bpp-phyl3  3.0.0
Functions
bpp::numeric Namespace Reference

Functions

template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value>::type>
T & cwise (T &t)
 
ExtendedFloat & cwise (ExtendedFloat &t)
 
const ExtendedFloat & cwise (const ExtendedFloat &t)
 
template<typename Derived >
auto cwise (const Eigen::MatrixBase< Derived > &m) -> decltype(m.array())
 
template<typename Derived >
auto cwise (Eigen::MatrixBase< Derived > &m) -> decltype(m.array())
 
auto cwise (const Eigen::RowVectorXi &m) -> decltype(m.template cast< double >().array())
 
template<int R, int C>
ExtendedFloatArray< R, C > cwise (const ExtendedFloatMatrix< R, C > &m)
 
template<int R, int C>
ExtendedFloatArrayWrapper< R, C > cwise (ExtendedFloatMatrix< R, C > &m)
 
void checkDimensionIsSquare (const MatrixDimension &dim)
 
template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value>::type>
T zero (const Dimension< T > &)
 
template<typename T = void>
char zero (const Dimension< char > &)
 
template<typename T = void>
std::string zero (const Dimension< std::string > &)
 
template<typename T = void>
Parameter & zero (const Dimension< Parameter > &)
 
template<typename T = void>
ExtendedFloat zero (const Dimension< ExtendedFloat > &)
 
template<typename T , int Rows, int Cols>
auto zero (const Dimension< Eigen::Matrix< T, Rows, Cols >> &dim) -> decltype(Eigen::Matrix< T, Rows, Cols >::Zero(dim.rows, dim.cols))
 
template<int R, int C, template< int R2=R, int C2=C > class MatType>
auto zero (const Dimension< ExtendedFloatEigen< R, C, MatType >> &dim) -> decltype(ExtendedFloatEigen< R, C, MatType >::Zero(dim.rows, dim.cols))
 
template<typename T = void>
TransitionFunction zero (const Dimension< TransitionFunction > &dim)
 
template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value>::type>
T one (const Dimension< T > &)
 
template<typename T = void>
char one (const Dimension< char > &)
 
template<typename T = void>
std::string one (const Dimension< std::string > &)
 
template<typename T = void>
Parameter & one (const Dimension< Parameter > &)
 
template<typename T = void>
ExtendedFloat one (const Dimension< ExtendedFloat > &)
 
template<typename T , int Rows, int Cols>
auto one (const Dimension< Eigen::Matrix< T, Rows, Cols >> &dim) -> decltype(Eigen::Matrix< T, Rows, Cols >::Ones(dim.rows, dim.cols))
 
template<int R, int C, template< int R2=2, int C2=C > class MatType>
auto one (const Dimension< ExtendedFloatEigen< R, C, MatType >> &dim) -> decltype(ExtendedFloatEigen< R, C, MatType >::Ones(dim.rows, dim.cols))
 
template<typename T = void>
TransitionFunction one (const Dimension< TransitionFunction > &dim)
 
template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value>::type>
T identity (const Dimension< T > &)
 
template<typename T , typename = typename std::enable_if<std::is_same<T, ExtendedFloat>::value>::type>
T identity (const Dimension< ExtendedFloat > &)
 
template<typename T , int Rows, int Cols>
auto identity (const Dimension< Eigen::Matrix< T, Rows, Cols >> &dim) -> decltype(Eigen::Matrix< T, Rows, Cols >::Identity(dim.rows, dim.cols))
 
template<int R, int C, template< int R2=R, int C2=C > class MatType>
auto identity (const Dimension< ExtendedFloatEigen< R, C, MatType >> &dim) -> decltype(ExtendedFloatEigen< R, C, MatType >::Identity(dim.rows))
 
bool isinf (const double &d)
 
bool isinf (const ExtendedFloat &d)
 
template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value || std::is_same<T, ExtendedFloat>::value>::type>
bool isIdentity (const T &t)
 
template<typename T = void>
bool isIdentity (const std::string &t)
 
template<typename Derived >
bool isIdentity (const Eigen::MatrixBase< Derived > &m)
 
