A simple implementation of hidden Markov models recursion, in DataFlow implementation. More...

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

Inheritance diagram for bpp::HmmLikelihood_DF:

Collaboration diagram for bpp::HmmLikelihood_DF:

Public Member Functions
	HmmLikelihood_DF (Context &context, std::shared_ptr< HmmStateAlphabet > hiddenAlphabet, std::shared_ptr< HmmTransitionMatrix > transitionMatrix, std::shared_ptr< HmmPhyloEmissionProbabilities > emissionProbabilities, const std::string &prefix="")
	Build a new HmmLikelihood_DF object. More...

	HmmLikelihood_DF (const HmmLikelihood_DF &lik)

virtual	~HmmLikelihood_DF ()

HmmLikelihood_DF *	clone () const

void	makeLikelihoods ()

const HmmStateAlphabet &	hmmStateAlphabet () const

HmmStateAlphabet &	hmmStateAlphabet ()

const Eigen::MatrixXd &	getHmmTransitionMatrix () const

const HmmPhyloEmissionProbabilities &	getHmmEmissionProbabilities () const

HmmPhyloEmissionProbabilities &	getHmmEmissionProbabilities ()

void	setParameters (const ParameterList &pl)

void	setNamespace (const std::string &nameSpace)

const Eigen::MatrixXd &	getHiddenStatesPosteriorProbabilities () const

Eigen::VectorXd	getHiddenStatesPosteriorProbabilitiesForASite (size_t site) const

DataLik	getLikelihoodForASite (size_t site) const

SiteLikelihoodsRef	getSiteLikelihoods (bool shrunk=false)

void	setSiteLikelihoods (SiteLikelihoodsRef ll, bool shrunk=false)

DataLik	getLikelihoodForASite (size_t pos, bool shrunk=false)

DataLik	getLogLikelihoodForASite (size_t pos, bool shrunk=false)

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

void	cleanAllLikelihoods ()

ValueRef< DataLik >	getLikelihoodNode ()

virtual bool	isInitialized () const

const Context &	getContext () const

void	setLikelihoodNode (ValueRef< DataLik > ll)

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

const ParameterList &	getIndependentParameters () const

size_t	getNumberOfIndependentParameters () const

void	aliasParameters (const std::string &p1, const std::string &p2)

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

void	unaliasParameters (const std::string &p1, const std::string &p2)

ParameterList	getAliasedParameters (const ParameterList &pl) const

ParameterList	getFromParameters (const ParameterList &pl) const

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

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

std::string	getNamespace () const override

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

virtual void	fireParameterChanged (const ParameterList &parameters)

Protected Member Functions
Context &	getContext_ ()

ValueRef< DataLik >	getLikelihoodNode_ ()

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

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

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_ ()

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

Protected Attributes
std::shared_ptr< HmmStateAlphabet >	hiddenAlphabet_
	The alphabet describing the hidden states. More...

std::shared_ptr< HmmPhyloEmissionProbabilities >	emissionProbabilities_

std::shared_ptr< ConfiguredTransitionMatrix >	matrix_

ValueRef< Eigen::VectorXd >	hmmEq_

ValueRef< Eigen::MatrixXd >	hmmTrans_

ValueRef< MatrixLik >	hmmEmis_

ValueRef< RowLik >	forwardLik_

ValueRef< Eigen::MatrixXd >	backwardLik_

ValueRef< Eigen::MatrixXd >	hiddenPostProb_

Eigen::Index	nbStates_

Eigen::Index	nbSites_

SiteLikelihoodsRef	siteLikelihoods_

SiteLikelihoodsRef	patternedSiteLikelihoods_

ValueRef< DataLik >	likelihood_

Private Attributes
Context &	context_

ParameterList	independentParameters_

std::map< std::string, std::shared_ptr< AliasParameterListener > >	aliasListenersRegister_

ParameterList	parameters_

std::string	prefix_

Detailed Description

A simple implementation of hidden Markov models recursion, in DataFlow implementation.

This class builds DF objects linked with HMM computation, and owns a HmmLikelihoodComputation object.

Definition at line 32 of file HmmLikelihood_DF.h.

Constructor & Destructor Documentation

◆ HmmLikelihood_DF() [1/2]

HmmLikelihood_DF::HmmLikelihood_DF	(	Context &	context,
		std::shared_ptr< HmmStateAlphabet >	hiddenAlphabet,
		std::shared_ptr< HmmTransitionMatrix >	transitionMatrix,
		std::shared_ptr< HmmPhyloEmissionProbabilities >	emissionProbabilities,
		const std::string &	prefix = `""`
	)

Build a new HmmLikelihood_DF object.

