Interface for discrete distribution objects. More...

#include <Bpp/Numeric/Prob/DiscreteDistribution.h>

Inheritance diagram for bpp::DiscreteDistribution:

Collaboration diagram for bpp::DiscreteDistribution:

Public Member Functions
	DiscreteDistribution ()

virtual	~DiscreteDistribution ()

DiscreteDistribution *	clone () const =0
	Create a copy of this object and send a pointer to it. More...

virtual std::string	getName () const =0
	Get the name of the distribution. More...

virtual size_t	getNumberOfCategories () const =0

virtual void	setNumberOfCategories (size_t nbClasses)=0
	sets the number of categories and discretizes if there is a change in this number. More...

virtual double	getValueCategory (double value) const =0

virtual size_t	getCategoryIndex (double value) const =0

virtual double	getCategory (size_t categoryIndex) const =0

virtual double	getProbability (size_t categoryIndex) const =0

virtual double	getProbability (double category) const =0

virtual Vdouble	getCategories () const =0

virtual Vdouble	getProbabilities () const =0

virtual void	set (double category, double probability)=0
	Set the probability associated to a class. More...

virtual void	add (double category, double probability)=0
	Modify the probability associated to a class. More...

virtual double	getInfCumulativeProbability (double category) const =0

virtual double	getIInfCumulativeProbability (double category) const =0

virtual double	getSupCumulativeProbability (double category) const =0

virtual double	getSSupCumulativeProbability (double category) const =0

virtual double	rand () const =0
	Draw a random number from this distribution. More...

virtual double	randC () const =0
	Draw a random number from the continuous version of this distribution, if it exists. More...

virtual double	qProb (double x) const =0
	Return the quantile of the continuous version of the distribution, ie y such that . More...

virtual double	pProb (double x) const =0
	Return the cumulative quantile of the continuous version of the distribution, ie . More...

virtual double	Expectation (double a) const =0
	Return a primitive function used for the expectation of the continuous version of the distribution, ie $E(X\|...<=X<a) = \int_{...}^a t.dProb(t) dt$ . More...

virtual void	setMedian (bool median)=0
	Sets the median value to true to say that the value in a class is proportional to the median value of the class, the proportionality factor being such that the sum of the values equals the expectation of the distribution. If it is set to false, the value is the mean value in the class. More...

virtual void	discretize ()=0
	Discretizes the distribution in equiprobable classes. More...

virtual Vdouble	getBounds () const =0

virtual double	getBound (size_t) const =0

virtual double	getLowerBound () const
	methods about the range of the definition More...

virtual double	getUpperBound () const

virtual bool	strictLowerBound () const

virtual bool	strictUpperBound () const

virtual void	restrictToConstraint (const Constraint &c)=0
	Restricts the distribution to the domain where the constraint is respected, in addition of other predefined constraints. More...

virtual void	print (OutputStream &out) const =0
	Print the distribution (categories and corresponding probabilities) to a stream. More...

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

virtual void	aliasParameters (const std::string &p1, const std::string &p2)=0
	Set two parameters as 'aliased'. More...

virtual void	aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
	alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. More...

virtual void	unaliasParameters (const std::string &p1, const std::string &p2)=0
	Detach two parameters previously set as 'aliased'. More...

virtual const ParameterList &	getIndependentParameters () const =0
	Get the minimal list of parameters to set the model. More...

virtual std::vector< std::string >	getAlias (const std::string &name) const =0

virtual std::map< std::string, std::string >	getAliases () const =0

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
	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...

virtual void	setAllParametersValues (const ParameterList &parameters)=0
	Set the parameters values to be equals to those of parameters. More...

virtual void	setParameterValue (const std::string &name, double value)=0
	Set the value of parameter with name name to be equal to value. More...

virtual void	setParametersValues (const ParameterList &parameters)=0
	Update the parameters from parameters. More...

virtual bool	matchParametersValues (const ParameterList &parameters)=0
	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...

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

Detailed Description

Interface for discrete distribution objects.

A discrete distribution usually contains a finite set of categories and a probability associated to each.

Each category (or class) is defined by two bounds, and sometimes by a mean or a median value.

