Function wrapper that remove simple constraints on parameters. Also transform first order derivatives. More...

#include <Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h>

Inheritance diagram for bpp::ReparametrizationDerivableFirstOrderWrapper:

Collaboration diagram for bpp::ReparametrizationDerivableFirstOrderWrapper:

Public Member Functions
	ReparametrizationDerivableFirstOrderWrapper (std::shared_ptr< FirstOrderDerivable > function, bool verbose=true)
	Build a new reparametrization wrapper for the given function, using all available parameters. More...

	ReparametrizationDerivableFirstOrderWrapper (std::shared_ptr< FirstOrderDerivable > function, const ParameterList &parameters, bool verbose=true)
	Build a new reparametrization wrapper for the given function, using only the specified parameters. More...

virtual	~ReparametrizationDerivableFirstOrderWrapper ()

ReparametrizationDerivableFirstOrderWrapper *	clone () const
	Create a copy of this object and send a pointer to it. More...

void	enableFirstOrderDerivatives (bool yn)
	Tell if derivatives must be computed. More...

bool	enableFirstOrderDerivatives () const
	Tell if derivatives must be computed. More...

double	getFirstOrderDerivative (const std::string &variable) const
	Get the derivative of the function at the current point. More...

virtual double	df (const std::string &variable, const ParameterList &parameters)
	Get the value of the first derivative of the function according to a given set of parameters. More...

virtual void	setParameters (const ParameterList &parameters)=0
	Set the point where the function must be computed. More...

virtual double	getValue () const =0
	Get the value of the function at the current point. More...

virtual double	f (const ParameterList &parameters)
	Get the value of the function according to a given set of parameters. More...

virtual bool	hasParameter (const std::string &name) const =0
	Tell if there is a parameter with specified name. More...

virtual const ParameterList &	getParameters () const =0
	Get all parameters available. More...

virtual const Parameter &	parameter (const std::string &name) const =0
	Get the parameter with specified name. More...

virtual double	getParameterValue (const std::string &name) const =0
	Get the value for parameter of name 'name'. More...

virtual void	setAllParametersValues (const ParameterList &parameters)=0
	Set the parameters values to be equals to those of parameters. More...

virtual void	setParameterValue (const std::string &name, double value)=0
	Set the value of parameter with name name to be equal to value. More...

virtual void	setParametersValues (const ParameterList &parameters)=0
	Update the parameters from parameters. More...

virtual bool	matchParametersValues (const ParameterList &parameters)=0
	Update the parameters from parameters. More...

virtual void	removeConstraint (const std::string &name)=0
	Remove the constraint associated with one parameter, if any. More...

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
	Set/Change the constraint associated with one parameter. More...

virtual size_t	getNumberOfParameters () const =0
	Get the number of parameters. More...

virtual void	setNamespace (const std::string &prefix)=0
	Set the namespace for the parameter names. More...

virtual std::string	getNamespace () const =0

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
	Resolves a parameter name according to the current namespace. More...

virtual const FunctionInterface &	function () const

virtual FunctionInterface &	function ()

virtual std::shared_ptr< const FunctionInterface >	getFunction () const

virtual std::shared_ptr< FunctionInterface >	getFunction ()

void	setParameters (const ParameterList &parameters)
	Set the point where the function must be computed. More...

double	getValue () const
	Get the value of the function at the current point. More...

void	fireParameterChanged (const ParameterList &parameters)
	Notify the class when one or several parameters have changed. More...

bool	hasParameter (const std::string &name) const override
	Tell if there is a parameter with specified name. More...

const ParameterList &	getParameters () const override
	Get all parameters available. More...

const Parameter &	parameter (const std::string &name) const override
	Get the parameter with specified name. More...

double	getParameterValue (const std::string &name) const override
	Get the value for parameter of name 'name'. More...

void	setAllParametersValues (const ParameterList &parameters) override
	Set the parameters values to be equals to those of parameters. More...

void	setParameterValue (const std::string &name, double value) override
	Set the value of parameter with name name to be equal to value. More...

void	setParametersValues (const ParameterList &parameters) override
	Update the parameters from parameters. More...

bool	matchParametersValues (const ParameterList &parameters) override
	Update the parameters from parameters. More...

void	removeConstraint (const std::string &name) override
	Remove the constraint associated with one parameter, if any. More...

