| rtree {ape} | R Documentation |
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.
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 |
either an R function used to generate the branch lengths
(rtree or NULL to give no branch lengths) or the
coalescence times (rcoal). For the latter, a genuine
coalescent tree is simulated by default. |
... |
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 Emmanuel.Paradis@mpl.ird.fr
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))