Hi, I've trying to fit some BiSSE models in diversitree onto a set of fairly
large trees (>9k species) stored as a multiphylo object. However, due to the
size of the trees it quickly becomes a very time-consuming task to fit such
models to each individual tree.
Given that the implementation in diversitree uses an MCMC approach, I would
imagine that it is pretty straightforward in principle to fit the model
sampling trees from the multiphylo object in proportion to their probability
(in the same way as the parameter estimation). However, this doesn't seem to be
implemented in diversitree.
Is there a quick change to the relevant code that would run MCMC analyses of
BiSSE models in diversitree, or alternative another package that would fit
these but incorporating phylogenetic uncertainty using a set of phylogenies.
Thanks,
Kev
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