TreeSearch (version 0.4.0)

TBR: Tree bisection and reconnection (TBR)

Description

TBR performs a single random TBR iteration.

Usage

TBR(tree, edgeToBreak = NULL, mergeEdges = NULL)
TBRSwap(parent, child, nEdge = length(parent), edgeToBreak = NULL,
  mergeEdges = NULL)
TBRMoves(parent, child, nEdge = length(parent), avoid = NULL,
  retainRoot = FALSE)
AllTBR(parent, child, nEdge = length(parent), avoid = NULL,
  retainRoot = FALSE)
RootedTBR(tree, edgeToBreak = NULL, mergeEdges = NULL)
RootedTBRSwap(parent, child, nEdge = length(parent),
  edgeToBreak = NULL, mergeEdges = NULL)

Arguments

tree

A bifurcating tree of class phylo, with all nodes resolved;

edgeToBreak

(optional) integer specifying the index of an edge to bisect/prune, generated randomly if not specified. Alternatively, set to -1 to return a complete list of all trees one step from the input tree.

mergeEdges

(optional) vector of length 1 or 2, listing edge(s) to be joined: In SPR, this is where the pruned subtree will be reconnected. In TBR, these edges will be reconnected (so must be on opposite sides of edgeToBreak); if only a single edge is specified, the second will be chosen at random

parent

Integer vector corresponding to the first column of the edge matrix of a tree of class phylo, i.e. tree$edge[, 1].

child

Integer vector corresponding to the second column of the edge matrix of a tree of class phylo, i.e. tree$edge[, 2].

nEdge

(optional) Number of edges.

avoid

Integer vector specifying which edges should not be broken

retainRoot

logical specifying whether taxa may be swapped across the root

Value

This function returns a tree in phyDat format that has undergone one TBR iteration.

a list containing two elements, corresponding in turn to the rearranged parent and child parameters

a matrix with two columns, each row listing an edge that can be broken and an edge into which it can be merged

a list of trees, in parent-child format

Functions

• TBRSwap: faster version that takes and returns parent and child parameters

• TBRMoves: Possible TBR moves

• AllTBR: All unique trees one TBR move away

• RootedTBR: Perform TBR rearrangement, retaining position of root

• RootedTBRSwap: faster version that takes and returns parent and child parameters

Details

Branch lengths are not (yet) supported.

All nodes in a tree must be bifurcating; ape::collapse.singles and ape::multi2di may help.

References

The TBR algorithm is summarized in Felsenstein2004TreeSearch

See Also

RootedTBR(): useful when the position of the root node should be retained.

Other tree rearrangement functions: NNI, SPR

Examples

# NOT RUN {
{
library('ape')
tree <- rtree(20, br=NULL)
TBR(tree)
}
# }