bpp-phyl3 3.0.0
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
bpp::AbstractWrappedSubstitutionModel Class Referenceabstract

#include <Bpp/Phyl/Model/AbstractWrappedModel.h>

+ Inheritance diagram for bpp::AbstractWrappedSubstitutionModel:
+ Collaboration diagram for bpp::AbstractWrappedSubstitutionModel:

Public Member Functions

 AbstractWrappedSubstitutionModel (const std::string &prefix)
 
virtual ~AbstractWrappedSubstitutionModel ()
 
const TransitionModelInterface & transitionModel () const
 
const FrequencySetInterface & frequencySet () const override
 
const BranchModelInterface & model () const override
 
virtual std::string getName () const override
 Get the name of the model. More...
 
void setNamespace (const std::string &prefix)
 
bool hasIndependentParameter (const std::string &name) const
 
const ParameterList & getIndependentParameters () const
 
size_t getNumberOfIndependentParameters () const
 
void aliasParameters (const std::string &p1, const std::string &p2)
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 
ParameterList getFromParameters (const ParameterList &pl) const
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const
 
std::string getFrom (const std::string &name) const
 
bool hasParameter (const std::string &name) const override
 
const ParameterList & getParameters () const override
 
const Parameter & parameter (const std::string &name) const override
 
const std::shared_ptr< Parameter > & getParameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const override
 
void setAllParametersValues (const ParameterList &parameters) override
 
void setParameterValue (const std::string &name, double value) override
 
void setParametersValues (const ParameterList &parameters) override
 
bool matchParametersValues (const ParameterList &parameters) override
 
void removeConstraint (const std::string &name) override
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 
size_t getNumberOfParameters () const override
 
std::string getNamespace () const override
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 
virtual void fireParameterChanged (const ParameterList &parameters)
 
virtual Clonable * clone () const=0
 
BranchModelInterface * clone () const =0
 
TransitionModelInterface * clone () const =0
 
virtual double getInitValue (size_t i, int state) const =0
 
virtual const Eigen::VectorXd & Lik_t (const Eigen::VectorXd &values, double t) const =0
 
const Eigen::VectorXd & Lik_t (const Eigen::VectorXd &values, double t) const override
 
virtual const Eigen::VectorXd & dLik_dt (const Eigen::VectorXd &values, double t) const =0
 
const Eigen::VectorXd & dLik_dt (const Eigen::VectorXd &values, double t) const override
 
virtual const Eigen::VectorXd & d2Lik_dt2 (const Eigen::VectorXd &values, double t) const =0
 
const Eigen::VectorXd & d2Lik_dt2 (const Eigen::VectorXd &values, double t) const override
 
virtual double getRate () const =0
 Get the rate. More...
 
virtual void setRate (double rate)=0
 Set the rate of the model (must be positive). More...
 
virtual void addRateParameter ()=0
 
virtual double freq (size_t i) const =0
 
virtual double Pij_t (size_t i, size_t j, double t) const =0
 
virtual double dPij_dt (size_t i, size_t j, double t) const =0
 
virtual double d2Pij_dt2 (size_t i, size_t j, double t) const =0
 
virtual const Vdouble & getFrequencies () const =0
 
virtual bool computeFrequencies () const =0
 
virtual void computeFrequencies (bool yn)=0
 Set if equilibrium frequencies should be computed. More...
 
virtual const Matrix< double > & getPij_t (double t) const =0
 
virtual const Matrix< double > & getdPij_dt (double t) const =0
 
virtual const Matrix< double > & getd2Pij_dt2 (double t) const =0
 
virtual void setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0)=0
 Set equilibrium frequencies equal to the frequencies estimated from the data. More...
 
virtual void setFreq (std::map< int, double > &frequencies)=0
 Set equilibrium frequencies. More...
 
virtual const SubstitutionModelInterface & substitutionModel () const =0
 
SubstitutionModelInterface * clone () const override=0
 
virtual double Qij (size_t i, size_t j) const =0
 A method for computing all necessary matrices. More...
 
virtual const Matrix< double > & generator () const =0
 
virtual const Matrix< double > & exchangeabilityMatrix () const =0
 
virtual double Sij (size_t i, size_t j) const =0
 
virtual void enableEigenDecomposition (bool yn)=0
 Set if eigenValues and Vectors must be computed. More...
 
virtual bool enableEigenDecomposition ()=0
 Tell if eigenValues and Vectors must be computed. More...
 
virtual const Vdouble & getEigenValues () const =0
 
virtual const Vdouble & getIEigenValues () const =0
 
virtual bool isDiagonalizable () const =0
 
virtual bool isNonSingular () const =0
 
virtual const Matrix< double > & getRowLeftEigenVectors () const =0
 
virtual const Matrix< double > & getColumnRightEigenVectors () const =0
 
virtual void setScalable (bool scalable)=0
 sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example. More...
 
virtual bool isScalable () const =0
 returns if model is scalable More...
 
virtual double getScale () const =0
 Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...
 
virtual void setScale (double scale)=0
 Multiplies the current generator by the given scale. More...
 
virtual void normalize ()=0
 Normalize the generator. More...
 
virtual void setDiagonal ()=0
 set the diagonal of the generator such that sum on each line equals 0. More...
 
const std::vector< int > & getAlphabetStates () const override
 
const StateMapInterface & stateMap () const override
 
std::shared_ptr< const StateMapInterface > getStateMap () const override
 
int getAlphabetStateAsInt (size_t i) const override
 
std::string getAlphabetStateAsChar (size_t i) const override
 
std::vector< size_t > getModelStates (int code) const override
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
std::vector< size_t > getModelStates (const std::string &code) const override
 Get the state in the model corresponding to a particular state in the alphabet. More...
 
const Alphabet & alphabet () const override
 
std::shared_ptr< const Alphabet > getAlphabet () const override
 
size_t getNumberOfStates () const override
 Get the number of states. More...
 

