ape: rtree – R documentation

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rtree

Generate Random Trees

Description

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

Usage

rtree(n, rooted = TRUE, tip.label = NULL, br = runif, equiprob = FALSE, ...)
rtopology(n, rooted = FALSE, tip.label = NULL, br = runif, ...)
rcoal(n, tip.label = NULL, br = "coalescent", ...)
rmtree(N, n, rooted = TRUE, tip.label = NULL, br = runif,
       equiprob = FALSE, ...)
rmtopology(N, n, rooted = FALSE, 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.
`equiprob`	(new since ape 5.4-1) a logical specifying whether topologies are generated in equal frequencies. If, `FALSE`, the unbalanced topologies are generated in higher proportions than the balanced ones.
`...`	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 option equiprob = TRUE generates unlabelled topologies in equal frequencies. This is more complicated for the labelled topologies (see the vignette “RandomTopologies”).

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 or rmtopology.

Author(s)

Emmanuel Paradis

References

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

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

ape

Analyses of Phylogenetics and Evolution

v5.5

GPL-2 | GPL-3

Authors

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24