Partial implementation of the TransitionModel interface. More...

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

Inheritance diagram for bpp::AbstractTransitionModel:

Collaboration diagram for bpp::AbstractTransitionModel:

Public Member Functions
	AbstractTransitionModel (std::shared_ptr< const Alphabet > alpha, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)

	AbstractTransitionModel (const AbstractTransitionModel &model)=default

AbstractTransitionModel &	operator= (const AbstractTransitionModel &model)=default

virtual	~AbstractTransitionModel ()

const Alphabet &	alphabet () const override

std::shared_ptr< const Alphabet >	getAlphabet () const override

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

size_t	getNumberOfStates () const override
	Get the number of states. More...

const std::vector< int > &	getAlphabetStates () const override

std::string	getAlphabetStateAsChar (size_t index) const override

int	getAlphabetStateAsInt (size_t index) 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 Vdouble &	getFrequencies () const override

bool	computeFrequencies () const override

virtual const Matrix< double > &	getPij_t (double t) const override=0

virtual const Matrix< double > &	getdPij_dt (double t) const override=0

virtual const Matrix< double > &	getd2Pij_dt2 (double t) const override=0

virtual double	freq (size_t i) const override

virtual double	Pij_t (size_t i, size_t j, double t) const override

virtual double	dPij_dt (size_t i, size_t j, double t) const override

virtual double	d2Pij_dt2 (size_t i, size_t j, double t) const override

double	getInitValue (size_t i, int state) const override

void	setFreqFromData (const SequenceDataInterface &data, double pseudoCount=0) override
	Set equilibrium frequencies equal to the frequencies estimated from the data. More...

virtual void	setFreq (std::map< int, double > &freqs) override
	Set equilibrium frequencies. More...

const FrequencySetInterface &	frequencySet () const override

virtual void	fireParameterChanged (const ParameterList &parameters) override
	Tells the model that a parameter value has changed. More...

void	addRateParameter () override
	add a "rate" parameter to the model, that handles the overall rate of the process. More...

void	setVerboseLevel (short level)

short	verboseLevel () const

virtual double	getRate () const override
	The rate of the substitution process. More...

virtual void	setRate (double rate) override
	Set the rate of the model (must be positive). More...

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 void	computeFrequencies (bool yn)=0

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

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

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 Clonable *	clone () const=0

Protected Member Functions
virtual void	updateMatrices_ ()=0
	Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...

Vdouble &	getFrequencies_ () override

virtual ParameterList &	getParameters_ ()=0

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

Protected Attributes
std::shared_ptr< const Alphabet >	alphabet_
	The alphabet relevant to this model. More...

std::shared_ptr< const StateMapInterface >	stateMap_
	The map of model states with alphabet states. More...

size_t	size_
	The number of states. More...

double	rate_
	The rate of the model (default: 1). The generator (and all its vectorial components) is independent of the rate, since it should be normalized. More...

Vdouble	freq_
	The vector $\pi_e$ of equilibrium frequencies. More...

RowMatrix< double >	pijt_
	These ones are for bookkeeping: More...

RowMatrix< double >	dpijt_

RowMatrix< double >	d2pijt_

short	verboseLevel_

Private Attributes
Eigen::VectorXd	lik_

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Detailed Description

Partial implementation of the TransitionModel interface.

This abstract class provides some fields, namely:

alphabet_: a pointer toward the alphabet,
size_: the size of the alphabet, a parameter frequently called during various computations,
rate_: the rate of the model
generator_, leftEigenVectors_, rightEigenVectors_: useful matrices,
eigenValues_, iEigenValues_, freq_: useful vectors.
isDiagonalizable_ : boolean value useful for computation of the exponential

Access methods for these fields are implemented.

This class also provides the updateMatrices_() method, which computes eigen values and vectors and fills the corresponding vector (eigenValues_) and matrices (leftEigenVectors_ and rightEigenVectors_) from the generator.

The freq_ vector and generator_ matrices are hence the only things to provide to create a substitution model. It is also possible to redefine one of these methods for better efficiency. The Pij_t, dPij_dt and d2Pij_dt2 are particularly inefficient since the matrix formula is used to compute all probabilities, and then the result for the initial and final state of interest is retrieved.

