Five points numerical derivative function wrapper. More...

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

Inheritance diagram for bpp::FivePointsNumericalDerivative:

Collaboration diagram for bpp::FivePointsNumericalDerivative:

Public Member Functions
	FivePointsNumericalDerivative (Function *function)

	FivePointsNumericalDerivative (DerivableFirstOrder *function)

	FivePointsNumericalDerivative (DerivableSecondOrder *function)

virtual	~FivePointsNumericalDerivative ()

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

double	getValue () const
	Get the value of the function at the current point. More...

double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const
	Get the value of the cross derivative of the function according to a given set of parameters. 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 numerically. More...

void	enableSecondOrderCrossDerivatives (bool yn)

bool	enableSecondOrderCrossDerivatives () const

virtual double	d2f (const std::string &variable, const ParameterList &parameters)
	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)
	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)
	Get the value of the first derivative 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...

bool	hasParameter (const std::string &name) const
	Tell if there is a parameter with specified name. More...

virtual const ParameterList &	getParameters () const =0
	Get all parameters available. More...

const ParameterList &	getParameters () const
	Get all parameters available. More...

virtual const Parameter &	getParameter (const std::string &name) const =0
	Get the parameter with specified name. More...

const Parameter &	getParameter (const std::string &name) const
	Get the parameter with specified name. More...

virtual double	getParameterValue (const std::string &name) const =0
	Get the value for parameter of name 'name'. More...

double	getParameterValue (const std::string &name) const
	Get the value for parameter of name 'name'. More...

virtual size_t	getNumberOfParameters () const =0
	Get the number of parameters. More...

size_t	getNumberOfParameters () const
	Get the number of parameters. More...

virtual void	setNamespace (const std::string &prefix)=0
	Set the namespace for the parameter names. More...

void	setNamespace (const std::string &prefix)
	Set the namespace for the parameter names. More...

virtual std::string	getNamespace () const =0

std::string	getNamespace () const

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const =0
	Resolves a parameter name according to the current namespace. More...

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

The Parametrizable interface.
double	f (const ParameterList &parameters)
	Get the value of the function according to a given set of parameters. More...

void	setParameters (const ParameterList &parameters)
	Set the point where the function must be computed. More...

void	setAllParametersValues (const ParameterList &parameters)
	Set the parameters values to be equals to those of parameters. More...

void	setParameterValue (const std::string &name, double value)
	Set the value of parameter with name name to be equal to value. More...

void	setParametersValues (const ParameterList &parameters)
	Update the parameters from parameters. More...

bool	matchParametersValues (const ParameterList &parameters)
	Update the parameters from parameters. More...

Protected Member Functions
void	updateDerivatives (const ParameterList parameters)
	Compute derivatives. More...

virtual ParameterList &	getParameters_ ()=0
	Get all parameters available. More...

ParameterList &	getParameters_ ()
	Get all parameters available. 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_

Private Attributes
double	f1_

double	f2_

double	f3_

double	f4_

double	f5_

Detailed Description

Five points numerical derivative function wrapper.

Numerical derivatives use three points to compute the derivatives. is the focus point, $x_{-2} = x_0-2h$ , $x_{-1} = x_0-h$ , $x_{+1}=x_0+h$ and $x_{+2} = x_0+2h$ are other points, with function values , $f_{-2}$ , $f_{-1}$ , $f_{+1}$ and $f_{+2}$ respectively. The derivatives are then computed using the central formulas:

$\begin{eqnarray*} \dfrac{\partial f}{\partial x } &=& \dfrac{f_{-2}-8f_{-1}+8f_{+1}-f_{+2}}{12h}\\ \dfrac{\partial^2 f}{\partial x^2} &=& \dfrac{-f_{-2}+16f_{-1}-30f_0+16f_{+1}-f_{+2}}{12h^2}\\ \end{eqnarray*}$

In case of border limit (when $x_{-2}$ or $x_{+2}$ are not computable), the foreward and backward three points computations are performed, respectively:

