bpp-core  2.2.0
Classes | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
bpp::AbstractDiscreteDistribution Class Referenceabstract

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="")
 
 AbstractDiscreteDistribution (size_t nbClasses, double precision, const std::string &prefix="")
 
 AbstractDiscreteDistribution (const AbstractDiscreteDistribution &adde)
 
AbstractDiscreteDistribution & operator= (const AbstractDiscreteDistribution &adde)
 
virtual ~AbstractDiscreteDistribution ()
 
virtual void restrictToConstraint (const Constraint &c)
 Restricts the distribution to the domain where the constraint is respected, in addition of other predefined constraints. More...
 
DiscreteDistribution * clone () const =0
 Create a copy of this object and send a pointer to it. More...
 
virtual std::string getName () const =0
 Get the name of the distribution. More...
 
virtual 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 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
 
void fireParameterChanged (const ParameterList &parameters)
 Notify the class when one or several parameters have changed. More...
 
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...
 
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
 
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 throw (Exception)
 Draw a random number from the continuous version of this distribution, if it exists. More...
 
double getBound (size_t i) const throw (IndexOutOfBoundsException)
 
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...
 

Protected Member Functions

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_ ()
 

Protected Attributes

size_t numberOfCategories_
 
std::map< double, double, Order > distribution_
 
std::vector< double > bounds_
 
IntervalConstraint intMinMax_
 the interval where the distribution is defined/restricted. More...
 
bool median_
 

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 59 of file AbstractDiscreteDistribution.h.

Constructor & Destructor Documentation

◆ AbstractDiscreteDistribution() [1/3]

AbstractDiscreteDistribution::AbstractDiscreteDistribution ( size_t  nbClasses,
const std::string &  prefix = "" 
)

Definition at line 49 of file AbstractDiscreteDistribution.cpp.

◆ AbstractDiscreteDistribution() [2/3]

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

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

Definition at line 58 of file AbstractDiscreteDistribution.cpp.

◆ AbstractDiscreteDistribution() [3/3]

AbstractDiscreteDistribution::AbstractDiscreteDistribution ( const AbstractDiscreteDistribution &  adde)

Definition at line 67 of file AbstractDiscreteDistribution.cpp.

◆ ~AbstractDiscreteDistribution()

virtual bpp::AbstractDiscreteDistribution::~AbstractDiscreteDistribution ( )
inlinevirtual

Definition at line 146 of file AbstractDiscreteDistribution.h.

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
categoryThe class value.
probabilityThe class probability.

Implements bpp::DiscreteDistribution.

Definition at line 181 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ 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_.

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)
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
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.

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

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
p1Original parameter.
p2Aliased parameter.
Exceptions
ParameterNotFoundExceptionif p1 or p2 do not correspond to existing parameters.
Exceptionwhen 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
unparsedParamsthe map of the links : <A,B> matches for A->B aliasing.
verboseverbosity

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().

◆ clone()

DiscreteDistribution* bpp::DiscreteDistribution::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::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::BetaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::UniformDiscreteDistribution, and bpp::ConstantDistribution.

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

◆ 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 AbstractDiscreteDistribution::discretize ( )
virtual

Discretizes the distribution in equiprobable classes.

Implements bpp::DiscreteDistribution.

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

Definition at line 307 of file AbstractDiscreteDistribution.cpp.

References bounds_, distribution_, bpp::DiscreteDistribution::Expectation(), bpp::IntervalConstraint::getLowerBound(), bpp::IntervalConstraint::getUpperBound(), intMinMax_, median_, numberOfCategories_, bpp::DiscreteDistribution::pProb(), precision(), bpp::DiscreteDistribution::qProb(), bpp::IntervalConstraint::strictLowerBound(), bpp::IntervalConstraint::strictUpperBound(), and bpp::NumConstants::TINY().

