bpp-phyl3: bpp::RHomogeneousMixedTreeLikelihood Class Reference

Definition at line 89 of file RHomogeneousMixedTreeLikelihood.h.

References bpp::RHomogeneousTreeLikelihood::RHomogeneousMixedTreeLikelihood.

◆ computeAllTransitionProbabilities()

void RHomogeneousMixedTreeLikelihood::computeAllTransitionProbabilities ( )

protectedvirtual

This method is used by fireParameterChanged method.

Reimplemented from bpp::AbstractHomogeneousTreeLikelihood.

Definition at line 285 of file RHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

◆ computeDownSubtreeD2Likelihood()

void RHomogeneousMixedTreeLikelihood::computeDownSubtreeD2Likelihood ( const Node * node )

protectedvirtual

Reimplemented from bpp::RHomogeneousTreeLikelihood.

Definition at line 276 of file RHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

◆ computeDownSubtreeDLikelihood()

void RHomogeneousMixedTreeLikelihood::computeDownSubtreeDLikelihood ( const Node * node )

protectedvirtual

Reimplemented from bpp::RHomogeneousTreeLikelihood.

Definition at line 268 of file RHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

◆ computeSubtreeLikelihood()

void RHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood ( const Node * node )

protectedvirtual

Compute the likelihood for a subtree defined by the Tree::Node node.

Parameters

node	The root of the subtree.

Reimplemented from bpp::RHomogeneousTreeLikelihood.

Definition at line 260 of file RHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

◆ computeTransitionProbabilitiesForNode()

void RHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode ( const Node * node )

protectedvirtual

This method is used by fireParameterChanged method.

Reimplemented from bpp::AbstractHomogeneousTreeLikelihood.

Definition at line 294 of file RHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

◆ computeTreeD2Likelihood()

void RHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood ( const std::string & variable )

virtual

Reimplemented from bpp::RHomogeneousTreeLikelihood.

Definition at line 252 of file RHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

◆ computeTreeDLikelihood()

void RHomogeneousMixedTreeLikelihood::computeTreeDLikelihood ( const std::string & variable )

virtual

Reimplemented from bpp::RHomogeneousTreeLikelihood.

Definition at line 228 of file RHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

◆ computeTreeLikelihood()

void RHomogeneousMixedTreeLikelihood::computeTreeLikelihood ( )

Definition at line 161 of file RHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

◆ data() [1/2]

const AlignmentDataInterface& bpp::AbstractTreeLikelihood::data ( ) const

inlinevirtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns: The site container where the sequences are stored.

Definition at line 262 of file AbstractTreeLikelihood.h.

◆ data() [2/2]

virtual const AlignmentDataInterface& bpp::TreeLikelihoodInterface::data ( ) const

pure virtualinherited

Get the dataset for which the likelihood must be evaluated.

Returns: The site container where the sequences are stored.

Implemented in bpp::AbstractTreeLikelihood.

◆ displayLikelihood()

void RHomogeneousMixedTreeLikelihood::displayLikelihood ( const Node * node )

protectedvirtual

This method is mainly for debugging purpose.

Parameters

node	The node at which likelihood values must be displayed.

Reimplemented from bpp::RHomogeneousTreeLikelihood.

Definition at line 303 of file RHomogeneousMixedTreeLikelihood.cpp.

References treeLikelihoodsContainer_.

◆ displayLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray ( const VVVdouble & likelihoodArray )

staticinherited

Print the likelihood array to terminal (debugging tool).

Parameters

likelihoodArray the likelihood array.

Definition at line 251 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

Referenced by bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), and bpp::RNonHomogeneousTreeLikelihood::displayLikelihood().

◆ enableDerivatives() [1/2]

void bpp::AbstractTreeLikelihood::enableDerivatives ( bool yn )

inlinevirtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

References bpp::ParameterList::addParameters(), bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::RHomogeneousTreeLikelihood::getLogLikelihood(), bpp::AbstractParametrizable::getParameters(), bpp::ParameterList::includeParameters(), bpp::RHomogeneousTreeLikelihood::minusLogLik_, bpp::AbstractHomogeneousTreeLikelihood::model_, probas_, and treeLikelihoodsContainer_.

Definition at line 270 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood().

