Discretized Dirichlet distribution. If the distribution is in n dimensions, the domain is the n-1 simplex. More...

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

Inheritance diagram for bpp::DirichletDiscreteDistribution:

Collaboration diagram for bpp::DirichletDiscreteDistribution:

Public Member Functions
	DirichletDiscreteDistribution (std::vector< size_t > vn, Vdouble valpha)
	Build a new discretized Dirichlet distribution. More...

	~DirichletDiscreteDistribution ()

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

std::string	getName () const

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

size_t	getNumberOfCategories () const

Vdouble	getValueCategory (Vdouble &Vvalue) const

VVdouble	getCategories () const

virtual double	getProbability (Vdouble &category) const

Vdouble	rand () const
	Draw a random vector from this distribution. More...

Vdouble	randC () const
	Draw a random vector from the continuous version of this distribution. 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 throw (ParameterNotFoundException, Exception)
	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 throw (ParameterNotFoundException, Exception)
	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 bool	hasParameter (const std::string &name) const =0
	Tell if there is a parameter with specified name. More...

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

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

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

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

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

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

virtual bool	matchParametersValues (const ParameterList &parameters)=0 throw (ConstraintException)
	Update the parameters from parameters. More...

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

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

virtual std::string	getNamespace () const =0

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

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

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) throw (ParameterNotFoundException, Exception)
	Set two parameters as 'aliased'. 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) throw (ParameterNotFoundException, Exception)
	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...

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

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

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

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

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

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

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

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

void	setParametersValues (const ParameterList &parameters) throw (ParameterNotFoundException, ConstraintException)
	Update the parameters from parameters. More...

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

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

std::string	getNamespace () const

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

Protected Member Functions
void	applyParameters ()

void	discretize (Vdouble &valpha)

void	addParameter_ (Parameter *parameter)

void	addParameters_ (const ParameterList &parameters)

void	deleteParameter_ (size_t index) throw (IndexOutOfBoundsException)

void	deleteParameter_ (std::string &name) throw (IndexOutOfBoundsException)

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

void	resetParameters_ ()

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

Parameter &	getParameter_ (size_t index) throw (IndexOutOfBoundsException)

const Parameter &	getParameter_ (size_t index) const throw (IndexOutOfBoundsException)

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

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

ParameterList &	getParameters_ ()

Private Attributes
std::vector< BetaDiscreteDistribution *>	vpBDD_

Detailed Description

Discretized Dirichlet distribution. If the distribution is in n dimensions, the domain is the n-1 simplex.

The discretization is made in the order of these dimensions. Then the order of the dimensions is not neutral on the resulting categories.

Here is an example of the discretization process: if the distribution is in 3 dimensions, and the number of categories is 4 in the first dimension, 3 in the second and 5 in the third, the first interval is split in 4 equi-probable intervals, and each interval is split on the second dimension in 3 equi-probable intervals, and each of the 12 resulting 2D intervals is split in 5 equi-probable 3D-intervals. Eventually, there are 60 equi-probable categories.

In the same example, if the distribution is followed by the random vector $ (X_1,X_2,X_3) $ , the 1D distribution used for $ X_1 $ is the marginal distribution, which discretized values are say, $ v_1^1, v_1^2, v_1^3, v_1^4 $ , then the four 1D distributions used for $ X_2 $ are the conditional marginal distributions $ (X_2|X_1=v_1^1), (X_2|X_1=v_1^2), (X_2|X_1=v_1^3), (X_2|X_1=v_1^4) $ . And in a similar way for $ X_3 $ , with the 12 resulting conditions on $ X_1 $ and $ X_2 $ .

It uses the AbstractDiscreteDistribution comparator class to deal with double precision. By default, category values that differ less than 10E-9 will be considered identical.

The successive discretization process is done using the distributions, if the parameters are $(\alpha_1, ..., \alpha_n)$ :

$ X_1 $ follows Beta( $\alpha_1, \sum_{i=2}^n \alpha_i$ ).

$ X_j $ follows $(1-\sum_{i=1}^{j-1} X_i)$ * Beta( $\alpha_j, \sum_{i=j+1}^n \alpha_i$ ).

$X_n = 1 - \sum_{i=1}^{n-1} X_i$ .

The parameters are: alpha_1, ... alpha_n $\in [0.0001;\infty[$ .

Definition at line 101 of file DirichletDiscreteDistribution.h.

Constructor & Destructor Documentation

◆ DirichletDiscreteDistribution()

DirichletDiscreteDistribution::DirichletDiscreteDistribution	(	std::vector< size_t >	vn,
		Vdouble	valpha
	)

Build a new discretized Dirichlet distribution.