$\begin{eqnarray*} \dfrac{\partial f}{\partial x } &=& \dfrac{f_{+1}-f_0}{h}\\ \dfrac{\partial^2 f}{\partial x^2} &=& \dfrac{f_{+2}-2f_{+1}+f_0}{h^2}\\ \end{eqnarray*}$

and

$\begin{eqnarray*} \dfrac{\partial f}{\partial x } &=& \dfrac{f_0-f_{-1}}{h}\\ \dfrac{\partial^2 f}{\partial x^2} &=& \dfrac{f_0-2f_{-1}+f_{-2}}{h^2}\\ \end{eqnarray*}$

The parameter is computed in a parameter dependent manner: $h = x \times e$ , with $x \neq 0$ being the current parameter value. If , . Default value is provided for and corresponds to the _h field. The default value works fine in most cases, but you may want to change it using the setInterval method.

Warning: cross second order derivatives are not implemented with the five points method.

See also: AbstractNumericalDerivative

Definition at line 87 of file FivePointsNumericalDerivative.h.

Constructor & Destructor Documentation

◆ FivePointsNumericalDerivative() [1/3]

bpp::FivePointsNumericalDerivative::FivePointsNumericalDerivative ( Function * function )

inline

Definition at line 94 of file FivePointsNumericalDerivative.h.

Referenced by clone().

◆ FivePointsNumericalDerivative() [2/3]

bpp::FivePointsNumericalDerivative::FivePointsNumericalDerivative ( DerivableFirstOrder * function )

inline

Definition at line 101 of file FivePointsNumericalDerivative.h.

◆ FivePointsNumericalDerivative() [3/3]

bpp::FivePointsNumericalDerivative::FivePointsNumericalDerivative ( DerivableSecondOrder * function )

inline

Definition at line 108 of file FivePointsNumericalDerivative.h.

◆ ~FivePointsNumericalDerivative()

virtual bpp::FivePointsNumericalDerivative::~FivePointsNumericalDerivative ( )

inlinevirtual

Definition at line 115 of file FivePointsNumericalDerivative.h.

Member Function Documentation

◆ clone()

FivePointsNumericalDerivative* bpp::FivePointsNumericalDerivative::clone ( ) const

inlinevirtual

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

Returns: A pointer toward the copy object.

Implements bpp::AbstractNumericalDerivative.

Definition at line 117 of file FivePointsNumericalDerivative.h.

References FivePointsNumericalDerivative().

◆ d2f() [1/2]

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

inlinevirtualinherited

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

Parameters

variable	The name of the variable in $\frac{\partial^2 f}{\partial x^2}$ .
parameters	The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Definition at line 228 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
	)

inlinevirtualinherited

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

Parameters

variable1	The name of the variable in $\frac{\partial^2 f}{\partial x \partial y}$ .
variable2	The name of the variable in $\frac{\partial^2 f}{\partial x \partial y}$ .
parameters	The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Definition at line 255 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
	)

inlinevirtualinherited

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

Parameters

variable	The name of the variable in $\frac{df}{dx}$ .
parameters	The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Definition at line 173 of file Functions.h.

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

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractNumericalDerivative::enableFirstOrderDerivatives ( ) const

inlinevirtualinherited

Tell if derivatives must be computed.

Returns: yes/no

Implements bpp::DerivableFirstOrder.

Definition at line 163 of file AbstractNumericalDerivative.h.

References bpp::AbstractNumericalDerivative::computeD1_.

◆ enableFirstOrderDerivatives() [2/2]

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

inlinevirtualinherited

Tell if derivatives must be computed.

Parameters

yn yes/no

Implements bpp::DerivableFirstOrder.

Definition at line 162 of file AbstractNumericalDerivative.h.

References bpp::AbstractNumericalDerivative::computeD1_.

◆ enableSecondOrderCrossDerivatives() [1/2]

bool bpp::AbstractNumericalDerivative::enableSecondOrderCrossDerivatives ( ) const

inlineinherited

Definition at line 254 of file AbstractNumericalDerivative.h.

References bpp::AbstractNumericalDerivative::computeCrossD2_.

◆ enableSecondOrderCrossDerivatives() [2/2]

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

inlineinherited

Definition at line 253 of file AbstractNumericalDerivative.h.

References bpp::AbstractNumericalDerivative::computeCrossD2_.

