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 override
	Tell if there is a parameter with specified name. More...

const ParameterList &	getParameters () const override
	Get all parameters available. More...

const Parameter &	parameter (const std::string &name) const override
	Get the parameter with specified name. More...

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

double	getParameterValue (const std::string &name) const override
	Get the value for parameter of name 'name'. More...

void	setAllParametersValues (const ParameterList &parameters) override
	Set the parameters values to be equals to those of parameters. More...

void	setParameterValue (const std::string &name, double value) override
	Set the value of parameter with name name to be equal to value. More...

void	setParametersValues (const ParameterList &parameters) override
	Update the parameters from parameters. More...

bool	matchParametersValues (const ParameterList &parameters) override
	Update the parameters from parameters. More...

void	removeConstraint (const std::string &name) override
	Remove the constraint associated with one parameter, if any. More...

void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
	Set/Change the constraint associated with one parameter. More...

size_t	getNumberOfParameters () const override
	Get the number of parameters. More...

std::string	getNamespace () const override

std::string	getParameterNameWithoutNamespace (const std::string &name) const override
	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 > &	getParameter (size_t i) const

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

Parameter &	getParameter_ (const std::string &name)

Parameter &	getParameter_ (size_t index)

const Parameter &	getParameter_ (size_t index) const

Parameter &	getParameterWithNamespace_ (const std::string &name)

const Parameter &	getParameterWithNamespace_ (const std::string &name) const

ParameterList &	getParameters_ () override
	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...

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 66 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

dim	The number of probabilities.
method	tells the method of parametrization (default 0) 0: No parametrization 1: Global ratio 2: Local ratio 3: Binary
allowNull	if null probabilites are allowed (default: false)
name	The name passed to AbstractParameterAliasable constructor.

Definition at line 84 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

probas	The vector of probabilities.
method	tells the method of parametrization (default 0) 0: No parametrization 1: Global ratio 2: Local ratio 3: Binary
allowNull	if null probabilites are allowed (default: false)
name	The name passed to AbstractParameterAliasable constructor.

Definition at line 12 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 125 of file Simplex.h.

Member Function Documentation

◆ addParameter_()

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

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 196 of file AbstractParameterAliasable.h.

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

◆ addParameters_()

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

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 202 of file AbstractParameterAliasable.h.

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

Referenced by 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

p1	name of the parameter to which the other parameter is aliased
p2	name of the aliased parameter, which will be deleted from independent parameters list

Implements bpp::ParameterAliasable.

Definition at line 67 of file AbstractParameterAliasable.cpp.

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

unparsedParams	the map of the links : <A,B> matches for A->B aliasing.
verbose	verbosity

Implements bpp::ParameterAliasable.

Definition at line 120 of file AbstractParameterAliasable.cpp.

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

◆ clone()

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 127 of file Simplex.h.

References fireParameterChanged(), and Simplex().

◆ deleteParameter_() [1/2]

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

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 237 of file AbstractParameterAliasable.h.

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

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

◆ deleteParameter_() [2/2]

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

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 245 of file AbstractParameterAliasable.h.

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

◆ deleteParameters_()

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

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 252 of file AbstractParameterAliasable.h.

◆ dimension()

size_t bpp::Simplex::dimension ( ) const

inline

Definition at line 132 of file Simplex.h.

References dim_, and setFrequencies().

◆ fireParameterChanged()

void Simplex::fireParameterChanged ( const ParameterList & parameters )

virtual

Notify the class when one or several parameters have changed.

Parameters

parameters A ParameterList object with parameters that changed.

Reimplemented from bpp::AbstractParametrizable.

Reimplemented in bpp::OrderedSimplex.

Definition at line 132 of file Simplex.cpp.

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

Referenced by clone(), bpp::OrderedSimplex::fireParameterChanged(), and bpp::OrderedSimplex::OrderedSimplex().

◆ 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

name	The name of the parameter to look for.

Implements bpp::ParameterAliasable.

Definition at line 204 of file AbstractParameterAliasable.cpp.

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

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

◆ getAliasedParameters()

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

inherited

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

Definition at line 244 of file AbstractParameterAliasable.cpp.

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

◆ getAliases()

std::map< std::string, std::string > AbstractParameterAliasable::getAliases ( ) const

virtualinherited

Returns: the map of the aliases.

Implements bpp::ParameterAliasable.

Definition at line 225 of file AbstractParameterAliasable.cpp.

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

◆ getFrequencies() [1/2]

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

inline

Definition at line 136 of file Simplex.h.

References vProb_.

Referenced by bpp::OrderedSimplex::fireParameterChanged(), and bpp::OrderedSimplex::OrderedSimplex().

◆ getFrequencies() [2/2]

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

inline

Definition at line 138 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

name	The name of the parameter to look for.

Definition at line 280 of file AbstractParameterAliasable.cpp.

References bpp::AbstractParameterAliasable::aliasListenersRegister_.

