From a model, compute transition probabilities given there is at least a change of a category (ie a non null number in a register) in the branch. More...

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

Inheritance diagram for bpp::OneChangeRegisterTransitionModel:

Collaboration diagram for bpp::OneChangeRegisterTransitionModel:

Public Member Functions
	OneChangeRegisterTransitionModel (std::unique_ptr< SubstitutionModelInterface > originalModel, const SubstitutionRegisterInterface &reg, size_t numReg)

	OneChangeRegisterTransitionModel (std::unique_ptr< SubstitutionModelInterface > originalModel, const SubstitutionRegisterInterface &reg, std::vector< size_t > vNumRegs)
	Constructor. More...

	OneChangeRegisterTransitionModel (const OneChangeRegisterTransitionModel &fmsm)

OneChangeRegisterTransitionModel &	operator= (const OneChangeRegisterTransitionModel &fmsm)

virtual	~OneChangeRegisterTransitionModel ()

OneChangeRegisterTransitionModel *	clone () const override

void	fireParameterChanged (const ParameterList &parameters) 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 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	freq (size_t i) const override

const Vdouble &	getFrequencies () const override

const FrequencySetInterface &	frequencySet () const override

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

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

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...

const std::string &	getRegisterName () const

const std::vector< size_t > &	getRegisterNumbers () const

const SubstitutionModelInterface &	substitutionModel () const

const TransitionModelInterface &	transitionModel () const override

const BranchModelInterface &	model () const override

bool	computeFrequencies () const override

void	computeFrequencies (bool yn) override

virtual void	addRateParameter () override

virtual void	setNamespace (const std::string &prefix) 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


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
void	updateMatrices_ ()

Vdouble &	getFrequencies_ () override

SubstitutionModelInterface &	substitutionModel_ ()

TransitionModelInterface &	transitionModel_ () override

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

Protected Attributes
std::unique_ptr< SubstitutionModelInterface >	subModel_
	The related model. More...

size_t	size_

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

RowMatrix< double >	dpij_t

RowMatrix< double >	d2pij_t

std::string	nestedPrefix_

Private Attributes
RowMatrix< uint >	noChangedStates_

std::unique_ptr< AnonymousSubstitutionModel >	modelChanged_

std::string	registerName_

std::vector< size_t >	vNumRegs_

ParameterList	independentParameters_

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

ParameterList	parameters_

std::string	prefix_

Eigen::VectorXd	lik_

Detailed Description

From a model, compute transition probabilities given there is at least a change of a category (ie a non null number in a register) in the branch.

It has the same parameters as the SubModel.

See also: SubstitutionRegister

Definition at line 24 of file OneChangeRegisterTransitionModel.h.

Constructor & Destructor Documentation

◆ OneChangeRegisterTransitionModel() [1/3]

OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel	(	std::unique_ptr< SubstitutionModelInterface >	originalModel,
		const SubstitutionRegisterInterface &	reg,
		size_t	numReg
	)

Definition at line 13 of file OneChangeRegisterTransitionModel.cpp.

References bpp::AbstractWrappedModel::alphabet(), bpp::SubstitutionRegisterInterface::getNumberOfSubstitutionTypes(), bpp::RowMatrix< class >::getRow(), bpp::SubstitutionRegisterInterface::getType(), modelChanged_, noChangedStates_, bpp::AbstractFromSubstitutionModelTransitionModel::size_, and updateMatrices_().

Referenced by clone().

◆ OneChangeRegisterTransitionModel() [2/3]

OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel	(	std::unique_ptr< SubstitutionModelInterface >	originalModel,
		const SubstitutionRegisterInterface &	reg,
		std::vector< size_t >	vNumRegs
	)

Constructor.

Parameters

originalModel	the substitution model used
reg	the register in which the considered type of event is defined.
vNumRegs	the vector of numbers of the considered event in the register.

Definition at line 49 of file OneChangeRegisterTransitionModel.cpp.

References bpp::AbstractWrappedModel::getAlphabet(), bpp::SubstitutionRegisterInterface::getNumberOfSubstitutionTypes(), bpp::RowMatrix< class >::getRow(), bpp::SubstitutionRegisterInterface::getType(), modelChanged_, noChangedStates_, bpp::AbstractFromSubstitutionModelTransitionModel::size_, updateMatrices_(), and vNumRegs_.

◆ OneChangeRegisterTransitionModel() [3/3]

bpp::OneChangeRegisterTransitionModel::OneChangeRegisterTransitionModel ( const OneChangeRegisterTransitionModel & fmsm )

inline

Definition at line 78 of file OneChangeRegisterTransitionModel.h.

◆ ~OneChangeRegisterTransitionModel()

virtual bpp::OneChangeRegisterTransitionModel::~OneChangeRegisterTransitionModel ( )

inlinevirtual

Definition at line 103 of file OneChangeRegisterTransitionModel.h.

Member Function Documentation

◆ addRateParameter()

virtual void bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter ( )

inlineoverridevirtualinherited

Implements bpp::BranchModelInterface.

