The Strand Symmetric Reversible substitution model for nucleotides. More...

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

Inheritance diagram for bpp::SSR:

Collaboration diagram for bpp::SSR:

Public Member Functions
	SSR (const NucleicAlphabet *alpha, double beta=1., double gamma=1., double delta=1., double theta=0.5)

virtual	~SSR ()

SSR *	clone () const

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

void	updateMatrices ()
	Compute and diagonalize the matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices. More...

void	setFreq (std::map< int, double > &)
	This method is redefined to actualize the corresponding parameters theta too. More...

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

const Alphabet *	getAlphabet () const

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

int	getAlphabetChar (size_t i) const
	Get the char in the alphabet corresponding to a given state in the model. 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 const Vdouble &	getFrequencies () const

const Matrix< double > &	getGenerator () const

const Matrix< double > &	getExchangeabilityMatrix () const

double	Sij (size_t i, size_t j) const

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

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

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

const Vdouble &	getEigenValues () const

const Vdouble &	getIEigenValues () const

bool	isDiagonalizable () const

bool	isNonSingular () const

const Matrix< double > &	getRowLeftEigenVectors () const

const Matrix< double > &	getColumnRightEigenVectors () const

virtual double	freq (size_t i) const

virtual double	Qij (size_t i, size_t j) const

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

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

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

void	setFreqFromData (const SequenceContainer &data, double pseudoCount=0)
	Set equilibrium frequencies equal to the frequencies estimated from the data. 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 void	fireParameterChanged (const ParameterList &parameters)
	Tells the model that a parameter value has changed. More...

void	addRateParameter ()

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...

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
	Get the rate. More...

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

size_t	getNumberOfIndependentParameters () const

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

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

const ParameterList &	getIndependentParameters () const

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

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	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
const Alphabet *	alphabet_
	The alphabet relevant to this model. More...

size_t	size_
	The size of the generator, i.e. the number of states. More...

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

std::vector< int >	chars_
	The list of supported chars. More...

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

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

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

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

RowMatrix< double >	dpijt_

RowMatrix< double >	d2pijt_

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

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

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

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

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

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

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

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

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

Private Attributes
double	beta_

double	gamma_

double	delta_

double	theta_

double	piA_

double	piC_

double	piG_

double	piT_

Detailed Description

The Strand Symmetric Reversible substitution model for nucleotides.

We use a parametrization derived from Hobolth et al 2007

$S = \begin{pmatrix} \cdots & \beta & 1 & \gamma \\ \beta & \cdots & \delta & 1 \\ 1 & \delta & \cdots & \beta \\ \gamma & 1 & \beta & \cdots \\ \end{pmatrix}$

The equilibrium frequencies

$\pi = \left(1-\frac{\theta}{2}, \frac{\theta}{2}, \frac{\theta}{2}, 1-\frac{\theta}{2}\right)$

This models hence includes four parameters, three relative rates $\beta, \gamma, \delta$ and the GC content $\theta$ .

Normalization: we set $f$ to 1, and scale the matrix so that $\sum_i Q_{i,i}\pi_i = -1$ . The normalized generator is obtained by taking the dot product of $S$ and $\pi$ :

$Q = S . \pi = \frac{1}{P}\begin{pmatrix} -\gamma\pi_T-\pi_G-\beta\pi_C & \beta\pi_C & \pi_G & \gamma\pi_T \\ \beta\pi_A & -\pi_T-\delta\pi_G-\beta\pi_A & \delta\pi_G & \pi_T \\ \pi_A & \delta\pi_C & -\beta\pi_T-\delta\pi_C-\pi_A & \beta\pi_T \\ \gamma\pi_A & \pi_C & \beta\pi_G & -\beta\pi_G-\pi_C-\gamma\pi_A \\ \end{pmatrix}$

where P is the normalization constant. For now, the generator of this model is diagonalized numericaly. See AbstractSubstitutionModel for details of how the probabilities are computed.

