Partial implementation of the DiscreteDistribution interface. More...

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

Inheritance diagram for bpp::AbstractDiscreteDistribution:

Collaboration diagram for bpp::AbstractDiscreteDistribution:

Classes
class	Order
	Comparator class for AbstractDiscreteDistribution. More...

Public Member Functions
	AbstractDiscreteDistribution (size_t nbClasses, const std::string &prefix="", short discretization=DISCRETIZATION_EQUAL_PROB)

	AbstractDiscreteDistribution (size_t nbClasses, double precision, const std::string &prefix="", short discretization=DISCRETIZATION_EQUAL_PROB)

	AbstractDiscreteDistribution (const AbstractDiscreteDistribution &adde)

AbstractDiscreteDistribution &	operator= (const AbstractDiscreteDistribution &adde)

virtual	~AbstractDiscreteDistribution ()

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

DiscreteDistributionInterface *	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 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 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 &	parameter (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 void	removeConstraint (const std::string &name)=0
	Remove the constraint associated with one parameter, if any. More...

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
	Set/Change the constraint associated with one parameter. More...

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

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

virtual std::string	getNamespace () const =0

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

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

bool	hasIndependentParameter (const std::string &name) const

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

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

void	aliasParameters (const std::string &p1, const std::string &p2)
	alias the parameters. More...

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

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

ParameterList	getAliasedParameters (const ParameterList &pl) const
	Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list. More...

ParameterList	getFromParameters (const ParameterList &pl) const
	Return the list of the names of the parameters from which the parameters of the list are aliased (directly or not). More...

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

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

std::string	getFrom (const std::string &name) const

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

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

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

const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const

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

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

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

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

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

void	removeConstraint (const std::string &name) override
	Remove the constraint associated with one parameter, if any. More...

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
	Set/Change the constraint associated with one parameter. More...

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

std::string	getNamespace () const override

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

virtual void	fireParameterChanged (const ParameterList &parameters)
	Notify the class when one or several parameters have changed. More...

The DiscreteDistribution interface.
size_t	getNumberOfCategories () const

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

double	getCategory (size_t categoryIndex) const

double	getProbability (size_t categoryIndex) const

double	getProbability (double category) const

Vdouble	getCategories () const

Vdouble	getProbabilities () const

double	getValueCategory (double value) const

size_t	getCategoryIndex (double value) const

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

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

double	getInfCumulativeProbability (double category) const

double	getIInfCumulativeProbability (double category) const

double	getSupCumulativeProbability (double category) const

double	getSSupCumulativeProbability (double category) const

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

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

double	getBound (size_t i) const

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

double	getUpperBound () const

bool	strictLowerBound () const

bool	strictUpperBound () const

Vdouble	getBounds () const

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

double	precision () const

void	setMedian (bool median)
	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 ()
	Discretizes the distribution in equiprobable classes. More...

Static Public Attributes
static short	DISCRETIZATION_EQUAL_PROB = 1

static short	DISCRETIZATION_EQUAL_INTERVAL = 2

static short	DISCRETIZATION_EQUAL_PROB_WHEN_POSSIBLE = 3

Protected Member Functions
void	discretizeEqualProportions ()

void	discretizeEqualIntervals ()

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

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	shareParameter_ (const std::shared_ptr< Parameter > &parameter)

void	shareParameters_ (const ParameterList &parameters)

void	includeParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index)

void	deleteParameter_ (std::string &name)

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

void	resetParameters_ ()

const std::shared_ptr< Parameter > &	getParameter (size_t i) const

std::shared_ptr< Parameter > &	getParameter (size_t i)

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

ParameterList &	getParameters_ () override
	Get all parameters available. More...

Protected Attributes
size_t	numberOfCategories_

std::map< double, double, Order >	distribution_

std::vector< double >	bounds_

std::shared_ptr< IntervalConstraint >	intMinMax_
	the interval where the distribution is defined/restricted. More...

bool	median_

short	discretizationScheme_

Detailed Description

Partial implementation of the DiscreteDistribution interface.

This class uses a map to store the cateogry values as keys and probabilities as values. It uses its own comparator class to deal with double precision. By default, category values that differ less than 10E-9 will be considered identical.

