reorder-methods: reordering trees within phylobase objects
In phylobase: Base package for phylogenetic structures and comparative data

Description Usage Arguments Details Value Note Author(s) See Also Examples

Methods for reordering trees into various traversal orders

reorder(x, ...)

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

`x`	a `phylo4` or `phylo4d` object
`order`	The desired traversal order; currently only “preorder” and “postorder” are allowed for `phylo4` and `phylo4d` objects.
`...`	optional: extra arguments supplied to `FUN`

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.

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

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

See http://ape.mpl.ird.fr/misc/FormatTreeR_28July2008.pdf

Peter Cowan, Jim Regetz

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

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

      ancestor descendant
 [1,]        0          6
 [2,]        6          7
 [3,]        7          3
 [4,]        7          8
 [5,]        8          1
 [6,]        8          2
 [7,]        6          9
 [8,]        9          4
 [9,]        9          5
      ancestor descendant
 [1,]        7          3
 [2,]        8          1
 [3,]        8          2
 [4,]        7          8
 [5,]        6          7
 [6,]        9          4
 [7,]        9          5
 [8,]        6          9
 [9,]        0          6