Parameter transformation from ] a, b [ to ]-inf, + inf [. More...

#include <Bpp/Numeric/TransformedParameter.h>

Inheritance diagram for bpp::IntervalTransformedParameter:

Collaboration diagram for bpp::IntervalTransformedParameter:

Public Member Functions
	IntervalTransformedParameter (const std::string &name, double value, double lowerBound=0, double upperBound=1, double scale=1, bool hyper=true)
	Build a new IntervalTransformedParameter, with given bounds and scale. More...

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

void	setOriginalValue (double value)
	Set the value of the parameter using the orignal coordinate system. More...

double	getOriginalValue () const

double	getFirstOrderDerivative () const

double	getSecondOrderDerivative () const

virtual void	setName (const std::string &name)
	Set the name of this parameter. More...

virtual void	setValue (double value)
	Set the value of this parameter. More...

void	setPrecision (double precision)
	Set the precision of this parameter. More...

virtual const std::string &	getName () const
	Get the name of this parameter. More...

virtual double	getValue () const
	Get the value of this parameter. More...

virtual double	getPrecision () const
	Get the precision of this parameter. More...

virtual std::shared_ptr< const ConstraintInterface >	getConstraint () const
	Return the constraint associated to this parameter if there is one. More...

virtual std::shared_ptr< ConstraintInterface >	getConstraint ()
	Return the constraint associated to this parameter if there is one. More...

virtual const ConstraintInterface &	constraint () const
	Return the constraint associated to this parameter if there is one. More...

virtual ConstraintInterface &	constraint ()
	Return the constraint associated to this parameter if there is one. More...

virtual bool	hasConstraint () const
	Tells if this parameter has a constraint. More...

virtual std::shared_ptr< ConstraintInterface >	removeConstraint ()
	Remove the constraint associated to this parameter. More...

virtual void	setConstraint (std::shared_ptr< ConstraintInterface > constraint)
	Set a constraint to this parameter. More...

virtual void	addParameterListener (std::shared_ptr< ParameterListener > listener)
	Add a new listener to this parameter. More...

virtual void	removeParameterListener (const std::string &listenerId)
	Remove all listeners with a given id from this parameter. More...

virtual bool	hasParameterListener (const std::string &listenerId)
	Tell is there is a listener with a given id from this parameter. More...

Static Public Attributes
static const std::shared_ptr< IntervalConstraint >	R_PLUS

static const std::shared_ptr< IntervalConstraint >	R_PLUS_STAR

static const std::shared_ptr< IntervalConstraint >	R_MINUS

static const std::shared_ptr< IntervalConstraint >	R_MINUS_STAR

static const std::shared_ptr< IntervalConstraint >	PROP_CONSTRAINT_IN

static const std::shared_ptr< IntervalConstraint >	PROP_CONSTRAINT_EX

Protected Member Functions
void	fireParameterNameChanged (ParameterEvent &event)

void	fireParameterValueChanged (ParameterEvent &event)

void	fireParameterConstraintChanged (ParameterEvent &event)

Protected Attributes
std::string	name_

double	value_

double	precision_

std::shared_ptr< ConstraintInterface >	constraint_

std::vector< std::shared_ptr< ParameterListener > >	listeners_

Private Attributes
double	scale_

double	lowerBound_

double	upperBound_

bool	hyper_

double	tiny_

Detailed Description

Parameter transformation from ] a, b [ to ]-inf, + inf [.

The equation of the tranformation is

$x' = s\tan\left(\pi\frac{x-a}{b-a} - \frac{\pi}{2}\right)$

The 'a' and 'b' parameters are the lower and upper bounds and 's' is a scaling factor set to 1 by default. If the hyperbolic option is set to true (the default), then the following transformation is used instead:

$x' = s\,\text{atanh}\left(2\frac{x-a}{b-a} - 1\right)$

Definition at line 165 of file TransformedParameter.h.

