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

#include <Bpp/Numeric/TransformedParameter.h>

Inheritance diagram for bpp::RTransformedParameter:

Collaboration diagram for bpp::RTransformedParameter:

Public Member Functions
	RTransformedParameter (const std::string &name, double value, double bound=0, bool positive=true, double scale=1)
	Build a new RTransformedParameter, with given bound and scale. More...

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

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

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

virtual void	addParameterListener (ParameterListener *listener, bool attachListener=true)
	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< Constraint >	constraint_

std::vector< ParameterListener * >	listeners_

std::vector< bool >	listenerAttach_

Private Attributes
double	scale_

double	bound_

bool	positive_

Detailed Description

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

The equation of the tranformation is

$x' = \begin{cases} \log(a\cdot(x-b)) & \text{if $x < b+1$},\\ a(x-1-b) & \text{if $a \geq b+1$}. \end{cases}$

for a transformation from ] b, +inf [ to ]-inf, + inf [. The 'b' parameter is the lower bound and 'a' is a scaling factor set to 1 by default. For a transformation from ] -inf, b [, the transformation is then

$x' = \begin{cases} -\log(-a\cdot(x-b)) & \text{if $x < b-1$},\\ -a(x-1-b) & \text{if $a \geq b-1$}. \end{cases}$

Definition at line 117 of file TransformedParameter.h.

Constructor & Destructor Documentation

◆ RTransformedParameter()

bpp::RTransformedParameter::RTransformedParameter	(	const std::string &	name,
		double	value,
		double	bound = `0`,
		bool	positive = `true`,
		double	scale = `1`
	)

inline

Build a new RTransformedParameter, with given bound and scale.

Parameters

name	the name of the parameter.
value	the value of th eparameter, in orginal coordinates.
bound	the inerval bound to use.
positive	tell if the original interval is positive or negative.
scale	the scaling factor.

Definition at line 135 of file TransformedParameter.h.

References setOriginalValue().

Referenced by clone().

Member Function Documentation

◆ addParameterListener()

virtual void bpp::Parameter::addParameterListener	(	ParameterListener *	listener,
		bool	attachListener = `true`
	)

inlinevirtualinherited

Add a new listener to this parameter.

Parameters

listener	The listener to add.
attachListener	Tell if the parameter will own this listener. If so, deep copies will be made when cloning the parameter, and the listener will be destroyed upon destruction of the parameter or upon removal. Alternatively, only superficial copies will be made, and the listener will persist if the parameter is destroyed.

Definition at line 278 of file Parameter.h.

References bpp::Parameter::listenerAttach_, and bpp::Parameter::listeners_.

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

◆ clone()

RTransformedParameter* bpp::RTransformedParameter::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 144 of file TransformedParameter.h.

References RTransformedParameter().

◆ fireParameterConstraintChanged()

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

inlineprotectedinherited

Definition at line 316 of file Parameter.h.

References bpp::Parameter::listeners_.

◆ fireParameterNameChanged()

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

inlineprotectedinherited

Definition at line 300 of file Parameter.h.

References bpp::Parameter::listeners_.

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

◆ fireParameterValueChanged()

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

inlineprotectedinherited

Definition at line 308 of file Parameter.h.

References bpp::Parameter::listeners_.

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

◆ getConstraint() [1/2]

virtual std::shared_ptr<Constraint> 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 242 of file Parameter.h.

References bpp::Parameter::constraint_.

◆ getConstraint() [2/2]

virtual const std::shared_ptr<Constraint> 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 233 of file Parameter.h.

References bpp::Parameter::constraint_.

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

◆ getFirstOrderDerivative()

double bpp::RTransformedParameter::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 166 of file TransformedParameter.h.

References bpp::Parameter::getValue(), positive_, and scale_.

◆ getName()

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

inlinevirtualinherited

Get the name of this parameter.

Returns: The parameter name.

Definition at line 211 of file Parameter.h.

References bpp::Parameter::name_.

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

◆ getOriginalValue()

double bpp::RTransformedParameter::getOriginalValue ( ) const

inlinevirtual

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

Implements bpp::TransformedParameter.

Definition at line 156 of file TransformedParameter.h.

References bound_, bpp::Parameter::getValue(), positive_, and scale_.

◆ getPrecision()

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

inlinevirtualinherited

Get the precision of this parameter.

Returns: The precision value.

Definition at line 225 of file Parameter.h.

References bpp::Parameter::precision_.

◆ getSecondOrderDerivative()

double bpp::RTransformedParameter::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 176 of file TransformedParameter.h.

References bpp::Parameter::getValue(), positive_, and scale_.

◆ getValue()

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

inlinevirtualinherited

Get the value of this parameter.

Returns: The parameter value.

Definition at line 218 of file Parameter.h.

