Rev Language Reference

fnFreeK(RealPos[][] transition_rates, Bool rescaled, String matrixExponentialMethod)

transition_rates :	RealPos[][] (pass by const reference)
	Transition rates between states.
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

RateMatrix

This function accepts both a vector or a matrix of non-negative, real numbers in the first argument to automatically generate a rate matrix with corresponding substitution rates, returning a rate matrix object. The function will fill rates in the matrix from left to right as provided in the first argument, skipping the diagonal when using a vector as input. For this reason, using a vector of lengths 2 to 5 will create a 2-by-2 rate matrix but a vector of length 6 will create a 3-by-3 rate matrix as fnFreeK will have enough values to fill the matrix. Using a matrix in fnFreeK will create a rate matrix object with rates assigned using their respective position in the provided matrix. Users can specify if matrix should be normalized in the second argument using a boolean variable (default TRUE). Lastly users can specify what matrix exponential method to use (default eigen) with a string. Possible options include: scalingAndSquaring scalingAndSquaringPade scalingAndSquaringTaylor uniformization eigen

# Define vector to pass, this will create a 2-by-2 matrix
x <- v(0.5, 0,5)
# Use fnFreeK to create rate matrix
# Note the second argument is true in this case so rates will be normalized
fnFreeK(x)
[ [ -1.0000, 1.0000 ] ,
  [ 1.0000, -1.0000 ] ]

# Case where rates are not normalized
x <- v(0.5, 0.5)
fnFreeK(x, false)
[ [ -0.5000, 0.5000 ] ,
  [ 0.5000, -0.5000 ] ]

# Define matrix for 3-by-3 rate matrix object
x <- v([0, .6, .4], [.2, 0, .4], [.3, .3, 0])
# Create rate matrix object
fnFreeK(x)
[ [ -1.0000, 0.6000, 0.4000 ] ,
  [ 0.2000, -0.6000, 0.4000 ] ,
  [ 0.3000, 0.3000, -0.6000 ] ]

• RateMatrix
• fnFreeBinary
• fnFreeSymmetricRateMatrix