Referenced by bpp::BetaDiscreteDistribution::BetaDiscreteDistribution(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution(), restrictToConstraint(), setMedian(), setNumberOfCategories(), bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution(), and bpp::UniformDiscreteDistribution::UniformDiscreteDistribution().

◆ Expectation()

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

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

◆ fireParameterChanged()

void bpp::AbstractParameterAliasable::fireParameterChanged ( const ParameterList &  parameters)
inlinevirtualinherited

Notify the class when one or several parameters have changed.

Parameters
parametersA ParameterList object with parameters that changed.

Implements bpp::AbstractParametrizable.

Reimplemented in bpp::Simplex, bpp::ParametrizableCollection< N >, bpp::MixtureOfDiscreteDistributions, bpp::SimpleDiscreteDistribution, bpp::DirichletDiscreteDistribution, bpp::TruncatedExponentialDiscreteDistribution, bpp::InvariantMixedDiscreteDistribution, bpp::BetaDiscreteDistribution, bpp::ExponentialDiscreteDistribution, bpp::GammaDiscreteDistribution, bpp::GaussianDiscreteDistribution, bpp::ConstantDistribution, and bpp::UniformDiscreteDistribution.

Definition at line 206 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::getParameters(), bpp::AbstractParameterAliasable::independentParameters_, and bpp::ParameterList::matchParametersValues().

Referenced by bpp::ConstantDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::DirichletDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), and bpp::Simplex::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
nameThe 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
nameThe 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().

◆ getBound()

double bpp::AbstractDiscreteDistribution::getBound ( size_t  ) const
throw (IndexOutOfBoundsException
)
inlinevirtual
Returns
the i th internal bound

Implements bpp::DiscreteDistribution.

Definition at line 178 of file AbstractDiscreteDistribution.h.

References bounds_, and numberOfCategories_.

Referenced by getBounds().

◆ getBounds()

Vdouble AbstractDiscreteDistribution::getBounds ( ) const
virtual
Returns
A vector of all the bounds

Implements bpp::DiscreteDistribution.

Definition at line 444 of file AbstractDiscreteDistribution.cpp.

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

◆ getCategories()

Vdouble AbstractDiscreteDistribution::getCategories ( ) const
virtual
Returns
A vector with all classes values.

Implements bpp::DiscreteDistribution.

Definition at line 142 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ getCategory()

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

Implements bpp::DiscreteDistribution.

Definition at line 111 of file AbstractDiscreteDistribution.cpp.

References distribution_.

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

◆ getFrom()

string AbstractParameterAliasable::getFrom ( const std::string &  name) const
inherited
Returns
The name of the parameter from which a given parameter is aliased.
Parameters
nameThe name of the parameter to look for.

Definition at line 306 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_.

◆ getIInfCumulativeProbability()

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

Implements bpp::DiscreteDistribution.

Definition at line 230 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ 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_.

◆ getInfCumulativeProbability()

double AbstractDiscreteDistribution::getInfCumulativeProbability ( double  category) const
virtual
Returns
$Pr(x < \mbox{category})$.
Parameters
categoryThe class value.

Implements bpp::DiscreteDistribution.

Definition at line 215 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ getLowerBound()

double bpp::AbstractDiscreteDistribution::getLowerBound ( ) const
inlinevirtual

methods about the range of the definition

Returns
The lowest value.

Reimplemented from bpp::DiscreteDistribution.

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

Definition at line 192 of file AbstractDiscreteDistribution.h.

References bpp::IntervalConstraint::getLowerBound(), and intMinMax_.

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

◆ getName()

virtual std::string bpp::DiscreteDistribution::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::write().

◆ 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 AbstractDiscreteDistribution::getNumberOfCategories ( ) const
virtual
Returns
The number of categories.

Implements bpp::DiscreteDistribution.

Definition at line 91 of file AbstractDiscreteDistribution.cpp.

References numberOfCategories_.

