Abstract Kronecker Word Model. More...

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

Inheritance diagram for bpp::AbstractKroneckerWordSubstitutionModel:

Collaboration diagram for bpp::AbstractKroneckerWordSubstitutionModel:

Public Member Functions
	AbstractKroneckerWordSubstitutionModel (ModelList &modelList, const std::string &prefix)
	Build a new AbstractKroneckerWordSubstitutionModel object from a vector of pointers to SubstitutionModels, allowing for all substitutions. More...

	AbstractKroneckerWordSubstitutionModel (ModelList &modelList, const std::vector< std::set< size_t >> &vPos, const std::string &prefix)
	Build a new AbstractKroneckerWordSubstitutionModel object from a vector of pointers to SubstitutionModels, allowing for a given vector of simultaneous substitutions. More...

	AbstractKroneckerWordSubstitutionModel (std::unique_ptr< SubstitutionModelInterface > pmodel, unsigned int num, const std::string &prefix)
	Build a new AbstractWordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models, allowing for all substitutions. More...

	AbstractKroneckerWordSubstitutionModel (std::unique_ptr< SubstitutionModelInterface > pmodel, unsigned int num, const std::vector< std::set< size_t >> &vPos, const std::string &prefix)
	Build a new AbstractWordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models, allowing for a given vector of simultaneous substitutions. More...

virtual	~AbstractKroneckerWordSubstitutionModel ()

	AbstractKroneckerWordSubstitutionModel (const AbstractKroneckerWordSubstitutionModel &)

AbstractKroneckerWordSubstitutionModel &	operator= (const AbstractKroneckerWordSubstitutionModel &)

void	setNamespace (const std::string &prefix)

const SubstitutionModelInterface &	nModel (size_t i) const
	returns the ith model, or throw an exception if i is not a valid number. More...

size_t	getNumberOfModels () const

virtual void	setFreq (std::map< int, double > &freqs)
	Estimation of the parameters of the models so that the equilibrium frequencies match the given ones. More...

bool	computeFrequencies () const

void	computeFrequencies (bool yn)

const Matrix< double > &	generator () const

const Matrix< double > &	exchangeabilityMatrix () const

const Matrix< double > &	getPij_t (double t) const

const Matrix< double > &	getdPij_dt (double t) const

const Matrix< double > &	getd2Pij_dt2 (double t) const

double	Sij (size_t i, size_t j) const

const Vdouble &	getEigenValues () const

const Vdouble &	getIEigenValues () const

bool	isDiagonalizable () const

bool	isNonSingular () const

const Matrix< double > &	getRowLeftEigenVectors () const

const Matrix< double > &	getColumnRightEigenVectors () const

virtual double	Qij (size_t i, size_t j) const
	A method for computing all necessary matrices. More...

void	enableEigenDecomposition (bool yn)
	Set if eigenValues and Vectors must be computed. More...

bool	enableEigenDecomposition ()
	Tell if eigenValues and Vectors must be computed. More...

void	setScalable (bool scalable)
	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
	returns if model is scalable More...

double	getScale () const
	return scale More...

void	setScale (double scale)
	Multiplies the current generator by the given scale. More...

void	normalize ()
	normalize the generator More...

void	setDiagonal ()
	set the diagonal of the generator such that sum on each line equals 0. More...

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

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...

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 Clonable *	clone () const=0

SubstitutionModelInterface *	clone () const override=0

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

virtual size_t	getNumberOfIndependentParameters () const=0

size_t	getNumberOfIndependentParameters () const

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

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

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

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

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

virtual const ParameterList &	getIndependentParameters () const=0

const ParameterList &	getIndependentParameters () const

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

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

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

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

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

bool	hasParameter (const std::string &name) const override

virtual const ParameterList &	getParameters () const=0

const ParameterList &	getParameters () const override

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

const Parameter &	parameter (const std::string &name) const override

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

double	getParameterValue (const std::string &name) const override

virtual void	setAllParametersValues (const ParameterList &parameters)=0

void	setAllParametersValues (const ParameterList &parameters) override

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

void	setParameterValue (const std::string &name, double value) override

virtual void	setParametersValues (const ParameterList &parameters)=0

void	setParametersValues (const ParameterList &parameters) override

virtual bool	matchParametersValues (const ParameterList &parameters)=0

bool	matchParametersValues (const ParameterList &parameters) override

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

void	removeConstraint (const std::string &name) override

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

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

virtual size_t	getNumberOfParameters () const=0

size_t	getNumberOfParameters () const override

virtual std::string	getNamespace () const=0

std::string	getNamespace () const override

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

std::string	getParameterNameWithoutNamespace (const std::string &name) const override

bool	hasIndependentParameter (const std::string &name) const

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

std::string	getFrom (const std::string &name) const

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

Protected Member Functions
void	initGenerators_ ()

bool	checkChangingPositions_ ()
	checks that the vector of changing positions is valid More...

	AbstractKroneckerWordSubstitutionModel (std::shared_ptr< const Alphabet > alph, std::shared_ptr< const StateMapInterface > stateMap, const std::string &prefix)
	Constructor for the derived classes only. More...

void	setChangingPositions (const std::vector< std::set< size_t >> &vPos)

void	updateMatrices_ ()
	Diagonalize the matrix, and fill the eigenValues_, iEigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...

virtual void	completeMatrices_ ()=0
	Called by updateMatrices to handle specific modifications for inheriting classes. More...

