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

A Simplex object, used to define sets of probabilities that sum 1. More...

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

+ Inheritance diagram for bpp::Simplex:
+ Collaboration diagram for bpp::Simplex:

Public Member Functions

 Simplex (size_t dim, unsigned short method=0, bool allowNull=false, const std::string &name="Simplex.")
 Builds a new Simplex object from a number of probabilities. They are initialized equal. More...
 
 Simplex (const std::vector< double > &probas, unsigned short method=0, bool allowNull=false, const std::string &name="Simplex.")
 Builds a new Simplex object from a vector of probabilities. More...
 
virtual ~Simplex ()
 
Simplex * clone () const
 Create a copy of this object and send a pointer to it. More...
 
void fireParameterChanged (const ParameterList &parameters)
 Notify the class when one or several parameters have changed. More...
 
size_t dimension () const
 
void setFrequencies (const std::vector< double > &)
 
const std::vector< double > & getFrequencies () const
 
std::vector< double > & getFrequencies ()
 
double prob (size_t i) const
 
unsigned short getMethod () const
 
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 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

size_t dim_
 The dimension+1 of the space simplex (ie the number of probabilities). More...
 
unsigned short method_
 the method of parametrization. More...
 
std::vector< double > vProb_
 
std::vector< double > valpha_
 just used with local ratio (method 2) More...
 
ParameterList independentParameters_
 
std::map< std::string, AliasParameterListener * > aliasListenersRegister_
 
ParameterList parameters_
 
std::string prefix_
 

Detailed Description

A Simplex object, used to define sets of probabilities that sum 1.

The probabilities are denoted $p_i$ for $i \in <1,n>$.

If they are parametrized, the parameters are called "theta1", ..., "theta(n-1)".

Three ways of parametrization are available:

Global ratio:

$\forall i<n, \theta_i=\frac{p_i}{1-(p_1+...+p_{i-1})}$.

In the reverse, $\forall i<n, p_i= (1-\theta_1).(1-\theta_2)...\theta_{i}$ and $p_n=(1-\theta_1).(1-\theta_2)...(1-\theta_{n-1})$.

Local ratio:

$\theta_i = \frac{p_i}{p_i+p_{i+1}} \forall i \in 1..\textrm{n-1}$.

In the reverse if we denote $\alpha_i=\frac{1-\theta_i}{\theta_i}$, $p_i=\frac{\alpha_1...\alpha_{i-1}}{1+\sum_{k=1}^{n-1}\alpha_1...\alpha_k}$.

Binary:

This parametrization is based on the binary coding.

Given $a_b...a_1$ the writing of i in binary, we denote $i_k=a_k...a_1$.

Given $a_b...a_1$ the writing of i in binary where $a_b=1$, we denote $1_i=\sum_j\{p_{j+1} \text{ such that } j_b=1i_{b-1}\}$ and $0_i=\sum_j\{p_{j+1} \text{ such that } j_b=0i_{b-1}\}$, and then we define:

$\theta_i=\frac{1_i}{1_i+0_i}$

and on the reverse, we denote $\theta'_{0i_{b-1}}=1-\theta_i$ and $\theta'_{1i_{b-1}}=\theta_i$.

Then, if $c=ceil(log_2(n))$, for $i \in <0,n-1>$.

$p_{i+1}=\theta'_{i_c}....\theta'_{i_1} $

Definition at line 103 of file Simplex.h.

Constructor & Destructor Documentation

◆ Simplex() [1/2]

Simplex::Simplex ( size_t  dim,
unsigned short  method = 0,
bool  allowNull = false,
const std::string &  name = "Simplex." 
)

Builds a new Simplex object from a number of probabilities. They are initialized equal.

Parameters
dimThe number of probabilities.
methodtells the method of parametrization (default 0) 0: No parametrization 1: Global ratio 2: Local ratio 3: Binary
allowNullif null probabilites are allowed (default: false)
nameThe name passed to AbstractParameterAliasable constructor.

Definition at line 121 of file Simplex.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), dim_, method_, bpp::Parameter::PROP_CONSTRAINT_EX, bpp::Parameter::PROP_CONSTRAINT_IN, setFrequencies(), bpp::TextTools::toString(), valpha_, and vProb_.

Referenced by clone().

◆ Simplex() [2/2]

Simplex::Simplex ( const std::vector< double > &  probas,
unsigned short  method = 0,
bool  allowNull = false,
const std::string &  name = "Simplex." 
)

Builds a new Simplex object from a vector of probabilities.

Parameters
probasThe vector of probabilities.
methodtells the method of parametrization (default 0) 0: No parametrization 1: Global ratio 2: Local ratio 3: Binary
allowNullif null probabilites are allowed (default: false)
nameThe name passed to AbstractParameterAliasable constructor.

Definition at line 49 of file Simplex.cpp.

References bpp::AbstractParameterAliasable::addParameter_(), dim_, method_, bpp::Parameter::PROP_CONSTRAINT_EX, bpp::Parameter::PROP_CONSTRAINT_IN, bpp::NumConstants::SMALL(), bpp::VectorTools::sum(), bpp::TextTools::toString(), valpha_, and vProb_.

