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

View source: R/evol.rate.mcmc.R

minSplitR 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.

See Also

evol.rate.mcmc, posterior.evolrate


liamrevell/phytools documentation built on March 4, 2024, 3:27 a.m.