posterior.evolrate {phytools}

Analysis of the posterior sample from evol.rate.mcmc

Description

Analyzes posterior sample from evol.rate.mcmc.

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 burn-in excluded).

tips

list of tips in state \sigma_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).

Details

This function 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 (\sigma_1^2) and tipward (\sigma_2^2) from the average split.

Value

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

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

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