template<int R, int C, template< int R2=R, int C2=C > class MatType>
bool isIdentity (const ExtendedFloatEigen< R, C, MatType > &efm)
 
template<typename R , typename F , typename = typename std::enable_if<std::is_arithmetic<R>::value || std::is_same<R, ExtendedFloat>::value>::type>
R convert (const F &from, const Dimension< R > &)
 
template<typename T , int Rows, int Cols, typename F , typename = typename std::enable_if<std::is_arithmetic<F>::value>::type>
auto convert (const F &from, const Dimension< Eigen::Matrix< T, Rows, Cols >> &dim) -> decltype(Eigen::Matrix< T, Rows, Cols >::Constant(dim.rows, dim.cols, from))
 
template<int R, int C, template< int R2=R, int C2=C > class MatType, typename F , typename = typename std::enable_if<std::is_same<F, ExtendedFloat>::value || std::is_arithmetic<F>::value>::type>
auto convert (const F &from, const Dimension< ExtendedFloatEigen< R, C, MatType >> &dim) -> decltype(ExtendedFloatEigen< R, C, MatType >::Constant(dim.rows, dim.cols, from))
 
TransitionFunction convert (double from, const Dimension< TransitionFunction > &dim)
 
template<typename T , int R, int C, typename DerivedF >
const Eigen::Matrix< T, R, C > convert (const Eigen::MatrixBase< DerivedF > &from, const Dimension< Eigen::Matrix< T, R, C >> &dim, typename std::enable_if< std::is_same< DerivedF, Eigen::RowVectorXi >::value||std::is_same< DerivedF, Eigen::VectorXi >::value >::type *=0)
 
template<int R, int C, typename DerivedF >
const ExtendedFloatMatrix< R, C > convert (const Eigen::MatrixBase< DerivedF > &from, const Dimension< ExtendedFloatMatrix< R, C >> &dim, typename std::enable_if< std::is_same< DerivedF, Eigen::RowVectorXi >::value||std::is_same< DerivedF, Eigen::VectorXi >::value >::type *=0)
 
template<typename T , int Rows, int Cols, typename DerivedF >
const DerivedF & convert (const Eigen::MatrixBase< DerivedF > &from, const Dimension< Eigen::Matrix< T, Rows, Cols >> &dim, typename std::enable_if<!(std::is_same< DerivedF, Eigen::RowVectorXi >::value||std::is_same< DerivedF, Eigen::VectorXi >::value)>::type *=0)
 
template<int R, int C, typename DerivedF >
const ExtendedFloatMatrix< R, C > convert (const Eigen::MatrixBase< DerivedF > &from, const Dimension< ExtendedFloatMatrix< R, C >> &dim, typename std::enable_if<!(std::is_same< DerivedF, Eigen::RowVectorXi >::value||std::is_same< DerivedF, Eigen::VectorXi >::value)>::type *=0)
 
template<int R, int C, typename DerivedF >
const DerivedF & convert (const ExtendedFloatEigenBase< DerivedF > &from, const Dimension< ExtendedFloatMatrix< R, C >> &dim)
 
template<int R, int C>
const Eigen::Matrix< double, R, C > convert (const ExtendedFloatMatrix< R, C > &from, const Dimension< Eigen::Matrix< double, R, C >> &dim)
 
template<typename R , typename F >
void convert (R &r, const F &from, const Dimension< R > &dim)
 
template<typename R >
void convert (R &r, const R &from, const Dimension< R > &dim)
 
template<typename T , typename = typename std::enable_if<std::is_floating_point<T>::value>::type>
T inverse (T t)
 
ExtendedFloat inverse (const ExtendedFloat &t)
 
template<typename Derived >
Derived inverse (ExtendedFloatEigenBase< Derived > base)
 
template<typename T , typename = typename std::enable_if<std::is_floating_point<T>::value>::type>
T log (T t)
 
template<typename T , typename = typename std::enable_if<std::is_floating_point<T>::value>::type>
T exp (T t)
 
template<typename T >
std::string debug (const T &t, typename std::enable_if< std::is_arithmetic< T >::value >::type *=0)
 
template<typename T >
std::string debug (const Parameter &t)
 
template<typename T = std::string>
std::string debug (const std::string &t)
 
