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 root an unrooted tree at
the root node (i.e., the node with node number Ntip(tree)+1).
All the best, Liam
Liam J. Revell, Assistant Professor of Biology
University of Massachusetts Boston
web: http://faculty.umb.edu/liam.revell/
email: liam.rev...@umb.edu
blog: http://blog.phytools.org
On 3/19/2015 3:12 PM, Luiz Max Carvalho wrote:
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 = 7, resolve.root = TRUE)
output: Phylogenetic tree with 5 tips and 4 internal nodes.
Tip labels:
[1] t4 t3 t2 t5 t1
Rooted; includes branch lengths.
I don't understand why rooting at node 6 throws an error, while using node
7 is fine. What am I missing?
Cheers,
Luiz
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