SubModel taken from a MixedTransitionModel, kept in the context of the MixedTransitionModel (see FromMixtureSubstitutionModel for an out of context subModel). So "rate" and "scale" are set for the MixedTransitionModel. More...

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

Inheritance diagram for bpp::InMixedSubstitutionModel:

Collaboration diagram for bpp::InMixedSubstitutionModel:

Public Member Functions
	InMixedSubstitutionModel (std::unique_ptr< MixedTransitionModelInterface > mixedModel, const std::string &subModelName, const std::string &mixtDesc)

	InMixedSubstitutionModel (std::unique_ptr< MixedTransitionModelInterface > mixedModel, size_t subModelNumber, const std::string &mixtDesc)

	InMixedSubstitutionModel (const InMixedSubstitutionModel &fmsm)

InMixedSubstitutionModel &	operator= (const InMixedSubstitutionModel &fmsm)

InMixedSubstitutionModel *	clone () const override

const MixedTransitionModelInterface &	mixedModel () const

const SubstitutionModelInterface &	substitutionModel () const override

size_t	getSubModelNumber () const

bool	computeFrequencies () const override

void	computeFrequencies (bool yn) override

bool	isScalable () const override
	returns if model is scalable More...

void	setScalable (bool scalable) override
	sets if model is scalable, ie scale can be changed. Default : true, set to false to avoid normalization for example. More...

double	getScale () const override
	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) override
	Multiplies the current generator by the given scale. More...

void	normalize () override
	Normalize the generator. More...

void	setDiagonal () override
	set the diagonal of the generator such that sum on each line equals 0. More...

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

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

void	addRateParameter () override

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

const TransitionModelInterface &	transitionModel () const

const FrequencySetInterface &	frequencySet () const override

const BranchModelInterface &	model () const override

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

const ParameterList &	getIndependentParameters () const

size_t	getNumberOfIndependentParameters () const

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

void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)

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

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

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

virtual std::map< std::string, std::string >	getAliases () const

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

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

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

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

void	setAllParametersValues (const ParameterList &parameters) override

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

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

void	removeConstraint (const std::string &name) override

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override

size_t	getNumberOfParameters () const override

std::string	getNamespace () const override

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

virtual const Eigen::VectorXd &	Lik_t (const Eigen::VectorXd &values, double t) const =0

const Eigen::VectorXd &	Lik_t (const Eigen::VectorXd &values, double t) const override

virtual const Eigen::VectorXd &	dLik_dt (const Eigen::VectorXd &values, double t) const =0

const Eigen::VectorXd &	dLik_dt (const Eigen::VectorXd &values, double t) const override

virtual const Eigen::VectorXd &	d2Lik_dt2 (const Eigen::VectorXd &values, double t) const =0

const Eigen::VectorXd &	d2Lik_dt2 (const Eigen::VectorXd &values, double t) const override


double	freq (size_t i) const override

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

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

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

const Vdouble &	getFrequencies () const override

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

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

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

double	getInitValue (size_t i, int state) const override

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

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

double	Qij (size_t i, size_t j) const override
	Methods to supersede SubstitutionModel methods. More...

const Matrix< double > &	generator () const override

const Matrix< double > &	exchangeabilityMatrix () const override

double	Sij (size_t i, size_t j) const override

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

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

bool	isDiagonalizable () const override

bool	isNonSingular () const override

const Vdouble &	getEigenValues () const override

const Vdouble &	getIEigenValues () const override

const Matrix< double > &	getRowLeftEigenVectors () const override

const Matrix< double > &	getColumnRightEigenVectors () const override


void	fireParameterChanged (const ParameterList &parameters) override
	Methods to supersede AbstractSubstitutionnModel methods. More...

void	setNamespace (const std::string &name) override


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

const StateMapInterface &	stateMap () const override

std::shared_ptr< const StateMapInterface >	getStateMap () const override

int	getAlphabetStateAsInt (size_t i) const override

std::string	getAlphabetStateAsChar (size_t i) const override

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

const Alphabet &	alphabet () const override

std::shared_ptr< const Alphabet >	getAlphabet () const override

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

Protected Member Functions
Vdouble &	getFrequencies_ () override

MixedTransitionModelInterface &	mixedModel_ ()

