rtree: Generates Random Trees

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

View source: R/rtree.R

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

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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, ...)

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

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.

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

References

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

See Also

stree, rlineage

Examples

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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(1)
par(mar = c(5, 4, 4, 2))

Example output



ape documentation built on May 2, 2019, 3:22 a.m.