Constructor & Destructor Documentation

◆ IntervalTransformedParameter()

bpp::IntervalTransformedParameter::IntervalTransformedParameter	(	const std::string &	name,
		double	value,
		double	lowerBound = `0`,
		double	upperBound = `1`,
		double	scale = `1`,
		bool	hyper = `true`
	)

inline

Build a new IntervalTransformedParameter, with given bounds and scale.

Parameters

name	the name of the parameter.
value	the value of th eparameter, in orginal coordinates.
lowerBound	the inerval lower bound to use.
upperBound	the inerval lower bound to use.
scale	the scaling factor.
hyper	tell if the hyberbolic function should be used (true by default).

Definition at line 186 of file TransformedParameter.h.

Member Function Documentation

◆ addParameterListener()

virtual void bpp::Parameter::addParameterListener ( std::shared_ptr< ParameterListener > listener )

inlinevirtualinherited

Add a new listener to this parameter.

Parameters

listener The listener to add.

Definition at line 261 of file Parameter.h.

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

◆ clone()

IntervalTransformedParameter* bpp::IntervalTransformedParameter::clone ( ) const

inlinevirtual

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

Returns: A pointer toward the copy object.

Implements bpp::TransformedParameter.

Definition at line 197 of file TransformedParameter.h.

◆ constraint() [1/2]

virtual const ConstraintInterface& bpp::Parameter::constraint ( ) const

inlinevirtualinherited

Return the constraint associated to this parameter if there is one.

Returns: A referec toward the constraint if there is one, otherwise throw an exception.

Definition at line 203 of file Parameter.h.

Referenced by bpp::Parameter::setConstraint().

◆ constraint() [2/2]

virtual ConstraintInterface& bpp::Parameter::constraint ( )

inlinevirtualinherited

Return the constraint associated to this parameter if there is one.

Returns: A referec toward the constraint if there is one, otherwise throw an exception.

Definition at line 225 of file Parameter.h.

◆ fireParameterConstraintChanged()

void bpp::Parameter::fireParameterConstraintChanged ( ParameterEvent & event )

inlineprotectedinherited

Definition at line 298 of file Parameter.h.

◆ fireParameterNameChanged()

void bpp::Parameter::fireParameterNameChanged ( ParameterEvent & event )

inlineprotectedinherited

Definition at line 282 of file Parameter.h.

◆ fireParameterValueChanged()

void bpp::Parameter::fireParameterValueChanged ( ParameterEvent & event )

inlineprotectedinherited

Definition at line 290 of file Parameter.h.

Referenced by bpp::Parameter::setValue().

◆ getConstraint() [1/2]

virtual std::shared_ptr<const ConstraintInterface> bpp::Parameter::getConstraint ( ) const

inlinevirtualinherited

Return the constraint associated to this parameter if there is one.

Returns: A shared pointer toward the constraint, or NULL if there is no constraint.

Definition at line 196 of file Parameter.h.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::ReparametrizationFunctionWrapper::init_(), bpp::ParameterList::matchParametersValues(), bpp::AliasParameterListener::parameterConstraintChanged(), bpp::ParameterList::setParametersValues(), and bpp::ParameterList::testParametersValues().

◆ getConstraint() [2/2]

virtual std::shared_ptr<ConstraintInterface> bpp::Parameter::getConstraint ( )

inlinevirtualinherited

Return the constraint associated to this parameter if there is one.

Returns: A shared pointer toward the constraint, or NULL if there is no constraint.

Definition at line 218 of file Parameter.h.

◆ getFirstOrderDerivative()

double bpp::IntervalTransformedParameter::getFirstOrderDerivative ( ) const

inlinevirtual

Returns: The first order derivative of the transformation at the original point.

Exceptions

NotImplementedException if the transformation does not support derivation or if the derivation was not implemented.

Implements bpp::TransformedParameter.

Definition at line 218 of file TransformedParameter.h.

References bpp::Parameter::getValue(), and bpp::NumConstants::PI().

◆ getName()

virtual const std::string& bpp::Parameter::getName ( ) const

inlinevirtualinherited

Get the name of this parameter.

Returns: The parameter name.

Definition at line 174 of file Parameter.h.

