bpp-core  2.2.0
Public Member Functions | Protected Member Functions | Private Member Functions | List of all members
bpp::ReparametrizationDerivableSecondOrderWrapper Class Referenceabstract

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

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

+ Inheritance diagram for bpp::ReparametrizationDerivableSecondOrderWrapper:
+ Collaboration diagram for bpp::ReparametrizationDerivableSecondOrderWrapper:

Public Member Functions

 ReparametrizationDerivableSecondOrderWrapper (DerivableSecondOrder *function, bool verbose=true)
 Build a new reparametrization wrapper for the given function, using all available parameters. More...
 
 ReparametrizationDerivableSecondOrderWrapper (DerivableSecondOrder *function, const ParameterList &parameters, bool verbose=true)
 Build a new reparametrization wrapper for the given function, using only the specified parameters. More...
 
virtual ~ReparametrizationDerivableSecondOrderWrapper ()
 
ReparametrizationDerivableSecondOrderWrapper * clone () const
 Create a copy of this object and send a pointer to it. More...
 
void enableSecondOrderDerivatives (bool yn)
 Tell if derivatives must be computed. More...
 
bool enableSecondOrderDerivatives () const
 Tell if derivatives must be computed. More...
 
double getSecondOrderDerivative (const std::string &variable) const throw (Exception)
 Get the second order derivative of the function at the current point. More...
 
double getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const throw (Exception)
 Get the value of the cross derivative of the function according to a given set of parameters. More...
 
virtual double d2f (const std::string &variable, const ParameterList &parameters) throw (Exception)
 Get the value of the second order derivative of the function according to a given set of parameters. More...
 
virtual double d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters) throw (Exception)
 Get the value of the cross derivative of the function according to a given set of parameters. More...
 
virtual void enableFirstOrderDerivatives (bool yn)=0
 Tell if derivatives must be computed. More...
 
virtual bool enableFirstOrderDerivatives () const =0
 Tell if derivatives must be computed. More...
 
virtual double getFirstOrderDerivative (const std::string &variable) const =0 throw (Exception)
 Get the derivative of the function at the current point. More...
 
virtual double df (const std::string &variable, const ParameterList &parameters) throw (Exception)
 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 throw (ParameterNotFoundException, ConstraintException, Exception)
 Set the point where the function must be computed. More...
 
virtual double getValue () const =0 throw (Exception)
 Get the value of the function at the current point. More...
 
virtual double f (const ParameterList &parameters) throw (Exception)
 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 & getParameter (const std::string &name) const =0 throw (ParameterNotFoundException)
 Get the parameter with specified name. More...
 
virtual double getParameterValue (const std::string &name) const =0 throw (ParameterNotFoundException)
 Get the value for parameter of name 'name'. More...
 
virtual void setAllParametersValues (const ParameterList &parameters)=0 throw (ParameterNotFoundException, ConstraintException)
 Set the parameters values to be equals to those of parameters. More...
 
virtual void setParameterValue (const std::string &name, double value)=0 throw (ParameterNotFoundException, ConstraintException)
 Set the value of parameter with name name to be equal to value. More...
 
virtual void setParametersValues (const ParameterList &parameters)=0 throw (ParameterNotFoundException, ConstraintException)
 Update the parameters from parameters. More...
 
virtual bool matchParametersValues (const ParameterList &parameters)=0 throw (ConstraintException)
 Update the parameters from parameters. 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...
 
