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

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

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

+ Inheritance diagram for bpp::DirichletDiscreteDistribution:
+ Collaboration diagram for bpp::DirichletDiscreteDistribution:

Public Member Functions

 DirichletDiscreteDistribution (std::vector< size_t > vn, Vdouble valpha)
 Build a new discretized Dirichlet distribution. More...
 
 ~DirichletDiscreteDistribution ()
 
DirichletDiscreteDistribution * clone () const
 Create a copy of this object and send a pointer to it. More...
 
std::string getName () const
 
void fireParameterChanged (const ParameterList &parameters)
 Notify the class when one or several parameters have changed. More...
 
size_t getNumberOfCategories () const
 
Vdouble getValueCategory (Vdouble &Vvalue) const
 
VVdouble getCategories () const
 
virtual double getProbability (Vdouble &category) const
 
Vdouble rand () const
 Draw a random vector from this distribution. More...
 
Vdouble randC () const
 Draw a random vector from the continuous version of this distribution. More...
 
virtual size_t getNumberOfIndependentParameters () const =0
 Get the number of independent parameters. More...
 
virtual void aliasParameters (const std::string &p1, const std::string &p2)=0
 Set two parameters as 'aliased'. More...
 
virtual void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)=0
 alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. More...
 
virtual void unaliasParameters (const std::string &p1, const std::string &p2)=0
 Detach two parameters previously set as 'aliased'. More...
 
virtual const ParameterList & getIndependentParameters () const =0
 Get the minimal list of parameters to set the model. More...
 
virtual std::vector< std::string > getAlias (const std::string &name) const =0
 
virtual std::map< std::string, std::string > getAliases () const =0
 
virtual bool hasParameter (const std::string &name) const =0
 Tell if there is a parameter with specified name. More...
 
virtual const ParameterList & getParameters () const =0
 Get all parameters available. More...
 
virtual const Parameter & getParameter (const std::string &name) const =0
 Get the parameter with specified name. More...
 
virtual double getParameterValue (const std::string &name) const =0
 Get the value for parameter of name 'name'. More...
 
virtual void setAllParametersValues (const ParameterList &parameters)=0
 Set the parameters values to be equals to those of parameters. More...
 
virtual void setParameterValue (const std::string &name, double value)=0
 Set the value of parameter with name name to be equal to value. More...
 
virtual void setParametersValues (const ParameterList &parameters)=0
 Update the parameters from parameters. More...
 
virtual bool matchParametersValues (const ParameterList &parameters)=0
 Update the parameters from parameters. More...
 
virtual size_t getNumberOfParameters () const =0
 Get the number of parameters. More...
 
virtual void setNamespace (const std::string &prefix)=0
 Set the namespace for the parameter names. More...
 
virtual std::string getNamespace () const =0
 
virtual std::string getParameterNameWithoutNamespace (const std::string &name) const =0
 Resolves a parameter name according to the current namespace. More...
 
void setNamespace (const std::string &prefix)
 Set the namespace for the parameter names. More...
 
bool hasIndependentParameter (const std::string &name) const
 
const ParameterList & getIndependentParameters () const
 Get the minimal list of parameters to set the model. More...
 
size_t getNumberOfIndependentParameters () const
 Get the number of independent parameters. More...
 
void aliasParameters (const std::string &p1, const std::string &p2)
 alias the parameters. More...
 
void aliasParameters (std::map< std::string, std::string > &unparsedParams, bool verbose)
 alias the parameters following the links described in a map, and update the object accordingly. Cycles in aliasing are detected and forbidden. More...
 
void unaliasParameters (const std::string &p1, const std::string &p2)
 Detach two parameters previously set as 'aliased'. More...
 
ParameterList getAliasedParameters (const ParameterList &pl) const
 Return the list of the names of the parameters that are aliased (directly or not) to one of the parameters of the list. More...
 
