Wraps a dataflow graph as a function: resultNode = f(variableNodes). More...

#include <Bpp/Phyl/Likelihood/PhyloLikelihoods/SingleProcessPhyloLikelihood.h>

Inheritance diagram for bpp::SingleProcessPhyloLikelihood:

Collaboration diagram for bpp::SingleProcessPhyloLikelihood:

Public Member Functions
	SingleProcessPhyloLikelihood (Context &context, std::shared_ptr< LikelihoodCalculationSingleProcess > likCal, const ParameterList &variableNodes, size_t nProc=0, size_t nData=0)

	SingleProcessPhyloLikelihood (Context &context, std::shared_ptr< LikelihoodCalculationSingleProcess > likCal, size_t nProc=0, size_t nData=0)
	: the parameters the independent parameters of the LikelihoodCalculation More...

SingleProcessPhyloLikelihood *	clone () const override

void	setData (std::shared_ptr< const AlignmentDataInterface > sites, size_t nData=0) override
	Set the dataset for which the likelihood must be evaluated. More...

std::shared_ptr< const AlignmentDataInterface >	getShrunkData () const
	return a pointer to the compressed data. More...

std::shared_ptr< const AlignmentDataInterface >	getData () const override
	return a pointer to the original data. More...

size_t	getNumberOfSites () const override
	Get the number of sites in the dataset. More...

size_t	getNumberOfDistinctSites () const

size_t	getNumberOfClasses () const
	Get the number of model classes. More...

std::shared_ptr< const Alphabet >	getAlphabet () const override
	Get the alphabet associated to the dataset. More...

std::shared_ptr< const ParametrizablePhyloTree >	tree () const

const SubstitutionProcessInterface &	substitutionProcess () const
	Return the ref to the SubstitutionProcess used to build the phylolikelihood. More...

std::shared_ptr< const SubstitutionProcessInterface >	getSubstitutionProcess () const
	Return a smarter pointer to the SubstitutionProcess used to build the phylolikelihood. More...

size_t	getSubstitutionProcessNumber () const

bool	isInitialized () const override

LikelihoodCalculation &	likelihoodCalculation () const override

std::shared_ptr< LikelihoodCalculation >	getLikelihoodCalculation () const override

AlignedLikelihoodCalculation &	alignedLikelihoodCalculation () const override

std::shared_ptr< AlignedLikelihoodCalculation >	getAlignedLikelihoodCalculation () const override

LikelihoodCalculationSingleProcess &	likelihoodCalculationSingleProcess () const

std::shared_ptr< LikelihoodCalculationSingleProcess >	getLikelihoodCalculationSingleProcess () const

ValueRef< RowLik >	getFirstOrderDerivativeVector (const std::string &variable) const

ValueRef< RowLik >	firstOrderDerivativeVector (const std::string &variable) const

ValueRef< RowLik >	getSecondOrderDerivativeVector (const std::string &variable) const

ValueRef< RowLik >	getSecondOrderDerivativeVector (const std::string &variable1, const std::string &variable2) const

ValueRef< RowLik >	secondOrderDerivativeVector (const std::string &variable1, const std::string &variable2) const

VVdouble	getPosteriorProbabilitiesPerSitePerClass () const
	Get the posterior probabilities of each class, for each site. More...

Vdouble	getPosteriorProbabilitiesForSitePerClass (size_t pos) const

VVDataLik	getLikelihoodPerSitePerClass () const

std::vector< size_t >	getClassWithMaxPostProbPerSite () const

Vdouble	getPosteriorRatePerSite () const

Vdouble	getPosteriorStateFrequencies (uint nodeId)

size_t	getNData () const
	Get the number of dataset concerned. More...

void	setNData (size_t nData)

size_t	getNumberOfStates () const
	Get the number the states. More...

DataLik	getLikelihoodForASite (size_t site) const
	Get the likelihood for a site (on uncompressed data) More...

double	getLogLikelihoodForASite (size_t site) const
	Get the log likelihood for a site, and its derivatives. More...

VDataLik	getLikelihoodPerSite () const
	Get the likelihood for each site. More...

const Context &	context () const override

Context &	context () override

ValueRef< DataLik >	getLikelihoodNode () const override

virtual void	enableSecondOrderDerivatives (bool yn)=0

virtual bool	enableSecondOrderDerivatives () const=0

virtual void	enableSecondOrderDerivatives (bool yn) override

bool	enableSecondOrderDerivatives () const override

virtual double	getSecondOrderDerivative (const std::string &variable) const=0

virtual double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const=0

double	getSecondOrderDerivative (const std::string &variable) const override

double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const override

virtual double	d2f (const std::string &variable, const ParameterList &parameters)

virtual double	d2f (const std::string &variable1, const std::string &variable2, const ParameterList &parameters)

virtual void	enableFirstOrderDerivatives (bool yn)=0

virtual bool	enableFirstOrderDerivatives () const=0

virtual void	enableFirstOrderDerivatives (bool yn) override
	Tell if derivatives must be computed: for Function inheritance. More...