SubstitutionModelInterface &	substitutionModel_ () override

TransitionModelInterface &	transitionModel_ ()

BranchModelInterface &	model_ ()

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

void	deleteParameters_ (const std::vector< std::string > &names)

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_ () override

Private Attributes
std::unique_ptr< MixedTransitionModelInterface >	mixedModelPtr_
	The MixedOfTransitionModels. More...

size_t	subModelNumber_
	the number of the submodel More...

std::string	mixtName_
	The name of the mixture model (for io purpose). More...

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Eigen::VectorXd	lik_

Detailed Description

SubModel taken from a MixedTransitionModel, kept in the context of the MixedTransitionModel (see FromMixtureSubstitutionModel for an out of context subModel). So "rate" and "scale" are set for the MixedTransitionModel.

But method getRate returns the specific rate of the subModel.

It owns the MixedTransitionModel.

It has the same parameters as the MixedTransitionModel.

Definition at line 28 of file InMixedSubstitutionModel.h.

Constructor & Destructor Documentation

◆ InMixedSubstitutionModel() [1/3]

InMixedSubstitutionModel::InMixedSubstitutionModel	(	std::unique_ptr< MixedTransitionModelInterface >	mixedModel,
		const std::string &	subModelName,
		const std::string &	mixtDesc
	)

Definition at line 12 of file InMixedSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), mixedModelPtr_, and subModelNumber_.

◆ InMixedSubstitutionModel() [2/3]

InMixedSubstitutionModel::InMixedSubstitutionModel	(	std::unique_ptr< MixedTransitionModelInterface >	mixedModel,
		size_t	subModelNumber,
		const std::string &	mixtDesc
	)

Definition at line 30 of file InMixedSubstitutionModel.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), mixedModelPtr_, and bpp::TextTools::toString().

◆ InMixedSubstitutionModel() [3/3]

InMixedSubstitutionModel::InMixedSubstitutionModel ( const InMixedSubstitutionModel & fmsm )

Definition at line 51 of file InMixedSubstitutionModel.cpp.

Member Function Documentation

◆ addRateParameter()

void bpp::InMixedSubstitutionModel::addRateParameter ( )

inlineoverridevirtual

Implements bpp::BranchModelInterface.

Definition at line 214 of file InMixedSubstitutionModel.h.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::BranchModelInterface::addRateParameter(), bpp::AbstractParameterAliasable::getNamespace(), getRate(), mixedModel(), mixedModel_(), and bpp::Parameter::R_PLUS_STAR.

◆ alphabet()

const Alphabet& bpp::AbstractWrappedModel::alphabet ( ) const

inlineoverridevirtualinherited

Returns: A reference to the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 53 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::alphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::alphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ clone()

InMixedSubstitutionModel* bpp::InMixedSubstitutionModel::clone ( ) const

inlineoverridevirtual

Implements bpp::SubstitutionModelInterface.

Definition at line 62 of file InMixedSubstitutionModel.h.

References bpp::AbstractLkTransitionModel::InMixedSubstitutionModel.

◆ computeFrequencies() [1/2]

bool bpp::InMixedSubstitutionModel::computeFrequencies ( ) const

inlineoverridevirtual

Returns: Says if equilibrium frequencies should be computed

Implements bpp::TransitionModelInterface.

Definition at line 80 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::computeFrequencies(), and mixedModel().

◆ computeFrequencies() [2/2]

void bpp::InMixedSubstitutionModel::computeFrequencies ( bool yn )

inlineoverridevirtual

Returns: Set if equilibrium frequencies should be computed from the generator

Implements bpp::TransitionModelInterface.

Definition at line 89 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::computeFrequencies(), and mixedModel_().

