Dear Chris,
phangorn might provide a solution for your problem. You can define
user-specific data via a contrast matrix and use this matrix to create a
phyDat object. You can then use parsimony or maximum likelihood (maybe
also Bayesian?) in phangorn to reconstruct ancestral states. I actually
Dear Krzysztof,
I would agree with Liam that it would be most sensible to treat {02} as an
intermediate condition between {0} and {2}. I have not explored
phytools::make.simmap() in detail so I apologize in advance, if what I suggest
below can be done there (probably then in an easier way).