Definition at line 23 of file AbstractDiscreteDistribution.h.

Constructor & Destructor Documentation

◆ AbstractDiscreteDistribution() [1/3]

AbstractDiscreteDistribution::AbstractDiscreteDistribution	(	size_t	nbClasses,
		const std::string &	prefix = `""`,
		short	discretization = `DISCRETIZATION_EQUAL_PROB`
	)

Definition at line 16 of file AbstractDiscreteDistribution.cpp.

◆ AbstractDiscreteDistribution() [2/3]

AbstractDiscreteDistribution::AbstractDiscreteDistribution	(	size_t	nbClasses,
		double	precision,
		const std::string &	prefix = `""`,
		short	discretization = `DISCRETIZATION_EQUAL_PROB`
	)

With additional precision value to discriminate categories (default 1e-12)

Definition at line 26 of file AbstractDiscreteDistribution.cpp.

◆ AbstractDiscreteDistribution() [3/3]

AbstractDiscreteDistribution::AbstractDiscreteDistribution ( const AbstractDiscreteDistribution & adde )

Definition at line 36 of file AbstractDiscreteDistribution.cpp.

◆ ~AbstractDiscreteDistribution()

virtual bpp::AbstractDiscreteDistribution::~AbstractDiscreteDistribution ( )

inlinevirtual

Definition at line 111 of file AbstractDiscreteDistribution.h.

References add(), getCategories(), getCategory(), getCategoryIndex(), getIInfCumulativeProbability(), getInfCumulativeProbability(), getNumberOfCategories(), getProbabilities(), getProbability(), getSSupCumulativeProbability(), getSupCumulativeProbability(), getValueCategory(), rand(), and setNumberOfCategories().

Member Function Documentation

◆ add()

void AbstractDiscreteDistribution::add	(	double	category,
		double	probability
	)

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.

Implements bpp::DiscreteDistributionInterface.

Definition at line 151 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by ~AbstractDiscreteDistribution().

◆ addParameter_()

void bpp::AbstractParameterAliasable::addParameter_ ( Parameter * parameter )

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 196 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::addParameter_(), bpp::Parameter::getName(), and bpp::ParameterList::shareParameter().

Referenced by bpp::ParametrizableCollection< N >::addObject(), bpp::BetaDiscreteDistribution::BetaDiscreteDistribution(), bpp::ConstantDistribution::ConstantDistribution(), bpp::DirichletDiscreteDistribution::DirichletDiscreteDistribution(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), bpp::Simplex::Simplex(), and bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution().

◆ addParameters_()

void bpp::AbstractParameterAliasable::addParameters_ ( const ParameterList & parameters )

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 202 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::addParameters_(), bpp::AliasParameterListener::getName(), bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().

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

◆ aliasParameters() [1/4]

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.

Referenced by bpp::ParameterAliasable::~ParameterAliasable().

◆ aliasParameters() [2/4]

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.

◆ aliasParameters() [3/4]

void AbstractParameterAliasable::aliasParameters	(	const std::string &	p1,
		const std::string &	p2
	)

virtualinherited

alias the parameters.

Parameters

p1	name of the parameter to which the other parameter is aliased
p2	name of the aliased parameter, which will be deleted from independent parameters list

Implements bpp::ParameterAliasable.

Definition at line 67 of file AbstractParameterAliasable.cpp.

Referenced by bpp::ParametrizableCollection< N >::addObject(), and bpp::AbstractParameterAliasable::aliasParameters().

◆ aliasParameters() [4/4]

void AbstractParameterAliasable::aliasParameters	(	std::map< std::string, std::string > &	unparsedParams,
		bool	verbose
	)

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

Implements bpp::ParameterAliasable.

Definition at line 120 of file AbstractParameterAliasable.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::ParameterList::clone(), bpp::Parameter::clone(), bpp::ApplicationTools::displayResult(), bpp::AbstractParametrizable::getParameters(), bpp::Parameter::getValue(), bpp::ParameterList::hasParameter(), bpp::AbstractParametrizable::matchParametersValues(), bpp::ParameterList::parameter(), bpp::ParameterList::size(), and bpp::TextTools::toString().

