phytools: minSplit – R documentation

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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.

Author(s)

Liam Revell liam.revell@umb.edu

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.