Vdouble &	getFrequencies_ () override

virtual ParameterList &	getParameters_ ()=0

ParameterList &	getParameters_ () override

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

Protected Attributes
std::vector< std::shared_ptr< SubstitutionModelInterface > >	VSubMod_

std::vector< std::string >	VnestedPrefix_

std::vector< double >	Vrate_

bool	isScalable_
	If the model is scalable (ie generator can be normalized automatically). More...

RowMatrix< double >	generator_
	The generator matrix of the model. More...

bool	computeFreq_
	if the Frequencies must be computed from the generator More...

RowMatrix< double >	exchangeability_
	The exchangeability matrix of the model, defined as $S_{ij}=\frac{Q_{ij}}{\pi_j}$ . When the model is reversible, this matrix is symmetric. More...

bool	eigenDecompose_
	Tell if the eigen decomposition should be performed. More...

Vdouble	eigenValues_
	The vector of eigen values. More...

Vdouble	iEigenValues_
	The vector of the imaginary part of the eigen values. More...

bool	isDiagonalizable_
	boolean value for diagonalizability in R of the generator_ More...

RowMatrix< double >	rightEigenVectors_
	The matrix made of right eigen vectors (by column). More...

bool	isNonSingular_
	boolean value for non-singularity of rightEigenVectors_ More...

RowMatrix< double >	leftEigenVectors_
	The matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular. More...

std::vector< RowMatrix< double > >	vPowGen_
	vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular). More...

RowMatrix< double >	tmpMat_
	For computational issues. More...

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 Member Functions
void	fillBasicGenerator_ ()
	First fill of the generator, from the position model. More...

Private Attributes
std::vector< std::set< size_t > >	sChangingPos_
	vector of sets of simultaneously changing positions. More...

std::vector< RowMatrix< double > >	vGenerators_
	vector of generators for computation purposes More...

bool	newAlphabet_
	boolean flag to check if a specific WordAlphabet has been built More...

Eigen::VectorXd	lik_

ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Detailed Description

Abstract Kronecker Word Model.

Objects of this class are built from several substitution models. Each model corresponds to a position in the word. No model is directly accessible.

A substitution rate between words is the product of the rates of changing letters of position generators.

Either all substitutions are allowed, or any subset of them is allowed. For example, in case of 3 words model, if is the generator of the position model, either all substitutions are allowed (ie generator is $Q_1 \otimes Q_1 \otimes Q_1$ with is with diagonal of 1), or all and only three letters substitutions are allowed (ie generator is $Q_0 \otimes Q_0 \otimes Q_0$ with is with diagonal of 0), or all and only two letters substitutions are allowed (generator is $I \otimes Q_0 \otimes Q_0 + Q_0 \otimes I \otimes Q_0 + Q_0 \otimes Q_0 \otimes I$ ), or all and only two neighbors letters substitutions are allowed (generator is $I \otimes Q_0 \otimes Q_0 + Q_0 \otimes Q_0 \otimes I$ ).

Default construction is all substitutions, but a vector of vectors of simultaneously changing positions can be given.

Definition at line 44 of file AbstractKroneckerWordSubstitutionModel.h.

Constructor & Destructor Documentation

◆ AbstractKroneckerWordSubstitutionModel() [1/6]

AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel	(	ModelList &	modelList,
		const std::string &	prefix
	)

Build a new AbstractKroneckerWordSubstitutionModel object from a vector of pointers to SubstitutionModels, allowing for all substitutions.

Parameters

modelList	the list of substitution models to use, in the order of the positions in the words from left to right. All the models must be different objects to avoid parameters redundancy, otherwise only the first model is used. The used models are owned by the instance.
prefix	the Namespace.

Definition at line 16 of file AbstractKroneckerWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::enableEigenDecomposition(), initGenerators_(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

◆ AbstractKroneckerWordSubstitutionModel() [2/6]

AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel	(	ModelList &	modelList,
		const std::vector< std::set< size_t >> &	vPos,
		const std::string &	prefix
	)

Build a new AbstractKroneckerWordSubstitutionModel object from a vector of pointers to SubstitutionModels, allowing for a given vector of simultaneous substitutions.

Parameters

modelList	the list of substitution models to use, in the order of the positions in the words from left to right. All the models must be different objects to avoid parameters redundancy, otherwise only the first model is used. The used models are owned by the instance.
vPos	a vector of sets of simultaneously changing positions.
prefix	the Namespace.

Definition at line 33 of file AbstractKroneckerWordSubstitutionModel.cpp.

References checkChangingPositions_(), bpp::AbstractSubstitutionModel::enableEigenDecomposition(), initGenerators_(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

◆ AbstractKroneckerWordSubstitutionModel() [3/6]

AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel	(	std::unique_ptr< SubstitutionModelInterface >	pmodel,
		unsigned int	num,
		const std::string &	prefix
	)

Build a new AbstractWordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models, allowing for all substitutions.

Parameters

pmodel	A pointer to the substitution model to use in all the positions. It will be owned by the instance.
num	The number of models involved.
prefix	the Namespace.