◆ enableDerivatives() [2/2]

virtual void bpp::TreeLikelihoodInterface::enableDerivatives ( bool yn )

pure virtualinherited

Tell if derivatives must be computed.

This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.

Parameters

yn	Yes or no.

Implemented in bpp::AbstractTreeLikelihood.

◆ enableFirstOrderDerivatives() [1/2]

bool bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( ) const

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 273 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

◆ enableFirstOrderDerivatives() [2/2]

void bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives ( bool yn )

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 271 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.

◆ enableSecondOrderDerivatives() [1/2]

bool bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( ) const

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 274 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

◆ enableSecondOrderDerivatives() [2/2]

void bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives ( bool yn )

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 272 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.

◆ fireParameterChanged()

void RHomogeneousMixedTreeLikelihood::fireParameterChanged ( const ParameterList & params )

virtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 134 of file RHomogeneousMixedTreeLikelihood.cpp.

◆ getAlphabet() [1/2]

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

inlinevirtualinherited

Get the alphabet associated to the dataset.

Returns: the alphabet associated to the dataset.

Definition at line 263 of file AbstractTreeLikelihood.h.

◆ getAlphabet() [2/2]

virtual std::shared_ptr<const Alphabet> bpp::TreeLikelihoodInterface::getAlphabet ( ) const

pure virtualinherited

Get the alphabet associated to the dataset.

Returns: the alphabet associated to the dataset.

Implemented in bpp::AbstractTreeLikelihood.

◆ getAlphabetStateAsChar()

std::string bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsChar ( size_t i ) const

inlinevirtualinherited

Returns: the alphabet state corresponding to the given model state.

Definition at line 132 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getAlphabetStateAsInt()

int bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStateAsInt ( size_t i ) const

inlinevirtualinherited

Returns: the alphabet state corresponding to the given model state.

Definition at line 130 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getAlphabetStates()

const std::vector<int>& bpp::AbstractHomogeneousTreeLikelihood::getAlphabetStates ( ) const

inlinevirtualinherited

Returns: the alphabet states corresponding to all model states.

Definition at line 128 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getBranchLengthsParameters()

ParameterList AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters ( ) const

virtualinherited

Get the branch lengths parameters.

Returns: A ParameterList with all branch lengths.

References bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 213 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::ParameterList::getCommonParametersWith(), bpp::AbstractParametrizable::getParameters(), and bpp::AbstractTreeLikelihood::initialized_.

◆ getD2LikelihoodForASite()

double RHomogeneousTreeLikelihood::getD2LikelihoodForASite ( size_t site ) const

virtualinherited

Definition at line 535 of file RHomogeneousTreeLikelihood.cpp.

Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite().

◆ getD2LikelihoodForASiteForARateClass()

double RHomogeneousMixedTreeLikelihood::getD2LikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const

virtual

Reimplemented from bpp::RHomogeneousTreeLikelihood.

Definition at line 239 of file RHomogeneousMixedTreeLikelihood.cpp.

References probas_, and treeLikelihoodsContainer_.

◆ getD2LogLikelihood()

double RHomogeneousTreeLikelihood::getD2LogLikelihood ( ) const

virtualinherited

Definition at line 556 of file RHomogeneousTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.

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

◆ getD2LogLikelihoodForASite()

double RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite ( size_t site ) const

virtualinherited

Definition at line 548 of file RHomogeneousTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), and bpp::pow().

Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihood().

◆ getDerivableParameters() [1/2]

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters ( ) const

virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns: A ParameterList.

References bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 37 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getBranchLengthsParameters(), and bpp::AbstractTreeLikelihood::initialized_.

◆ getDerivableParameters() [2/2]

virtual ParameterList bpp::TreeLikelihoodInterface::getDerivableParameters ( ) const

pure virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns: A ParameterList.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getDLikelihoodForASite()

double RHomogeneousTreeLikelihood::getDLikelihoodForASite ( size_t site ) const

virtualinherited

Definition at line 282 of file RHomogeneousTreeLikelihood.cpp.

Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), and bpp::RHomogeneousTreeLikelihood::getDLogLikelihoodForASite().

