TreeTools: GenerateTree – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

GenerateTree

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)

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.

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.

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]))

TreeTools

Create, Modify and Analyse Phylogenetic Trees

v1.4.4

GPL (>= 3)

Authors

Martin R. Smith [aut, cre, cph] (<https://orcid.org/0000-0001-5660-1727>), Emmanuel Paradis [cph] (<https://orcid.org/0000-0003-3092-2199>)

Initial release