Definition at line 54 of file AbstractKroneckerWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::enableEigenDecomposition(), initGenerators_(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

◆ AbstractKroneckerWordSubstitutionModel() [4/6]

AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel	(	std::unique_ptr< SubstitutionModelInterface >	pmodel,
		unsigned int	num,
		const std::vector< std::set< size_t >> &	vPos,
		const std::string &	prefix
	)

Build a new AbstractWordSubstitutionModel object from a pointer to an SubstitutionModel and a number of desired models, allowing for a given vector of simultaneous substitutions.

Parameters

pmodel	A pointer to the substitution model to use in all the positions. It will be owned by the instance.
num	The number of models involved.
vPos	a vector of vectors of simultaneously changing positions.
prefix	the Namespace.

Definition at line 72 of file AbstractKroneckerWordSubstitutionModel.cpp.

References checkChangingPositions_(), bpp::AbstractSubstitutionModel::enableEigenDecomposition(), initGenerators_(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

◆ ~AbstractKroneckerWordSubstitutionModel()

virtual bpp::AbstractKroneckerWordSubstitutionModel::~AbstractKroneckerWordSubstitutionModel ( )

inlinevirtual

Definition at line 145 of file AbstractKroneckerWordSubstitutionModel.h.

◆ AbstractKroneckerWordSubstitutionModel() [5/6]

AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel ( const AbstractKroneckerWordSubstitutionModel & wrsm )

Definition at line 110 of file AbstractKroneckerWordSubstitutionModel.cpp.

References initGenerators_().

◆ AbstractKroneckerWordSubstitutionModel() [6/6]

AbstractKroneckerWordSubstitutionModel::AbstractKroneckerWordSubstitutionModel	(	std::shared_ptr< const Alphabet >	alph,
		std::shared_ptr< const StateMapInterface >	stateMap,
		const std::string &	prefix
	)

protected

Constructor for the derived classes only.

Definition at line 94 of file AbstractKroneckerWordSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::enableEigenDecomposition(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

Member Function Documentation

◆ addRateParameter()

void AbstractTransitionModel::addRateParameter ( )

overridevirtualinherited

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 bpp::AbstractTransitionModel::rate_.

◆ alphabet()

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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::alphabet_.

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

◆ checkChangingPositions_()

bool AbstractKroneckerWordSubstitutionModel::checkChangingPositions_ ( )

protected

checks that the vector of changing positions is valid

Definition at line 157 of file AbstractKroneckerWordSubstitutionModel.cpp.

References sChangingPos_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by AbstractKroneckerWordSubstitutionModel(), and setChangingPositions().

◆ clone() [1/2]

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

pure virtualinherited

Implements bpp::BranchModelInterface.

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

◆ clone() [2/2]

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

overridepure virtualinherited

Implements bpp::TransitionModelInterface.

◆ completeMatrices_()

virtual void bpp::AbstractWordSubstitutionModel::completeMatrices_ ( )

protectedpure virtualinherited

Called by updateMatrices to handle specific modifications for inheriting classes.

Implemented in bpp::WordSubstitutionModel, bpp::KroneckerWordSubstitutionModel, bpp::AbstractKroneckerCodonSubstitutionModel, and bpp::AbstractCodonSubstitutionModel.

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

◆ computeFrequencies() [1/2]

bool bpp::AbstractSubstitutionModel::computeFrequencies ( ) const

inlinevirtualinherited

Returns: Says if equilibrium frequencies should be computed

Reimplemented from bpp::AbstractTransitionModel.

Definition at line 404 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::computeFreq_.

Referenced by bpp::CodonAdHocSubstitutionModel::CodonAdHocSubstitutionModel(), bpp::CodonDistanceFrequenciesSubstitutionModel::CodonDistanceFrequenciesSubstitutionModel(), bpp::CodonDistancePhaseFrequenciesSubstitutionModel::CodonDistancePhaseFrequenciesSubstitutionModel(), bpp::CodonDistanceSubstitutionModel::CodonDistanceSubstitutionModel(), bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), bpp::F81::F81(), bpp::gBGC::gBGC(), bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::KroneckerCodonDistanceFrequenciesSubstitutionModel(), bpp::KroneckerCodonDistanceSubstitutionModel::KroneckerCodonDistanceSubstitutionModel(), bpp::L95::L95(), bpp::POMO::POMO(), bpp::RN95::RN95(), bpp::RN95s::RN95s(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::WordSubstitutionModel::WordSubstitutionModel(), and bpp::YpR::YpR().

◆ computeFrequencies() [2/2]

void bpp::AbstractSubstitutionModel::computeFrequencies ( bool yn )

inlinevirtualinherited

Returns: Set if equilibrium frequencies should be computed

Implements bpp::TransitionModelInterface.

Definition at line 406 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::computeFreq_.

◆ 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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::getdPij_dt().

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

◆ enableEigenDecomposition() [1/2]

bool bpp::AbstractSubstitutionModel::enableEigenDecomposition ( )

inlinevirtualinherited

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 434 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractDFPSubstitutionModel::AbstractDFPSubstitutionModel(), AbstractKroneckerWordSubstitutionModel(), bpp::KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), and bpp::WordSubstitutionModel::WordSubstitutionModel().

◆ enableEigenDecomposition() [2/2]

void bpp::AbstractSubstitutionModel::enableEigenDecomposition ( bool yn )

inlinevirtualinherited

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 432 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

◆ exchangeabilityMatrix()

const Matrix<double>& bpp::AbstractSubstitutionModel::exchangeabilityMatrix ( ) const

inlinevirtualinherited

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 $S . \pi$ .