◆ ~Simplex()

virtual bpp::Simplex::~Simplex ( )
inlinevirtual

Definition at line 162 of file Simplex.h.

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(), bpp::DirichletDiscreteDistribution::DirichletDiscreteDistribution(), bpp::ExponentialDiscreteDistribution::ExponentialDiscreteDistribution(), bpp::GammaDiscreteDistribution::GammaDiscreteDistribution(), bpp::GaussianDiscreteDistribution::GaussianDiscreteDistribution(), bpp::InvariantMixedDiscreteDistribution::InvariantMixedDiscreteDistribution(), bpp::MixtureOfDiscreteDistributions::MixtureOfDiscreteDistributions(), bpp::SimpleDiscreteDistribution::SimpleDiscreteDistribution(), 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() [1/2]

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() [2/2]

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().

◆ clone()

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

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

Returns
A pointer toward the copy object.

Implements bpp::Clonable.

Definition at line 164 of file Simplex.h.

References Simplex().

◆ 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_().

◆ dimension()

size_t bpp::Simplex::dimension ( ) const
inline

Definition at line 169 of file Simplex.h.

References dim_.

◆ fireParameterChanged()

void Simplex::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 169 of file Simplex.cpp.

References dim_, bpp::AbstractParametrizable::getParameterValue(), method_, bpp::NumConstants::TINY(), bpp::TextTools::toString(), valpha_, and vProb_.

◆ getAlias()

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().

◆ 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()

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().

◆ getFrequencies() [1/2]

std::vector<double>& bpp::Simplex::getFrequencies ( )
inline

Definition at line 175 of file Simplex.h.

References vProb_.

◆ getFrequencies() [2/2]

const std::vector<double>& bpp::Simplex::getFrequencies ( ) const
inline

Definition at line 173 of file Simplex.h.

References vProb_.

◆ 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()

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_.

◆ getMethod()

unsigned short bpp::Simplex::getMethod ( ) const
inline

Definition at line 179 of file Simplex.h.

References method_.

◆ getNamespace()

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(), setFrequencies(), bpp::AbstractParameterAliasable::setNamespace(), and bpp::BppODiscreteDistributionFormat::writeDiscreteDistribution().

◆ getNumberOfIndependentParameters()

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().

◆ getNumberOfParameters()

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().

◆ getParameter()

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_() [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()

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_().

◆ getParameters()

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_()

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=().

◆ getParameterValue()

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 bpp::DirichletDiscreteDistribution::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(), fireParameterChanged(), bpp::TruncatedExponentialDiscreteDistribution::fireParameterChanged(), bpp::BetaDiscreteDistribution::randC(), bpp::ExponentialDiscreteDistribution::randC(), bpp::GammaDiscreteDistribution::randC(), bpp::TruncatedExponentialDiscreteDistribution::randC(), and bpp::ConstantDistribution::restrictToConstraint().

◆ 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().

◆ 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_.

◆ 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()

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().

◆ 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()

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(), setFrequencies(), bpp::TestFunction::setParameters(), bpp::ReparametrizationFunctionWrapper::setParameters(), and bpp::FullHmmTransitionMatrix::setTransitionProbabilities().

◆ prob()

double bpp::Simplex::prob ( size_t  i) const
inline

Definition at line 177 of file Simplex.h.

References vProb_.

◆ 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()

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().

◆ setFrequencies()

void Simplex::setFrequencies ( const std::vector< double > &  probas)

Definition at line 246 of file Simplex.cpp.

References bpp::ParameterList::addParameter(), dim_, bpp::AbstractParametrizable::getNamespace(), bpp::AbstractParametrizable::matchParametersValues(), method_, bpp::NumConstants::SMALL(), bpp::VectorTools::sum(), bpp::TextTools::toString(), and valpha_.

Referenced by Simplex().

◆ setNamespace()

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().

◆ setParametersValues()

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().

◆ setParameterValue()

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().

◆ 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()

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().

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().

◆ dim_

size_t bpp::Simplex::dim_
private

The dimension+1 of the space simplex (ie the number of probabilities).

Definition at line 111 of file Simplex.h.

Referenced by dimension(), fireParameterChanged(), setFrequencies(), and Simplex().

◆ 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().

◆ method_

unsigned short bpp::Simplex::method_
private

the method of parametrization.

0: No parametrization 1: Global ratio 2: Local ratio 3: Binary

Definition at line 121 of file Simplex.h.

Referenced by fireParameterChanged(), getMethod(), setFrequencies(), and Simplex().

◆ 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().

◆ valpha_

std::vector<double> bpp::Simplex::valpha_
private

just used with local ratio (method 2)

Definition at line 128 of file Simplex.h.

Referenced by fireParameterChanged(), setFrequencies(), and Simplex().

◆ vProb_

std::vector<double> bpp::Simplex::vProb_
private

Definition at line 123 of file Simplex.h.

Referenced by fireParameterChanged(), getFrequencies(), prob(), and Simplex().

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