bool	enableFirstOrderDerivatives () const override

virtual double	getFirstOrderDerivative (const std::string &variable) const=0

double	getFirstOrderDerivative (const std::string &variable) const override

virtual double	df (const std::string &variable, const ParameterList &parameters)

virtual void	setParameters (const ParameterList &parameters)=0

void	setParameters (const ParameterList &parameters) override

virtual double	getValue () const=0

double	getValue () const override

virtual double	f (const ParameterList &parameters)

virtual bool	hasParameter (const std::string &name) const=0

virtual const ParameterList &	getParameters () const=0

virtual const Parameter &	parameter (const std::string &name) const=0

virtual double	getParameterValue (const std::string &name) const=0

virtual void	setAllParametersValues (const ParameterList &parameters)=0

virtual void	setParameterValue (const std::string &name, double value)=0

virtual void	setParametersValues (const ParameterList &parameters)=0

virtual bool	matchParametersValues (const ParameterList &parameters)=0

virtual void	removeConstraint (const std::string &name)=0

virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0

virtual size_t	getNumberOfParameters () const=0

virtual void	setNamespace (const std::string &prefix)=0

virtual std::string	getNamespace () const=0

virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0

void	shareParameters (const ParameterList &variableNodes)
	Share Parameters, that are DF_parameters. More...

ValueRef< DataLik >	firstOrderDerivativeNode (const std::string &variable) const

ValueRef< DataLik >	secondOrderDerivativeNode (const std::string &variable1, const std::string &variable2) const

bool	hasParameter (const std::string &name) const override

const ParameterList &	getParameters () const override

const Parameter &	parameter (const std::string &name) const override

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

double	getParameterValue (const std::string &name) const override

void	setAllParametersValues (const ParameterList &parameters) override

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

void	setParametersValues (const ParameterList &parameters) override

bool	matchParametersValues (const ParameterList &parameters) override

void	removeConstraint (const std::string &name) override

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

size_t	getNumberOfParameters () const override

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

std::string	getNamespace () const override

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

virtual void	fireParameterChanged (const ParameterList &parameters)

Retrieve some particular independent parameters subsets.
ParameterList	getNonDerivableParameters () const override

ParameterList	getDerivableParameters () const override

ParameterList	getBranchLengthParameters () const override
	Get the independent branch lengths parameters. More...

ParameterList	getSubstitutionModelParameters () const override
	Get the independent parameters associated to substitution model(s). More...

ParameterList	getRateDistributionParameters () const override
	Get the independent parameters associated to the rate distribution(s). More...

ParameterList	getRootFrequenciesParameters () const override
	Get the independent parameters associated to the root frequencies(s). More...

The likelihood functions.
virtual DataLik	getLikelihoodForASite (size_t site) const =0
	Get the likelihood for a site. More...

virtual double	getLogLikelihoodForASite (size_t site) const =0
	Get the log likelihood for a site, and its derivatives. More...

virtual VDataLik	getLikelihoodPerSite () const =0
	Get the likelihood for each site. More...

The data functions
virtual const Context &	context () const =0

virtual Context &	context ()=0

The likelihood functions.
virtual ValueRef< DataLik >	getLikelihoodNode () const =0

double	getLogLikelihood () const
	Get the logarithm of the likelihood for the whole dataset. More...

Protected Member Functions
virtual ParameterList &	getParameters_ ()=0

void	setNumberOfSites (size_t nbSites)

Node_DF &	accessVariableNode (const std::string &name) const

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

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

virtual void	addParameter_ (Parameter *parameter)

virtual void	addParameters_ (const ParameterList &parameters)

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

virtual void	shareParameters_ (const ParameterList &parameters)

virtual void	includeParameters_ (const ParameterList &parameters)

virtual void	deleteParameter_ (size_t index)

virtual void	deleteParameter_ (std::string &name)

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

void	resetParameters_ ()

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

Static Protected Member Functions
static Node_DF &	accessVariableNode (const Parameter &param)

Protected Attributes
std::shared_ptr< LikelihoodCalculationSingleProcess >	likCal_

size_t	nProc_
	the Substitution Process number More...

std::unordered_map< std::string, ValueRef< RowLik > >	firstOrderDerivativeVectors_
	For Dataflow computing. More...

std::unordered_map< std::pair< std::string, std::string >, ValueRef< RowLik >, StringPairHash >	secondOrderDerivativeVectors_

size_t	nbStates_

size_t	nData_
	Number of the concerned data. More...

size_t	nbSites_

Context &	context_

DataLik	minusLogLik_
	the value More...

std::unordered_map< std::string, ValueRef< DataLik > >	firstOrderDerivativeNodes_
	For Dataflow computing. More...

std::unordered_map< std::pair< std::string, std::string >, ValueRef< DataLik >, StringPairHash >	secondOrderDerivativeNodes_

Private Attributes
ParameterList	parameters_

std::string	prefix_

Detailed Description

Wraps a dataflow graph as a function: resultNode = f(variableNodes).

Definition at line 29 of file SingleProcessPhyloLikelihood.h.

Constructor & Destructor Documentation

◆ SingleProcessPhyloLikelihood() [1/2]

bpp::SingleProcessPhyloLikelihood::SingleProcessPhyloLikelihood	(	Context &	context,
		std::shared_ptr< LikelihoodCalculationSingleProcess >	likCal,
		const ParameterList &	variableNodes,
		size_t	nProc = `0`,
		size_t	nData = `0`
	)

inline

Definition at line 52 of file SingleProcessPhyloLikelihood.h.

References bpp::AbstractParametrizable::shareParameters_().

Referenced by clone().