◆ getDLikelihoodForASiteForARateClass()

double RHomogeneousMixedTreeLikelihood::getDLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const

virtual

Reimplemented from bpp::RHomogeneousTreeLikelihood.

Definition at line 216 of file RHomogeneousMixedTreeLikelihood.cpp.

References probas_, and treeLikelihoodsContainer_.

◆ getDLogLikelihood()

double RHomogeneousTreeLikelihood::getDLogLikelihood ( ) const

virtualinherited

Definition at line 303 of file RHomogeneousTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::getDLogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.

Referenced by bpp::RHomogeneousTreeLikelihood::getFirstOrderDerivative().

◆ getDLogLikelihoodForASite()

double RHomogeneousTreeLikelihood::getDLogLikelihoodForASite ( size_t site ) const

virtualinherited

Definition at line 295 of file RHomogeneousTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), and bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite().

Referenced by bpp::RHomogeneousTreeLikelihood::getDLogLikelihood().

◆ getFirstOrderDerivative()

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

virtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 317 of file RHomogeneousTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::computeTreeDLikelihood(), bpp::RHomogeneousTreeLikelihood::getDLogLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::getRateDistributionParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), and bpp::AbstractParametrizable::hasParameter().

◆ getLikelihood()

double RHomogeneousTreeLikelihood::getLikelihood ( ) const

virtualinherited

Get the likelihood for the whole dataset.

Returns: The likelihood of the dataset.

Definition at line 118 of file RHomogeneousTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.

◆ getLikelihoodForASite()

double RHomogeneousTreeLikelihood::getLikelihoodForASite ( size_t site ) const

virtualinherited

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns: The likelihood for site site.

References bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 148 of file RHomogeneousTreeLikelihood.cpp.

Referenced by bpp::RHomogeneousTreeLikelihood::getD2LogLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLogLikelihoodForASite(), and bpp::RHomogeneousTreeLikelihood::getLikelihood().

◆ getLikelihoodForASiteForARateClass()

double RHomogeneousMixedTreeLikelihood::getLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const

virtual

Get the likelihood for a site knowing its rate class.

Parameters

site	The site index.
rateClass	The rate class index.

Returns: The likelihood for the specified site and rate class.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 172 of file RHomogeneousMixedTreeLikelihood.cpp.

References probas_, and treeLikelihoodsContainer_.

Referenced by getLogLikelihoodForASiteForARateClass().

◆ getLikelihoodForASiteForARateClassForAState()

double RHomogeneousMixedTreeLikelihood::getLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const

virtual

Get the likelihood for a site knowing its rate class and its ancestral state.

Parameters

site	The site index.
rateClass	The rate class index.
state	The ancestral state.

Returns: The likelihood for the specified site and rate class and ancestral state.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 192 of file RHomogeneousMixedTreeLikelihood.cpp.

References probas_, and treeLikelihoodsContainer_.

Referenced by getLogLikelihoodForASiteForARateClassForAState().

◆ getLikelihoodForASiteForAState() [1/2]

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const

virtualinherited

Get the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns: The likelihood for site site and state state.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 75 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getLikelihoodForASiteForAState() [2/2]

virtual double bpp::TreeLikelihoodInterface::getLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const

pure virtualinherited

Get the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns: The likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodPerSitePerState().

◆ getLikelihoodPerSite() [1/2]

Vdouble AbstractTreeLikelihood::getLikelihoodPerSite ( ) const

virtualinherited

Get the likelihood for each site.

Returns: A vector with all likelihoods for each site.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Definition at line 11 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite().

◆ getLikelihoodPerSite() [2/2]

virtual Vdouble bpp::TreeLikelihoodInterface::getLikelihoodPerSite ( ) const

pure virtualinherited

Get the likelihood for each site.

Returns: A vector with all likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

◆ getLikelihoodPerSitePerRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass ( ) const

virtualinherited

Get the likelihood for each site and each rate class.

Returns: A two-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 57 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbPerSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite().

◆ getLikelihoodPerSitePerRateClassPerState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState ( ) const

virtualinherited

Get the likelihood for each site and each rate class and each state.

Returns: A three-dimension vector with all likelihoods.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 120 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

◆ getLikelihoodPerSitePerState() [1/2]

VVdouble AbstractTreeLikelihood::getLikelihoodPerSitePerState ( ) const

virtualinherited

Get the likelihood for each site and for each state.