◆ d2Lik_dt2() [1/2]

virtual const Eigen::VectorXd& bpp::BranchModelInterface::d2Lik_dt2	(	const Eigen::VectorXd &	values,
		double	t
	)		const

pure virtualinherited

Implemented in bpp::AbstractLkTransitionModel, bpp::TransitionModelInterface, bpp::TransitionFromTransitionModel, and bpp::MultinomialFromTransitionModel.

◆ d2Lik_dt2() [2/2]

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::d2Lik_dt2	(	const Eigen::VectorXd &	values,
		double	t
	)		const

inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 64 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and bpp::AbstractLkTransitionModel::lik_.

◆ d2Pij_dt2()

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

inlineoverridevirtual

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::TransitionModelInterface.

Definition at line 120 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::d2Pij_dt2(), and bpp::AbstractWrappedSubstitutionModel::transitionModel().

◆ dLik_dt() [1/2]

virtual const Eigen::VectorXd& bpp::BranchModelInterface::dLik_dt	(	const Eigen::VectorXd &	values,
		double	t
	)		const

pure virtualinherited

Implemented in bpp::AbstractLkTransitionModel, bpp::TransitionModelInterface, bpp::TransitionFromTransitionModel, and bpp::MultinomialFromTransitionModel.

◆ dLik_dt() [2/2]

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::dLik_dt	(	const Eigen::VectorXd &	values,
		double	t
	)		const

inlineoverridevirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 47 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getdPij_dt(), and bpp::AbstractLkTransitionModel::lik_.

◆ dPij_dt()

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

inlineoverridevirtual

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::TransitionModelInterface.

Definition at line 119 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::dPij_dt(), and bpp::AbstractWrappedSubstitutionModel::transitionModel().

◆ enableEigenDecomposition() [1/2]

bool bpp::InMixedSubstitutionModel::enableEigenDecomposition ( )

inlineoverridevirtual

Tell if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 160 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::enableEigenDecomposition(), and substitutionModel_().

◆ enableEigenDecomposition() [2/2]

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

inlineoverridevirtual

Set if eigenValues and Vectors must be computed.

Implements bpp::SubstitutionModelInterface.

Definition at line 158 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::enableEigenDecomposition(), and substitutionModel_().

◆ exchangeabilityMatrix()

const Matrix<double>& bpp::InMixedSubstitutionModel::exchangeabilityMatrix ( ) const

inlineoverridevirtual

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::SubstitutionModelInterface.

Definition at line 154 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::exchangeabilityMatrix(), and substitutionModel().

◆ fireParameterChanged()

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

inlineoverridevirtual

Methods to supersede AbstractSubstitutionnModel methods.

Tells the model that a parameter value has changed.

This updates the matrices consequently.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 235 of file InMixedSubstitutionModel.h.

References bpp::ParameterAliasable::matchParametersValues(), and mixedModel_().

◆ freq()

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

inlineoverridevirtual

@ brief Methods to supersede WrappedSubstitutionModel methods.

Implements bpp::TransitionModelInterface.

Definition at line 116 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::freq(), and bpp::AbstractWrappedSubstitutionModel::transitionModel().

◆ frequencySet()

const FrequencySetInterface& bpp::AbstractWrappedTransitionModel::frequencySet ( ) const

inlineoverridevirtualinherited

Returns: Get the FrequencySet of equilibrium of this model.

Exceptions

Exception if no FrequenceSet is associated to this model.

Reimplemented from bpp::AbstractWrappedModel.

Reimplemented in bpp::RegisterRatesSubstitutionModel, bpp::OneChangeTransitionModel, bpp::OneChangeRegisterTransitionModel, and bpp::YN98.

Definition at line 93 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::frequencySet(), and bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::RegisterRatesSubstitutionModel::frequencySet().

◆ generator()

const Matrix<double>& bpp::InMixedSubstitutionModel::generator ( ) const

inlineoverridevirtual

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. Additionally, the rate_ attribute 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::SubstitutionModelInterface.

Definition at line 152 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::generator(), and substitutionModel().

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::AbstractWrappedModel::getAlphabet ( ) const

inlineoverridevirtualinherited

Returns: A pointer toward the alphabet associated to this model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 55 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabet(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabet(), and bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel().

