From a transition model, compute the transition function probabilities. More...

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

Inheritance diagram for bpp::TransitionFromTransitionModel:

Collaboration diagram for bpp::TransitionFromTransitionModel:

Public Member Functions
	TransitionFromTransitionModel (std::shared_ptr< TransitionModelInterface > originalModel)

	TransitionFromTransitionModel (const TransitionFromTransitionModel &fmsm)

TransitionFromTransitionModel &	operator= (const TransitionFromTransitionModel &fmsm)

virtual	~TransitionFromTransitionModel ()

TransitionFromTransitionModel *	clone () const override

void	fireParameterChanged (const ParameterList &parameters) override

const BranchModelInterface &	model () const override

const TransitionModelInterface &	transitionModel () const

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

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

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

void	setFreqFromData (const SequenceDataInterface &data, double pseudoCount)

virtual void	setFreq (std::map< int, double > &m)

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

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

double	getInitValue (size_t i, int state) const override

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

void	addRateParameter () override

void	setNamespace (const std::string &prefix)

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


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...

const FrequencySetInterface &	frequencySet () const override

Protected Member Functions
BranchModelInterface &	model_ ()

TransitionModelInterface &	transitionModel_ ()

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::shared_ptr< TransitionModelInterface >	subModel_
	The related model. More...

size_t	size_

double	tref_
	Reference time to avoid recomuputation of transition matrix when time has not changed. If <0, it means that transition matrix should be recomputed (for ex if parameters have changed). More...

const Matrix< double > *	Pij_t
	Transition Matrices owned by the submodel. More...

const Matrix< double > *	dPij_dt

const Matrix< double > *	d2Pij_dt2

Eigen::VectorXd	Pi_
	Used return vectors. More...

Eigen::VectorXd	dPi_

Eigen::VectorXd	d2Pi_

ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Detailed Description

From a transition model, compute the transition function probabilities.

This class is (up to now) mostly for test purpose.

It has the same parameters as the SubModel.

Definition at line 21 of file TransitionFromTransitionModel.h.

Constructor & Destructor Documentation

◆ TransitionFromTransitionModel() [1/2]

bpp::TransitionFromTransitionModel::TransitionFromTransitionModel ( std::shared_ptr< TransitionModelInterface > originalModel )

inline

Definition at line 58 of file TransitionFromTransitionModel.h.

References bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::getNamespace(), and subModel_.

Referenced by clone().

◆ TransitionFromTransitionModel() [2/2]

bpp::TransitionFromTransitionModel::TransitionFromTransitionModel ( const TransitionFromTransitionModel & fmsm )

inline

Definition at line 69 of file TransitionFromTransitionModel.h.

◆ ~TransitionFromTransitionModel()

virtual bpp::TransitionFromTransitionModel::~TransitionFromTransitionModel ( )

inlinevirtual

Definition at line 92 of file TransitionFromTransitionModel.h.

Member Function Documentation

◆ addRateParameter()

void bpp::TransitionFromTransitionModel::addRateParameter ( )

inlineoverridevirtual

Implements bpp::BranchModelInterface.

Definition at line 142 of file TransitionFromTransitionModel.h.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::BranchModelInterface::addRateParameter(), bpp::AbstractParameterAliasable::getNamespace(), getRate(), model(), model_(), 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()

TransitionFromTransitionModel* bpp::TransitionFromTransitionModel::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 94 of file TransitionFromTransitionModel.h.

References TransitionFromTransitionModel().

◆ d2Lik_dt2()

const Eigen::VectorXd & TransitionFromTransitionModel::d2Lik_dt2	(	const Eigen::VectorXd &	from,
		double	t
	)		const

overridevirtual

Implements bpp::BranchModelInterface.

Definition at line 59 of file TransitionFromTransitionModel.cpp.

References to().

◆ dLik_dt()

const Eigen::VectorXd & TransitionFromTransitionModel::dLik_dt	(	const Eigen::VectorXd &	from,
		double	t
	)		const

overridevirtual

Implements bpp::BranchModelInterface.