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
	Set/Change the constraint associated with one parameter. More...

size_t	getNumberOfParameters () const override
	Get the number of parameters. More...

void	setNamespace (const std::string &prefix) override
	Set the namespace for the parameter names. More...

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override
	Resolves a parameter name according to the current namespace. More...

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

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0
	Get all parameters available. More...

ParameterList &	getParameters_ () override
	Get all parameters available. More...

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

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

virtual void	addParameter_ (Parameter *parameter)

virtual void	addParameters_ (const ParameterList &parameters)

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

virtual void	shareParameters_ (const ParameterList &parameters)

virtual void	includeParameters_ (const ParameterList &parameters)

virtual void	deleteParameter_ (size_t index)

virtual void	deleteParameter_ (std::string &name)

virtual 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

Protected Attributes
std::shared_ptr< FunctionInterface >	function_

ParameterList	functionParameters_

Private Member Functions
void	init_ (bool verbose)

Detailed Description

Function wrapper that remove simple constraints on parameters. Also transform first order derivatives.

This function takes as input another function and reparametrize it when possible. currently, only constraint of the type ]a, b[ where a and b can be +/- inf.

Definition at line 113 of file ReparametrizationFunctionWrapper.h.

Constructor & Destructor Documentation

◆ ReparametrizationDerivableFirstOrderWrapper() [1/2]

bpp::ReparametrizationDerivableFirstOrderWrapper::ReparametrizationDerivableFirstOrderWrapper	(	std::shared_ptr< FirstOrderDerivable >	function,
		bool	verbose = `true`
	)

inline

Build a new reparametrization wrapper for the given function, using all available parameters.

Parameters

function	The function to reparametrize.
verbose	Print some information.

Definition at line 124 of file ReparametrizationFunctionWrapper.h.

◆ ReparametrizationDerivableFirstOrderWrapper() [2/2]

bpp::ReparametrizationDerivableFirstOrderWrapper::ReparametrizationDerivableFirstOrderWrapper	(	std::shared_ptr< FirstOrderDerivable >	function,
		const ParameterList &	parameters,
		bool	verbose = `true`
	)

inline

Build a new reparametrization wrapper for the given function, using only the specified parameters.

Parameters

function	The function to reparametrize.
parameters	The list of parameters that will be reparametrized. The intersection with the list of function parameters will be used in the reparametrized function. Any other parameters (in the given list or in the original function) will be ignored.
verbose	Print some information.

Definition at line 137 of file ReparametrizationFunctionWrapper.h.

◆ ~ReparametrizationDerivableFirstOrderWrapper()

virtual bpp::ReparametrizationDerivableFirstOrderWrapper::~ReparametrizationDerivableFirstOrderWrapper ( )

inlinevirtual

Definition at line 141 of file ReparametrizationFunctionWrapper.h.

Member Function Documentation

◆ addParameter_()

virtual void bpp::AbstractParametrizable::addParameter_ ( Parameter * parameter )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 111 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameter().

Referenced by bpp::AbstractParameterAliasable::addParameter_(), and bpp::AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix().

◆ addParameters_()

virtual void bpp::AbstractParametrizable::addParameters_ ( const ParameterList & parameters )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 117 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameters().

Referenced by bpp::AbstractParameterAliasable::addParameters_(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::LogsumHmmLikelihood::LogsumHmmLikelihood(), bpp::LowMemoryRescaledHmmLikelihood::LowMemoryRescaledHmmLikelihood(), and bpp::RescaledHmmLikelihood::RescaledHmmLikelihood().

◆ clone()

ReparametrizationDerivableFirstOrderWrapper* bpp::ReparametrizationDerivableFirstOrderWrapper::clone ( ) const

inlinevirtual

Create a copy of this object and send a pointer to it.

Returns: A pointer toward the copy object.

Implements bpp::FirstOrderDerivable.

Reimplemented in bpp::ReparametrizationDerivableSecondOrderWrapper.

Definition at line 143 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::init_().

◆ deleteParameter_() [1/2]

virtual void bpp::AbstractParametrizable::deleteParameter_ ( size_t index )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 137 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter(), and bpp::ParameterList::size().

Referenced by bpp::AbstractParameterAliasable::deleteParameter_().