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

◆ 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
nameThe name of the parameter to look for.
Returns
The parameter with given name.
Exceptions
ParameterNotFoundExceptionif 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
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().

◆ getParameter_() [1/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string &  name)
throw (ParameterNotFoundException
)
inlineprotectedinherited
Parameters
nameThe name of the parameter.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf 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
nameThe 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().

Referenced by bpp::DirichletDiscreteDistribution::applyParameters(), bpp::ConstantDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::AutoCorrelationTransitionMatrix::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::FullHmmTransitionMatrix::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::Simplex::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::BetaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

◆ 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
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(), and bpp::BppODiscreteDistributionFormat::read().

◆ getParameterWithNamespace_() [1/2]

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name)
throw (ParameterNotFoundException
)
inlineprotectedinherited
Parameters
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf 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
nameThe name of the parameter, including its namespace.
Returns
A reference toward the corresponding parameter.
Exceptions
ParameterNotFoundExceptionIf no parameter with that name is found in the list.

Definition at line 194 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

◆ getProbabilities()

Vdouble AbstractDiscreteDistribution::getProbabilities ( ) const
virtual
Returns
A vector with all probabilities.

Implements bpp::DiscreteDistribution.

Definition at line 158 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ getProbability() [1/2]

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

Implements bpp::DiscreteDistribution.

Definition at line 123 of file AbstractDiscreteDistribution.cpp.

References distribution_.

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

◆ getProbability() [2/2]

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

Implements bpp::DiscreteDistribution.

Definition at line 135 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ getSSupCumulativeProbability()

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

Implements bpp::DiscreteDistribution.

Definition at line 264 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ getSupCumulativeProbability()

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

Implements bpp::DiscreteDistribution.

Definition at line 247 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ getUpperBound()

double bpp::AbstractDiscreteDistribution::getUpperBound ( ) const
inlinevirtual
Returns
The highest value.

Reimplemented from bpp::DiscreteDistribution.

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

Definition at line 197 of file AbstractDiscreteDistribution.h.

References bpp::IntervalConstraint::getUpperBound(), and intMinMax_.

Referenced by 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::DiscreteDistribution.

Definition at line 289 of file AbstractDiscreteDistribution.cpp.

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

◆ 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
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().

◆ hasParameter() [2/2]

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

Tell if there is a parameter with specified name.

Parameters
nameThe 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
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.

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

◆ operator=()

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

Definition at line 77 of file AbstractDiscreteDistribution.cpp.

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

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

◆ pProb()

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

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

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

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

◆ precision()

double bpp::AbstractDiscreteDistribution::precision ( ) const
inline

Definition at line 216 of file AbstractDiscreteDistribution.h.

References distribution_.

Referenced by discretize(), 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
outThe outstream where to print the distribution.

Implements bpp::DiscreteDistribution.

Definition at line 279 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ qProb()

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

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

◆ 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::DiscreteDistribution.

Definition at line 197 of file AbstractDiscreteDistribution.cpp.

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

◆ randC()

double bpp::AbstractDiscreteDistribution::randC ( ) const
throw (Exception
)
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
ExceptionIf there is no continuous version of this distribution.

Implements bpp::DiscreteDistribution.

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

Definition at line 171 of file AbstractDiscreteDistribution.h.

◆ 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().

◆ restrictToConstraint()

void AbstractDiscreteDistribution::restrictToConstraint ( const Constraint &  c)
virtual

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

Parameters
cThe Constraint to respect.

Implements bpp::DiscreteDistribution.

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

Definition at line 454 of file AbstractDiscreteDistribution.cpp.

References discretize(), and intMinMax_.

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

◆ 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
categoryThe class value.
probabilityThe class probability.

Implements bpp::DiscreteDistribution.

Definition at line 174 of file AbstractDiscreteDistribution.cpp.

References distribution_.

◆ 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
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.

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
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::InfinityFunctionWrapper::setAllParametersValues().

