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Subtree pruning and rearrangement (SPR)

Source: R/SPR.R
SPR.Rd

Perform one SPR rearrangement on a tree

Usage

SPR(tree, edgeToBreak = NULL, mergeEdge = NULL)

SPRMoves(tree, edgeToBreak = integer(0))

# S3 method for class 'phylo'
SPRMoves(tree, edgeToBreak = integer(0))

# S3 method for class 'matrix'
SPRMoves(tree, edgeToBreak = integer(0))

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

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) 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.

TBRMoves() returns a list of all trees one SPR move away from tree, with edges and nodes in preorder, rooted on the first-labelled tip.

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

Details

Equivalent to kSPR() in the phangorn package, 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.

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

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

References

The SPR algorithm is summarized in Felsenstein J (2004). Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.

See also

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

Other tree rearrangement functions: NNI(), TBR()

Author

Martin R. Smith

Examples

{
tree <- ape::rtree(20, br=FALSE)
SPR(tree)
}
#> 
#> Phylogenetic tree with 20 tips and 19 internal nodes.
#> 
#> Tip labels:
#>   t12, t7, t19, t5, t6, t1, ...
#> 
#> Rooted; includes branch lengths.