Implements bpp::SubstitutionModelInterface.

Definition at line 410 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ fillBasicGenerator_()

void AbstractKroneckerWordSubstitutionModel::fillBasicGenerator_ ( )

privatevirtual

First fill of the generator, from the position model.

Reimplemented from bpp::AbstractWordSubstitutionModel.

Definition at line 170 of file AbstractKroneckerWordSubstitutionModel.cpp.

References bpp::MatrixTools::add(), bpp::MatrixTools::fillDiag(), bpp::AbstractSubstitutionModel::generator(), bpp::AbstractSubstitutionModel::generator_, bpp::MatrixTools::getId(), bpp::AbstractTransitionModel::getNumberOfStates(), bpp::MatrixTools::kroneckerMult(), sChangingPos_, vGenerators_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

◆ fireParameterChanged()

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

inlineoverridevirtualinherited

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(), bpp::AbstractTransitionModel::rate_, bpp::ParameterList::size(), and bpp::AbstractTransitionModel::updateMatrices_().

◆ freq()

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

inlineoverridevirtualinherited

Returns: Equilibrium frequency associated to character i.

See also: getFrequencies(), getStates()

Implements bpp::TransitionModelInterface.

Definition at line 195 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

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

◆ frequencySet()

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

inlineoverridevirtualinherited

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.

◆ generator()

const Matrix<double>& bpp::AbstractSubstitutionModel::generator ( ) const

inlinevirtualinherited

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 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()

Implements bpp::SubstitutionModelInterface.

Definition at line 408 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

Referenced by fillBasicGenerator_().

◆ getAlphabet()

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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::alphabet_.

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

◆ getAlphabetStateAsChar()

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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::stateMap_.

◆ getAlphabetStateAsInt()

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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::stateMap_.

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

◆ getAlphabetStates()

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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::stateMap_.

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

◆ getColumnRightEigenVectors()

const Matrix<double>& bpp::AbstractSubstitutionModel::getColumnRightEigenVectors ( ) const

inlinevirtualinherited

Returns: A matrix with right eigen vectors. Each column in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModelInterface.

Definition at line 428 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

◆ getd2Pij_dt2()

const Matrix< double > & AbstractSubstitutionModel::getd2Pij_dt2 ( double t ) const

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()

Implements bpp::AbstractTransitionModel.

Reimplemented in 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.

Definition at line 557 of file AbstractSubstitutionModel.cpp.

Referenced by bpp::JCprot::getd2Pij_dt2().

◆ getdPij_dt()

const Matrix< double > & AbstractSubstitutionModel::getdPij_dt ( double t ) const

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()

Implements bpp::AbstractTransitionModel.

Reimplemented in 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.

Definition at line 486 of file AbstractSubstitutionModel.cpp.

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

◆ getEigenValues()

const Vdouble& bpp::AbstractSubstitutionModel::getEigenValues ( ) const

inlinevirtualinherited

Returns: A vector with all real parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModelInterface.

Definition at line 418 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

◆ getFrequencies()

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

inlineoverridevirtualinherited

Returns: A vector of all equilibrium frequencies.

See also: freq()

Implements bpp::TransitionModelInterface.

Definition at line 187 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

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

◆ getFrequencies_()

Vdouble& bpp::AbstractTransitionModel::getFrequencies_ ( )

inlineoverrideprotectedvirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 268 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::freq_.

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

◆ getIEigenValues()

const Vdouble& bpp::AbstractSubstitutionModel::getIEigenValues ( ) const

inlinevirtualinherited

Returns: A vector with all imaginary parts of the eigen values of the generator of this model;

Implements bpp::SubstitutionModelInterface.

Definition at line 420 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

◆ getInitValue()

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

overridevirtualinherited

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 bpp::AbstractTransitionModel::alphabet_, bpp::AbstractTransitionModel::getAlphabetStateAsInt(), and bpp::AbstractTransitionModel::size_.

◆ getModelStates() [1/2]

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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::stateMap_.

◆ getModelStates() [2/2]

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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::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().

◆ getNumberOfModels()

size_t bpp::AbstractWordSubstitutionModel::getNumberOfModels ( ) const

inlineinherited

Definition at line 196 of file AbstractWordSubstitutionModel.h.

References bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::BppOSubstitutionModelFormat::write().

◆ getNumberOfStates()

size_t bpp::AbstractTransitionModel::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, 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 bpp::AbstractTransitionModel::stateMap_.

Referenced by bpp::AbstractCodonSubstitutionModel::completeMatrices_(), bpp::AbstractKroneckerCodonSubstitutionModel::completeMatrices_(), 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()

const Matrix< double > & AbstractSubstitutionModel::getPij_t ( double t ) const

virtualinherited

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

See also: Pij_t()

Implements bpp::AbstractTransitionModel.

Reimplemented in 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.

Definition at line 395 of file AbstractSubstitutionModel.cpp.

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

◆ getRate()

double AbstractTransitionModel::getRate ( ) const

overridevirtualinherited

The rate of the substitution process.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 45 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractTransitionModel::rate_.

◆ getRowLeftEigenVectors()

const Matrix<double>& bpp::AbstractSubstitutionModel::getRowLeftEigenVectors ( ) const

inlinevirtualinherited

Returns: A matrix with left eigen vectors. Each row in the matrix stands for an eigen vector.

