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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fixed small mistakes and clarified rate.mat and p #50
I proposed some changes to the documentation of rate.mat and p that make clearer what format they are supposed to be in, and how they relate to each other.
I also added a simple example for that based off of the previous example.
In minor corrections, I corrected rate.class to rate.cat and clarified that S and F in the explanation of fixing root probabilities are the names of the hidden states.
This is the result of few of us trying to resolve our initial confusions, and we thought these additions might clear it up a bit better for novices, but feel free to edit out anything (or everything) if it is too long or inaccurate.
I proposed some changes to the documentation of
rate.matandpthat make clearer what format they are supposed to be in, and how they relate to each other.I also added a simple example for that based off of the previous example.
In minor corrections, I corrected
rate.classtorate.catand clarified that S and F in the explanation of fixing root probabilities are the names of the hidden states.This is the result of few of us trying to resolve our initial confusions, and we thought these additions might clear it up a bit better for novices, but feel free to edit out anything (or everything) if it is too long or inaccurate.