Definition at line 37 of file TransitionFromTransitionModel.cpp.

References to().

◆ fireParameterChanged()

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

inlineoverridevirtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 97 of file TransitionFromTransitionModel.h.

References bpp::AbstractParameterAliasable::fireParameterChanged(), bpp::AbstractParameterAliasable::matchParametersValues(), model_(), and tref_.

◆ frequencySet()

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

inlineoverridevirtualinherited

Returns: Get the FrequencySet of equilibrium of this model.

Exceptions

Exception if no FrequenceSet is associated to this model.

Implements bpp::BranchModelInterface.

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

Definition at line 59 of file AbstractWrappedModel.h.

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

Referenced by bpp::YN98::frequencySet().

◆ 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().

◆ getInitValue()

double bpp::TransitionFromTransitionModel::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 132 of file TransitionFromTransitionModel.h.

References bpp::BranchModelInterface::getInitValue(), and transitionModel().

◆ 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::TransitionFromTransitionModel::getName ( ) const

inlineoverridevirtual

Get the name of the model.

Returns: The name of this model.

Reimplemented from bpp::AbstractWrappedModel.

Definition at line 137 of file TransitionFromTransitionModel.h.

◆ 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().

◆ getRate()

double bpp::TransitionFromTransitionModel::getRate ( ) const

inlineoverridevirtual

Get the rate.

Implements bpp::BranchModelInterface.

Definition at line 128 of file TransitionFromTransitionModel.h.

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

Referenced by addRateParameter().

◆ 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().

◆ Lik_t()

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

overridevirtual

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.

Implements bpp::BranchModelInterface.

Definition at line 14 of file TransitionFromTransitionModel.cpp.

References to().

◆ model()

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

inlineoverridevirtual

Implements bpp::WrappedModelInterface.

Definition at line 104 of file TransitionFromTransitionModel.h.

References subModel_.

Referenced by addRateParameter().

◆ model_()

BranchModelInterface& bpp::TransitionFromTransitionModel::model_ ( )

inlineprotected

Definition at line 149 of file TransitionFromTransitionModel.h.

References subModel_.

Referenced by addRateParameter(), and fireParameterChanged().

◆ operator=()

TransitionFromTransitionModel& bpp::TransitionFromTransitionModel::operator= ( const TransitionFromTransitionModel & fmsm )

inline

Definition at line 77 of file TransitionFromTransitionModel.h.

References d2Pi_, dPi_, bpp::AbstractParameterAliasable::operator=(), Pi_, size_, subModel_, and tref_.

◆ setFreq()

virtual void bpp::TransitionFromTransitionModel::setFreq ( std::map< int, double > & m )

inlinevirtual

Definition at line 123 of file TransitionFromTransitionModel.h.

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

◆ setFreqFromData()

void bpp::TransitionFromTransitionModel::setFreqFromData	(	const SequenceDataInterface &	data,
		double	pseudoCount
	)

inline

Definition at line 118 of file TransitionFromTransitionModel.h.

References bpp::TransitionModelInterface::setFreqFromData(), and transitionModel_().

◆ setRate()

void bpp::TransitionFromTransitionModel::setRate ( double rate )

inlineoverridevirtual

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

Parameters

rate	must be positive.

Implements bpp::BranchModelInterface.

Definition at line 130 of file TransitionFromTransitionModel.h.

References bpp::BranchModelInterface::setRate(), and transitionModel_().

◆ stateMap()

const StateMapInterface& bpp::AbstractWrappedModel::stateMap ( ) const

inlineoverridevirtualinherited

Returns: The mapping of model states with alphabet states.

Implements bpp::BranchModelInterface.

Reimplemented in bpp::RegisterRatesSubstitutionModel.

Definition at line 40 of file AbstractWrappedModel.h.

