The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004). More...

#include <Bpp/Phyl/Model/Codon/YNGKP_M1.h>

Inheritance diagram for bpp::YNGKP_M1:

Collaboration diagram for bpp::YNGKP_M1:

Public Member Functions
	YNGKP_M1 (const GeneticCode gc, FrequenciesSet codonFreqs)

virtual	~YNGKP_M1 ()

YNGKP_M1 *	clone () const

	YNGKP_M1 (const YNGKP_M1 &)

YNGKP_M1 &	operator= (const YNGKP_M1 &)

const SubstitutionModel &	getModel () const

const MixedSubstitutionModel &	getMixedModel () const

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

const SubstitutionModel *	getNModel (size_t i) const
	Returns a specific model from the mixture. More...

SubstitutionModel *	getNModel (size_t i)

double	getNProbability (size_t i) const
	Returns the probability of a specific model from the mixture. More...

const std::vector< double > &	getProbabilities () const
	Returns the vector of the probabilities of the submodels of the mixture. More...

void	setNProbability (size_t i, double prob)
	Sets the probabilities of the submodels of the mixture. More...

size_t	getNumberOfModels () const
	Returns the number of submodels. More...

void	setVRates (const Vdouble &vd)
	sets the rates of the submodels. More...

void	normalizeVRates ()
	normalizes the rates of the submodels. More...

const std::vector< double > &	getVRates () const
	Returns the vector of all the rates of the mixture. More...

double	getNRate (size_t i) const
	Returns the rate of a specific model from the mixture. More...

Vint	getSubmodelNumbers (std::string &desc) const

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

const std::vector< int > &	getAlphabetChars () const

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

int	getAlphabetChar (size_t i) const
	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...

std::vector< size_t >	getModelStates (int i) const
	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	freq (size_t i) const

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

virtual double	Qij (size_t i, size_t j) const

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

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

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

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

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

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

virtual const Vdouble &	getFrequencies () const =0

virtual const Vdouble &	getFrequencies () const

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

const Matrix< double > &	getGenerator () const

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

const Matrix< double > &	getExchangeabilityMatrix () const

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

double	Sij (size_t i, size_t j) const

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

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

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

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

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

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

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...

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

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

virtual const Vdouble &	getEigenValues () const =0

const Vdouble &	getEigenValues () const

virtual const Vdouble &	getIEigenValues () const =0

const Vdouble &	getIEigenValues () const

virtual bool	isDiagonalizable () const =0

bool	isDiagonalizable () const

virtual bool	isNonSingular () const =0

bool	isNonSingular () const

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

const Matrix< double > &	getRowLeftEigenVectors () const

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

const Matrix< double > &	getColumnRightEigenVectors () const

virtual const Alphabet *	getAlphabet () const =0

const Alphabet *	getAlphabet () const

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

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

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

double	getInitValue (size_t i, int state) const throw (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...

double	getScale () const
	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...

void	setScale (double scale)
	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...

double	getRate () const
	Get the rate. More...

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

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

virtual void	addRateParameter ()=0

void	addRateParameter ()

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

void	setFreqFromData (const SequenceContainer &data, double pseudoCount=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...

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

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

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

size_t	getNumberOfIndependentParameters () const

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

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

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

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

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

void	setNamespace (const std::string &prefix)

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

const ParameterList &	getParameters () const

const Parameter &	getParameter (const std::string &name) const

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

void	setAllParametersValues (const ParameterList &parameters)

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

void	setParametersValues (const ParameterList &parameters)

bool	matchParametersValues (const ParameterList &parameters)

size_t	getNumberOfParameters () const

std::string	getNamespace () const

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

Protected Member Functions
void	updateMatrices ()

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	resetParameters_ ()

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

ParameterList &	getParameters_ ()

Protected Attributes
std::map< std::string, std::string >	mapParNamesFromPmodel_
	Tools to make the link between the Parameters of the object and those of pmixmodel_. More...