A discrete distribution may contain one or several parameters. The probabilities associated to each class usually depends on the parameter values. In some cases, the number and/or bounds of the classes may also depend on the parameters values, depending on the kind of discretization used.

Definition at line 69 of file DiscreteDistribution.h.

Constructor & Destructor Documentation

◆ DiscreteDistribution()

bpp::DiscreteDistribution::DiscreteDistribution ( )

inline

Definition at line 73 of file DiscreteDistribution.h.

◆ ~DiscreteDistribution()

virtual bpp::DiscreteDistribution::~DiscreteDistribution ( )

inlinevirtual

Definition at line 74 of file DiscreteDistribution.h.

Member Function Documentation

◆ add()

virtual void bpp::DiscreteDistribution::add	(	double	category,
		double	probability
	)

pure virtual

Modify the probability associated to a class.

If the category does not exist, a new category is created with the corresponding probability. if the category exists, add 'probability' to the existing probability. The sum of all probabilities is not checked.

Parameters

category	The class value.
probability	The class probability.

Implemented in bpp::AbstractDiscreteDistribution.

◆ aliasParameters() [1/2]

virtual void bpp::ParameterAliasable::aliasParameters	(	const std::string &	p1,
		const std::string &	p2
	)

pure virtualinherited

Set two parameters as 'aliased'.

The values of the two parameters will be synchronized, so that setting the value of one parameter will automatically set the value of the other one accordingly.

Parameters

p1	Original parameter.
p2	Aliased parameter.

Exceptions

ParameterNotFoundException	if p1 or p2 do not correspond to existing parameters.
Exception	when trying to perform non-valid association.

Implemented in bpp::AbstractParameterAliasable.

◆ aliasParameters() [2/2]

virtual void bpp::ParameterAliasable::aliasParameters	(	std::map< std::string, std::string > &	unparsedParams,
		bool	verbose
	)

pure virtualinherited

alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden.

Parameters

unparsedParams	the map of the links : <A,B> matches for A->B aliasing.
verbose	verbosity

Implemented in bpp::AbstractParameterAliasable.

◆ clone()

DiscreteDistribution* bpp::DiscreteDistribution::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::Clonable.

Implemented in bpp::UniformDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::ConstantDistribution, and bpp::BetaDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::operator=().

◆ discretize()

virtual void bpp::DiscreteDistribution::discretize ( )

pure virtual

Discretizes the distribution in equiprobable classes.

Implemented in bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::ConstantDistribution, and bpp::AbstractDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::discretize().

◆ Expectation()

virtual double bpp::DiscreteDistribution::Expectation ( double a ) const

pure virtual

Return a primitive function used for the expectation of the continuous version of the distribution, ie $E(X|...<=X<a) = \int_{...}^a t.dProb(t) dt$ .

Implemented in bpp::UniformDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::ConstantDistribution, and bpp::BetaDiscreteDistribution.

Referenced by bpp::AbstractDiscreteDistribution::discretize(), and bpp::InvariantMixedDiscreteDistribution::Expectation().

◆ getAlias()

virtual std::vector<std::string> bpp::ParameterAliasable::getAlias ( const std::string & name ) const

pure virtualinherited

Returns: The list of names of the parameters that are aliased with a given parameter. Depending on the implementation, the function may be recursive or not...

Parameters

name	The name of the parameter to look for.

Implemented in bpp::AbstractParameterAliasable.

Referenced by bpp::BppOParametrizableFormat::write().

◆ getAliases()

virtual std::map<std::string, std::string> bpp::ParameterAliasable::getAliases ( ) const

pure virtualinherited

Returns: the map of the aliases.

Implemented in bpp::AbstractParameterAliasable.

◆ getBound()

virtual double bpp::DiscreteDistribution::getBound ( size_t ) const

pure virtual

Returns: the i th internal bound

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::updateDistribution().

◆ getBounds()

virtual Vdouble bpp::DiscreteDistribution::getBounds ( ) const

pure virtual

Returns: A vector of all the bounds

Implemented in bpp::AbstractDiscreteDistribution.

◆ getCategories()

virtual Vdouble bpp::DiscreteDistribution::getCategories ( ) const

pure virtual

Returns: A vector with all classes values.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::updateDistribution().

