poweRbal (version 0.0.1.1)

enum2cladewise: Function to modify the node enumeration in rooted binary trees

Description

enum2cladewise - Changes the node enumeration to cladewise enumeration, i.e., starting from the root we follow the rule:
Go to the left child; if that does not exist or was already visited go (up again and) to the right child.
The nodes in the rooted binary tree can be nearly arbitrarily enumerated (distinct nodes should have distinct values and the values should be positive, i.e., >0).

Usage

enum2cladewise(phy, root = NULL)

Value

enum2cladewise A single tree of class phylo is returned with cladewise node enumeration.

Arguments

phy

A rooted binary tree of class phylo.

root

Integer value (default = NULL) that should only be specified if the root is known precisely (not necessary, but speeds up computation).

Examples

# Example with cladewise enumeration:
phy_alreadycladew <- list(edge = matrix(c(6,7, 7,8, 8,1, 8,2,
                                          7,9, 9,3, 9,4, 6,5),
                                 byrow = TRUE, ncol = 2),
                          tip.label = rep(" ",5), Nnode = 4)
attr(phy_alreadycladew, "class") <- "phylo"
enum2cladewise(phy_alreadycladew, root = 6)$edge
ape::plot.phylo(phy_alreadycladew)
# Example with other node enumeration:
phy_example <- list(edge = matrix(c(1,55, 55,12, 12,2, 12,10, 55,9,
                                    9,13, 9,60, 1,3),
                                  byrow = TRUE, ncol = 2),
                    tip.label = rep(" ",5), Nnode = 4,
                    edge.length = rep(1, 8))
attr(phy_example, "class") <- "phylo"
# The reenumeration works with and without specifying the root:
enum2cladewise(phy_example, root = 1)$edge
ape::plot.phylo(enum2cladewise(phy_example))