◆ clone()

DiscreteDistributionInterface* bpp::DiscreteDistributionInterface::clone ( ) const

pure virtualinherited

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

Referenced by bpp::DiscreteDistributionInterface::~DiscreteDistributionInterface().

◆ deleteParameter_() [1/2]

void bpp::AbstractParameterAliasable::deleteParameter_ ( size_t index )

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 237 of file AbstractParameterAliasable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), and bpp::ParameterList::hasParameter().

Referenced by bpp::ParametrizableCollection< N >::removeObject().

◆ deleteParameter_() [2/2]

void bpp::AbstractParameterAliasable::deleteParameter_ ( std::string & name )

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 245 of file AbstractParameterAliasable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), and bpp::ParameterList::hasParameter().

◆ deleteParameters_()

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

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 252 of file AbstractParameterAliasable.h.

◆ discretize()

void AbstractDiscreteDistribution::discretize ( )

virtual

Discretizes the distribution in equiprobable classes.

Implements bpp::DiscreteDistributionInterface.

Reimplemented in bpp::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::SimpleDiscreteDistribution, and bpp::ConstantDistribution.

Definition at line 494 of file AbstractDiscreteDistribution.cpp.

References bounds_, DISCRETIZATION_EQUAL_INTERVAL, DISCRETIZATION_EQUAL_PROB, discretizationScheme_, discretizeEqualIntervals(), discretizeEqualProportions(), intMinMax_, and numberOfCategories_.

◆ discretizeEqualIntervals()

void AbstractDiscreteDistribution::discretizeEqualIntervals ( )

protected

Definition at line 454 of file AbstractDiscreteDistribution.cpp.

References bounds_, distribution_, intMinMax_, numberOfCategories_, and bpp::DiscreteDistributionInterface::pProb().

Referenced by discretize(), and setMedian().

◆ discretizeEqualProportions()

void AbstractDiscreteDistribution::discretizeEqualProportions ( )

protected

Definition at line 294 of file AbstractDiscreteDistribution.cpp.

References bounds_, distribution_, bpp::DiscreteDistributionInterface::Expectation(), intMinMax_, median_, numberOfCategories_, bpp::DiscreteDistributionInterface::pProb(), precision(), bpp::DiscreteDistributionInterface::qProb(), and bpp::NumConstants::TINY().

Referenced by discretize(), and setMedian().

◆ Expectation()

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

pure virtualinherited

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

Referenced by discretizeEqualProportions(), and bpp::DiscreteDistributionInterface::~DiscreteDistributionInterface().

◆ fireParameterChanged()

virtual void bpp::AbstractParametrizable::fireParameterChanged ( const ParameterList & parameters )

inlinevirtualinherited

Notify the class when one or several parameters have changed.

Parameters

parameters A ParameterList object with parameters that changed.

Definition at line 108 of file AbstractParametrizable.h.

◆ getAlias() [1/2]

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::ParametrizableCollection< N >::addObject(), bpp::BppOParametrizableFormat::write(), and bpp::ParameterAliasable::~ParameterAliasable().

◆ getAlias() [2/2]

vector< string > AbstractParameterAliasable::getAlias ( const std::string & name ) const

virtualinherited

Returns: The list of names of the parameters that are aliased with a given parameter. The implementation is recursive, which means that in the case of A->B->C, getalias(C) will return both A and B.

Parameters

name	The name of the parameter to look for.

Implements bpp::ParameterAliasable.

Definition at line 204 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_, and bpp::VectorTools::append().

Referenced by bpp::AbstractParameterAliasable::getAliases(), and bpp::ParametrizableCollection< N >::removeObject().

◆ getAliasedParameters()

ParameterList AbstractParameterAliasable::getAliasedParameters ( const ParameterList & pl ) const

inherited

Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list.

Definition at line 244 of file AbstractParameterAliasable.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::ParameterList::hasParameter(), and bpp::AbstractParametrizable::parameter().

◆ getAliases() [1/2]

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

pure virtualinherited

Returns: the map of the aliases.

Implemented in bpp::AbstractParameterAliasable.