Note: This class is dedicated to "simple" substitution models, for which the number of states is equivalent to the number of characters in the alphabet. Consider using the MarkovModulatedSubstitutionModel for more complexe cases.

Definition at line 113 of file AbstractSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractTransitionModel() [1/2]

AbstractTransitionModel::AbstractTransitionModel	(	std::shared_ptr< const Alphabet >	alpha,
		std::shared_ptr< const StateMapInterface >	stateMap,
		const std::string &	prefix
	)

Definition at line 21 of file AbstractSubstitutionModel.cpp.

References computeFrequencies(), freq_, and size_.

◆ AbstractTransitionModel() [2/2]

bpp::AbstractTransitionModel::AbstractTransitionModel ( const AbstractTransitionModel & model )

default

◆ ~AbstractTransitionModel()

virtual bpp::AbstractTransitionModel::~AbstractTransitionModel ( )

inlinevirtual

Definition at line 164 of file AbstractSubstitutionModel.h.

Member Function Documentation

◆ addRateParameter()

void AbstractTransitionModel::addRateParameter ( )

overridevirtual

add a "rate" parameter to the model, that handles the overall rate of the process.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 63 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::getNamespace(), bpp::Parameter::R_PLUS_STAR, and rate_.

◆ alphabet()

const Alphabet& bpp::AbstractTransitionModel::alphabet ( ) const

inlineoverridevirtual

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 167 of file AbstractSubstitutionModel.h.

References alphabet_.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), and bpp::AbstractWordSubstitutionModel::operator=().

◆ 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]

bool bpp::AbstractTransitionModel::computeFrequencies ( ) const

inlineoverridevirtual

Returns: Says if equilibrium frequencies should be computed

Implements bpp::TransitionModelInterface.

Reimplemented in bpp::AbstractSubstitutionModel.

Definition at line 189 of file AbstractSubstitutionModel.h.

Referenced by AbstractTransitionModel().

◆ computeFrequencies() [2/2]

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

pure virtualinherited

Returns: Set if equilibrium frequencies should be computed

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

◆ d2Lik_dt2()

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::AbstractTransitionModel::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlineoverridevirtual

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()

Implements bpp::TransitionModelInterface.

Reimplemented in bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 199 of file AbstractSubstitutionModel.h.

References getd2Pij_dt2().

Referenced by bpp::JCprot::d2Pij_dt2().

◆ dLik_dt()

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::AbstractTransitionModel::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlineoverridevirtual

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()

Implements bpp::TransitionModelInterface.

Reimplemented in bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 198 of file AbstractSubstitutionModel.h.

References getdPij_dt().

Referenced by bpp::JCprot::dPij_dt().

◆ fireParameterChanged()

virtual void bpp::AbstractTransitionModel::fireParameterChanged ( const ParameterList & parameters )

inlineoverridevirtual

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 217 of file AbstractSubstitutionModel.h.

References bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), rate_, bpp::ParameterList::size(), and updateMatrices_().

◆ freq()

virtual double bpp::AbstractTransitionModel::freq ( size_t i ) const

inlineoverridevirtual

Returns: Equilibrium frequency associated to character i.

See also: getFrequencies(), getStates()

Implements bpp::TransitionModelInterface.

Definition at line 195 of file AbstractSubstitutionModel.h.

References freq_.

Referenced by bpp::CodonSameAARateSubstitutionModel::compute_().

◆ frequencySet()

const FrequencySetInterface& bpp::AbstractTransitionModel::frequencySet ( ) const

inlineoverridevirtual

Returns: Get the FrequencySet of equilibrium of this model.

Exceptions

Exception if no FrequenceSet is associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::EquiprobableSubstitutionModel, bpp::D1WalkSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 207 of file AbstractSubstitutionModel.h.

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractTransitionModel::getAlphabet ( ) const

inlineoverridevirtual

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 169 of file AbstractSubstitutionModel.h.

References alphabet_.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices_(), and bpp::RE08::getInitValue().

◆ getAlphabetStateAsChar()

std::string bpp::AbstractTransitionModel::getAlphabetStateAsChar ( size_t index ) const

inlineoverridevirtual

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 179 of file AbstractSubstitutionModel.h.

