TreeTools: Neworder – R documentation

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Neworder

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, nb.edge, 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

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

Create, Modify and Analyse Phylogenetic Trees

v1.4.4

GPL (>= 3)

Authors

Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)

Initial release