template<typename T = ExtendedFloat>
std::string debug (const ExtendedFloat &t)
 
template<typename Derived >
std::string debug (const Eigen::MatrixBase< Derived > &m)
 
template<typename Derived >
std::string debug (const ExtendedFloatEigenBase< Derived > &m)
 
template<typename T = TransitionFunction>
std::string debug (const TransitionFunction &f)
 
template<typename T >
std::size_t hash (T t, typename std::enable_if< std::is_floating_point< T >::value||std::is_integral< T >::value >::type *=0)
 
std::size_t hash (const ExtendedFloat &ef)
 
template<typename T = std::string>
std::size_t hash (const std::string &t)
 
template<typename Derived >
std::size_t hash (const Eigen::MatrixBase< Derived > &m)
 
template<typename Derived >
std::size_t hash (const ExtendedFloatEigenBase< Derived > &efm)
 

Function Documentation

◆ checkDimensionIsSquare()

void bpp::numeric::checkDimensionIsSquare ( const MatrixDimension &  dim)

Definition at line 163 of file DataFlowNumeric.cpp.

References bpp::MatrixDimension::cols, bpp::MatrixDimension::rows, and bpp::to_string().

Referenced by identity().

◆ convert() [1/12]

template<typename T , int R, int C, typename DerivedF >
const Eigen::Matrix<T, R, C> bpp::numeric::convert ( const Eigen::MatrixBase< DerivedF > &  from,
const Dimension< Eigen::Matrix< T, R, C >> &  dim,
typename std::enable_if< std::is_same< DerivedF, Eigen::RowVectorXi >::value||std::is_same< DerivedF, Eigen::VectorXi >::value >::type *  = 0 
)

From Matrix Xi

Definition at line 630 of file DataFlowNumeric.h.

◆ convert() [2/12]

template<typename T , int Rows, int Cols, typename DerivedF >
const DerivedF& bpp::numeric::convert ( const Eigen::MatrixBase< DerivedF > &  from,
const Dimension< Eigen::Matrix< T, Rows, Cols >> &  dim,
typename std::enable_if<!(std::is_same< DerivedF, Eigen::RowVectorXi >::value||std::is_same< DerivedF, Eigen::VectorXi >::value)>::type *  = 0 
)

From Eigen

Definition at line 653 of file DataFlowNumeric.h.

◆ convert() [3/12]

template<int R, int C, typename DerivedF >
const ExtendedFloatMatrix<R, C> bpp::numeric::convert ( const Eigen::MatrixBase< DerivedF > &  from,
const Dimension< ExtendedFloatMatrix< R, C >> &  dim,
typename std::enable_if< std::is_same< DerivedF, Eigen::RowVectorXi >::value||std::is_same< DerivedF, Eigen::VectorXi >::value >::type *  = 0 
)

Definition at line 639 of file DataFlowNumeric.h.

◆ convert() [4/12]

template<int R, int C, typename DerivedF >
const ExtendedFloatMatrix<R, C> bpp::numeric::convert ( const Eigen::MatrixBase< DerivedF > &  from,
const Dimension< ExtendedFloatMatrix< R, C >> &  dim,
typename std::enable_if<!(std::is_same< DerivedF, Eigen::RowVectorXi >::value||std::is_same< DerivedF, Eigen::VectorXi >::value)>::type *  = 0 
)

Definition at line 661 of file DataFlowNumeric.h.

◆ convert() [5/12]

template<int R, int C, typename DerivedF >
const DerivedF& bpp::numeric::convert ( const ExtendedFloatEigenBase< DerivedF > &  from,
const Dimension< ExtendedFloatMatrix< R, C >> &  dim 
)

From ExtendedFloatEigen

Definition at line 673 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigenBase< Derived >::derived().

◆ convert() [6/12]

template<int R, int C>
const Eigen::Matrix<double, R, C> bpp::numeric::convert ( const ExtendedFloatMatrix< R, C > &  from,
const Dimension< Eigen::Matrix< double, R, C >> &  dim 
)

Definition at line 680 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::exponent_part(), bpp::ExtendedFloatEigen< R, C, EigenType >::float_part(), and bpp::ExtendedFloat::radix.

