Specialisation interface for nucleotide substitution model. More...

#include <Bpp/Phyl/Model/Nucleotide/NucleotideSubstitutionModel.h>

Inheritance diagram for bpp::NucleotideSubstitutionModel:

Collaboration diagram for bpp::NucleotideSubstitutionModel:

Public Member Functions
virtual	~NucleotideSubstitutionModel ()

NucleotideSubstitutionModel *	clone () const =0

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

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

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

virtual int	getAlphabetChar (size_t i) const =0
	Get the char in the alphabet corresponding to a given state in the model. More...

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

virtual double	freq (size_t i) const =0

virtual double	Qij (size_t i, size_t j) const =0

virtual double	Pij_t (size_t i, size_t j, double t) const =0

virtual double	dPij_dt (size_t i, size_t j, double t) const =0

virtual double	d2Pij_dt2 (size_t i, size_t j, double t) const =0

virtual const Vdouble &	getFrequencies () const =0

virtual const Matrix< double > &	getGenerator () const =0

virtual const Matrix< double > &	getExchangeabilityMatrix () const =0

virtual double	Sij (size_t i, size_t j) const =0

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

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

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

virtual void	enableEigenDecomposition (bool yn)=0
	Set if eigenValues and Vectors must be computed. More...

virtual bool	enableEigenDecomposition ()=0
	Tell if eigenValues and Vectors must be computed. More...

virtual const Vdouble &	getEigenValues () const =0

virtual const Vdouble &	getIEigenValues () const =0

virtual bool	isDiagonalizable () const =0

virtual bool	isNonSingular () const =0

virtual const Matrix< double > &	getRowLeftEigenVectors () const =0

virtual const Matrix< double > &	getColumnRightEigenVectors () const =0

virtual const Alphabet *	getAlphabet () const =0

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

virtual double	getScale () const =0
	Get the scalar product of diagonal elements of the generator and the frequencies vector. If the generator is normalized, then scale=1. Otherwise each element must be multiplied by 1/scale. More...

virtual void	setScale (double scale)=0
	Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector. More...

virtual double	getRate () const =0
	Get the rate. More...

virtual void	setRate (double rate)=0
	Set the rate of the model (must be positive). More...

virtual void	addRateParameter ()=0

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

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

virtual const FrequenciesSet *	getFrequenciesSet () const
	If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0. More...

virtual size_t	getNumberOfIndependentParameters () const =0

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

Detailed Description

Specialisation interface for nucleotide substitution model.

Definition at line 54 of file NucleotideSubstitutionModel.h.

Constructor & Destructor Documentation

virtual bpp::NucleotideSubstitutionModel::~NucleotideSubstitutionModel ( )

inlinevirtual

Definition at line 58 of file NucleotideSubstitutionModel.h.

Member Function Documentation

virtual void bpp::SubstitutionModel::addRateParameter ( )

pure virtualinherited

Implemented in bpp::AbstractSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter().

NucleotideSubstitutionModel* bpp::NucleotideSubstitutionModel::clone ( ) const

pure virtual

Implements bpp::SubstitutionModel.

Implemented in bpp::HKY85, bpp::F84, bpp::T92, bpp::K80, bpp::GTR, bpp::RN95, bpp::TN93, bpp::JCnuc, bpp::RN95s, bpp::SSR, bpp::L95, and bpp::gBGC.

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

virtual double bpp::SubstitutionModel::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const

pure virtualinherited

Returns: The second order derivative of the probability of change from state i to state j with respect to time t, at time t.

See Also: getd2Pij_dt2(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::d2Pij_dt2(), and bpp::RE08::d2Pij_dt2().

virtual double bpp::SubstitutionModel::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const

pure virtualinherited

Returns: The first order derivative of the probability of change from state i to state j with respect to time t, at time t.

See Also: getdPij_dt(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::RE08::d2Pij_dt2(), bpp::AbstractBiblioSubstitutionModel::dPij_dt(), and bpp::RE08::dPij_dt().

virtual void bpp::SubstitutionModel::enableEigenDecomposition ( bool yn )

pure virtualinherited

Set if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::AbstractCodonSubstitutionModel(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition(), bpp::gBGC::gBGC(), and bpp::YpR::YpR().

virtual bool bpp::SubstitutionModel::enableEigenDecomposition ( )

pure virtualinherited

Tell if eigenValues and Vectors must be computed.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

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

pure virtualinherited

Returns: Equilibrium frequency associated to character i.

