R: Generate pectinate, balanced or random trees

GenerateTree {TreeTools}

R Documentation

Generate pectinate, balanced or random trees

Description

RandomTree(), PectinateTree(), BalancedTree() and StarTree() generate trees with the specified shapes and leaf labels.

Usage

RandomTree(tips, root = FALSE, nodes)

PectinateTree(tips)

BalancedTree(tips)

StarTree(tips)

Arguments

`tips`	An integer specifying the number of tips, or a character vector naming the tips, or any other object from which `TipLabels()` can extract leaf labels.
`root`	Character or integer specifying tip to use as root, if desired; or `FALSE` for an unrooted tree.
`nodes`	Number of nodes to generate. The default and maximum, `tips - 1`, generates a binary tree; setting a lower value will induce polytomies.

Value

Each function returns an unweighted binary tree of class phylo with the specified leaf labels. Trees are rooted unless root = FALSE.

RandomTree() returns a topology drawn at random from the uniform distribution (i.e. each binary tree is drawn with equal probability). Trees are generated by inserting each tip in term at a randomly selected edge in the tree. Random numbers are generated using a Mersenne Twister. If root = FALSE, the tree will be unrooted, with the first tip in a basal position. Otherwise, the tree will be rooted on root.

PectinateTree() returns a pectinate (caterpillar) tree.

BalancedTree() returns a balanced (symmetrical) tree, in preorder.

StarTree() returns a completely unresolved (star) tree.

Author(s)

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

RandomTree(LETTERS[1:10])

data('Lobo')
RandomTree(Lobo.phy)

plot(PectinateTree(LETTERS[1:10]))

plot(BalancedTree(LETTERS[1:10]))
plot(StarTree(LETTERS[1:10]))

[Package TreeTools version 1.7.2 Index]