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averageTree

Compute an average tree from a set of trees and related operations

Description

These functions compute average trees or consensus trees by various criteria.

Usage

averageTree(trees, start=NULL, method="quadratic.path.difference",
   tol=1e-12, quiet=FALSE, ...)
ls.consensus(trees, start=NULL, tol=1e-12, quiet=FALSE, ...)
minTreeDist(tree, trees, method="quadratic.path.difference", ...)

Arguments

trees

object of class "multiPhylo".
tree

object of class "phylo". For minTreeDist the tree on which to find the edge lengths that minimize the distance to the phylogenies in trees.
start

starting tree for optimization.
method

distance criterion for minimization. Options are "symmetric.difference", "branch.score.difference", "path.difference", and "quadratic.path.difference".
tol

tolerance value for optimization.
quiet

logical value indicating whether to run "quietly" or not.
...

other arguments to be passed internally.

Value

An object of class "phylo" with edge lengths.

Author(s)

phytools

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70
GPL (>= 2)
Authors
Liam J. Revell
Initial release
2020-9-19

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