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thej022214 / corHMM

Fits a generalized form of the covarion model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as “hidden” states in a Markov process.
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Add support for multi-state individual traits in rate.mat.maker #9

Closed jcoliver closed 4 years ago

jcoliver commented 5 years ago

The command rate.mat.maker(rate.cat = 1, ntraits = 1, nstates = 3, model = "ARD") Results in the following rate index matrix:

    (0) (1)
(0)  NA   2
(1)   1  NA

However, for a three-state character, should the output not be something like:

    (0) (1) (2)
(0)  NA   3   5
(1)   1  NA   6
(2)   2   4  NA