Returns: A 2d vector with all likelihoods for each site and for each state.

Definition at line 35 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

◆ getLikelihoodPerSitePerState() [2/2]

virtual VVdouble bpp::TreeLikelihoodInterface::getLikelihoodPerSitePerState ( ) const

pure virtualinherited

Get the likelihood for each site and for each state.

Returns: A 2d vector with all likelihoods for each site and for each state.

Implemented in bpp::AbstractTreeLikelihood.

◆ getLogLikelihood()

double RHomogeneousTreeLikelihood::getLogLikelihood ( ) const

virtualinherited

Get the logarithm of the likelihood for the whole dataset.

Returns: The logarithm of the likelihood of the dataset.

Definition at line 130 of file RHomogeneousTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractHomogeneousTreeLikelihood::nbSites_.

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

◆ getLogLikelihoodForASite()

double RHomogeneousTreeLikelihood::getLogLikelihoodForASite ( size_t site ) const

virtualinherited

Get the logarithm of the likelihood for a site.

Parameters

site	The site index to analyse.

Returns: The logarithm of the likelihood for site site.

References bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), bpp::log(), bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 160 of file RHomogeneousTreeLikelihood.cpp.

Referenced by bpp::RHomogeneousTreeLikelihood::getLogLikelihood().

◆ getLogLikelihoodForASiteForARateClass()

double RHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClass	(	size_t	site,
		size_t	rateClass
	)		const

virtual

Get the logarithm of the likelihood for a site knowing its rate class.

Parameters

site	The site index.
rateClass	The rate class index.

Returns: The logarithm of the likelihood for the specified site and rate class.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 184 of file RHomogeneousMixedTreeLikelihood.cpp.

References getLikelihoodForASiteForARateClass(), and bpp::log().

◆ getLogLikelihoodForASiteForARateClassForAState()

double RHomogeneousMixedTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState	(	size_t	site,
		size_t	rateClass,
		int	state
	)		const

virtual

Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state.

Parameters

site	The site index.
rateClass	The rate class index.
state	The ancestral state.

Returns: The logarithm of the likelihood for the specified site and rate class and ancestral state..

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 204 of file RHomogeneousMixedTreeLikelihood.cpp.

References getLikelihoodForASiteForARateClassForAState(), and bpp::log().

◆ getLogLikelihoodForASiteForAState() [1/2]

double AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const

virtualinherited

Get the logarithm of the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns: The logarithm of the likelihood for site site and state state.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::log(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 88 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getLogLikelihoodForASiteForAState() [2/2]

virtual double bpp::TreeLikelihoodInterface::getLogLikelihoodForASiteForAState	(	size_t	site,
		int	state
	)		const

pure virtualinherited

Get the logarithm of the likelihood for a site and for a state.

Parameters

site	The site index to analyse.
state	The state to consider.

Returns: The logarithm of the likelihood for site site and state state.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::AbstractTreeLikelihood::getLogLikelihoodPerSitePerState().

◆ getLogLikelihoodPerSite() [1/2]

Vdouble AbstractTreeLikelihood::getLogLikelihoodPerSite ( ) const

virtualinherited

Get the logarithm of the likelihood for each site.

Returns: A vector with all log likelihoods for each site.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodForASiteForARateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

Definition at line 23 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLogLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

◆ getLogLikelihoodPerSite() [2/2]

virtual Vdouble bpp::TreeLikelihoodInterface::getLogLikelihoodPerSite ( ) const

pure virtualinherited

Get the logarithm of the likelihood for each site.

Returns: A vector with all log likelihoods for each site.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::PairedSiteLikelihoods::appendModel().

◆ getLogLikelihoodPerSitePerRateClass()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClass ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and each rate class.

Returns: A two-dimension vector with all log likelihoods: V[i][j] = likelihood of site i and rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 102 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getLogLikelihoodPerSitePerRateClassPerState()

VVVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and each rate class and each state.

Returns: A three-dimension vector with all log likelihoods: V[i][j][k} = likelihood of site i and rate class j and state k.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 143 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

◆ getLogLikelihoodPerSitePerState() [1/2]

VVdouble AbstractTreeLikelihood::getLogLikelihoodPerSitePerState ( ) const

virtualinherited

Get the logarithm of the likelihood for each site and for each state.