See Also: getFrequencies(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), bpp::RE08::d2Pij_dt2(), bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::RE08::dPij_dt(), bpp::AbstractBiblioSubstitutionModel::freq(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::RE08::getdPij_dt(), bpp::RE08::getPij_t(), bpp::RE08::getPij_t(), bpp::RE08::Pij_t(), bpp::RE08::Pij_t(), bpp::RE08::updateMatrices(), bpp::RE08::updateMatrices(), and bpp::RE08::updateMatrices().

virtual const Alphabet* bpp::SubstitutionModel::getAlphabet ( ) const

pure virtualinherited

Returns: Get the alphabet associated to this model.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

virtual int bpp::SubstitutionModel::getAlphabetChar ( size_t i ) const

pure virtualinherited

Get the char in the alphabet corresponding to a given state in the model.

In most cases, this method will return i.

Parameters

i	The index of the state.

Returns: The corresponding state in the alphabet.

See Also: MarkovModulatedSubstitutionModel; getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetChar(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), bpp::MarginalAncestralStateReconstruction::getAncestralSequenceForNode(), and bpp::NonHomogeneousSequenceSimulator::multipleEvolve().

virtual const std::vector<int>& bpp::SubstitutionModel::getAlphabetChars ( ) const

pure virtualinherited

Returns: The supported states of the model, as a vector of int codes.

See Also: Alphabet

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getAlphabetChars(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Matrix<double>& bpp::SubstitutionModel::getColumnRightEigenVectors ( ) const

pure virtualinherited

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getColumnRightEigenVectors(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

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

pure virtualinherited

Returns: All second order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See Also: d2Pij_dt2()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getd2Pij_dt2(), and bpp::RE08::getd2Pij_dt2().

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

pure virtualinherited

Returns: Get all first order derivatives of the probability of change from state i to state j with respect to time t, at time t.

See Also: dPij_dt()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::RE08::getd2Pij_dt2(), bpp::AbstractBiblioSubstitutionModel::getdPij_dt(), and bpp::RE08::getdPij_dt().

virtual const Vdouble& bpp::SubstitutionModel::getEigenValues ( ) const

pure virtualinherited

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), bpp::AbstractBiblioSubstitutionModel::getEigenValues(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Matrix<double>& bpp::SubstitutionModel::getExchangeabilityMatrix ( ) const

pure virtualinherited

Returns: The matrix of exchangeability terms. It is recommended that exchangeability matrix be normalized so that the normalized generator be obtained directly by the dot product $S . \pi$ .

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getExchangeabilityMatrix(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Vdouble& bpp::SubstitutionModel::getFrequencies ( ) const

pure virtualinherited

Returns: A vector of all equilibrium frequencies.

See Also: freq()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::AbstractBiblioSubstitutionModel::getFrequencies(), bpp::TwoTreeLikelihood::getRootFrequencies(), bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies(), bpp::NonHomogeneousSequenceSimulator::NonHomogeneousSequenceSimulator(), bpp::MarkovModulatedSubstitutionModel::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const FrequenciesSet* bpp::SubstitutionModel::getFrequenciesSet ( ) const

inlinevirtualinherited

If the model owns a FrequenciesSet, returns a pointer to it, otherwise return 0.

Reimplemented in bpp::JCprot, bpp::AbstractBiblioSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::AbstractCodonPhaseFrequenciesSubstitutionModel, and bpp::AbstractCodonFrequenciesSubstitutionModel.

Definition at line 463 of file SubstitutionModel.h.

Referenced by bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet(), and bpp::BppOSubstitutionModelFormat::write().

virtual const Matrix<double>& bpp::SubstitutionModel::getGenerator ( ) const

pure virtualinherited

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

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

See Also: Qij()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::AbstractBiblioSubstitutionModel::getGenerator(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::RE08::updateMatrices(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

virtual const Vdouble& bpp::SubstitutionModel::getIEigenValues ( ) const

pure virtualinherited

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getIEigenValues().

virtual double bpp::SubstitutionModel::getInitValue	(	size_t	i,
		int	state
	)		const throw (IndexOutOfBoundsException, BadIntException)

pure virtualinherited

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

Parameters

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

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

Exceptions

IndexOutOfBoundsException	if array position is out of range.
BadIntException	if states are not allowed in the associated alphabet.

See Also: getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getInitValue().

virtual std::vector<size_t> bpp::SubstitutionModel::getModelStates ( int i ) const

pure virtualinherited

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

Parameters

i	The alphabet char to check.

