1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
|
## is.binary.tree.R (2023-02-07)
## Test for Binary Tree
## Copyright 2016-2023 Emmanuel Paradis
## This file is part of the R-package `ape'.
## See the file ../COPYING for licensing issues.
is.binary <- function(phy) UseMethod("is.binary")
is.binary.phylo <- function(phy)
{
n <- length(phy$tip.label)
m <- phy$Nnode
dgr <- tabulate(phy$edge, n + m)
ref <- c(rep.int(1L, n), rep.int(3L, m))
## the root is assumed to be numbered n+1
if (.is.rooted_ape(phy, n)) ref[n + 1L] <- 2L
## can use identical() as long as tabulate() returns integers
identical(dgr, ref)
}
is.binary.tree <- function(phy)
{
message("!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!\nis.binary.tree() is deprecated; using is.binary() instead.\n\nis.binary.tree() will be removed soon: see ?is.binary and update your code.\n!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!")
is.binary(phy)
}
is.binary.multiPhylo <- function(phy)
{
phy <- unclass(phy)
n <- length(attr(phy, "TipLabel"))
if (n)
n - sapply(phy, "[[", "Nnode") + is.rooted.multiPhylo(phy) == 2
else
sapply(phy, is.binary.phylo)
}
|