◆ getAlphabetStateAsChar()

std::string bpp::AbstractWrappedModel::getAlphabetStateAsChar ( size_t index ) const

inlineoverridevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 46 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsChar(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsChar().

◆ getAlphabetStateAsInt()

int bpp::AbstractWrappedModel::getAlphabetStateAsInt ( size_t index ) const

inlineoverridevirtualinherited

Parameters

index The model state.

Returns: The corresponding alphabet state as character code.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 44 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStateAsInt(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStateAsInt().

◆ getAlphabetStates()

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

inlineoverridevirtualinherited

@ brief Methods to supersede TransitionModel methods.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 38 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getAlphabetStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getAlphabetStates().

◆ getColumnRightEigenVectors()

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

inlineoverridevirtual

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

Implements bpp::SubstitutionModelInterface.

Definition at line 172 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::getColumnRightEigenVectors(), and substitutionModel().

◆ getd2Pij_dt2()

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

inlineoverridevirtual

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::TransitionModelInterface.

Definition at line 128 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::getd2Pij_dt2(), and bpp::AbstractWrappedSubstitutionModel::transitionModel().

◆ getdPij_dt()

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

inlineoverridevirtual

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::TransitionModelInterface.

Definition at line 126 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::getdPij_dt(), and bpp::AbstractWrappedSubstitutionModel::transitionModel().

◆ getEigenValues()

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

inlineoverridevirtual

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

Implements bpp::SubstitutionModelInterface.

Definition at line 166 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::getEigenValues(), and substitutionModel().

◆ getFrequencies()

const Vdouble& bpp::InMixedSubstitutionModel::getFrequencies ( ) const

inlineoverridevirtual

Returns: A vector of all equilibrium frequencies.

See also: freq()

Implements bpp::TransitionModelInterface.

Definition at line 122 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::getFrequencies(), and bpp::AbstractWrappedSubstitutionModel::transitionModel().

◆ getFrequencies_()

Vdouble& bpp::InMixedSubstitutionModel::getFrequencies_ ( )

inlineoverrideprotectedvirtual

Implements bpp::TransitionModelInterface.

Definition at line 95 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::getFrequencies_(), and mixedModel_().

◆ getIEigenValues()

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

inlineoverridevirtual

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

Implements bpp::SubstitutionModelInterface.

Definition at line 168 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::getIEigenValues(), and substitutionModel().

◆ getInitValue()

double bpp::InMixedSubstitutionModel::getInitValue	(	size_t	i,
		int	state
	)		const

inlineoverridevirtual

This method is used to initialize likelihoods in recursions. 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::BranchModelInterface.

Definition at line 130 of file InMixedSubstitutionModel.h.

References bpp::BranchModelInterface::getInitValue(), and bpp::AbstractWrappedTransitionModel::model().

◆ getModelStates() [1/2]

std::vector<size_t> bpp::AbstractWrappedModel::getModelStates ( const std::string & code ) const

inlineoverridevirtualinherited

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

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 50 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

◆ getModelStates() [2/2]

std::vector<size_t> bpp::AbstractWrappedModel::getModelStates ( int code ) const

inlineoverridevirtualinherited

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

Parameters

code	The alphabet state to check.

Returns: A vector of indices of model states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 48 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getModelStates(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getModelStates().

◆ getName()

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

inlineoverridevirtual

Get the name of the model.

Returns: The name of this model.

Reimplemented from bpp::AbstractWrappedModel.

Definition at line 250 of file InMixedSubstitutionModel.h.

References mixedModelPtr_.

◆ getNumberOfStates()

size_t bpp::AbstractWrappedModel::getNumberOfStates ( ) const

inlineoverridevirtualinherited

Get the number of states.

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

See also: getAlphabetChars for the list of supported states.

Returns: The number of different states in the model.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 57 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getNumberOfStates(), and bpp::WrappedModelInterface::model().

◆ getPij_t()

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

inlineoverridevirtual

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

See also: Pij_t()

Implements bpp::TransitionModelInterface.

Definition at line 124 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::getPij_t(), and bpp::AbstractWrappedSubstitutionModel::transitionModel().

