bpp-core3  3.0.0
Public Member Functions | Static Public Attributes | Protected Member Functions | Protected Attributes | Private Attributes | List of all members
bpp::InvariantMixedDiscreteDistribution Class Referenceabstract

Discrete mixed distribution, with a one-category fixed value (called "invariant") and a user-specified multi-categories distribution. More...

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

+ Inheritance diagram for bpp::InvariantMixedDiscreteDistribution:
+ Collaboration diagram for bpp::InvariantMixedDiscreteDistribution:

Public Member Functions

 InvariantMixedDiscreteDistribution (std::unique_ptr< DiscreteDistributionInterface > dist, double p, double invariant=0.)
 Build a new InvariantMixedDiscreteDistribution object. More...
 
virtual ~InvariantMixedDiscreteDistribution ()
 
 InvariantMixedDiscreteDistribution (const InvariantMixedDiscreteDistribution &imdd)
 
InvariantMixedDiscreteDistribution & operator= (const InvariantMixedDiscreteDistribution &imdd)
 
InvariantMixedDiscreteDistribution * clone () const
 Create a copy of this object and send a pointer to it. More...
 
std::string getName () const
 Get the name of the distribution. More...
 
void fireParameterChanged (const ParameterList &parameters)
 Notify the class when one or several parameters have changed. More...
 
void setNamespace (const std::string &prefix)
 Set the namespace for the parameter names. More...
 
void setNumberOfCategories (size_t nbClasses)
 
const DiscreteDistributionInterface & variableSubDistribution () const
 
double qProb (double x) const
 Return the quantile of the continuous version of the distribution, ie y such that $ Prob(X<y)=x $. More...
 
double pProb (double x) const
 Return the cumulative quantile of the continuous version of the distribution, ie $ Prob(X<x) $. More...
 
double Expectation (double a) const
 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...
 
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...
 
void discretize ()
 Discretizes the distribution in equiprobable classes. More...
 
void restrictToConstraint (const ConstraintInterface &c)
 Restricts the distribution to the domain where the constraint is respected, in addition of other predefined constraints. More...
 
virtual size_t getNumberOfIndependentParameters () const =0
 Get the number of independent parameters. More...
 
size_t getNumberOfIndependentParameters () const
 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...
 
void aliasParameters (const std::string &p1, const std::string &p2)
 alias the parameters. More...
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. More...
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 Detach two parameters previously set as 'aliased'. More...
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 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...
 
const ParameterList & getIndependentParameters () const
 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::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const =0
 
virtual std::map< std::string, std::string > getAliases () const
 
virtual bool hasParameter (const std::string &name) const =0
 Tell if there is a parameter with specified name. More...
 
bool hasParameter (const std::string &name) const override
 Tell if there is a parameter with specified name. More...
 
virtual const ParameterList & getParameters () const =0
 Get all parameters available. More...
 
const ParameterList & getParameters () const override
 Get all parameters available. More...
 
virtual const Parameter & parameter (const std::string &name) const =0
 Get the parameter with specified name. More...
 
const Parameter & parameter (const std::string &name) const override
 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...
 
double getParameterValue (const std::string &name) const override
 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...
 
void setAllParametersValues (const ParameterList &parameters) override
 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...
 
void setParameterValue (const std::string &name, double value) override
 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...
 
void setParametersValues (const ParameterList &parameters) override
 Update the parameters from parameters. More...
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 Update the parameters from parameters. More...
 
bool matchParametersValues (const ParameterList &parameters) override
 Update the parameters from parameters. More...
 
virtual void removeConstraint (const std::string &name)=0
 Remove the constraint associated with one parameter, if any. More...
 
void removeConstraint (const std::string &name) override
 Remove the constraint associated with one parameter, if any. More...
 
virtual void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
 Set/Change the constraint associated with one parameter. More...
 
void setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
 Set/Change the constraint associated with one parameter. More...
 
virtual size_t getNumberOfParameters () const =0
 Get the number of parameters. More...
 
size_t getNumberOfParameters () const override
 Get the number of parameters. More...
 
virtual std::string getNamespace () const =0
 
std::string getNamespace () const override
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
 Resolves a parameter name according to the current namespace. More...
 
std::string getParameterNameWithoutNamespace (const std::string &name) const override
 Resolves a parameter name according to the current namespace. More...
 
bool hasIndependentParameter (const std::string &name) const
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list. More...
 