References bpp::Parameter::value_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::ParametersStopCondition::getCurrentTolerance(), bpp::NumCalcApplicationTools::getDefaultValue(), getFirstOrderDerivative(), bpp::IntervalTransformedParameter::getFirstOrderDerivative(), getOriginalValue(), bpp::IntervalTransformedParameter::getOriginalValue(), bpp::PlaceboTransformedParameter::getOriginalValue(), bpp::AbstractParametrizable::getParameterValue(), bpp::ParameterList::getParameterValue(), getSecondOrderDerivative(), bpp::IntervalTransformedParameter::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 249 of file Parameter.h.

References bpp::Parameter::constraint_.

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 165 of file Parameter.cpp.

References bpp::Parameter::listeners_.

◆ removeConstraint()

std::shared_ptr< Constraint > 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 140 of file Parameter.cpp.

References bpp::Parameter::constraint_.

Referenced by 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 149 of file Parameter.cpp.

References bpp::Parameter::listenerAttach_, and bpp::Parameter::listeners_.

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

◆ setConstraint()

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

virtualinherited

Set a constraint to this parameter.

Parameters

constraint a pointer to the constraint (may be null)

Constraint:

Definition at line 131 of file Parameter.cpp.

References bpp::Parameter::constraint_, and bpp::Parameter::value_.

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

◆ 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 185 of file Parameter.h.

References bpp::Parameter::fireParameterNameChanged(), and bpp::Parameter::name_.

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

◆ setOriginalValue()

void bpp::RTransformedParameter::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 147 of file TransformedParameter.h.

References bound_, positive_, scale_, and bpp::Parameter::setValue().

Referenced by RTransformedParameter().

◆ setPrecision()

void Parameter::setPrecision ( double precision )

inherited

Set the precision of this parameter.

Parameters

precision the new parameter precision.

Precision:

Definition at line 124 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 110 of file Parameter.cpp.

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

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

Member Data Documentation

◆ bound_

double bpp::RTransformedParameter::bound_

private

Definition at line 122 of file TransformedParameter.h.

Referenced by getOriginalValue(), and setOriginalValue().

◆ constraint_

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

protectedinherited

Definition at line 140 of file Parameter.h.

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

◆ listenerAttach_

std::vector<bool> bpp::Parameter::listenerAttach_

protectedinherited

Definition at line 142 of file Parameter.h.

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

◆ listeners_

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

protectedinherited

Definition at line 141 of file Parameter.h.

Referenced by bpp::Parameter::addParameterListener(), bpp::Parameter::fireParameterConstraintChanged(), bpp::Parameter::fireParameterNameChanged(), bpp::Parameter::fireParameterValueChanged(), bpp::Parameter::hasParameterListener(), bpp::Parameter::operator=(), bpp::Parameter::Parameter(), bpp::Parameter::removeParameterListener(), and bpp::Parameter::~Parameter().

◆ name_

std::string bpp::Parameter::name_

protectedinherited

Definition at line 137 of file Parameter.h.

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

◆ positive_

bool bpp::RTransformedParameter::positive_

private

Definition at line 123 of file TransformedParameter.h.

Referenced by getFirstOrderDerivative(), getOriginalValue(), getSecondOrderDerivative(), and setOriginalValue().

◆ precision_

double bpp::Parameter::precision_

protectedinherited

Definition at line 139 of file Parameter.h.

Referenced by bpp::Parameter::getPrecision(), 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 330 of file Parameter.h.

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

◆ PROP_CONSTRAINT_IN

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

staticinherited

Definition at line 329 of file Parameter.h.

Referenced by 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 327 of file Parameter.h.

◆ R_MINUS_STAR

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

staticinherited

Definition at line 328 of file Parameter.h.

◆ R_PLUS

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

staticinherited

Definition at line 325 of file Parameter.h.

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

◆ R_PLUS_STAR

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

staticinherited

Definition at line 326 of file Parameter.h.

Referenced by bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution().

◆ scale_

double bpp::RTransformedParameter::scale_

private

Definition at line 121 of file TransformedParameter.h.

Referenced by getFirstOrderDerivative(), getOriginalValue(), getSecondOrderDerivative(), and setOriginalValue().

◆ value_

double bpp::Parameter::value_

protectedinherited

Definition at line 138 of file Parameter.h.

Referenced by bpp::Parameter::getValue(), 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

◆ RTransformedParameter()

Member Function Documentation

◆ addParameterListener()

◆ clone()

◆ 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

◆ bound_

◆ constraint_

◆ listenerAttach_

◆ listeners_

◆ name_

◆ positive_

◆ precision_

◆ PROP_CONSTRAINT_EX

◆ PROP_CONSTRAINT_IN

◆ R_MINUS

◆ R_MINUS_STAR

◆ R_PLUS

◆ R_PLUS_STAR

◆ scale_

◆ value_