phytools: posterior.evolrate – R documentation

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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 (σ_1^2) and tipward (σ_2^2) from 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 σ_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 liam.revell@umb.edu

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.