Parameters

vn	the vector of the dim-1 numbers of categories to use.
valpha	the vector of the dim alpha parameters.

Constructor:

Definition at line 55 of file DirichletDiscreteDistribution.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), discretize(), bpp::TextTools::toString(), and vpBDD_.

Referenced by clone().

◆ ~DirichletDiscreteDistribution()

DirichletDiscreteDistribution::~DirichletDiscreteDistribution ( )

Definition at line 81 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

Member Function Documentation

◆ addParameter_()

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

inlineprotectedinherited

Definition at line 212 of file AbstractParameterAliasable.h.

References bpp::ParameterList::addParameter(), bpp::AbstractParametrizable::addParameter_(), bpp::Parameter::clone(), and bpp::AbstractParameterAliasable::independentParameters_.

◆ addParameters_()

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

inlineprotectedinherited

Definition at line 218 of file AbstractParameterAliasable.h.

References bpp::ParameterList::addParameters(), bpp::AbstractParametrizable::addParameters_(), and bpp::AbstractParameterAliasable::independentParameters_.

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
	)
throw	(	ParameterNotFoundException,
		Exception
	)

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() [2/4]

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
	)
throw	(	ParameterNotFoundException,
		Exception
	)

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.

Implements bpp::ParameterAliasable.

Definition at line 103 of file AbstractParameterAliasable.cpp.

References bpp::Parameter::addParameterListener(), bpp::Parameter::getConstraint(), bpp::Constraint::getDescription(), and bpp::Parameter::hasConstraint().

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

◆ 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 151 of file AbstractParameterAliasable.cpp.

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

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

◆ applyParameters()

void DirichletDiscreteDistribution::applyParameters ( )

protected

Definition at line 99 of file DirichletDiscreteDistribution.cpp.

References discretize(), bpp::AbstractParametrizable::getParameterValue(), bpp::TextTools::toString(), and vpBDD_.

Referenced by fireParameterChanged().

◆ clone()

DirichletDiscreteDistribution* bpp::DirichletDiscreteDistribution::clone ( ) const

inlinevirtual

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

Returns: A pointer toward the copy object.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 119 of file DirichletDiscreteDistribution.h.

References DirichletDiscreteDistribution().

◆ deleteParameter_() [1/2]

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

inlineprotectedinherited

Definition at line 224 of file AbstractParameterAliasable.h.

References bpp::ParameterList::deleteParameter(), bpp::AbstractParametrizable::deleteParameter_(), bpp::Parameter::getName(), bpp::AbstractParametrizable::getParameter_(), bpp::ParameterList::hasParameter(), and bpp::AbstractParameterAliasable::independentParameters_.

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

◆ deleteParameter_() [2/2]

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

inlineprotectedinherited

Definition at line 232 of file AbstractParameterAliasable.h.

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

◆ deleteParameters_()

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

inlineprotectedinherited

Definition at line 239 of file AbstractParameterAliasable.h.

References bpp::AbstractParameterAliasable::deleteParameter_().

◆ discretize()

void DirichletDiscreteDistribution::discretize ( Vdouble & valpha )

protected

Definition at line 113 of file DirichletDiscreteDistribution.cpp.

References bpp::ParameterList::addParameter(), bpp::ParameterList::setParameterValue(), and vpBDD_.

Referenced by applyParameters(), and DirichletDiscreteDistribution().

◆ fireParameterChanged()

void DirichletDiscreteDistribution::fireParameterChanged ( const ParameterList & parameters )

virtual

Notify the class when one or several parameters have changed.

Parameters

parameters A ParameterList object with parameters that changed.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 91 of file DirichletDiscreteDistribution.cpp.

References applyParameters(), and bpp::AbstractParameterAliasable::fireParameterChanged().

◆ 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(), and bpp::BppOParametrizableFormat::write().

◆ 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 245 of file AbstractParameterAliasable.cpp.

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

Referenced by 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 266 of file AbstractParameterAliasable.cpp.

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

◆ getCategories()

VVdouble DirichletDiscreteDistribution::getCategories ( ) const

Definition at line 195 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ 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 306 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_.

◆ 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::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::BppODiscreteDistributionFormat::write(), and bpp::BppOParametrizableFormat::write().

◆ 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 162 of file AbstractParameterAliasable.h.

References bpp::AbstractParameterAliasable::independentParameters_.

◆ getName()

std::string bpp::DirichletDiscreteDistribution::getName ( ) const

inline

Definition at line 128 of file DirichletDiscreteDistribution.h.

