def makeQdDefn(self, word_probs, mprobs_matrix, rate_params):
expm = NonParamDefn('expm')
exp = ExpDefn(expm)
calcExMat = CalcDefn(lambda: self.calcExchangeabilityMatrix,
name='calculate_exchangeability_matrix')()
Qd = CalcDefn(CalcQd, name='Qd')(exp, calcExMat, word_probs,
mprobs_matrix, *rate_params)
return Qd
def makeQdDefn(self, word_probs, mprobs_matrix, rate_params):
"""Diagonalized Q, ie: rate matrix prepared for exponentiation"""
Q = CalcDefn(self.calcQ, name='Q')(word_probs, mprobs_matrix, *rate_params)
expm = NonParamDefn('expm')
exp = ExpDefn(expm)
Qd = CallDefn(exp, Q, name='Qd')
return Qd
def makeContinuousPsubDefn(self, word_probs, mprobs_matrix, distance,
rate_params):
Qd = self.makeQdDefn(word_probs, mprobs_matrix, rate_params)
Q = CalcDefn(lambda cQd, t: cQd.getQ(t), name='Q')(Qd, distance)
P = CalcDefn(lambda cQd, Q: cQd.getP(), name='psubs')(Qd, Q)
return P