Warning: the HmmTransitionMatrix and HmmEmissionProbabilities object passed as argument must be non-null and point toward the same HmmStateAlphabet instance.

Definition at line 14 of file HmmLikelihood_DF.cpp.

References bpp::AbstractParameterAliasable::addParameters_(), backwardLik_, context_, bpp::NumericMutable< T >::create(), bpp::ForwardHmmLikelihood_DF::create(), bpp::BackwardHmmLikelihood_DF::create(), bpp::ConfiguredParameter::create(), emissionProbabilities_, forwardLik_, bpp::LikelihoodCalculation::getContext_(), hiddenAlphabet_, hiddenPostProb_, hmmEmis_, hmmEq_, hmmTrans_, matrix_, nbSites_, nbStates_, bpp::LikelihoodCalculation::setLikelihoodNode(), bpp::AlignedLikelihoodCalculation::setSiteLikelihoods(), bpp::ParameterList::shareParameter(), bpp::AbstractParameterAliasable::shareParameters_(), and bpp::ThreePoints.

Referenced by clone().

◆ HmmLikelihood_DF() [2/2]

bpp::HmmLikelihood_DF::HmmLikelihood_DF ( const HmmLikelihood_DF & lik )

inline

Definition at line 126 of file HmmLikelihood_DF.h.

◆ ~HmmLikelihood_DF()

virtual bpp::HmmLikelihood_DF::~HmmLikelihood_DF ( )

inlinevirtual

Definition at line 141 of file HmmLikelihood_DF.h.

Member Function Documentation

◆ cleanAllLikelihoods()

void bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods ( )

inlinevirtualinherited

Reimplemented from bpp::LikelihoodCalculation.

Reimplemented in bpp::LikelihoodCalculationSingleProcess, and bpp::LikelihoodCalculationOnABranch.

Definition at line 235 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::cleanAllLikelihoods(), bpp::Context::erase(), bpp::LikelihoodCalculation::getContext_(), bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_, and bpp::AlignedLikelihoodCalculation::siteLikelihoods_.

Referenced by bpp::LikelihoodCalculationOnABranch::cleanAllLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::cleanAllLikelihoods().

◆ clone()

HmmLikelihood_DF* bpp::HmmLikelihood_DF::clone ( ) const

inlinevirtual

Reimplemented from bpp::AlignedLikelihoodCalculation.

Definition at line 143 of file HmmLikelihood_DF.h.

References HmmLikelihood_DF().

◆ getContext()

const Context& bpp::LikelihoodCalculation::getContext ( ) const

inlineinherited

Definition at line 76 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::context_.

◆ getContext_()

Context& bpp::LikelihoodCalculation::getContext_ ( )

inlineprotectedinherited

Definition at line 110 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::context_.

◆ getHiddenStatesPosteriorProbabilities()

const Eigen::MatrixXd& bpp::HmmLikelihood_DF::getHiddenStatesPosteriorProbabilities ( ) const

inline

Definition at line 171 of file HmmLikelihood_DF.h.

References hiddenPostProb_.

◆ getHiddenStatesPosteriorProbabilitiesForASite()

Eigen::VectorXd bpp::HmmLikelihood_DF::getHiddenStatesPosteriorProbabilitiesForASite ( size_t site ) const

inline

Definition at line 176 of file HmmLikelihood_DF.h.

References hiddenPostProb_.

Referenced by getLikelihoodForASite().

◆ getHmmEmissionProbabilities() [1/2]

HmmPhyloEmissionProbabilities& bpp::HmmLikelihood_DF::getHmmEmissionProbabilities ( )

inline

Definition at line 162 of file HmmLikelihood_DF.h.

References emissionProbabilities_.

◆ getHmmEmissionProbabilities() [2/2]

const HmmPhyloEmissionProbabilities& bpp::HmmLikelihood_DF::getHmmEmissionProbabilities ( ) const

inline

Definition at line 160 of file HmmLikelihood_DF.h.

References emissionProbabilities_.

◆ getHmmTransitionMatrix()

const Eigen::MatrixXd& bpp::HmmLikelihood_DF::getHmmTransitionMatrix ( ) const

inline

Definition at line 158 of file HmmLikelihood_DF.h.