◆ deleteParameter_() [2/2]

virtual void bpp::AbstractParametrizable::deleteParameter_ ( std::string & name )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 144 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter().

◆ deleteParameters_()

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

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 149 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameters().

◆ df()

virtual double bpp::FirstOrderDerivable::df	(	const std::string &	variable,
		const ParameterList &	parameters
	)

inlinevirtualinherited

Get the value of the first derivative of the function according to a given set of parameters.

Parameters

variable	The name of the variable in $\frac{df}{dx}$ .
parameters	The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Definition at line 138 of file Functions.h.

References bpp::FunctionInterface::setParameters().

◆ enableFirstOrderDerivatives() [1/2]

void bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives ( bool yn )

inlinevirtual

Tell if derivatives must be computed.

Parameters

yn yes/no

Implements bpp::FirstOrderDerivable.

Definition at line 149 of file ReparametrizationFunctionWrapper.h.

References enableFirstOrderDerivatives(), and bpp::ReparametrizationFunctionWrapper::function_.

Referenced by enableFirstOrderDerivatives().

◆ enableFirstOrderDerivatives() [2/2]

bool bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives ( ) const

inlinevirtual

Tell if derivatives must be computed.

Returns: yes/no

Implements bpp::FirstOrderDerivable.

Definition at line 151 of file ReparametrizationFunctionWrapper.h.

References enableFirstOrderDerivatives(), and bpp::ReparametrizationFunctionWrapper::function_.

Referenced by enableFirstOrderDerivatives().

◆ f()

virtual double bpp::FunctionInterface::f ( const ParameterList & parameters )

inlinevirtualinherited

Get the value of the function according to a given set of parameters.

Parameters

parameters The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Reimplemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, and bpp::AbstractNumericalDerivative.

Definition at line 82 of file Functions.h.

References bpp::FunctionInterface::getValue(), and bpp::FunctionInterface::setParameters().

Referenced by bpp::NumTools::uniRoot().

◆ fireParameterChanged()

void ReparametrizationFunctionWrapper::fireParameterChanged ( const ParameterList & parameters )

virtualinherited

Notify the class when one or several parameters have changed.

Parameters

parameters A ParameterList object with parameters that changed.

Reimplemented from bpp::AbstractParametrizable.

Definition at line 141 of file ReparametrizationFunctionWrapper.cpp.

References bpp::ApplicationTools::error, and bpp::Parameter::setValue().

Referenced by bpp::ReparametrizationFunctionWrapper::getValue().

◆ function() [1/2]

virtual const FunctionInterface& bpp::ReparametrizationFunctionWrapper::function ( ) const

inlinevirtualinherited

Definition at line 82 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_.

◆ function() [2/2]

virtual FunctionInterface& bpp::ReparametrizationFunctionWrapper::function ( )

inlinevirtualinherited

Definition at line 84 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_.

◆ getFirstOrderDerivative()

double bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative ( const std::string & variable ) const

inlinevirtual

Get the derivative of the function at the current point.

Parameters

variable The name of the variable in $\frac{df}{dx}$ .

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implements bpp::FirstOrderDerivable.

Definition at line 153 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_, and bpp::AbstractParametrizable::parameter().

◆ getFunction() [1/2]

virtual std::shared_ptr<const FunctionInterface> bpp::ReparametrizationFunctionWrapper::getFunction ( ) const

inlinevirtualinherited

Definition at line 86 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_.

◆ getFunction() [2/2]

virtual std::shared_ptr<FunctionInterface> bpp::ReparametrizationFunctionWrapper::getFunction ( )

inlinevirtualinherited

Definition at line 88 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_.

◆ getNamespace() [1/2]

std::string bpp::AbstractParametrizable::getNamespace ( ) const

inlineoverridevirtualinherited

Returns: The current namespace used. This is an empty string if no namespace is currently defined.

Implements bpp::Parametrizable.

Definition at line 99 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::Simplex::setFrequencies(), and bpp::AbstractParameterAliasable::setNamespace().

◆ getNamespace() [2/2]

virtual std::string bpp::Parametrizable::getNamespace ( ) const

pure virtualinherited

Returns: The current namespace used. This is an empty string if no namespace is currently defined.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ getNumberOfParameters() [1/2]

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlineoverridevirtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

Implements bpp::Parametrizable.