Implements bpp::SubstitutionModelInterface.

Definition at line 426 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

◆ getScale()

double AbstractSubstitutionModel::getScale ( ) const

virtualinherited

return scale

Implements bpp::SubstitutionModelInterface.

Definition at line 632 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::diag(), bpp::AbstractTransitionModel::freq_, and bpp::AbstractSubstitutionModel::generator_.

Referenced by bpp::AbstractSubstitutionModel::normalize().

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractTransitionModel::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 173 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::stateMap_.

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

◆ initGenerators_()

void AbstractKroneckerWordSubstitutionModel::initGenerators_ ( )

protected

Definition at line 142 of file AbstractKroneckerWordSubstitutionModel.cpp.

References vGenerators_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(), and AbstractKroneckerWordSubstitutionModel().

◆ isDiagonalizable()

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const

inlinevirtualinherited

Returns: True if the model is diagonalizable in R.

Implements bpp::SubstitutionModelInterface.

Definition at line 422 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

◆ isNonSingular()

bool bpp::AbstractSubstitutionModel::isNonSingular ( ) const

inlinevirtualinherited

Returns: True is the model is non-singular.

Implements bpp::SubstitutionModelInterface.

Definition at line 424 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

◆ isScalable()

virtual bool bpp::AbstractSubstitutionModel::isScalable ( ) const

inlinevirtualinherited

returns if model is scalable

Implements bpp::SubstitutionModelInterface.

Definition at line 469 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isScalable_.

Referenced by bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ 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_.

◆ nModel()

const SubstitutionModelInterface& bpp::AbstractWordSubstitutionModel::nModel ( size_t i ) const

inlineinherited

returns the ith model, or throw an exception if i is not a valid number.

Definition at line 188 of file AbstractWordSubstitutionModel.h.

References bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::BppOSubstitutionModelFormat::write().

◆ normalize()

void AbstractSubstitutionModel::normalize ( )

virtualinherited

normalize the generator

Implements bpp::SubstitutionModelInterface.

Definition at line 673 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::getScale(), bpp::AbstractSubstitutionModel::isScalable_, and bpp::AbstractSubstitutionModel::setScale().

Referenced by bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::AbstractReversibleSubstitutionModel::updateMatrices_(), and bpp::gBGC::updateMatrices_().

◆ operator=()

AbstractKroneckerWordSubstitutionModel & AbstractKroneckerWordSubstitutionModel::operator= ( const AbstractKroneckerWordSubstitutionModel & model )

Definition at line 121 of file AbstractKroneckerWordSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::operator=(), bpp::AbstractWordSubstitutionModel::operator=(), sChangingPos_, and vGenerators_.

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

◆ Pij_t()

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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::getPij_t().

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

◆ Qij()

virtual double bpp::AbstractSubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const

inlinevirtualinherited

A method for computing all necessary matrices.

Returns: The rate in the generator of change from state i to state j.

See also: getStates();

Implements bpp::SubstitutionModelInterface.

Definition at line 430 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

◆ setChangingPositions()

void AbstractKroneckerWordSubstitutionModel::setChangingPositions ( const std::vector< std::set< size_t >> & vPos )

protected

Definition at line 133 of file AbstractKroneckerWordSubstitutionModel.cpp.

References checkChangingPositions_(), and sChangingPos_.

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

◆ setDiagonal()

void AbstractSubstitutionModel::setDiagonal ( )

virtualinherited

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

Implements bpp::SubstitutionModelInterface.

Definition at line 654 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::generator_, RowMatrix< double >::getRow(), and bpp::AbstractTransitionModel::size_.

Referenced by bpp::CodonSameAARateSubstitutionModel::compute_(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::AbstractReversibleSubstitutionModel::updateMatrices_(), bpp::AbstractDFPSubstitutionModel::updateMatrices_(), bpp::POMO::updateMatrices_(), and bpp::RegisterRatesSubstitutionModel::updateMatrices_().

◆ setFreq()

void AbstractWordSubstitutionModel::setFreq ( std::map< int, double > & freqs )

virtualinherited

Estimation of the parameters of the models so that the equilibrium frequencies match the given ones.

Parameters

freqs map of the frequencies

When there is one submodel for all the positions, the submodel parameters are fit on the means of the frequencies on each position. Otherwise, each model is fit on the frequencies on its corresponding position in the word.

Reimplemented from bpp::AbstractTransitionModel.

Reimplemented in bpp::SENCA, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFrequenciesSubstitutionModel, and bpp::CodonAdHocSubstitutionModel.

Definition at line 349 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractTransitionModel::getNumberOfStates(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractParameterAliasable::matchParametersValues(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

◆ setFreqFromData()

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

overridevirtualinherited

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 bpp::AbstractTransitionModel::setFreq().

◆ setNamespace()

void AbstractWordSubstitutionModel::setNamespace ( const std::string & prefix )

virtualinherited

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::CodonAdHocSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::SENCA, bpp::KroneckerCodonDistanceSubstitutionModel, bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, and bpp::CodonDistanceFrequenciesSubstitutionModel.

Definition at line 185 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::setNamespace(), bpp::TextTools::toString(), bpp::AbstractWordSubstitutionModel::VnestedPrefix_, and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::setNamespace(), bpp::KroneckerCodonDistanceSubstitutionModel::setNamespace(), bpp::CodonDistanceSubstitutionModel::setNamespace(), and bpp::AbstractCodonSubstitutionModel::setNamespace().