◆ SingleProcessPhyloLikelihood() [2/2]

bpp::SingleProcessPhyloLikelihood::SingleProcessPhyloLikelihood	(	Context &	context,
		std::shared_ptr< LikelihoodCalculationSingleProcess >	likCal,
		size_t	nProc = `0`,
		size_t	nData = `0`
	)

inline

: the parameters the independent parameters of the LikelihoodCalculation

Definition at line 68 of file SingleProcessPhyloLikelihood.h.

References likCal_, and bpp::AbstractParametrizable::shareParameters_().

Member Function Documentation

◆ accessVariableNode() [1/2]

static Node_DF& bpp::AbstractPhyloLikelihood::accessVariableNode ( const Parameter & param )

inlinestaticprotectedinherited

Definition at line 188 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), firstOrderDerivativeVector(), bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::secondOrderDerivativeVector(), and secondOrderDerivativeVector().

◆ accessVariableNode() [2/2]

Node_DF& bpp::AbstractPhyloLikelihood::accessVariableNode ( const std::string & name ) const

inlineprotectedinherited

Definition at line 193 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), and bpp::SecondOrderDerivable::parameter().

◆ alignedLikelihoodCalculation()

AlignedLikelihoodCalculation& bpp::SingleProcessPhyloLikelihood::alignedLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns: The LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 255 of file SingleProcessPhyloLikelihood.h.

References likCal_.

◆ clone()

SingleProcessPhyloLikelihood* bpp::SingleProcessPhyloLikelihood::clone ( ) const

inlineoverridevirtual

Implements bpp::AbstractParametrizable.

Definition at line 87 of file SingleProcessPhyloLikelihood.h.

References SingleProcessPhyloLikelihood().

◆ context() [1/4]

virtual const Context& bpp::PhyloLikelihoodInterface::context ( ) const

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ context() [2/4]

const Context& bpp::AbstractPhyloLikelihood::context ( ) const

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 73 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

◆ context() [3/4]

Context& bpp::AbstractPhyloLikelihood::context ( )

inlineoverridevirtualinherited

Implements bpp::PhyloLikelihoodInterface.

Definition at line 75 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::context_.

◆ context() [4/4]

virtual Context& bpp::PhyloLikelihoodInterface::context ( )

pure virtualinherited

Implemented in bpp::AbstractPhyloLikelihood.

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 115 of file AbstractPhyloLikelihood.h.

◆ enableFirstOrderDerivatives() [2/2]

virtual void bpp::AbstractPhyloLikelihood::enableFirstOrderDerivatives ( bool yn )

inlineoverridevirtualinherited

Tell if derivatives must be computed: for Function inheritance.

Implements bpp::SecondOrderDerivable.

Definition at line 113 of file AbstractPhyloLikelihood.h.

◆ enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 116 of file AbstractPhyloLikelihood.h.

◆ enableSecondOrderDerivatives() [2/2]

virtual void bpp::AbstractPhyloLikelihood::enableSecondOrderDerivatives ( bool yn )

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 114 of file AbstractPhyloLikelihood.h.

◆ firstOrderDerivativeNode()

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode ( const std::string & variable ) const

inlineinherited

Definition at line 139 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, bpp::AbstractPhyloLikelihood::firstOrderDerivativeNodes_, and bpp::AbstractPhyloLikelihood::getLikelihoodNode().

Referenced by bpp::AbstractPhyloLikelihood::getFirstOrderDerivative(), and bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode().

◆ firstOrderDerivativeVector()

ValueRef<RowLik> bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVector ( const std::string & variable ) const

inline

Definition at line 282 of file SingleProcessPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, firstOrderDerivativeVectors_, and getLikelihoodCalculationSingleProcess().

Referenced by getFirstOrderDerivativeVector(), and secondOrderDerivativeVector().

◆ getAlignedLikelihoodCalculation()

std::shared_ptr<AlignedLikelihoodCalculation> bpp::SingleProcessPhyloLikelihood::getAlignedLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 260 of file SingleProcessPhyloLikelihood.h.

References likCal_.

◆ getAlphabet()

std::shared_ptr<const Alphabet> bpp::SingleProcessPhyloLikelihood::getAlphabet ( ) const

inlineoverridevirtual

Get the alphabet associated to the dataset.

Returns: the alphabet associated to the dataset.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 134 of file SingleProcessPhyloLikelihood.h.

References bpp::StateMapInterface::getAlphabet(), likelihoodCalculationSingleProcess(), and bpp::LikelihoodCalculationSingleProcess::stateMap().

◆ getBranchLengthParameters()

ParameterList bpp::SingleProcessPhyloLikelihood::getBranchLengthParameters ( ) const

inlineoverridevirtual

Get the independent branch lengths parameters.

Returns: A ParameterList with all branch lengths.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 205 of file SingleProcessPhyloLikelihood.h.

References bpp::SubstitutionProcessInterface::getBranchLengthParameters(), likelihoodCalculationSingleProcess(), and bpp::LikelihoodCalculationSingleProcess::substitutionProcess().

◆ getClassWithMaxPostProbPerSite()

vector< size_t > SingleProcessPhyloLikelihood::getClassWithMaxPostProbPerSite ( ) const

Definition at line 82 of file SingleProcessPhyloLikelihood.cpp.

◆ getData()

std::shared_ptr<const AlignmentDataInterface> bpp::SingleProcessPhyloLikelihood::getData ( ) const

inlineoverridevirtual

return a pointer to the original data.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 112 of file SingleProcessPhyloLikelihood.h.

