Hi all,
There is indeed a bug in root(), but there seems to be an ambiguity
which needs to be solved: I think Luiz's command should give an error
for the reason I try to explain below.
As written in the help page, the option 'node' is an alternative to
'outgroup':
node: alternatively,
Maybe this is obvious, but even though your tree is unrooted, node 6 is
the root of the edge matrix for the tree (i.e., it has the node
number equal to Ntip(tree)+1) - thus:
t5-multi2di(t5)
will give you a resolved tree rooted at this node.
There seems to be a bug in root when you try to
Dear phylofolks,
I'm trying to root a tree on an internal (rather than a terminal) branch.
Here is a small example:
library(ape)
t5 - rmtree(N = 1, n = 5, rooted = FALSE)[[1]]
root(t5, node = 6, resolve.root = TRUE)
output: Error in if (i != N) { : argument is of length zero
root(t5, node =