◆ getCategory()

virtual double bpp::DiscreteDistribution::getCategory ( size_t categoryIndex ) const

pure virtual

Parameters

categoryIndex Class index.

Returns: The value associated to a given class.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), and bpp::InvariantMixedDiscreteDistribution::updateDistribution().

◆ getCategoryIndex()

virtual size_t bpp::DiscreteDistribution::getCategoryIndex ( double value ) const

pure virtual

Parameters

value

Returns: The index of the category the value is in. Throws a OutOfRangeException if the value is off the domain of the DiscreteDistribution.

Implemented in bpp::AbstractDiscreteDistribution.

◆ getIInfCumulativeProbability()

virtual double bpp::DiscreteDistribution::getIInfCumulativeProbability ( double category ) const

pure virtual

Returns: $Pr(x \leq \mbox{category})$ .

Parameters

category The class value.

Implemented in bpp::AbstractDiscreteDistribution.

◆ getIndependentParameters()

virtual const ParameterList& bpp::ParameterAliasable::getIndependentParameters ( ) const

pure virtualinherited

Get the minimal list of parameters to set the model.

If no parameters are aliased, this is the same a getParameters().

Returns: A minimal set of parameters.

Implemented in bpp::AbstractParameterAliasable.

Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

◆ getInfCumulativeProbability()

virtual double bpp::DiscreteDistribution::getInfCumulativeProbability ( double category ) const

pure virtual

Returns: $Pr(x < \mbox{category})$ .

Parameters

category The class value.

Implemented in bpp::AbstractDiscreteDistribution.

◆ getLowerBound()

virtual double bpp::DiscreteDistribution::getLowerBound ( ) const

inlinevirtual

methods about the range of the definition

Returns: The lowest value.

Reimplemented in bpp::SimpleDiscreteDistribution, bpp::ConstantDistribution, and bpp::AbstractDiscreteDistribution.

Definition at line 278 of file DiscreteDistribution.h.

References bpp::NumConstants::VERY_BIG().

Referenced by bpp::InvariantMixedDiscreteDistribution::updateDistribution().

◆ getName()

virtual std::string bpp::DiscreteDistribution::getName ( ) const

pure virtual

Get the name of the distribution.

Returns: The name of this distribution.

Implemented in bpp::UniformDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::ConstantDistribution, and bpp::BetaDiscreteDistribution.

Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

◆ getNamespace()

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().

◆ getNumberOfCategories()

virtual size_t bpp::DiscreteDistribution::getNumberOfCategories ( ) const

pure virtual

Returns: The number of categories.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

◆ getNumberOfIndependentParameters()

virtual size_t bpp::ParameterAliasable::getNumberOfIndependentParameters ( ) const

pure virtualinherited

Get the number of independent parameters.

Returns: The number of independent parameters. If no parameters are aliased, this is equivalent to the getNumberOfParameters() method.

Implemented in bpp::AbstractParameterAliasable.

◆ getNumberOfParameters()

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()

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()

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()

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_()

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()

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().

◆ getProbabilities()

virtual Vdouble bpp::DiscreteDistribution::getProbabilities ( ) const

pure virtual

Returns: A vector with all probabilities.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::updateDistribution().

◆ getProbability() [1/2]

virtual double bpp::DiscreteDistribution::getProbability ( double category ) const

pure virtual

Parameters

category The value associated to the class.

Returns: The probability associated to a given class.

Implemented in bpp::AbstractDiscreteDistribution.

◆ getProbability() [2/2]

virtual double bpp::DiscreteDistribution::getProbability ( size_t categoryIndex ) const

pure virtual

Parameters

categoryIndex Class index.

Returns: The probability associated to a given class.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by bpp::BppODiscreteDistributionFormat::initialize_().

◆ getSSupCumulativeProbability()

virtual double bpp::DiscreteDistribution::getSSupCumulativeProbability ( double category ) const

pure virtual

Returns: $Pr(x \geq \mbox{category})$ .

Parameters

category The class value.

Implemented in bpp::AbstractDiscreteDistribution.

◆ getSupCumulativeProbability()

virtual double bpp::DiscreteDistribution::getSupCumulativeProbability ( double category ) const

pure virtual

Returns: $Pr(x > \mbox{category})$ .