Referenced by bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::addParameter_(), bpp::ParameterList::getCommonParametersWith(), bpp::ParametersStopCondition::getCurrentTolerance(), bpp::NumCalcApplicationTools::getDefaultValue(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), bpp::ReparametrizationFunctionWrapper::init_(), bpp::ParametersStopCondition::isToleranceReached(), bpp::ParameterList::parameter(), bpp::AliasParameterListener::parameterConstraintChanged(), bpp::AliasParameterListener::parameterValueChanged(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

◆ getOriginalValue()

double bpp::IntervalTransformedParameter::getOriginalValue ( ) const

inlinevirtual

Returns: The current value of the parameter in orignal coordinates.

Implements bpp::TransformedParameter.

Definition at line 208 of file TransformedParameter.h.

References bpp::Parameter::getValue(), and bpp::NumConstants::PI().

◆ getPrecision()

virtual double bpp::Parameter::getPrecision ( ) const

inlinevirtualinherited

Get the precision of this parameter.

Returns: The precision value.

Definition at line 188 of file Parameter.h.

◆ getSecondOrderDerivative()

double bpp::IntervalTransformedParameter::getSecondOrderDerivative ( ) const

inlinevirtual

Returns: The second order derivative of the transformation at the original point.

Exceptions

NotImplementedException if the transformation does not support derivation or if the derivation was not implemented.

Implements bpp::TransformedParameter.

Definition at line 226 of file TransformedParameter.h.

References bpp::Parameter::getValue(), and bpp::NumConstants::PI().

◆ getValue()

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

inlinevirtualinherited

Get the value of this parameter.

Returns: The parameter value.

Definition at line 181 of file Parameter.h.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::ParametersStopCondition::getCurrentTolerance(), bpp::NumCalcApplicationTools::getDefaultValue(), bpp::RTransformedParameter::getFirstOrderDerivative(), getFirstOrderDerivative(), bpp::RTransformedParameter::getOriginalValue(), getOriginalValue(), bpp::PlaceboTransformedParameter::getOriginalValue(), bpp::AbstractParametrizable::getParameterValue(), bpp::ParameterList::getParameterValue(), bpp::RTransformedParameter::getSecondOrderDerivative(), getSecondOrderDerivative(), bpp::TestFunction::getValue(), bpp::ReparametrizationFunctionWrapper::init_(), bpp::ParametersStopCondition::isToleranceReached(), bpp::ParameterList::matchParametersValues(), bpp::ParameterList::setAllParametersValues(), bpp::ParameterList::setParametersValues(), and bpp::ParameterList::testParametersValues().

◆ hasConstraint()

virtual bool bpp::Parameter::hasConstraint ( ) const

inlinevirtualinherited

Tells if this parameter has a constraint.

Returns: True if this parameter has a contraint.

Definition at line 238 of file Parameter.h.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::ParameterList::matchParametersValues(), bpp::ParameterList::setParametersValues(), and bpp::ParameterList::testParametersValues().

◆ hasParameterListener()

bool Parameter::hasParameterListener ( const std::string & listenerId )

virtualinherited

Tell is there is a listener with a given id from this parameter.

Parameters

listenerId The id of listener to remove.

Returns: True if at list one listener with the given id was found.

Definition at line 104 of file Parameter.cpp.

References bpp::Parameter::listeners_, bpp::Parameter::PROP_CONSTRAINT_EX, bpp::Parameter::PROP_CONSTRAINT_IN, bpp::Parameter::R_MINUS, bpp::Parameter::R_MINUS_STAR, bpp::Parameter::R_PLUS, and bpp::Parameter::R_PLUS_STAR.

◆ removeConstraint()

std::shared_ptr< ConstraintInterface > Parameter::removeConstraint ( )

virtualinherited

Remove the constraint associated to this parameter.

Warning! The contraint objet is not deleted.

Returns: A pointer toward the formerly used contraint.

Definition at line 85 of file Parameter.cpp.

References bpp::Parameter::constraint_.