ParameterList	lParPmodel_

Private Member Functions
SubstitutionModel &	getModel ()

MixedSubstitutionModel &	getMixedModel ()

Private Attributes
std::auto_ptr < MixtureOfASubstitutionModel >	pmixmodel_

int	synfrom_

int	synto_

Detailed Description

The Yang et al (2000) M1 substitution model for codons, with the more realistic modification in Wong & al (2004).

Author: Laurent Guéguen

This model is a mixture of models as described in YN98 class, the mixture being defined on the selection parameter to allow it to vary among sites. A site is either negatively selected $0 < \omega_0 < 1$ (with probability $p_0 $ ), or neutral ( $\omega_1 = 1$ ) with probability $1-p_0 $ .

The synonymous rates must be the same between both models, so the overall rates of the models are modified to respect this constraint and such that the mean rate of the mixed model equals one.

This model includes 3 parameters ( $\kappa$ , $ p0 $ and $\omega$ ). The codon frequencies $\pi_j$ are either observed or infered.

References:

Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen (2000) Genetics 155:431-449.

Wong, W. S. W., Z. Yang, N. Goldman, and R. Nielsen. (2004) Genetics 168:1041–1051.

Definition at line 79 of file YNGKP_M1.h.

Constructor & Destructor Documentation

YNGKP_M1::YNGKP_M1	(	const GeneticCode *	gc,
		FrequenciesSet *	codonFreqs
	)

Definition at line 51 of file YNGKP_M1.cpp.

Referenced by clone().

YNGKP_M1::~YNGKP_M1 ( )

virtual

Definition at line 140 of file YNGKP_M1.cpp.

YNGKP_M1::YNGKP_M1 ( const YNGKP_M1 & mod2 )

Definition at line 123 of file YNGKP_M1.cpp.

Member Function Documentation

void AbstractBiblioSubstitutionModel::addRateParameter ( )

virtualinherited

Implements bpp::SubstitutionModel.

Definition at line 84 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractParameterAliasable::getNamespace(), bpp::AbstractParameterAliasable::getParameters(), bpp::AbstractBiblioSubstitutionModel::getRate(), bpp::AbstractBiblioSubstitutionModel::lParPmodel_, bpp::AbstractBiblioSubstitutionModel::lParPmodel_, and bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_.

virtual void bpp::SubstitutionModel::addRateParameter ( )

pure virtualinherited

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

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

YNGKP_M1* bpp::YNGKP_M1::clone ( ) const

inlinevirtual

Implements bpp::AbstractBiblioMixedSubstitutionModel.

Definition at line 100 of file YNGKP_M1.h.

References YNGKP_M1().

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

inlinevirtualinherited

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::SubstitutionModel.

Definition at line 106 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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

inlinevirtualinherited

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::SubstitutionModel.

Definition at line 105 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

inlinevirtualinherited

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 122 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

bool bpp::AbstractBiblioSubstitutionModel::enableEigenDecomposition ( )

inlinevirtualinherited

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 124 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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 void bpp::AbstractBiblioSubstitutionModel::fireParameterChanged ( const ParameterList & parameters )

inlinevirtualinherited

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 171 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::AbstractParameterAliasable::getNamespace(), bpp::ParameterList::size(), bpp::ParameterList::size(), and bpp::AbstractBiblioSubstitutionModel::updateMatrices().

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

inlinevirtualinherited

Returns: Equilibrium frequency associated to character i.

See Also: getFrequencies(), getStates()

Implements bpp::SubstitutionModel.

Definition at line 100 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

const Alphabet* bpp::AbstractBiblioSubstitutionModel::getAlphabet ( ) const

inlinevirtualinherited

Returns: Get the alphabet associated to this model.

Implements bpp::SubstitutionModel.

Definition at line 147 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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.

int bpp::AbstractBiblioSubstitutionModel::getAlphabetChar ( size_t i ) const

inlinevirtualinherited

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()

Implements bpp::SubstitutionModel.

Definition at line 96 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

inlinevirtualinherited

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

See Also: Alphabet

Implements bpp::SubstitutionModel.

Definition at line 94 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

inlinevirtualinherited

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

Implements bpp::SubstitutionModel.

Definition at line 135 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

inlinevirtualinherited

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::SubstitutionModel.

