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
39
40
41
42
43
44
45
46
47
48
|
\name{collapse.singles}
\alias{collapse.singles}
\alias{has.singles}
\title{Collapse Single Nodes}
\description{
\code{collapse.singles} deletes the single nodes (i.e., with a single
descendant) in a tree.
\code{has.singles} tests for the presence of single node(s) in a tree.
}
\usage{
collapse.singles(tree, root.edge = FALSE)
has.singles(tree)
}
\arguments{
\item{tree}{an object of class \code{"phylo"}.}
\item{root.edge}{whether to get the singleton edges from the root
until the first bifurcating node and put them as \code{root.edge} of
the returned tree. By default, this is ignored or if the tree has no
edge lengths (see examples).}
}
\value{
an object of class \code{"phylo"}.
}
\author{Emmanuel Paradis, Klaus Schliep}
\seealso{
\code{\link{plot.phylo}}, \code{\link{read.tree}}
}
\examples{
## a tree with 3 tips and 3 nodes:
e <- c(4L, 6L, 6L, 5L, 5L, 6L, 1L, 5L, 3L, 2L)
dim(e) <- c(5, 2)
tr <- structure(list(edge = e, tip.label = LETTERS[1:3], Nnode = 3L),
class = "phylo")
tr
has.singles(tr)
## the following shows that node #4 (ie, the root) is a singleton
## and node #6 is the first bifurcating node
tr$edge
## A bifurcating tree has less nodes than it has tips:
## the following used to fail with ape 4.1 or lower:
plot(tr)
collapse.singles(tr) # only 2 nodes
## give branch lengths to use the 'root.edge' option:
tr$edge.length <- runif(5)
str(collapse.singles(tr, TRUE)) # has a 'root.edge'
}
\keyword{manip}
|