◆ setRate()

void AbstractTransitionModel::setRate ( double rate )

overridevirtualinherited

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

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

◆ setScalable()

void bpp::AbstractSubstitutionModel::setScalable ( bool scalable )

inlinevirtualinherited

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

Implements bpp::SubstitutionModelInterface.

Definition at line 461 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isScalable_.

◆ setScale()

void AbstractSubstitutionModel::setScale ( double scale )

virtualinherited

Multiplies the current generator by the given scale.

Parameters

scale the scale by which the generator is multiplied.

Implements bpp::SubstitutionModelInterface.

Definition at line 641 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::eigenValues_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractSubstitutionModel::iEigenValues_, bpp::AbstractSubstitutionModel::isScalable_, and bpp::MatrixTools::scale().

Referenced by bpp::AbstractSubstitutionModel::normalize(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::F84::updateMatrices_(), bpp::HKY85::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::K80::updateMatrices_(), bpp::L95::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::T92::updateMatrices_(), bpp::TN93::updateMatrices_(), bpp::POMO::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ setVerboseLevel()

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

inlineinherited

Definition at line 239 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::verboseLevel_.

◆ Sij()

double bpp::AbstractSubstitutionModel::Sij	(	size_t	i,
		size_t	j
	)		const

inlinevirtualinherited

Returns: The exchangeability between state i and state j.

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

Implements bpp::SubstitutionModelInterface.

Definition at line 416 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

◆ stateMap()

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

inlineoverridevirtualinherited

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 bpp::AbstractTransitionModel::stateMap_.

◆ updateMatrices_()

void AbstractWordSubstitutionModel::updateMatrices_ ( )

protectedvirtualinherited

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.

Now check inversion and diagonalization

Reimplemented from bpp::AbstractSubstitutionModel.

Reimplemented in bpp::WordSubstitutionModel, and bpp::AbstractCodonSubstitutionModel.

Definition at line 209 of file AbstractWordSubstitutionModel.cpp.

References bpp::AbstractWordSubstitutionModel::completeMatrices_(), bpp::AbstractSubstitutionModel::computeFrequencies(), bpp::AbstractSubstitutionModel::enableEigenDecomposition(), bpp::AbstractSubstitutionModel::exchangeability_, bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::AbstractTransitionModel::freq_, bpp::AbstractSubstitutionModel::generator_, bpp::AbstractTransitionModel::getNumberOfStates(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractSubstitutionModel::normalize(), bpp::AbstractSubstitutionModel::setDiagonal(), bpp::AbstractTransitionModel::size_, bpp::AbstractSubstitutionModel::updateMatrices_(), and bpp::AbstractWordSubstitutionModel::VSubMod_.

Referenced by bpp::KroneckerCodonDistanceFrequenciesSubstitutionModel::KroneckerCodonDistanceFrequenciesSubstitutionModel(), bpp::KroneckerCodonDistanceSubstitutionModel::KroneckerCodonDistanceSubstitutionModel(), bpp::KroneckerWordSubstitutionModel::KroneckerWordSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::updateMatrices_(), and bpp::WordSubstitutionModel::updateMatrices_().

◆ verboseLevel()

short bpp::AbstractTransitionModel::verboseLevel ( ) const

inlineinherited

Definition at line 241 of file AbstractSubstitutionModel.h.

References bpp::AbstractTransitionModel::verboseLevel_.

Member Data Documentation

◆ alphabet_

std::shared_ptr<const Alphabet> bpp::AbstractTransitionModel::alphabet_

protectedinherited

The alphabet relevant to this model.

Definition at line 121 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractTransitionModel::alphabet(), bpp::POMO::getAllelicAlphabet(), bpp::AbstractTransitionModel::getAlphabet(), bpp::AbstractTransitionModel::getInitValue(), bpp::RE08::getInitValue(), bpp::AbstractNucleotideSubstitutionModel::getNucleicAlphabet(), bpp::AbstractReversibleNucleotideSubstitutionModel::getNucleicAlphabet(), bpp::RE08Nucleotide::getNucleicAlphabet(), bpp::AbstractProteinSubstitutionModel::getProteicAlphabet(), bpp::AbstractReversibleProteinSubstitutionModel::getProteicAlphabet(), bpp::RE08Protein::getProteicAlphabet(), and bpp::AbstractWordSubstitutionModel::operator=().

◆ computeFreq_

bool bpp::AbstractSubstitutionModel::computeFreq_

protectedinherited

if the Frequencies must be computed from the generator

Definition at line 303 of file AbstractSubstitutionModel.h.

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

◆ d2pijt_

RowMatrix<double> bpp::AbstractTransitionModel::d2pijt_

mutableprotectedinherited

Definition at line 150 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), and bpp::AbstractMixedTransitionModel::getd2Pij_dt2().

◆ dpijt_

RowMatrix<double> bpp::AbstractTransitionModel::dpijt_

mutableprotectedinherited

Definition at line 149 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), and bpp::AbstractMixedTransitionModel::getdPij_dt().

◆ eigenDecompose_

bool bpp::AbstractSubstitutionModel::eigenDecompose_

protectedinherited

Tell if the eigen decomposition should be performed.

Definition at line 315 of file AbstractSubstitutionModel.h.