Definition at line 120 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

inlinevirtualinherited

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::SubstitutionModel.

Definition at line 118 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

inlinevirtualinherited

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

Implements bpp::SubstitutionModel.

Definition at line 130 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

Definition at line 112 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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::AbstractBiblioSubstitutionModel::getFrequencies ( ) const

inlinevirtualinherited

Returns: A vector of all equilibrium frequencies.

See Also: freq()

Implements bpp::SubstitutionModel.

Definition at line 108 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

const FrequenciesSet* bpp::AbstractBiblioSubstitutionModel::getFrequenciesSet ( ) const

inlinevirtualinherited

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

Reimplemented from bpp::SubstitutionModel.

Definition at line 153 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

Referenced by YNGKP_M1(), bpp::YNGKP_M2::YNGKP_M2(), bpp::YNGKP_M3::YNGKP_M3(), bpp::YNGKP_M7::YNGKP_M7(), and bpp::YNGKP_M8::YNGKP_M8().

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().

const Matrix<double>& bpp::AbstractBiblioSubstitutionModel::getGenerator ( ) 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. 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()

Implements bpp::SubstitutionModel.

Definition at line 110 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

inlinevirtualinherited

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

Implements bpp::SubstitutionModel.

Definition at line 132 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

double bpp::AbstractBiblioSubstitutionModel::getInitValue	(	size_t	i,
		int	state
	)		const throw (BadIntException)

inlinevirtualinherited

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();

Implements bpp::SubstitutionModel.

Definition at line 151 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

const MixedSubstitutionModel& bpp::YNGKP_M1::getMixedModel ( ) const

inlinevirtual

Implements bpp::AbstractBiblioMixedSubstitutionModel.

Definition at line 112 of file YNGKP_M1.h.

References pmixmodel_.

MixedSubstitutionModel& bpp::YNGKP_M1::getMixedModel ( )

inlineprivatevirtual

Implements bpp::AbstractBiblioMixedSubstitutionModel.

Definition at line 119 of file YNGKP_M1.h.

References pmixmodel_.

const SubstitutionModel& bpp::YNGKP_M1::getModel ( ) const

inlinevirtual

Implements bpp::AbstractBiblioSubstitutionModel.

Definition at line 110 of file YNGKP_M1.h.

References pmixmodel_.

SubstitutionModel& bpp::YNGKP_M1::getModel ( )

inlineprivatevirtual

Implements bpp::AbstractBiblioSubstitutionModel.

Definition at line 117 of file YNGKP_M1.h.

References pmixmodel_.

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

inlinevirtualinherited

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.

Implements bpp::SubstitutionModel.

Definition at line 98 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

std::string bpp::YNGKP_M1::getName ( ) const

inlinevirtual

Get the name of the model.

Returns: The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 114 of file YNGKP_M1.h.

const SubstitutionModel* bpp::AbstractBiblioMixedSubstitutionModel::getNModel ( size_t i ) const

inlinevirtualinherited

Returns a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 77 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel().

SubstitutionModel* bpp::AbstractBiblioMixedSubstitutionModel::getNModel ( size_t i )

inlinevirtualinherited

Implements bpp::MixedSubstitutionModel.

Definition at line 82 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel().

double bpp::AbstractBiblioMixedSubstitutionModel::getNProbability ( size_t i ) const

inlinevirtualinherited

Returns the probability of a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 90 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel().

double bpp::AbstractBiblioMixedSubstitutionModel::getNRate ( size_t i ) const

inlinevirtualinherited

Returns the rate of a specific model from the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 154 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel().

size_t bpp::AbstractBiblioMixedSubstitutionModel::getNumberOfModels ( ) const

inlinevirtualinherited

Returns the number of submodels.

Implements bpp::MixedSubstitutionModel.

Definition at line 119 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel().

size_t bpp::AbstractBiblioSubstitutionModel::getNumberOfStates ( ) const

inlinevirtualinherited

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.

Definition at line 149 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

inlinevirtualinherited

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

See Also: Pij_t()

Implements bpp::SubstitutionModel.