Parameters

category The class value.

Implemented in bpp::AbstractDiscreteDistribution.

◆ getUpperBound()

virtual double bpp::DiscreteDistribution::getUpperBound ( ) const

inlinevirtual

Returns: The highest value.

Reimplemented in bpp::SimpleDiscreteDistribution, bpp::ConstantDistribution, and bpp::AbstractDiscreteDistribution.

Definition at line 286 of file DiscreteDistribution.h.

References bpp::NumConstants::VERY_BIG().

Referenced by bpp::InvariantMixedDiscreteDistribution::updateDistribution().

◆ getValueCategory()

virtual double bpp::DiscreteDistribution::getValueCategory ( double value ) const

pure virtual

Parameters

value

Returns: The value of the category the value is in. Throws a OutOfRangeException if the value is off the domain of the DiscreteDistribution.

Implemented in bpp::AbstractDiscreteDistribution.

◆ hasParameter()

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()

virtual bool bpp::Parametrizable::matchParametersValues ( const ParameterList & parameters )

pure virtualinherited

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.

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

Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::BppODiscreteDistributionFormat::initialize_(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

◆ pProb()

virtual double bpp::DiscreteDistribution::pProb ( double x ) const

pure virtual

Return the cumulative quantile of the continuous version of the distribution, ie .

Implemented in bpp::UniformDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::ConstantDistribution, and bpp::BetaDiscreteDistribution.

Referenced by bpp::AbstractDiscreteDistribution::discretize(), bpp::InvariantMixedDiscreteDistribution::pProb(), and bpp::InvariantMixedDiscreteDistribution::qProb().

◆ print()

virtual void bpp::DiscreteDistribution::print ( OutputStream & out ) const

pure virtual

Print the distribution (categories and corresponding probabilities) to a stream.

Parameters

out	The outstream where to print the distribution.

Implemented in bpp::AbstractDiscreteDistribution.

◆ qProb()

virtual double bpp::DiscreteDistribution::qProb ( double x ) const

pure virtual

Return the quantile of the continuous version of the distribution, ie y such that .

Implemented in bpp::UniformDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::ConstantDistribution, and bpp::BetaDiscreteDistribution.

Referenced by bpp::AbstractDiscreteDistribution::discretize(), and bpp::InvariantMixedDiscreteDistribution::qProb().

◆ rand()

virtual double bpp::DiscreteDistribution::rand ( ) const

pure virtual

Draw a random number from this distribution.

This number will be one of the class values, drawn according to the class probabilities.

Returns: A random number according to this distribution.

Implemented in bpp::AbstractDiscreteDistribution.

◆ randC()

virtual double bpp::DiscreteDistribution::randC ( ) const

pure virtual

Draw a random number from the continuous version of this distribution, if it exists.

Uses the continuous version of this distribution to draw a random number.

Returns: A random number according to this distribution.

Exceptions

Exception If there is no continuous version of this distribution.

Implemented in bpp::UniformDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::ConstantDistribution, bpp::BetaDiscreteDistribution, and bpp::AbstractDiscreteDistribution.

◆ restrictToConstraint()

virtual void bpp::DiscreteDistribution::restrictToConstraint ( const Constraint & c )

pure virtual

Restricts the distribution to the domain where the constraint is respected, in addition of other predefined constraints.

If the domain interval is modified, the discretization process is launched.

Parameters

c	The Constraint to respect.

Implemented in bpp::TruncatedExponentialDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::ConstantDistribution, and bpp::AbstractDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::restrictToConstraint().

◆ set()

virtual void bpp::DiscreteDistribution::set	(	double	category,
		double	probability
	)

pure virtual

Set the probability associated to a class.

If the category does not exist, a new category is created with the corresponding probability. If the category already exist, its probability is set to 'probability'. The sum of all probabilities is not checked.

Parameters

category	The class value.
probability	The class probability.

Implemented in bpp::AbstractDiscreteDistribution.

◆ setAllParametersValues()

virtual void bpp::Parametrizable::setAllParametersValues ( const ParameterList & parameters )

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

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.

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

Referenced by bpp::AbstractNumericalDerivative::setAllParametersValues(), bpp::FunctionWrapper::setAllParametersValues(), and bpp::InfinityFunctionWrapper::setAllParametersValues().

