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) throw (ConstraintException)
	Set the value of the parameter using the orignal coordinate system. More...

double	getOriginalValue () const

double	getFirstOrderDerivative () const throw (NotImplementedException)

double	getSecondOrderDerivative () const throw (NotImplementedException)

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

virtual void	setValue (double value) throw (ConstraintException)
	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 Constraint *	getConstraint () const
	Return the constraint associated to this parameter if there is one. More...

virtual 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 const Constraint *	removeConstraint ()
	Remove the constraint associated to this parameter. More...

virtual void	setConstraint (Constraint *constraint, bool attach=false)
	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 IntervalConstraint	R_PLUS

static const IntervalConstraint	R_PLUS_STAR

static const IntervalConstraint	R_MINUS

static const IntervalConstraint	R_MINUS_STAR

static const IntervalConstraint	PROP_CONSTRAINT_IN

static const IntervalConstraint	PROP_CONSTRAINT_EX

Protected Member Functions
void	fireParameterNameChanged (ParameterEvent &event)

void	fireParameterValueChanged (ParameterEvent &event)

Protected Attributes
std::string	name_

double	value_

double	precision_

Constraint *	constraint_

bool	attach_

std::vector< ParameterListener * >	listeners_

std::vector< bool >	listenerAttach_

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 205 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 226 of file TransformedParameter.h.

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 298 of file Parameter.h.

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

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 237 of file TransformedParameter.h.

◆ fireParameterNameChanged()

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

inlineprotectedinherited

Definition at line 320 of file Parameter.h.

References bpp::Parameter::listeners_.

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

◆ fireParameterValueChanged()

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

inlineprotectedinherited

Definition at line 325 of file Parameter.h.

References bpp::Parameter::listeners_.

◆ getConstraint() [1/2]

virtual const Constraint* bpp::Parameter::getConstraint ( ) const

inlinevirtualinherited

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

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

Definition at line 255 of file Parameter.h.

References bpp::Parameter::constraint_.

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

◆ getConstraint() [2/2]

virtual Constraint* bpp::Parameter::getConstraint ( )

inlinevirtualinherited

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

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

Definition at line 262 of file Parameter.h.

References bpp::Parameter::constraint_.

◆ getFirstOrderDerivative()

double bpp::IntervalTransformedParameter::getFirstOrderDerivative	(		)	const
throw	(	NotImplementedException
	)

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 258 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 234 of file Parameter.h.

References bpp::Parameter::name_.

Referenced by bpp::ParameterList::deleteParameter(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), 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::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 248 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 248 of file Parameter.h.

References bpp::Parameter::precision_.

◆ getSecondOrderDerivative()

double bpp::IntervalTransformedParameter::getSecondOrderDerivative	(		)	const
throw	(	NotImplementedException
	)

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 266 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 241 of file Parameter.h.

References bpp::Parameter::value_.

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 269 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 187 of file Parameter.cpp.

References bpp::Parameter::listeners_.

◆ removeConstraint()

const 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 163 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 172 of file Parameter.cpp.

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

◆ setConstraint()

void Parameter::setConstraint	(	Constraint *	constraint,
		bool	attach = `false`
	)

virtualinherited

Set a constraint to this parameter.

Parameters

constraint	a pointer to the constraint (may be null)
attach	says if the constraint is attached to the Parameter (default: false).

Constraint:

Definition at line 143 of file Parameter.cpp.

References bpp::Parameter::attach_, bpp::Parameter::constraint_, bpp::Constraint::isCorrect(), and bpp::Parameter::value_.

Referenced by bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::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 208 of file Parameter.h.

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

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

◆ setOriginalValue()

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

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 240 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 136 of file Parameter.cpp.

References bpp::Parameter::precision_.

◆ setValue()

void Parameter::setValue	(	double	value	)
throw	(	ConstraintException
	)

virtualinherited

Set the value of this parameter.

Parameters

value the new parameter value.

Value:

Reimplemented in bpp::AutoParameter.

Definition at line 123 of file Parameter.cpp.

Referenced by bpp::NewtonBacktrackOneDimension::doStep(), bpp::GoldenSectionSearch::doStep(), bpp::BrentOneDimension::doStep(), bpp::ReparametrizationFunctionWrapper::fireParameterChanged(), bpp::ParameterList::matchParametersValues(), 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

◆ attach_

bool bpp::Parameter::attach_

protectedinherited

Definition at line 143 of file Parameter.h.

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

◆ constraint_

Constraint* bpp::Parameter::constraint_

protectedinherited

Definition at line 142 of file Parameter.h.

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

◆ hyper_

bool bpp::IntervalTransformedParameter::hyper_

private

Definition at line 212 of file TransformedParameter.h.

◆ listenerAttach_

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

protectedinherited

Definition at line 145 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 144 of file Parameter.h.

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

◆ lowerBound_

double bpp::IntervalTransformedParameter::lowerBound_

private

Definition at line 210 of file TransformedParameter.h.

◆ name_

std::string bpp::Parameter::name_

protectedinherited

Definition at line 139 of file Parameter.h.

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

◆ precision_

double bpp::Parameter::precision_

protectedinherited

Definition at line 141 of file Parameter.h.

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

◆ PROP_CONSTRAINT_EX

const IntervalConstraint Parameter::PROP_CONSTRAINT_EX

staticinherited

Definition at line 337 of file Parameter.h.

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

◆ PROP_CONSTRAINT_IN

const IntervalConstraint Parameter::PROP_CONSTRAINT_IN

staticinherited

Definition at line 336 of file Parameter.h.

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

◆ R_MINUS

const IntervalConstraint Parameter::R_MINUS

staticinherited

Definition at line 334 of file Parameter.h.

◆ R_MINUS_STAR

const IntervalConstraint Parameter::R_MINUS_STAR

staticinherited

Definition at line 335 of file Parameter.h.

◆ R_PLUS

const IntervalConstraint Parameter::R_PLUS

staticinherited

Definition at line 332 of file Parameter.h.

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

◆ R_PLUS_STAR

const IntervalConstraint Parameter::R_PLUS_STAR

staticinherited

Definition at line 333 of file Parameter.h.

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

◆ scale_

double bpp::IntervalTransformedParameter::scale_

private

Definition at line 209 of file TransformedParameter.h.

◆ tiny_

double bpp::IntervalTransformedParameter::tiny_

private

Definition at line 213 of file TransformedParameter.h.

◆ upperBound_

double bpp::IntervalTransformedParameter::upperBound_

private

Definition at line 211 of file TransformedParameter.h.

◆ value_

double bpp::Parameter::value_

protectedinherited

Definition at line 140 of file Parameter.h.

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

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()

◆ 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

◆ attach_

◆ constraint_

◆ hyper_

◆ listenerAttach_

◆ listeners_

◆ lowerBound_

◆ name_

◆ precision_

◆ PROP_CONSTRAINT_EX

◆ PROP_CONSTRAINT_IN

◆ R_MINUS

◆ R_MINUS_STAR

◆ R_PLUS

◆ R_PLUS_STAR

◆ scale_

◆ tiny_

◆ upperBound_

◆ value_