rtree {ape}R Documentation

Generates Random Trees

Description

These functions generate trees by splitting randomly the edges (rtree) or randomly clustering the tips (rcoal). rtree generates general (non-ultrametric) trees, and rcoal generates coalescent (ultrametric) trees.

Usage

rtree(n, rooted = TRUE, tip.label = NULL, br = runif, ...)
rcoal(n, tip.label = NULL, br = "coalescent", ...)
rmtree(N, n, rooted = TRUE, tip.label = NULL, br = runif, ...)

Arguments

n an integer giving the number of tips in the tree.
rooted a logical indicating whether the tree should be rooted (the default).
tip.label a character vector giving the tip labels; if not specified, the tips "t1", "t2", ..., are given.
br an R function used to generate the branch lengths (rtree; use NULL to simulate only a topology), or the coalescence times (rcoal). For the latter, a genuine coalescent tree is simulated by default.
... further argument(s) to be passed to br.
N an integer giving the number of trees to generate.

Details

The trees generated are bifurcating. If rooted = FALSE in (rtree), the tree is trifurcating at its root.

The default function to generate branch lengths in rtree is runif. If further arguments are passed to br, they need to be tagged (e.g., min = 0, max = 10).

rmtree calls successively rtree and set the class of the returned object appropriately.

Value

An object of class "phylo" or of class "multiPhylo" in the case of rmtree.

Author(s)

Emmanuel Paradis Emmanuel.Paradis@mpl.ird.fr

Examples

layout(matrix(1:9, 3, 3))
### Nine random trees:
for (i in 1:9) plot(rtree(20))
### Nine random cladograms:
for (i in 1:9) plot(rtree(20, FALSE), type = "c")
### generate 4 random trees of bird orders:
data(bird.orders)
layout(matrix(1:4, 2, 2))
for (i in 1:4)
  plot(rcoal(23, tip.label = bird.orders$tip.label), no.margin = TRUE)
layout(matrix(1))

[Package ape version 2.3 Index]