RandomTree(), PectinateTree(), BalancedTree() and StarTree()
generate trees with the specified shapes and leaf labels.
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
FALSEfor 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.
See also
Other tree generation functions:
ConstrainedNJ(),
NJTree(),
TreeNumber,
TrivialTree
Examples
RandomTree(LETTERS[1:10])
#>
#> Phylogenetic tree with 10 tips and 8 internal nodes.
#>
#> Tip labels:
#> A, B, C, D, E, F, ...
#>
#> Unrooted; no branch lengths.
data("Lobo")
RandomTree(Lobo.phy)
#>
#> Phylogenetic tree with 48 tips and 46 internal nodes.
#>
#> Tip labels:
#> Tubiluchus_Priapulida, Cricocosmia, Aysheaia, Siberion, Onychodictyon_ferox, Onychodictyon_gracilis, ...
#>
#> Unrooted; no branch lengths.
plot(PectinateTree(LETTERS[1:10]))
plot(BalancedTree(LETTERS[1:10]))
plot(StarTree(LETTERS[1:10]))
