RenumberTree: Reorder trees

Description

Reorder() is a wrapper for ape:::.reorder_ape. Calling this C function directly is approximately twice as fast as using ape::cladewise or ape::postorder

Usage

RenumberTree(parent, child)
RenumberEdges(parent, child, ...)
Cladewise(tree, nTip, edge)
# S3 method for phylo
Cladewise(tree, nTip = length(tree$tip.label), edge = tree$edge)
# S3 method for list
Cladewise(tree, nTip, edge)
# S3 method for multiPhylo
Cladewise(tree, nTip, edge)
# S3 method for matrix
Cladewise(tree, nTip = min(tree[, 1]) - 1L, edge)
ApePostorder(tree, nTip, edge)
# S3 method for phylo
ApePostorder(tree, nTip = length(tree$tip.label), edge = tree$edge)
# S3 method for list
ApePostorder(tree, nTip, edge)
# S3 method for multiPhylo
ApePostorder(tree, nTip, edge)
Postorder(tree, force = FALSE, renumber = FALSE)
# S3 method for phylo
Postorder(tree, force = FALSE, renumber = FALSE)
# S3 method for list
Postorder(tree, force = FALSE, renumber = FALSE)
# S3 method for multiPhylo
Postorder(tree, force = FALSE, renumber = FALSE)
# S3 method for numeric
Postorder(tree, force = FALSE, renumber = FALSE)
PostorderEdges(edge, renumber = FALSE)
Pruningwise(tree, nTip, edge)
# S3 method for phylo
Pruningwise(tree, nTip = length(tree$tip.label), edge = tree$edge)
# S3 method for list
Pruningwise(tree, nTip, edge)
# S3 method for multiPhylo
Pruningwise(tree, nTip, edge)
Preorder(tree)
# S3 method for phylo
Preorder(tree)
# S3 method for numeric
Preorder(tree)
# S3 method for multiPhylo
Preorder(tree)
# S3 method for list
Preorder(tree)

Arguments

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].

…

Deprecated; included for compatibility with previous versions.

tree

A tree of class phylo.

nTip

Integer specifying number of tips (leaves).

edge

Two-column matrix listing the parent and child of each edge in a tree, corresponding to tree$edge. Optional in Cladewise().

force

Logical specifying whether to rearrange trees already in postorder, in order to ensure edges are ordered in the 'TreeTools' fashion.

renumber

Logical specifying whether to renumber nodes such that they increase in number away from the root.

Value

RenumberTree() returns an edge matrix for a tree of class phylo following the preorder convention for edge and node numbering.

RenumberEdges() formats the output of RenumberTree() into a list whose two entries correspond to the new parent and child vectors.

ApePostorder(), Cladewise(), Postorder(), Preorder() and Pruningwise() each return a tree of class phylo with nodes following the specified numbering scheme.

Postorder.numeric accepts a numeric matrix corresponding to the edge entry of a tree of class phylo, and returns a two-column array corresponding to tree, with edges listed in postorder

Functions

Cladewise: Reorder tree cladewise.
ApePostorder: Reorder tree in Postorder using ape's postorder function, which is robust to unconventional node numbering.
Postorder: Reorder tree in Postorder. Edge lengths are not retained.
Pruningwise: Reorder tree Pruningwise.
Preorder: Reorder tree in Preorder (special case of cladewise).

Details

Cladewise(), ApePostorder() and Pruningwise() are convenience functions to the corresponding functions in 'ape'. Single nodes may need to be collapsed using ape::collapse.singles first. 'ape' functions can cause crashes if nodes are numbered unconventionally -- sometimes encountered after using tree rearrangement functions, e.g. phangorn::SPR.

Preorder() is more robust: it supports polytomies, nodes can be numbered in any sequence, and edges can be listed in any order in the input tree. Its output is guaranteed to be identical for any tree of an equivalent topology, allowing unique trees to be detected by comparing sorted edge matrices alone.

A tree in preorder is numbered starting from the root node. Each node is numbered in the sequence in which it is encountered, and each edge is listed in the sequence in which it is visited.

At each node, child edges are sorted from left to right in order of the lowest-numbered leaf in the subtree subtended by each edge; i.e. an edge that leads eventually to tip 1 will be to the left of an edge leading to a subtree containing tip 2.

Numbering begins by following the leftmost edge of the root node, and sorting its descendant subtree into preorder. Then, the next edge at the root node is followed, and its descendants sorted into preorder, until each edge has been visited.

RenumberTree() and RenumberEdges() are wrappers for the C function preorder_edges_and_nodes(); they do not perform the same checks on input as Preorder() and are intended for use where performance is at a premium.

Postorder() is modified from the 'ape' function to return a specific order: edges are listed from the node that subtends the smallest subtree to the one that subtends the largest (i.e. the root node), with all of a node's descendant edges listed adjacently. If a tree is already in postorder, it will not be rearranged unless force = TRUE.

Methods applied to numeric inputs do not check input for sanity, so should be used with caution: malformed input may cause undefined results, including crashing R.

Trees with >8191 leaves require additional memory and are not handled at present. If you need to process such large trees, please contact the maintainer for advice.