◆ getRate()

double bpp::InMixedSubstitutionModel::getRate ( ) const

inlineoverridevirtual

Get the rate.

Implements bpp::BranchModelInterface.

Definition at line 204 of file InMixedSubstitutionModel.h.

References bpp::BranchModelInterface::getRate(), and bpp::AbstractWrappedSubstitutionModel::transitionModel().

Referenced by addRateParameter().

◆ getRowLeftEigenVectors()

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

inlineoverridevirtual

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

Implements bpp::SubstitutionModelInterface.

Definition at line 170 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::getRowLeftEigenVectors(), and substitutionModel().

◆ getScale()

double bpp::InMixedSubstitutionModel::getScale ( ) const

inlineoverridevirtual

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::SubstitutionModelInterface.

Definition at line 189 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::getScale(), and substitutionModel().

◆ getStateMap()

std::shared_ptr<const StateMapInterface> bpp::AbstractWrappedModel::getStateMap ( ) const

inlineoverridevirtualinherited

Returns: A shared_ptr to the mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 42 of file AbstractWrappedModel.h.

References bpp::BranchModelInterface::getStateMap(), and bpp::WrappedModelInterface::model().

Referenced by bpp::RegisterRatesSubstitutionModel::getStateMap().

◆ getSubModelNumber()

size_t bpp::InMixedSubstitutionModel::getSubModelNumber ( ) const

inline

Definition at line 75 of file InMixedSubstitutionModel.h.

References subModelNumber_.

Referenced by bpp::BppOSubstitutionModelFormat::write().

◆ isDiagonalizable()

bool bpp::InMixedSubstitutionModel::isDiagonalizable ( ) const

inlineoverridevirtual

Returns: True if the model is diagonalizable in R.

Implements bpp::SubstitutionModelInterface.

Definition at line 162 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::isDiagonalizable(), and substitutionModel().

◆ isNonSingular()

bool bpp::InMixedSubstitutionModel::isNonSingular ( ) const

inlineoverridevirtual

Returns: True is the model is non-singular.

Implements bpp::SubstitutionModelInterface.

Definition at line 164 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::isNonSingular(), and substitutionModel().

◆ isScalable()

bool bpp::InMixedSubstitutionModel::isScalable ( ) const

inlineoverridevirtual

returns if model is scalable

Implements bpp::SubstitutionModelInterface.

Definition at line 178 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::isScalable(), and substitutionModel().

◆ Lik_t() [1/2]

virtual const Eigen::VectorXd& bpp::BranchModelInterface::Lik_t	(	const Eigen::VectorXd &	values,
		double	t
	)		const

pure virtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters

values	An vector of states on the site.
t	time

Exceptions

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

Implemented in bpp::AbstractLkTransitionModel, bpp::TransitionModelInterface, bpp::TransitionFromTransitionModel, and bpp::MultinomialFromTransitionModel.

◆ Lik_t() [2/2]

const Eigen::VectorXd& bpp::AbstractLkTransitionModel::Lik_t	(	const Eigen::VectorXd &	values,
		double	t
	)		const

inlineoverridevirtualinherited

This method is used to compute likelihoods in recursions. It computes the probability of a vector given a start state.

Parameters

values	An vector of states on the site.
t	the branch length

Implements bpp::TransitionModelInterface.

Definition at line 30 of file AbstractSubstitutionModel.h.

References bpp::TransitionModelInterface::getPij_t(), and bpp::AbstractLkTransitionModel::lik_.

◆ mixedModel()

const MixedTransitionModelInterface& bpp::InMixedSubstitutionModel::mixedModel ( ) const

inline

Definition at line 65 of file InMixedSubstitutionModel.h.

References mixedModelPtr_.

Referenced by addRateParameter(), computeFrequencies(), and bpp::BppOSubstitutionModelFormat::write().

◆ mixedModel_()

MixedTransitionModelInterface& bpp::InMixedSubstitutionModel::mixedModel_ ( )

inlineprotected

Definition at line 100 of file InMixedSubstitutionModel.h.