◆ convert() [7/12]

template<typename T , int Rows, int Cols, typename F , typename = typename std::enable_if<std::is_arithmetic<F>::value>::type>
auto bpp::numeric::convert ( const F &  from,
const Dimension< Eigen::Matrix< T, Rows, Cols >> &  dim 
) -> decltype (Eigen::Matrix<T, Rows, Cols>::Constant (dim.rows, dim.cols, from))

Definition at line 604 of file DataFlowNumeric.h.

◆ convert() [8/12]

template<int R, int C, template< int R2=R, int C2=C > class MatType, typename F , typename = typename std::enable_if<std::is_same<F, ExtendedFloat>::value || std::is_arithmetic<F>::value>::type>
auto bpp::numeric::convert ( const F &  from,
const Dimension< ExtendedFloatEigen< R, C, MatType >> &  dim 
) -> decltype (ExtendedFloatEigen<R, C, MatType>::Constant (dim.rows, dim.cols, from))

Definition at line 613 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::Constant().

◆ convert() [9/12]

template<typename R , typename F , typename = typename std::enable_if<std::is_arithmetic<R>::value || std::is_same<R, ExtendedFloat>::value>::type>
R bpp::numeric::convert ( const F &  from,
const Dimension< R > &   
)

Definition at line 597 of file DataFlowNumeric.h.

Referenced by bpp::TransitionFunctionFromModel::compute(), bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), bpp::RewardMappingTools::computeRewardVectors(), convert(), and bpp::copyEigenToBpp().

◆ convert() [10/12]

TransitionFunction bpp::numeric::convert ( double  from,
const Dimension< TransitionFunction > &  dim 
)
inline

Definition at line 620 of file DataFlowNumeric.h.

◆ convert() [11/12]

template<typename R , typename F >
void bpp::numeric::convert ( R &  r,
const F &  from,
const Dimension< R > &  dim 
)

General call

Definition at line 691 of file DataFlowNumeric.h.

References convert().

◆ convert() [12/12]

template<typename R >
void bpp::numeric::convert ( R &  r,
const R &  from,
const Dimension< R > &  dim 
)

Definition at line 697 of file DataFlowNumeric.h.

◆ cwise() [1/8]

template<typename Derived >
auto bpp::numeric::cwise ( const Eigen::MatrixBase< Derived > &  m) -> decltype (m.array ())

Definition at line 44 of file DataFlowCWise.h.

◆ cwise() [2/8]

auto bpp::numeric::cwise ( const Eigen::RowVectorXi &  m) -> decltype (m.template cast<double>().array ())
inline

Definition at line 54 of file DataFlowCWise.h.

◆ cwise() [3/8]

const ExtendedFloat& bpp::numeric::cwise ( const ExtendedFloat &  t)
inline

Definition at line 39 of file DataFlowCWise.h.

◆ cwise() [4/8]

template<int R, int C>
ExtendedFloatArray<R, C> bpp::numeric::cwise ( const ExtendedFloatMatrix< R, C > &  m)
inline

Definition at line 60 of file DataFlowCWise.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::exponent_part(), and bpp::ExtendedFloatEigen< R, C, EigenType >::float_part().

◆ cwise() [5/8]

template<typename Derived >
auto bpp::numeric::cwise ( Eigen::MatrixBase< Derived > &  m) -> decltype (m.array ())

Definition at line 49 of file DataFlowCWise.h.

◆ cwise() [6/8]

ExtendedFloat& bpp::numeric::cwise ( ExtendedFloat &  t)
inline

Definition at line 34 of file DataFlowCWise.h.

◆ cwise() [7/8]

template<int R, int C>
ExtendedFloatArrayWrapper<R, C> bpp::numeric::cwise ( ExtendedFloatMatrix< R, C > &  m)
inline

Definition at line 67 of file DataFlowCWise.h.

◆ cwise() [8/8]

template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value>::type>
T& bpp::numeric::cwise ( T &  t)

Definition at line 29 of file DataFlowCWise.h.

