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

Description Usage Arguments Value Author(s) References See Also

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

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. Used to be called min.split() but was changed to avoid conflict with the generic min.

Usage

1
minSplit(tree, split.list, method="sum", printD=FALSE)

Arguments

tree

a phylogeny stored as 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 [email protected]

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


liamrevell/phytools documentation built on Nov. 22, 2018, 5:21 p.m.