averageTree: Compute an average tree from a set of trees and related...
In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)
averageTree R Documentation
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 liam.revell@umb.edu
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.
phytools documentation built on June 22, 2024, 10:39 a.m.
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| averageTree | R Documentation |
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 |
tree |
object of class |
start |
starting tree for optimization. |
method |
distance criterion for minimization. Options are |
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 liam.revell@umb.edu
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.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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