Protected Member Functions

TransitionModelInterface & transitionModel_ ()
 
virtual SubstitutionModelInterface & substitutionModel_ ()=0
 
BranchModelInterface & model_ ()
 
const std::shared_ptr< Parameter > & getParameter (size_t i) const
 
std::shared_ptr< Parameter > & getParameter (size_t i)
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
Parameter & getParameter_ (const std::string &name)
 
Parameter & getParameter_ (size_t index)
 
const Parameter & getParameter_ (size_t index) const
 
Parameter & getParameterWithNamespace_ (const std::string &name)
 
const Parameter & getParameterWithNamespace_ (const std::string &name) const
 
ParameterList & getParameters_ () override
 
virtual Vdouble & getFrequencies_ ()=0
 

Private Attributes

ParameterList independentParameters_
 
std::map< std::string, std::shared_ptr< AliasParameterListener > > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 
Eigen::VectorXd lik_
 

Detailed Description

Definition at line 187 of file AbstractWrappedModel.h.

Constructor & Destructor Documentation

◆ AbstractWrappedSubstitutionModel()

bpp::AbstractWrappedSubstitutionModel::AbstractWrappedSubstitutionModel ( const std::string &  prefix)
inline

Definition at line 192 of file AbstractWrappedModel.h.

◆ ~AbstractWrappedSubstitutionModel()

virtual bpp::AbstractWrappedSubstitutionModel::~AbstractWrappedSubstitutionModel ( )
inlinevirtual

Definition at line 196 of file AbstractWrappedModel.h.

Member Function Documentation

◆ addRateParameter()

virtual void bpp::BranchModelInterface::addRateParameter ( )
pure virtualinherited

Implemented in bpp::AbstractBiblioTransitionModel, bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractTransitionModel, bpp::FromMixtureSubstitutionModel, bpp::G2001, bpp::InMixedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::TransitionFromTransitionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::InMixedSubstitutionModel::addRateParameter(), bpp::MultinomialFromTransitionModel::addRateParameter(), bpp::TransitionFromTransitionModel::addRateParameter(), and bpp::BppOSubstitutionModelFormat::updateParameters_().

◆ alphabet()

const Alphabet & bpp::AbstractWrappedModel::alphabet ( ) const
inlineoverridevirtualinherited
Returns
A reference to the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 53 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::alphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::alphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ clone() [1/3]

BranchModelInterface * bpp::BranchModelInterface::clone ( ) const
pure virtualinherited

Implements bpp::ParameterAliasable.

Implemented in bpp::BinarySubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::F84, bpp::HKY85, bpp::LG10_EX_EHO::EmbeddedModel, bpp::LG10_EX_EHO, bpp::TwoParameterBinarySubstitutionModel, bpp::TransitionModelInterface, bpp::AnonymousSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::DFP07, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::GY94, bpp::KCM, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::MG94, bpp::RELAX, bpp::SENCA, bpp::TripletSubstitutionModel, bpp::YN98, bpp::YNGP_M1, bpp::YNGP_M10, bpp::YNGP_M2, bpp::YNGP_M3, bpp::YNGP_M7, bpp::YNGP_M8, bpp::YNGP_M9, bpp::D1WalkSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::FromMixtureSubstitutionModel, bpp::G2001, bpp::InMixedSubstitutionModel, bpp::KroneckerWordSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::MixtureOfATransitionModel, bpp::MixtureOfSubstitutionModels, bpp::MixtureOfTransitionModels, bpp::MultinomialFromTransitionModel, bpp::F81, bpp::gBGC, bpp::GTR, bpp::JCnuc, bpp::K80, bpp::L95, bpp::RN95, bpp::RN95s, bpp::SSR, bpp::T92, bpp::TN93, bpp::YpR_Sym, bpp::YpR_Gen, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::POMO, bpp::Coala, bpp::DSO78, bpp::JCprot, bpp::JTT92, bpp::LG08, bpp::LGL08_CAT::EmbeddedModel, bpp::LGL08_CAT, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_EHO, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EX2, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EX3, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_UL2, bpp::LLG08_UL3::EmbeddedModel, bpp::LLG08_UL3, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::RE08, bpp::RE08Nucleotide, bpp::RE08Protein, bpp::RE08Codon, bpp::RegisterRatesSubstitutionModel, bpp::TransitionFromTransitionModel, bpp::TS98, bpp::WordSubstitutionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractReversibleSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::CodonSubstitutionModelInterface, bpp::CodonReversibleSubstitutionModelInterface, bpp::YNGP_M, bpp::MarkovModulatedSubstitutionModel, bpp::MixedTransitionModelInterface, bpp::NucleotideSubstitutionModelInterface, bpp::NucleotideReversibleSubstitutionModelInterface, bpp::AbstractNucleotideSubstitutionModel, bpp::AbstractReversibleNucleotideSubstitutionModel, bpp::ProteinSubstitutionModelInterface, bpp::ProteinReversibleSubstitutionModelInterface, bpp::AbstractProteinSubstitutionModel, bpp::AbstractReversibleProteinSubstitutionModel, bpp::SubstitutionModelInterface, and bpp::ReversibleSubstitutionModelInterface.

Referenced by bpp::SubstitutionProcessCollection::addOnePerBranchSubstitutionProcess(), and bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess().

◆ clone() [2/3]

TransitionModelInterface * bpp::TransitionModelInterface::clone ( ) const
pure virtualinherited

Implements bpp::BranchModelInterface.