References mixedModelPtr_.

Referenced by addRateParameter(), computeFrequencies(), fireParameterChanged(), getFrequencies_(), setFreq(), setFreqFromData(), setNamespace(), setRate(), and substitutionModel_().

◆ model()

const BranchModelInterface& bpp::AbstractWrappedTransitionModel::model ( ) const

inlineoverridevirtualinherited

Implements bpp::WrappedModelInterface.

Definition at line 98 of file AbstractWrappedModel.h.

References bpp::WrappedTransitionModelInterface::transitionModel().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), getInitValue(), bpp::FromMixtureSubstitutionModel::getName(), bpp::RegisterRatesSubstitutionModel::getRate(), bpp::AbstractBiblioSubstitutionModel::operator=(), bpp::AbstractBiblioTransitionModel::operator=(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setFreq(), bpp::AbstractBiblioTransitionModel::setNamespace(), and bpp::BppOSubstitutionModelFormat::write().

◆ model_()

BranchModelInterface& bpp::AbstractWrappedTransitionModel::model_ ( )

inlineprotectedinherited

Definition at line 85 of file AbstractWrappedModel.h.

References bpp::AbstractWrappedTransitionModel::transitionModel_().

Referenced by bpp::AbstractBiblioTransitionModel::addRateParameter(), bpp::FromMixtureSubstitutionModel::addRateParameter(), bpp::AbstractBiblioTransitionModel::fireParameterChanged(), bpp::FromMixtureSubstitutionModel::fireParameterChanged(), bpp::RegisterRatesSubstitutionModel::RegisterRatesSubstitutionModel(), bpp::AbstractBiblioTransitionModel::setNamespace(), bpp::FromMixtureSubstitutionModel::setNamespace(), bpp::RegisterRatesSubstitutionModel::setRate(), and bpp::AbstractBiblioTransitionModel::updateMatrices_().

◆ normalize()

void bpp::InMixedSubstitutionModel::normalize ( )

inlineoverridevirtual

Normalize the generator.

Implements bpp::SubstitutionModelInterface.

Definition at line 194 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::normalize(), and substitutionModel_().

◆ operator=()

InMixedSubstitutionModel & InMixedSubstitutionModel::operator= ( const InMixedSubstitutionModel & fmsm )

Definition at line 64 of file InMixedSubstitutionModel.cpp.

References mixedModelPtr_, mixtName_, bpp::AbstractParameterAliasable::operator=(), and subModelNumber_.

◆ Pij_t()

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

inlineoverridevirtual

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

See also: getPij_t(), getStates()

Implements bpp::TransitionModelInterface.

Definition at line 118 of file InMixedSubstitutionModel.h.

References bpp::TransitionModelInterface::Pij_t(), and bpp::AbstractWrappedSubstitutionModel::transitionModel().

◆ Qij()

double bpp::InMixedSubstitutionModel::Qij	(	size_t	i,
		size_t	j
	)		const

inlineoverridevirtual

Methods to supersede SubstitutionModel methods.

Implements bpp::SubstitutionModelInterface.

Definition at line 150 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::Qij(), and substitutionModel().

◆ setDiagonal()

void bpp::InMixedSubstitutionModel::setDiagonal ( )

inlineoverridevirtual

set the diagonal of the generator such that sum on each line equals 0.

Implements bpp::SubstitutionModelInterface.

Definition at line 199 of file InMixedSubstitutionModel.h.

References bpp::SubstitutionModelInterface::setDiagonal(), and substitutionModel_().

◆ setFreq()

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

inlineoverridevirtual

Set equilibrium frequencies.

Parameters

frequencies The map of the frequencies to use.

Implements bpp::TransitionModelInterface.

Definition at line 140 of file InMixedSubstitutionModel.h.

References mixedModel_(), and bpp::TransitionModelInterface::setFreq().

◆ setFreqFromData()

void bpp::InMixedSubstitutionModel::setFreqFromData	(	const SequenceDataInterface &	data,
		double	pseudoCount = `0`
	)

inlineoverridevirtual

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