ParameterList getFromParameters (const ParameterList &pl) const
 Return the list of the names of the parameters from which the parameters of the list are aliased (directly or not). More...
 
std::string getFrom (const std::string &name) const
 
const std::shared_ptr< Parameter > & getParameter (const std::string &name) const
 
The DiscreteDistribution interface.
size_t getNumberOfCategories () const
 
double getCategory (size_t categoryIndex) const
 
double getProbability (size_t categoryIndex) const
 
double getProbability (double category) const
 
Vdouble getCategories () const
 
Vdouble getProbabilities () const
 
double getValueCategory (double value) const
 
size_t getCategoryIndex (double value) const
 
void set (double category, double probability)
 Set the probability associated to a class. More...
 
void add (double category, double probability)
 Modify the probability associated to a class. More...
 
double getInfCumulativeProbability (double category) const
 
double getIInfCumulativeProbability (double category) const
 
double getSupCumulativeProbability (double category) const
 
double getSSupCumulativeProbability (double category) const
 
double rand () const
 Draw a random number from this distribution. More...
 
double randC () const
 Draw a random number from the continuous version of this distribution, if it exists. More...
 
double getBound (size_t i) const
 
double getLowerBound () const
 methods about the range of the definition More...
 
double getUpperBound () const
 
bool strictLowerBound () const
 
bool strictUpperBound () const
 
Vdouble getBounds () const
 
void print (OutputStream &out) const
 Print the distribution (categories and corresponding probabilities) to a stream. More...
 
double precision () const
 

Static Public Attributes

static short DISCRETIZATION_EQUAL_PROB = 1
 
static short DISCRETIZATION_EQUAL_INTERVAL = 2
 
static short DISCRETIZATION_EQUAL_PROB_WHEN_POSSIBLE = 3
 

Protected Member Functions

void updateDistribution ()
 
void discretizeEqualProportions ()
 
void discretizeEqualIntervals ()
 
virtual ParameterList & getParameters_ ()=0
 Get all parameters available. More...
 
ParameterList & getParameters_ () override
 Get all parameters available. More...
 
void addParameter_ (Parameter *parameter)
 
void addParameters_ (const ParameterList &parameters)
 
void shareParameter_ (const std::shared_ptr< Parameter > &parameter)
 
void shareParameters_ (const ParameterList &parameters)
 
void includeParameters_ (const ParameterList &parameters)
 
void deleteParameter_ (size_t index)
 
void deleteParameter_ (std::string &name)
 
void deleteParameters_ (const std::vector< std::string > &names)
 
void resetParameters_ ()
 
const std::shared_ptr< Parameter > & getParameter (size_t i) const
 
std::shared_ptr< Parameter > & getParameter (size_t i)
 
Parameter & getParameter_ (const std::string &name)
 
Parameter & getParameter_ (size_t index)
 
const Parameter & getParameter_ (size_t index) const
 
Parameter & getParameterWithNamespace_ (const std::string &name)
 
const Parameter & getParameterWithNamespace_ (const std::string &name) const
 

Protected Attributes

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

Private Attributes

std::unique_ptr< DiscreteDistributionInterface > dist_
 
double invariant_
 
double p_
 
std::string nestedPrefix_
 

Detailed Description

Discrete mixed distribution, with a one-category fixed value (called "invariant") and a user-specified multi-categories distribution.

The term "invariant" comes from the use of such distributions in phylogenetics: the fixed category corresponds to a value of 0 and describes invariant positions in an alignment.

Definition at line 19 of file InvariantMixedDiscreteDistribution.h.

Constructor & Destructor Documentation

◆ InvariantMixedDiscreteDistribution() [1/2]

InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution ( std::unique_ptr< DiscreteDistributionInterface >  dist,
double  p,
double  invariant = 0. 
)

Build a new InvariantMixedDiscreteDistribution object.

Parameters
distThe distribution to use. The mixed distribution will "own" this distribution object. This means that the distribution will be cloned in case of copy of this instance, and will be deleted with this instance.
pThe probability of being in the invariant category.
invariantThe value of the invariant category (typically 0, but other values may be specified).

Definition at line 13 of file InvariantMixedDiscreteDistribution.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), dist_, nestedPrefix_, bpp::Parameter::PROP_CONSTRAINT_IN, and updateDistribution().

Referenced by clone().

◆ ~InvariantMixedDiscreteDistribution()

virtual bpp::InvariantMixedDiscreteDistribution::~InvariantMixedDiscreteDistribution ( )
inlinevirtual

Definition at line 39 of file InvariantMixedDiscreteDistribution.h.