References hmmTrans_.

◆ getLikelihoodForASite() [1/2]

DataLik bpp::AlignedLikelihoodCalculation::getLikelihoodForASite	(	size_t	pos,
		bool	shrunk = `false`
	)

inlineinherited

Definition at line 198 of file LikelihoodCalculation.h.

References bpp::AlignedLikelihoodCalculation::makeLikelihoods(), bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_, and bpp::AlignedLikelihoodCalculation::siteLikelihoods_.

Referenced by bpp::AbstractAlignedPhyloLikelihood::getLikelihoodForASite(), and bpp::AlignedLikelihoodCalculation::getLogLikelihoodForASite().

◆ getLikelihoodForASite() [2/2]

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

inline

Definition at line 182 of file HmmLikelihood_DF.h.

References getHiddenStatesPosteriorProbabilitiesForASite(), and hmmEmis_.

◆ getLikelihoodNode()

ValueRef<DataLik> bpp::LikelihoodCalculation::getLikelihoodNode ( )

inlineinherited

Definition at line 63 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::likelihood_, and bpp::LikelihoodCalculation::makeLikelihoods().

◆ getLikelihoodNode_()

ValueRef<DataLik> bpp::LikelihoodCalculation::getLikelihoodNode_ ( )

inlineprotectedinherited

Definition at line 115 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::likelihood_.

Referenced by bpp::LikelihoodCalculationSingleProcess::getForwardLikelihoodsAtNodeForClass(), and bpp::LikelihoodCalculationSingleProcess::getSiteLikelihoodsTree_().

◆ getLikelihoodPerSite()

VDataLik bpp::AlignedLikelihoodCalculation::getLikelihoodPerSite ( )

inlineinherited

Get the likelihood for each site.

Returns: A vector with all site likelihoods.

Definition at line 221 of file LikelihoodCalculation.h.

References bpp::copyEigenToBpp(), and bpp::AlignedLikelihoodCalculation::getSiteLikelihoods().

◆ getLogLikelihoodForASite()

DataLik bpp::AlignedLikelihoodCalculation::getLogLikelihoodForASite	(	size_t	pos,
		bool	shrunk = `false`
	)

inlineinherited

Definition at line 209 of file LikelihoodCalculation.h.

References bpp::AlignedLikelihoodCalculation::getLikelihoodForASite(), and bpp::log().

◆ getSiteLikelihoods()

SiteLikelihoodsRef bpp::AlignedLikelihoodCalculation::getSiteLikelihoods ( bool shrunk = false )

inlineinherited

Definition at line 165 of file LikelihoodCalculation.h.

References bpp::AlignedLikelihoodCalculation::makeLikelihoods(), bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_, and bpp::AlignedLikelihoodCalculation::siteLikelihoods_.

Referenced by bpp::AlignedPhyloLikelihoodMixture::AlignedPhyloLikelihoodMixture(), and bpp::AlignedLikelihoodCalculation::getLikelihoodPerSite().

◆ hmmStateAlphabet() [1/2]

HmmStateAlphabet& bpp::HmmLikelihood_DF::hmmStateAlphabet ( )

inline

Definition at line 150 of file HmmLikelihood_DF.h.

References hiddenAlphabet_.

◆ hmmStateAlphabet() [2/2]

const HmmStateAlphabet& bpp::HmmLikelihood_DF::hmmStateAlphabet ( ) const

inline

Definition at line 148 of file HmmLikelihood_DF.h.

References hiddenAlphabet_.

◆ isInitialized()

virtual bool bpp::LikelihoodCalculation::isInitialized ( ) const

inlinevirtualinherited

Definition at line 71 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::likelihood_.

Referenced by bpp::SubstitutionMappingTools::computeCounts(), bpp::SubstitutionMappingTools::computeNormalizations(), bpp::RewardMappingTools::computeRewardVectors(), bpp::OnABranchPhyloLikelihood::isInitialized(), bpp::OneProcessSequencePhyloLikelihood::isInitialized(), bpp::SingleProcessPhyloLikelihood::isInitialized(), and bpp::LikelihoodCalculationSingleProcess::setData().

◆ makeLikelihoods()

void bpp::HmmLikelihood_DF::makeLikelihoods ( )

inlinevirtual

Reimplemented from bpp::AlignedLikelihoodCalculation.