ParameterList getFromParameters (const ParameterList &pl) const
 Return the list of the names of the parameters from which the parameters of the list are aliased (directly or not). More...
 
virtual std::vector< std::string > getAlias (const std::string &name) const
 
virtual std::map< std::string, std::string > getAliases () const
 
std::string getFrom (const std::string &name) const
 
bool hasParameter (const std::string &name) const
 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
 Get the parameter with specified name. More...
 
const std::shared_ptr< Parameter > & getSharedParameter (const std::string &name) const
 
double getParameterValue (const std::string &name) const
 Get the value for parameter of name 'name'. More...
 
void setAllParametersValues (const ParameterList &parameters)
 Set the parameters values to be equals to those of parameters. More...
 
void setParameterValue (const std::string &name, double value)
 Set the value of parameter with name name to be equal to value. More...
 
void setParametersValues (const ParameterList &parameters)
 Update the parameters from parameters. More...
 
bool matchParametersValues (const ParameterList &parameters)
 Update the parameters from parameters. More...
 
size_t getNumberOfParameters () const
 Get the number of parameters. More...
 
std::string getNamespace () const
 
std::string getParameterNameWithoutNamespace (const std::string &name) const
 Resolves a parameter name according to the current namespace. More...
 

Protected Member Functions

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

Private Attributes

std::vector< BetaDiscreteDistribution * > vpBDD_
 
ParameterList independentParameters_
 
std::map< std::string, AliasParameterListener * > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

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

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

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

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

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

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

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

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

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

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

Definition at line 103 of file DirichletDiscreteDistribution.h.

Constructor & Destructor Documentation

◆ DirichletDiscreteDistribution()

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

Build a new discretized Dirichlet distribution.

Parameters
vnthe vector of the dim-1 numbers of categories to use.
valphathe vector of the dim alpha parameters.

Constructor:

Definition at line 57 of file DirichletDiscreteDistribution.cpp.

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

Referenced by clone().

◆ ~DirichletDiscreteDistribution()

DirichletDiscreteDistribution::~DirichletDiscreteDistribution ( )

Definition at line 83 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

Member Function Documentation

◆ addParameter_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 244 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::addParameter_(), bpp::Parameter::getName(), bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParameterAliasable::independentParameters_, and bpp::ParameterList::shareParameter().

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

◆ addParameters_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 250 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::addParameters_(), bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParameterAliasable::independentParameters_, bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().

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

◆ aliasParameters() [1/4]

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 119 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(), and bpp::ParameterList::size().

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

◆ aliasParameters() [2/4]

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.

◆ aliasParameters() [3/4]

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 173 of file AbstractParameterAliasable.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::Parameter::clone(), bpp::Clonable::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().

◆ aliasParameters() [4/4]

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.

◆ applyParameters()

void DirichletDiscreteDistribution::applyParameters ( )
protected

Definition at line 101 of file DirichletDiscreteDistribution.cpp.

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

Referenced by fireParameterChanged().

◆ clone()

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

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

Returns
A pointer toward the copy object.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 121 of file DirichletDiscreteDistribution.h.

References DirichletDiscreteDistribution().

◆ deleteParameter_() [1/2]

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 285 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)
inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 293 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)
inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 300 of file AbstractParameterAliasable.h.

References bpp::AbstractParameterAliasable::deleteParameter_().

◆ discretize()

void DirichletDiscreteDistribution::discretize ( Vdouble &  valpha)
protected

Definition at line 115 of file DirichletDiscreteDistribution.cpp.

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

Referenced by applyParameters(), and DirichletDiscreteDistribution().

◆ fireParameterChanged()

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

Notify the class when one or several parameters have changed.

Parameters
parametersA ParameterList object with parameters that changed.

Reimplemented from bpp::AbstractParametrizable.

Definition at line 93 of file DirichletDiscreteDistribution.cpp.

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

◆ getAlias() [1/2]

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 260 of file AbstractParameterAliasable.cpp.

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

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

◆ getAlias() [2/2]

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::BppOParametrizableFormat::write().

◆ 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 304 of file AbstractParameterAliasable.cpp.