◆ getFromParameters()

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

inherited

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

Definition at line 297 of file AbstractParameterAliasable.cpp.

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

◆ 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 135 of file AbstractParameterAliasable.h.

◆ getMethod()

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

inline

Definition at line 142 of file Simplex.h.

References method_.

◆ getNamespace()

std::string bpp::AbstractParametrizable::getNamespace ( ) const

inlineoverridevirtualinherited

Returns: The current namespace used. This is an empty string if no namespace is currently defined.

Implements bpp::Parametrizable.

Definition at line 99 of file AbstractParametrizable.h.

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

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

◆ 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 137 of file AbstractParameterAliasable.h.

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

◆ getNumberOfParameters()

size_t bpp::AbstractParametrizable::getNumberOfParameters ( ) const

inlineoverridevirtualinherited

Get the number of parameters.

See also: getNumberOfIndependentParameters If some parameters are aliased.

Returns: The number of parameters.

Implements bpp::Parametrizable.

Definition at line 95 of file AbstractParametrizable.h.

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

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

◆ getParameter() [1/3]

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

inlineinherited

Definition at line 48 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

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

◆ getParameter() [2/3]

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

inlineprotectedinherited

Returns: The shared_ptr parameter at a given position.

Warning: No check is performed on the validity of the index given as input!

Definition at line 211 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter() [3/3]

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

inlineprotectedinherited

Definition at line 216 of file AbstractParametrizable.h.

References bpp::ParameterList::getParameter().

◆ getParameter_() [1/3]

Parameter& bpp::AbstractParametrizable::getParameter_ ( const std::string & name )

inlineprotectedinherited

Parameters

name	The name of the parameter.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 164 of file AbstractParametrizable.h.

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

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

◆ getParameter_() [2/3]

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

inlineprotectedinherited

Definition at line 190 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameter_() [3/3]

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

inlineprotectedinherited

Definition at line 197 of file AbstractParametrizable.h.

References bpp::ParameterList::size().

◆ getParameterNameWithoutNamespace()

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

overridevirtualinherited

Resolves a parameter name according to the current namespace.

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

Implements bpp::Parametrizable.

Definition at line 28 of file AbstractParametrizable.cpp.

References bpp::TextTools::startsWith().

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

◆ getParameters()

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

inlineoverridevirtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 41 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameters_()

ParameterList& bpp::AbstractParametrizable::getParameters_ ( )

inlineoverrideprotectedvirtualinherited

Get all parameters available.

See also: getIndependentParameters if some parameters are aliased.

Returns: A list with all parameters available.

Implements bpp::Parametrizable.

Definition at line 205 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameters_.

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

◆ getParameterValue()

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

inlineoverridevirtualinherited

Get the value for parameter of name 'name'.

Parameters

name	The name of the parameter.

Returns: the value of parameter name.

Implements bpp::Parametrizable.

Definition at line 53 of file AbstractParametrizable.h.

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

◆ getParameterWithNamespace_() [1/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 176 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::getParameter_().

◆ getParameterWithNamespace_() [2/2]

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

inlineprotectedinherited

Parameters

name	The name of the parameter, including its namespace.

Returns: A reference toward the corresponding parameter.

Exceptions

ParameterNotFoundException If no parameter with that name is found in the list.

Definition at line 185 of file AbstractParametrizable.h.

References bpp::AbstractParametrizable::parameter().

◆ hasIndependentParameter()

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

inlineinherited

Definition at line 133 of file AbstractParameterAliasable.h.

References bpp::ParameterList::hasParameter().

◆ hasParameter()

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

inlineoverridevirtualinherited

Tell if there is a parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: y/n.

Implements bpp::Parametrizable.

Definition at line 39 of file AbstractParametrizable.h.

References bpp::ParameterList::hasParameter().

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

◆ includeParameters_()

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

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 227 of file AbstractParameterAliasable.h.

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

◆ matchParametersValues()

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

inlineoverridevirtualinherited

Update the parameters from parameters.

Only common parameters with parameters will be updated.

Parameters

parameters A list of parameters.

Returns: True if at least one parameter value has been changed.

Exceptions

ConstraintException If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 76 of file AbstractParametrizable.h.

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

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

◆ parameter()

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

inlineoverridevirtualinherited

Get the parameter with specified name.

Parameters

name	The name of the parameter to look for.

Returns: The parameter with given name.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 43 of file AbstractParametrizable.h.

References bpp::ParameterList::parameter().

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

◆ prob()

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

inline

Definition at line 140 of file Simplex.h.

◆ removeConstraint()

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

inlineoverridevirtualinherited

Remove the constraint associated with one parameter, if any.

Parameters

name	The name of the parameter to look for.

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 85 of file AbstractParametrizable.h.

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

◆ resetParameters_()

void bpp::AbstractParameterAliasable::resetParameters_ ( )

inlineprotectedinherited

Definition at line 262 of file AbstractParameterAliasable.h.