References stateMap_.

◆ getAlphabetStateAsInt()

int bpp::AbstractTransitionModel::getAlphabetStateAsInt ( size_t index ) const

inlineoverridevirtual

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 181 of file AbstractSubstitutionModel.h.

References stateMap_.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), and getInitValue().

◆ getAlphabetStates()

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

inlineoverridevirtual

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

See also: Alphabet

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 177 of file AbstractSubstitutionModel.h.

References stateMap_.

Referenced by bpp::DFP07::DFP07(), bpp::YNGP_M3::YNGP_M3(), and bpp::YNGP_M8::YNGP_M8().

◆ getd2Pij_dt2()

virtual const Matrix<double>& bpp::AbstractTransitionModel::getd2Pij_dt2 ( double t ) const

overridepure virtual

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()

Implements bpp::TransitionModelInterface.

Implemented in bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by d2Pij_dt2().

◆ getdPij_dt()

virtual const Matrix<double>& bpp::AbstractTransitionModel::getdPij_dt ( double t ) const

overridepure virtual

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()

Implements bpp::TransitionModelInterface.

Implemented in bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by dPij_dt().

◆ getFrequencies()

const Vdouble& bpp::AbstractTransitionModel::getFrequencies ( ) const

inlineoverridevirtual

Returns: A vector of all equilibrium frequencies.

See also: freq()

Implements bpp::TransitionModelInterface.

Definition at line 187 of file AbstractSubstitutionModel.h.

References freq_.

Referenced by bpp::SENCA::setFreq().

◆ getFrequencies_()

Vdouble& bpp::AbstractTransitionModel::getFrequencies_ ( )

inlineoverrideprotectedvirtual

Implements bpp::TransitionModelInterface.

Definition at line 268 of file AbstractSubstitutionModel.h.

References freq_.

Referenced by bpp::CodonDistanceFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::fireParameterChanged(), bpp::CodonDistanceFrequenciesSubstitutionModel::setFreq(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::setFreq(), and bpp::DFPDistanceFrequenciesSubstitutionModel::setFreq().

◆ getInitValue()

double AbstractTransitionModel::getInitValue	(	size_t	i,
		int	state
	)		const

overridevirtual

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();

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RE08.

Definition at line 70 of file AbstractSubstitutionModel.cpp.

References alphabet_, getAlphabetStateAsInt(), and size_.

◆ getModelStates() [1/2]

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

inlineoverridevirtual

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.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 185 of file AbstractSubstitutionModel.h.

References stateMap_.

◆ getModelStates() [2/2]

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

inlineoverridevirtual

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.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 183 of file AbstractSubstitutionModel.h.

References stateMap_.

◆ 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::LegacyPhylogeneticsApplicationTools::setSubstitutionModelParametersInitialValuesWithAliases(), bpp::ModelPath::toString(), and bpp::BppOSubstitutionModelFormat::write().

◆ getNumberOfStates()

size_t bpp::AbstractTransitionModel::getNumberOfStates ( ) const

inlineoverridevirtual

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, bpp::RE08Codon, bpp::RE08Protein, bpp::RE08Nucleotide, bpp::YpR, bpp::gBGC, bpp::DFPDistanceFrequenciesSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, and bpp::BinarySubstitutionModel.

Definition at line 175 of file AbstractSubstitutionModel.h.

References stateMap_.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), bpp::AbstractKroneckerCodonSubstitutionModel::completeMatrices_(), bpp::AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractMixedTransitionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::AbstractMixedTransitionModel::getdPij_dt(), bpp::RE08Nucleotide::getNumberOfStates(), bpp::RE08Protein::getNumberOfStates(), bpp::RE08Codon::getNumberOfStates(), bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractMixedTransitionModel::getPij_t(), bpp::AbstractWordSubstitutionModel::setFreq(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::MixtureOfATransitionModel::updateMatrices_(), and bpp::MixtureOfTransitionModels::updateMatrices_().

◆ getPij_t()

virtual const Matrix<double>& bpp::AbstractTransitionModel::getPij_t ( double t ) const

overridepure virtual

Returns: All probabilities of change from state i to state j during time t.

See also: Pij_t()

Implements bpp::TransitionModelInterface.