References bpp::LikelihoodCalculationSingleProcess::getData(), and likelihoodCalculationSingleProcess().

◆ getDerivableParameters()

ParameterList bpp::SingleProcessPhyloLikelihood::getDerivableParameters ( ) const

inlineoverridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 195 of file SingleProcessPhyloLikelihood.h.

References bpp::SubstitutionProcessInterface::getBranchLengthParameters(), likelihoodCalculationSingleProcess(), and bpp::LikelihoodCalculationSingleProcess::substitutionProcess().

◆ getFirstOrderDerivative()

double bpp::AbstractPhyloLikelihood::getFirstOrderDerivative ( const std::string & variable ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 131 of file AbstractPhyloLikelihood.h.

References bpp::convert(), and bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode().

◆ getFirstOrderDerivativeVector()

ValueRef<RowLik> bpp::SingleProcessPhyloLikelihood::getFirstOrderDerivativeVector ( const std::string & variable ) const

inline

Definition at line 277 of file SingleProcessPhyloLikelihood.h.

References firstOrderDerivativeVector().

◆ getLikelihoodCalculation()

std::shared_ptr<LikelihoodCalculation> bpp::SingleProcessPhyloLikelihood::getLikelihoodCalculation ( ) const

inlineoverridevirtual

Returns: A shared pointer toward the LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 250 of file SingleProcessPhyloLikelihood.h.

References likCal_.

◆ getLikelihoodCalculationSingleProcess()

std::shared_ptr<LikelihoodCalculationSingleProcess> bpp::SingleProcessPhyloLikelihood::getLikelihoodCalculationSingleProcess ( ) const

inline

Definition at line 270 of file SingleProcessPhyloLikelihood.h.

References likCal_.

Referenced by firstOrderDerivativeVector().

◆ getLikelihoodForASite() [1/2]

DataLik bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite ( size_t site ) const

inlinevirtualinherited

Get the likelihood for a site (on uncompressed data)

Parameters

site	The site index to analyse.

Returns: The likelihood for site site.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 143 of file AlignedPhyloLikelihood.h.

References bpp::AlignedPhyloLikelihoodInterface::alignedLikelihoodCalculation(), and bpp::AlignedLikelihoodCalculation::getLikelihoodForASite().

◆ getLikelihoodForASite() [2/2]

virtual DataLik bpp::AlignedPhyloLikelihoodInterface::getLikelihoodForASite ( size_t site ) const

pure virtualinherited

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns: The likelihood for site site.

Implemented in bpp::AbstractAlignedPhyloLikelihood.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::getLikelihoodForASiteForAPhyloLikelihood().

◆ getLikelihoodNode() [1/2]

virtual ValueRef<DataLik> bpp::PhyloLikelihoodInterface::getLikelihoodNode ( ) const

pure virtualinherited

Returns: the LikDF node where the Likelihood is computed.

Implemented in bpp::AbstractPhyloLikelihood.

◆ getLikelihoodNode() [2/2]

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::getLikelihoodNode ( ) const

inlineoverridevirtualinherited

Returns: the LikDF node where the Likelihood is computed.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 100 of file AbstractPhyloLikelihood.h.

References bpp::PhyloLikelihoodInterface::getLikelihoodCalculation().

Referenced by bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), and bpp::AbstractPhyloLikelihood::getValue().

◆ getLikelihoodPerSite() [1/2]

VDataLik bpp::AbstractAlignedPhyloLikelihood::getLikelihoodPerSite ( ) const

inlinevirtualinherited

Get the likelihood for each site.

Returns: A vector with all site likelihoods.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 167 of file AlignedPhyloLikelihood.h.

References bpp::AlignedPhyloLikelihoodInterface::getAlignedLikelihoodCalculation().

Referenced by bpp::MixtureProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), and bpp::OneProcessSequencePhyloLikelihood::getPosteriorRatePerSite().

◆ getLikelihoodPerSite() [2/2]

virtual VDataLik bpp::AlignedPhyloLikelihoodInterface::getLikelihoodPerSite ( ) const

pure virtualinherited

Get the likelihood for each site.

Returns: A vector with all site likelihoods.

Implemented in bpp::AbstractAlignedPhyloLikelihood.

◆ getLikelihoodPerSitePerClass()

VVDataLik SingleProcessPhyloLikelihood::getLikelihoodPerSitePerClass ( ) const

Definition at line 72 of file SingleProcessPhyloLikelihood.cpp.

References bpp::copyEigenToBpp().

◆ getLogLikelihood()

double bpp::PhyloLikelihoodInterface::getLogLikelihood ( ) const

inlineinherited

Get the logarithm of the likelihood for the whole dataset.

Returns: The logarithm of the likelihood of the dataset.

Definition at line 66 of file PhyloLikelihood.h.

References bpp::SecondOrderDerivable::getValue().

◆ getLogLikelihoodForASite() [1/2]

double bpp::AbstractAlignedPhyloLikelihood::getLogLikelihoodForASite ( size_t site ) const

inlinevirtualinherited

Get the log likelihood for a site, and its derivatives.

Parameters

site	The site index to analyse.

Returns: The (D)log likelihood for site site.

Implements bpp::AlignedPhyloLikelihoodInterface.

Definition at line 154 of file AlignedPhyloLikelihood.h.

References bpp::convert(), and bpp::AlignedPhyloLikelihoodInterface::getAlignedLikelihoodCalculation().

