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

Numerical derivative function wrapper, partial implementation. More...

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

+ Inheritance diagram for bpp::AbstractNumericalDerivative:
+ Collaboration diagram for bpp::AbstractNumericalDerivative:

Public Member Functions

 AbstractNumericalDerivative (Function *function)
 
 AbstractNumericalDerivative (DerivableFirstOrder *function)
 
 AbstractNumericalDerivative (DerivableSecondOrder *function)
 
 AbstractNumericalDerivative (const AbstractNumericalDerivative &ad)
 
AbstractNumericalDerivative & operator= (const AbstractNumericalDerivative &ad)
 
virtual ~AbstractNumericalDerivative ()
 
AbstractNumericalDerivative * clone () const =0
 Create a copy of this object and send a pointer to it. More...
 
void setInterval (double h)
 Set the interval value used in numerical approximation. More...
 
double getInterval () const
 
void setParametersToDerivate (const std::vector< std::string > &variables)
 Set the list of parameters to derivate. More...
 
void enableSecondOrderCrossDerivatives (bool yn)
 
bool enableSecondOrderCrossDerivatives () const
 
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 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 double getValue () const =0 throw (Exception)
 Get the value of the function at the current point. 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 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...
 
bool hasParameter (const std::string &name) const
 Tell if there is a parameter with specified name. More...
 
const ParameterList & getParameters () const throw (Exception)
 Get all parameters available. More...
 
const Parameter & getParameter (const std::string &name) const throw (ParameterNotFoundException)
 Get the parameter with specified name. More...
 
double getValue () const throw (Exception)
 Get the value of the function at the current point. More...
 
double getParameterValue (const std::string &name) const throw (ParameterNotFoundException)
 Get the value for parameter of name 'name'. 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...
 
The DerivableFirstOrder interface
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...
 
The DerivableSecondOrder interface
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...
 
The Parametrizable interface.
double f (const ParameterList &parameters) throw (Exception)
 Get the value of the function according to a given set of parameters. More...
 
void setParameters (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
 Set the point where the function must be computed. 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...
 

Protected Member Functions

virtual void updateDerivatives (const ParameterList parameters)=0
 Compute derivatives. More...
 

Protected Attributes

DerivableFirstOrder * function1_
 
DerivableSecondOrder * function2_
 
double h_
 
std::vector< std::string > variables_
 
std::map< std::string, size_t > index_
 
std::vector< double > der1_
 
std::vector< double > der2_
 
RowMatrix< double > crossDer2_
 
bool computeD1_
 
bool computeD2_
 
bool computeCrossD2_
 
Function * function_
 

Detailed Description

Numerical derivative function wrapper, partial implementation.

This class provides a wrapper for Function object, implementing the DerivableSecondOrder interface (Although no cross derivative is implemented for now). Derivations of this class can be used as full DerivableSecondOrder objects, with derivative functions.

Three kinds of constructors are provided: one with a Function object, another with a DerivableFirstOrder object, and one with a DerivableSecondOrder object. In the first case, all derivatives will be computed numerically. In the second case, first order derivative will be computed numerically only if no appropriate analytical derivative is available, second order derivative will always be computed numerically. In the last case, first and second order derivative will be computed numerically only if no appropriate analytical derivative is available.

Definition at line 66 of file AbstractNumericalDerivative.h.

Constructor & Destructor Documentation

◆ AbstractNumericalDerivative() [1/4]

bpp::AbstractNumericalDerivative::AbstractNumericalDerivative ( Function *  function)
inline

Definition at line 82 of file AbstractNumericalDerivative.h.

◆ AbstractNumericalDerivative() [2/4]

bpp::AbstractNumericalDerivative::AbstractNumericalDerivative ( DerivableFirstOrder *  function)
inline

Definition at line 87 of file AbstractNumericalDerivative.h.

◆ AbstractNumericalDerivative() [3/4]

bpp::AbstractNumericalDerivative::AbstractNumericalDerivative ( DerivableSecondOrder *  function)
inline

Definition at line 92 of file AbstractNumericalDerivative.h.

◆ AbstractNumericalDerivative() [4/4]

bpp::AbstractNumericalDerivative::AbstractNumericalDerivative ( const AbstractNumericalDerivative &  ad)
inline

Definition at line 97 of file AbstractNumericalDerivative.h.

◆ ~AbstractNumericalDerivative()

virtual bpp::AbstractNumericalDerivative::~AbstractNumericalDerivative ( )
inlinevirtual

Definition at line 119 of file AbstractNumericalDerivative.h.

Member Function Documentation

◆ clone()

AbstractNumericalDerivative* bpp::AbstractNumericalDerivative::clone ( ) const
pure virtual

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

Returns
A pointer toward the copy object.

Implements bpp::DerivableSecondOrder.