◆ getNamespace() [1/2]

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

inlinevirtualinherited

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

Implements bpp::Parametrizable.

Definition at line 125 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::prefix_.

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

◆ getNamespace() [2/2]

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

pure virtualinherited

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

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

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

◆ getNumberOfCategories()

size_t DirichletDiscreteDistribution::getNumberOfCategories ( ) const

virtual

Returns: The number of categories

Implements bpp::MultipleDiscreteDistribution.

Definition at line 140 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ 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.

◆ 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 164 of file AbstractParameterAliasable.h.

References bpp::AbstractParameterAliasable::independentParameters_, and bpp::ParameterList::size().

◆ getNumberOfParameters() [1/2]

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlinevirtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

Implements bpp::Parametrizable.

Definition at line 121 of file AbstractParametrizable.h.

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

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

◆ getNumberOfParameters() [2/2]

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

pure virtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

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

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

◆ getParameter() [1/2]

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

inlinevirtualinherited

Get the parameter with specified name.

Parameters

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 79 of file AbstractParametrizable.h.

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

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

◆ getParameter() [2/2]

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

pure virtualinherited

Get the parameter with specified name.

Parameters

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::FunctionWrapper::getParameter().

◆ getParameter_() [1/3]

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

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 175 of file AbstractParametrizable.h.

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

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

◆ getParameter_() [2/3]

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

inlineprotectedinherited

Definition at line 199 of file AbstractParametrizable.h.

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

◆ getParameter_() [3/3]

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

inlineprotectedinherited

Definition at line 205 of file AbstractParametrizable.h.

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

◆ getParameterNameWithoutNamespace() [1/2]

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

virtualinherited

Resolves a parameter name according to the current namespace.

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

Implements bpp::Parametrizable.

Definition at line 63 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

◆ getParameterNameWithoutNamespace() [2/2]

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

pure virtualinherited

Resolves a parameter name according to the current namespace.

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

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

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

◆ getParameters() [1/2]

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

inlinevirtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 77 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameters() [2/2]

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

pure virtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

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

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

◆ getParameters_()

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineprotectedinherited

Definition at line 212 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameterValue() [1/2]

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

inlinevirtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 84 of file AbstractParametrizable.h.

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

◆ getParameterValue() [2/2]

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

pure virtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

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

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

◆ getParameterWithNamespace_() [1/2]

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

inlineprotectedinherited

Parameters

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::getParameter_().

◆ getParameterWithNamespace_() [2/2]

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

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 194 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

◆ getProbability()

double DirichletDiscreteDistribution::getProbability ( Vdouble & category ) const

virtual

Parameters

category The vector of values associated to the class.

Returns: The probability associated to a given class.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 177 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ getValueCategory()

Vdouble DirichletDiscreteDistribution::getValueCategory ( Vdouble & Vvalue ) const

virtual

Parameters

Vvalue

Returns: The vector of categoryIndex of the classes the value is in. Throws a ConstraintException if the value is off the domain of the DirichletDiscreteDistribution.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 154 of file DirichletDiscreteDistribution.cpp.

References bpp::NumConstants::VERY_TINY(), and vpBDD_.

◆ 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::FunctionWrapper::hasParameter().

◆ hasParameter() [2/2]

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

inlinevirtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: y/n.

Implements bpp::Parametrizable.

Definition at line 75 of file AbstractParametrizable.h.

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

◆ matchParametersValues() [1/2]

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

inlinevirtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

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 111 of file AbstractParametrizable.h.

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

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

◆ matchParametersValues() [2/2]

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

pure virtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

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::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

◆ rand()

Vdouble DirichletDiscreteDistribution::rand ( ) const

virtual

Draw a random vector from this distribution.

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

Returns: A random number according to this distribution.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 249 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ randC()

Vdouble DirichletDiscreteDistribution::randC ( ) const

virtual

Draw a random vector from the continuous version of this distribution.

Returns: A random vector according to this distribution.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 266 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ resetParameters_()

void bpp::AbstractParameterAliasable::resetParameters_ ( )

inlineprotectedinherited

Definition at line 249 of file AbstractParameterAliasable.h.

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

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

◆ setAllParametersValues() [1/2]

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

inlinevirtualinherited

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters

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 90 of file AbstractParametrizable.h.

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

◆ setAllParametersValues() [2/2]

virtual void bpp::Parametrizable::setAllParametersValues	(	const ParameterList &	parameters	)
throw	(	ParameterNotFoundException,
		ConstraintException
	)

pure virtualinherited

Set the parameters values to be equals to those of parameters.

The list must contain exactly the same parameters (ie same names) than the parameters available.

