Partial implementation of the Markov-modulated class of substitution models. More...

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

Inheritance diagram for bpp::MarkovModulatedSubstitutionModel:

Collaboration diagram for bpp::MarkovModulatedSubstitutionModel:

Public Member Functions
	MarkovModulatedSubstitutionModel (ReversibleSubstitutionModel *model, unsigned int nbRates, bool normalizeRateChanges, const std::string &prefix)
	Build a new MarkovModulatedSubstitutionModel object. More...

	MarkovModulatedSubstitutionModel (const MarkovModulatedSubstitutionModel &model)

MarkovModulatedSubstitutionModel &	operator= (const MarkovModulatedSubstitutionModel &model)

virtual	~MarkovModulatedSubstitutionModel ()

MarkovModulatedSubstitutionModel *	clone () const =0

const Alphabet *	getAlphabet () const

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

const StateMap &	getStateMap () const

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

std::string	getAlphabetStateAsChar (size_t index) const

int	getAlphabetStateAsInt (size_t index) const

std::vector< size_t >	getModelStates (int code) const
	Get the state in the model corresponding to a particular state in the alphabet. More...

std::vector< size_t >	getModelStates (const std::string &code) const
	Get the state in the model corresponding to a particular state in the alphabet. More...

const Vdouble &	getFrequencies () const

const Matrix< double > &	getExchangeabilityMatrix () const

const Matrix< double > &	getGenerator () const

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

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

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

const Vdouble &	getEigenValues () const

const Vdouble &	getIEigenValues () const

bool	isDiagonalizable () const

bool	isNonSingular () const

const Matrix< double > &	getRowLeftEigenVectors () const

const Matrix< double > &	getColumnRightEigenVectors () const

double	freq (size_t i) const

double	Sij (size_t i, size_t j) const

double	Qij (size_t i, size_t j) const

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

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

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...

const ReversibleSubstitutionModel *	getNestedModel () const

size_t	getRate (size_t i) const
	Get the rate category corresponding to a particular state in the compound model. More...

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

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

void	setScale (double scale)
	Multiplies the current generator by the given scale. 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	setNamespace (const std::string &prefix)

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

virtual void	addRateParameter ()=0

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

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

Protected Member Functions
virtual void	updateMatrices ()

virtual void	updateRatesModel ()=0
	Update the rates vector, generator and equilibrium frequencies. More...

Protected Attributes
ReversibleSubstitutionModel *	model_

MarkovModulatedStateMap	stateMap_

size_t	nbStates_

size_t	nbRates_

RowMatrix< double >	ratesGenerator_

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

RowMatrix< double >	exchangeability_
	The exchangeability matrix of the model. More...

RowMatrix< double >	leftEigenVectors_
	The matrix made of left eigen vectors (by row). More...

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

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

Vdouble	iEigenValues_
	The vector of imaginary parts of the eigen values (zero in case of reversible pmodel). More...

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

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

RowMatrix< double >	dpijt_

RowMatrix< double >	d2pijt_

Vdouble	freq_
	The vector of equilibrium frequencies. More...

bool	normalizeRateChanges_

std::string	nestedPrefix_

Rate generator.
These variables must be initialized in the constructor of the derived class.
RowMatrix< double >	rates_

RowMatrix< double >	ratesExchangeability_

Vdouble	ratesFreq_

Detailed Description

Partial implementation of the Markov-modulated class of substitution models.

This class wraps a substitution model and provide a matrix describing rate changes. The rate matrix must be initialized by derived classes of this class. Using these matrices, the diagonalization procedure of Galtier and Jean-Marie is used.

Such models can be described using two matrices: a substitution matrix, $M$ , with size $m$ , which is a "standard" substitution model of any alphabet type, and a rate matrix $G$ of size $g$ . The generator of the markov-modulated model, $Q$ can be written using Kronecker matrix operands:

$Q=D_R \otimes M + G \otimes I_m,$

where $D_R$ is the diagonal matrix of all rates, and $I_m$ is the identity matrix of size $m$ .

This generator is normalized so that branch lengths are measured in unit of mean number of substitutions per site, where susbstitution here means "change of alphabet state". Rate changes are not counted.