Referenced by bpp::CWiseAdd< R, std::tuple< T0, T1 > >::compute(), bpp::CWiseAdd< R, ReductionOf< T > >::compute(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::compute(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::compute(), bpp::CombineDeltaShifted< T >::compute(), bpp::CWiseSub< R, std::tuple< T0, T1 > >::compute(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::compute(), bpp::CWiseMean< R, ReductionOf< T >, P >::compute(), bpp::CWiseMul< R, ReductionOf< T > >::compute(), bpp::CWiseInverse< T >::compute(), bpp::CWiseLog< T >::compute(), bpp::CWiseExp< T >::compute(), bpp::CWiseConstantPow< T >::compute(), bpp::LogSumExp< R, T0, T1 >::compute(), bpp::ShiftDelta< T >::compute(), bpp::ForwardHmmLikelihood_DF::compute(), bpp::ForwardHmmDLikelihood_DF::compute(), bpp::ForwardHmmD2Likelihood_DF::compute(), bpp::BackwardHmmLikelihood_DF::compute(), bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), bpp::RewardMappingTools::computeRewardVectors(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorProbabilitiesPerSitePerClass(), and bpp::SingleProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerClass().

◆ debug() [1/7]

template<typename Derived >
std::string bpp::numeric::debug ( const Eigen::MatrixBase< Derived > &  m)

Definition at line 794 of file DataFlowNumeric.h.

References isIdentity(), one(), bpp::to_string(), and zero().

◆ debug() [2/7]

template<typename T = ExtendedFloat>
std::string bpp::numeric::debug ( const ExtendedFloat &  t)

Definition at line 787 of file DataFlowNumeric.h.

References bpp::to_string().

◆ debug() [3/7]

template<typename Derived >
std::string bpp::numeric::debug ( const ExtendedFloatEigenBase< Derived > &  m)

Definition at line 824 of file DataFlowNumeric.h.

References debug(), bpp::ExtendedFloatEigenBase< Derived >::derived(), and bpp::to_string().

◆ debug() [4/7]

template<typename T >
std::string bpp::numeric::debug ( const Parameter &  t)

Definition at line 772 of file DataFlowNumeric.h.

References bpp::Parameter::getValue(), and bpp::to_string().

◆ debug() [5/7]

template<typename T = std::string>
std::string bpp::numeric::debug ( const std::string &  t)

Definition at line 780 of file DataFlowNumeric.h.

◆ debug() [6/7]

template<typename T >
std::string bpp::numeric::debug ( const T &  t,
typename std::enable_if< std::is_arithmetic< T >::value >::type *  = 0 
)

Definition at line 764 of file DataFlowNumeric.h.

References bpp::to_string().

Referenced by debug(), bpp::ProbabilitiesFromDiscreteDistribution::debugInfo(), bpp::FrequenciesFromFrequencySet::debugInfo(), bpp::EquilibriumFrequenciesFromModel::debugInfo(), bpp::TransitionMatrixFromModel::debugInfo(), bpp::TransitionFunctionFromModel::debugInfo(), bpp::ProbabilitiesFromMixedModel::debugInfo(), bpp::Sequence_DF::debugInfo(), bpp::FrequenciesFromSimplex::debugInfo(), bpp::EquilibriumFrequenciesFromTransitionMatrix::debugInfo(), bpp::TransitionMatrixFromTransitionMatrix::debugInfo(), bpp::CWiseFill< R, T >::debugInfo(), bpp::CWisePattern< R >::debugInfo(), bpp::CWiseMatching< R, ReductionOf< T > >::debugInfo(), bpp::CWiseCompound< R, ReductionOf< T > >::debugInfo(), bpp::CWiseApply< R, T, F >::debugInfo(), bpp::CWiseAdd< R, std::tuple< T0, T1 > >::debugInfo(), bpp::CWiseSub< R, std::tuple< T0, T1 > >::debugInfo(), bpp::CWiseAdd< R, ReductionOf< T > >::debugInfo(), bpp::CWiseAdd< R, T >::debugInfo(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::debugInfo(), bpp::CWiseMean< R, ReductionOf< T >, P >::debugInfo(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::debugInfo(), bpp::CWiseMul< R, ReductionOf< T > >::debugInfo(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::debugInfo(), bpp::CWiseNegate< T >::debugInfo(), bpp::CWiseInverse< T >::debugInfo(), bpp::CWiseLog< T >::debugInfo(), bpp::CWiseExp< T >::debugInfo(), bpp::CWiseConstantPow< T >::debugInfo(), bpp::ScalarProduct< R, T0, T1 >::debugInfo(), bpp::SumOfLogarithms< F >::debugInfo(), bpp::LogSumExp< R, T0, T1 >::debugInfo(), bpp::MatrixProduct< R, T0, T1 >::debugInfo(), bpp::ShiftDelta< T >::debugInfo(), bpp::CombineDeltaShifted< T >::debugInfo(), bpp::CondLikelihood::debugInfo(), bpp::ForwardHmmLikelihood_DF::debugInfo(), bpp::ForwardHmmDLikelihood_DF::debugInfo(), bpp::ForwardHmmD2Likelihood_DF::debugInfo(), and bpp::BackwardHmmLikelihood_DF::debugInfo().