The parameters are named "beta", "gamma", "delta", and "theta" and their values may be retrieved with the command

getParameterValue("beta")

for instance.

Reference:

Hobolth A, Christensen O Fm Mailund T, Schierup M H (2007), PLoS_ Genetics_ 3(2) e7.
Yap VB, Speed TP (1995), Journal_ Of Molecular Evolution_ 58(1) 12-18

Definition at line 98 of file SSR.h.

Constructor & Destructor Documentation

SSR::SSR	(	const NucleicAlphabet *	alpha,
		double	beta = `1.`,
		double	gamma = `1.`,
		double	delta = `1.`,
		double	theta = `0.5`
	)

Definition at line 55 of file SSR.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameter_(), and updateMatrices().

Referenced by clone().

virtual bpp::SSR::~SSR ( )

inlinevirtual

Definition at line 112 of file SSR.h.

Member Function Documentation

void AbstractSubstitutionModel::addRateParameter ( )

virtualinherited

Implements bpp::SubstitutionModel.

Definition at line 434 of file AbstractSubstitutionModel.cpp.

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

virtual void bpp::SubstitutionModel::addRateParameter ( )

pure virtualinherited

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

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

SSR* bpp::SSR::clone ( ) const

inlinevirtual

Implements bpp::AbstractReversibleSubstitutionModel.

Definition at line 119 of file SSR.h.

References SSR().

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::AbstractSubstitutionModel::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.

Reimplemented in bpp::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 280 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getd2Pij_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 double bpp::AbstractSubstitutionModel::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.

Reimplemented in bpp::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 279 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getdPij_dt().

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

inlinevirtualinherited

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 288 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

bool bpp::AbstractSubstitutionModel::enableEigenDecomposition ( )

inlinevirtualinherited

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModel.

Definition at line 290 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenDecompose_.

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::AbstractSubstitutionModel::fireParameterChanged ( const ParameterList & parameters )

inlinevirtualinherited

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Reimplemented in bpp::JCprot, bpp::YpR, bpp::RE08, bpp::CodonDistanceFrequenciesSubstitutionModel, bpp::CodonDistancePhaseFrequenciesSubstitutionModel, bpp::CodonDistanceFitnessPhaseFrequenciesSubstitutionModel, bpp::CodonDistanceSubstitutionModel, bpp::UserProteinSubstitutionModel, bpp::WAG01, bpp::DSO78, bpp::JTT92, bpp::LG08, bpp::gBGC, bpp::CodonRateFrequenciesSubstitutionModel, and bpp::CodonRateSubstitutionModel.

Definition at line 297 of file AbstractSubstitutionModel.h.

References bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::SubstitutionModel::getName(), bpp::ParameterList::size(), and bpp::AbstractSubstitutionModel::updateMatrices().

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 double bpp::AbstractSubstitutionModel::freq ( size_t i ) const

inlinevirtualinherited

Returns: Equilibrium frequency associated to character i.

See Also: getFrequencies(), getStates()

Implements bpp::SubstitutionModel.

Definition at line 274 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

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

inlinevirtualinherited

Returns: Get the alphabet associated to this model.

Implements bpp::SubstitutionModel.

Definition at line 242 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::alphabet_.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::WordSubstitutionModel::completeMatrices(), bpp::AbstractWordSubstitutionModel::extractAlph(), bpp::AbstractWordSubstitutionModel::getNumberOfStates(), and bpp::AbstractWordSubstitutionModel::operator=().

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().

int bpp::AbstractSubstitutionModel::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 246 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::chars_.

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 std::vector<int>& bpp::AbstractSubstitutionModel::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 244 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::chars_.

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

inlinevirtualinherited

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

Implements bpp::SubstitutionModel.

Definition at line 272 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::rightEigenVectors_.