Implemented in bpp::BinarySubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::F84, bpp::HKY85, bpp::LG10_EX_EHO::EmbeddedModel, bpp::LG10_EX_EHO, bpp::TwoParameterBinarySubstitutionModel, bpp::AnonymousSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::DFP07, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::GY94, bpp::KCM, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::MG94, bpp::RELAX, bpp::SENCA, bpp::TripletSubstitutionModel, bpp::YN98, bpp::YNGP_M1, bpp::YNGP_M10, bpp::YNGP_M2, bpp::YNGP_M3, bpp::YNGP_M7, bpp::YNGP_M8, bpp::YNGP_M9, bpp::D1WalkSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::FromMixtureSubstitutionModel, bpp::G2001, bpp::InMixedSubstitutionModel, bpp::KroneckerWordSubstitutionModel, bpp::MixtureOfASubstitutionModel, bpp::MixtureOfATransitionModel, bpp::MixtureOfSubstitutionModels, bpp::MixtureOfTransitionModels, bpp::F81, bpp::gBGC, bpp::GTR, bpp::JCnuc, bpp::K80, bpp::L95, bpp::RN95, bpp::RN95s, bpp::SSR, bpp::T92, bpp::TN93, bpp::YpR_Sym, bpp::YpR_Gen, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::POMO, bpp::Coala, bpp::DSO78, bpp::JCprot, bpp::JTT92, bpp::LG08, bpp::LGL08_CAT::EmbeddedModel, bpp::LGL08_CAT, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_EHO, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EX2, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_EX3, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_UL2, bpp::LLG08_UL3::EmbeddedModel, bpp::LLG08_UL3, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::RE08, bpp::RE08Nucleotide, bpp::RE08Protein, bpp::RE08Codon, bpp::RegisterRatesSubstitutionModel, bpp::TS98, bpp::WordSubstitutionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractReversibleSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::CodonSubstitutionModelInterface, bpp::CodonReversibleSubstitutionModelInterface, bpp::YNGP_M, bpp::MarkovModulatedSubstitutionModel, bpp::MixedTransitionModelInterface, bpp::NucleotideSubstitutionModelInterface, bpp::NucleotideReversibleSubstitutionModelInterface, bpp::AbstractNucleotideSubstitutionModel, bpp::AbstractReversibleNucleotideSubstitutionModel, bpp::ProteinSubstitutionModelInterface, bpp::ProteinReversibleSubstitutionModelInterface, bpp::AbstractProteinSubstitutionModel, bpp::AbstractReversibleProteinSubstitutionModel, bpp::SubstitutionModelInterface, and bpp::ReversibleSubstitutionModelInterface.

Referenced by bpp::AbstractSinglePhyloSubstitutionMapping::addModel(), bpp::MixtureOfATransitionModel::MixtureOfATransitionModel(), and bpp::AbstractMixedTransitionModel::operator=().

◆ clone() [3/3]

SubstitutionModelInterface * bpp::SubstitutionModelInterface::clone ( ) const
overridepure virtualinherited

Implements bpp::TransitionModelInterface.

Implemented in bpp::BinarySubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::F84, bpp::HKY85, bpp::LG10_EX_EHO::EmbeddedModel, bpp::TwoParameterBinarySubstitutionModel, bpp::AnonymousSubstitutionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::GY94, bpp::KCM, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::MG94, bpp::SENCA, bpp::TripletSubstitutionModel, bpp::YN98, bpp::D1WalkSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::FromMixtureSubstitutionModel, bpp::G2001, bpp::InMixedSubstitutionModel, bpp::KroneckerWordSubstitutionModel, bpp::F81, bpp::gBGC, bpp::GTR, bpp::JCnuc, bpp::K80, bpp::L95, bpp::RN95, bpp::RN95s, bpp::SSR, bpp::T92, bpp::TN93, bpp::YpR_Sym, bpp::YpR_Gen, bpp::POMO, bpp::Coala, bpp::DSO78, bpp::JCprot, bpp::JTT92, bpp::LG08, bpp::LGL08_CAT::EmbeddedModel, bpp::LLG08_EHO::EmbeddedModel, bpp::LLG08_EX2::EmbeddedModel, bpp::LLG08_EX3::EmbeddedModel, bpp::LLG08_UL2::EmbeddedModel, bpp::LLG08_UL3::EmbeddedModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::RE08, bpp::RE08Nucleotide, bpp::RE08Protein, bpp::RE08Codon, bpp::RegisterRatesSubstitutionModel, bpp::TS98, bpp::WordSubstitutionModel, bpp::AbstractReversibleSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::AbstractDFPSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, bpp::CodonSubstitutionModelInterface, bpp::CodonReversibleSubstitutionModelInterface, bpp::MarkovModulatedSubstitutionModel, bpp::NucleotideSubstitutionModelInterface, bpp::NucleotideReversibleSubstitutionModelInterface, bpp::AbstractNucleotideSubstitutionModel, bpp::AbstractReversibleNucleotideSubstitutionModel, bpp::ProteinSubstitutionModelInterface, bpp::ProteinReversibleSubstitutionModelInterface, bpp::AbstractProteinSubstitutionModel, bpp::AbstractReversibleProteinSubstitutionModel, and bpp::ReversibleSubstitutionModelInterface.

◆ computeFrequencies() [1/2]

virtual bool bpp::TransitionModelInterface::computeFrequencies ( ) const
pure virtualinherited
Returns
Says if equilibrium frequencies should be computed

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::computeFrequencies(), bpp::InMixedSubstitutionModel::computeFrequencies(), bpp::RELAX::RELAX(), bpp::SENCA::SENCA(), bpp::YNGP_M1::YNGP_M1(), bpp::YNGP_M10::YNGP_M10(), bpp::YNGP_M2::YNGP_M2(), bpp::YNGP_M3::YNGP_M3(), bpp::YNGP_M7::YNGP_M7(), bpp::YNGP_M8::YNGP_M8(), and bpp::YNGP_M9::YNGP_M9().

◆ computeFrequencies() [2/2]

virtual void bpp::TransitionModelInterface::computeFrequencies ( bool  yn)
pure virtualinherited

Set if equilibrium frequencies should be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

◆ d2Lik_dt2() [1/2]

virtual const Eigen::VectorXd & bpp::BranchModelInterface::d2Lik_dt2 ( const Eigen::VectorXd &  values,
double  t 
) const
pure virtualinherited

Implemented in bpp::MultinomialFromTransitionModel, bpp::TransitionFromTransitionModel, bpp::TransitionModelInterface, and bpp::AbstractLkTransitionModel.

