collapse.singles {ape} | R Documentation |
This function deletes the single nodes (i.e., with a single descendant) in a tree.
collapse.singles(tree, root.edge = FALSE)
tree |
an object of class |
root.edge |
whether to get the singleton edges from the root
until the first bifurcating node and put them as |
an object of class "phylo"
.
Emmanuel Paradis
## 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 ## the following shows that node #4 (ie, the root) is a singleton ## and node #6 is the first bifurcating node tr$edge ## Normally, a tree has less nodes than it has tips: ## > plot(tr) ## Error in plot.phylo(tr) : ## there are single (non-splitting) nodes in your tree; ## you may need to use collapse.singles() collapse.singles(tr) # only 2 nodes ## give branch lengths to use the 'root.edge' option: tr$edge.length <- runif(5) str(collapse.singles(tr, TRUE)) # has a 'root.edge'