bpp-core  2.4.0
bpp::DiscreteDistribution Class Referenceabstract

Interface for discrete distribution objects. More...

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

+ Inheritance diagram for bpp::DiscreteDistribution:
+ Collaboration diagram for bpp::DiscreteDistribution:

Public Member Functions

 DiscreteDistribution ()
 
virtual ~DiscreteDistribution ()
 
DiscreteDistributionclone () const =0
 Create a copy of this object and send a pointer to it. More...
 
virtual std::string getName () const =0
 Get the name of the distribution. More...
 
virtual size_t getNumberOfCategories () const =0
 
virtual void setNumberOfCategories (size_t nbClasses)=0
 sets the number of categories and discretizes if there is a change in this number. More...
 
virtual double getValueCategory (double value) const =0
 
virtual double getCategory (size_t categoryIndex) const =0
 
virtual double getProbability (size_t categoryIndex) const =0
 
virtual double getProbability (double category) const =0
 
virtual Vdouble getCategories () const =0
 
virtual Vdouble getProbabilities () const =0
 
virtual void set (double category, double probability)=0
 Set the probability associated to a class. More...
 
virtual void add (double category, double probability)=0
 Modify the probability associated to a class. More...
 
virtual double getInfCumulativeProbability (double category) const =0
 
virtual double getIInfCumulativeProbability (double category) const =0
 
virtual double getSupCumulativeProbability (double category) const =0
 
virtual double getSSupCumulativeProbability (double category) const =0
 
virtual double rand () const =0
 Draw a random number from this distribution. More...
 
virtual double randC () const =0
 Draw a random number from the continuous version of this distribution, if it exists. More...
 
virtual double qProb (double x) const =0
 Return the quantile of the continuous version of the distribution, ie y such that $ Prob(X<y)=x $. More...
 
virtual double pProb (double x) const =0
 Return the cumulative quantile of the continuous version of the distribution, ie $ Prob(X<x) $. More...
 
virtual double Expectation (double a) const =0
 Return a primitive function used for the expectation of the continuous version of the distribution, ie $ E(X|...<=X<a) = \int_{...}^a t.dProb(t) dt $. More...
 
virtual void setMedian (bool median)=0
 Sets the median value to true to say that the value in a class is proportional to the median value of the class, the proportionality factor being such that the sum of the values equals the expectation of the distribution. If it is set to false, the value is the mean value in the class. More...
 
virtual void discretize ()=0
 Discretizes the distribution in equiprobable classes. More...
 
virtual Vdouble getBounds () const =0
 
virtual double getBound (size_t) const =0
 
virtual double getLowerBound () const
 methods about the range of the definition More...
 
virtual double getUpperBound () const
 
virtual bool strictLowerBound () const
 
virtual bool strictUpperBound () const
 
virtual void restrictToConstraint (const Constraint &c)=0
 Restricts the distribution to the domain where the constraint is respected, in addition of other predefined constraints. More...
 
virtual void print (OutputStream &out) const =0
 Print the distribution (categories and corresponding probabilities) to a stream. More...
 
virtual size_t getNumberOfIndependentParameters () const =0
 Get the number of independent parameters. More...
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 Set two parameters as 'aliased'. More...
 
virtual void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
 alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. More...
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 Detach two parameters previously set as 'aliased'. More...
 
virtual const ParameterListgetIndependentParameters () 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 ParameterListgetParameters () const =0
 Get all parameters available. More...
 
virtual const ParametergetParameter (const std::string &name) const =0
 Get the parameter with specified name. More...
 
virtual double getParameterValue (const std::string &name) const =0
 Get the value for parameter of name 'name'. More...
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 Set the parameters values to be equals to those of parameters. More...
 
virtual void setParameterValue (const std::string &name, double value)=0
 Set the value of parameter with name name to be equal to value. More...
 
virtual void setParametersValues (const ParameterList &parameters)=0
 Update the parameters from parameters. More...
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 Update the parameters from parameters. More...
 
virtual size_t getNumberOfParameters () const =0
 Get the number of parameters. More...
 
virtual void setNamespace (const std::string &prefix)=0
 Set the namespace for the parameter names. More...
 
virtual std::string getNamespace () const =0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
 Resolves a parameter name according to the current namespace. More...
 

