51 AbstractParameterAliasable(
"JC69."),
67 for (
size_t i = 0; i < 4; ++i)
69 for (
size_t j = 0; j < 4; ++j)
81 for (
size_t i = 0; i < 4; i++)
85 for (
size_t i = 1; i < 4; i++)
87 for (
size_t j = 0; j < 4; j++)
96 for (
size_t i = 0; i < 4; i++)
100 for (
size_t i = 1; i < 4; i++)
104 for (
size_t i = 0; i < 3; i++)
106 for (
size_t j = 1; j < 4; j++)
121 return 1. / 4. + 3. / 4. * exp(-
rate_ * 4. / 3. * d);
123 return 1. / 4. - 1. / 4. * exp(-
rate_ * 4. / 3. * d);
133 return 1. / 3. * exp(-
rate_ * 4. / 3. * d) *
rate_;
151 for (
size_t i = 0; i <
size_; i++)
153 for (
size_t j = 0; j <
size_; j++)
155 p_(i, j) = (i == j) ? 1. / 4. + 3. / 4. *
exp_ : 1. / 4. - 1. / 4. *
exp_;
164 for (
size_t i = 0; i <
size_; i++)
166 for (
size_t j = 0; j <
size_; j++)
177 for (
size_t i = 0; i <
size_; i++)
179 for (
size_t j = 0; j <
size_; j++)
RowMatrix< double > exchangeability_
The exchangeability matrix of the model, defined as . When the model is reversible, this matrix is symetric.
This class implements a state map where all resolved states are modeled.
RowMatrix< double > rightEigenVectors_
The matrix made of right eigen vectors (by column).
Vdouble eigenValues_
The vector of eigen values.
Vdouble freq_
The vector of equilibrium frequencies.
const Matrix< double > & getd2Pij_dt2(double d) const
Partial implementation of the ReversibleSubstitutionModel interface.
RowMatrix< double > leftEigenVectors_
The matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular.
RowMatrix< double > generator_
The generator matrix of the model.
double rate_
The rate of the model (default: 1). The generator (and all its vectorial components) is independent o...
double d2Pij_dt2(size_t i, size_t j, double d) const
size_t size_
The size of the generator, i.e. the number of states.
double dPij_dt(size_t i, size_t j, double d) const
JCnuc(const NucleicAlphabet *alpha)
const Matrix< double > & getdPij_dt(double d) const
const Matrix< double > & getPij_t(double d) const
double Pij_t(size_t i, size_t j, double d) const