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

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

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 [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, posterior.evolrate

phytools documentation built on June 22, 2024, 10:39 a.m.