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

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

◆ setAllParametersValues()

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

inlineoverridevirtualinherited

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

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

Parameters

parameters A list with all parameters.

Exceptions

ParameterNotFoundException	If a some parameter in the list is not in params.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 58 of file AbstractParametrizable.h.

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

◆ setConstraint()

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

inlineoverridevirtualinherited

Set/Change the constraint associated with one parameter.

Parameters

name	The name of the parameter to look for.
constraint	A pointer to the constraint (may be null)

Exceptions

ParameterNotFoundException if no parameter with this name is found.

Implements bpp::Parametrizable.

Definition at line 90 of file AbstractParametrizable.h.

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

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

◆ setFrequencies()

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

Definition at line 209 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 dimension(), bpp::OrderedSimplex::OrderedSimplex(), bpp::OrderedSimplex::setFrequencies(), and Simplex().

◆ setNamespace()

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

virtualinherited

Set the namespace for the parameter names.

Parameters

prefix The '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 186 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 )

inlineoverridevirtualinherited

Update the parameters from parameters.

parameters must be a subset of all parameters available.

Parameters

parameters A list containing all parameters to update.

Exceptions

ParameterNotFoundException	If a some parameter in params is not in the list.
ConstraintException	If a value in parameters does not match the constraint in the corresponding parameter in the list.

Implements bpp::Parametrizable.

Definition at line 70 of file AbstractParametrizable.h.

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

Referenced by bpp::LowMemoryRescaledHmmLikelihood::setParameters(), bpp::RescaledHmmLikelihood::setParameters(), and bpp::LogsumHmmLikelihood::setParameters().

◆ setParameterValue()

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

inlineoverridevirtualinherited

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

Parameters

name	the name of the parameter to set.
value	The value of the parameter.

Exceptions

ParameterNotFoundException	If no parameter in the list has the name name.
ConstraintException	If value does not match the constraint associated to parameter name.

Implements bpp::Parametrizable.

Definition at line 64 of file AbstractParametrizable.h.

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

◆ shareParameter_()

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

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 212 of file AbstractParameterAliasable.h.

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

◆ shareParameters_()

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

inlineprotectedvirtualinherited

Reimplemented from bpp::AbstractParametrizable.

Definition at line 218 of file AbstractParameterAliasable.h.

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

◆ 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

p1	Original parameter.
p2	Aliased parameter.

Exceptions

ParameterNotFoundException	if p1 or p2 do not correspond to existing parameters.
Exception	when trying to perform non-valid dissociation.

Implements bpp::ParameterAliasable.

Definition at line 168 of file AbstractParameterAliasable.cpp.

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

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

Member Data Documentation

◆ dim_

size_t bpp::Simplex::dim_

private

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

Definition at line 74 of file Simplex.h.

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

◆ 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 84 of file Simplex.h.

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

◆ valpha_

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

private

just used with local ratio (method 2)

Definition at line 91 of file Simplex.h.

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

◆ vProb_

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

private

Definition at line 86 of file Simplex.h.

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

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

Bpp/Numeric/Prob/Simplex.h
Bpp/Numeric/Prob/Simplex.cpp

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ Simplex() [1/2]

◆ Simplex() [2/2]

◆ ~Simplex()

Member Function Documentation

◆ addParameter_()

◆ addParameters_()

◆ aliasParameters() [1/2]

◆ aliasParameters() [2/2]

◆ clone()

◆ deleteParameter_() [1/2]

◆ deleteParameter_() [2/2]

◆ deleteParameters_()

◆ dimension()

◆ fireParameterChanged()

◆ getAlias()

◆ getAliasedParameters()

◆ getAliases()

◆ getFrequencies() [1/2]

◆ getFrequencies() [2/2]

◆ getFrom()

◆ getFromParameters()

◆ getIndependentParameters()

◆ getMethod()

◆ getNamespace()

◆ getNumberOfIndependentParameters()

◆ getNumberOfParameters()

◆ getParameter() [1/3]

◆ getParameter() [2/3]

◆ getParameter() [3/3]

◆ getParameter_() [1/3]

◆ getParameter_() [2/3]

◆ getParameter_() [3/3]

◆ getParameterNameWithoutNamespace()

◆ getParameters()

◆ getParameters_()

◆ getParameterValue()

◆ getParameterWithNamespace_() [1/2]

◆ getParameterWithNamespace_() [2/2]

◆ hasIndependentParameter()

◆ hasParameter()

◆ includeParameters_()

◆ matchParametersValues()

◆ parameter()

◆ prob()

◆ removeConstraint()

◆ resetParameters_()

◆ setAllParametersValues()

◆ setConstraint()

◆ setFrequencies()

◆ setNamespace()

◆ setParametersValues()

◆ setParameterValue()

◆ shareParameter_()

◆ shareParameters_()

◆ unaliasParameters()

Member Data Documentation

◆ dim_

◆ method_

◆ valpha_

◆ vProb_