◆ InvariantMixedDiscreteDistribution() [2/2]

bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution ( const InvariantMixedDiscreteDistribution &  imdd)
inline

Definition at line 41 of file InvariantMixedDiscreteDistribution.h.

Member Function Documentation

◆ add()

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

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::DiscreteDistributionInterface.

Definition at line 151 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

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

◆ addParameter_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 196 of file AbstractParameterAliasable.h.

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

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

◆ addParameters_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 202 of file AbstractParameterAliasable.h.

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

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

◆ aliasParameters() [1/4]

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

Set two parameters as 'aliased'.

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

Parameters
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().

◆ 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 
)
virtualinherited

alias the parameters.

Parameters
p1name of the parameter to which the other parameter is aliased
p2name of the aliased parameter, which will be deleted from independent parameters list

Implements bpp::ParameterAliasable.

Definition at line 67 of file AbstractParameterAliasable.cpp.

References bpp::Parameter::addParameterListener(), bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::ParameterList::deleteParameter(), bpp::ApplicationTools::displayWarning(), bpp::Parameter::getConstraint(), bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractParametrizable::getParameters_(), bpp::Parameter::hasConstraint(), bpp::AbstractParametrizable::hasParameter(), bpp::ParameterList::hasParameter(), bpp::AbstractParameterAliasable::independentParameters_, bpp::Parameter::setConstraint(), bpp::ParameterList::shareParameters(), bpp::ParameterList::size(), and bpp::ParameterList::whichParameterHasName().

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

◆ aliasParameters() [4/4]

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

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

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

Implements bpp::ParameterAliasable.

Definition at line 120 of file AbstractParameterAliasable.cpp.

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

◆ clone()

InvariantMixedDiscreteDistribution* bpp::InvariantMixedDiscreteDistribution::clone ( ) const
inlinevirtual

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

Returns
A pointer toward the copy object.

Implements bpp::DiscreteDistributionInterface.

Definition at line 59 of file InvariantMixedDiscreteDistribution.h.

References InvariantMixedDiscreteDistribution().

◆ deleteParameter_() [1/2]

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 237 of file AbstractParameterAliasable.h.

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

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

◆ deleteParameter_() [2/2]

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 245 of file AbstractParameterAliasable.h.

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

◆ deleteParameters_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 252 of file AbstractParameterAliasable.h.

◆ discretize()

void bpp::InvariantMixedDiscreteDistribution::discretize ( )
inlinevirtual

Discretizes the distribution in equiprobable classes.

Reimplemented from bpp::AbstractDiscreteDistribution.

Definition at line 110 of file InvariantMixedDiscreteDistribution.h.

References restrictToConstraint(), and updateDistribution().

◆ discretizeEqualIntervals()

void AbstractDiscreteDistribution::discretizeEqualIntervals ( )
protectedinherited

Definition at line 454 of file AbstractDiscreteDistribution.cpp.

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

Referenced by bpp::AbstractDiscreteDistribution::discretize(), and bpp::AbstractDiscreteDistribution::setMedian().

◆ discretizeEqualProportions()

void AbstractDiscreteDistribution::discretizeEqualProportions ( )
protectedinherited

Definition at line 294 of file AbstractDiscreteDistribution.cpp.

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

Referenced by bpp::AbstractDiscreteDistribution::discretize(), and bpp::AbstractDiscreteDistribution::setMedian().

◆ Expectation()

double bpp::InvariantMixedDiscreteDistribution::Expectation ( double  a) const
inlinevirtual

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 $.

Implements bpp::DiscreteDistributionInterface.

Definition at line 95 of file InvariantMixedDiscreteDistribution.h.

References p_.

◆ fireParameterChanged()

void InvariantMixedDiscreteDistribution::fireParameterChanged ( const ParameterList &  parameters)
virtual

Notify the class when one or several parameters have changed.

Parameters
parametersA ParameterList object with parameters that changed.

Reimplemented from bpp::AbstractParametrizable.

Definition at line 31 of file InvariantMixedDiscreteDistribution.cpp.

References dist_, bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::getParameterValue(), p_, and updateDistribution().

Referenced by getName().

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

◆ getAlias() [2/2]

vector< string > AbstractParameterAliasable::getAlias ( const std::string &  name) const
virtualinherited
Returns
The list of names of the parameters that are aliased with a given parameter. The implementation is recursive, which means that in the case of A->B->C, getalias(C) will return both A and B.
Parameters
nameThe name of the parameter to look for.