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

◆ eigenValues_

Vdouble bpp::AbstractSubstitutionModel::eigenValues_

protectedinherited

The vector of eigen values.

Definition at line 320 of file AbstractSubstitutionModel.h.

◆ exchangeability_

RowMatrix<double> bpp::AbstractSubstitutionModel::exchangeability_

protectedinherited

The exchangeability matrix of the model, defined as $S_{ij}=\frac{Q_{ij}}{\pi_j}$ . When the model is reversible, this matrix is symmetric.

Definition at line 310 of file AbstractSubstitutionModel.h.

◆ freq_

Vdouble bpp::AbstractTransitionModel::freq_

protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 143 of file AbstractSubstitutionModel.h.

◆ generator_

RowMatrix<double> bpp::AbstractSubstitutionModel::generator_

protectedinherited

The generator matrix of the model.

Definition at line 298 of file AbstractSubstitutionModel.h.

◆ iEigenValues_

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_

protectedinherited

The vector of the imaginary part of the eigen values.

Definition at line 325 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getIEigenValues(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::setScale(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isDiagonalizable_

bool bpp::AbstractSubstitutionModel::isDiagonalizable_

protectedinherited

boolean value for diagonalizability in R of the generator_

Definition at line 330 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isDiagonalizable(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isNonSingular_

bool bpp::AbstractSubstitutionModel::isNonSingular_

protectedinherited

boolean value for non-singularity of rightEigenVectors_

Definition at line 340 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::isNonSingular(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ isScalable_

bool bpp::AbstractSubstitutionModel::isScalable_

protectedinherited

If the model is scalable (ie generator can be normalized automatically).

Definition at line 293 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::isScalable(), bpp::AbstractSubstitutionModel::normalize(), bpp::AbstractSubstitutionModel::operator=(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractSubstitutionModel::setScalable(), and bpp::AbstractSubstitutionModel::setScale().

◆ leftEigenVectors_

RowMatrix<double> bpp::AbstractSubstitutionModel::leftEigenVectors_

protectedinherited

The matrix made of left eigen vectors (by row) if rightEigenVectors_ is non-singular.

Definition at line 346 of file AbstractSubstitutionModel.h.

◆ 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().

◆ newAlphabet_

bool bpp::AbstractWordSubstitutionModel::newAlphabet_

privateinherited

boolean flag to check if a specific WordAlphabet has been built

Definition at line 109 of file AbstractWordSubstitutionModel.h.

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

◆ pijt_

RowMatrix<double> bpp::AbstractTransitionModel::pijt_

mutableprotectedinherited

These ones are for bookkeeping:

Definition at line 148 of file AbstractSubstitutionModel.h.

Referenced by bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), and bpp::AbstractMixedTransitionModel::getPij_t().

◆ rate_

double bpp::AbstractTransitionModel::rate_

protectedinherited

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

Definition at line 138 of file AbstractSubstitutionModel.h.

◆ rightEigenVectors_

RowMatrix<double> bpp::AbstractSubstitutionModel::rightEigenVectors_

protectedinherited

The matrix made of right eigen vectors (by column).

Definition at line 335 of file AbstractSubstitutionModel.h.

◆ sChangingPos_

std::vector<std::set< size_t> > bpp::AbstractKroneckerWordSubstitutionModel::sChangingPos_

private

vector of sets of simultaneously changing positions.

Shortcut : if empty, any number of any positions can change simultaneously

Definition at line 54 of file AbstractKroneckerWordSubstitutionModel.h.

Referenced by checkChangingPositions_(), fillBasicGenerator_(), operator=(), and setChangingPositions().

◆ size_

size_t bpp::AbstractTransitionModel::size_

protectedinherited

The number of states.

Definition at line 131 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractReversibleSubstitutionModel::AbstractReversibleSubstitutionModel(), bpp::AbstractTransitionModel::AbstractTransitionModel(), bpp::D1WalkSubstitutionModel::D1WalkSubstitutionModel(), bpp::EquiprobableSubstitutionModel::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::EquiprobableSubstitutionModel::dPij_dt(), bpp::RE08::dPij_dt(), bpp::EquiprobableSubstitutionModel::getd2Pij_dt2(), bpp::JCnuc::getd2Pij_dt2(), bpp::JCprot::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::EquiprobableSubstitutionModel::getdPij_dt(), bpp::JCnuc::getdPij_dt(), bpp::JCprot::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractTransitionModel::getInitValue(), bpp::RE08::getInitValue(), bpp::EquiprobableSubstitutionModel::getPij_t(), bpp::JCnuc::getPij_t(), bpp::JCprot::getPij_t(), bpp::RE08::getPij_t(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::EquiprobableSubstitutionModel::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::RE08(), bpp::AbstractSubstitutionModel::setDiagonal(), bpp::T92::T92(), bpp::TN93::TN93(), bpp::AbstractWordSubstitutionModel::updateMatrices_(), bpp::EquiprobableSubstitutionModel::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), bpp::RE08::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ stateMap_

std::shared_ptr<const StateMapInterface> bpp::AbstractTransitionModel::stateMap_

protectedinherited

The map of model states with alphabet states.