Implemented in bpp::AbstractMixedTransitionModel, bpp::AbstractSubstitutionModel, bpp::WordSubstitutionModel, bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Referenced by Pij_t().

◆ getRate()

double AbstractTransitionModel::getRate ( ) const

overridevirtual

The rate of the substitution process.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 45 of file AbstractSubstitutionModel.cpp.

References rate_.

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractTransitionModel::getStateMap ( ) const

inlineoverridevirtual

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

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 173 of file AbstractSubstitutionModel.h.

References stateMap_.

Referenced by bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), and bpp::EquiprobableSubstitutionModel::EquiprobableSubstitutionModel().

◆ Lik_t()

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

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 bpp::AbstractLkTransitionModel::lik_.

◆ operator=()

AbstractTransitionModel& bpp::AbstractTransitionModel::operator= ( const AbstractTransitionModel & model )

default

Referenced by bpp::AbstractMixedTransitionModel::operator=(), and bpp::AbstractSubstitutionModel::operator=().

◆ Pij_t()

virtual double bpp::AbstractTransitionModel::Pij_t	(	size_t	i,
		size_t	j,
		double	t
	)		const

inlineoverridevirtual

Returns: The probability of change from state i to state j during time t.

See also: getPij_t(), getStates()

Implements bpp::TransitionModelInterface.

Reimplemented in bpp::RE08, bpp::JCprot, bpp::TN93, bpp::T92, bpp::K80, bpp::JCnuc, bpp::F81, bpp::EquiprobableSubstitutionModel, bpp::TwoParameterBinarySubstitutionModel, bpp::HKY85, bpp::F84, and bpp::BinarySubstitutionModel.

Definition at line 197 of file AbstractSubstitutionModel.h.

References getPij_t().

Referenced by bpp::JCprot::Pij_t().

◆ setFreq()

void AbstractTransitionModel::setFreq ( std::map< int, double > & frequencies )

overridevirtual

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

Implements bpp::TransitionModelInterface.

Definition at line 98 of file AbstractSubstitutionModel.cpp.

References freq_, and updateMatrices_().

Referenced by bpp::SENCA::setFreq(), and setFreqFromData().

◆ setFreqFromData()

void AbstractTransitionModel::setFreqFromData	(	const SequenceDataInterface &	data,
		double	pseudoCount = `0`
	)

overridevirtual

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

Implements bpp::TransitionModelInterface.

Reimplemented in bpp::RE08, bpp::WAG01, bpp::UserProteinSubstitutionModel, bpp::LG08, bpp::JTT92, bpp::JCprot, bpp::DSO78, bpp::Coala, bpp::K80, and bpp::JCnuc.

Definition at line 88 of file AbstractSubstitutionModel.cpp.

References bpp::SequenceContainerTools::getFrequencies(), and setFreq().

◆ setRate()

void AbstractTransitionModel::setRate ( double rate )

overridevirtual

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

Parameters

rate	must be positive.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel, and bpp::AbstractMixedTransitionModel.

Definition at line 52 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::hasParameter(), rate_, bpp::AbstractParameterAliasable::setParameterValue(), and bpp::TextTools::toString().

Referenced by bpp::AbstractMixedTransitionModel::setRate().

◆ setVerboseLevel()

void bpp::AbstractTransitionModel::setVerboseLevel ( short level )

inline

Definition at line 239 of file AbstractSubstitutionModel.h.

References verboseLevel_.

◆ stateMap()

const StateMapInterface& bpp::AbstractTransitionModel::stateMap ( ) const

inlineoverridevirtual

Returns: The mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 171 of file AbstractSubstitutionModel.h.

References stateMap_.

◆ updateMatrices_()

virtual void bpp::AbstractTransitionModel::updateMatrices_ ( )

protectedpure virtual

Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.

The generator_ matrix and freq_ vector must be initialized.

Eigen values and vectors are computed from the generator and assigned to the eigenValues_ for the real part, iEigenValues_ for the imaginary part, rightEigenVectors_ and leftEigenVectors_ variables. isDiagonalizable_ checks if the generator_ is diagonalizable in R.

The optional rate parameter is not taken into account in this method to prevent unnecessary computation.

!! Here there is no normalization of the generator.