Definition at line 107 of file AbstractFromSubstitutionModelTransitionModel.h.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::BranchModelInterface::addRateParameter(), bpp::AbstractParameterAliasable::getNamespace(), bpp::BranchModelInterface::getRate(), bpp::AbstractFromSubstitutionModelTransitionModel::model(), bpp::AbstractFromSubstitutionModelTransitionModel::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 OneChangeRegisterTransitionModel().

◆ clone()

OneChangeRegisterTransitionModel* bpp::OneChangeRegisterTransitionModel::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParameterAliasable.

Definition at line 105 of file OneChangeRegisterTransitionModel.h.

References OneChangeRegisterTransitionModel().

◆ computeFrequencies() [1/2]

bool bpp::AbstractFromSubstitutionModelTransitionModel::computeFrequencies ( ) const

inlineoverridevirtualinherited

Returns: Says if equilibrium frequencies should be computed

Implements bpp::TransitionModelInterface.

Definition at line 69 of file AbstractFromSubstitutionModelTransitionModel.h.

References bpp::AbstractFromSubstitutionModelTransitionModel::subModel_.

◆ computeFrequencies() [2/2]

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

inlineoverridevirtualinherited

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

Implements bpp::TransitionModelInterface.

Definition at line 78 of file AbstractFromSubstitutionModelTransitionModel.h.

References bpp::AbstractFromSubstitutionModelTransitionModel::subModel_.

◆ 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 OneChangeRegisterTransitionModel::d2Pij_dt2	(	size_t	i,
		size_t	j,
		double	t
	)		const

overridevirtual

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 174 of file OneChangeRegisterTransitionModel.cpp.

References bpp::TransitionModelInterface::d2Pij_dt2(), bpp::TransitionModelInterface::dPij_dt(), bpp::SubstitutionModelInterface::generator(), bpp::BranchModelInterface::getRate(), modelChanged_, bpp::TransitionModelInterface::Pij_t(), bpp::AbstractFromSubstitutionModelTransitionModel::size_, bpp::AbstractFromSubstitutionModelTransitionModel::substitutionModel(), and bpp::AbstractFromSubstitutionModelTransitionModel::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 OneChangeRegisterTransitionModel::dPij_dt	(	size_t	i,
		size_t	j,
		double	t
	)		const

overridevirtual

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 136 of file OneChangeRegisterTransitionModel.cpp.

References bpp::SubstitutionModelInterface::generator(), bpp::BranchModelInterface::getRate(), modelChanged_, Pij_t(), bpp::AbstractFromSubstitutionModelTransitionModel::size_, bpp::AbstractFromSubstitutionModelTransitionModel::substitutionModel(), and bpp::AbstractFromSubstitutionModelTransitionModel::transitionModel().

◆ fireParameterChanged()

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

inlineoverridevirtual

Reimplemented from bpp::AbstractFromSubstitutionModelTransitionModel.

Definition at line 111 of file OneChangeRegisterTransitionModel.h.

References bpp::AbstractFromSubstitutionModelTransitionModel::fireParameterChanged(), and updateMatrices_().

◆ freq()

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

inlineoverridevirtual

Returns: Equilibrium frequency associated to character i.

See also: getFrequencies(), getStates()

Implements bpp::TransitionModelInterface.

Definition at line 127 of file OneChangeRegisterTransitionModel.h.

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

◆ frequencySet()

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

inlineoverridevirtual

Returns: Get the FrequencySet of equilibrium of this model.

Exceptions

Exception if no FrequenceSet is associated to this model.

Reimplemented from bpp::AbstractWrappedTransitionModel.

Definition at line 137 of file OneChangeRegisterTransitionModel.h.

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

◆ 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 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().

◆ getd2Pij_dt2()

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

overridevirtual

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 366 of file OneChangeRegisterTransitionModel.cpp.

References bpp::AbstractFromSubstitutionModelTransitionModel::d2pij_t, bpp::SubstitutionModelInterface::generator(), bpp::TransitionModelInterface::getd2Pij_dt2(), bpp::TransitionModelInterface::getdPij_dt(), bpp::TransitionModelInterface::getPij_t(), bpp::BranchModelInterface::getRate(), RowMatrix< double >::getRow(), modelChanged_, bpp::AbstractFromSubstitutionModelTransitionModel::size_, bpp::AbstractFromSubstitutionModelTransitionModel::substitutionModel(), and bpp::AbstractFromSubstitutionModelTransitionModel::transitionModel().

◆ getdPij_dt()

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

overridevirtual

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 287 of file OneChangeRegisterTransitionModel.cpp.

References bpp::AbstractFromSubstitutionModelTransitionModel::dpij_t, bpp::SubstitutionModelInterface::generator(), bpp::TransitionModelInterface::getdPij_dt(), bpp::TransitionModelInterface::getPij_t(), bpp::BranchModelInterface::getRate(), RowMatrix< double >::getRow(), modelChanged_, bpp::AbstractFromSubstitutionModelTransitionModel::size_, bpp::AbstractFromSubstitutionModelTransitionModel::substitutionModel(), and bpp::AbstractFromSubstitutionModelTransitionModel::transitionModel().