Definition at line 95 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::setNamespace(), and bpp::ParameterList::size().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::AbstractParameterAliasable::operator=(), bpp::ConstantDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

◆ getNumberOfParameters() [2/2]

virtual size_t bpp::Parametrizable::getNumberOfParameters ( ) const

pure virtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::AbstractParametrizable, and bpp::DirectionFunction.

Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution(), and bpp::Parametrizable::~Parametrizable().

◆ getParameter() [1/3]

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

inlineinherited

Definition at line 48 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::operator=(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ getParameter() [2/3]

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

inlineprotectedinherited

Returns: The shared_ptr parameter at a given position.

Warning: No check is performed on the validity of the index given as input!

Definition at line 211 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter() [3/3]

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

inlineprotectedinherited

Definition at line 216 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter_() [1/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string & name )

inlineprotectedinherited

Parameters

name	The name of the parameter.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 164 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::hasParameter(), and bpp::ParameterList::parameter().

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::AbstractParametrizable::removeConstraint(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::InvariantMixedDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::AbstractParametrizable::setConstraint(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ getParameter_() [2/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t index )

inlineprotectedinherited

Definition at line 190 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameter_() [3/3]

const Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t index ) const

inlineprotectedinherited

Definition at line 197 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameterNameWithoutNamespace() [1/2]

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

overridevirtualinherited

Resolves a parameter name according to the current namespace.

Returns: The parameter name without the namespace prefix, if any.

Implements bpp::Parametrizable.

Definition at line 28 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParametrizable::getNamespace(), and bpp::AbstractParameterAliasable::operator=().

◆ getParameterNameWithoutNamespace() [2/2]

virtual std::string bpp::Parametrizable::getParameterNameWithoutNamespace ( const std::string & name ) const

pure virtualinherited

Resolves a parameter name according to the current namespace.

Returns: The parameter name without the namespace prefix, if any.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::Parametrizable::~Parametrizable().

◆ getParameters() [1/2]

const ParameterList& bpp::AbstractParametrizable::getParameters ( ) const

inlineoverridevirtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 41 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), and bpp::ParametrizableCollection< N >::removeObject().

◆ getParameters() [2/2]

virtual const ParameterList& bpp::Parametrizable::getParameters ( ) const

pure virtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::DirectionFunction, and bpp::AbstractParametrizable.

Referenced by bpp::ParameterAliasableAdapter::getIndependentParameters(), bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::Parametrizable::~Parametrizable().

◆ getParameters_() [1/2]

virtual ParameterList& bpp::Parametrizable::getParameters_ ( )

protectedpure virtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implemented in bpp::FunctionWrapper, bpp::AbstractParametrizable, and bpp::DirectionFunction.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ getParameters_() [2/2]

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineoverrideprotectedvirtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 205 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), and bpp::AbstractParameterAliasable::operator=().

◆ getParameterValue() [1/2]

double bpp::AbstractParametrizable::getParameterValue ( const std::string & name ) const

inlineoverridevirtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 53 of file AbstractParametrizable.h.

References bpp::Parameter::getValue(), and bpp::AbstractParametrizable::parameter().

◆ getParameterValue() [2/2]

virtual double bpp::Parametrizable::getParameterValue ( const std::string & name ) const

pure virtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), and bpp::Parametrizable::~Parametrizable().

◆ getParameterWithNamespace_() [1/2]

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string & name )

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 176 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

const Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string & name ) const

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 185 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameter().

◆ getValue() [1/2]

virtual double bpp::FunctionInterface::getValue ( ) const

pure virtualinherited

Get the value of the function at the current point.

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implemented in bpp::TestFunction, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::ReparametrizationFunctionWrapper, bpp::ThreePointsNumericalDerivative, bpp::FivePointsNumericalDerivative, bpp::TwoPointsNumericalDerivative, and bpp::DirectionFunction.

Referenced by bpp::FunctionInterface::f(), bpp::AbstractNumericalDerivative::f(), bpp::InfinityFunctionWrapper::f(), and bpp::FunctionInterface::~FunctionInterface().

◆ getValue() [2/2]

double bpp::ReparametrizationFunctionWrapper::getValue ( ) const

inlinevirtualinherited

Get the value of the function at the current point.

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implements bpp::FunctionInterface.