Referenced by bpp::AbstractParametrizable::removeConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

◆ removeParameterListener()

void Parameter::removeParameterListener ( const std::string & listenerId )

virtualinherited

Remove all listeners with a given id from this parameter.

Parameters

listenerId The id of listener to remove.

Definition at line 94 of file Parameter.cpp.

References bpp::Parameter::listeners_.

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

◆ setConstraint()

void Parameter::setConstraint ( std::shared_ptr< ConstraintInterface > constraint )

virtualinherited

Set a constraint to this parameter.

Parameters

constraint A pointer to the constraint (may be null)

Constraint:

Definition at line 76 of file Parameter.cpp.

References bpp::Parameter::constraint(), bpp::Parameter::constraint_, and bpp::Parameter::value_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AliasParameterListener::parameterConstraintChanged(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), and bpp::AbstractParametrizable::setConstraint().

◆ setName()

virtual void bpp::Parameter::setName ( const std::string & name )

inlinevirtualinherited

Set the name of this parameter.

Parameters

name	the new parameter name.

Definition at line 148 of file Parameter.h.

Referenced by bpp::ParametrizableCollection< N >::addObject(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

◆ setOriginalValue()

void bpp::IntervalTransformedParameter::setOriginalValue ( double value )

inlinevirtual

Set the value of the parameter using the orignal coordinate system.

Parameters

value Parameter value in original coordinates.

Exceptions

ConstraintException if the value is not correct.

Implements bpp::TransformedParameter.

Definition at line 200 of file TransformedParameter.h.

References bpp::NumConstants::PI(), and bpp::Parameter::setValue().

◆ setPrecision()

void Parameter::setPrecision ( double precision )

inherited

Set the precision of this parameter.

Parameters

precision the new parameter precision.

Precision:

Definition at line 69 of file Parameter.cpp.

References bpp::Parameter::precision_.

Referenced by bpp::Parameter::Parameter().

◆ setValue()

void Parameter::setValue ( double value )

virtualinherited

Set the value of this parameter.

Parameters

value the new parameter value.

Value:

Reimplemented in bpp::AutoParameter.

Definition at line 55 of file Parameter.cpp.

References bpp::Parameter::constraint_, bpp::Parameter::fireParameterValueChanged(), bpp::Parameter::precision_, and bpp::Parameter::value_.

Referenced by bpp::GoldenSectionSearch::doInit(), bpp::BrentOneDimension::doInit(), bpp::NewtonBacktrackOneDimension::doStep(), bpp::GoldenSectionSearch::doStep(), bpp::BrentOneDimension::doStep(), bpp::ReparametrizationFunctionWrapper::fireParameterChanged(), bpp::ParameterList::matchParametersValues(), bpp::Parameter::Parameter(), bpp::AliasParameterListener::parameterValueChanged(), bpp::ParameterList::setAllParametersValues(), bpp::RTransformedParameter::setOriginalValue(), setOriginalValue(), bpp::PlaceboTransformedParameter::setOriginalValue(), bpp::ParameterList::setParametersValues(), bpp::ParameterList::setParameterValue(), and bpp::AutoParameter::setValue().

Member Data Documentation

◆ constraint_

std::shared_ptr<ConstraintInterface> bpp::Parameter::constraint_

protectedinherited

Definition at line 104 of file Parameter.h.

Referenced by bpp::Parameter::operator=(), bpp::Parameter::removeConstraint(), bpp::Parameter::setConstraint(), bpp::AutoParameter::setValue(), and bpp::Parameter::setValue().

◆ hyper_

bool bpp::IntervalTransformedParameter::hyper_

private

Definition at line 172 of file TransformedParameter.h.

◆ listeners_

std::vector< std::shared_ptr<ParameterListener> > bpp::Parameter::listeners_

protectedinherited

Definition at line 105 of file Parameter.h.

Referenced by bpp::Parameter::hasParameterListener(), bpp::Parameter::operator=(), and bpp::Parameter::removeParameterListener().

◆ lowerBound_

double bpp::IntervalTransformedParameter::lowerBound_

private

Definition at line 170 of file TransformedParameter.h.

