Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states.
Covarion model for Binary data
alpha, switchRate, vfrequencies, hfrequencies, mode, rates, eigenSystem, frequencies
 
type: beast.core.parameter.RealParameter |
the rate of evolution in slow mode |
Required input |
 
type: beast.core.parameter.RealParameter |
the rate of flipping between slow and fast modes |
Required input |
 
type: beast.core.parameter.RealParameter |
the frequencies of the visible states |
Required input |
 
type: beast.core.parameter.RealParameter |
the frequencies of the hidden rates |
Optional input |
 
type: beast.evolution.substitutionmodel.BinaryCovarion$MODE |
one of BEAST, REVERSIBLE, TUFFLESTEEL BEAST = implementation as in BEAST 1 REVERSIBLE = like BEAST 1 implementation, but using frequencies to make it reversible TUFFLEYSTEEL = Tuffley & Steel (1996) impementation (no rates for |
Optional input |
 
type: beast.core.Function |
Rate parameter which defines the transition rate matrix. Only the off-diagonal entries need to be specified (diagonal makes row sum to zero in a rate matrix). Entry i specifies the rate from floor(i/(n-1)) to i%(n-1)+delta where n is the number of states and delta=1 if floor(i/(n-1)) <= i%(n-1) and 0 otherwise. |
Optional input |
 
type: java.lang.String |
Name of the class used for creating an EigenSystem |
Optional input. Default: beast.evolution.substitutionmodel.DefaultEigenSystem |
 
type: beast.evolution.substitutionmodel.Frequencies |
substitution model equilibrium state frequencies |
Optional input |