Returns: A 2d vector with all log likelihoods for each site and for each state.

Definition at line 52 of file AbstractTreeLikelihood.cpp.

References bpp::TreeLikelihoodInterface::getLogLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihoodInterface::getNumberOfStates().

◆ getLogLikelihoodPerSitePerState() [2/2]

virtual VVdouble bpp::TreeLikelihoodInterface::getLogLikelihoodPerSitePerState ( ) const

pure virtualinherited

Get the logarithm of the likelihood for each site and for each state.

Returns: A 2d vector with all log likelihoods for each site and for each state.

Implemented in bpp::AbstractTreeLikelihood.

◆ getMaximumBranchLength()

virtual double bpp::AbstractHomogeneousTreeLikelihood::getMaximumBranchLength ( ) const

inlinevirtualinherited

Definition at line 239 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_.

◆ getMinimumBranchLength()

virtual double bpp::AbstractHomogeneousTreeLikelihood::getMinimumBranchLength ( ) const

inlinevirtualinherited

Definition at line 238 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_.

◆ getModel() [1/4]

std::shared_ptr<TransitionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getModel ( )

inlinevirtualinherited

Returns: The substitution model attached to this instance.

Definition at line 171 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getModel() [2/4]

std::shared_ptr<const TransitionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getModel ( ) const

inlinevirtualinherited

Returns: The substitution model attached to this instance.

Definition at line 168 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getModel() [3/4]

std::shared_ptr<TransitionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getModel	(	int	nodeId,
		size_t	siteIndex
	)

inlineinherited

Definition at line 172 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getModel() [4/4]

std::shared_ptr<const TransitionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getModel	(	int	nodeId,
		size_t	siteIndex
	)		const

inlineinherited

Definition at line 169 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getModelForSite() [1/2]

std::shared_ptr<TransitionModelInterface> bpp::HomogeneousTreeLikelihood::getModelForSite	(	int	nodeId,
		size_t	siteIndex
	)

inlinevirtualinherited

Get the substitution model associated to a given node and alignment column.

Parameters

nodeId	The id of the request node.
siteIndex	The index of the alignment position.

See also: getSiteIndex

Returns: A pointer toward the corresponding model.

Exceptions

NodeNotFoundException This exception may be thrown if the node is not found (depending on the implementation).

Definition at line 35 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getModel().

◆ getModelForSite() [2/2]

std::shared_ptr<const TransitionModelInterface> bpp::HomogeneousTreeLikelihood::getModelForSite	(	int	nodeId,
		size_t	siteIndex
	)		const

inlinevirtualinherited

Get the substitution model associated to a given node and alignment column.

Parameters

nodeId	The id of the request node.
siteIndex	The index of the alignment position.

See also: getSiteIndex

Returns: A pointer toward the corresponding model.

Definition at line 30 of file HomogeneousTreeLikelihood.h.

References bpp::HomogeneousTreeLikelihood::getModel().

◆ getNewBranchModelIterator()

ConstBranchModelIterator* bpp::AbstractHomogeneousTreeLikelihood::getNewBranchModelIterator ( int nodeId ) const

inlinevirtualinherited

Definition at line 149 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractHomogeneousTreeLikelihood::nbDistinctSites_.

◆ getNewSiteModelIterator()

ConstSiteModelIterator* bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator ( size_t siteIndex ) const

inlinevirtualinherited

Definition at line 154 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_, and bpp::AbstractTreeLikelihood::tree_.

◆ getNonDerivableParameters() [1/2]

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters ( ) const

virtualinherited

All non derivable parameters.

Usually, this contains all substitution model parameters and rate distribution.

Returns: A ParameterList.

References bpp::ParameterList::addParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::TreeLikelihoodInterface::getSubstitutionModelParameters(), and bpp::AbstractTreeLikelihood::initialized_.

Definition at line 46 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getNonDerivableParameters() [2/2]

virtual ParameterList bpp::TreeLikelihoodInterface::getNonDerivableParameters ( ) const

pure virtualinherited

All non derivable parameters.

Usually, this contains all substitution model parameters and rate distribution.