◆ debug() [7/7]

template<typename T = TransitionFunction>
std::string bpp::numeric::debug ( const TransitionFunction &  f)

Definition at line 832 of file DataFlowNumeric.h.

Referenced by bpp::NumericConstant< T >::debugInfo(), bpp::NumericMutable< T >::debugInfo(), bpp::Convert< R, F >::debugInfo(), bpp::Identity< R >::debugInfo(), bpp::NumericConstant< T >::description(), and bpp::NumericMutable< T >::description().

◆ exp()

template<typename T , typename = typename std::enable_if<std::is_floating_point<T>::value>::type>
T bpp::numeric::exp ( T  t)

Definition at line 747 of file DataFlowNumeric.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), and bpp::AbstractSubstitutionModel::getPij_t().

◆ hash() [1/5]

template<typename Derived >
std::size_t bpp::numeric::hash ( const Eigen::MatrixBase< Derived > &  m)

Definition at line 861 of file DataFlowNumeric.h.

References bpp::combineHash().

◆ hash() [2/5]

std::size_t bpp::numeric::hash ( const ExtendedFloat &  ef)
inline

Definition at line 848 of file DataFlowNumeric.h.

References bpp::combineHash(), bpp::ExtendedFloat::exponent_part(), bpp::ExtendedFloat::float_part(), and hash().

◆ hash() [3/5]

template<typename Derived >
std::size_t bpp::numeric::hash ( const ExtendedFloatEigenBase< Derived > &  efm)

Definition at line 875 of file DataFlowNumeric.h.

References bpp::combineHash(), bpp::ExtendedFloatEigenBase< Derived >::derived(), and hash().

◆ hash() [4/5]

template<typename T = std::string>
std::size_t bpp::numeric::hash ( const std::string &  t)

Definition at line 856 of file DataFlowNumeric.h.

◆ hash() [5/5]

template<typename T >
std::size_t bpp::numeric::hash ( T  t,
typename std::enable_if< std::is_floating_point< T >::value||std::is_integral< T >::value >::type *  = 0 
)

Definition at line 843 of file DataFlowNumeric.h.

Referenced by hash().

◆ identity() [1/4]

template<typename T , int Rows, int Cols>
auto bpp::numeric::identity ( const Dimension< Eigen::Matrix< T, Rows, Cols >> &  dim) -> decltype (Eigen::Matrix<T, Rows, Cols>::Identity (dim.rows, dim.cols))

Definition at line 526 of file DataFlowNumeric.h.

References checkDimensionIsSquare().

◆ identity() [2/4]

template<typename T , typename = typename std::enable_if<std::is_same<T, ExtendedFloat>::value>::type>
T bpp::numeric::identity ( const Dimension< ExtendedFloat > &  )

Definition at line 520 of file DataFlowNumeric.h.

◆ identity() [3/4]

template<int R, int C, template< int R2=R, int C2=C > class MatType>
auto bpp::numeric::identity ( const Dimension< ExtendedFloatEigen< R, C, MatType >> &  dim) -> decltype (ExtendedFloatEigen<R, C, MatType>::Identity (dim.rows))

Definition at line 534 of file DataFlowNumeric.h.