◆ d2Lik_dt2() [2/2]

const Eigen::VectorXd & bpp::AbstractLkTransitionModel::d2Lik_dt2 ( const Eigen::VectorXd &  values,
double  t 
) const
inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 64 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and bpp::AbstractLkTransitionModel::lik_.

◆ d2Pij_dt2()

virtual double bpp::TransitionModelInterface::d2Pij_dt2 ( size_t  i,
size_t  j,
double  t 
) const
pure virtualinherited
Returns
The second order derivative of the probability of change from state i to state j with respect to time t, at time t.
See also
getd2Pij_dt2(), getStates()

Implemented in bpp::BinarySubstitutionModel, bpp::F84, bpp::HKY85, bpp::TwoParameterBinarySubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::JCnuc, bpp::K80, bpp::T92, bpp::TN93, bpp::JCprot, bpp::RE08, bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, and bpp::OneChangeTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::d2Pij_dt2(), bpp::InMixedSubstitutionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), and bpp::OneChangeTransitionModel::d2Pij_dt2().

◆ dLik_dt() [1/2]

virtual const Eigen::VectorXd & bpp::BranchModelInterface::dLik_dt ( const Eigen::VectorXd &  values,
double  t 
) const
pure virtualinherited

Implemented in bpp::MultinomialFromTransitionModel, bpp::TransitionFromTransitionModel, bpp::TransitionModelInterface, and bpp::AbstractLkTransitionModel.

◆ dLik_dt() [2/2]

const Eigen::VectorXd & bpp::AbstractLkTransitionModel::dLik_dt ( const Eigen::VectorXd &  values,
double  t 
) const
inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 47 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getdPij_dt(), and bpp::AbstractLkTransitionModel::lik_.

◆ dPij_dt()

virtual double bpp::TransitionModelInterface::dPij_dt ( size_t  i,
size_t  j,
double  t 
) const
pure virtualinherited
Returns
The first order derivative of the probability of change from state i to state j with respect to time t, at time t.
See also
getdPij_dt(), getStates()

Implemented in bpp::BinarySubstitutionModel, bpp::F84, bpp::HKY85, bpp::TwoParameterBinarySubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::JCnuc, bpp::K80, bpp::T92, bpp::TN93, bpp::JCprot, bpp::RE08, bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, and bpp::OneChangeTransitionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeTransitionModel::d2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::dPij_dt(), and bpp::InMixedSubstitutionModel::dPij_dt().

◆ enableEigenDecomposition() [1/2]

virtual bool bpp::SubstitutionModelInterface::enableEigenDecomposition ( )
pure virtualinherited

Tell if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel().

◆ enableEigenDecomposition() [2/2]

virtual void bpp::SubstitutionModelInterface::enableEigenDecomposition ( bool  yn)
pure virtualinherited

Set if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::enableEigenDecomposition(), and bpp::InMixedSubstitutionModel::enableEigenDecomposition().

◆ exchangeabilityMatrix()

virtual const Matrix< double > & bpp::SubstitutionModelInterface::exchangeabilityMatrix ( ) const
pure virtualinherited
Returns
The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::Coala::Coala(), bpp::AbstractTotallyWrappedSubstitutionModel::exchangeabilityMatrix(), and bpp::InMixedSubstitutionModel::exchangeabilityMatrix().

◆ freq()

virtual double bpp::TransitionModelInterface::freq ( size_t  i) const
pure virtualinherited
Returns
Equilibrium frequency associated to character i.
See also
getFrequencies(), getStates()

Implemented in bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, and bpp::OneChangeTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::freq(), bpp::InMixedSubstitutionModel::freq(), bpp::OneChangeRegisterTransitionModel::freq(), and bpp::OneChangeTransitionModel::freq().

◆ frequencySet()

const FrequencySetInterface & bpp::AbstractWrappedTransitionModel::frequencySet ( ) const
inlineoverridevirtualinherited
Returns
Get the FrequencySet of equilibrium of this model.
Exceptions
Exceptionif no FrequenceSet is associated to this model.

Reimplemented from bpp::AbstractWrappedModel.

Reimplemented in bpp::YN98, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, and bpp::RegisterRatesSubstitutionModel.

Definition at line 92 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::frequencySet(), and bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::RegisterRatesSubstitutionModel::frequencySet().

◆ generator()

virtual const Matrix< double > & bpp::SubstitutionModelInterface::generator ( ) const
pure virtualinherited
Returns
The normalized Markov generator matrix, i.e. all normalized rates of changes from state i to state j. The generator is normalized so that (i) $ \forall i; \sum_j Q_{i,j} = 0 $, meaning that $ $ \forall i; Q_{i,i} = -\sum_{j \neq i}Q_{i,j}$, and (ii) $ \sum_i Q_{i,i} \times \pi_i = -1$. This means that, under normalization, the mean rate of replacement at equilibrium is 1 and that time $t$ are measured in units of expected number of changes per site. Additionally, the rate_ attribute provides the possibility to increase or decrease this mean rate.

See Kosiol and Goldman (2005), Molecular Biology And Evolution 22(2) 193-9.

See also
Qij()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::OneChangeTransitionModel::dPij_dt(), bpp::AbstractTotallyWrappedSubstitutionModel::generator(), bpp::InMixedSubstitutionModel::generator(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeTransitionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::OneChangeTransitionModel::getPij_t(), bpp::OneChangeRegisterTransitionModel::Pij_t(), bpp::OneChangeRegisterTransitionModel::updateMatrices_(), and bpp::RegisterRatesSubstitutionModel::updateMatrices_().

◆ getAlphabet()

std::shared_ptr< const Alphabet > bpp::AbstractWrappedModel::getAlphabet ( ) const
inlineoverridevirtualinherited
Returns
A pointer toward the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 55 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ getAlphabetStateAsChar()

std::string bpp::AbstractWrappedModel::getAlphabetStateAsChar ( size_t  index) const
inlineoverridevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 46 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsChar(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsChar().

