Hi
I am trying to reconstruct anestral character states with the *ace* function
of the *ape* package. I have a discrete character which among the taxa of my
phylogeny is present or not (1or 0).
When I use the "ER" model assuming equal transition rates between the two
states I get good results. But for confidence I wanted to conduct also a
Maximum Likelihood analysis with the "ARD" model assuming rates to vary and
finally compare the two results. *The problem is that some of my likelihoods
for the states of the ancestors are negative using the ARD model. *Does
somebody know why?
Thanks a lot,
Betty
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