One final comment on this. Since the conditional scaled likelihoods of
the subtree and the marginal ancestral state reconstruction are
equivalent at the root node of the tree, a computationally simple (but
slow) method for getting the marginal ancestral state reconstructions is
to move the
Hi Andres.
To answer your question at its face value, the line of code you want is:
anc-setNames(apply(ANC$lik.anc,1,function(x)
names(which.max(x))),length(tree$tip.label)+1:tree$Nnode)
(The setNames ensures that your resultant vector gets the node numbers
for names.)
This message really