Referenced by bpp::ParameterAliasable::~ParameterAliasable().

◆ getAliases() [2/2]

std::map< std::string, std::string > AbstractParameterAliasable::getAliases ( ) const

virtualinherited

Returns: the map of the aliases.

Implements bpp::ParameterAliasable.

Definition at line 225 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_, and bpp::AbstractParameterAliasable::getAlias().

◆ getBound()

double bpp::AbstractDiscreteDistribution::getBound ( size_t ) const

inlinevirtual

Returns: the i th internal bound

Implements bpp::DiscreteDistributionInterface.

Definition at line 141 of file AbstractDiscreteDistribution.h.

Referenced by getBounds().

◆ getBounds()

Vdouble AbstractDiscreteDistribution::getBounds ( ) const

virtual

Returns: A vector of all the bounds

Implements bpp::DiscreteDistributionInterface.

Definition at line 527 of file AbstractDiscreteDistribution.cpp.

References getBound(), getLowerBound(), getUpperBound(), and numberOfCategories_.

Referenced by strictUpperBound().

◆ getCategories()

Vdouble AbstractDiscreteDistribution::getCategories ( ) const

virtual

Returns: A vector with all classes values.

Implements bpp::DiscreteDistributionInterface.

Definition at line 112 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by ~AbstractDiscreteDistribution().

◆ getCategory()

double AbstractDiscreteDistribution::getCategory ( size_t categoryIndex ) const

virtual

Parameters

categoryIndex Class index.

Returns: The value associated to a given class.

Implements bpp::DiscreteDistributionInterface.

Definition at line 81 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by ~AbstractDiscreteDistribution().

◆ getCategoryIndex()

size_t AbstractDiscreteDistribution::getCategoryIndex ( double value ) const

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.

Implements bpp::DiscreteDistributionInterface.

Definition at line 278 of file AbstractDiscreteDistribution.cpp.

References bounds_, intMinMax_, and bpp::TextTools::toString().

Referenced by ~AbstractDiscreteDistribution().

◆ getFrom()

string AbstractParameterAliasable::getFrom ( const std::string & name ) const

inherited

Returns: The name of the parameter from which a given parameter is aliased.

Parameters

name	The name of the parameter to look for.

Definition at line 280 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_.

◆ getFromParameters()

ParameterList AbstractParameterAliasable::getFromParameters ( const ParameterList & pl ) const

inherited

Return the list of the names of the parameters from which the parameters of the list are aliased (directly or not).

Definition at line 297 of file AbstractParameterAliasable.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::ParameterList::hasParameter(), and bpp::AbstractParametrizable::parameter().

◆ getIInfCumulativeProbability()

double AbstractDiscreteDistribution::getIInfCumulativeProbability ( double category ) const

virtual

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

Parameters

category The class value.

Implements bpp::DiscreteDistributionInterface.

Definition at line 200 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by ~AbstractDiscreteDistribution().

◆ getIndependentParameters() [1/2]

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::BppOParametrizableFormat::write(), bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution(), and bpp::ParameterAliasable::~ParameterAliasable().

◆ getIndependentParameters() [2/2]

const ParameterList& bpp::AbstractParameterAliasable::getIndependentParameters ( ) const

inlinevirtualinherited

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.

Implements bpp::ParameterAliasable.

Definition at line 135 of file AbstractParameterAliasable.h.

◆ getInfCumulativeProbability()

double AbstractDiscreteDistribution::getInfCumulativeProbability ( double category ) const

virtual

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

Parameters

category The class value.

Implements bpp::DiscreteDistributionInterface.

Definition at line 185 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by ~AbstractDiscreteDistribution().

◆ getLowerBound()

double bpp::AbstractDiscreteDistribution::getLowerBound ( ) const

inlinevirtual

methods about the range of the definition

Returns: The lowest value.

Reimplemented from bpp::DiscreteDistributionInterface.

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

Definition at line 153 of file AbstractDiscreteDistribution.h.

Referenced by bpp::BetaDiscreteDistribution::fireParameterChanged(), getBounds(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().

◆ getName()

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

pure virtualinherited

Get the name of the distribution.

Returns: The name of this distribution.