Implements bpp::ParameterAliasable.

Definition at line 204 of file AbstractParameterAliasable.cpp.

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

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

◆ getAliasedParameters()

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

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

Definition at line 244 of file AbstractParameterAliasable.cpp.

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

◆ getAliases() [1/2]

virtual std::map<std::string, std::string> bpp::ParameterAliasable::getAliases ( ) const
pure virtualinherited
Returns
the map of the aliases.

Implemented in bpp::AbstractParameterAliasable.

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

◆ getAliases() [2/2]

std::map< std::string, std::string > AbstractParameterAliasable::getAliases ( ) const
virtualinherited
Returns
the map of the aliases.

Implements bpp::ParameterAliasable.

Definition at line 225 of file AbstractParameterAliasable.cpp.

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

◆ getBound()

double bpp::AbstractDiscreteDistribution::getBound ( size_t  ) const
inlinevirtualinherited
Returns
the i th internal bound

Implements bpp::DiscreteDistributionInterface.

Definition at line 141 of file AbstractDiscreteDistribution.h.

Referenced by bpp::AbstractDiscreteDistribution::getBounds().

◆ getBounds()

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 527 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::getBound(), bpp::AbstractDiscreteDistribution::getLowerBound(), bpp::AbstractDiscreteDistribution::getUpperBound(), and bpp::AbstractDiscreteDistribution::numberOfCategories_.

Referenced by bpp::AbstractDiscreteDistribution::strictUpperBound().

◆ getCategories()

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 112 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

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

◆ getCategory()

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 81 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

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

◆ getCategoryIndex()

size_t AbstractDiscreteDistribution::getCategoryIndex ( double  value) const
virtualinherited
Parameters
value
Returns
The index of the category the value is in. Throws a OutOfRangeException if the value is off the domain of the DiscreteDistribution.

Implements bpp::DiscreteDistributionInterface.

Definition at line 278 of file AbstractDiscreteDistribution.cpp.

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

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

◆ getFrom()

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

Definition at line 280 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_.

◆ getFromParameters()

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

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

Definition at line 297 of file AbstractParameterAliasable.cpp.

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

◆ getIInfCumulativeProbability()

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 200 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

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

◆ getIndependentParameters() [1/2]

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

Get the minimal list of parameters to set the model.

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

Returns
A minimal set of parameters.

Implemented in bpp::AbstractParameterAliasable.

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

◆ getIndependentParameters() [2/2]

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

Get the minimal list of parameters to set the model.

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

Returns
A minimal set of parameters.

Implements bpp::ParameterAliasable.

Definition at line 135 of file AbstractParameterAliasable.h.

◆ getInfCumulativeProbability()

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 185 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

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

◆ getLowerBound()

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

methods about the range of the definition

Returns
The lowest value.

Reimplemented from bpp::DiscreteDistributionInterface.

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

Definition at line 153 of file AbstractDiscreteDistribution.h.

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

◆ getName()

std::string bpp::InvariantMixedDiscreteDistribution::getName ( ) const
inlinevirtual

Get the name of the distribution.

Returns
The name of this distribution.

Implements bpp::DiscreteDistributionInterface.

Definition at line 62 of file InvariantMixedDiscreteDistribution.h.

References fireParameterChanged(), and setNamespace().

◆ getNamespace() [1/2]

std::string bpp::AbstractParametrizable::getNamespace ( ) const
inlineoverridevirtualinherited
Returns
The current namespace used. This is an empty string if no namespace is currently defined.

Implements bpp::Parametrizable.

Definition at line 99 of file AbstractParametrizable.h.

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

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

◆ getNamespace() [2/2]

virtual std::string bpp::Parametrizable::getNamespace ( ) const
pure virtualinherited
Returns
The current namespace used. This is an empty string if no namespace is currently defined.

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

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

◆ getNumberOfCategories()

size_t AbstractDiscreteDistribution::getNumberOfCategories ( ) const
virtualinherited
Returns
The number of categories.

Implements bpp::DiscreteDistributionInterface.

Definition at line 61 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::numberOfCategories_.

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

◆ getNumberOfIndependentParameters() [1/2]

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

Get the number of independent parameters.

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

Implemented in bpp::AbstractParameterAliasable.

