reorder-methods: reordering trees within phylobase objects

In fmichonneau/phylobase: Base Package for Phylogenetic Structures and Comparative Data

reordering trees within phylobase objects

Description

Methods for reordering trees into various traversal orders

Usage

reorder(x, ...)

## S4 method for signature 'phylo4'
reorder(x, order = c("preorder", "postorder"))

Arguments

x	a phylo4 or phylo4d object
...	additional optional elements (not in use)
order	The desired traversal order; currently only “preorder” and “postorder” are allowed for phylo4 and phylo4d objects.

Details

The reorder method takes a phylo4 or phylo4d tree and orders the edge matrix (i.e. edges(x)) in the requested traversal order. Currently only two orderings are permitted, and both require rooted trees. In postorder, a node's descendants come before that node, thus the root, which is ancestral to all nodes, comes last. In preorder, a node is visited before its descendants, thus the root comes first.

Value

A phylo4 or phylo4d object with the edge, label, length and data slots ordered as order, which is itself recorded in the order slot.

Note

The preorder parameter corresponds to cladewise in the ape package, and postorder corresponds (almost) to pruningwise.

Author(s)

Peter Cowan, Jim Regetz

See Also

reorder.phylo in the ape package. ancestors ancestor siblings children descendants

Examples

phy <- phylo4(ape::rtree(5))
edges(reorder(phy, "preorder"))
edges(reorder(phy, "postorder"))

fmichonneau/phylobase documentation built on Feb. 3, 2024, 2:29 a.m.