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

◆ getAliases() [1/2]

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

Implements bpp::ParameterAliasable.

Definition at line 283 of file AbstractParameterAliasable.cpp.

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

◆ getAliases() [2/2]

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

Implemented in bpp::AbstractParameterAliasable.

◆ getCategories()

VVdouble DirichletDiscreteDistribution::getCategories ( ) const

Definition at line 197 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ getFrom()

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

Definition at line 344 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 363 of file AbstractParameterAliasable.cpp.

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

◆ getIndependentParameters() [1/2]

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 171 of file AbstractParameterAliasable.h.

References bpp::AbstractParameterAliasable::independentParameters_.

◆ getIndependentParameters() [2/2]

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

◆ getName()

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

Definition at line 130 of file DirichletDiscreteDistribution.h.

◆ getNamespace() [1/2]

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

Implements bpp::Parametrizable.

Definition at line 125 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::prefix_.

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

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

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

◆ getNumberOfCategories()

size_t DirichletDiscreteDistribution::getNumberOfCategories ( ) const
virtual
Returns
The number of categories

Implements bpp::MultipleDiscreteDistribution.

Definition at line 142 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ getNumberOfIndependentParameters() [1/2]

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 173 of file AbstractParameterAliasable.h.

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

◆ getNumberOfIndependentParameters() [2/2]

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.

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

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

◆ getParameter() [1/2]

const Parameter& bpp::AbstractParametrizable::getParameter ( const std::string &  name) const
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::AbstractParameterAliasable::getFromParameters(), 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
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::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

Referenced by bpp::FunctionWrapper::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 190 of file AbstractParametrizable.h.

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

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

◆ getParameter_() [2/3]

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

Definition at line 216 of file AbstractParametrizable.h.

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

◆ getParameter_() [3/3]

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

Definition at line 223 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 65 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), and bpp::AbstractParameterAliasable::shareParameters_().

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

Referenced by bpp::FunctionWrapper::getParameterNameWithoutNamespace(), 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::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::ParametrizableAdapter, bpp::FunctionWrapper, bpp::DirectionFunction, and bpp::AbstractParametrizable.

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

◆ getParameters_() [1/2]

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

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 231 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameters_() [2/2]

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::DirectionFunction, and bpp::AbstractParametrizable.

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

◆ getParameterValue() [1/2]

double bpp::AbstractParametrizable::getParameterValue ( const std::string &  name) const
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 89 of file AbstractParametrizable.h.

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

Referenced by applyParameters(), bpp::AutoCorrelationTransitionMatrix::fireParameterChanged(), bpp::BetaDiscreteDistribution::fireParameterChanged(), bpp::ConstantDistribution::fireParameterChanged(), bpp::ExponentialDiscreteDistribution::fireParameterChanged(), bpp::GammaDiscreteDistribution::fireParameterChanged(), bpp::GaussianDiscreteDistribution::fireParameterChanged(), bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::MixtureOfDiscreteDistributions::fireParameterChanged(), bpp::SimpleDiscreteDistribution::fireParameterChanged(), bpp::Simplex::fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::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::ParametrizableAdapter, bpp::FunctionWrapper, and bpp::AbstractParametrizable.

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

◆ 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 202 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 211 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter().

◆ getProbability()

double DirichletDiscreteDistribution::getProbability ( Vdouble &  category) const
virtual
Parameters
categoryThe vector of values associated to the class.
Returns
The probability associated to a given class.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 179 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ getSharedParameter() [1/3]

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

Definition at line 84 of file AbstractParametrizable.h.

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

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), bpp::AbstractParameterAliasable::shareParameters_(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ getSharedParameter() [2/3]

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

Definition at line 242 of file AbstractParametrizable.h.

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

◆ getSharedParameter() [3/3]

const std::shared_ptr<Parameter>& bpp::AbstractParametrizable::getSharedParameter ( 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 237 of file AbstractParametrizable.h.