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 > & AbstractSubstitutionModel::getd2Pij_dt2 ( double t ) const

virtualinherited

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

See Also: d2Pij_dt2()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 275 of file AbstractSubstitutionModel.cpp.

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

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 > & AbstractSubstitutionModel::getdPij_dt ( double t ) const

virtualinherited

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

See Also: dPij_dt()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 206 of file AbstractSubstitutionModel.cpp.

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

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::AbstractSubstitutionModel::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 262 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::eigenValues_.

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::AbstractSubstitutionModel::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 254 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

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::AbstractSubstitutionModel::getFrequencies ( ) const

inlinevirtualinherited

Returns: A vector of all equilibrium frequencies.

See Also: freq()

Implements bpp::SubstitutionModel.

Definition at line 250 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::freq_.

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().

const Matrix<double>& bpp::AbstractSubstitutionModel::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 252 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

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::AbstractSubstitutionModel::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 264 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::iEigenValues_.

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 AbstractSubstitutionModel::getInitValue	(	size_t	i,
		int	state
	)		const throw (IndexOutOfBoundsException, BadIntException)

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();

Implements bpp::SubstitutionModel.

Reimplemented in bpp::RE08.

Definition at line 350 of file AbstractSubstitutionModel.cpp.

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().

std::vector<size_t> bpp::AbstractSubstitutionModel::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 248 of file AbstractSubstitutionModel.h.

References bpp::VectorTools::whichAll().

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

inlinevirtual

Get the name of the model.

Returns: The name of this model.

Implements bpp::SubstitutionModel.

Definition at line 122 of file SSR.h.

virtual size_t bpp::NucleotideSubstitutionModel::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.

Reimplemented in bpp::gBGC.

Definition at line 68 of file NucleotideSubstitutionModel.h.

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

virtualinherited

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

See Also: Pij_t()

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel, bpp::F84, bpp::HKY85, bpp::JCprot, bpp::T92, bpp::K80, bpp::RN95, bpp::TN93, bpp::RE08, bpp::JCnuc, bpp::RN95s, bpp::BinarySubstitutionModel, and bpp::WordSubstitutionModel.

Definition at line 135 of file AbstractSubstitutionModel.cpp.

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

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().

double AbstractSubstitutionModel::getRate ( ) const

virtualinherited

Get the rate.

Implements bpp::SubstitutionModel.

Definition at line 416 of file AbstractSubstitutionModel.cpp.

References bpp::AbstractSubstitutionModel::rate_.

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::AbstractSubstitutionModel::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 270 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::leftEigenVectors_.

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 AbstractSubstitutionModel::getScale ( ) const

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.

Implements bpp::SubstitutionModel.

Definition at line 401 of file AbstractSubstitutionModel.cpp.

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

Referenced by bpp::AbstractReversibleSubstitutionModel::updateMatrices().

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().

bool bpp::AbstractSubstitutionModel::isDiagonalizable ( ) const

inlinevirtualinherited

Returns: True if the model is diagonalizable in R.

Implements bpp::SubstitutionModel.

Definition at line 266 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isDiagonalizable_.

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::AbstractSubstitutionModel::isNonSingular ( ) const

inlinevirtualinherited

Returns: True is the model is non-singular.

Implements bpp::SubstitutionModel.

Definition at line 268 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::isNonSingular_.

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::AbstractSubstitutionModel::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.

Reimplemented in bpp::RE08, bpp::JCnuc, and bpp::BinarySubstitutionModel.

Definition at line 278 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::getPij_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 double bpp::AbstractSubstitutionModel::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.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 276 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::generator_.

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

virtual

This method is redefined to actualize the corresponding parameters theta too.

Reimplemented from bpp::AbstractSubstitutionModel.

Definition at line 111 of file SSR.cpp.

References piC_, piG_, piG_, bpp::AbstractParameterAliasable::setParameterValue(), and updateMatrices().

void AbstractSubstitutionModel::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 367 of file AbstractSubstitutionModel.cpp.