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 throw (Exception)
 Get the derivative of the function at the current point. More...
 
void setParameters (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
 Set the point where the function must be computed. More...
 
double getValue () const throw (Exception)
 Get the value of the function at the current point. More...
 
bool hasParameter (const std::string &name) const
 Tell if there is a parameter with specified name. More...
 
const ParameterList & getParameters () const
 Get all parameters available. More...
 
const Parameter & getParameter (const std::string &name) const throw (ParameterNotFoundException)
 Get the parameter with specified name. More...
 
double getParameterValue (const std::string &name) const throw (ParameterNotFoundException)
 Get the value for parameter of name 'name'. More...
 
void setAllParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
 Set the parameters values to be equals to those of parameters. More...
 
void setParameterValue (const std::string &name, double value) throw (ParameterNotFoundException, ConstraintException)
 Set the value of parameter with name name to be equal to value. More...
 
void setParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
 Update the parameters from parameters. More...
 
bool matchParametersValues (const ParameterList &parameters) throw (ConstraintException)
 Update the parameters from parameters. More...
 
size_t getNumberOfParameters () const
 Get the number of parameters. More...
 
void setNamespace (const std::string &prefix)
 Set the namespace for the parameter names. More...
 
std::string getNamespace () const
 
std::string getParameterNameWithoutNamespace (const std::string &name) const
 Resolves a parameter name according to the current namespace. More...
 
virtual const Function & getFunction () const
 
virtual Function & getFunction ()
 
void fireParameterChanged (const ParameterList &parameters)
 Notify the class when one or several parameters have changed. More...
 

Protected Member Functions

void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index) throw (IndexOutOfBoundsException)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
Parameter & getParameter_ (const std::string &name) throw (ParameterNotFoundException)
 
Parameter & getParameter_ (size_t index) throw (IndexOutOfBoundsException)
 
const Parameter & getParameter_ (size_t index) const throw (IndexOutOfBoundsException)
 
Parameter & getParameterWithNamespace_ (const std::string &name) throw (ParameterNotFoundException)
 
const Parameter & getParameterWithNamespace_ (const std::string &name) const throw (ParameterNotFoundException)
 
ParameterList & getParameters_ ()
 

Private Member Functions

void init_ (bool verbose)
 

Detailed Description

Function wrapper that remove simple constraints on parameters. Also transform first and second 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 209 of file ReparametrizationFunctionWrapper.h.

Constructor & Destructor Documentation

◆ ReparametrizationDerivableSecondOrderWrapper() [1/2]

bpp::ReparametrizationDerivableSecondOrderWrapper::ReparametrizationDerivableSecondOrderWrapper ( DerivableSecondOrder *  function,
bool  verbose = true 
)
inline

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

Parameters
functionThe function to reparametrize.
verbosePrint some information.

Definition at line 221 of file ReparametrizationFunctionWrapper.h.

Referenced by clone().

◆ ReparametrizationDerivableSecondOrderWrapper() [2/2]

bpp::ReparametrizationDerivableSecondOrderWrapper::ReparametrizationDerivableSecondOrderWrapper ( DerivableSecondOrder *  function,
const ParameterList &  parameters,
bool  verbose = true 
)
inline

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

Parameters
functionThe function to reparametrize.
parametersThe 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.
verbosePrint some information.

Definition at line 234 of file ReparametrizationFunctionWrapper.h.

◆ ~ReparametrizationDerivableSecondOrderWrapper()

virtual bpp::ReparametrizationDerivableSecondOrderWrapper::~ReparametrizationDerivableSecondOrderWrapper ( )
inlinevirtual

Definition at line 238 of file ReparametrizationFunctionWrapper.h.

Member Function Documentation

◆ addParameter_()

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

Definition at line 137 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameter(), and bpp::AbstractParametrizable::parameters_.

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

◆ addParameters_()

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

Definition at line 143 of file AbstractParametrizable.h.

References bpp::ParameterList::addParameters(), and bpp::AbstractParametrizable::parameters_.

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

◆ clone()

ReparametrizationDerivableSecondOrderWrapper* bpp::ReparametrizationDerivableSecondOrderWrapper::clone ( ) const
inlinevirtual

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

Returns
A pointer toward the copy object.

Implements bpp::DerivableSecondOrder.

Definition at line 243 of file ReparametrizationFunctionWrapper.h.

References ReparametrizationDerivableSecondOrderWrapper().