◆ getLogLikelihoodForASite() [2/2]

virtual double bpp::AlignedPhyloLikelihoodInterface::getLogLikelihoodForASite ( size_t site ) const

pure virtualinherited

Get the log likelihood for a site, and its derivatives.

Parameters

site	The site index to analyse.

Returns: The (D)log likelihood for site site.

Implemented in bpp::AbstractAlignedPhyloLikelihood.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::getLogLikelihoodForASiteForAPhyloLikelihood(), and bpp::PhylogeneticsApplicationTools::printAnalysisInformation().

◆ getNData()

size_t bpp::AbstractSingleDataPhyloLikelihood::getNData ( ) const

inlinevirtualinherited

Get the number of dataset concerned.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 126 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nData_.

◆ getNonDerivableParameters()

ParameterList bpp::SingleProcessPhyloLikelihood::getNonDerivableParameters ( ) const

inlineoverridevirtual

Implements bpp::PhyloLikelihoodInterface.

Definition at line 190 of file SingleProcessPhyloLikelihood.h.

References bpp::SubstitutionProcessInterface::getNonDerivableParameters(), likelihoodCalculationSingleProcess(), and bpp::LikelihoodCalculationSingleProcess::substitutionProcess().

◆ getNumberOfClasses()

size_t bpp::SingleProcessPhyloLikelihood::getNumberOfClasses ( ) const

inline

Get the number of model classes.

Definition at line 131 of file SingleProcessPhyloLikelihood.h.

References bpp::SubstitutionProcessInterface::getNumberOfClasses(), and substitutionProcess().

◆ getNumberOfDistinctSites()

size_t bpp::SingleProcessPhyloLikelihood::getNumberOfDistinctSites ( ) const

inline

Definition at line 122 of file SingleProcessPhyloLikelihood.h.

References bpp::LikelihoodCalculationSingleProcess::getNumberOfDistinctSites(), and likelihoodCalculationSingleProcess().

◆ getNumberOfSites()

size_t bpp::SingleProcessPhyloLikelihood::getNumberOfSites ( ) const

inlineoverridevirtual

Get the number of sites in the dataset.

Returns: the number of sites in the dataset.

Reimplemented from bpp::AbstractAlignedPhyloLikelihood.

Definition at line 117 of file SingleProcessPhyloLikelihood.h.

References bpp::LikelihoodCalculationSingleProcess::getNumberOfSites(), and likelihoodCalculationSingleProcess().

◆ getNumberOfStates()

size_t bpp::AbstractSingleDataPhyloLikelihood::getNumberOfStates ( ) const

inlinevirtualinherited

Get the number the states.

Implements bpp::SingleDataPhyloLikelihoodInterface.

Definition at line 136 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nbStates_.

◆ getPosteriorProbabilitiesForSitePerClass()

Vdouble SingleProcessPhyloLikelihood::getPosteriorProbabilitiesForSitePerClass ( size_t pos ) const

Definition at line 12 of file SingleProcessPhyloLikelihood.cpp.

References bpp::convert(), and bpp::VectorTools::sum().

◆ getPosteriorProbabilitiesPerSitePerClass()

VVdouble SingleProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerClass ( ) const

Get the posterior probabilities of each class, for each site.

Returns: A 2D-vector (Sites X Class) of all posterior probabilities.

Definition at line 38 of file SingleProcessPhyloLikelihood.cpp.

References bpp::copyBppToEigen(), bpp::copyEigenToBpp(), bpp::numeric::cwise(), and bpp::ExtendedFloatEigen< R, C, EigenType >::sum().

◆ getPosteriorRatePerSite()

Vdouble SingleProcessPhyloLikelihood::getPosteriorRatePerSite ( ) const

Definition at line 96 of file SingleProcessPhyloLikelihood.cpp.

References bpp::convert().

◆ getPosteriorStateFrequencies()

Vdouble SingleProcessPhyloLikelihood::getPosteriorStateFrequencies ( uint nodeId )

Definition at line 119 of file SingleProcessPhyloLikelihood.cpp.

References bpp::copyEigenToBpp().

◆ getRateDistributionParameters()

ParameterList bpp::SingleProcessPhyloLikelihood::getRateDistributionParameters ( ) const

inlineoverridevirtual

Get the independent parameters associated to the rate distribution(s).

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 225 of file SingleProcessPhyloLikelihood.h.

References bpp::SubstitutionProcessInterface::getRateDistributionParameters(), likelihoodCalculationSingleProcess(), and bpp::LikelihoodCalculationSingleProcess::substitutionProcess().

◆ getRootFrequenciesParameters()

ParameterList bpp::SingleProcessPhyloLikelihood::getRootFrequenciesParameters ( ) const

inlineoverridevirtual

Get the independent parameters associated to the root frequencies(s).

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 236 of file SingleProcessPhyloLikelihood.h.

References bpp::SubstitutionProcessInterface::getRootFrequenciesParameters(), likelihoodCalculationSingleProcess(), and bpp::LikelihoodCalculationSingleProcess::substitutionProcess().

◆ getSecondOrderDerivative() [1/2]

double bpp::AbstractPhyloLikelihood::getSecondOrderDerivative ( const std::string & variable ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 155 of file AbstractPhyloLikelihood.h.

◆ getSecondOrderDerivative() [2/2]

double bpp::AbstractPhyloLikelihood::getSecondOrderDerivative	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 160 of file AbstractPhyloLikelihood.h.

