Fantastic, thank you. Yes, diversitree works well for my data. I fit a
3-state model, comparing symmetric vs. asymmetric rates and found that the
asymmetric rates model was the best fit. The marginal likelihood node
reconstructions make more sense than did the results from ace.
Thank you for your
Hi Katharine.
You can also do ancestral state estimation for the model "ARD" using the
packages diversitree. There is a worked example on my blog here:
http://blog.phytools.org/2016/09/possible-bug-in-acemodelard-and-other.html
(also highlighting a possible bug in ace for model="ARD" & other