◆ getAlphabetStateAsInt()

int bpp::AbstractWrappedModel::getAlphabetStateAsInt ( size_t  index) const
inlineoverridevirtualinherited
Parameters
indexThe model state.
Returns
The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 44 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsInt(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsInt().

◆ getAlphabetStates()

const std::vector< int > & bpp::AbstractWrappedModel::getAlphabetStates ( ) const
inlineoverridevirtualinherited

@ brief Methods to supersede TransitionModel methods.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 38 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStates().

◆ getColumnRightEigenVectors()

virtual const Matrix< double > & bpp::SubstitutionModelInterface::getColumnRightEigenVectors ( ) const
pure virtualinherited
Returns
A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getColumnRightEigenVectors(), and bpp::InMixedSubstitutionModel::getColumnRightEigenVectors().

◆ getd2Pij_dt2()

virtual const Matrix< double > & bpp::TransitionModelInterface::getd2Pij_dt2 ( double  t) const
pure virtualinherited
Returns
All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See also
d2Pij_dt2()

Implemented in bpp::BinarySubstitutionModel, bpp::F84, bpp::HKY85, bpp::TwoParameterBinarySubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::JCnuc, bpp::K80, bpp::T92, bpp::TN93, bpp::JCprot, bpp::RE08, bpp::WordSubstitutionModel, bpp::AbstractSubstitutionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::MultinomialFromTransitionModel::d2Lik_dt2(), bpp::TransitionFromTransitionModel::d2Lik_dt2(), bpp::AbstractLkTransitionModel::d2Lik_dt2(), bpp::AbstractTotallyWrappedTransitionModel::getd2Pij_dt2(), bpp::InMixedSubstitutionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), and bpp::OneChangeTransitionModel::getd2Pij_dt2().

◆ getdPij_dt()

virtual const Matrix< double > & bpp::TransitionModelInterface::getdPij_dt ( double  t) const
pure virtualinherited
Returns
Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.
See also
dPij_dt()

Implemented in bpp::BinarySubstitutionModel, bpp::F84, bpp::HKY85, bpp::TwoParameterBinarySubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::JCnuc, bpp::K80, bpp::T92, bpp::TN93, bpp::JCprot, bpp::RE08, bpp::WordSubstitutionModel, bpp::AbstractSubstitutionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::MultinomialFromTransitionModel::dLik_dt(), bpp::TransitionFromTransitionModel::dLik_dt(), bpp::AbstractLkTransitionModel::dLik_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeTransitionModel::getd2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::getdPij_dt(), bpp::InMixedSubstitutionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), and bpp::OneChangeTransitionModel::getdPij_dt().

◆ getEigenValues()

virtual const Vdouble & bpp::SubstitutionModelInterface::getEigenValues ( ) const
pure virtualinherited
Returns
A vector with all real parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getEigenValues(), and bpp::InMixedSubstitutionModel::getEigenValues().

◆ getFrequencies()

virtual const Vdouble & bpp::TransitionModelInterface::getFrequencies ( ) const
pure virtualinherited
Returns
A vector of all equilibrium frequencies.
See also
freq()

Implemented in bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, and bpp::OneChangeTransitionModel.

Referenced by bpp::EquilibriumFrequenciesFromModel::compute(), bpp::AbstractTotallyWrappedTransitionModel::getFrequencies(), bpp::InMixedSubstitutionModel::getFrequencies(), bpp::OneChangeRegisterTransitionModel::getFrequencies(), and bpp::OneChangeTransitionModel::getFrequencies().

◆ getFrequencies_()

virtual Vdouble & bpp::TransitionModelInterface::getFrequencies_ ( )
protectedpure virtualinherited

Implemented in bpp::AbstractFromSubstitutionModelTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::getFrequencies_(), and bpp::InMixedSubstitutionModel::getFrequencies_().

◆ getIEigenValues()

virtual const Vdouble & bpp::SubstitutionModelInterface::getIEigenValues ( ) const
pure virtualinherited
Returns
A vector with all imaginary parts of the eigen values of the generator of this model;

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getIEigenValues(), and bpp::InMixedSubstitutionModel::getIEigenValues().

◆ getInitValue()

virtual double bpp::BranchModelInterface::getInitValue ( size_t  i,
int  state 
) const
pure virtualinherited

This method is used to initialize likelihoods in recursions. It typically sends 1 if i = state, 0 otherwise, where i is one of the possible states of the alphabet allowed in the model and state is the observed state in the considered sequence/site.

Parameters
ithe index of the state in the model.
stateAn observed state in the sequence/site.
Returns
1 or 0 depending if the two states are compatible.
Exceptions
IndexOutOfBoundsExceptionif array position is out of range.
BadIntExceptionif states are not allowed in the associated alphabet.
See also
getStates();

Implemented in bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RE08, and bpp::TransitionFromTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::getInitValue(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::MultinomialFromTransitionModel::getInitValue(), bpp::OneChangeRegisterTransitionModel::getInitValue(), bpp::OneChangeTransitionModel::getInitValue(), and bpp::TransitionFromTransitionModel::getInitValue().

◆ getModelStates() [1/2]

std::vector< size_t > bpp::AbstractWrappedModel::getModelStates ( const std::string &  code) const
inlineoverridevirtualinherited

Get the state in the model corresponding to a particular state in the alphabet.

Parameters
codeThe alphabet state to check.
Returns
A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 50 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

◆ getModelStates() [2/2]

std::vector< size_t > bpp::AbstractWrappedModel::getModelStates ( int  code) const
inlineoverridevirtualinherited

Get the state in the model corresponding to a particular state in the alphabet.

Parameters
codeThe alphabet state to check.
Returns
A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 48 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getModelStates().

◆ getName()

virtual std::string bpp::AbstractWrappedModel::getName ( ) const
inlineoverridevirtualinherited

Get the name of the model.