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

Implements bpp::DiscreteDistribution.

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

Definition at line 218 of file AbstractDiscreteDistribution.h.

References discretize(), and median_.

◆ setNamespace() [1/2]

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

Set the namespace for the parameter names.

Parameters
prefixThe '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
prefixThe '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().

◆ 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::DiscreteDistribution.

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

Definition at line 96 of file AbstractDiscreteDistribution.cpp.

References discretize(), and numberOfCategories_.

◆ 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
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.

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
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::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
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.

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
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::InfinityFunctionWrapper::setParameterValue().

◆ strictLowerBound()

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

Reimplemented from bpp::DiscreteDistribution.

Definition at line 202 of file AbstractDiscreteDistribution.h.

References intMinMax_, and bpp::IntervalConstraint::strictLowerBound().

◆ strictUpperBound()

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

Reimplemented from bpp::DiscreteDistribution.

Definition at line 207 of file AbstractDiscreteDistribution.h.

References intMinMax_, and bpp::IntervalConstraint::strictUpperBound().

◆ 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
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.

◆ 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
p1Original parameter.
p2Aliased parameter.
Exceptions
ParameterNotFoundExceptionif p1 or p2 do not correspond to existing parameters.
Exceptionwhen 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

◆ bounds_

std::vector<double> bpp::AbstractDiscreteDistribution::bounds_
protected

Definition at line 117 of file AbstractDiscreteDistribution.h.

Referenced by bpp::SimpleDiscreteDistribution::discretize(), discretize(), getBound(), getValueCategory(), operator=(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().

◆ distribution_

std::map<double, double, Order> bpp::AbstractDiscreteDistribution::distribution_
protected

These fields must be initialized in the constructor of the derived classes.

Definition at line 115 of file AbstractDiscreteDistribution.h.

Referenced by add(), bpp::ConstantDistribution::ConstantDistribution(), bpp::SimpleDiscreteDistribution::discretize(), discretize(), bpp::SimpleDiscreteDistribution::Expectation(), bpp::ConstantDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), getCategories(), getCategory(), getIInfCumulativeProbability(), getInfCumulativeProbability(), bpp::SimpleDiscreteDistribution::getLowerBound(), getProbabilities(), getProbability(), getSSupCumulativeProbability(), getSupCumulativeProbability(), bpp::SimpleDiscreteDistribution::getUpperBound(), getValueCategory(), operator=(), bpp::SimpleDiscreteDistribution::pProb(), precision(), print(), bpp::SimpleDiscreteDistribution::qProb(), rand(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), set(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().

◆ intMinMax_

IntervalConstraint bpp::AbstractDiscreteDistribution::intMinMax_
protected

the interval where the distribution is defined/restricted.

Definition at line 124 of file AbstractDiscreteDistribution.h.

Referenced by bpp::BetaDiscreteDistribution::BetaDiscreteDistribution(), discretize(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), getLowerBound(), getUpperBound(), getValueCategory(), operator=(), bpp::UniformDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::BetaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), restrictToConstraint(), strictLowerBound(), strictUpperBound(), bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution(), bpp::UniformDiscreteDistribution::UniformDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().

◆ median_

bool bpp::AbstractDiscreteDistribution::median_
protected

Tells if the values in the classes is associated to the median or not (default: false)

Definition at line 131 of file AbstractDiscreteDistribution.h.

Referenced by discretize(), operator=(), bpp::InvariantMixedDiscreteDistribution::setMedian(), bpp::MixtureOfDiscreteDistributions::setMedian(), and setMedian().

◆ numberOfCategories_

size_t bpp::AbstractDiscreteDistribution::numberOfCategories_
protected

Definition at line 111 of file AbstractDiscreteDistribution.h.

Referenced by bpp::SimpleDiscreteDistribution::discretize(), discretize(), getBound(), getBounds(), getNumberOfCategories(), operator=(), setNumberOfCategories(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().

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