References bpp::convert(), and bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode().

◆ getSecondOrderDerivativeVector() [1/2]

ValueRef<RowLik> bpp::SingleProcessPhyloLikelihood::getSecondOrderDerivativeVector ( const std::string & variable ) const

inline

Definition at line 297 of file SingleProcessPhyloLikelihood.h.

◆ getSecondOrderDerivativeVector() [2/2]

ValueRef<RowLik> bpp::SingleProcessPhyloLikelihood::getSecondOrderDerivativeVector	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inline

Definition at line 302 of file SingleProcessPhyloLikelihood.h.

References secondOrderDerivativeVector().

◆ getShrunkData()

std::shared_ptr<const AlignmentDataInterface> bpp::SingleProcessPhyloLikelihood::getShrunkData ( ) const

inline

return a pointer to the compressed data.

Definition at line 103 of file SingleProcessPhyloLikelihood.h.

References bpp::LikelihoodCalculationSingleProcess::getShrunkData(), and likelihoodCalculationSingleProcess().

◆ getSubstitutionModelParameters()

ParameterList bpp::SingleProcessPhyloLikelihood::getSubstitutionModelParameters ( ) const

inlineoverridevirtual

Get the independent parameters associated to substitution model(s).

Returns: A ParameterList.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 215 of file SingleProcessPhyloLikelihood.h.

References bpp::SubstitutionProcessInterface::getSubstitutionModelParameters(), likelihoodCalculationSingleProcess(), and bpp::LikelihoodCalculationSingleProcess::substitutionProcess().

◆ getSubstitutionProcess()

std::shared_ptr<const SubstitutionProcessInterface> bpp::SingleProcessPhyloLikelihood::getSubstitutionProcess ( ) const

inline

Return a smarter pointer to the SubstitutionProcess used to build the phylolikelihood.

Warning; the process parameter values may not be up to date with some of the LikelihoodCalculationSingleProcess

Definition at line 170 of file SingleProcessPhyloLikelihood.h.

References bpp::LikelihoodCalculationSingleProcess::getSubstitutionProcess(), and likelihoodCalculationSingleProcess().

◆ getSubstitutionProcessNumber()

size_t bpp::SingleProcessPhyloLikelihood::getSubstitutionProcessNumber ( ) const

inline

Definition at line 175 of file SingleProcessPhyloLikelihood.h.

References nProc_.

◆ getValue()

double bpp::AbstractPhyloLikelihood::getValue ( ) const

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 124 of file AbstractPhyloLikelihood.h.

References bpp::convert(), bpp::AbstractPhyloLikelihood::getLikelihoodNode(), and bpp::AbstractPhyloLikelihood::minusLogLik_.

◆ isInitialized()

bool bpp::SingleProcessPhyloLikelihood::isInitialized ( ) const

inlineoverridevirtual

Returns: 'true' is the likelihood function has been initialized.

Reimplemented from bpp::AbstractPhyloLikelihood.

Definition at line 180 of file SingleProcessPhyloLikelihood.h.

References bpp::LikelihoodCalculation::isInitialized(), and likelihoodCalculationSingleProcess().

◆ likelihoodCalculation()

LikelihoodCalculation& bpp::SingleProcessPhyloLikelihood::likelihoodCalculation ( ) const

inlineoverridevirtual

Returns: The LikelihoodCalculation.

Implements bpp::PhyloLikelihoodInterface.

Definition at line 245 of file SingleProcessPhyloLikelihood.h.

References likCal_.

◆ likelihoodCalculationSingleProcess()

LikelihoodCalculationSingleProcess& bpp::SingleProcessPhyloLikelihood::likelihoodCalculationSingleProcess ( ) const

inline

Definition at line 265 of file SingleProcessPhyloLikelihood.h.

References likCal_.

Referenced by getAlphabet(), getBranchLengthParameters(), getData(), getDerivableParameters(), getNonDerivableParameters(), getNumberOfDistinctSites(), getNumberOfSites(), getRateDistributionParameters(), getRootFrequenciesParameters(), getShrunkData(), getSubstitutionModelParameters(), getSubstitutionProcess(), isInitialized(), setData(), substitutionProcess(), and tree().

◆ secondOrderDerivativeNode()

ValueRef<DataLik> bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inlineinherited

Definition at line 168 of file AbstractPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), and bpp::AbstractPhyloLikelihood::secondOrderDerivativeNodes_.

Referenced by bpp::AbstractPhyloLikelihood::getSecondOrderDerivative().

◆ secondOrderDerivativeVector()

ValueRef<RowLik> bpp::SingleProcessPhyloLikelihood::secondOrderDerivativeVector	(	const std::string &	variable1,
		const std::string &	variable2
	)		const

inline

Definition at line 308 of file SingleProcessPhyloLikelihood.h.

References bpp::AbstractPhyloLikelihood::accessVariableNode(), bpp::AbstractPhyloLikelihood::context_, firstOrderDerivativeVector(), and secondOrderDerivativeVectors_.

Referenced by getSecondOrderDerivativeVector().

◆ setData()

void bpp::SingleProcessPhyloLikelihood::setData	(	std::shared_ptr< const AlignmentDataInterface >	sites,
		size_t	nData = `0`
	)

inlineoverridevirtual

Set the dataset for which the likelihood must be evaluated.

