| Renumber {TreeTools} | R Documentation |
Renumber a tree's nodes and tips
Description
Renumber() numbers the nodes and tips in a tree to conform with the
phylo standards.
Usage
Renumber(tree)
Arguments
tree |
A tree of class |
Details
The ape class phylo is not formally defined, but expects trees' internal
representation to conform to certain principles: for example, nodes should
be numbered sequentially, with values increasing away from the root.
Renumber() attempts to reformat any tree into a representation that will
not cause ape functions to produce unwanted results or to crash R.
Value
Renumber() returns a tree of class phylo, numbered in a
Cladewise fashion consistent with the expectations of ape functions.
Author(s)
Martin R. Smith (martin.smith@durham.ac.uk)
See Also
Preorder() provides a faster and simpler alternative, but also
rotates nodes.
Other tree manipulation:
AddTip(),
CollapseNode(),
ConsensusWithout(),
DropTip(),
EnforceOutgroup(),
ImposeConstraint(),
KeptPaths(),
KeptVerts(),
LeafLabelInterchange(),
MakeTreeBinary(),
RenumberTips(),
RenumberTree(),
RootTree(),
SortTree(),
Subtree(),
TipTimedTree(),
TrivialTree
Examples
tree <- RandomTree(letters[1:10])
Renumber(tree)