Implemented in bpp::ThreePointsNumericalDerivative, bpp::FivePointsNumericalDerivative, and bpp::TwoPointsNumericalDerivative.

◆ 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().

◆ 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() [1/2]

void bpp::AbstractNumericalDerivative::enableFirstOrderDerivatives ( bool  yn)
inlinevirtual

Tell if derivatives must be computed.

Parameters
ynyes/no

Implements bpp::DerivableFirstOrder.

Definition at line 159 of file AbstractNumericalDerivative.h.

References computeD1_.

◆ enableFirstOrderDerivatives() [2/2]

bool bpp::AbstractNumericalDerivative::enableFirstOrderDerivatives ( ) const
inlinevirtual

Tell if derivatives must be computed.

Returns
yes/no

Implements bpp::DerivableFirstOrder.

Definition at line 160 of file AbstractNumericalDerivative.h.

References computeD1_.

◆ enableSecondOrderCrossDerivatives() [1/2]

void bpp::AbstractNumericalDerivative::enableSecondOrderCrossDerivatives ( bool  yn)
inline

Definition at line 268 of file AbstractNumericalDerivative.h.

References computeCrossD2_.

◆ enableSecondOrderCrossDerivatives() [2/2]

bool bpp::AbstractNumericalDerivative::enableSecondOrderCrossDerivatives ( ) const
inline

Definition at line 269 of file AbstractNumericalDerivative.h.

References computeCrossD2_.

◆ enableSecondOrderDerivatives() [1/2]

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

Tell if derivatives must be computed.

Parameters
ynyes/no

Implements bpp::DerivableSecondOrder.

Definition at line 185 of file AbstractNumericalDerivative.h.

References computeD2_.

◆ enableSecondOrderDerivatives() [2/2]

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

Tell if derivatives must be computed.

Returns
yes/no

Implements bpp::DerivableSecondOrder.

Definition at line 186 of file AbstractNumericalDerivative.h.

References computeD2_.

◆ f()

double bpp::AbstractNumericalDerivative::f ( const ParameterList &  parameters)
throw (Exception
)
inlinevirtual

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 from bpp::Function.

Definition at line 227 of file AbstractNumericalDerivative.h.

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

◆ getFirstOrderDerivative()

double bpp::AbstractNumericalDerivative::getFirstOrderDerivative ( const std::string &  variable) const
throw (Exception
)
inlinevirtual

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 162 of file AbstractNumericalDerivative.h.

References computeD1_, der1_, function1_, bpp::DerivableFirstOrder::getFirstOrderDerivative(), and index_.

◆ getInterval()

double bpp::AbstractNumericalDerivative::getInterval ( ) const
inline
Returns
The interval value used in numerical approximation.

Definition at line 136 of file AbstractNumericalDerivative.h.

References h_.

◆ getNamespace() [1/2]

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().

◆ getNamespace() [2/2]

std::string bpp::FunctionWrapper::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 360 of file Functions.h.

References bpp::FunctionWrapper::function_, and bpp::Parametrizable::getNamespace().

◆ getNumberOfParameters() [1/2]

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().

◆ getNumberOfParameters() [2/2]

size_t bpp::FunctionWrapper::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 350 of file Functions.h.

References bpp::FunctionWrapper::function_, and bpp::Parametrizable::getNumberOfParameters().

◆ getParameter() [1/2]

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() [2/2]

const Parameter& bpp::FunctionWrapper::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 306 of file Functions.h.

References bpp::FunctionWrapper::function_, and bpp::Parametrizable::getParameter().

◆ getParameterNameWithoutNamespace() [1/2]

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().

◆ getParameterNameWithoutNamespace() [2/2]

std::string bpp::FunctionWrapper::getParameterNameWithoutNamespace ( const std::string &  name) const
inlinevirtualinherited

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 365 of file Functions.h.

References bpp::FunctionWrapper::function_, and bpp::Parametrizable::getParameterNameWithoutNamespace().

◆ getParameters() [1/2]

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(), setParameterValue(), bpp::AbstractOptimizer::step(), and bpp::BppOParametrizableFormat::write().

◆ getParameters() [2/2]

const ParameterList& bpp::FunctionWrapper::getParameters ( ) const
throw (Exception
)
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 301 of file Functions.h.

References bpp::FunctionWrapper::function_, and bpp::Parametrizable::getParameters().

◆ getParameterValue() [1/2]

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().

◆ getParameterValue() [2/2]

double bpp::FunctionWrapper::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 321 of file Functions.h.

References bpp::FunctionWrapper::function_, and bpp::Parametrizable::getParameterValue().

◆ getSecondOrderDerivative() [1/2]

double bpp::AbstractNumericalDerivative::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.

Reimplemented in bpp::TwoPointsNumericalDerivative.

