44 #include "../AbstractSubstitutionModel.h" 46 #include <Bpp/Numeric/Constraints.h> 49 #include <Bpp/Seq/Alphabet/NucleicAlphabet.h> 121 mutable RowMatrix<double>
p_;
125 RN95s(
const NucleicAlphabet* alphabet,
133 #ifndef NO_VIRTUAL_COV 141 double Pij_t (
size_t i,
size_t j,
double d)
const;
142 double dPij_dt (
size_t i,
size_t j,
double d)
const;
143 double d2Pij_dt2(
size_t i,
size_t j,
double d)
const;
144 const Matrix<double>&
getPij_t (
double d)
const;
145 const Matrix<double>&
getdPij_dt (
double d)
const;
148 std::string
getName()
const {
return "RN95s"; }
156 void setFreq(std::map<int, double>&);
const Matrix< double > & getdPij_dt(double d) const
const Matrix< double > & getPij_t(double d) const
double dPij_dt(size_t i, size_t j, double d) const
Partial implementation of the SubstitutionModel interface.
double d2Pij_dt2(size_t i, size_t j, double d) const
void updateMatrices()
Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVe...
std::string getName() const
Get the name of the model.
Intersection of models RN95 and L95.
double Pij_t(size_t i, size_t j, double d) const
RN95s(const NucleicAlphabet *alphabet, double alpha=1, double beta=1, double gamma=1, double delta=1)
Specialisation interface for nucleotide substitution model.
const Matrix< double > & getd2Pij_dt2(double d) const
void setFreq(std::map< int, double > &)
This method takes the average value between observed and .