Renumber() numbers the nodes and tips in a tree to conform with the
phylo standards.
Arguments
- tree
A tree of class
phylo.
Value
Renumber() returns a tree of class phylo, numbered in a
Cladewise fashion consistent with the expectations of ape functions.
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.
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)
#>
#> Phylogenetic tree with 10 tips and 8 internal nodes.
#>
#> Tip labels:
#> f, g, i, j, c, d, ...
#>
#> Unrooted; no branch length.