In addition to the ideas so far, there is also corHMM.
https://rdrr.io/cran/corHMM/man/corHMM.html is the main help for this, but you
can also use corHMM::ancRECON, corHMM:rayDISC, and corHMM:corDISC.
corHMM::plotRECON can plot ancestral state reconstructions.
For tip uncertainty, you can do
Hi Chris,
I sent this message a few days ago but can't see any sign that it was
received so trying again. Apologies if anyone ends up seeing both.
To the question- in addition to the other (good) solutions given in this
thread, both HiSSE (R package) and BayesTraits (stand alone software) can
