Wrappers for the C functions called by
ape::reorder.phylo.
These call the C functions directly, so are faster – but don't perform
as many checks on user input. Bad input could crash R.
Usage
NeworderPruningwise(nTip, nNode, parent, child, nEdge)
NeworderPhylo(nTip, parent, child, nEdge, whichwise)Arguments
- nTip, nNode, nEdge
Integer specifying the number of tips, nodes and edges in the input tree.
- 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].- whichwise
Integer specifying whether to order edges (1) cladewise; or (2) in postorder.
Value
NeworderPruningwise returns an integer vector specifying the
pruningwise order of edges within a tree.
NeworderPhylo returns an integer vector specifying the order
of edges under the ordering sequence specified by whichwise.
See also
Other C wrappers:
RenumberTree()
Examples
nTip <- 8L
tree <- BalancedTree(nTip)
edge <- tree[["edge"]]
pruningwise <- NeworderPruningwise(nTip, tree$Nnode, edge[, 1], edge[, 2],
dim(edge)[1])
cladewise <- NeworderPhylo(nTip, edge[, 1], edge[, 2], dim(edge)[1], 1L)
postorder <- NeworderPhylo(nTip, edge[, 1], edge[, 2], dim(edge)[1], 2L)
tree[["edge"]] <- tree[["edge"]][pruningwise, ]