◆ name_

std::string bpp::Parameter::name_

protectedinherited

Definition at line 101 of file Parameter.h.

Referenced by bpp::Parameter::operator=(), and bpp::AutoParameter::setValue().

◆ precision_

double bpp::Parameter::precision_

protectedinherited

Definition at line 103 of file Parameter.h.

Referenced by bpp::Parameter::operator=(), bpp::Parameter::setPrecision(), and bpp::Parameter::setValue().

◆ PROP_CONSTRAINT_EX

const std::shared_ptr< IntervalConstraint > Parameter::PROP_CONSTRAINT_EX

staticinherited

Definition at line 312 of file Parameter.h.

Referenced by bpp::AutoCorrelationTransitionMatrix::AutoCorrelationTransitionMatrix(), bpp::Parameter::hasParameterListener(), and bpp::Simplex::Simplex().

◆ PROP_CONSTRAINT_IN

const std::shared_ptr< IntervalConstraint > Parameter::PROP_CONSTRAINT_IN

staticinherited

Definition at line 311 of file Parameter.h.

Referenced by bpp::Parameter::hasParameterListener(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), and bpp::Simplex::Simplex().

◆ R_MINUS

const std::shared_ptr< IntervalConstraint > Parameter::R_MINUS

staticinherited

Definition at line 309 of file Parameter.h.

Referenced by bpp::Parameter::hasParameterListener().

◆ R_MINUS_STAR

const std::shared_ptr< IntervalConstraint > Parameter::R_MINUS_STAR

staticinherited

Definition at line 310 of file Parameter.h.

Referenced by bpp::Parameter::hasParameterListener().

◆ R_PLUS

const std::shared_ptr< IntervalConstraint > Parameter::R_PLUS

staticinherited

Definition at line 307 of file Parameter.h.

Referenced by bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::Parameter::hasParameterListener(), and bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution().

◆ R_PLUS_STAR

const std::shared_ptr< IntervalConstraint > Parameter::R_PLUS_STAR

staticinherited

Definition at line 308 of file Parameter.h.

Referenced by bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution(), and bpp::Parameter::hasParameterListener().

◆ scale_

double bpp::IntervalTransformedParameter::scale_

private

Definition at line 169 of file TransformedParameter.h.

◆ tiny_

double bpp::IntervalTransformedParameter::tiny_

private

Definition at line 173 of file TransformedParameter.h.

◆ upperBound_

double bpp::IntervalTransformedParameter::upperBound_

private

Definition at line 171 of file TransformedParameter.h.

◆ value_

double bpp::Parameter::value_

protectedinherited

Definition at line 102 of file Parameter.h.

Referenced by bpp::Parameter::operator=(), bpp::Parameter::setConstraint(), and bpp::Parameter::setValue().

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

Bpp/Numeric/TransformedParameter.h

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ IntervalTransformedParameter()

Member Function Documentation

◆ addParameterListener()

◆ clone()

◆ constraint() [1/2]

◆ constraint() [2/2]

◆ fireParameterConstraintChanged()

◆ fireParameterNameChanged()

◆ fireParameterValueChanged()

◆ getConstraint() [1/2]

◆ getConstraint() [2/2]

◆ getFirstOrderDerivative()

◆ getName()

◆ getOriginalValue()

◆ getPrecision()

◆ getSecondOrderDerivative()

◆ getValue()

◆ hasConstraint()

◆ hasParameterListener()

◆ removeConstraint()

◆ removeParameterListener()

◆ setConstraint()

◆ setName()

◆ setOriginalValue()

◆ setPrecision()

◆ setValue()

Member Data Documentation

◆ constraint_

◆ hyper_

◆ listeners_

◆ lowerBound_

◆ name_

◆ precision_

◆ PROP_CONSTRAINT_EX

◆ PROP_CONSTRAINT_IN

◆ R_MINUS

◆ R_MINUS_STAR

◆ R_PLUS

◆ R_PLUS_STAR

◆ scale_

◆ tiny_

◆ upperBound_

◆ value_