averageTree: Compute an average tree from a set of trees and related...

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

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

Description

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.

Details

The function averageTree tries to find the (hypothetical) tree topology and branch lengths that has a minimum distance to all the trees in an input set, according to some user-specified tree distance measure.

The function ls.consensus computes the least-squares consensus tree (Lapointe & Cucumel, 1997) from a set of input trees.

Finally, the function minTreeDist finds the tree in the input set that is a minimum distance to all the other trees in the set. (This contrasts with averageTree which can return a tree not in the input set.)

Value

An object of class "phylo" with edge lengths.

Author(s)

Liam Revell [e-mail]

References

Lapointe, F.-J., G. Cucumel (1997) The average consensus procedure: Combination of weighted trees containing identical or overlapping sets of taxa. Systematic Biology, 46, 306-312.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

liamrevell/phytools documentation built on April 8, 2024, 9:59 p.m.