I suggest you ...

Implement SIMMAP in R

SIMMAP creates a stochastic simulation of discrete character trait evolution on a phylogenetic tree. This is a realization from the Bayesian posterior distribution of possible transitions given the tip data and the tree.

Desired functions:
A) Stochastic simulation under a given model
B) Infer the stochastic model

Notes:
a) Should implement an arbitrary size finite state Markov model
b) Should provide fast visualization or realizations

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    CarlAdminCarl (Admin, Comparative Phylogenetics) shared this idea  ·   ·  Admin →

    1 comment

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      • CarlAdminCarl (Admin, Comparative Phylogenetics) commented  · 

        This should be incorporated into the ouch package as a way of generating possible paintings. Will require either a simmap that allows changes only at nodes or a modification of the ouch code to allow changes along a branch.

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