Definition at line 99 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::fireParameterChanged().

◆ hasParameter() [1/2]

virtual bool bpp::Parametrizable::hasParameter ( const std::string & name ) const

pure virtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: y/n.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ hasParameter() [2/2]

bool bpp::AbstractParametrizable::hasParameter ( const std::string & name ) const

inlineoverridevirtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: y/n.

Implements bpp::Parametrizable.

Definition at line 39 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter().

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::AbstractParametrizable::getParameter_(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ includeParameters_()

virtual void bpp::AbstractParametrizable::includeParameters_ ( const ParameterList & parameters )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 132 of file AbstractParametrizable.h.

References bpp::ParameterList::includeParameters().

Referenced by bpp::AbstractParameterAliasable::includeParameters_().

◆ init_()

void bpp::ReparametrizationDerivableFirstOrderWrapper::init_ ( bool verbose )

private

◆ matchParametersValues() [1/2]

bool bpp::AbstractParametrizable::matchParametersValues ( const ParameterList & parameters )

inlineoverridevirtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

parameters A list of parameters.

Returns: True if at least one parameter value has been changed.

Exceptions

ConstraintException If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 76 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::ParameterList::matchParametersValues(), and bpp::ParameterList::shareSubList().

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::Simplex::setFrequencies(), bpp::ReparametrizationFunctionWrapper::setParameters(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

◆ matchParametersValues() [2/2]

virtual bool bpp::Parametrizable::matchParametersValues ( const ParameterList & parameters )

pure virtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

parameters A list of parameters.

Returns: True if at least one parameter value has been changed.

Exceptions

ConstraintException If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), bpp::TestFunction::setParameters(), and bpp::Parametrizable::~Parametrizable().

◆ parameter() [1/2]

const Parameter& bpp::AbstractParametrizable::parameter ( const std::string & name ) const

inlineoverridevirtualinherited

Get the parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: The parameter with given name.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 43 of file AbstractParametrizable.h.

References bpp::ParameterList::parameter().

Referenced by bpp::AbstractParameterAliasable::getAliasedParameters(), getFirstOrderDerivative(), bpp::AbstractParameterAliasable::getFromParameters(), bpp::AbstractParametrizable::getParameterValue(), bpp::AbstractParametrizable::getParameterWithNamespace_(), and bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative().

◆ parameter() [2/2]

virtual const Parameter& bpp::Parametrizable::parameter ( const std::string & name ) const

pure virtualinherited

Get the parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: The parameter with given name.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::TestFunction::getValue(), and bpp::Parametrizable::~Parametrizable().

◆ removeConstraint() [1/2]

void bpp::AbstractParametrizable::removeConstraint ( const std::string & name )

inlineoverridevirtualinherited

Remove the constraint associated with one parameter, if any.

Parameters

name	The name of the parameter to look for.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 85 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::removeConstraint().

◆ removeConstraint() [2/2]

virtual void bpp::Parametrizable::removeConstraint ( const std::string & name )

pure virtualinherited

Remove the constraint associated with one parameter, if any.

Parameters

name	The name of the parameter to look for.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ resetParameters_()

void bpp::AbstractParametrizable::resetParameters_ ( )

inlineprotectedinherited

Definition at line 154 of file AbstractParametrizable.h.

References bpp::ParameterList::reset().

Referenced by bpp::AbstractParameterAliasable::resetParameters_().

◆ setAllParametersValues() [1/2]

void bpp::AbstractParametrizable::setAllParametersValues ( const ParameterList & parameters )

inlineoverridevirtualinherited

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters

parameters A list with all parameters.

Exceptions

ParameterNotFoundException	If a some parameter in the list is not in params.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 58 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), and bpp::ParameterList::setAllParametersValues().

◆ setAllParametersValues() [2/2]

virtual void bpp::Parametrizable::setAllParametersValues ( const ParameterList & parameters )

pure virtualinherited

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters

parameters A list with all parameters.

Exceptions

ParameterNotFoundException	If a some parameter in the list is not in params.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setConstraint() [1/2]

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

inlineoverridevirtualinherited

Set/Change the constraint associated with one parameter.

Parameters

name	The name of the parameter to look for.
constraint	A pointer to the constraint (may be null)

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 90 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::setConstraint().