Galtier N. and Jean-Marie A., Markov-modulated Markov chains and the covarion process of molecular evolution (2004). Journal of Computational Biology, 11:727-33.

Definition at line 75 of file MarkovModulatedSubstitutionModel.h.

Constructor & Destructor Documentation

◆ MarkovModulatedSubstitutionModel() [1/2]

bpp::MarkovModulatedSubstitutionModel::MarkovModulatedSubstitutionModel	(	ReversibleSubstitutionModel *	model,
		unsigned int	nbRates,
		bool	normalizeRateChanges,
		const std::string &	prefix
	)

inline

Build a new MarkovModulatedSubstitutionModel object.

Parameters

model	The substitution model to use. Can be of any alphabet type, and will be owned by this instance.
nbRates	The number of rate classes
normalizeRateChanges	Tells if the branch lengths must be computed in terms of rate and state NB: In most cases, this parameter should be set to false.
prefix	The parameter namespace to be forwarded to the AbstractParametrizable constructor. changes instead of state change only.

Definition at line 161 of file MarkovModulatedSubstitutionModel.h.

References model_, and nestedPrefix_.

◆ MarkovModulatedSubstitutionModel() [2/2]

MarkovModulatedSubstitutionModel::MarkovModulatedSubstitutionModel ( const MarkovModulatedSubstitutionModel & model )

Definition at line 51 of file MarkovModulatedSubstitutionModel.cpp.

◆ ~MarkovModulatedSubstitutionModel()

virtual bpp::MarkovModulatedSubstitutionModel::~MarkovModulatedSubstitutionModel ( )

inlinevirtual

Definition at line 178 of file MarkovModulatedSubstitutionModel.h.

References model_.

Member Function Documentation

◆ addRateParameter()

virtual void bpp::SubstitutionModel::addRateParameter ( )

pure virtualinherited

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

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

◆ clone()

MarkovModulatedSubstitutionModel* bpp::MarkovModulatedSubstitutionModel::clone ( ) const

pure virtual

Implements bpp::ReversibleSubstitutionModel.

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

◆ d2Pij_dt2()

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

inlinevirtual

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()

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

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ MarkovModulatedSubstitutionModel() [1/2]

◆ MarkovModulatedSubstitutionModel() [2/2]

◆ ~MarkovModulatedSubstitutionModel()

Member Function Documentation

◆ addRateParameter()

◆ clone()

◆ d2Pij_dt2()

◆ dPij_dt()

◆ enableEigenDecomposition() [1/2]

◆ enableEigenDecomposition() [2/2]

◆ fireParameterChanged()

◆ freq()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getColumnRightEigenVectors()

◆ getd2Pij_dt2()

◆ getdPij_dt()

◆ getEigenValues()

◆ getExchangeabilityMatrix()

◆ getFrequencies()

◆ getFrequenciesSet()

◆ getGenerator()

◆ getIEigenValues()

◆ getInitValue()

◆ getModelStates() [1/2]

◆ getModelStates() [2/2]

◆ getName()

◆ getNestedModel()

◆ getNumberOfStates()

◆ getPij_t()

◆ getRate() [1/2]

◆ getRate() [2/2]

◆ getRowLeftEigenVectors()

◆ getScale()

◆ getStateMap()

◆ isDiagonalizable()

◆ isNonSingular()

◆ operator=()

◆ Pij_t()

◆ Qij()

◆ setFreq()

◆ setFreqFromData()

◆ setNamespace()

◆ setRate()

◆ setScale()

◆ Sij()

◆ updateMatrices()

◆ updateRatesModel()

Member Data Documentation

◆ d2pijt_

◆ dpijt_

◆ eigenDecompose_

◆ eigenValues_

◆ exchangeability_

◆ freq_

◆ generator_

◆ iEigenValues_

◆ leftEigenVectors_

◆ model_

◆ nbRates_

◆ nbStates_

◆ nestedPrefix_

◆ normalizeRateChanges_

◆ pijt_

◆ rates_

◆ ratesExchangeability_

◆ ratesFreq_

◆ ratesGenerator_

◆ rightEigenVectors_

◆ stateMap_