Hi Jake & Diego,
Maybe a very small modification to ace() could help to accomodate some of these
issues. Currently, ace(type = "discrete") checks the branch lengths of the tree
and throws an error if any of them is zero or negative. I think zero-length
branches could be allowed. This seems quit
Hi Diego,
If your tree has polytomies and the branches have no length information, I am
not sure if likelihood model-based reconstruction is right.
The ace function (and all other similar functions based on likelihood) will
assume that your branch lengths represent some kind biological informat
Dear colleagues,
I am trying to estimate ancestral states for two binary characters in a
full morphology-based phylogenetic tree. I am using ace function,
type="discrete" and kappa=0 as arguments. Unfortunately, I am dealing with
two problems about this issue: my topology have three polytomies and
