AllSPR {TreeSearch}

All SPR trees

Description

All SPR trees

Usage

AllSPR(parent, child, nEdge, notDuplicateRoot, edgeToBreak)

Arguments

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

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

notDuplicateRoot

logical vector of length nEdge, specifying for each edge whether it is the second edge leading to the root (in which case its breaking will be equivalent to breaking the other root edge... except insofar as it moves the position of the root.)

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.

Value

AllSPR() returns a list of edge matrices for all trees one SPR rearrangement from the starting tree

Author(s)

Martin R. Smith