Returns: A ParameterList.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

◆ getNumberOfClasses()

size_t bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses ( ) const

inlinevirtualinherited

Get the number of classes.

Returns: The number of classes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 90 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getNumberOfSites() [1/2]

size_t bpp::AbstractTreeLikelihood::getNumberOfSites ( ) const

inlinevirtualinherited

Get the number of sites in the dataset.

Returns: the number of sites in the dataset.

Definition at line 268 of file AbstractTreeLikelihood.h.

◆ getNumberOfSites() [2/2]

virtual size_t bpp::TreeLikelihoodInterface::getNumberOfSites ( ) const

pure virtualinherited

Get the number of sites in the dataset.

Returns: the number of sites in the dataset.

Implemented in bpp::AbstractTreeLikelihood.

◆ getNumberOfStates()

size_t bpp::AbstractHomogeneousTreeLikelihood::getNumberOfStates ( ) const

inlinevirtualinherited

Returns: the number of model states of the underlying Markov chain.

References bpp::AbstractTreeLikelihood::getLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 126 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getPosteriorProbabilitiesPerRate()

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate ( ) const

virtualinherited

Get the posterior probability for each site of belonging to a particular rate class.

Returns: A two-dimension vector with all posterior probabilities: V[i][j] = probability for site i of belonging to rate class j.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 166 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getPosteriorRatePerSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite ( ) const

virtualinherited

Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.

Returns: A vector with all rates.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 184 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::getLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getRateClassWithMaxPostProbPerSite()

vector< size_t > AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbPerSite ( ) const

virtualinherited

Get the posterior rate class (the one with maximum posterior probability) for each site.

Returns: A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 203 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), and bpp::AbstractTreeLikelihood::getNumberOfSites().

◆ getRateDistribution() [1/2]

std::shared_ptr<DiscreteDistributionInterface> bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( )

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns: A pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 75 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getRateDistribution() [2/2]

std::shared_ptr<const DiscreteDistributionInterface> bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution ( ) const

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns: A const pointer toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 70 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getRateDistributionParameters()

ParameterList bpp::AbstractHomogeneousTreeLikelihood::getRateDistributionParameters ( ) const

inlinevirtualinherited

Get the parameters associated to the rate distribution.

Returns: A ParameterList object with all rate distribution parameters.

Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 140 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters().

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::getFirstOrderDerivative(), bpp::RHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative(), bpp::RHomogeneousTreeLikelihood::getSecondOrderDerivative(), and bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative().

◆ getRateWithMaxPostProbPerSite()

Vdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite ( ) const

virtualinherited

Get the posterior rate (the one with maximum posterior probability) for each site.

Returns: A vector with all rate classes indexes.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 217 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ getRootFrequencies()

const std::vector<double>& bpp::AbstractHomogeneousTreeLikelihood::getRootFrequencies ( size_t siteIndex ) const

inlinevirtualinherited

Get the values of the frequencies for each state in the alphabet at the root node.

For reversible models, these are the equilibrium frequencies. For non-reversible models, these usually are distinct parameters.

For models without site partitioning, the set of frequencies is the same for all positions. For partition models, the frequencies may differ from one site to another.

Parameters

siteIndex The index of the alignment position.

See also: getSiteIndex

Returns: A vector with ancestral frequencies for each state in the alphabet;

References bpp::RHomogeneousTreeLikelihood::computeTreeD2Likelihood(), bpp::RHomogeneousTreeLikelihood::getD2LogLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::getRateDistributionParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), and bpp::AbstractParametrizable::hasParameter().

Definition at line 145 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getSecondOrderDerivative() [1/2]

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

virtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 569 of file RHomogeneousTreeLikelihood.cpp.

◆ getSecondOrderDerivative() [2/2]

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

inlinevirtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 176 of file RHomogeneousTreeLikelihood.h.

◆ getSiteIndex()

size_t bpp::RHomogeneousTreeLikelihood::getSiteIndex ( size_t site ) const

inlinevirtualinherited

Get the index (used for inner computations) of a given site (original alignment column).

Parameters

site	An alignment position.

Returns: The site index corresponding to the given input alignment position.

Definition at line 160 of file RHomogeneousTreeLikelihood.h.

References bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), and bpp::RHomogeneousTreeLikelihood::likelihoodData_.

◆ getSubstitutionModel() [1/2]

virtual std::shared_ptr<const SubstitutionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel ( ) const

inlinevirtualinherited

Get a SubstitutionModel pointer toward the model associated to this instance, if possible.

Performs a cast operation on the pointer. Return NULL if cast failed.

Returns: A SubstitutionModel pointer toward the model associated to this instance.

Definition at line 183 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getSubstitutionModel() [2/2]

virtual std::shared_ptr<const SubstitutionModelInterface> bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModel	(	int	nodeId,
		size_t	siteIndex
	)		const

inlinevirtualinherited

Get a SubstitutionModel pointer toward the model associated to this instance, if possible.

Performs a cast operation on the pointer. Return NULL if cast failed.

Returns: A SubstitutionModel pointer toward the model associated to this instance.

Parameters

nodeId	Id of the node
siteIndex	Position of the site

Definition at line 197 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getSubstitutionModelParameters()

ParameterList AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters ( ) const

virtualinherited

Get the parameters associated to substitution model(s).

Returns: A ParameterList.

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::getFirstOrderDerivative(), bpp::RHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRHomogeneousMixedTreeLikelihood::getSecondOrderDerivative(), bpp::RHomogeneousTreeLikelihood::getSecondOrderDerivative(), and bpp::DRHomogeneousTreeLikelihood::getSecondOrderDerivative().

Definition at line 222 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractHomogeneousTreeLikelihood::model_.

◆ getTransitionProbabilities() [1/2]

VVdouble AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities	(	int	nodeId,
		size_t	siteIndex
	)		const

virtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node and site.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The index of the alignment position.

See also: getSiteIndex

Returns: An array of dimension 2, where a[x][y] is the probability of substituting from x to y.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::TreeLikelihoodInterface::getNumberOfStates(), bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface::getTransitionProbabilitiesPerRateClass(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Definition at line 275 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ getTransitionProbabilities() [2/2]

virtual VVdouble bpp::TreeLikelihoodInterface::getTransitionProbabilities	(	int	nodeId,
		size_t	siteIndex
	)		const

pure virtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node and site.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The index of the alignment position.

See also: getSiteIndex

Returns: An array of dimension 2, where a[x][y] is the probability of substituting from x to y.

Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Referenced by bpp::TreeLikelihoodTools::getAncestralFrequencies_().

◆ getTransitionProbabilitiesPerRateClass()

VVVdouble bpp::AbstractHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass	(	int	nodeId,
		size_t	siteIndex
	)		const

inlinevirtualinherited

Retrieves all Pij(t) for a particular branch, defined by the upper node.

These intermediate results may be used by other methods.

Parameters

nodeId	The node defining the branch of interest.
siteIndex	The position in the alignment.

Returns: An array of dimension 3, where a[c][x][y] is the probability of substituting from x to y while being in rate class c.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 147 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::pxy_.

◆ getValue()

double RHomogeneousTreeLikelihood::getValue ( ) const

virtualinherited

Implements bpp::SecondOrderDerivable.

Definition at line 257 of file RHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::isInitialized(), and bpp::RHomogeneousTreeLikelihood::minusLogLik_.

◆ hasLikelihoodData() [1/2]

bool bpp::AbstractTreeLikelihood::hasLikelihoodData ( ) const

inlinevirtualinherited

Returns: True if the TreeLikelihood object has a LikelihoodData.

Definition at line 261 of file AbstractTreeLikelihood.h.

References bpp::ParameterList::addParameter(), bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::ApplicationTools::displayWarning(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::ParameterList::reset(), and bpp::TextTools::toString().

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::init().

◆ hasLikelihoodData() [2/2]

virtual bool bpp::TreeLikelihoodInterface::hasLikelihoodData ( ) const

pure virtualinherited

Returns: True if the TreeLikelihood object has a LikelihoodData.

Implemented in bpp::AbstractTreeLikelihood.

◆ init_()

void RHomogeneousTreeLikelihood::init_ ( bool usePatterns )

privateinherited

Method called by constructors.

Definition at line 54 of file RHomogeneousTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::likelihoodData_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood().

