averageTree | R Documentation |
Compute average trees or consensus trees by various criteria.
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", ...)
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. |
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.)
An object of class "phylo"
with edge lengths.
Liam Revell liam.revell@umb.edu
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. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
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