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

◆ getValueCategory()

Vdouble DirichletDiscreteDistribution::getValueCategory ( Vdouble &  Vvalue) const
virtual
Parameters
Vvalue
Returns
The vector of categoryIndex of the classes the value is in. Throws a ConstraintException if the value is off the domain of the DirichletDiscreteDistribution.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 156 of file DirichletDiscreteDistribution.cpp.

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

◆ hasIndependentParameter()

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

Definition at line 169 of file AbstractParameterAliasable.h.

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

◆ hasParameter() [1/2]

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_.

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

◆ hasParameter() [2/2]

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

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

◆ includeParameters_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 275 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::includeParameters_(), bpp::AbstractParameterAliasable::independentParameters_, bpp::ParameterList::shareParameter(), and bpp::ParameterList::size().

◆ matchParametersValues() [1/2]

bool bpp::AbstractParametrizable::matchParametersValues ( const ParameterList &  parameters)
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 112 of file AbstractParametrizable.h.

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

Referenced by bpp::AbstractParameterAliasable::aliasParameters(), bpp::Simplex::setFrequencies(), bpp::TestFunction::setParameters(), 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::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

Referenced by bpp::InvariantMixedDiscreteDistribution::fireParameterChanged(), bpp::LogsumHmmLikelihood::fireParameterChanged(), bpp::BppODiscreteDistributionFormat::initialize_(), bpp::AbstractNumericalDerivative::matchParametersValues(), bpp::FunctionWrapper::matchParametersValues(), and bpp::InfinityFunctionWrapper::matchParametersValues().

◆ rand()

Vdouble DirichletDiscreteDistribution::rand ( ) const
virtual

Draw a random vector from this distribution.

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

Returns
A random number according to this distribution.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 251 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ randC()

Vdouble DirichletDiscreteDistribution::randC ( ) const
virtual

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

Returns
A random vector according to this distribution.

Implements bpp::MultipleDiscreteDistribution.

Definition at line 268 of file DirichletDiscreteDistribution.cpp.

References vpBDD_.

◆ resetParameters_()

void bpp::AbstractParameterAliasable::resetParameters_ ( )
inlineprotectedinherited

Definition at line 310 of file AbstractParameterAliasable.h.

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

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

◆ setAllParametersValues() [1/2]

void bpp::AbstractParametrizable::setAllParametersValues ( const ParameterList &  parameters)
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 94 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)
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::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

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

◆ setNamespace() [1/2]

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

Set the namespace for the parameter names.

Parameters
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 240 of file AbstractParameterAliasable.cpp.

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

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

◆ setNamespace() [2/2]

virtual void bpp::Parametrizable::setNamespace ( const std::string &  prefix)
pure virtualinherited

Set the namespace for the parameter names.

Parameters
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::MixtureOfDiscreteDistributions, bpp::InvariantMixedDiscreteDistribution, bpp::ParametrizableAdapter, bpp::FunctionWrapper, bpp::AbstractParametrizable, bpp::AbstractParameterAliasable, bpp::RescaledHmmLikelihood, bpp::LowMemoryRescaledHmmLikelihood, and bpp::LogsumHmmLikelihood.

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

◆ setParametersValues() [1/2]

void bpp::AbstractParametrizable::setParametersValues ( const ParameterList &  parameters)
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 106 of file AbstractParametrizable.h.

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

Referenced by bpp::LogsumHmmLikelihood::setParameters(), bpp::LowMemoryRescaledHmmLikelihood::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::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

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

◆ setParameterValue() [1/2]

void bpp::AbstractParametrizable::setParameterValue ( const std::string &  name,
double  value 
)
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 100 of file AbstractParametrizable.h.

References bpp::ParameterList::createSubList(), bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::parameters_, bpp::AbstractParametrizable::prefix_, 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::ParametrizableAdapter, bpp::InfinityFunctionWrapper, bpp::FunctionWrapper, bpp::AbstractNumericalDerivative, and bpp::AbstractParametrizable.

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

◆ shareParameter_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 260 of file AbstractParameterAliasable.h.

