TreeSearch (version 0.2.2)

SPR: Subtree Pruning and Rearrangement

Description

Perform one SPR rearrangement on a tree

Usage

SPR(tree, edgeToBreak = NULL, mergeEdge = NULL)
SPRSwap(parent, child, nEdge = length(parent), nNode = nEdge/2L,
  edgeToBreak = NULL, mergeEdge = NULL)
RootedSPR(tree, edgeToBreak = NULL, mergeEdge = NULL)
RootedSPRSwap(parent, child, nEdge = length(parent), nNode = nEdge/2L,
  edgeToBreak = NULL, mergeEdge = NULL)

Arguments

tree

A tree of class phylo.

edgeToBreak

the index of an edge to bisect, generated randomly if not specified.

mergeEdge

the index of an edge on which to merge the broken edge.

parent

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

child

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

nEdge

(optional) integer specifying the number of edges of a tree of class phylo, i.e. dim(tree$edge)[1]

nNode

(optional) Number of nodes.

Value

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

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

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

Functions

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

• RootedSPR: Perform SPR rearrangement, retaining position of root

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

Details

Equivalent to phangorn's kSPR, but faster. Note that rearrangements that only change the position of the root WILL be returned by SPR. If the position of the root is irrelevant (as in Fitch parsimony, for example) then this function will occasionally return a functionally equivalent topology. RootIrrelevantSPR will search tree space more efficiently in these cases. Branch lengths are not (yet) supported.

References

The SPR algorithm is summarized in Felsenstein2004TreeSearch

See Also

RootedSPR useful when the position of the root node should be retained.

TBR

NNI

Examples

# NOT RUN {
{
tree <- ape::rtree(20, br=FALSE)
SPR(tree)
}
# }