Returns
The name of this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::LG10_EX_EHO, bpp::DFP07, bpp::GY94, bpp::KCM, bpp::MG94, bpp::RELAX, bpp::YN98, bpp::YNGP_M1, bpp::YNGP_M10, bpp::YNGP_M2, bpp::YNGP_M3, bpp::YNGP_M7, bpp::YNGP_M8, bpp::YNGP_M9, bpp::FromMixtureSubstitutionModel, bpp::InMixedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::LGL08_CAT, bpp::LLG08_EHO, bpp::LLG08_EX2, bpp::LLG08_EX3, bpp::LLG08_UL2, bpp::LLG08_UL3, bpp::RegisterRatesSubstitutionModel, and bpp::TransitionFromTransitionModel.

Definition at line 67 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getName(), and bpp::WrappedModelInterface::model().

Referenced by bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ getNumberOfStates()

size_t bpp::AbstractWrappedModel::getNumberOfStates ( ) const
inlineoverridevirtualinherited

Get the number of states.

For most models, this equals the size of the alphabet.

See also
getAlphabetChars for the list of supported states.
Returns
The number of different states in the model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 57 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getNumberOfStates(), and bpp::WrappedModelInterface::model().

◆ getPij_t()

virtual const Matrix< double > & bpp::TransitionModelInterface::getPij_t ( double  t) const
pure virtualinherited
Returns
All probabilities of change from state i to state j during time t.
See also
Pij_t()

Implemented in bpp::BinarySubstitutionModel, bpp::F84, bpp::HKY85, bpp::TwoParameterBinarySubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::JCnuc, bpp::K80, bpp::T92, bpp::TN93, bpp::JCprot, bpp::RE08, bpp::WordSubstitutionModel, bpp::AbstractSubstitutionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, and bpp::AbstractTransitionModel.

Referenced by bpp::MultinomialFromTransitionModel::d2Lik_dt2(), bpp::MultinomialFromTransitionModel::dLik_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeTransitionModel::getdPij_dt(), bpp::AbstractTotallyWrappedTransitionModel::getPij_t(), bpp::InMixedSubstitutionModel::getPij_t(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::OneChangeTransitionModel::getPij_t(), bpp::MultinomialFromTransitionModel::Lik_t(), bpp::TransitionFromTransitionModel::Lik_t(), and bpp::AbstractLkTransitionModel::Lik_t().

◆ getRate()

virtual double bpp::BranchModelInterface::getRate ( ) const
pure virtualinherited

Get the rate.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::G2001, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::TransitionFromTransitionModel, and bpp::TS98.

Referenced by bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeTransitionModel::d2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::dPij_dt(), bpp::OneChangeTransitionModel::dPij_dt(), bpp::OneChangeRegisterTransitionModel::getd2Pij_dt2(), bpp::OneChangeTransitionModel::getd2Pij_dt2(), bpp::OneChangeRegisterTransitionModel::getdPij_dt(), bpp::OneChangeTransitionModel::getdPij_dt(), bpp::OneChangeRegisterTransitionModel::getPij_t(), bpp::OneChangeTransitionModel::getPij_t(), bpp::AbstractTotallyWrappedTransitionModel::getRate(), bpp::InMixedSubstitutionModel::getRate(), bpp::MultinomialFromTransitionModel::getRate(), bpp::OneChangeRegisterTransitionModel::getRate(), bpp::OneChangeTransitionModel::getRate(), bpp::RegisterRatesSubstitutionModel::getRate(), bpp::TransitionFromTransitionModel::getRate(), and bpp::OneChangeTransitionModel::Pij_t().

◆ getRowLeftEigenVectors()

virtual const Matrix< double > & bpp::SubstitutionModelInterface::getRowLeftEigenVectors ( ) const
pure virtualinherited
Returns
A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getRowLeftEigenVectors(), and bpp::InMixedSubstitutionModel::getRowLeftEigenVectors().

◆ getScale()

virtual double bpp::SubstitutionModelInterface::getScale ( ) const
pure virtualinherited

Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale.

Returns
Minus the scalar product of diagonal elements and the frequencies vector.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::getScale(), and bpp::InMixedSubstitutionModel::getScale().

◆ getStateMap()

std::shared_ptr< const StateMapInterface > bpp::AbstractWrappedModel::getStateMap ( ) const
inlineoverridevirtualinherited
Returns
A shared_ptr to the mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 42 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getStateMap(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getStateMap().

◆ isDiagonalizable()

virtual bool bpp::SubstitutionModelInterface::isDiagonalizable ( ) const
pure virtualinherited
Returns
True if the model is diagonalizable in R.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isDiagonalizable(), and bpp::InMixedSubstitutionModel::isDiagonalizable().

◆ isNonSingular()

virtual bool bpp::SubstitutionModelInterface::isNonSingular ( ) const
pure virtualinherited
Returns
True is the model is non-singular.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isNonSingular(), and bpp::InMixedSubstitutionModel::isNonSingular().

◆ isScalable()

virtual bool bpp::SubstitutionModelInterface::isScalable ( ) const
pure virtualinherited

returns if model is scalable

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::isScalable(), and bpp::InMixedSubstitutionModel::isScalable().

◆ Lik_t() [1/2]

virtual const Eigen::VectorXd & bpp::BranchModelInterface::Lik_t ( const Eigen::VectorXd &  values,
double  t 
) const
pure virtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters
valuesAn vector of states on the site.
ttime
Exceptions
IndexOutOfBoundsExceptionif array position is out of range.
BadIntExceptionif states are not allowed in the associated alphabet.

Implemented in bpp::MultinomialFromTransitionModel, bpp::TransitionFromTransitionModel, bpp::TransitionModelInterface, and bpp::AbstractLkTransitionModel.

◆ Lik_t() [2/2]

const Eigen::VectorXd & bpp::AbstractLkTransitionModel::Lik_t ( const Eigen::VectorXd &  values,
double  t 
) const
inlineoverridevirtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters
valuesAn vector of states on the site.
tthe branch length

Implements bpp::TransitionModelInterface.

Definition at line 30 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getPij_t(), and bpp::AbstractLkTransitionModel::lik_.

◆ model()

const BranchModelInterface & bpp::AbstractWrappedTransitionModel::model ( ) const
inlineoverridevirtualinherited

Implements bpp::WrappedModelInterface.