Parameters

sites	The data set to use.
nData	the number of the data

Reimplemented from bpp::AbstractSingleDataPhyloLikelihood.

Definition at line 93 of file SingleProcessPhyloLikelihood.h.

References likelihoodCalculationSingleProcess(), bpp::LikelihoodCalculationSingleProcess::setData(), and bpp::AbstractSingleDataPhyloLikelihood::setData().

◆ setNData()

void bpp::AbstractSingleDataPhyloLikelihood::setNData ( size_t nData )

inlineinherited

Definition at line 131 of file SingleDataPhyloLikelihood.h.

References bpp::AbstractSingleDataPhyloLikelihood::nData_.

◆ setNumberOfSites()

void bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites ( size_t nbSites )

inlineprotectedinherited

Definition at line 173 of file AlignedPhyloLikelihood.h.

References bpp::AbstractAlignedPhyloLikelihood::nbSites_.

Referenced by bpp::AbstractAlignedPhyloLikelihoodSet::AbstractAlignedPhyloLikelihoodSet(), bpp::AbstractAlignedPhyloLikelihoodSet::addPhyloLikelihood(), and bpp::AbstractSingleDataPhyloLikelihood::setData().

◆ setParameters()

void bpp::AbstractPhyloLikelihood::setParameters ( const ParameterList & parameters )

inlineoverridevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 95 of file AbstractPhyloLikelihood.h.

References bpp::SecondOrderDerivable::setParametersValues().

◆ shareParameters()

void bpp::AbstractPhyloLikelihood::shareParameters ( const ParameterList & variableNodes )

inlineinherited

Share Parameters, that are DF_parameters.

Definition at line 90 of file AbstractPhyloLikelihood.h.

References bpp::SecondOrderDerivable::getParameters_(), and bpp::ParameterList::shareParameters().

Referenced by bpp::AbstractPhyloLikelihood::AbstractPhyloLikelihood(), and bpp::AbstractPhyloLikelihood::operator=().

◆ substitutionProcess()

const SubstitutionProcessInterface& bpp::SingleProcessPhyloLikelihood::substitutionProcess ( ) const

inline

Return the ref to the SubstitutionProcess used to build the phylolikelihood.

Warning; the process parameter values may not be up to date with some of the LikelihoodCalculationSingleProcess

Definition at line 158 of file SingleProcessPhyloLikelihood.h.

References likelihoodCalculationSingleProcess(), and bpp::LikelihoodCalculationSingleProcess::substitutionProcess().

Referenced by getNumberOfClasses().

◆ tree()

std::shared_ptr<const ParametrizablePhyloTree> bpp::SingleProcessPhyloLikelihood::tree ( ) const

inline

Definition at line 146 of file SingleProcessPhyloLikelihood.h.

References bpp::SubstitutionProcessInterface::getParametrizablePhyloTree(), likelihoodCalculationSingleProcess(), and bpp::LikelihoodCalculationSingleProcess::substitutionProcess().

Member Data Documentation

◆ context_

Context& bpp::AbstractPhyloLikelihood::context_

protectedinherited

Definition at line 34 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihoodSet::addPhyloLikelihood(), bpp::AbstractPhyloLikelihood::context(), bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::firstOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::firstOrderDerivativeVector(), firstOrderDerivativeVector(), bpp::PhyloLikelihoodFormula::makeLikelihoodsFromOperator(), bpp::AbstractPhyloLikelihood::operator=(), bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode(), bpp::OnABranchPhyloLikelihood::secondOrderDerivativeVector(), bpp::OneProcessSequencePhyloLikelihood::secondOrderDerivativeVector(), and secondOrderDerivativeVector().

◆ firstOrderDerivativeNodes_

std::unordered_map<std::string, ValueRef<DataLik> > bpp::AbstractPhyloLikelihood::firstOrderDerivativeNodes_

mutableprotectedinherited

For Dataflow computing.

Definition at line 44 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::firstOrderDerivativeNode().

◆ firstOrderDerivativeVectors_

std::unordered_map<std::string, ValueRef<RowLik> > bpp::SingleProcessPhyloLikelihood::firstOrderDerivativeVectors_

mutableprotected

For Dataflow computing.

Definition at line 45 of file SingleProcessPhyloLikelihood.h.

Referenced by firstOrderDerivativeVector().

◆ likCal_

std::shared_ptr<LikelihoodCalculationSingleProcess> bpp::SingleProcessPhyloLikelihood::likCal_

mutableprotected

Definition at line 35 of file SingleProcessPhyloLikelihood.h.

Referenced by alignedLikelihoodCalculation(), getAlignedLikelihoodCalculation(), getLikelihoodCalculation(), getLikelihoodCalculationSingleProcess(), likelihoodCalculation(), likelihoodCalculationSingleProcess(), and SingleProcessPhyloLikelihood().

◆ minusLogLik_

DataLik bpp::AbstractPhyloLikelihood::minusLogLik_

mutableprotectedinherited

the value

Definition at line 39 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::getValue(), and bpp::AbstractPhyloLikelihood::operator=().

◆ nbSites_

size_t bpp::AbstractAlignedPhyloLikelihood::nbSites_

protectedinherited

Definition at line 111 of file AlignedPhyloLikelihood.h.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), bpp::AbstractAlignedPhyloLikelihood::getNumberOfSites(), bpp::MixtureProcessPhyloLikelihood::getPosteriorProbabilitiesPerSitePerProcess(), bpp::AbstractAlignedPhyloLikelihood::operator=(), and bpp::AbstractAlignedPhyloLikelihood::setNumberOfSites().