◆ d2f() [1/2]

virtual double bpp::DerivableSecondOrder::d2f ( const std::string &  variable,
const ParameterList &  parameters 
)
throw (Exception
)
inlinevirtualinherited

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

Parameters
variableThe name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x^2} $.
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Definition at line 236 of file Functions.h.

References bpp::DerivableSecondOrder::getSecondOrderDerivative(), and bpp::Function::setParameters().

◆ d2f() [2/2]

virtual double bpp::DerivableSecondOrder::d2f ( const std::string &  variable1,
const std::string &  variable2,
const ParameterList &  parameters 
)
throw (Exception
)
inlinevirtualinherited

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

Parameters
variable1The name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
variable2The name of the $ y $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Definition at line 263 of file Functions.h.

References bpp::DerivableSecondOrder::getSecondOrderDerivative(), and bpp::Function::setParameters().

◆ deleteParameter_() [1/2]

void bpp::AbstractParametrizable::deleteParameter_ ( size_t  index)
throw (IndexOutOfBoundsException
)
inlineprotectedinherited

Definition at line 148 of file AbstractParametrizable.h.

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

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

◆ deleteParameter_() [2/2]

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

Definition at line 155 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameter(), and bpp::AbstractParametrizable::parameters_.

◆ deleteParameters_()

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

Definition at line 160 of file AbstractParametrizable.h.

References bpp::ParameterList::deleteParameters(), and bpp::AbstractParametrizable::parameters_.

◆ df()

virtual double bpp::DerivableFirstOrder::df ( const std::string &  variable,
const ParameterList &  parameters 
)
throw (Exception
)
inlinevirtualinherited

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

Parameters
variableThe name of the $ x $ variable in $ \frac{df}{dx} $.
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Definition at line 176 of file Functions.h.

References bpp::DerivableFirstOrder::getFirstOrderDerivative(), and bpp::Function::setParameters().

◆ enableFirstOrderDerivatives() [1/4]

virtual void bpp::DerivableFirstOrder::enableFirstOrderDerivatives ( bool  yn)
pure virtualinherited

Tell if derivatives must be computed.

Parameters
ynyes/no

Implemented in bpp::DerivableFirstOrderWrapper, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::AbstractHmmLikelihood, and bpp::AbstractNumericalDerivative.

Referenced by bpp::ConjugateGradientMultiDimensions::doStep(), and bpp::BfgsMultiDimensions::doStep().

◆ enableFirstOrderDerivatives() [2/4]

virtual bool bpp::DerivableFirstOrder::enableFirstOrderDerivatives ( ) const
pure virtualinherited

Tell if derivatives must be computed.

Returns
yes/no

Implemented in bpp::DerivableFirstOrderWrapper, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::AbstractHmmLikelihood, and bpp::AbstractNumericalDerivative.

◆ enableFirstOrderDerivatives() [3/4]

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

Tell if derivatives must be computed.

Parameters
ynyes/no

Implements bpp::DerivableFirstOrder.

Definition at line 190 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives(), and bpp::ReparametrizationFunctionWrapper::getFunction().

Referenced by bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives().

◆ enableFirstOrderDerivatives() [4/4]

bool bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives ( ) const
inlinevirtualinherited

Tell if derivatives must be computed.

Returns
yes/no

Implements bpp::DerivableFirstOrder.

Definition at line 192 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives(), and bpp::ReparametrizationFunctionWrapper::getFunction().

Referenced by bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives().

◆ enableSecondOrderDerivatives() [1/2]

void bpp::ReparametrizationDerivableSecondOrderWrapper::enableSecondOrderDerivatives ( bool  yn)
inlinevirtual

Tell if derivatives must be computed.

Parameters
ynyes/no

Implements bpp::DerivableSecondOrder.

Definition at line 250 of file ReparametrizationFunctionWrapper.h.

References enableSecondOrderDerivatives(), and bpp::ReparametrizationFunctionWrapper::getFunction().

Referenced by enableSecondOrderDerivatives().

