{ape}R Documentation

Collapse Single Nodes

Description deletes the single nodes (i.e., with a single descendant) in a tree. tests for the presence of single node(s) in a tree.

Usage, root.edge = FALSE)



an object of class "phylo".


whether to get the singleton edges from the root until the first bifurcating node and put them as root.edge of the returned tree. By default, this is ignored or if the tree has no edge lengths (see examples).


an object of class "phylo".


Emmanuel Paradis, Klaus Schliep

See Also

plot.phylo, read.tree


## 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")
## the following shows that node #4 (ie, the root) is a singleton
## and node #6 is the first bifurcating node
## A bifurcating tree has less nodes than it has tips:
## the following used to fail with ape 4.1 or lower:
plot(tr) # only 2 nodes
## give branch lengths to use the 'root.edge' option:
tr$edge.length <- runif(5)
str(, TRUE)) # has a 'root.edge'

[Package ape version 5.5 Index]