Partial implementation of the TransitionModel interface, with function for likelihood computations. More...

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

Inheritance diagram for bpp::AbstractLkTransitionModel:

Collaboration diagram for bpp::AbstractLkTransitionModel:

Public Member Functions
	AbstractLkTransitionModel ()

virtual	~AbstractLkTransitionModel ()

const Eigen::VectorXd &	Lik_t (const Eigen::VectorXd &values, double t) const override

const Eigen::VectorXd &	dLik_dt (const Eigen::VectorXd &values, double t) const override

const Eigen::VectorXd &	d2Lik_dt2 (const Eigen::VectorXd &values, double t) const override

TransitionModelInterface *	clone () const =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 std::string	getName () const =0
	Get the name of the model. More...

virtual const std::vector< int > &	getAlphabetStates () const =0

virtual const StateMapInterface &	stateMap () const =0

virtual std::shared_ptr< const StateMapInterface >	getStateMap () const =0

virtual std::vector< size_t >	getModelStates (int code) const =0
	Get the state in the model corresponding to a particular state in the alphabet. More...

virtual std::vector< size_t >	getModelStates (const std::string &code) const =0
	Get the state in the model corresponding to a particular state in the alphabet. More...

virtual int	getAlphabetStateAsInt (size_t index) const =0

virtual std::string	getAlphabetStateAsChar (size_t index) const =0

virtual const Alphabet &	alphabet () const =0

virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0

virtual const FrequencySetInterface &	frequencySet () const =0

virtual size_t	getNumberOfStates () const =0
	Get the number of states. More...

virtual double	getInitValue (size_t i, int state) const =0

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 size_t	getNumberOfIndependentParameters () const=0

virtual void	aliasParameters (const std::string &p1, const std::string &p2)=0

virtual void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0

virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0

virtual const ParameterList &	getIndependentParameters () const=0

virtual std::vector< std::string >	getAlias (const std::string &name) const=0

virtual std::map< std::string, std::string >	getAliases () const=0

virtual bool	hasParameter (const std::string &name) const=0

virtual const ParameterList &	getParameters () const=0

virtual const Parameter &	parameter (const std::string &name) const=0

virtual double	getParameterValue (const std::string &name) const=0

virtual void	setAllParametersValues (const ParameterList &parameters)=0

virtual void	setParameterValue (const std::string &name, double value)=0

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

virtual void	removeConstraint (const std::string &name)=0

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

virtual size_t	getNumberOfParameters () const=0

virtual void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

Protected Member Functions
virtual Vdouble &	getFrequencies_ ()=0

virtual ParameterList &	getParameters_ ()=0

Private Attributes
Eigen::VectorXd	lik_

Friends
class	AbstractTotallyWrappedTransitionModel

class	AbstractFromSubstitutionModelTransitionModel

class	InMixedSubstitutionModel

Detailed Description

Partial implementation of the TransitionModel interface, with function for likelihood computations.

Definition at line 19 of file AbstractSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractLkTransitionModel()

bpp::AbstractLkTransitionModel::AbstractLkTransitionModel ( )

inline

Definition at line 26 of file AbstractSubstitutionModel.h.

◆ ~AbstractLkTransitionModel()

virtual bpp::AbstractLkTransitionModel::~AbstractLkTransitionModel ( )

inlinevirtual

Definition at line 27 of file AbstractSubstitutionModel.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()

virtual const Alphabet & bpp::BranchModelInterface::alphabet ( ) const

pure virtualinherited

Returns: A reference to the alphabet associated to this model.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::alphabet(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), and bpp::SENCA::setFreq().

◆ clone()

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

pure virtualinherited

Implements bpp::BranchModelInterface.

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

◆ 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()

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

inlineoverridevirtual

Implements bpp::TransitionModelInterface.

Definition at line 64 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and 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()

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

inlineoverridevirtual

Implements bpp::TransitionModelInterface.

Definition at line 47 of file AbstractSubstitutionModel.h.

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

◆ 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()

virtual const FrequencySetInterface & bpp::BranchModelInterface::frequencySet ( ) const

pure virtualinherited

Returns: Get the FrequencySet of equilibrium of this model.

Exceptions

Exception if no FrequenceSet is associated to this model.

Implemented in bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::AbstractBiblioMixedTransitionModel, bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::AbstractWrappedTransitionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::YN98, bpp::D1WalkSubstitutionModel, bpp::EquiprobableSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::OneChangeRegisterTransitionModel, bpp::OneChangeTransitionModel, bpp::DSO78, bpp::JCprot, bpp::JTT92, bpp::LG08, bpp::UserProteinSubstitutionModel, bpp::WAG01, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::RE08Codon::codonFrequencySet(), bpp::AbstractWrappedModel::frequencySet(), bpp::AbstractWrappedTransitionModel::frequencySet(), bpp::OneChangeRegisterTransitionModel::frequencySet(), bpp::OneChangeTransitionModel::frequencySet(), and bpp::BppOSubstitutionModelFormat::write().