◆ enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractNumericalDerivative::enableSecondOrderDerivatives ( ) const

inlinevirtualinherited

Tell if derivatives must be computed.

Returns: yes/no

Implements bpp::DerivableSecondOrder.

Definition at line 184 of file AbstractNumericalDerivative.h.

References bpp::AbstractNumericalDerivative::computeD2_.

◆ enableSecondOrderDerivatives() [2/2]

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

inlinevirtualinherited

Tell if derivatives must be computed.

Parameters

yn yes/no

Implements bpp::DerivableSecondOrder.

Definition at line 183 of file AbstractNumericalDerivative.h.

References bpp::AbstractNumericalDerivative::computeD2_.

◆ f()

double bpp::AbstractNumericalDerivative::f ( const ParameterList & parameters )

inlinevirtualinherited

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

Parameters

parameters The parameter set to pass to the function.

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Reimplemented from bpp::Function.

Definition at line 217 of file AbstractNumericalDerivative.h.

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

◆ getFirstOrderDerivative()

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

inlinevirtualinherited

Get the derivative of the function at the current point.

Parameters

variable The name of the variable in $\frac{df}{dx}$ .

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implements bpp::DerivableFirstOrder.

Definition at line 165 of file AbstractNumericalDerivative.h.

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

◆ getInterval()

double bpp::AbstractNumericalDerivative::getInterval ( ) const

inlineinherited

Returns: The interval value used in numerical approximation.

Definition at line 137 of file AbstractNumericalDerivative.h.

References bpp::AbstractNumericalDerivative::h_.

◆ getNamespace() [1/2]

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 347 of file Functions.h.

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

◆ 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::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

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

◆ getNumberOfParameters() [1/2]

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 337 of file Functions.h.

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

◆ 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::ParametrizableAdapter, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.

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

◆ getParameter() [1/2]

const Parameter& bpp::FunctionWrapper::getParameter ( const std::string & name ) const

inlinevirtualinherited

Get the parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: The parameter with given name.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 297 of file Functions.h.

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

◆ getParameter() [2/2]

virtual const Parameter& bpp::Parametrizable::getParameter ( const std::string & name ) const

pure virtualinherited

Get the parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: The parameter with given name.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

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

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

◆ getParameterNameWithoutNamespace() [1/2]

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 352 of file Functions.h.

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

◆ 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::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), and bpp::BppOParametrizableFormat::write().

◆ getParameters() [1/2]

const ParameterList& bpp::FunctionWrapper::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 292 of file Functions.h.

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

◆ 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::ParametrizableAdapter, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.

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

◆ getParameters_() [1/2]

ParameterList& bpp::FunctionWrapper::getParameters_ ( )

inlineprotectedvirtualinherited

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 358 of file Functions.h.

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

◆ getParameters_() [2/2]

virtual ParameterList& bpp::Parametrizable::getParameters_ ( )

protectedpure 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::DirectionFunction, and bpp::AbstractParametrizable.

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

◆ getParameterValue() [1/2]

double bpp::FunctionWrapper::getParameterValue ( const std::string & name ) const

inlinevirtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 312 of file Functions.h.

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

◆ getParameterValue() [2/2]

virtual double bpp::Parametrizable::getParameterValue ( const std::string & name ) const

pure virtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

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

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

◆ getSecondOrderDerivative() [1/2]

double bpp::AbstractNumericalDerivative::getSecondOrderDerivative ( const std::string & variable ) const

inlinevirtualinherited

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

Parameters

variable The name of the variable in $\frac{\partial^2 f}{\partial x^2}$ .

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implements bpp::DerivableSecondOrder.

Reimplemented in bpp::TwoPointsNumericalDerivative.

Definition at line 186 of file AbstractNumericalDerivative.h.

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

◆ getSecondOrderDerivative() [2/2]

double bpp::FivePointsNumericalDerivative::getSecondOrderDerivative	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inlinevirtual

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

Parameters

variable1	The name of the variable in $\frac{\partial^2 f}{\partial x \partial y}$ .
variable2	The name of the variable in $\frac{\partial^2 f}{\partial x \partial y}$ .

Returns: The value of the function with the given parameter set.

Exceptions

Exception If an error occured.