Parameters

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

◆ 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 218 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParameterAliasable::independentParameters_, bpp::AbstractParametrizable::setNamespace(), bpp::ParameterList::size(), 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::AbstractParameterAliasable, bpp::MixtureOfDiscreteDistributions, bpp::AbstractParametrizable, and bpp::InvariantMixedDiscreteDistribution.

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

◆ setParametersValues() [1/2]

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

inlinevirtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

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 104 of file AbstractParametrizable.h.

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

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

◆ setParametersValues() [2/2]

virtual void bpp::Parametrizable::setParametersValues	(	const ParameterList &	parameters	)
throw	(	ParameterNotFoundException,
		ConstraintException
	)

pure virtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

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::AbstractNumericalDerivative::setParametersValues(), bpp::FunctionWrapper::setParametersValues(), and bpp::InfinityFunctionWrapper::setParametersValues().

◆ setParameterValue() [1/2]

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

inlinevirtualinherited

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

Parameters

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 97 of file AbstractParametrizable.h.

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

◆ setParameterValue() [2/2]

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

pure virtualinherited

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

Parameters

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

◆ unaliasParameters() [1/2]

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

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.

◆ unaliasParameters() [2/2]

void AbstractParameterAliasable::unaliasParameters	(	const std::string &	p1,
		const std::string &	p2
	)
throw	(	ParameterNotFoundException,
		Exception
	)

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.

Implements bpp::ParameterAliasable.

Definition at line 198 of file AbstractParameterAliasable.cpp.

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

Member Data Documentation

◆ vpBDD_

std::vector<BetaDiscreteDistribution* > bpp::DirichletDiscreteDistribution::vpBDD_

private

Definition at line 106 of file DirichletDiscreteDistribution.h.

Referenced by applyParameters(), DirichletDiscreteDistribution(), discretize(), getCategories(), getNumberOfCategories(), getProbability(), getValueCategory(), rand(), randC(), and ~DirichletDiscreteDistribution().

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

Bpp/Numeric/Prob/DirichletDiscreteDistribution.h
Bpp/Numeric/Prob/DirichletDiscreteDistribution.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DirichletDiscreteDistribution()

◆ ~DirichletDiscreteDistribution()

Member Function Documentation

◆ addParameter_()

◆ addParameters_()

◆ aliasParameters() [1/4]

◆ aliasParameters() [2/4]

◆ aliasParameters() [3/4]

◆ aliasParameters() [4/4]

◆ applyParameters()

◆ clone()

◆ deleteParameter_() [1/2]

◆ deleteParameter_() [2/2]

◆ deleteParameters_()

◆ discretize()

◆ fireParameterChanged()

◆ getAlias() [1/2]

◆ getAlias() [2/2]

◆ getAliasedParameters()

◆ getCategories()

◆ getFrom()

◆ getIndependentParameters() [1/2]

◆ getIndependentParameters() [2/2]

◆ getName()

◆ getNamespace() [1/2]

◆ getNamespace() [2/2]

◆ getNumberOfCategories()

◆ getNumberOfIndependentParameters() [1/2]

◆ getNumberOfIndependentParameters() [2/2]

◆ getNumberOfParameters() [1/2]

◆ getNumberOfParameters() [2/2]

◆ getParameter() [1/2]

◆ getParameter() [2/2]

◆ getParameter_() [1/3]

◆ getParameter_() [2/3]

◆ getParameter_() [3/3]

◆ getParameterNameWithoutNamespace() [1/2]

◆ getParameterNameWithoutNamespace() [2/2]

◆ getParameters() [1/2]

◆ getParameters() [2/2]

◆ getParameters_()

◆ getParameterValue() [1/2]

◆ getParameterValue() [2/2]

◆ getParameterWithNamespace_() [1/2]

◆ getParameterWithNamespace_() [2/2]

◆ getProbability()

◆ getValueCategory()

◆ hasParameter() [1/2]

◆ hasParameter() [2/2]

◆ matchParametersValues() [1/2]

◆ matchParametersValues() [2/2]

◆ rand()

◆ randC()

◆ resetParameters_()

◆ setAllParametersValues() [1/2]

◆ setAllParametersValues() [2/2]

◆ setNamespace() [1/2]

◆ setNamespace() [2/2]

◆ setParametersValues() [1/2]

◆ setParametersValues() [2/2]

◆ setParameterValue() [1/2]

◆ setParameterValue() [2/2]

◆ unaliasParameters() [1/2]

◆ unaliasParameters() [2/2]

Member Data Documentation

◆ vpBDD_