References checkDimensionIsSquare(), and bpp::ExtendedFloatEigen< R, C, EigenType >::Identity().

◆ identity() [4/4]

template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value>::type>
T bpp::numeric::identity ( const Dimension< T > &  )

Definition at line 514 of file DataFlowNumeric.h.

Referenced by bpp::MatrixProduct< R, T0, T1 >::create(), and isIdentity().

◆ inverse() [1/3]

ExtendedFloat bpp::numeric::inverse ( const ExtendedFloat &  t)
inline

Definition at line 721 of file DataFlowNumeric.h.

References bpp::ExtendedFloat::exponent_part(), and bpp::ExtendedFloat::float_part().

◆ inverse() [2/3]

template<typename Derived >
Derived bpp::numeric::inverse ( ExtendedFloatEigenBase< Derived >  base)

Definition at line 729 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigenBase< Derived >::derived().

◆ inverse() [3/3]

template<typename T , typename = typename std::enable_if<std::is_floating_point<T>::value>::type>
T bpp::numeric::inverse ( T  t)

Definition at line 716 of file DataFlowNumeric.h.

Referenced by bpp::CWiseInverse< T >::compute().

◆ isIdentity() [1/4]

template<typename Derived >
bool bpp::numeric::isIdentity ( const Eigen::MatrixBase< Derived > &  m)

Definition at line 567 of file DataFlowNumeric.h.

References identity().

◆ isIdentity() [2/4]

template<int R, int C, template< int R2=R, int C2=C > class MatType>
bool bpp::numeric::isIdentity ( const ExtendedFloatEigen< R, C, MatType > &  efm)

Definition at line 574 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::exponent_part(), bpp::ExtendedFloatEigen< R, C, EigenType >::float_part(), and isIdentity().

Referenced by bpp::NumericConstant< T >::hasNumericalProperty().

◆ isIdentity() [3/4]

template<typename T = void>
bool bpp::numeric::isIdentity ( const std::string &  t)

Definition at line 561 of file DataFlowNumeric.h.

◆ isIdentity() [4/4]

template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value || std::is_same<T, ExtendedFloat>::value>::type>
bool bpp::numeric::isIdentity ( const T &  t)

Definition at line 555 of file DataFlowNumeric.h.

Referenced by debug(), and isIdentity().

◆ isinf() [1/2]

bool bpp::numeric::isinf ( const double &  d)
inline

Definition at line 543 of file DataFlowNumeric.h.

References isinf().

Referenced by bpp::LogSumExp< R, T0, T1 >::compute(), bpp::SubstitutionMappingTools::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), and bpp::DecompositionReward::computeRewards_().

◆ isinf() [2/2]

bool bpp::numeric::isinf ( const ExtendedFloat &  d)
inline

Definition at line 548 of file DataFlowNumeric.h.

References bpp::ExtendedFloat::exponent_part(), and bpp::ExtendedFloat::float_part().

Referenced by isinf().

◆ log()

template<typename T , typename = typename std::enable_if<std::is_floating_point<T>::value>::type>
T bpp::numeric::log ( T  t)

Definition at line 740 of file DataFlowNumeric.h.

Referenced by bpp::MultinomialFromTransitionModel::compute_d2Multinomial_dt2_(), bpp::MultinomialFromTransitionModel::compute_dMultinomial_dt_(), bpp::MultinomialFromTransitionModel::compute_Multinomial_(), bpp::HierarchicalClustering::getBestPair(), bpp::NeighborJoining::getBestPair(), bpp::PGMA::getBestPair(), bpp::PhylogeneticsApplicationTools::printAnalysisInformation(), and bpp::IOPhymlPairedSiteLikelihoods::readPairedSiteLikelihoods().

◆ one() [1/8]

template<typename T = void>
char bpp::numeric::one ( const Dimension< char > &  )

Definition at line 467 of file DataFlowNumeric.h.

◆ one() [2/8]

template<typename T , int Rows, int Cols>
auto bpp::numeric::one ( const Dimension< Eigen::Matrix< T, Rows, Cols >> &  dim) -> decltype (Eigen::Matrix<T, Rows, Cols>::Ones (dim.rows, dim.cols))

Definition at line 491 of file DataFlowNumeric.h.

