These functions generate trees by splitting randomly the edges
rtopology) or randomly clustering the tips
rtopology generate general
rcoal generates coalescent trees. The algorithms are
described in Paradis (2012) and in a vignette in this package.
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, ...)
an integer giving the number of tips in the tree.
a logical indicating whether the tree should be rooted (the default).
a character vector giving the tip labels; if not specified, the tips "t1", "t2", ..., are given.
one of the following: (i) an R function used to generate the
branch lengths (
(new since ape 5.4-1) a logical specifying
whether topologies are generated in equal frequencies. If,
further argument(s) to be passed to
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.
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
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
the case of
Paradis, E. (2012) Analysis of Phylogenetics and Evolution with R (Second Edition). New York: Springer.
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))
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