◆ nbStates_

size_t bpp::AbstractSingleDataPhyloLikelihood::nbStates_

protectedinherited

Definition at line 87 of file SingleDataPhyloLikelihood.h.

Referenced by bpp::AbstractSingleDataPhyloLikelihood::getNumberOfStates(), bpp::OneProcessSequencePhyloLikelihood::getPosteriorStateFrequencies(), bpp::AbstractSingleDataPhyloLikelihood::operator=(), and bpp::AbstractSingleDataPhyloLikelihood::setData().

◆ nData_

size_t bpp::AbstractSingleDataPhyloLikelihood::nData_

protectedinherited

Number of the concerned data.

Definition at line 92 of file SingleDataPhyloLikelihood.h.

Referenced by bpp::AbstractSingleDataPhyloLikelihood::getNData(), bpp::AbstractSingleDataPhyloLikelihood::operator=(), bpp::AbstractSingleDataPhyloLikelihood::setData(), and bpp::AbstractSingleDataPhyloLikelihood::setNData().

◆ nProc_

size_t bpp::SingleProcessPhyloLikelihood::nProc_

protected

the Substitution Process number

Definition at line 40 of file SingleProcessPhyloLikelihood.h.

Referenced by getSubstitutionProcessNumber().

◆ secondOrderDerivativeNodes_

std::unordered_map<std::pair<std::string, std::string>, ValueRef<DataLik>, StringPairHash> bpp::AbstractPhyloLikelihood::secondOrderDerivativeNodes_

mutableprotectedinherited

Definition at line 48 of file AbstractPhyloLikelihood.h.

Referenced by bpp::AbstractPhyloLikelihood::secondOrderDerivativeNode().

◆ secondOrderDerivativeVectors_

std::unordered_map<std::pair<std::string, std::string>, ValueRef<RowLik>, StringPairHash> bpp::SingleProcessPhyloLikelihood::secondOrderDerivativeVectors_

mutableprotected

Definition at line 49 of file SingleProcessPhyloLikelihood.h.

Referenced by secondOrderDerivativeVector().

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

Bpp/Phyl/Likelihood/PhyloLikelihoods/SingleProcessPhyloLikelihood.h
Bpp/Phyl/Likelihood/PhyloLikelihoods/SingleProcessPhyloLikelihood.cpp

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SingleProcessPhyloLikelihood() [1/2]

◆ SingleProcessPhyloLikelihood() [2/2]

Member Function Documentation

◆ accessVariableNode() [1/2]

◆ accessVariableNode() [2/2]

◆ alignedLikelihoodCalculation()

◆ clone()

◆ context() [1/4]

◆ context() [2/4]

◆ context() [3/4]

◆ context() [4/4]

◆ enableFirstOrderDerivatives() [1/2]

◆ enableFirstOrderDerivatives() [2/2]

◆ enableSecondOrderDerivatives() [1/2]

◆ enableSecondOrderDerivatives() [2/2]

◆ firstOrderDerivativeNode()

◆ firstOrderDerivativeVector()

◆ getAlignedLikelihoodCalculation()

◆ getAlphabet()

◆ getBranchLengthParameters()

◆ getClassWithMaxPostProbPerSite()

◆ getData()

◆ getDerivableParameters()

◆ getFirstOrderDerivative()

◆ getFirstOrderDerivativeVector()

◆ getLikelihoodCalculation()

◆ getLikelihoodCalculationSingleProcess()

◆ getLikelihoodForASite() [1/2]

◆ getLikelihoodForASite() [2/2]

◆ getLikelihoodNode() [1/2]

◆ getLikelihoodNode() [2/2]

◆ getLikelihoodPerSite() [1/2]

◆ getLikelihoodPerSite() [2/2]

◆ getLikelihoodPerSitePerClass()

◆ getLogLikelihood()

◆ getLogLikelihoodForASite() [1/2]

◆ getLogLikelihoodForASite() [2/2]

◆ getNData()

◆ getNonDerivableParameters()

◆ getNumberOfClasses()

◆ getNumberOfDistinctSites()

◆ getNumberOfSites()

◆ getNumberOfStates()

◆ getPosteriorProbabilitiesForSitePerClass()

◆ getPosteriorProbabilitiesPerSitePerClass()

◆ getPosteriorRatePerSite()

◆ getPosteriorStateFrequencies()

◆ getRateDistributionParameters()

◆ getRootFrequenciesParameters()

◆ getSecondOrderDerivative() [1/2]

◆ getSecondOrderDerivative() [2/2]

◆ getSecondOrderDerivativeVector() [1/2]

◆ getSecondOrderDerivativeVector() [2/2]

◆ getShrunkData()

◆ getSubstitutionModelParameters()

◆ getSubstitutionProcess()

◆ getSubstitutionProcessNumber()

◆ getValue()

◆ isInitialized()

◆ likelihoodCalculation()

◆ likelihoodCalculationSingleProcess()

◆ secondOrderDerivativeNode()

◆ secondOrderDerivativeVector()

◆ setData()

◆ setNData()

◆ setNumberOfSites()

◆ setParameters()

◆ shareParameters()

◆ substitutionProcess()

◆ tree()

Member Data Documentation

◆ context_

◆ firstOrderDerivativeNodes_