Referenced by bpp::SimpleDiscreteDistribution::restrictToConstraint().

◆ setConstraint() [2/2]

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

pure virtualinherited

Set/Change the constraint associated with one parameter.

Parameters

name	The name of the parameter to look for.
constraint	A pointer to the constraint (may be null)

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setNamespace() [1/2]

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

overridevirtualinherited

Set the namespace for the parameter names.

Parameters

prefix The 'namespace', that is a prefix to add to all parameter names. If parameter names are already prefixed, the new prefix will be used instead.

Implements bpp::Parametrizable.

Reimplemented in bpp::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 10 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParameterAliasable::setNamespace(), bpp::LowMemoryRescaledHmmLikelihood::setNamespace(), bpp::LogsumHmmLikelihood::setNamespace(), and bpp::RescaledHmmLikelihood::setNamespace().

◆ setNamespace() [2/2]

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

pure virtualinherited

Set the namespace for the parameter names.

Parameters

prefix The 'namespace', that is a prefix to add to all parameter names. If parameter names are already prefixed, the new prefix will be used instead.

Implemented in bpp::FunctionWrapper, bpp::ParametrizableAdapter, bpp::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, bpp::AbstractParametrizable, and bpp::InvariantMixedDiscreteDistribution.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setParameters() [1/2]

virtual void bpp::FunctionInterface::setParameters ( const ParameterList & parameters )

pure virtualinherited

Set the point where the function must be computed.

Parameters

parameters The parameter set to pass to the function.

Implemented in bpp::TestFunction, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::ReparametrizationFunctionWrapper, and bpp::DirectionFunction.

Referenced by bpp::SecondOrderDerivable::d2f(), bpp::InfinityDerivableSecondOrderWrapper::d2f(), bpp::FirstOrderDerivable::df(), bpp::InfinityDerivableFirstOrderWrapper::df(), bpp::FunctionInterface::f(), bpp::AbstractNumericalDerivative::f(), bpp::InfinityFunctionWrapper::f(), and bpp::FunctionInterface::~FunctionInterface().

◆ setParameters() [2/2]

void bpp::ReparametrizationFunctionWrapper::setParameters ( const ParameterList & parameters )

inlinevirtualinherited

Set the point where the function must be computed.

Parameters

parameters The parameter set to pass to the function.

Implements bpp::FunctionInterface.

Definition at line 90 of file ReparametrizationFunctionWrapper.h.

References bpp::ParameterList::createSubList(), bpp::ParameterList::getParameterNames(), and bpp::AbstractParametrizable::matchParametersValues().

◆ setParametersValues() [1/2]

void bpp::AbstractParametrizable::setParametersValues ( const ParameterList & parameters )

inlineoverridevirtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

parameters A list containing all parameters to update.

Exceptions

ParameterNotFoundException	If a some parameter in params is not in the list.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 70 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), and bpp::ParameterList::setParametersValues().

Referenced by bpp::LowMemoryRescaledHmmLikelihood::setParameters(), bpp::LogsumHmmLikelihood::setParameters(), and bpp::RescaledHmmLikelihood::setParameters().

◆ setParametersValues() [2/2]

virtual void bpp::Parametrizable::setParametersValues ( const ParameterList & parameters )

pure virtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

parameters A list containing all parameters to update.

Exceptions

ParameterNotFoundException	If a some parameter in params is not in the list.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setParameterValue() [1/2]

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

inlineoverridevirtualinherited

Set the value of parameter with name name to be equal to value.

Parameters

name	the name of the parameter to set.
value	The value of the parameter.

Exceptions

ParameterNotFoundException	If no parameter in the list has the name name.
ConstraintException	If value does not match the constraint associated to parameter name.

Implements bpp::Parametrizable.

Definition at line 64 of file AbstractParametrizable.h.

References bpp::ParameterList::createSubList(), bpp::AbstractParametrizable::fireParameterChanged(), and bpp::ParameterList::setParameterValue().

◆ setParameterValue() [2/2]

virtual void bpp::Parametrizable::setParameterValue	(	const std::string &	name,
		double	value
	)

pure virtualinherited

Set the value of parameter with name name to be equal to value.

Parameters

name	the name of the parameter to set.
value	The value of the parameter.

Exceptions

ParameterNotFoundException	If no parameter in the list has the name name.
ConstraintException	If value does not match the constraint associated to parameter name.