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

Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution(), and bpp::DiscreteDistributionInterface::~DiscreteDistributionInterface().

◆ getNamespace() [1/2]

std::string bpp::AbstractParametrizable::getNamespace ( ) const

inlineoverridevirtualinherited

Returns: The current namespace used. This is an empty string if no namespace is currently defined.

Implements bpp::Parametrizable.

Definition at line 99 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), and bpp::AbstractParametrizable::prefix_.

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

◆ getNamespace() [2/2]

virtual std::string bpp::Parametrizable::getNamespace ( ) const

pure virtualinherited

Returns: The current namespace used. This is an empty string if no namespace is currently defined.

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

Referenced by bpp::Parametrizable::~Parametrizable().

◆ getNumberOfCategories()

size_t AbstractDiscreteDistribution::getNumberOfCategories ( ) const

virtual

Returns: The number of categories.

Implements bpp::DiscreteDistributionInterface.

Definition at line 61 of file AbstractDiscreteDistribution.cpp.

References numberOfCategories_.

Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution(), and ~AbstractDiscreteDistribution().

◆ getNumberOfIndependentParameters() [1/2]

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.

Referenced by bpp::ParameterAliasable::~ParameterAliasable().

◆ getNumberOfIndependentParameters() [2/2]

size_t bpp::AbstractParameterAliasable::getNumberOfIndependentParameters ( ) const

inlinevirtualinherited

Get the number of independent parameters.

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

Implements bpp::ParameterAliasable.

Definition at line 137 of file AbstractParameterAliasable.h.

References bpp::AliasParameterListener::getAlias(), bpp::AliasParameterListener::getFrom(), and bpp::ParameterList::size().

◆ getNumberOfParameters() [1/2]

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlineoverridevirtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

Implements bpp::Parametrizable.

Definition at line 95 of file AbstractParametrizable.h.

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

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::AbstractParameterAliasable::operator=(), bpp::ConstantDistribution::restrictToConstraint(), and bpp::SimpleDiscreteDistribution::restrictToConstraint().

◆ getNumberOfParameters() [2/2]

virtual size_t bpp::Parametrizable::getNumberOfParameters ( ) const

pure virtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

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

Referenced by bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution(), and bpp::Parametrizable::~Parametrizable().

◆ getParameter() [1/3]

const std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getParameter ( const std::string & name ) const

inlineinherited

Definition at line 48 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

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

◆ getParameter() [2/3]

const std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getParameter ( size_t i ) const

inlineprotectedinherited

Returns: The shared_ptr parameter at a given position.

Warning: No check is performed on the validity of the index given as input!

Definition at line 211 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter() [3/3]

std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getParameter ( size_t i )

inlineprotectedinherited

Definition at line 216 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter_() [1/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string & name )

inlineprotectedinherited

Parameters

name	The name of the parameter.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 164 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::hasParameter(), and bpp::ParameterList::parameter().

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParametrizable::getParameterWithNamespace_(), bpp::AbstractParametrizable::removeConstraint(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::InvariantMixedDiscreteDistribution::restrictToConstraint(), bpp::AbstractParametrizable::setConstraint(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ getParameter_() [2/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t index )

inlineprotectedinherited

Definition at line 190 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameter_() [3/3]

const Parameter& bpp::AbstractParametrizable::getParameter_ ( size_t index ) const

inlineprotectedinherited

Definition at line 197 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameterNameWithoutNamespace() [1/2]

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

overridevirtualinherited

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 28 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

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

◆ getParameterNameWithoutNamespace() [2/2]

virtual std::string bpp::Parametrizable::getParameterNameWithoutNamespace ( const std::string & name ) const

pure virtualinherited

Resolves a parameter name according to the current namespace.

Returns: The parameter name without the namespace prefix, if any.

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

Referenced by bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::Parametrizable::~Parametrizable().

◆ getParameters() [1/2]

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

inlineoverridevirtualinherited

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 41 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::FullHmmTransitionMatrix::FullHmmTransitionMatrix(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), and bpp::ParametrizableCollection< N >::removeObject().

