rtree: Generates Random Trees

Description

These functions generate trees by splitting randomly the edges (rtree) or randomly clustering the tips (rcoal). rtree generates general trees, and rcoal generates coalescent trees. The algorithms are described in Paradis (2012).

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

Value

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

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.

References

Paradis, E. (2012) Analysis of Phylogenetics and Evolution with R (Second Edition). New York: Springer.

Examples

Run this code

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))

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