Definition at line 97 of file AbstractWrappedModel.h.

References bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::InMixedSubstitutionModel::getInitValue(), bpp::FromMixtureSubstitutionModel::getName(), bpp::RegisterRatesSubstitutionModel::getRate(), bpp::AbstractBiblioSubstitutionModel::operator=(), bpp::AbstractBiblioTransitionModel::operator=(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setFreq(), bpp::AbstractBiblioTransitionModel::setNamespace(), and bpp::BppOSubstitutionModelFormat::write().

◆ model_()

BranchModelInterface & bpp::AbstractWrappedTransitionModel::model_ ( )
inlineprotectedinherited

Definition at line 84 of file AbstractWrappedModel.h.

References bpp::AbstractWrappedTransitionModel::transitionModel_().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::FromMixtureSubstitutionModel::fireParameterChanged(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setNamespace(), bpp::FromMixtureSubstitutionModel::setNamespace(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ normalize()

virtual void bpp::SubstitutionModelInterface::normalize ( )
pure virtualinherited

Normalize the generator.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::normalize(), and bpp::InMixedSubstitutionModel::normalize().

◆ Pij_t()

virtual double bpp::TransitionModelInterface::Pij_t ( size_t  i,
size_t  j,
double  t 
) const
pure virtualinherited
Returns
The probability of change from state i to state j during time t.
See also
getPij_t(), getStates()

Implemented in bpp::BinarySubstitutionModel, bpp::F84, bpp::HKY85, bpp::TwoParameterBinarySubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::F81, bpp::JCnuc, bpp::K80, bpp::T92, bpp::TN93, bpp::JCprot, bpp::RE08, bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, and bpp::OneChangeTransitionModel.

Referenced by bpp::OneChangeRegisterTransitionModel::d2Pij_dt2(), bpp::OneChangeTransitionModel::d2Pij_dt2(), bpp::AbstractTotallyWrappedTransitionModel::Pij_t(), bpp::InMixedSubstitutionModel::Pij_t(), and bpp::OneChangeRegisterTransitionModel::Pij_t().

◆ Qij()

virtual double bpp::SubstitutionModelInterface::Qij ( size_t  i,
size_t  j 
) const
pure virtualinherited

A method for computing all necessary matrices.

Returns
The rate in the generator of change from state i to state j.
See also
getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::YpR::checkModel(), bpp::OneChangeTransitionModel::d2Pij_dt2(), bpp::DFP07::DFP07(), bpp::OneChangeTransitionModel::getd2Pij_dt2(), bpp::OneChangeTransitionModel::getdPij_dt(), bpp::OneChangeTransitionModel::Pij_t(), bpp::AbstractTotallyWrappedSubstitutionModel::Qij(), bpp::InMixedSubstitutionModel::Qij(), bpp::RELAX::RELAX(), bpp::DFP07::updateMatrices_(), bpp::RELAX::updateMatrices_(), bpp::YNGP_M1::updateMatrices_(), bpp::YNGP_M10::updateMatrices_(), bpp::YNGP_M2::updateMatrices_(), bpp::YNGP_M3::updateMatrices_(), bpp::YNGP_M7::updateMatrices_(), bpp::YNGP_M8::updateMatrices_(), bpp::YNGP_M9::updateMatrices_(), bpp::YNGP_M1::YNGP_M1(), bpp::YNGP_M10::YNGP_M10(), bpp::YNGP_M2::YNGP_M2(), bpp::YNGP_M3::YNGP_M3(), bpp::YNGP_M7::YNGP_M7(), bpp::YNGP_M8::YNGP_M8(), and bpp::YNGP_M9::YNGP_M9().

◆ setDiagonal()

virtual void bpp::SubstitutionModelInterface::setDiagonal ( )
pure virtualinherited

set the diagonal of the generator such that sum on each line equals 0.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setDiagonal(), and bpp::InMixedSubstitutionModel::setDiagonal().

◆ setFreq()

virtual void bpp::TransitionModelInterface::setFreq ( std::map< int, double > &  frequencies)
pure virtualinherited

Set equilibrium frequencies.

Parameters
frequenciesThe map of the frequencies to use.

Implemented in bpp::F84, bpp::MixtureOfATransitionModel, bpp::MixtureOfTransitionModels, bpp::L95, bpp::RN95, bpp::RN95s, bpp::SSR, bpp::D1WalkSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::BinarySubstitutionModel, bpp::HKY85, bpp::AbstractTransitionModel, bpp::F81, bpp::GTR, bpp::T92, bpp::TN93, bpp::AbstractBiblioTransitionModel, bpp::AbstractMixedTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::CodonAdHocSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonSameAARateSubstitutionModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::KCM, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::MG94, bpp::SENCA, bpp::YN98, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::POMO, bpp::RE08, bpp::RE08Codon, bpp::OneChangeRegisterTransitionModel, and bpp::OneChangeTransitionModel.

Referenced by bpp::AbstractTotallyWrappedTransitionModel::setFreq(), bpp::InMixedSubstitutionModel::setFreq(), bpp::RE08Codon::setFreq(), bpp::MultinomialFromTransitionModel::setFreq(), bpp::TransitionFromTransitionModel::setFreq(), bpp::OneChangeRegisterTransitionModel::setFreq(), bpp::OneChangeTransitionModel::setFreq(), and bpp::AbstractTotallyWrappedTransitionModel::setFreqFromData().

◆ setFreqFromData()

virtual void bpp::TransitionModelInterface::setFreqFromData ( const SequenceDataInterface &  data,
double  pseudoCount = 0 
)
pure virtualinherited

Set equilibrium frequencies equal to the frequencies estimated from the data.

Parameters
dataThe sequences to use.
pseudoCountA quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as

\[ \pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)} \]

Implemented in bpp::AbstractMixedTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::AbstractBiblioTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::JCnuc, bpp::K80, bpp::Coala, bpp::DSO78, bpp::JCprot, bpp::JTT92, bpp::LG08, bpp::UserProteinSubstitutionModel, bpp::WAG01, and bpp::RE08.