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

◆ getNumberOfIndependentParameters() [2/2]

size_t bpp::AbstractParameterAliasable::getNumberOfIndependentParameters ( ) const
inlinevirtualinherited

Get the number of independent parameters.

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

Implements bpp::ParameterAliasable.

Definition at line 137 of file AbstractParameterAliasable.h.

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

◆ getNumberOfParameters() [1/2]

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const
inlineoverridevirtualinherited

Get the number of parameters.

See also
getNumberOfIndependentParameters If some parameters are aliased.
Returns
The number of parameters.

Implements bpp::Parametrizable.

Definition at line 95 of file AbstractParametrizable.h.

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

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

◆ getNumberOfParameters() [2/2]

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

Get the number of parameters.

See also
getNumberOfIndependentParameters If some parameters are aliased.
Returns
The number of parameters.

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

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

◆ getParameter() [1/3]

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

Definition at line 48 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

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

◆ getParameter() [2/3]

const std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getParameter ( size_t  i) const
inlineprotectedinherited
Returns
The shared_ptr parameter at a given position.
Warning
No check is performed on the validity of the index given as input!

Definition at line 211 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter() [3/3]

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

Definition at line 216 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter_() [1/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string &  name)
inlineprotectedinherited
Parameters
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 164 of file AbstractParametrizable.h.

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

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

◆ getParameter_() [2/3]

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

Definition at line 190 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameter_() [3/3]

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

Definition at line 197 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameterNameWithoutNamespace() [1/2]

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

Resolves a parameter name according to the current namespace.

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

Implements bpp::Parametrizable.

Definition at line 28 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

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

◆ getParameterNameWithoutNamespace() [2/2]

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

Resolves a parameter name according to the current namespace.

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

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

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

◆ getParameters() [1/2]

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

Get all parameters available.

See also
getIndependentParameters if some parameters are aliased.
Returns
A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 41 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameters() [2/2]

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

Get all parameters available.

See also
getIndependentParameters if some parameters are aliased.
Returns
A list with all parameters available.

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

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

◆ getParameters_() [1/2]

virtual ParameterList& bpp::Parametrizable::getParameters_ ( )
protectedpure virtualinherited

Get all parameters available.

See also
getIndependentParameters if some parameters are aliased.
Returns
A list with all parameters available.

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

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

◆ getParameters_() [2/2]

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )
inlineoverrideprotectedvirtualinherited

Get all parameters available.

See also
getIndependentParameters if some parameters are aliased.
Returns
A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 205 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameterValue() [1/2]

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

Get the value for parameter of name 'name'.

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

Implements bpp::Parametrizable.

Definition at line 53 of file AbstractParametrizable.h.

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

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

◆ getParameterValue() [2/2]

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

◆ getParameterWithNamespace_() [1/2]

Parameter& bpp::AbstractParametrizable::getParameterWithNamespace_ ( const std::string &  name)
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 176 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

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

◆ getProbabilities()

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 128 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

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

◆ getProbability() [1/2]

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 93 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

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

◆ getProbability() [2/2]

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 105 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

◆ getSSupCumulativeProbability()

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 234 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

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

◆ getSupCumulativeProbability()

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 217 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

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

◆ getUpperBound()

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

Reimplemented from bpp::DiscreteDistributionInterface.

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

Definition at line 158 of file AbstractDiscreteDistribution.h.

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

◆ getValueCategory()

double AbstractDiscreteDistribution::getValueCategory ( double  value) const
virtualinherited
Parameters
value
Returns
The value of the category the value is in. Throws a OutOfRangeException if the value is off the domain of the DiscreteDistribution.

Implements bpp::DiscreteDistributionInterface.

Definition at line 259 of file AbstractDiscreteDistribution.cpp.

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

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

◆ hasIndependentParameter()

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

Definition at line 133 of file AbstractParameterAliasable.h.

References bpp::ParameterList::hasParameter().

◆ hasParameter() [1/2]

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

Tell if there is a parameter with specified name.

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

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

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

◆ hasParameter() [2/2]

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

Tell if there is a parameter with specified name.

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

Implements bpp::Parametrizable.

Definition at line 39 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter().

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

◆ includeParameters_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 227 of file AbstractParameterAliasable.h.

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

◆ matchParametersValues() [1/2]

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

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters
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 76 of file AbstractParametrizable.h.

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

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

◆ matchParametersValues() [2/2]

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

Update the parameters from parameters.

Only common parameters with parameters will be updated.