◆ getParameters() [2/2]

virtual const ParameterList& bpp::Parametrizable::getParameters ( ) const

pure virtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

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

Referenced by bpp::ParameterAliasableAdapter::getIndependentParameters(), bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), bpp::BppOParametrizableFormat::write(), and bpp::Parametrizable::~Parametrizable().

◆ getParameters_() [1/2]

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::AbstractParametrizable, and bpp::DirectionFunction.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ getParameters_() [2/2]

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineoverrideprotectedvirtualinherited

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 205 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameterValue() [1/2]

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

inlineoverridevirtualinherited

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 53 of file AbstractParametrizable.h.

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

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

Referenced by bpp::BppODiscreteDistributionFormat::readDiscreteDistribution(), and bpp::Parametrizable::~Parametrizable().

◆ getParameterWithNamespace_() [1/2]

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string & name )

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 176 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

const Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string & name ) const

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 185 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameter().

◆ getProbabilities()

Vdouble AbstractDiscreteDistribution::getProbabilities ( ) const

virtual

Returns: A vector with all probabilities.

Implements bpp::DiscreteDistributionInterface.

Definition at line 128 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by ~AbstractDiscreteDistribution().

◆ getProbability() [1/2]

double AbstractDiscreteDistribution::getProbability ( size_t categoryIndex ) const

virtual

Parameters

categoryIndex Class index.

Returns: The probability associated to a given class.

Implements bpp::DiscreteDistributionInterface.

Definition at line 93 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by ~AbstractDiscreteDistribution().

◆ getProbability() [2/2]

double AbstractDiscreteDistribution::getProbability ( double category ) const

virtual

Parameters

category The value associated to the class.

Returns: The probability associated to a given class.

Implements bpp::DiscreteDistributionInterface.

Definition at line 105 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ getSSupCumulativeProbability()

double AbstractDiscreteDistribution::getSSupCumulativeProbability ( double category ) const

virtual

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

Parameters

category The class value.

Implements bpp::DiscreteDistributionInterface.

Definition at line 234 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by ~AbstractDiscreteDistribution().

◆ getSupCumulativeProbability()

double AbstractDiscreteDistribution::getSupCumulativeProbability ( double category ) const

virtual

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

Parameters

category The class value.

Implements bpp::DiscreteDistributionInterface.

Definition at line 217 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by ~AbstractDiscreteDistribution().

◆ getUpperBound()

double bpp::AbstractDiscreteDistribution::getUpperBound ( ) const

inlinevirtual

Returns: The highest value.

Reimplemented from bpp::DiscreteDistributionInterface.

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

Definition at line 158 of file AbstractDiscreteDistribution.h.

Referenced by bpp::BetaDiscreteDistribution::fireParameterChanged(), getBounds(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().

◆ getValueCategory()

double AbstractDiscreteDistribution::getValueCategory ( double value ) const

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.

Implements bpp::DiscreteDistributionInterface.

Definition at line 259 of file AbstractDiscreteDistribution.cpp.

References bounds_, distribution_, intMinMax_, and bpp::TextTools::toString().

Referenced by ~AbstractDiscreteDistribution().

◆ hasIndependentParameter()

bool bpp::AbstractParameterAliasable::hasIndependentParameter ( const std::string & name ) const

inlineinherited

Definition at line 133 of file AbstractParameterAliasable.h.

References bpp::ParameterList::hasParameter().

◆ 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

name	The name of the parameter to look for.

Returns: y/n.

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

Referenced by bpp::Parametrizable::~Parametrizable().

◆ hasParameter() [2/2]

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

inlineoverridevirtualinherited

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 39 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter().

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::AbstractParametrizable::getParameter_(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ includeParameters_()

void bpp::AbstractParameterAliasable::includeParameters_ ( const ParameterList & parameters )

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 227 of file AbstractParameterAliasable.h.

References bpp::AliasParameterListener::getName(), bpp::AbstractParametrizable::includeParameters_(), bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().

◆ matchParametersValues() [1/2]

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

inlineoverridevirtualinherited

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 76 of file AbstractParametrizable.h.

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

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

◆ matchParametersValues() [2/2]

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

Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), bpp::TestFunction::setParameters(), and bpp::Parametrizable::~Parametrizable().