Implemented in bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ shareParameter_()

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

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 122 of file AbstractParametrizable.h.

References bpp::ParameterList::shareParameter().

Referenced by bpp::AbstractParameterAliasable::shareParameter_().

◆ shareParameters_()

virtual void bpp::AbstractParametrizable::shareParameters_ ( const ParameterList & parameters )

inlineprotectedvirtualinherited

Reimplemented in bpp::AbstractParameterAliasable.

Definition at line 127 of file AbstractParametrizable.h.

References bpp::ParameterList::shareParameters().

Referenced by bpp::AbstractParameterAliasable::shareParameters_().

Member Data Documentation

◆ function_

std::shared_ptr<FunctionInterface> bpp::ReparametrizationFunctionWrapper::function_

protectedinherited

Definition at line 26 of file ReparametrizationFunctionWrapper.h.

Referenced by enableFirstOrderDerivatives(), bpp::ReparametrizationDerivableSecondOrderWrapper::enableSecondOrderDerivatives(), bpp::ReparametrizationFunctionWrapper::function(), getFirstOrderDerivative(), bpp::ReparametrizationFunctionWrapper::getFunction(), bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative(), and bpp::ReparametrizationFunctionWrapper::operator=().

◆ functionParameters_

ParameterList bpp::ReparametrizationFunctionWrapper::functionParameters_

protectedinherited

Definition at line 27 of file ReparametrizationFunctionWrapper.h.

Referenced by bpp::ReparametrizationFunctionWrapper::operator=().

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

Bpp/Numeric/Function/ReparametrizationFunctionWrapper.h

Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ ReparametrizationDerivableFirstOrderWrapper() [1/2]

◆ ReparametrizationDerivableFirstOrderWrapper() [2/2]

◆ ~ReparametrizationDerivableFirstOrderWrapper()

Member Function Documentation

◆ addParameter_()

◆ addParameters_()

◆ clone()

◆ deleteParameter_() [1/2]

◆ deleteParameter_() [2/2]

◆ deleteParameters_()

◆ df()

◆ enableFirstOrderDerivatives() [1/2]

◆ enableFirstOrderDerivatives() [2/2]

◆ f()

◆ fireParameterChanged()

◆ function() [1/2]

◆ function() [2/2]

◆ getFirstOrderDerivative()

◆ getFunction() [1/2]

◆ getFunction() [2/2]

◆ getNamespace() [1/2]

◆ getNamespace() [2/2]

◆ getNumberOfParameters() [1/2]

◆ getNumberOfParameters() [2/2]

◆ getParameter() [1/3]

◆ getParameter() [2/3]

◆ getParameter() [3/3]

◆ getParameter_() [1/3]

◆ getParameter_() [2/3]

◆ getParameter_() [3/3]

◆ getParameterNameWithoutNamespace() [1/2]

◆ getParameterNameWithoutNamespace() [2/2]

◆ getParameters() [1/2]

◆ getParameters() [2/2]

◆ getParameters_() [1/2]

◆ getParameters_() [2/2]

◆ getParameterValue() [1/2]

◆ getParameterValue() [2/2]

◆ getParameterWithNamespace_() [1/2]

◆ getParameterWithNamespace_() [2/2]

◆ getValue() [1/2]

◆ getValue() [2/2]

◆ hasParameter() [1/2]

◆ hasParameter() [2/2]

◆ includeParameters_()

◆ init_()

◆ matchParametersValues() [1/2]

◆ matchParametersValues() [2/2]

◆ parameter() [1/2]

◆ parameter() [2/2]

◆ removeConstraint() [1/2]

◆ removeConstraint() [2/2]

◆ resetParameters_()

◆ setAllParametersValues() [1/2]

◆ setAllParametersValues() [2/2]

◆ setConstraint() [1/2]

◆ setConstraint() [2/2]

◆ setNamespace() [1/2]

◆ setNamespace() [2/2]

◆ setParameters() [1/2]

◆ setParameters() [2/2]

◆ setParametersValues() [1/2]

◆ setParametersValues() [2/2]

◆ setParameterValue() [1/2]

◆ setParameterValue() [2/2]

◆ shareParameter_()

◆ shareParameters_()

Member Data Documentation

◆ function_

◆ functionParameters_