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

◆ operator=()

InvariantMixedDiscreteDistribution& bpp::InvariantMixedDiscreteDistribution::operator= ( const InvariantMixedDiscreteDistribution &  imdd)
inline

Definition at line 49 of file InvariantMixedDiscreteDistribution.h.

References dist_, invariant_, nestedPrefix_, bpp::AbstractDiscreteDistribution::operator=(), and p_.

◆ parameter() [1/2]

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

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 43 of file AbstractParametrizable.h.

References bpp::ParameterList::parameter().

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

◆ parameter() [2/2]

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

Get the parameter with specified name.

Parameters
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::TestFunction::getValue(), and bpp::Parametrizable::~Parametrizable().

◆ pProb()

double bpp::InvariantMixedDiscreteDistribution::pProb ( double  x) const
inlinevirtual

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 90 of file InvariantMixedDiscreteDistribution.h.

References p_.

◆ precision()

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

Definition at line 177 of file AbstractDiscreteDistribution.h.

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

◆ print()

void AbstractDiscreteDistribution::print ( OutputStream &  out) const
virtualinherited

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

Parameters
outThe outstream where to print the distribution.

Implements bpp::DiscreteDistributionInterface.

Definition at line 249 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

Referenced by bpp::AbstractDiscreteDistribution::strictUpperBound().

◆ qProb()

double bpp::InvariantMixedDiscreteDistribution::qProb ( double  x) const
inlinevirtual

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

Implements bpp::DiscreteDistributionInterface.

Definition at line 85 of file InvariantMixedDiscreteDistribution.h.

◆ rand()

double AbstractDiscreteDistribution::rand ( ) const
virtualinherited

Draw a random number from this distribution.

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

Returns
A random number according to this distribution.

Implements bpp::DiscreteDistributionInterface.

Definition at line 167 of file AbstractDiscreteDistribution.cpp.

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

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

◆ randC()

double bpp::AbstractDiscreteDistribution::randC ( ) const
inlinevirtualinherited

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::DiscreteDistributionInterface.

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

Definition at line 135 of file AbstractDiscreteDistribution.h.

◆ removeConstraint() [1/2]

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

Remove the constraint associated with one parameter, if any.

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

Implements bpp::Parametrizable.

Definition at line 85 of file AbstractParametrizable.h.

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

◆ removeConstraint() [2/2]

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

Remove the constraint associated with one parameter, if any.

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

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

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

◆ resetParameters_()

void bpp::AbstractParameterAliasable::resetParameters_ ( )
inlineprotectedinherited

Definition at line 262 of file AbstractParameterAliasable.h.

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

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

◆ restrictToConstraint()

void InvariantMixedDiscreteDistribution::restrictToConstraint ( const ConstraintInterface &  c)
virtual

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

Parameters
cThe Constraint to respect.

Reimplemented from bpp::AbstractDiscreteDistribution.

Definition at line 113 of file InvariantMixedDiscreteDistribution.cpp.

References dist_, bpp::AbstractParametrizable::getParameter_(), invariant_, bpp::ConstraintInterface::isCorrect(), and updateDistribution().

Referenced by discretize().

◆ set()

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

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::DiscreteDistributionInterface.

Definition at line 144 of file AbstractDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::distribution_.

◆ setAllParametersValues() [1/2]

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

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

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

Parameters
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 58 of file AbstractParametrizable.h.

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

◆ setAllParametersValues() [2/2]

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

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

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

Parameters
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::Parametrizable::~Parametrizable().

◆ setConstraint() [1/2]

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

Set/Change the constraint associated with one parameter.

Parameters
nameThe name of the parameter to look for.
constraintA pointer to the constraint (may be null)
Exceptions
ParameterNotFoundExceptionif no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 90 of file AbstractParametrizable.h.

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

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

◆ setConstraint() [2/2]

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

Set/Change the constraint associated with one parameter.

Parameters
nameThe name of the parameter to look for.
constraintA pointer to the constraint (may be null)
Exceptions
ParameterNotFoundExceptionif no parameter with this name is found.

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

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

◆ setMedian()

void bpp::InvariantMixedDiscreteDistribution::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.

Reimplemented from bpp::AbstractDiscreteDistribution.

Definition at line 100 of file InvariantMixedDiscreteDistribution.h.

References bpp::AbstractDiscreteDistribution::median_, and updateDistribution().

◆ setNamespace()

void InvariantMixedDiscreteDistribution::setNamespace ( const std::string &  prefix)
virtual

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.