Definition at line 116 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

const std::vector<double>& bpp::AbstractBiblioMixedSubstitutionModel::getProbabilities ( ) const

inlinevirtualinherited

Returns the vector of the probabilities of the submodels of the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 101 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel().

double bpp::AbstractBiblioSubstitutionModel::getRate ( ) const

inlinevirtualinherited

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 137 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

Referenced by bpp::AbstractBiblioSubstitutionModel::addRateParameter(), bpp::LGL08_CAT::LGL08_CAT(), bpp::LLG08_EHO::LLG08_EHO(), bpp::LLG08_EX2::LLG08_EX2(), bpp::LLG08_EX3::LLG08_EX3(), bpp::LLG08_UL2::LLG08_UL2(), and bpp::LLG08_UL3::LLG08_UL3().

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().

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

inlinevirtualinherited

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

Implements bpp::SubstitutionModel.

Definition at line 134 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

double bpp::AbstractBiblioSubstitutionModel::getScale ( ) const

inlinevirtualinherited

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.

Implements bpp::SubstitutionModel.

Definition at line 184 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

Vint AbstractBiblioMixedSubstitutionModel::getSubmodelNumbers ( std::string & desc ) const

virtualinherited

Implements bpp::MixedSubstitutionModel.

Definition at line 62 of file AbstractBiblioMixedSubstitutionModel.cpp.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), and bpp::StringTokenizer::nextToken().

const std::vector<double>& bpp::AbstractBiblioMixedSubstitutionModel::getVRates ( ) const

inlinevirtualinherited

Returns the vector of all the rates of the mixture.

Implements bpp::MixedSubstitutionModel.

Definition at line 146 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel().

bool bpp::AbstractBiblioSubstitutionModel::isDiagonalizable ( ) const

inlinevirtualinherited

Returns: True if the model is diagonalizable in R.

Implements bpp::SubstitutionModel.

Definition at line 126 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

bool bpp::AbstractBiblioSubstitutionModel::isNonSingular ( ) const

inlinevirtualinherited

Returns: True is the model is non-singular.

Implements bpp::SubstitutionModel.

Definition at line 128 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

void bpp::AbstractBiblioMixedSubstitutionModel::normalizeVRates ( )

inlinevirtualinherited

normalizes the rates of the submodels.

Implements bpp::MixedSubstitutionModel.

Definition at line 137 of file AbstractBiblioMixedSubstitutionModel.h.

References bpp::AbstractBiblioMixedSubstitutionModel::getMixedModel().

YNGKP_M1 & YNGKP_M1::operator= ( const YNGKP_M1 & mod2 )

Definition at line 129 of file YNGKP_M1.cpp.

References bpp::AbstractBiblioSubstitutionModel::operator=(), pmixmodel_, pmixmodel_, synfrom_, synfrom_, synto_, and synto_.

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

inlinevirtualinherited

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

See Also: getPij_t(), getStates()

Implements bpp::SubstitutionModel.

Definition at line 104 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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::AbstractBiblioSubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const

inlinevirtualinherited

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

See Also: getStates();

Implements bpp::SubstitutionModel.

Definition at line 102 of file AbstractBiblioSubstitutionModel.h.

References bpp::AbstractBiblioSubstitutionModel::getModel().

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().

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

virtualinherited

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

Reimplemented from bpp::SubstitutionModel.

Definition at line 95 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, and bpp::AbstractParameterAliasable::matchParametersValues().

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().

void AbstractBiblioSubstitutionModel::setFreqFromData	(	const SequenceContainer &	data,
		double	pseudoCount = `0`
	)

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

Implements bpp::SubstitutionModel.

Definition at line 110 of file AbstractBiblioSubstitutionModel.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractBiblioSubstitutionModel::getModel(), bpp::AbstractParameterAliasable::getParameterNameWithoutNamespace(), bpp::AbstractParameterAliasable::getParameterValue(), bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, bpp::AbstractBiblioSubstitutionModel::mapParNamesFromPmodel_, and bpp::AbstractParameterAliasable::matchParametersValues().

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

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

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