)^2) from the average split.

Usage

1
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.

Author(s)

Liam Revell [email protected]

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

evol.rate.mcmc, minSplit


liamrevell/phytools documentation built on June 30, 2018, 8:15 a.m.