◆ operator=()

AbstractDiscreteDistribution & AbstractDiscreteDistribution::operator= ( const AbstractDiscreteDistribution & adde )

Definition at line 46 of file AbstractDiscreteDistribution.cpp.

References bounds_, discretizationScheme_, distribution_, intMinMax_, median_, numberOfCategories_, and bpp::AbstractParameterAliasable::operator=().

Referenced by bpp::ConstantDistribution::operator=(), bpp::UniformDiscreteDistribution::operator=(), bpp::GaussianDiscreteDistribution::operator=(), bpp::ExponentialDiscreteDistribution::operator=(), bpp::InvariantMixedDiscreteDistribution::operator=(), bpp::GammaDiscreteDistribution::operator=(), bpp::TruncatedExponentialDiscreteDistribution::operator=(), bpp::MixtureOfDiscreteDistributions::operator=(), and bpp::SimpleDiscreteDistribution::operator=().

◆ parameter() [1/2]

const Parameter& bpp::AbstractParametrizable::parameter ( const std::string & name ) const

inlineoverridevirtualinherited

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 43 of file AbstractParametrizable.h.

References bpp::ParameterList::parameter().

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

◆ parameter() [2/2]

virtual const Parameter& bpp::Parametrizable::parameter ( 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::FunctionWrapper, bpp::ParametrizableAdapter, and bpp::AbstractParametrizable.

Referenced by bpp::TestFunction::getValue(), and bpp::Parametrizable::~Parametrizable().

◆ pProb()

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

pure virtualinherited

Return the cumulative quantile of the continuous version of the distribution, ie $ Prob(X<x) $ .

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

Referenced by discretizeEqualIntervals(), discretizeEqualProportions(), and bpp::DiscreteDistributionInterface::~DiscreteDistributionInterface().

◆ precision()

double bpp::AbstractDiscreteDistribution::precision ( ) const

inline

Definition at line 177 of file AbstractDiscreteDistribution.h.

Referenced by discretizeEqualProportions(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), and bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution().

◆ print()

void AbstractDiscreteDistribution::print ( OutputStream & out ) const

virtual

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

Parameters

out	The outstream where to print the distribution.

Implements bpp::DiscreteDistributionInterface.

Definition at line 249 of file AbstractDiscreteDistribution.cpp.

References distribution_.

Referenced by strictUpperBound().

◆ qProb()

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

pure virtualinherited

Return the quantile of the continuous version of the distribution, ie y such that $ Prob(X<y)=x $ .

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

Referenced by discretizeEqualProportions(), and bpp::DiscreteDistributionInterface::~DiscreteDistributionInterface().

◆ rand()

double AbstractDiscreteDistribution::rand ( ) const

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.

Implements bpp::DiscreteDistributionInterface.

Definition at line 167 of file AbstractDiscreteDistribution.cpp.

References distribution_, and bpp::RandomTools::giveRandomNumberBetweenZeroAndEntry().

Referenced by ~AbstractDiscreteDistribution().

◆ randC()

double bpp::AbstractDiscreteDistribution::randC ( ) const

inlinevirtual

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.

Implements bpp::DiscreteDistributionInterface.

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

Definition at line 135 of file AbstractDiscreteDistribution.h.

◆ removeConstraint() [1/2]

void bpp::AbstractParametrizable::removeConstraint ( const std::string & name )

inlineoverridevirtualinherited

Remove the constraint associated with one parameter, if any.

Parameters

name	The name of the parameter to look for.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 85 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::removeConstraint().

◆ removeConstraint() [2/2]

virtual void bpp::Parametrizable::removeConstraint ( const std::string & name )

pure virtualinherited

Remove the constraint associated with one parameter, if any.

Parameters

name	The name of the parameter to look for.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

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

Referenced by bpp::Parametrizable::~Parametrizable().

◆ resetParameters_()

void bpp::AbstractParameterAliasable::resetParameters_ ( )

inlineprotectedinherited

Definition at line 262 of file AbstractParameterAliasable.h.

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

Referenced by bpp::ParametrizableCollection< N >::clear().