Definition at line 145 of file HmmLikelihood_DF.h.

◆ setLikelihoodNode()

void bpp::LikelihoodCalculation::setLikelihoodNode ( ValueRef< DataLik > ll )

inlineinherited

Definition at line 85 of file LikelihoodCalculation.h.

References bpp::LikelihoodCalculation::likelihood_.

Referenced by HmmLikelihood_DF(), bpp::LikelihoodCalculationOnABranch::makeLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_().

◆ setNamespace()

void HmmLikelihood_DF::setNamespace ( const std::string & nameSpace )

virtual

Reimplemented from bpp::AbstractParameterAliasable.

Definition at line 116 of file HmmLikelihood_DF.cpp.

References emissionProbabilities_, hiddenAlphabet_, matrix_, and bpp::AbstractParametrizable::setNamespace().

◆ setParameters()

void bpp::HmmLikelihood_DF::setParameters ( const ParameterList & pl )

inline

Definition at line 164 of file HmmLikelihood_DF.h.

References bpp::AbstractParameterAliasable::setParametersValues().

◆ setSiteLikelihoods()

void bpp::AlignedLikelihoodCalculation::setSiteLikelihoods	(	SiteLikelihoodsRef	ll,
		bool	shrunk = `false`
	)

inlineinherited

Definition at line 184 of file LikelihoodCalculation.h.

References bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_, and bpp::AlignedLikelihoodCalculation::siteLikelihoods_.

Referenced by HmmLikelihood_DF(), bpp::LikelihoodCalculationOnABranch::makeLikelihoods(), and bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_().

Member Data Documentation

◆ backwardLik_

ValueRef<Eigen::MatrixXd> bpp::HmmLikelihood_DF::backwardLik_

protected

DF Backward Likelihoods for sites per state

backwardLik_(i,j) corresponds to Pr(x_{j+1}...x_n | y_j=i)/Pr(x_{j+1}|x_1...x_j) where the x are the observed states, and y the hidden states.

Definition at line 95 of file HmmLikelihood_DF.h.

Referenced by HmmLikelihood_DF().

◆ context_

Context& bpp::HmmLikelihood_DF::context_

private

Definition at line 36 of file HmmLikelihood_DF.h.

Referenced by HmmLikelihood_DF().

◆ emissionProbabilities_

std::shared_ptr<HmmPhyloEmissionProbabilities> bpp::HmmLikelihood_DF::emissionProbabilities_

protected

Definition at line 44 of file HmmLikelihood_DF.h.

Referenced by getHmmEmissionProbabilities(), HmmLikelihood_DF(), and setNamespace().

◆ forwardLik_

ValueRef<RowLik> bpp::HmmLikelihood_DF::forwardLik_

protected

DF Conditional Likelihoods for sites:

Definition at line 84 of file HmmLikelihood_DF.h.

Referenced by HmmLikelihood_DF().

◆ hiddenAlphabet_

std::shared_ptr<HmmStateAlphabet> bpp::HmmLikelihood_DF::hiddenAlphabet_

protected

The alphabet describing the hidden states.

Definition at line 43 of file HmmLikelihood_DF.h.

Referenced by HmmLikelihood_DF(), hmmStateAlphabet(), and setNamespace().

◆ hiddenPostProb_

ValueRef<Eigen::MatrixXd> bpp::HmmLikelihood_DF::hiddenPostProb_

protected

Hidden Posterior Probabilities

hiddenPostProb_(i,j) corresponds to Pr(y_j=i | x_1...x_n) where the x are the observed states, and y the hidden states.

Definition at line 105 of file HmmLikelihood_DF.h.

Referenced by getHiddenStatesPosteriorProbabilities(), getHiddenStatesPosteriorProbabilitiesForASite(), and HmmLikelihood_DF().

◆ hmmEmis_

ValueRef<MatrixLik> bpp::HmmLikelihood_DF::hmmEmis_

protected

DF Matrix from emission likelihoods for computation

Definition at line 77 of file HmmLikelihood_DF.h.

Referenced by getLikelihoodForASite(), and HmmLikelihood_DF().

◆ hmmEq_

ValueRef<Eigen::VectorXd> bpp::HmmLikelihood_DF::hmmEq_

protected

DF equilibrium vector from transitionmatrix for computation

Definition at line 63 of file HmmLikelihood_DF.h.

Referenced by HmmLikelihood_DF().