Reimplemented from bpp::AbstractNumericalDerivative.

Definition at line 125 of file FivePointsNumericalDerivative.h.

◆ getValue()

double bpp::FivePointsNumericalDerivative::getValue ( ) const

inlinevirtual

Get the value of the function at the current point.

Returns: The value of the function.

Exceptions

Exception If no point is specified or if an error occured.

Implements bpp::Function.

Definition at line 120 of file FivePointsNumericalDerivative.h.

References f3_.

◆ hasParameter() [1/2]

bool bpp::FunctionWrapper::hasParameter ( const std::string & name ) const

inlinevirtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: y/n.

Implements bpp::Parametrizable.

Definition at line 282 of file Functions.h.

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

◆ hasParameter() [2/2]

virtual bool bpp::Parametrizable::hasParameter ( const std::string & name ) const

pure virtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: y/n.

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

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

◆ matchParametersValues()

bool bpp::AbstractNumericalDerivative::matchParametersValues ( const ParameterList & parameters )

inlinevirtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

parameters A list of parameters.

Returns: True if at least one parameter value has been changed.

Exceptions

ConstraintException If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 245 of file AbstractNumericalDerivative.h.

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

◆ setAllParametersValues()

void bpp::AbstractNumericalDerivative::setAllParametersValues ( const ParameterList & parameters )

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

parameters A list with all parameters.

Exceptions

ParameterNotFoundException	If a some parameter in the list is not in params.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 227 of file AbstractNumericalDerivative.h.

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

◆ setInterval()

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

inlineinherited

Set the interval value used in numerical approximation.

Default value is 0.0001.

Parameters

h	Interval value.

Definition at line 132 of file AbstractNumericalDerivative.h.

References bpp::AbstractNumericalDerivative::h_.

◆ setNamespace() [1/2]

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

inlinevirtualinherited

Set the namespace for the parameter names.

Parameters

prefix The '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 342 of file Functions.h.

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

◆ setNamespace() [2/2]

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

pure virtualinherited

Set the namespace for the parameter names.

Parameters

prefix The '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::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::ParametrizableAdapter, bpp::FunctionWrapper, bpp::AbstractParametrizable, bpp::AbstractParameterAliasable, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, and bpp::LogsumHmmLikelihood.

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

◆ setParameters()

void bpp::AbstractNumericalDerivative::setParameters ( const ParameterList & parameters )

inlinevirtualinherited

Set the point where the function must be computed.

Parameters

parameters The parameter set to pass to the function.

Implements bpp::Function.

Definition at line 222 of file AbstractNumericalDerivative.h.

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

Referenced by bpp::AbstractNumericalDerivative::f().

◆ setParametersToDerivate()

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

inlineinherited

Set the list of parameters to derivate numerically.

Parameters

variables A list of all parameter names.

Definition at line 144 of file AbstractNumericalDerivative.h.

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

◆ setParametersValues()

void bpp::AbstractNumericalDerivative::setParametersValues ( const ParameterList & parameters )

inlinevirtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

parameters A list containing all parameters to update.

Exceptions

ParameterNotFoundException	If a some parameter in params is not in the list.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 239 of file AbstractNumericalDerivative.h.

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

◆ setParameterValue()

void bpp::AbstractNumericalDerivative::setParameterValue	(	const std::string &	name,
		double	value
	)

inlinevirtualinherited

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

Parameters

name	the name of the parameter to set.
value	The value of the parameter.

Exceptions

ParameterNotFoundException	If no parameter in the list has the name name.
ConstraintException	If value does not match the constraint associated to parameter name.

Implements bpp::Parametrizable.

Definition at line 233 of file AbstractNumericalDerivative.h.

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

◆ updateDerivatives()

void FivePointsNumericalDerivative::updateDerivatives ( const ParameterList parameters )

protectedvirtual

Compute derivatives.

Parameters

parameters The 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.

Implements bpp::AbstractNumericalDerivative.

Definition at line 47 of file FivePointsNumericalDerivative.cpp.

References bpp::ParameterList::createSubList(), bpp::ParameterList::getParameterValue(), bpp::ParameterList::hasParameter(), and bpp::ParameterList::setParameters().