References bpp::SequenceContainerTools::getCounts(), bpp::AbstractSubstitutionModel::setFreq(), bpp::AbstractSubstitutionModel::size_, and bpp::AbstractSubstitutionModel::size_.

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().

void AbstractSubstitutionModel::setRate ( double rate )

virtualinherited

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

Parameters

rate	must be positive.

Implements bpp::SubstitutionModel.

Reimplemented in bpp::AbstractMixedSubstitutionModel.

Definition at line 423 of file AbstractSubstitutionModel.cpp.

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

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

virtual void bpp::SubstitutionModel::setRate ( double rate )

pure virtualinherited

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

Parameters

rate	must be positive.

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

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

void AbstractSubstitutionModel::setScale ( double scale )

virtualinherited

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

Implements bpp::SubstitutionModel.

Definition at line 410 of file AbstractSubstitutionModel.cpp.

References bpp::MatrixTools::scale().

virtual void bpp::SubstitutionModel::setScale ( double scale )

pure virtualinherited

Set the rate of the generator, defined as the scalar product of diagonal elements of the generator and the frequencies vector.

When the generator is normalized, scale=1. Otherwise each element is multiplied such that the correct scale is set.

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

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

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

inlinevirtualinherited

Returns: The exchangeability between state i and state j.

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

Implements bpp::SubstitutionModel.

Definition at line 256 of file AbstractSubstitutionModel.h.

References bpp::AbstractSubstitutionModel::exchangeability_.

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

pure virtualinherited

Returns: The exchangeability between state i and state j.

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

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

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

void SSR::updateMatrices ( )

virtual

Compute and diagonalize the $Q$ matrix, and fill the eigenValues_, leftEigenVectors_ and rightEigenVectors_ matrices.

The exchangeability_ matrix and freq_ vector must be initialized. This function computes the generator_ matrix with the formula

$Q = S \times \pi$

where $Q$ is the generator matrix, $S$ is the exchangeability matrix and $Pi$ the diagonal matrix with frequencies.

The generator is then scaled so that

$\sum_i Q_{i,i} \times \pi_i = -1$

( $\pi_i$ are the equilibrium frequencies).

Eigen values and vectors are computed from the scaled generator and assigned to the eigenValues_, rightEigenVectors_ and leftEigenVectors_ variables.

Reimplemented from bpp::AbstractReversibleSubstitutionModel.

Definition at line 76 of file SSR.cpp.

Referenced by setFreq(), and SSR().

Member Data Documentation

const Alphabet* bpp::AbstractSubstitutionModel::alphabet_

protectedinherited

The alphabet relevant to this model.

Definition at line 84 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractWordSubstitutionModel::AbstractWordSubstitutionModel(), bpp::AbstractCodonSubstitutionModel::completeMatrices(), bpp::AbstractSubstitutionModel::getAlphabet(), bpp::AbstractWordSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), and bpp::AbstractWordSubstitutionModel::~AbstractWordSubstitutionModel().

double bpp::SSR::beta_

private

Definition at line 103 of file SSR.h.

Referenced by updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), and updateMatrices().

std::vector<int> bpp::AbstractSubstitutionModel::chars_

protectedinherited

The list of supported chars.

Definition at line 102 of file AbstractSubstitutionModel.h.

Referenced by bpp::AbstractSubstitutionModel::AbstractSubstitutionModel(), bpp::AbstractSubstitutionModel::getAlphabetChar(), bpp::AbstractSubstitutionModel::getAlphabetChars(), bpp::AbstractSubstitutionModel::getModelStates(), bpp::AbstractSubstitutionModel::operator=(), bpp::AbstractSubstitutionModel::operator=(), and bpp::RE08::RE08().

RowMatrix<double> bpp::AbstractSubstitutionModel::d2pijt_

mutableprotectedinherited

Definition at line 129 of file AbstractSubstitutionModel.h.

double bpp::SSR::delta_

private

Definition at line 103 of file SSR.h.