◆ hmmTrans_

ValueRef<Eigen::MatrixXd> bpp::HmmLikelihood_DF::hmmTrans_

protected

DF Matrix from transitionmatrix for computation

Definition at line 70 of file HmmLikelihood_DF.h.

Referenced by getHmmTransitionMatrix(), and HmmLikelihood_DF().

◆ likelihood_

ValueRef<DataLik> bpp::LikelihoodCalculation::likelihood_

mutableprotectedinherited

Likelihoods

Definition at line 30 of file LikelihoodCalculation.h.

Referenced by bpp::LikelihoodCalculation::cleanAllLikelihoods(), bpp::LikelihoodCalculation::getLikelihoodNode(), bpp::LikelihoodCalculation::getLikelihoodNode_(), bpp::LikelihoodCalculation::isInitialized(), bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_(), and bpp::LikelihoodCalculation::setLikelihoodNode().

◆ matrix_

std::shared_ptr<ConfiguredTransitionMatrix> bpp::HmmLikelihood_DF::matrix_

protected

DF TransitionMatrix

Definition at line 56 of file HmmLikelihood_DF.h.

Referenced by HmmLikelihood_DF(), and setNamespace().

◆ nbSites_

Eigen::Index bpp::HmmLikelihood_DF::nbSites_

protected

Definition at line 107 of file HmmLikelihood_DF.h.

Referenced by HmmLikelihood_DF().

◆ nbStates_

Eigen::Index bpp::HmmLikelihood_DF::nbStates_

protected

Definition at line 107 of file HmmLikelihood_DF.h.

Referenced by HmmLikelihood_DF().

◆ patternedSiteLikelihoods_

SiteLikelihoodsRef bpp::AlignedLikelihoodCalculation::patternedSiteLikelihoods_

mutableprotectedinherited

Definition at line 155 of file LikelihoodCalculation.h.

Referenced by bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods(), bpp::AlignedLikelihoodCalculation::getLikelihoodForASite(), bpp::AlignedLikelihoodCalculation::getSiteLikelihoods(), bpp::LikelihoodCalculationOnABranch::makeLikelihoods(), bpp::LikelihoodCalculationSingleProcess::makeLikelihoodsAtRoot_(), and bpp::AlignedLikelihoodCalculation::setSiteLikelihoods().

◆ siteLikelihoods_

SiteLikelihoodsRef bpp::AlignedLikelihoodCalculation::siteLikelihoods_

mutableprotectedinherited

Site Likelihoods

Definition at line 149 of file LikelihoodCalculation.h.

Referenced by bpp::AlignedLikelihoodCalculation::cleanAllLikelihoods(), bpp::AlignedLikelihoodCalculation::getLikelihoodForASite(), bpp::AlignedLikelihoodCalculation::getSiteLikelihoods(), and bpp::AlignedLikelihoodCalculation::setSiteLikelihoods().

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

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ HmmLikelihood_DF() [1/2]

◆ HmmLikelihood_DF() [2/2]

◆ ~HmmLikelihood_DF()

Member Function Documentation

◆ cleanAllLikelihoods()

◆ clone()

◆ getContext()

◆ getContext_()

◆ getHiddenStatesPosteriorProbabilities()

◆ getHiddenStatesPosteriorProbabilitiesForASite()

◆ getHmmEmissionProbabilities() [1/2]

◆ getHmmEmissionProbabilities() [2/2]

◆ getHmmTransitionMatrix()

◆ getLikelihoodForASite() [1/2]

◆ getLikelihoodForASite() [2/2]

◆ getLikelihoodNode()

◆ getLikelihoodNode_()

◆ getLikelihoodPerSite()

◆ getLogLikelihoodForASite()

◆ getSiteLikelihoods()

◆ hmmStateAlphabet() [1/2]

◆ hmmStateAlphabet() [2/2]

◆ isInitialized()

◆ makeLikelihoods()

◆ setLikelihoodNode()

◆ setNamespace()

◆ setParameters()

◆ setSiteLikelihoods()

Member Data Documentation

◆ backwardLik_

◆ context_

◆ emissionProbabilities_

◆ forwardLik_

◆ hiddenAlphabet_

◆ hiddenPostProb_

◆ hmmEmis_

◆ hmmEq_

◆ hmmTrans_

◆ likelihood_

◆ matrix_

◆ nbSites_

◆ nbStates_

◆ patternedSiteLikelihoods_

◆ siteLikelihoods_