◆ enableSecondOrderDerivatives() [2/2]

bool bpp::ReparametrizationDerivableSecondOrderWrapper::enableSecondOrderDerivatives ( ) const
inlinevirtual

Tell if derivatives must be computed.

Returns
yes/no

Implements bpp::DerivableSecondOrder.

Definition at line 252 of file ReparametrizationFunctionWrapper.h.

References enableSecondOrderDerivatives(), and bpp::ReparametrizationFunctionWrapper::getFunction().

Referenced by enableSecondOrderDerivatives().

◆ f()

virtual double bpp::Function::f ( const ParameterList &  parameters)
throw (Exception
)
inlinevirtualinherited

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

Parameters
parametersThe parameter set to pass to the function.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

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

Definition at line 117 of file Functions.h.

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

Referenced by bpp::NewtonOneDimension::doStep(), bpp::ConjugateGradientMultiDimensions::doStep(), bpp::BfgsMultiDimensions::doStep(), bpp::PowellMultiDimensions::doStep(), bpp::NewtonBacktrackOneDimension::doStep(), bpp::GoldenSectionSearch::doStep(), bpp::BrentOneDimension::doStep(), bpp::DownhillSimplexMethod::doStep(), bpp::FunctionWrapper::f(), bpp::PowellMultiDimensions::optimize(), bpp::BrentOneDimension::optimize(), bpp::DownhillSimplexMethod::optimize(), bpp::AbstractOptimizer::step(), and bpp::DownhillSimplexMethod::tryExtrapolation().

◆ fireParameterChanged()

void ReparametrizationFunctionWrapper::fireParameterChanged ( const ParameterList &  parameters)
virtualinherited

Notify the class when one or several parameters have changed.

Parameters
parametersA ParameterList object with parameters that changed.

Implements bpp::AbstractParametrizable.

Definition at line 173 of file ReparametrizationFunctionWrapper.cpp.

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

◆ getFirstOrderDerivative() [1/2]

virtual double bpp::DerivableFirstOrder::getFirstOrderDerivative ( const std::string &  variable) const
throw (Exception
)
pure virtualinherited

Get the derivative of the function at the current point.

Parameters
variableThe name of the $ x $ variable in $ \frac{df}{dx} $.
Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implemented in bpp::DerivableFirstOrderWrapper, bpp::ReparametrizationDerivableFirstOrderWrapper, bpp::AbstractHmmLikelihood, and bpp::AbstractNumericalDerivative.

Referenced by bpp::DerivableFirstOrder::df(), bpp::NewtonOneDimension::doStep(), bpp::AbstractNumericalDerivative::getFirstOrderDerivative(), bpp::ConjugateGradientMultiDimensions::getGradient(), and bpp::BfgsMultiDimensions::getGradient().

◆ getFirstOrderDerivative() [2/2]

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

Get the derivative of the function at the current point.

Parameters
variableThe name of the $ x $ variable in $ \frac{df}{dx} $.
Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implements bpp::DerivableFirstOrder.

Definition at line 194 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::getFunction(), and bpp::AbstractParametrizable::getParameter().

Referenced by getSecondOrderDerivative().

◆ getFunction() [1/2]

virtual const Function& bpp::ReparametrizationFunctionWrapper::getFunction ( ) const
inlinevirtualinherited

Definition at line 120 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_.

Referenced by bpp::ReparametrizationDerivableFirstOrderWrapper::enableFirstOrderDerivatives(), enableSecondOrderDerivatives(), bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), and getSecondOrderDerivative().

◆ getFunction() [2/2]

virtual Function& bpp::ReparametrizationFunctionWrapper::getFunction ( )
inlinevirtualinherited

Definition at line 122 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_.

◆ getNamespace() [1/2]

std::string bpp::AbstractParametrizable::getNamespace ( ) const
inlinevirtualinherited
Returns
The current namespace used. This is an empty string if no namespace is currently defined.

Implements bpp::Parametrizable.

Definition at line 125 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::prefix_.