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

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

◆ transitionModel()

const TransitionModelInterface& bpp::TransitionFromTransitionModel::transitionModel ( ) const

inline

Definition at line 109 of file TransitionFromTransitionModel.h.

References subModel_.

Referenced by getInitValue(), and getRate().

◆ transitionModel_()

TransitionModelInterface& bpp::TransitionFromTransitionModel::transitionModel_ ( )

inlineprotected

Definition at line 154 of file TransitionFromTransitionModel.h.

References subModel_.

Referenced by setFreq(), setFreqFromData(), and setRate().

Member Data Documentation

◆ d2Pi_

Eigen::VectorXd bpp::TransitionFromTransitionModel::d2Pi_

private

Definition at line 55 of file TransitionFromTransitionModel.h.

Referenced by operator=().

◆ d2Pij_dt2

const Matrix<double> * bpp::TransitionFromTransitionModel::d2Pij_dt2

private

Definition at line 50 of file TransitionFromTransitionModel.h.

◆ dPi_

Eigen::VectorXd bpp::TransitionFromTransitionModel::dPi_

private

Definition at line 55 of file TransitionFromTransitionModel.h.

Referenced by operator=().

◆ dPij_dt

const Matrix<double> * bpp::TransitionFromTransitionModel::dPij_dt

private

Definition at line 50 of file TransitionFromTransitionModel.h.

◆ Pi_

Eigen::VectorXd bpp::TransitionFromTransitionModel::Pi_

mutableprivate

Used return vectors.

Definition at line 55 of file TransitionFromTransitionModel.h.

Referenced by operator=().

◆ Pij_t

const Matrix<double>* bpp::TransitionFromTransitionModel::Pij_t

mutableprivate

Transition Matrices owned by the submodel.

These ones are for bookkeeping:

Definition at line 50 of file TransitionFromTransitionModel.h.

◆ size_

size_t bpp::TransitionFromTransitionModel::size_

private

The number of states

Definition at line 33 of file TransitionFromTransitionModel.h.

Referenced by operator=().

◆ subModel_

std::shared_ptr<TransitionModelInterface> bpp::TransitionFromTransitionModel::subModel_

private

The related model.

Definition at line 28 of file TransitionFromTransitionModel.h.

Referenced by model(), model_(), operator=(), TransitionFromTransitionModel(), transitionModel(), and transitionModel_().

◆ tref_

double bpp::TransitionFromTransitionModel::tref_

mutableprivate

Reference time to avoid recomuputation of transition matrix when time has not changed. If <0, it means that transition matrix should be recomputed (for ex if parameters have changed).

Definition at line 41 of file TransitionFromTransitionModel.h.

Referenced by fireParameterChanged(), and operator=().

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

Bpp/Phyl/Model/TransitionFromTransitionModel.h
Bpp/Phyl/Model/TransitionFromTransitionModel.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TransitionFromTransitionModel() [1/2]

◆ TransitionFromTransitionModel() [2/2]

◆ ~TransitionFromTransitionModel()

Member Function Documentation

◆ addRateParameter()

◆ alphabet()

◆ clone()

◆ d2Lik_dt2()

◆ dLik_dt()

◆ fireParameterChanged()

◆ frequencySet()

◆ getAlphabet()

◆ getAlphabetStateAsChar()

◆ getAlphabetStateAsInt()

◆ getAlphabetStates()

◆ getInitValue()

◆ getModelStates() [1/2]

◆ getModelStates() [2/2]

◆ getName()

◆ getNumberOfStates()

◆ getRate()

◆ getStateMap()

◆ Lik_t()

◆ model()

◆ model_()

◆ operator=()

◆ setFreq()

◆ setFreqFromData()

◆ setRate()

◆ stateMap()

◆ transitionModel()

◆ transitionModel_()

Member Data Documentation

◆ d2Pi_

◆ d2Pij_dt2

◆ dPi_

◆ dPij_dt

◆ Pi_

◆ Pij_t

◆ size_

◆ subModel_

◆ tref_