Definition at line 126 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::CodonSameAARateSubstitutionModel::compute_(), bpp::AbstractTransitionModel::getAlphabetStateAsChar(), bpp::AbstractTransitionModel::getAlphabetStateAsInt(), bpp::AbstractTransitionModel::getAlphabetStates(), bpp::AbstractTransitionModel::getModelStates(), bpp::AbstractTransitionModel::getNumberOfStates(), bpp::AbstractTransitionModel::getStateMap(), and bpp::AbstractTransitionModel::stateMap().

◆ tmpMat_

RowMatrix<double> bpp::AbstractSubstitutionModel::tmpMat_

mutableprotectedinherited

For computational issues.

Definition at line 357 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ verboseLevel_

short bpp::AbstractTransitionModel::verboseLevel_

protectedinherited

Definition at line 152 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractTransitionModel::setVerboseLevel(), bpp::AbstractSubstitutionModel::updateMatrices_(), and bpp::AbstractTransitionModel::verboseLevel().

◆ vGenerators_

std::vector< RowMatrix<double> > bpp::AbstractKroneckerWordSubstitutionModel::vGenerators_

private

vector of generators for computation purposes

Definition at line 59 of file AbstractKroneckerWordSubstitutionModel.h.

Referenced by fillBasicGenerator_(), initGenerators_(), and operator=().

◆ VnestedPrefix_

std::vector<std::string> bpp::AbstractWordSubstitutionModel::VnestedPrefix_

protectedinherited

Definition at line 117 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractKroneckerCodonSubstitutionModel::AbstractKroneckerCodonSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::AbstractWordSubstitutionModel::setNamespace(), and bpp::TripletSubstitutionModel::TripletSubstitutionModel().

◆ vPowGen_

std::vector< RowMatrix<double> > bpp::AbstractSubstitutionModel::vPowGen_

protectedinherited

vector of the powers of generator_ for Taylor development (if rightEigenVectors_ is singular).

Definition at line 352 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::getd2Pij_dt2(), bpp::AbstractSubstitutionModel::getdPij_dt(), bpp::AbstractSubstitutionModel::getPij_t(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::updateMatrices_(), bpp::gBGC::updateMatrices_(), bpp::RN95::updateMatrices_(), bpp::RN95s::updateMatrices_(), and bpp::YpR::updateMatrices_().

◆ Vrate_

std::vector<double> bpp::AbstractWordSubstitutionModel::Vrate_

protectedinherited

Definition at line 119 of file AbstractWordSubstitutionModel.h.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractWordSubstitutionModel::fillBasicGenerator_(), bpp::WordSubstitutionModel::getd2Pij_dt2(), bpp::WordSubstitutionModel::getdPij_dt(), bpp::WordSubstitutionModel::getPij_t(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::TripletSubstitutionModel::TripletSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::updateMatrices_(), and bpp::WordSubstitutionModel::updateMatrices_().

◆ VSubMod_

std::vector<std::shared_ptr<SubstitutionModelInterface> > bpp::AbstractWordSubstitutionModel::VSubMod_

protectedinherited

Vector of shared_ptr, to allow multiple positions to share the same model.

Definition at line 115 of file AbstractWordSubstitutionModel.h.

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

Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.h
Bpp/Phyl/Model/AbstractKroneckerWordSubstitutionModel.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AbstractKroneckerWordSubstitutionModel() [1/6]

◆ AbstractKroneckerWordSubstitutionModel() [2/6]

◆ AbstractKroneckerWordSubstitutionModel() [3/6]

◆ AbstractKroneckerWordSubstitutionModel() [4/6]

◆ ~AbstractKroneckerWordSubstitutionModel()

◆ AbstractKroneckerWordSubstitutionModel() [5/6]

◆ AbstractKroneckerWordSubstitutionModel() [6/6]

Member Function Documentation

◆ addRateParameter()

◆ alphabet()

◆ checkChangingPositions_()

◆ clone() [1/2]

◆ clone() [2/2]

◆ completeMatrices_()

◆ computeFrequencies() [1/2]

◆ computeFrequencies() [2/2]

◆ d2Lik_dt2()

◆ d2Pij_dt2()

◆ dLik_dt()

◆ dPij_dt()

◆ enableEigenDecomposition() [1/2]

◆ enableEigenDecomposition() [2/2]

◆ exchangeabilityMatrix()

◆ fillBasicGenerator_()

◆ fireParameterChanged()

◆ freq()

◆ frequencySet()

◆ generator()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getColumnRightEigenVectors()

◆ getd2Pij_dt2()

◆ getdPij_dt()

◆ getEigenValues()

◆ getFrequencies()

◆ getFrequencies_()

◆ getIEigenValues()

◆ getInitValue()

◆ getModelStates() [1/2]

◆ getModelStates() [2/2]

◆ getName()

◆ getNumberOfModels()

◆ getNumberOfStates()

◆ getPij_t()

◆ getRate()

◆ getRowLeftEigenVectors()

◆ getScale()

◆ getStateMap()

◆ initGenerators_()

◆ isDiagonalizable()

◆ isNonSingular()

◆ isScalable()

◆ Lik_t()

◆ nModel()

◆ normalize()

◆ operator=()

◆ Pij_t()

◆ Qij()

◆ setChangingPositions()

◆ setDiagonal()

◆ setFreq()

◆ setFreqFromData()

◆ setNamespace()

◆ setRate()

◆ setScalable()

◆ setScale()

◆ setVerboseLevel()

◆ Sij()

◆ stateMap()

◆ updateMatrices_()

◆ verboseLevel()