Neworder: Reorder edges of a phylogenetic tree

In TreeTools: Create, Modify and Analyse Phylogenetic Trees

Reorder edges of a phylogenetic tree

Description

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.

Author(s)

• C algorithm: Emmanuel Paradis

• R wrapper: Martin R. Smith

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, ]

TreeTools documentation built on Sept. 11, 2024, 8:27 p.m.