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 104 of file InvariantMixedDiscreteDistribution.cpp.

References dist_, nestedPrefix_, and bpp::AbstractParameterAliasable::setNamespace().

Referenced by getName().

◆ setNumberOfCategories()

void bpp::InvariantMixedDiscreteDistribution::setNumberOfCategories ( size_t  nbClasses)
inlinevirtual

@ brief Sets the number of categories of the embedded distribution. The number of categories of this class equals this plus one if the invariant_ is not in the embedded distribution values.

Reimplemented from bpp::AbstractDiscreteDistribution.

Definition at line 74 of file InvariantMixedDiscreteDistribution.h.

References updateDistribution().

◆ setParametersValues() [1/2]

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

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters
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 70 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::fireParameterChanged(), 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)
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::Parametrizable::~Parametrizable().

◆ setParameterValue() [1/2]

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

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

Parameters
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 64 of file AbstractParametrizable.h.

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

◆ setParameterValue() [2/2]

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

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

Parameters
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::Parametrizable::~Parametrizable().

◆ shareParameter_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 212 of file AbstractParameterAliasable.h.

References bpp::ParameterList::shareParameter(), and bpp::AbstractParametrizable::shareParameter_().

◆ shareParameters_()

void bpp::AbstractParameterAliasable::shareParameters_ ( const ParameterList &  parameters)
inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 218 of file AbstractParameterAliasable.h.

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

◆ strictLowerBound()

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

Reimplemented from bpp::DiscreteDistributionInterface.

Definition at line 163 of file AbstractDiscreteDistribution.h.

◆ strictUpperBound()

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

Reimplemented from bpp::DiscreteDistributionInterface.

Definition at line 168 of file AbstractDiscreteDistribution.h.

References bpp::AbstractDiscreteDistribution::getBounds(), and bpp::AbstractDiscreteDistribution::print().

◆ unaliasParameters() [1/2]

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().

◆ unaliasParameters() [2/2]

void AbstractParameterAliasable::unaliasParameters ( const std::string &  p1,
const std::string &  p2 
)
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 168 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_, bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractParameterAliasable::independentParameters_, bpp::Parameter::removeParameterListener(), and bpp::ParameterList::shareParameter().

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

◆ updateDistribution()

void InvariantMixedDiscreteDistribution::updateDistribution ( )
protected

Definition at line 42 of file InvariantMixedDiscreteDistribution.cpp.

References bpp::AbstractDiscreteDistribution::bounds_, dist_, bpp::AbstractDiscreteDistribution::distribution_, bpp::AbstractDiscreteDistribution::getLowerBound(), bpp::AbstractDiscreteDistribution::intMinMax_, invariant_, bpp::AbstractDiscreteDistribution::numberOfCategories_, and p_.

Referenced by discretize(), fireParameterChanged(), InvariantMixedDiscreteDistribution(), restrictToConstraint(), setMedian(), and setNumberOfCategories().

◆ variableSubDistribution()

const DiscreteDistributionInterface& bpp::InvariantMixedDiscreteDistribution::variableSubDistribution ( ) const
inline
Returns
The nested, conditional, sub-distribution.

Definition at line 83 of file InvariantMixedDiscreteDistribution.h.

References dist_.

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

Member Data Documentation

◆ bounds_

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

Definition at line 82 of file AbstractDiscreteDistribution.h.

Referenced by bpp::SimpleDiscreteDistribution::discretize(), bpp::AbstractDiscreteDistribution::discretize(), bpp::AbstractDiscreteDistribution::discretizeEqualIntervals(), bpp::AbstractDiscreteDistribution::discretizeEqualProportions(), bpp::AbstractDiscreteDistribution::getCategoryIndex(), bpp::AbstractDiscreteDistribution::getValueCategory(), bpp::AbstractDiscreteDistribution::operator=(), updateDistribution(), and bpp::MixtureOfDiscreteDistributions::updateDistribution().

◆ DISCRETIZATION_EQUAL_INTERVAL

short AbstractDiscreteDistribution::DISCRETIZATION_EQUAL_INTERVAL = 2
staticinherited

Definition at line 29 of file AbstractDiscreteDistribution.h.

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

◆ DISCRETIZATION_EQUAL_PROB

short AbstractDiscreteDistribution::DISCRETIZATION_EQUAL_PROB = 1
staticinherited

Definition at line 28 of file AbstractDiscreteDistribution.h.