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

◆ 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::FunctionWrapper::getNamespace().

◆ getNumberOfParameters() [1/2]

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const
inlinevirtualinherited

Get the number of parameters.

See also
getNumberOfIndependentParameters If some parameters are aliased.
Returns
The number of parameters.

Implements bpp::Parametrizable.

Definition at line 121 of file AbstractParametrizable.h.

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

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), 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::FunctionWrapper::getNumberOfParameters(), and bpp::BppODiscreteDistributionFormat::write().

◆ getParameter() [1/2]

const Parameter& bpp::AbstractParametrizable::getParameter ( const std::string &  name) const
throw (ParameterNotFoundException
)
inlinevirtualinherited

Get the parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
The parameter with given name.
Exceptions
ParameterNotFoundExceptionif no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 79 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::getAliasedParameters(), bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::AbstractParametrizable::getParameterValue(), bpp::AbstractParametrizable::getParameterWithNamespace_(), getSecondOrderDerivative(), and bpp::TestFunction::getValue().

◆ getParameter() [2/2]

virtual const Parameter& bpp::Parametrizable::getParameter ( const std::string &  name) const
throw (ParameterNotFoundException
)
pure virtualinherited

Get the parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
The parameter with given name.
Exceptions
ParameterNotFoundExceptionif no parameter with this name is found.

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

Referenced by bpp::FunctionWrapper::getParameter().

◆ getParameter_() [1/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string &  name)
throw (ParameterNotFoundException
)
inlineprotectedinherited
Parameters
nameThe name of the parameter.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 175 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

Referenced by bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), and bpp::InvariantMixedDiscreteDistribution::restrictToConstraint().

◆ getParameter_() [2/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t  index)
throw (IndexOutOfBoundsException
)
inlineprotectedinherited

Definition at line 199 of file AbstractParametrizable.h.

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

◆ getParameter_() [3/3]

const Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t  index) const
throw (IndexOutOfBoundsException
)
inlineprotectedinherited

Definition at line 205 of file AbstractParametrizable.h.

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

◆ getParameterNameWithoutNamespace() [1/2]

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

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 63 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

◆ 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::FunctionWrapper::getParameterNameWithoutNamespace(), bpp::BppODiscreteDistributionFormat::read(), and bpp::BppOParametrizableFormat::write().

◆ getParameters() [1/2]

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

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 77 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::fireParameterChanged(), 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::NewtonOneDimension::doStep(), bpp::FunctionWrapper::getParameters(), bpp::BppODiscreteDistributionFormat::read(), bpp::AbstractNumericalDerivative::setParameterValue(), bpp::AbstractOptimizer::step(), and bpp::BppOParametrizableFormat::write().

◆ getParameters_()

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )
inlineprotectedinherited

Definition at line 212 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameterValue() [1/2]

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

Get the value for parameter of name 'name'.

Parameters
nameThe name of the parameter.
Returns
the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 84 of file AbstractParametrizable.h.

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

Referenced by bpp::DirichletDiscreteDistribution::applyParameters(), bpp::ConstantDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::AutoCorrelationTransitionMatrix::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::FullHmmTransitionMatrix::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::Simplex::fireParameterChanged(), bpp::GammaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::BetaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

◆ getParameterValue() [2/2]

virtual double bpp::Parametrizable::getParameterValue ( const std::string &  name) const
throw (ParameterNotFoundException
)
pure virtualinherited

Get the value for parameter of name 'name'.

Parameters
nameThe name of the parameter.
Returns
the value of parameter name.

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

Referenced by bpp::FunctionWrapper::getParameterValue(), and bpp::BppODiscreteDistributionFormat::read().

◆ getParameterWithNamespace_() [1/2]

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name)
throw (ParameterNotFoundException
)
inlineprotectedinherited
Parameters
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 185 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

const Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name) const
throw (ParameterNotFoundException
)
inlineprotectedinherited
Parameters
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 194 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

◆ getSecondOrderDerivative() [1/2]

double bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative ( const std::string &  variable) const
throw (Exception
)
inlinevirtual

Get the second order derivative of the function at the current point.