Returns: A vector of indices of model states.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getModelStates(), bpp::MarkovModulatedSubstitutionModel::getModelStates(), and bpp::MarginalAncestralStateReconstruction::recursiveMarginalAncestralStates().

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

pure virtualinherited

Get the name of the model.

Returns: The name of this model.

Referenced by bpp::AbstractCodonFitnessSubstitutionModel::AbstractCodonFitnessSubstitutionModel(), bpp::AbstractSubstitutionModel::fireParameterChanged(), bpp::gBGC::getName(), bpp::MixtureOfSubstitutionModels::getSubmodelNumbers(), bpp::BppOSubstitutionModelFormat::readMixed_(), bpp::AbstractWordSubstitutionModel::updateMatrices(), bpp::AbstractBiblioSubstitutionModel::updateMatrices(), and bpp::BppOSubstitutionModelFormat::write().

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

inlinevirtual

Get the number of states.

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

Returns: The number of different states in the model.

Implements bpp::SubstitutionModel.

Reimplemented in bpp::gBGC.

Definition at line 68 of file NucleotideSubstitutionModel.h.

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

pure virtualinherited

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

See Also: Pij_t()

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::MarkovModulatedSubstitutionModel, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, bpp::WordSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::LaplaceSubstitutionCount::computeCounts(), bpp::UniformizationSubstitutionCount::computeCounts_(), bpp::DecompositionSubstitutionCount::computeCounts_(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::RE08::getd2Pij_dt2(), bpp::RE08::getdPij_dt(), bpp::AbstractBiblioSubstitutionModel::getPij_t(), and bpp::RE08::getPij_t().

virtual double bpp::SubstitutionModel::getRate ( ) const

pure virtualinherited

Get the rate.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::G2001, bpp::AbstractBiblioSubstitutionModel, and bpp::TS98.

Referenced by bpp::AbstractBiblioSubstitutionModel::getRate(), and bpp::MarkovModulatedSubstitutionModel::getRate().

virtual const Matrix<double>& bpp::SubstitutionModel::getRowLeftEigenVectors ( ) const

pure virtualinherited

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::DecompositionSubstitutionCount::computeEigen_(), and bpp::AbstractBiblioSubstitutionModel::getRowLeftEigenVectors().

virtual double bpp::SubstitutionModel::getScale ( ) const

pure virtualinherited

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

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

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::getScale().

virtual bool bpp::SubstitutionModel::isDiagonalizable ( ) const

pure virtualinherited

Returns: True if the model is diagonalizable in R.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isDiagonalizable().

virtual bool bpp::SubstitutionModel::isNonSingular ( ) const

pure virtualinherited

Returns: True is the model is non-singular.

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::AbstractBiblioSubstitutionModel::isNonSingular().

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

pure virtualinherited

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

See Also: getPij_t(), getStates()

Implemented in bpp::AbstractSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::JCnuc, bpp::BinarySubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::RE08::d2Pij_dt2(), bpp::RE08::dPij_dt(), bpp::NonHomogeneousSequenceSimulator::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::SimpleMutationProcess::evolve(), bpp::OneJumpSubstitutionCount::getNumberOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::Pij_t(), and bpp::RE08::Pij_t().

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

pure virtualinherited

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

See Also: getStates();

Implemented in bpp::AbstractSubstitutionModel, bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, and bpp::AbstractBiblioSubstitutionModel.

Referenced by bpp::UniformizationSubstitutionCount::fillBMatrices_(), bpp::DecompositionSubstitutionCount::fillBMatrices_(), bpp::AbstractMutationProcess::getTimeBeforeNextMutationEvent(), bpp::AbstractBiblioSubstitutionModel::Qij(), bpp::UniformizationSubstitutionCount::setSubstitutionModel(), bpp::SimpleMutationProcess::SimpleMutationProcess(), bpp::UniformizationSubstitutionCount::UniformizationSubstitutionCount(), bpp::gBGC::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), bpp::YpR::updateMatrices(), and bpp::YpR::updateMatrices().

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

inlinevirtualinherited

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

Definition at line 455 of file SubstitutionModel.h.

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

virtual void bpp::SubstitutionModel::setFreqFromData	(	const SequenceContainer &	data,
		double	pseudoCount = `0`
	)

pure virtualinherited

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

Parameters

data	The sequences to use.
pseudoCount	A quantity $\psi$ to add to adjust the observed values in order to prevent issues due to missing states on small data set. The corrected frequencies shall be computed as $\pi_i = \frac{n_i+\psi}{\sum_j (f_j+\psi)}$