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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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Cases where removing dual transitions leaves no way to transition between all states. #18

Open jboyko opened 4 years ago

jboyko commented 4 years ago

These are probably estimable, but thrown an error during the ancestral state reconstruction. We should warn the user when this is the case and perhaps offer a default matrix where dual transitions are allowed. In my opinion, this is partially a matter of whether allowing these types transitions break the biological assumptions of the model.

jboyko commented 4 years ago

I think the best option is to give a warning that it's un-estimateable and add an option to get getRateMat4Dat to include dual transitions. Will add this soon.

Caetanods commented 4 years ago

If the MK model cannot visit some states, then you might not have an ergotic Markov Chain ( https://brilliant.org/wiki/ergodic-markov-chains/ ). I don't know if some of the assumptions of the MK model will be broken if this is the case.

jboyko commented 4 years ago

Bingo! That's exactly the issue. Now, how do we make an efficient test of ergodicity?