◆ getFrequencies()

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

inlineoverridevirtual

Returns: A vector of all equilibrium frequencies.

See also: freq()

Implements bpp::TransitionModelInterface.

Definition at line 132 of file OneChangeRegisterTransitionModel.h.

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

◆ getFrequencies_()

Vdouble& bpp::AbstractFromSubstitutionModelTransitionModel::getFrequencies_ ( )

inlineoverrideprotectedvirtualinherited

Implements bpp::TransitionModelInterface.

Definition at line 85 of file AbstractFromSubstitutionModelTransitionModel.h.

References bpp::AbstractFromSubstitutionModelTransitionModel::subModel_.

◆ getInitValue()

double bpp::OneChangeRegisterTransitionModel::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 156 of file OneChangeRegisterTransitionModel.h.

References bpp::BranchModelInterface::getInitValue(), and bpp::AbstractFromSubstitutionModelTransitionModel::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::OneChangeRegisterTransitionModel::getName ( ) const

inlineoverridevirtual

Get the name of the model.

Returns: The name of this model.

Reimplemented from bpp::AbstractWrappedModel.

Definition at line 161 of file OneChangeRegisterTransitionModel.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().

◆ getPij_t()

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

overridevirtual

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

See also: Pij_t()

Implements bpp::TransitionModelInterface.

Definition at line 228 of file OneChangeRegisterTransitionModel.cpp.

References bpp::SubstitutionModelInterface::generator(), bpp::TransitionModelInterface::getPij_t(), bpp::BranchModelInterface::getRate(), RowMatrix< double >::getRow(), modelChanged_, bpp::AbstractFromSubstitutionModelTransitionModel::pij_t, bpp::AbstractFromSubstitutionModelTransitionModel::size_, bpp::AbstractFromSubstitutionModelTransitionModel::substitutionModel(), and bpp::AbstractFromSubstitutionModelTransitionModel::transitionModel().

◆ getRate()

double bpp::OneChangeRegisterTransitionModel::getRate ( ) const

inlineoverridevirtual

Get the rate.

Implements bpp::BranchModelInterface.

Definition at line 152 of file OneChangeRegisterTransitionModel.h.

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

Referenced by Pij_t().

◆ getRegisterName()

const std::string& bpp::OneChangeRegisterTransitionModel::getRegisterName ( ) const

inline

Definition at line 166 of file OneChangeRegisterTransitionModel.h.

References registerName_.

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

◆ getRegisterNumbers()

const std::vector<size_t>& bpp::OneChangeRegisterTransitionModel::getRegisterNumbers ( ) const

inline

Definition at line 171 of file OneChangeRegisterTransitionModel.h.

References vNumRegs_.

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

◆ 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() [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_.

◆ model()

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

inlineoverridevirtualinherited

Implements bpp::WrappedModelInterface.

Definition at line 64 of file AbstractFromSubstitutionModelTransitionModel.h.

References bpp::AbstractFromSubstitutionModelTransitionModel::subModel_.

Referenced by bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), getInitValue(), bpp::OneChangeTransitionModel::getInitValue(), and bpp::BppOSubstitutionModelFormat::write().

◆ model_()

BranchModelInterface& bpp::AbstractFromSubstitutionModelTransitionModel::model_ ( )

inlineprotectedinherited

Definition at line 101 of file AbstractFromSubstitutionModelTransitionModel.h.

References bpp::AbstractFromSubstitutionModelTransitionModel::subModel_.

Referenced by bpp::AbstractFromSubstitutionModelTransitionModel::addRateParameter(), bpp::AbstractFromSubstitutionModelTransitionModel::fireParameterChanged(), and bpp::AbstractFromSubstitutionModelTransitionModel::setNamespace().

◆ operator=()

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

inline

Definition at line 90 of file OneChangeRegisterTransitionModel.h.

References modelChanged_, noChangedStates_, bpp::AbstractFromSubstitutionModelTransitionModel::operator=(), bpp::AbstractParameterAliasable::operator=(), registerName_, and vNumRegs_.

◆ Pij_t()

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

overridevirtual

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 116 of file OneChangeRegisterTransitionModel.cpp.

References bpp::SubstitutionModelInterface::generator(), getRate(), modelChanged_, bpp::TransitionModelInterface::Pij_t(), bpp::AbstractFromSubstitutionModelTransitionModel::size_, bpp::AbstractFromSubstitutionModelTransitionModel::substitutionModel(), and bpp::AbstractFromSubstitutionModelTransitionModel::transitionModel().

Referenced by dPij_dt().

◆ setFreq()

virtual void bpp::OneChangeRegisterTransitionModel::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 147 of file OneChangeRegisterTransitionModel.h.

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

◆ setFreqFromData()

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

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