◆ getAlphabet()

virtual std::shared_ptr< const Alphabet > bpp::BranchModelInterface::getAlphabet ( ) const

pure virtualinherited

Returns: A pointer toward the alphabet associated to this model.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::YpR::checkModel(), bpp::NonHomogeneousSubstitutionProcess::createHomogeneousSubstitutionProcess(), bpp::NonHomogeneousSubstitutionProcess::createNonHomogeneousSubstitutionProcess(), bpp::AbstractWrappedModel::getAlphabet(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::SENCA::setFreq(), bpp::NonHomogeneousSubstitutionProcess::setModel(), and bpp::BppOSubstitutionModelFormat::writeMixed_().

◆ getAlphabetStateAsChar()

virtual std::string bpp::BranchModelInterface::getAlphabetStateAsChar ( size_t index ) const

pure virtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implemented in bpp::AbstractWrappedModel, bpp::AbstractTransitionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsChar(), and bpp::SubstitutionModelSet::getAlphabetStateAsChar().

◆ getAlphabetStateAsInt()

virtual int bpp::BranchModelInterface::getAlphabetStateAsInt ( size_t index ) const

pure virtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implemented in bpp::AbstractWrappedModel, bpp::RegisterRatesSubstitutionModel, bpp::AbstractTransitionModel, and bpp::MarkovModulatedSubstitutionModel.

Referenced by bpp::AbstractWrappedModel::getAlphabetStateAsInt(), bpp::SubstitutionModelSet::getAlphabetStateAsInt(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), and bpp::DRASRTreeLikelihoodData::initLikelihoodsWithPatterns().

◆ getAlphabetStates()

virtual const std::vector< int > & bpp::BranchModelInterface::getAlphabetStates ( ) const

pure virtualinherited

Returns: The alphabet states of each state of the model, as a vector of int codes.

See also: Alphabet

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::getAlphabetStates(), and bpp::AbstractWrappedModel::getAlphabetStates().

◆ 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(), 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(), 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().

◆ 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_().

◆ 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

i	the index of the state in the model.
state	An observed state in the sequence/site.

Returns: 1 or 0 depending if the two states are compatible.

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if 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]

virtual std::vector< size_t > bpp::BranchModelInterface::getModelStates ( const std::string & code ) const

pure virtualinherited

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

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

◆ getModelStates() [2/2]

virtual std::vector< size_t > bpp::BranchModelInterface::getModelStates ( int code ) const

pure virtualinherited

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

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::getModelStates(), and bpp::AbstractWrappedModel::getModelStates().

◆ getName()

virtual std::string bpp::BranchModelInterface::getName ( ) const

pure virtualinherited

Get the name of the model.

Returns: The name of this model.

Referenced by bpp::YpR::checkModel(), bpp::TransitionMatrixFromModel::compute(), bpp::AbstractWrappedModel::getName(), bpp::FromMixtureSubstitutionModel::getName(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::BppOSubstitutionModelFormat::initialize_(), bpp::MixtureOfSubstitutionModels::MixtureOfSubstitutionModels(), bpp::MixtureOfATransitionModel::model(), bpp::SubstitutionProcessCollectionMember::setModelScenario(), bpp::LegacyPhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesWithAliases(), bpp::ModelPath::toString(), and bpp::BppOSubstitutionModelFormat::write().

◆ getNumberOfStates()

virtual size_t bpp::BranchModelInterface::getNumberOfStates ( ) const

pure virtualinherited

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.

Implemented in bpp::BinarySubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::gBGC, bpp::YpR, bpp::RE08Nucleotide, bpp::RE08Protein, bpp::RE08Codon, bpp::RegisterRatesSubstitutionModel, and bpp::AbstractDFPSubstitutionModel.

Referenced by bpp::NonHomogeneousSubstitutionProcess::addModel(), bpp::SubstitutionModelSet::addModel(), bpp::AbstractWrappedModel::getNumberOfStates(), bpp::DRASDRTreeLikelihoodData::initLikelihoods(), bpp::DRASRTreeLikelihoodData::initLikelihoods(), and bpp::NonHomogeneousSubstitutionProcess::setModel().

◆ 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 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().

◆ getStateMap()

virtual std::shared_ptr< const StateMapInterface > bpp::BranchModelInterface::getStateMap ( ) const

pure virtualinherited

Returns: A shared_ptr to the mapping of model states with alphabet states.

Implemented in bpp::AbstractTransitionModel, bpp::AbstractWrappedModel, bpp::MarkovModulatedSubstitutionModel, and bpp::RegisterRatesSubstitutionModel.

Referenced by bpp::SubstitutionModelSet::getStateMap(), bpp::SubstitutionProcessCollectionMember::getStateMap(), and bpp::AbstractWrappedModel::getStateMap().

◆ Lik_t()

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

inlineoverridevirtual

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

Parameters

values	An vector of states on the site.
t	the branch length

Implements bpp::TransitionModelInterface.

Definition at line 30 of file AbstractSubstitutionModel.h.

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

◆ 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().

◆ setFreq()

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

pure virtualinherited

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

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

data	The sequences to use.
pseudoCount	A 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 $\pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)}$