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). From a modelling
perspective you would want to say that the probability of a transition from {0}
to {02} is higher than that from {0} to {2} and of course the other way round.
This can be achieved in diversitree by supplying a custom parametrization of
the generator of the Markov process describing the discrete trait's evolution.
In order to do this one can write a wrapper function around the function in
diversitree that is responsible for calculating the likelihood for the chosen
model. This does take some playing around, but perhaps the code accompanying
our 2018 article could be useful: https://github.com/BISSE-TRS/ppbEcoli .
Best wishes
Krzysztof
Sent with Proton Mail secure email.
_______________________________________________
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
