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phytools (version 0.7-20)

minSplit: Finding the minimum (median) split in the posterior sample

Description

This function takes a phylogenetic tree and a list of splits and identifies the split with the smallest summed or summed squared distances to all the other splits.

Usage

minSplit(tree, split.list, method="sum", printD=FALSE)

Arguments

tree

an object of class "phylo".

split.list

either a matrix with two named columns, "node" and "bp"; a $mcmc matrix from evol.rate.mcmc(); or the entire raw output from evol.rate.mcmc().

method

an optional string indicating the criterion to minimize: options are "sum" and "sumsq".

printD

logical specifying whether to print distances to screen (FALSE by default).

Value

A list with the following components:

node

node for the minimum split.

bp

location on the branch leading to node of the minimum split.

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

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, posterior.evolrate