Detailed Description

Interface for discrete distribution objects.

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

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

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

Definition at line 68 of file DiscreteDistribution.h.

Constructor & Destructor Documentation

bpp::DiscreteDistribution::DiscreteDistribution ( )
inline

Definition at line 72 of file DiscreteDistribution.h.

Member Function Documentation

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

Modify the probability associated to a class.

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

Parameters
categoryThe class value.
probabilityThe class probability.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by ~DiscreteDistribution().

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
p1Original parameter.
p2Aliased parameter.
Exceptions
ParameterNotFoundExceptionif p1 or p2 do not correspond to existing parameters.
Exceptionwhen trying to perform non-valid association.

Implemented in bpp::AbstractParameterAliasable.

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

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
unparsedParamsthe map of the links : <A,B> matches for A->B aliasing.
verboseverbosity

Implemented in bpp::AbstractParameterAliasable.

virtual void bpp::DiscreteDistribution::discretize ( )
pure virtual
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
nameThe name of the parameter to look for.

Implemented in bpp::AbstractParameterAliasable.

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

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().

virtual double bpp::DiscreteDistribution::getBound ( size_t  ) const
pure virtual
virtual Vdouble bpp::DiscreteDistribution::getBounds ( ) const
pure virtual
Returns
A vector of all the bounds

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by ~DiscreteDistribution().

virtual Vdouble bpp::DiscreteDistribution::getCategories ( ) const
pure virtual
Returns
A vector with all classes values.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and ~DiscreteDistribution().

virtual double bpp::DiscreteDistribution::getCategory ( size_t  categoryIndex) const
pure virtual
Parameters
categoryIndexClass index.
Returns
The value associated to a given class.

Implemented in bpp::AbstractDiscreteDistribution.

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

virtual double bpp::DiscreteDistribution::getIInfCumulativeProbability ( double  category) const
pure virtual
Returns
$Pr(x \leq \mbox{category})$.
Parameters
categoryThe class value.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by ~DiscreteDistribution().

virtual const ParameterList& bpp::ParameterAliasable::getIndependentParameters ( ) const
pure virtualinherited
virtual double bpp::DiscreteDistribution::getInfCumulativeProbability ( double  category) const
pure virtual
Returns
$Pr(x < \mbox{category})$.
Parameters
categoryThe class value.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by ~DiscreteDistribution().

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

methods about the range of the definition

Returns
The lowest value.

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

Definition at line 269 of file DiscreteDistribution.h.

References bpp::NumConstants::VERY_BIG().

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

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(), and bpp::Parametrizable::~Parametrizable().

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().

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(), bpp::BppODiscreteDistributionFormat::write(), and bpp::Parametrizable::~Parametrizable().

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

Get the parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
The parameter with given name.
Exceptions
ParameterNotFoundExceptionif no parameter with this name is found.

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

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

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(), bpp::BppOParametrizableFormat::write(), and bpp::Parametrizable::~Parametrizable().

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

Get the value for parameter of name 'name'.

Parameters
nameThe name of the parameter.
Returns
the value of parameter name.

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

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

virtual Vdouble bpp::DiscreteDistribution::getProbabilities ( ) const
pure virtual
Returns
A vector with all probabilities.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and ~DiscreteDistribution().

virtual double bpp::DiscreteDistribution::getProbability ( size_t  categoryIndex) const
pure virtual
Parameters
categoryIndexClass index.
Returns
The probability associated to a given class.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by bpp::BppODiscreteDistributionFormat::initialize_(), and ~DiscreteDistribution().

virtual double bpp::DiscreteDistribution::getProbability ( double  category) const
pure virtual
Parameters
categoryThe value associated to the class.
Returns
The probability associated to a given class.