◆ setMedian()

virtual void bpp::DiscreteDistribution::setMedian ( bool median )

pure virtual

Sets the median value to true to say that the value in a class is proportional to the median value of the class, the proportionality factor being such that the sum of the values equals the expectation of the distribution. If it is set to false, the value is the mean value in the class.

If the median value is modified, the discretization process is launched.

Parameters

median tells how the value associated to each class is computed.

Implemented in bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, and bpp::AbstractDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::setMedian().

◆ setNamespace()

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().

◆ setNumberOfCategories()

virtual void bpp::DiscreteDistribution::setNumberOfCategories ( size_t nbClasses )

pure virtual

sets the number of categories and discretizes if there is a change in this number.

Implemented in bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, and bpp::AbstractDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::setNumberOfCategories().

◆ setParametersValues()

virtual void bpp::Parametrizable::setParametersValues ( const ParameterList & parameters )

pure virtualinherited

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.

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

Referenced by bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

◆ setParameterValue()

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

pure virtualinherited

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.

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

Referenced by bpp::AbstractNumericalDerivative::setParameterValue(), bpp::FunctionWrapper::setParameterValue(), and bpp::InfinityFunctionWrapper::setParameterValue().

◆ strictLowerBound()

virtual bool bpp::DiscreteDistribution::strictLowerBound ( ) const

inlinevirtual

Returns: The lowest value.

Reimplemented in bpp::AbstractDiscreteDistribution.

Definition at line 294 of file DiscreteDistribution.h.

Referenced by bpp::InvariantMixedDiscreteDistribution::updateDistribution().

◆ strictUpperBound()

virtual bool bpp::DiscreteDistribution::strictUpperBound ( ) const

inlinevirtual

Returns: The highest value.

Reimplemented in bpp::AbstractDiscreteDistribution.

Definition at line 302 of file DiscreteDistribution.h.

Referenced by bpp::InvariantMixedDiscreteDistribution::updateDistribution().

◆ unaliasParameters()

virtual void bpp::ParameterAliasable::unaliasParameters	(	const std::string &	p1,
		const std::string &	p2
	)

pure virtualinherited

Detach two parameters previously set as 'aliased'.

The values of the two parameters will now be independent.

Parameters

p1	Original parameter.
p2	Aliased parameter.

Exceptions

ParameterNotFoundException	if p1 or p2 do not correspond to existing parameters.
Exception	when trying to perform non-valid dissociation.

Implemented in bpp::AbstractParameterAliasable.

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

Bpp/Numeric/Prob/DiscreteDistribution.h

Public Member Functions

Protected Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ DiscreteDistribution()

◆ ~DiscreteDistribution()

Member Function Documentation

◆ add()

◆ aliasParameters() [1/2]

◆ aliasParameters() [2/2]

◆ clone()

◆ discretize()

◆ Expectation()

◆ getAlias()

◆ getAliases()

◆ getBound()

◆ getBounds()

◆ getCategories()

◆ getCategory()

◆ getCategoryIndex()

◆ getIInfCumulativeProbability()

◆ getIndependentParameters()

◆ getInfCumulativeProbability()

◆ getLowerBound()

◆ getName()

◆ getNamespace()

◆ getNumberOfCategories()

◆ getNumberOfIndependentParameters()

◆ getNumberOfParameters()

◆ getParameter()

◆ getParameterNameWithoutNamespace()

◆ getParameters()

◆ getParameters_()

◆ getParameterValue()

◆ getProbabilities()

◆ getProbability() [1/2]

◆ getProbability() [2/2]

◆ getSSupCumulativeProbability()

◆ getSupCumulativeProbability()

◆ getUpperBound()

◆ getValueCategory()

◆ hasParameter()

◆ matchParametersValues()

◆ pProb()

◆ print()

◆ qProb()

◆ rand()

◆ randC()

◆ restrictToConstraint()

◆ set()

◆ setAllParametersValues()

◆ setMedian()

◆ setNamespace()

◆ setNumberOfCategories()

◆ setParametersValues()

◆ setParameterValue()

◆ strictLowerBound()

◆ strictUpperBound()

◆ unaliasParameters()