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

◆ shareParameters_()

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

Reimplemented from bpp::AbstractParametrizable.

Definition at line 266 of file AbstractParameterAliasable.h.

References bpp::AbstractParametrizable::getParameterNameWithoutNamespace(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParameterAliasable::independentParameters_, bpp::ParameterList::shareParameter(), bpp::AbstractParametrizable::shareParameters_(), and bpp::ParameterList::size().

◆ unaliasParameters() [1/2]

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 221 of file AbstractParameterAliasable.cpp.

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

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

◆ unaliasParameters() [2/2]

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.

Member Data Documentation

◆ aliasListenersRegister_

std::map<std::string, AliasParameterListener*> bpp::AbstractParameterAliasable::aliasListenersRegister_
privateinherited

Contains all parameter listeners for maintening alias relationships. The registry will be updated appropriately upon cloning and deleting.

Definition at line 151 of file AbstractParameterAliasable.h.

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::getAlias(), bpp::AbstractParameterAliasable::getAliasedParameters(), bpp::AbstractParameterAliasable::getAliases(), bpp::AbstractParameterAliasable::getFrom(), bpp::AbstractParameterAliasable::getFromParameters(), bpp::AbstractParameterAliasable::operator=(), bpp::AbstractParameterAliasable::setNamespace(), bpp::AbstractParameterAliasable::unaliasParameters(), and bpp::AbstractParameterAliasable::~AbstractParameterAliasable().

◆ independentParameters_

ParameterList bpp::AbstractParameterAliasable::independentParameters_
mutableprivateinherited

Definition at line 145 of file AbstractParameterAliasable.h.

Referenced by bpp::AbstractParameterAliasable::AbstractParameterAliasable(), bpp::AbstractParameterAliasable::addParameter_(), bpp::AbstractParameterAliasable::addParameters_(), bpp::AbstractParameterAliasable::aliasParameters(), bpp::AbstractParameterAliasable::deleteParameter_(), bpp::AbstractParameterAliasable::getIndependentParameters(), bpp::AbstractParameterAliasable::getNumberOfIndependentParameters(), bpp::AbstractParameterAliasable::hasIndependentParameter(), bpp::AbstractParameterAliasable::includeParameters_(), bpp::AbstractParameterAliasable::operator=(), bpp::AbstractParameterAliasable::resetParameters_(), bpp::AbstractParameterAliasable::shareParameter_(), bpp::AbstractParameterAliasable::shareParameters_(), and bpp::AbstractParameterAliasable::unaliasParameters().

◆ parameters_

ParameterList bpp::AbstractParametrizable::parameters_
privateinherited

Definition at line 66 of file AbstractParametrizable.h.

Referenced by bpp::AbstractParametrizable::addParameter_(), bpp::AbstractParametrizable::addParameters_(), bpp::AbstractParametrizable::deleteParameter_(), bpp::AbstractParametrizable::deleteParameters_(), bpp::AbstractParametrizable::getNumberOfParameters(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractParametrizable::getParameters_(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::hasParameter(), bpp::AbstractParametrizable::includeParameters_(), bpp::AbstractParametrizable::matchParametersValues(), bpp::AbstractParametrizable::resetParameters_(), bpp::AbstractParametrizable::setAllParametersValues(), bpp::AbstractParametrizable::setParametersValues(), bpp::AbstractParametrizable::setParameterValue(), bpp::AbstractParametrizable::shareParameter_(), and bpp::AbstractParametrizable::shareParameters_().

◆ prefix_

std::string bpp::AbstractParametrizable::prefix_
privateinherited

Definition at line 67 of file AbstractParametrizable.h.

Referenced by bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::getParameter(), bpp::AbstractParametrizable::getParameter_(), bpp::AbstractParametrizable::getSharedParameter(), bpp::AbstractParametrizable::hasParameter(), and bpp::AbstractParametrizable::setParameterValue().

◆ vpBDD_

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

Definition at line 108 of file DirichletDiscreteDistribution.h.

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

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