Implemented in bpp::AbstractDiscreteDistribution.

virtual double bpp::DiscreteDistribution::getSSupCumulativeProbability ( double  category) const
pure virtual
Returns
$Pr(x \geq \mbox{category})$.
Parameters
categoryThe class value.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by ~DiscreteDistribution().

virtual double bpp::DiscreteDistribution::getSupCumulativeProbability ( double  category) const
pure virtual
Returns
$Pr(x > \mbox{category})$.
Parameters
categoryThe class value.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by ~DiscreteDistribution().

virtual double bpp::DiscreteDistribution::getUpperBound ( ) const
inlinevirtual
virtual double bpp::DiscreteDistribution::getValueCategory ( double  value) const
pure virtual
Parameters
value
Returns
The value of the category the value is in. Throws a OutOfRangeException if the value is off the domain of the DiscreteDistribution.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by ~DiscreteDistribution().

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

Tell if there is a parameter with specified name.

Parameters
nameThe name of the parameter to look for.
Returns
y/n.

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

Referenced by bpp::FunctionWrapper::hasParameter(), and bpp::Parametrizable::~Parametrizable().

virtual bool bpp::Parametrizable::matchParametersValues ( const ParameterList parameters)
pure virtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters
parametersA list of parameters.
Returns
True if at least one parameter value has been changed.
Exceptions
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

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

Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::BppODiscreteDistributionFormat::initialize_(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), bpp::TestFunction::setParameters(), and bpp::Parametrizable::~Parametrizable().

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

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

Parameters
outThe outstream where to print the distribution.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by strictUpperBound().

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

Draw a random number from this distribution.

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

Returns
A random number according to this distribution.

Implemented in bpp::AbstractDiscreteDistribution.

Referenced by ~DiscreteDistribution().

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

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

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

Returns
A random number according to this distribution.
Exceptions
ExceptionIf there is no continuous version of this distribution.

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

Referenced by ~DiscreteDistribution().

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

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

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

Parameters
cThe Constraint to respect.

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

Referenced by bpp::InvariantMixedDiscreteDistribution::restrictToConstraint(), and strictUpperBound().

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

Set the probability associated to a class.

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

Parameters
categoryThe class value.
probabilityThe class probability.

Implemented in bpp::AbstractDiscreteDistribution.

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
parametersA list with all parameters.
Exceptions
ParameterNotFoundExceptionIf a some parameter in the list is not in params.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

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

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

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

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

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

Parameters
mediantells how the value associated to each class is computed.

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

Referenced by bpp::BppODiscreteDistributionFormat::read(), bpp::InvariantMixedDiscreteDistribution::setMedian(), and ~DiscreteDistribution().

virtual void bpp::Parametrizable::setNamespace ( const std::string &  prefix)
pure virtualinherited
virtual void bpp::DiscreteDistribution::setNumberOfCategories ( size_t  nbClasses)
pure virtual

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

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

Referenced by bpp::InvariantMixedDiscreteDistribution::setNumberOfCategories(), and ~DiscreteDistribution().

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
parametersA list containing all parameters to update.
Exceptions
ParameterNotFoundExceptionIf a some parameter in params is not in the list.
ConstraintExceptionIf a value in parameters does not match the constraint in the corresponding parameter in the list.

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

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

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
namethe name of the parameter to set.
valueThe value of the parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter in the list has the name name.
ConstraintExceptionIf value does not match the constraint associated to parameter name.

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

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

virtual bool bpp::DiscreteDistribution::strictLowerBound ( ) const
inlinevirtual
Returns
The lowest value.

Reimplemented in bpp::AbstractDiscreteDistribution.

Definition at line 283 of file DiscreteDistribution.h.

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

virtual bool bpp::DiscreteDistribution::strictUpperBound ( ) const
inlinevirtual
Returns
The highest value.

Reimplemented in bpp::AbstractDiscreteDistribution.

Definition at line 290 of file DiscreteDistribution.h.

References print(), and restrictToConstraint().

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

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

Detach two parameters previously set as 'aliased'.

The values of the two parameters will now be independent.

Parameters
p1Original parameter.
p2Aliased parameter.
Exceptions
ParameterNotFoundExceptionif p1 or p2 do not correspond to existing parameters.
Exceptionwhen trying to perform non-valid dissociation.

Implemented in bpp::AbstractParameterAliasable.

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


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