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

◆ DISCRETIZATION_EQUAL_PROB_WHEN_POSSIBLE

short AbstractDiscreteDistribution::DISCRETIZATION_EQUAL_PROB_WHEN_POSSIBLE = 3
staticinherited

Definition at line 30 of file AbstractDiscreteDistribution.h.

◆ discretizationScheme_

short bpp::AbstractDiscreteDistribution::discretizationScheme_
protectedinherited

Discretization policy.

Definition at line 97 of file AbstractDiscreteDistribution.h.

Referenced by bpp::AbstractDiscreteDistribution::discretize(), and bpp::AbstractDiscreteDistribution::operator=().

◆ dist_

std::unique_ptr<DiscreteDistributionInterface> bpp::InvariantMixedDiscreteDistribution::dist_
private

Definition at line 23 of file InvariantMixedDiscreteDistribution.h.

Referenced by fireParameterChanged(), InvariantMixedDiscreteDistribution(), operator=(), restrictToConstraint(), setNamespace(), updateDistribution(), and variableSubDistribution().

◆ distribution_

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

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

Definition at line 80 of file AbstractDiscreteDistribution.h.

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

◆ intMinMax_

std::shared_ptr<IntervalConstraint> bpp::AbstractDiscreteDistribution::intMinMax_
protectedinherited

the interval where the distribution is defined/restricted.

Definition at line 87 of file AbstractDiscreteDistribution.h.

Referenced by bpp::BetaDiscreteDistribution::BetaDiscreteDistribution(), bpp::AbstractDiscreteDistribution::discretize(), bpp::AbstractDiscreteDistribution::discretizeEqualIntervals(), bpp::AbstractDiscreteDistribution::discretizeEqualProportions(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), bpp::AbstractDiscreteDistribution::getCategoryIndex(), bpp::AbstractDiscreteDistribution::getValueCategory(), bpp::AbstractDiscreteDistribution::operator=(), bpp::UniformDiscreteDistribution::randC(), bpp::BetaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), bpp::ConstantDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::restrictToConstraint(), bpp::SimpleDiscreteDistribution::restrictToConstraint(), bpp::AbstractDiscreteDistribution::restrictToConstraint(), bpp::TruncatedExponentialDiscreteDistribution::TruncatedExponentialDiscreteDistribution(), bpp::UniformDiscreteDistribution::UniformDiscreteDistribution(), bpp::MixtureOfDiscreteDistributions::updateDistribution(), and updateDistribution().

◆ invariant_

double bpp::InvariantMixedDiscreteDistribution::invariant_
private

Definition at line 24 of file InvariantMixedDiscreteDistribution.h.

Referenced by operator=(), restrictToConstraint(), and updateDistribution().

◆ median_

bool bpp::AbstractDiscreteDistribution::median_
protectedinherited

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

Definition at line 92 of file AbstractDiscreteDistribution.h.

Referenced by bpp::AbstractDiscreteDistribution::discretizeEqualProportions(), bpp::AbstractDiscreteDistribution::operator=(), setMedian(), and bpp::MixtureOfDiscreteDistributions::setMedian().

◆ nestedPrefix_

std::string bpp::InvariantMixedDiscreteDistribution::nestedPrefix_
private

Definition at line 25 of file InvariantMixedDiscreteDistribution.h.

Referenced by InvariantMixedDiscreteDistribution(), operator=(), and setNamespace().

◆ numberOfCategories_

size_t bpp::AbstractDiscreteDistribution::numberOfCategories_
protectedinherited

Definition at line 76 of file AbstractDiscreteDistribution.h.

Referenced by bpp::SimpleDiscreteDistribution::discretize(), bpp::AbstractDiscreteDistribution::discretize(), bpp::AbstractDiscreteDistribution::discretizeEqualIntervals(), bpp::AbstractDiscreteDistribution::discretizeEqualProportions(), bpp::AbstractDiscreteDistribution::getBounds(), bpp::AbstractDiscreteDistribution::getNumberOfCategories(), bpp::AbstractDiscreteDistribution::operator=(), bpp::AbstractDiscreteDistribution::setNumberOfCategories(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), bpp::MixtureOfDiscreteDistributions::updateDistribution(), and updateDistribution().

◆ p_

double bpp::InvariantMixedDiscreteDistribution::p_
private

Definition at line 24 of file InvariantMixedDiscreteDistribution.h.

Referenced by Expectation(), fireParameterChanged(), operator=(), pProb(), and updateDistribution().

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