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 = rexp, ...)
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 the coalescence times (rcoal ), or
NULL to gave no branch lengths in the tree. |
... |
further argument(s) to be passed to br . |
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
. In rcoal
rexp
is used to generate the
inter-node distances. If further arguments are passed to br
,
they need to be tagged (e.g., min = 0, max = 10
).
Emmanuel Paradis paradis@isem.univ-montp2.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))