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

minSplit {phytools}

R Documentation

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 elements:

`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. (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.