Referenced by updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), and updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::dpijt_

mutableprotectedinherited

Definition at line 128 of file AbstractSubstitutionModel.h.

bool bpp::AbstractSubstitutionModel::eigenDecompose_

protectedinherited

Tell if the eigen decomposition should be performed.

Definition at line 134 of file AbstractSubstitutionModel.h.

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

Vdouble bpp::AbstractSubstitutionModel::eigenValues_

protectedinherited

The vector of eigen values.

Definition at line 139 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::exchangeability_

protectedinherited

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

Definition at line 122 of file AbstractSubstitutionModel.h.

Vdouble bpp::AbstractSubstitutionModel::freq_

protectedinherited

The vector $\pi_e$ of equilibrium frequencies.

Definition at line 113 of file AbstractSubstitutionModel.h.

double bpp::SSR::gamma_

private

Definition at line 103 of file SSR.h.

Referenced by updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), and updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::generator_

protectedinherited

The generator matrix $Q$ of the model.

Definition at line 107 of file AbstractSubstitutionModel.h.

Vdouble bpp::AbstractSubstitutionModel::iEigenValues_

protectedinherited

The vector of the imaginary part of the eigen values.

Definition at line 144 of file AbstractSubstitutionModel.h.

bool bpp::AbstractSubstitutionModel::isDiagonalizable_

protectedinherited

boolean value for diagonalizability in R of the generator_

Definition at line 150 of file AbstractSubstitutionModel.h.

bool bpp::AbstractSubstitutionModel::isNonSingular_

protectedinherited

boolean value for non-singularity of rightEigenVectors_

Definition at line 161 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::leftEigenVectors_

protectedinherited

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

Definition at line 168 of file AbstractSubstitutionModel.h.

double bpp::SSR::piA_

private

Definition at line 103 of file SSR.h.

Referenced by updateMatrices(), updateMatrices(), updateMatrices(), and updateMatrices().

double bpp::SSR::piC_

private

Definition at line 103 of file SSR.h.

Referenced by setFreq(), setFreq(), updateMatrices(), and updateMatrices().

double bpp::SSR::piG_

private

Definition at line 103 of file SSR.h.

Referenced by setFreq(), setFreq(), updateMatrices(), updateMatrices(), updateMatrices(), and updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::pijt_

mutableprotectedinherited

These ones are for bookkeeping:

Definition at line 127 of file AbstractSubstitutionModel.h.

double bpp::SSR::piT_

private

Definition at line 103 of file SSR.h.

Referenced by updateMatrices(), updateMatrices(), updateMatrices(), and updateMatrices().

double bpp::AbstractSubstitutionModel::rate_

protectedinherited

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

Definition at line 97 of file AbstractSubstitutionModel.h.

RowMatrix<double> bpp::AbstractSubstitutionModel::rightEigenVectors_

protectedinherited

The $U^-1$ matrix made of right eigen vectors (by column).

Definition at line 155 of file AbstractSubstitutionModel.h.

size_t bpp::AbstractSubstitutionModel::size_

protectedinherited

The size of the generator, i.e. the number of states.

Definition at line 89 of file AbstractSubstitutionModel.h.

double bpp::SSR::theta_

private

Definition at line 103 of file SSR.h.

Referenced by updateMatrices(), updateMatrices(), updateMatrices(), updateMatrices(), and updateMatrices().

RowMatrix<double> bpp::AbstractSubstitutionModel::tmpMat_

mutableprotectedinherited

For computational issues.

Definition at line 182 of file AbstractSubstitutionModel.h.

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

protectedinherited

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

Definition at line 175 of file AbstractSubstitutionModel.h.

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

Bpp/Phyl/Model/Nucleotide/SSR.h
Bpp/Phyl/Model/Nucleotide/SSR.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation