Rev Language Reference



fnOrderedRateMatrix(Natural maxState, RealPos lambda, RealPos mu, Bool allowZeroState, Bool rescaled, String matrixExponentialMethod)


maxState : Natural (pass by const reference)
The maximum state for this rate matrix.
lambda : RealPos (pass by const reference)
The rate of gain.
Default : 1
mu : RealPos (pass by const reference)
The rate of loss.
Default : 1
allowZeroState : Bool (pass by value)
Can the character go into state 0.
Default : TRUE
rescaled : Bool (pass by value)
Should the matrix be normalized?
Default : TRUE
matrixExponentialMethod : String (pass by value)
The method used to compute the matrix exponential.
Default : eigen
Options : scalingAndSquaring|scalingAndSquaringPade|scalingAndSquaringTaylor|uniformization|eigen

Return Type