◆ restrictToConstraint()

void AbstractDiscreteDistribution::restrictToConstraint ( const ConstraintInterface & c )

virtual

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

Parameters

c	The Constraint to respect.

Implements bpp::DiscreteDistributionInterface.

Reimplemented in bpp::InvariantMixedDiscreteDistribution, bpp::SimpleDiscreteDistribution, bpp::MixtureOfDiscreteDistributions, bpp::TruncatedExponentialDiscreteDistribution, and bpp::ConstantDistribution.

Definition at line 539 of file AbstractDiscreteDistribution.cpp.

References discretize(), and intMinMax_.

Referenced by bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), and setMedian().

◆ set()

void AbstractDiscreteDistribution::set	(	double	category,
		double	probability
	)

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.

Implements bpp::DiscreteDistributionInterface.

Definition at line 144 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ setAllParametersValues() [1/2]

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

inlineoverridevirtualinherited

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 58 of file AbstractParametrizable.h.

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

◆ setAllParametersValues() [2/2]

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

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setConstraint() [1/2]

void bpp::AbstractParametrizable::setConstraint	(	const std::string &	name,
		std::shared_ptr< ConstraintInterface >	constraint
	)

inlineoverridevirtualinherited

Set/Change the constraint associated with one parameter.

Parameters

name	The name of the parameter to look for.
constraint	A pointer to the constraint (may be null)

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 90 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_(), and bpp::Parameter::setConstraint().

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

◆ setConstraint() [2/2]

virtual void bpp::Parametrizable::setConstraint	(	const std::string &	name,
		std::shared_ptr< ConstraintInterface >	constraint
	)

pure virtualinherited

Set/Change the constraint associated with one parameter.

Parameters

name	The name of the parameter to look for.
constraint	A pointer to the constraint (may be null)

Exceptions

ParameterNotFoundException if no parameter with this name is found.

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

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setMedian()

void bpp::AbstractDiscreteDistribution::setMedian ( bool median )

inlinevirtual

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.

Implements bpp::DiscreteDistributionInterface.

Reimplemented in bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 179 of file AbstractDiscreteDistribution.h.

References discretize(), discretizeEqualIntervals(), discretizeEqualProportions(), and restrictToConstraint().

◆ setNamespace() [1/2]

void AbstractParameterAliasable::setNamespace ( const std::string & prefix )

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.

Implements bpp::Parametrizable.

Reimplemented in bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 186 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::setNamespace(), and bpp::TextTools::startsWith().

Referenced by bpp::InvariantMixedDiscreteDistribution::setNamespace(), and bpp::MixtureOfDiscreteDistributions::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::FunctionWrapper, bpp::ParametrizableAdapter, bpp::LogsumHmmLikelihood, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, bpp::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, bpp::AbstractParametrizable, and bpp::InvariantMixedDiscreteDistribution.

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setNumberOfCategories()

void AbstractDiscreteDistribution::setNumberOfCategories ( size_t nbClasses )

virtual

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

Implements bpp::DiscreteDistributionInterface.

Reimplemented in bpp::MixtureOfDiscreteDistributions, and bpp::InvariantMixedDiscreteDistribution.

Definition at line 66 of file AbstractDiscreteDistribution.cpp.

References discretize(), and numberOfCategories_.

Referenced by ~AbstractDiscreteDistribution().

◆ setParametersValues() [1/2]

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

inlineoverridevirtualinherited

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 70 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), and bpp::ParameterList::setParametersValues().

Referenced by bpp::LowMemoryRescaledHmmLikelihood::setParameters(), bpp::RescaledHmmLikelihood::setParameters(), and bpp::LogsumHmmLikelihood::setParameters().

◆ setParametersValues() [2/2]

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

Referenced by bpp::Parametrizable::~Parametrizable().

◆ setParameterValue() [1/2]

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

inlineoverridevirtualinherited

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 64 of file AbstractParametrizable.h.

References bpp::ParameterList::createSubList(), bpp::AbstractParametrizable::fireParameterChanged(), and bpp::ParameterList::setParameterValue().

◆ setParameterValue() [2/2]

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

Referenced by bpp::Parametrizable::~Parametrizable().