Definition at line 188 of file AbstractNumericalDerivative.h.

References computeD2_, der2_, function2_, bpp::DerivableSecondOrder::getSecondOrderDerivative(), and index_.

◆ getSecondOrderDerivative() [2/2]

double bpp::AbstractNumericalDerivative::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.

Reimplemented in bpp::FivePointsNumericalDerivative, and bpp::TwoPointsNumericalDerivative.

Definition at line 204 of file AbstractNumericalDerivative.h.

References computeCrossD2_, crossDer2_, function2_, bpp::DerivableSecondOrder::getSecondOrderDerivative(), and index_.

◆ 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::FunctionWrapper::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.

Reimplemented in bpp::InfinityFunctionWrapper, bpp::ThreePointsNumericalDerivative, and bpp::TwoPointsNumericalDerivative.

Definition at line 311 of file Functions.h.

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

Referenced by f().

◆ 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::FunctionWrapper::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 290 of file Functions.h.

References bpp::FunctionWrapper::function_, and bpp::Parametrizable::hasParameter().

◆ matchParametersValues()

bool bpp::AbstractNumericalDerivative::matchParametersValues ( const ParameterList &  parameters)
throw (ConstraintException
)
inlinevirtual

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 259 of file AbstractNumericalDerivative.h.

References bpp::FunctionWrapper::function_, bpp::Parametrizable::matchParametersValues(), and updateDerivatives().

◆ operator=()

AbstractNumericalDerivative& bpp::AbstractNumericalDerivative::operator= ( const AbstractNumericalDerivative &  ad)
inline

Definition at line 102 of file AbstractNumericalDerivative.h.

References computeCrossD2_, computeD1_, computeD2_, crossDer2_, der1_, der2_, function1_, function2_, h_, index_, bpp::FunctionWrapper::operator=(), and variables_.

◆ setAllParametersValues()

void bpp::AbstractNumericalDerivative::setAllParametersValues ( const ParameterList &  parameters)
throw (ParameterNotFoundException,
ConstraintException
)
inlinevirtual

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 238 of file AbstractNumericalDerivative.h.

References bpp::FunctionWrapper::function_, bpp::Parametrizable::setAllParametersValues(), and updateDerivatives().

◆ setInterval()

void bpp::AbstractNumericalDerivative::setInterval ( double  h)
inline

Set the interval value used in numerical approximation.

Default value is 0.0001.

Parameters
hInterval value.

Definition at line 131 of file AbstractNumericalDerivative.h.

References h_.

◆ setNamespace() [1/2]

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().

◆ setNamespace() [2/2]

void bpp::FunctionWrapper::setNamespace ( const std::string &  prefix)
inlinevirtualinherited

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.

Definition at line 355 of file Functions.h.

References bpp::FunctionWrapper::function_, and bpp::Parametrizable::setNamespace().

◆ setParameters()

void bpp::AbstractNumericalDerivative::setParameters ( const ParameterList &  parameters)
throw (ParameterNotFoundException,
ConstraintException
)
inlinevirtual

Set the point where the function must be computed.

Parameters
parametersThe parameter set to pass to the function.

Implements bpp::Function.

Definition at line 232 of file AbstractNumericalDerivative.h.

References bpp::FunctionWrapper::function_, bpp::Function::setParameters(), and updateDerivatives().

Referenced by f().

◆ setParametersToDerivate()

void bpp::AbstractNumericalDerivative::setParametersToDerivate ( const std::vector< std::string > &  variables)
inline

Set the list of parameters to derivate.

Parameters
variablesA list of all parameter names.

Definition at line 143 of file AbstractNumericalDerivative.h.

References crossDer2_, der1_, der2_, index_, bpp::RowMatrix< Scalar >::resize(), and variables_.

◆ setParametersValues()

void bpp::AbstractNumericalDerivative::setParametersValues ( const ParameterList &  parameters)
throw (ParameterNotFoundException,
ConstraintException
)
inlinevirtual

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 252 of file AbstractNumericalDerivative.h.

References bpp::FunctionWrapper::function_, bpp::Parametrizable::setParametersValues(), and updateDerivatives().

◆ setParameterValue()

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

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 245 of file AbstractNumericalDerivative.h.

References bpp::FunctionWrapper::function_, bpp::Parametrizable::getParameters(), bpp::Parametrizable::setParameterValue(), bpp::ParameterList::subList(), and updateDerivatives().

◆ updateDerivatives()

virtual void bpp::AbstractNumericalDerivative::updateDerivatives ( const ParameterList  parameters)
protectedpure virtual

Compute derivatives.

Parameters
parametersThe point where to compute derivatives. It is NOT passed as references, as the inner parameters of the function will be changed when computing the numerical derivatives.