Referenced by bpp::TransitionFromTransitionModel::setFreqFromData(), bpp::OneChangeRegisterTransitionModel::setFreqFromData(), bpp::OneChangeTransitionModel::setFreqFromData(), bpp::MultinomialFromTransitionModel::setFreqFromData(), and bpp::InMixedSubstitutionModel::setFreqFromData().

◆ setRate()

virtual void bpp::BranchModelInterface::setRate ( double  rate)
pure virtualinherited

Set the rate of the model (must be positive).

Parameters
ratemust be positive.

Implemented in bpp::AbstractMixedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractTotallyWrappedTransitionModel, bpp::G2001, bpp::InMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::MultinomialFromTransitionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::RegisterRatesSubstitutionModel, bpp::TransitionFromTransitionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::AbstractTotallyWrappedTransitionModel::setRate(), bpp::InMixedSubstitutionModel::setRate(), bpp::MultinomialFromTransitionModel::setRate(), bpp::OneChangeRegisterTransitionModel::setRate(), bpp::OneChangeTransitionModel::setRate(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::TransitionFromTransitionModel::setRate().

◆ setScalable()

virtual void bpp::SubstitutionModelInterface::setScalable ( bool  scalable)
pure virtualinherited

sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setScalable(), and bpp::InMixedSubstitutionModel::setScalable().

◆ setScale()

virtual void bpp::SubstitutionModelInterface::setScale ( double  scale)
pure virtualinherited

Multiplies the current generator by the given scale.

Parameters
scalethe scale by which the generator is multiplied.

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::setScale(), and bpp::InMixedSubstitutionModel::setScale().

◆ Sij()

virtual double bpp::SubstitutionModelInterface::Sij ( size_t  i,
size_t  j 
) const
pure virtualinherited
Returns
The exchangeability between state i and state j.

By definition Sij(i,j) = Sij(j,i).

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractTotallyWrappedSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::Sij(), and bpp::InMixedSubstitutionModel::Sij().

◆ stateMap()

const StateMapInterface & bpp::AbstractWrappedModel::stateMap ( ) const
inlineoverridevirtualinherited
Returns
The mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 40 of file AbstractWrappedModel.h.

References bpp::WrappedModelInterface::model(), and bpp::BranchModelInterface::stateMap().

Referenced by bpp::RegisterRatesSubstitutionModel::stateMap().

◆ substitutionModel()

virtual const SubstitutionModelInterface & bpp::WrappedSubstitutionModelInterface::substitutionModel ( ) const
pure virtualinherited

Implemented in bpp::GY94, bpp::KCM, bpp::MG94, bpp::YN98, bpp::FromMixtureSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::exchangeabilityMatrix(), bpp::AbstractTotallyWrappedSubstitutionModel::generator(), bpp::AbstractTotallyWrappedSubstitutionModel::getColumnRightEigenVectors(), bpp::AbstractTotallyWrappedSubstitutionModel::getEigenValues(), bpp::AbstractTotallyWrappedSubstitutionModel::getIEigenValues(), bpp::AbstractTotallyWrappedSubstitutionModel::getRowLeftEigenVectors(), bpp::AbstractTotallyWrappedSubstitutionModel::getScale(), bpp::AbstractTotallyWrappedSubstitutionModel::isDiagonalizable(), bpp::AbstractTotallyWrappedSubstitutionModel::isNonSingular(), bpp::AbstractTotallyWrappedSubstitutionModel::isScalable(), bpp::AbstractTotallyWrappedSubstitutionModel::Qij(), bpp::AbstractTotallyWrappedSubstitutionModel::Sij(), and transitionModel().

◆ substitutionModel_()

virtual SubstitutionModelInterface & bpp::AbstractWrappedSubstitutionModel::substitutionModel_ ( )
protectedpure virtual

Implemented in bpp::GY94, bpp::KCM, bpp::MG94, bpp::YN98, bpp::FromMixtureSubstitutionModel, bpp::InMixedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::AbstractTotallyWrappedSubstitutionModel::enableEigenDecomposition(), bpp::AbstractTotallyWrappedSubstitutionModel::normalize(), bpp::AbstractTotallyWrappedSubstitutionModel::setDiagonal(), bpp::AbstractTotallyWrappedSubstitutionModel::setScalable(), bpp::AbstractTotallyWrappedSubstitutionModel::setScale(), and transitionModel_().

◆ transitionModel()

const TransitionModelInterface & bpp::AbstractWrappedSubstitutionModel::transitionModel ( ) const
inlinevirtual

Implements bpp::WrappedTransitionModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 198 of file AbstractWrappedModel.h.

References bpp::WrappedSubstitutionModelInterface::substitutionModel().

Referenced by bpp::InMixedSubstitutionModel::d2Pij_dt2(), bpp::InMixedSubstitutionModel::dPij_dt(), bpp::InMixedSubstitutionModel::freq(), bpp::InMixedSubstitutionModel::getd2Pij_dt2(), bpp::InMixedSubstitutionModel::getdPij_dt(), bpp::InMixedSubstitutionModel::getFrequencies(), bpp::InMixedSubstitutionModel::getPij_t(), bpp::InMixedSubstitutionModel::getRate(), and bpp::InMixedSubstitutionModel::Pij_t().

◆ transitionModel_()

TransitionModelInterface & bpp::AbstractWrappedSubstitutionModel::transitionModel_ ( )
inlineprotectedvirtual

Implements bpp::AbstractWrappedTransitionModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 204 of file AbstractWrappedModel.h.

References substitutionModel_().

Member Data Documentation

◆ lik_

Eigen::VectorXd bpp::AbstractLkTransitionModel::lik_
mutableprivateinherited

Definition at line 23 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractLkTransitionModel::d2Lik_dt2(), bpp::AbstractLkTransitionModel::dLik_dt(), and bpp::AbstractLkTransitionModel::Lik_t().

The documentation for this class was generated from the following file: