Abstract class for codon models. More...

#include <Bpp/Phyl/Model/Codon/CodonSubstitutionModel.h>

Inheritance diagram for bpp::CodonSubstitutionModel:

Collaboration diagram for bpp::CodonSubstitutionModel:

Public Member Functions
	CodonSubstitutionModel ()

virtual	~CodonSubstitutionModel ()

virtual CodonSubstitutionModel *	clone () const =0

virtual double	getCodonsMulRate (size_t, size_t) const =0
	Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides. 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 size_t	getNumberOfStates () const =0
	Get the number of states. More...

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

Abstract class for codon models.

Author: Laurent Guéguen

This class aims at defining methods needed for inheriting codon.

Definition at line 57 of file CodonSubstitutionModel.h.

Constructor & Destructor Documentation

bpp::CodonSubstitutionModel::CodonSubstitutionModel ( )

inline

Definition at line 61 of file CodonSubstitutionModel.h.

virtual bpp::CodonSubstitutionModel::~CodonSubstitutionModel ( )

inlinevirtual

Definition at line 62 of file CodonSubstitutionModel.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().

virtual CodonSubstitutionModel* bpp::CodonSubstitutionModel::clone ( ) const

pure virtual

Implements bpp::SubstitutionModel.

Implemented in bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::AbstractCodonSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::CodonRateFrequenciesSubstitutionModel, and bpp::CodonRateSubstitutionModel.

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 double bpp::CodonSubstitutionModel::getCodonsMulRate	(	size_t	,
		size_t
	)		const

pure virtual

Returns the multiplicative rate specific to two codons specified by their number. The respective generator rate is this rate multiplied by the rate defined by the model defined on nucleotides.

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::SubstitutionModel::getNumberOfStates ( ) const

pure virtualinherited

Get the number of states.

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

Returns: The number of different states in the model.

Implemented in bpp::AbstractMixedSubstitutionModel, bpp::MarkovModulatedSubstitutionModel, bpp::RE08, bpp::YpR, bpp::AbstractBiblioSubstitutionModel, bpp::AbstractWordSubstitutionModel, bpp::BinarySubstitutionModel, bpp::gBGC, bpp::NucleotideSubstitutionModel, and bpp::ProteinSubstitutionModel.

Referenced by bpp::OneJumpSubstitutionCount::getAllNumbersOfSubstitutions(), bpp::AbstractBiblioSubstitutionModel::getNumberOfStates(), bpp::BranchLikelihood::initModel(), bpp::RE08::RE08(), bpp::SimpleMutationProcess::SimpleMutationProcess(), and bpp::MarkovModulatedSubstitutionModel::updateMatrices().

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