Implemented in bpp::FivePointsNumericalDerivative, bpp::ThreePointsNumericalDerivative, and bpp::TwoPointsNumericalDerivative.

Referenced by matchParametersValues(), setAllParametersValues(), setParameters(), setParametersValues(), and setParameterValue().

Member Data Documentation

◆ computeCrossD2_

bool bpp::AbstractNumericalDerivative::computeCrossD2_
protected

Definition at line 79 of file AbstractNumericalDerivative.h.

Referenced by enableSecondOrderCrossDerivatives(), getSecondOrderDerivative(), and operator=().

◆ computeD1_

bool bpp::AbstractNumericalDerivative::computeD1_
protected

Definition at line 79 of file AbstractNumericalDerivative.h.

Referenced by enableFirstOrderDerivatives(), getFirstOrderDerivative(), and operator=().

◆ computeD2_

bool bpp::AbstractNumericalDerivative::computeD2_
protected

Definition at line 79 of file AbstractNumericalDerivative.h.

Referenced by enableSecondOrderDerivatives(), getSecondOrderDerivative(), and operator=().

◆ crossDer2_

RowMatrix<double> bpp::AbstractNumericalDerivative::crossDer2_
protected

Definition at line 78 of file AbstractNumericalDerivative.h.

Referenced by getSecondOrderDerivative(), operator=(), and setParametersToDerivate().

◆ der1_

std::vector<double> bpp::AbstractNumericalDerivative::der1_
protected

Definition at line 76 of file AbstractNumericalDerivative.h.

Referenced by getFirstOrderDerivative(), operator=(), and setParametersToDerivate().

◆ der2_

std::vector<double> bpp::AbstractNumericalDerivative::der2_
protected

Definition at line 77 of file AbstractNumericalDerivative.h.

Referenced by getSecondOrderDerivative(), operator=(), and setParametersToDerivate().

◆ function1_

DerivableFirstOrder* bpp::AbstractNumericalDerivative::function1_
protected

Definition at line 71 of file AbstractNumericalDerivative.h.

Referenced by getFirstOrderDerivative(), and operator=().

◆ function2_

DerivableSecondOrder* bpp::AbstractNumericalDerivative::function2_
protected

Definition at line 72 of file AbstractNumericalDerivative.h.

Referenced by getSecondOrderDerivative(), and operator=().

◆ function_

Function* bpp::FunctionWrapper::function_
protectedinherited

Definition at line 278 of file Functions.h.

Referenced by bpp::DerivableFirstOrderWrapper::enableFirstOrderDerivatives(), bpp::DerivableSecondOrderWrapper::enableSecondOrderDerivatives(), bpp::FunctionWrapper::f(), bpp::DerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::InfinityDerivableFirstOrderWrapper::getFirstOrderDerivative(), bpp::FunctionWrapper::getNamespace(), bpp::FunctionWrapper::getNumberOfParameters(), bpp::FunctionWrapper::getParameter(), bpp::FunctionWrapper::getParameterNameWithoutNamespace(), bpp::FunctionWrapper::getParameters(), bpp::FunctionWrapper::getParameterValue(), bpp::DerivableSecondOrderWrapper::getSecondOrderDerivative(), bpp::InfinityDerivableSecondOrderWrapper::getSecondOrderDerivative(), bpp::FunctionWrapper::getValue(), bpp::InfinityFunctionWrapper::getValue(), bpp::FunctionWrapper::hasParameter(), matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), bpp::InfinityFunctionWrapper::matchParametersValues(), bpp::FunctionWrapper::operator=(), setAllParametersValues(), bpp::FunctionWrapper::setAllParametersValues(), bpp::InfinityFunctionWrapper::setAllParametersValues(), bpp::FunctionWrapper::setNamespace(), setParameters(), bpp::FunctionWrapper::setParameters(), bpp::InfinityFunctionWrapper::setParameters(), setParametersValues(), bpp::FunctionWrapper::setParametersValues(), bpp::InfinityFunctionWrapper::setParametersValues(), setParameterValue(), bpp::FunctionWrapper::setParameterValue(), and bpp::InfinityFunctionWrapper::setParameterValue().

◆ h_

double bpp::AbstractNumericalDerivative::h_
protected

Definition at line 73 of file AbstractNumericalDerivative.h.

Referenced by getInterval(), operator=(), and setInterval().

◆ index_

std::map<std::string, size_t> bpp::AbstractNumericalDerivative::index_
mutableprotected

Definition at line 75 of file AbstractNumericalDerivative.h.

Referenced by getFirstOrderDerivative(), getSecondOrderDerivative(), operator=(), and setParametersToDerivate().

◆ variables_

std::vector<std::string> bpp::AbstractNumericalDerivative::variables_
protected

Definition at line 74 of file AbstractNumericalDerivative.h.

Referenced by operator=(), and setParametersToDerivate().

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