◆ one() [3/8]

template<typename T = void>
ExtendedFloat bpp::numeric::one ( const Dimension< ExtendedFloat > &  )

Definition at line 485 of file DataFlowNumeric.h.

◆ one() [4/8]

template<int R, int C, template< int R2=2, int C2=C > class MatType>
auto bpp::numeric::one ( const Dimension< ExtendedFloatEigen< R, C, MatType >> &  dim) -> decltype (ExtendedFloatEigen<R, C, MatType>::Ones (dim.rows, dim.cols))

Definition at line 498 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::Ones().

◆ one() [5/8]

template<typename T = void>
Parameter& bpp::numeric::one ( const Dimension< Parameter > &  )

Definition at line 479 of file DataFlowNumeric.h.

◆ one() [6/8]

template<typename T = void>
std::string bpp::numeric::one ( const Dimension< std::string > &  )

Definition at line 473 of file DataFlowNumeric.h.

◆ one() [7/8]

template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value>::type>
T bpp::numeric::one ( const Dimension< T > &  )

Definition at line 461 of file DataFlowNumeric.h.

Referenced by bpp::CWiseMul< R, ReductionOf< T > >::compute(), bpp::CWiseConstantPow< T >::create(), debug(), bpp::LikelihoodCalculationOnABranch::makeLikelihoods(), bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtDAGNode_(), and bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtNode_().

◆ one() [8/8]

template<typename T = void>
TransitionFunction bpp::numeric::one ( const Dimension< TransitionFunction > &  dim)

Definition at line 505 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::Ones().

Referenced by bpp::ConstantOne< T >::compute(), and bpp::NumericConstant< T >::hasNumericalProperty().

◆ zero() [1/8]

template<typename T = void>
char bpp::numeric::zero ( const Dimension< char > &  )

Definition at line 413 of file DataFlowNumeric.h.

◆ zero() [2/8]

template<typename T , int Rows, int Cols>
auto bpp::numeric::zero ( const Dimension< Eigen::Matrix< T, Rows, Cols >> &  dim) -> decltype (Eigen::Matrix<T, Rows, Cols>::Zero (dim.rows, dim.cols))

Definition at line 437 of file DataFlowNumeric.h.

◆ zero() [3/8]

template<typename T = void>
ExtendedFloat bpp::numeric::zero ( const Dimension< ExtendedFloat > &  )

Definition at line 431 of file DataFlowNumeric.h.

◆ zero() [4/8]

template<int R, int C, template< int R2=R, int C2=C > class MatType>
auto bpp::numeric::zero ( const Dimension< ExtendedFloatEigen< R, C, MatType >> &  dim) -> decltype (ExtendedFloatEigen<R, C, MatType>::Zero (dim.rows, dim.cols))

Definition at line 444 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::Zero().

◆ zero() [5/8]

template<typename T = void>
Parameter& bpp::numeric::zero ( const Dimension< Parameter > &  )

Definition at line 425 of file DataFlowNumeric.h.

◆ zero() [6/8]

template<typename T = void>
std::string bpp::numeric::zero ( const Dimension< std::string > &  )

Definition at line 419 of file DataFlowNumeric.h.

◆ zero() [7/8]

template<typename T , typename = typename std::enable_if<std::is_arithmetic<T>::value>::type>
T bpp::numeric::zero ( const Dimension< T > &  )

Definition at line 407 of file DataFlowNumeric.h.

Referenced by bpp::CWiseAdd< R, ReductionOf< T > >::compute(), bpp::CombineDeltaShifted< T >::compute(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::compute(), debug(), bpp::ForwardLikelihoodTree::makeForwardLikelihoodAtEdge(), bpp::LikelihoodCalculationOnABranch::makeLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_().

◆ zero() [8/8]

template<typename T = void>
TransitionFunction bpp::numeric::zero ( const Dimension< TransitionFunction > &  dim)

Definition at line 451 of file DataFlowNumeric.h.

References bpp::ExtendedFloatEigen< R, C, EigenType >::Zero().

Referenced by bpp::ConstantZero< T >::compute(), and bpp::NumericConstant< T >::hasNumericalProperty().