rtree: Generates Random Trees
In gjuggler/ape: Analyses of Phylogenetics and Evolution

Description Usage Arguments Details Value Author(s) See Also Examples

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.

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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, ...)

`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`	one of the following: (i) an R function used to generate the branch lengths (`rtree`; use `NULL` to simulate only a topology), or the coalescence times (`rcoal`); (ii) a character to simulate a genuine coalescent tree for `rcoal` (the default); or (iii) a numeric vector for the branch lengths or the coalescence times.
`...`	further argument(s) to be passed to `br`.
`N`	an integer giving the number of trees to generate.

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.

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

Emmanuel Paradis

stree, rlineage

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))