Parameters
variableThe name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x^2} $.
Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implements bpp::DerivableSecondOrder.

Definition at line 254 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::ReparametrizationFunctionWrapper::getFunction(), and bpp::AbstractParametrizable::getParameter().

Referenced by getSecondOrderDerivative().

◆ getSecondOrderDerivative() [2/2]

double bpp::ReparametrizationDerivableSecondOrderWrapper::getSecondOrderDerivative ( const std::string &  variable1,
const std::string &  variable2 
) const
throw (Exception
)
inlinevirtual

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

Parameters
variable1The name of the $ x $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
variable2The name of the $ y $ variable in $ \frac{\partial^2 f}{\partial x \partial y} $.
Returns
The value of the function with the given parameter set.
Exceptions
ExceptionIf an error occured.

Implements bpp::DerivableSecondOrder.

Definition at line 262 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::ReparametrizationFunctionWrapper::getFunction(), bpp::AbstractParametrizable::getParameter(), and getSecondOrderDerivative().

◆ getValue() [1/2]

virtual double bpp::Function::getValue ( ) const
throw (Exception
)
pure virtualinherited

Get the value of the function at the current point.

Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

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

Referenced by bpp::SimpleNewtonMultiDimensions::doStep(), bpp::SimpleMultiDimensions::doStep(), bpp::MetaOptimizer::doStep(), bpp::Function::f(), bpp::ReparametrizationFunctionWrapper::getValue(), bpp::FunctionWrapper::getValue(), and bpp::InfinityFunctionWrapper::getValue().

◆ getValue() [2/2]

double bpp::ReparametrizationFunctionWrapper::getValue ( ) const
throw (Exception
)
inlinevirtualinherited

Get the value of the function at the current point.

Returns
The value of the function.
Exceptions
ExceptionIf no point is specified or if an error occured.

Implements bpp::Function.

Definition at line 134 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_, and bpp::Function::getValue().

◆ 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
nameThe name of the parameter to look for.
Returns
y/n.

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

Referenced by bpp::FunctionWrapper::hasParameter().

◆ hasParameter() [2/2]

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

Tell if there is a parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
y/n.

Implements bpp::Parametrizable.

Definition at line 75 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter(), bpp::AbstractParametrizable::parameters_, and bpp::AbstractParametrizable::prefix_.

◆ init_()

void bpp::ReparametrizationDerivableSecondOrderWrapper::init_ ( bool  verbose)
private

◆ matchParametersValues() [1/2]

bool bpp::AbstractParametrizable::matchParametersValues ( const ParameterList &  parameters)
throw (ConstraintException
)
inlinevirtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters
parametersA list of parameters.
Returns
True if at least one parameter value has been changed.
Exceptions
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 111 of file AbstractParametrizable.h.

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

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

◆ matchParametersValues() [2/2]

virtual bool bpp::Parametrizable::matchParametersValues ( const ParameterList &  parameters)
throw (ConstraintException
)
pure virtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters
parametersA list of parameters.
Returns
True if at least one parameter value has been changed.
Exceptions
ConstraintExceptionIf 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::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

◆ resetParameters_()

void bpp::AbstractParametrizable::resetParameters_ ( )
inlineprotectedinherited

Definition at line 165 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_, and bpp::ParameterList::reset().

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

◆ setAllParametersValues() [1/2]

void bpp::AbstractParametrizable::setAllParametersValues ( const ParameterList &  parameters)
throw (ParameterNotFoundException,
ConstraintException
)
inlinevirtualinherited

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
parametersA list with all parameters.
Exceptions
ParameterNotFoundExceptionIf a some parameter in the list is not in params.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 90 of file AbstractParametrizable.h.

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

◆ setAllParametersValues() [2/2]

virtual void bpp::Parametrizable::setAllParametersValues ( const ParameterList &  parameters)
throw (ParameterNotFoundException,
ConstraintException
)
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
parametersA list with all parameters.
Exceptions
ParameterNotFoundExceptionIf a some parameter in the list is not in params.
ConstraintExceptionIf 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::AbstractNumericalDerivative::setAllParametersValues(), bpp::FunctionWrapper::setAllParametersValues(), and bpp::InfinityFunctionWrapper::setAllParametersValues().

◆ setNamespace() [1/2]

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

Set the namespace for the parameter names.

Parameters
prefixThe '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::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 45 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

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

◆ setNamespace() [2/2]

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

Set the namespace for the parameter names.

Parameters
prefixThe '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::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, bpp::AbstractParametrizable, and bpp::InvariantMixedDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::setNamespace(), and bpp::FunctionWrapper::setNamespace().

◆ setParameters() [1/2]

virtual void bpp::Function::setParameters ( const ParameterList &  parameters)
throw (ParameterNotFoundException,
ConstraintException,
Exception
)
pure virtualinherited

Set the point where the function must be computed.

Parameters
parametersThe parameter set to pass to the function.

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

Referenced by bpp::DerivableSecondOrder::d2f(), bpp::DerivableFirstOrder::df(), bpp::NewtonOneDimension::doStep(), bpp::PowellMultiDimensions::doStep(), bpp::Function::f(), bpp::ReparametrizationFunctionWrapper::setParameters(), bpp::AbstractNumericalDerivative::setParameters(), bpp::FunctionWrapper::setParameters(), and bpp::InfinityFunctionWrapper::setParameters().

◆ setParameters() [2/2]

void bpp::ReparametrizationFunctionWrapper::setParameters ( const ParameterList &  parameters)
throw (ParameterNotFoundException,
ConstraintException
)
inlinevirtualinherited

Set the point where the function must be computed.

Parameters
parametersThe parameter set to pass to the function.

Implements bpp::Function.

Definition at line 124 of file ReparametrizationFunctionWrapper.h.

References bpp::ReparametrizationFunctionWrapper::function_, bpp::ReparametrizationFunctionWrapper::functionParameters_, bpp::AbstractParametrizable::matchParametersValues(), bpp::Function::setParameters(), and bpp::ParameterList::subList().

◆ setParametersValues() [1/2]

void bpp::AbstractParametrizable::setParametersValues ( const ParameterList &  parameters)
throw (ParameterNotFoundException,
ConstraintException
)
inlinevirtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters
parametersA list containing all parameters to update.
Exceptions
ParameterNotFoundExceptionIf a some parameter in params is not in the list.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 104 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, 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)
throw (ParameterNotFoundException,
ConstraintException
)
pure virtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters
parametersA list containing all parameters to update.
Exceptions
ParameterNotFoundExceptionIf a some parameter in params is not in the list.
ConstraintExceptionIf 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::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

◆ setParameterValue() [1/2]

void bpp::AbstractParametrizable::setParameterValue ( const std::string &  name,
double  value 
)
throw (ParameterNotFoundException,
ConstraintException
)
inlinevirtualinherited

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

Parameters
namethe name of the parameter to set.
valueThe value of the parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter in the list has the name name.
ConstraintExceptionIf value does not match the constraint associated to parameter name.

Implements bpp::Parametrizable.

Definition at line 97 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, bpp::AbstractParametrizable::prefix_, bpp::ParameterList::setParameterValue(), and bpp::ParameterList::subList().

◆ setParameterValue() [2/2]

virtual void bpp::Parametrizable::setParameterValue ( const std::string &  name,
double  value 
)
throw (ParameterNotFoundException,
ConstraintException
)
pure virtualinherited

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

Parameters
namethe name of the parameter to set.
valueThe value of the parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter in the list has the name name.
ConstraintExceptionIf 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::AbstractNumericalDerivative::setParameterValue(), bpp::FunctionWrapper::setParameterValue(), and bpp::InfinityFunctionWrapper::setParameterValue().

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