◆ initBranchLengthsParameters()

void AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters ( bool verbose = true )

virtualinherited

Definition at line 270 of file AbstractHomogeneousTreeLikelihood.cpp.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength().

◆ initialize()

void RHomogeneousMixedTreeLikelihood::initialize ( )

virtual

Init the likelihood object.

This method is used to initialize all parameters. It is typically called after the constructor and the setData method. It contains virtual methods that can't be called in the constructor.

Exceptions

Exception if something bad happened, for instance if no data are associated to the likelihood function.

Reimplemented from bpp::AbstractHomogeneousTreeLikelihood.

Definition at line 113 of file RHomogeneousMixedTreeLikelihood.cpp.

References bpp::AbstractHomogeneousTreeLikelihood::initialize(), and treeLikelihoodsContainer_.

◆ initParameters()

void AbstractHomogeneousTreeLikelihood::initParameters ( )

virtualinherited

This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree.

Definition at line 231 of file AbstractHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::addParameters_(), bpp::AbstractHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::AbstractParametrizable::resetParameters_().

Referenced by bpp::AbstractHomogeneousTreeLikelihood::initialize().

◆ isInitialized() [1/2]

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const

inlinevirtualinherited

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

Definition at line 275 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::initialized_.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::getValue(), bpp::RHomogeneousTreeLikelihood::getValue(), bpp::RNonHomogeneousTreeLikelihood::getValue(), and bpp::DRHomogeneousTreeLikelihood::getValue().

◆ isInitialized() [2/2]

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

pure virtualinherited

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

Implemented in bpp::AbstractTreeLikelihood.

◆ likelihoodData() [1/2]

DRASRTreeLikelihoodData& bpp::RHomogeneousTreeLikelihood::likelihoodData ( )

inlinevirtualinherited

Returns: The underlying likelihood data structure.

Definition at line 182 of file RHomogeneousTreeLikelihood.h.

References bpp::RHomogeneousTreeLikelihood::likelihoodData_.

◆ likelihoodData() [2/2]

const DRASRTreeLikelihoodData& bpp::RHomogeneousTreeLikelihood::likelihoodData ( ) const

inlinevirtualinherited

Returns: The underlying likelihood data structure.

Definition at line 184 of file RHomogeneousTreeLikelihood.h.

References bpp::RHomogeneousTreeLikelihood::likelihoodData_.

◆ operator=()

RHomogeneousMixedTreeLikelihood & RHomogeneousMixedTreeLikelihood::operator= ( const RHomogeneousMixedTreeLikelihood & lik )

Definition at line 81 of file RHomogeneousMixedTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::operator=(), probas_, and treeLikelihoodsContainer_.

◆ rateDistribution() [1/2]

DiscreteDistributionInterface& bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution ( )

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns: A reference toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 85 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ rateDistribution() [2/2]

const DiscreteDistributionInterface& bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution ( ) const

inlinevirtualinherited

Get the rate distribution used for the computation.

Returns: A const reference toward the rate distribution of this instance.

Implements bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface.

Definition at line 80 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

◆ resetLikelihoodArray()

void AbstractDiscreteRatesAcrossSitesTreeLikelihood::resetLikelihoodArray ( VVVdouble & likelihoodArray )

staticinherited

Set all conditional likelihoods to 1.

Parameters

likelihoodArray the likelihood array.

Definition at line 231 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

◆ setData()

void RHomogeneousMixedTreeLikelihood::setData ( const AlignmentDataInterface & sites )

virtual

Set the dataset for which the likelihood must be evaluated.

Parameters

sites The data set to use.

References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_, and bpp::TextTools::toString().

Definition at line 123 of file RHomogeneousMixedTreeLikelihood.cpp.

References bpp::RHomogeneousTreeLikelihood::setData(), and treeLikelihoodsContainer_.

Referenced by RHomogeneousMixedTreeLikelihood().

◆ setMaximumBranchLength()

virtual void bpp::AbstractHomogeneousTreeLikelihood::setMaximumBranchLength ( double maximum )

inlinevirtualinherited

Definition at line 229 of file AbstractHomogeneousTreeLikelihood.h.

◆ setMinimumBranchLength()

virtual void bpp::AbstractHomogeneousTreeLikelihood::setMinimumBranchLength ( double minimum )

inlinevirtualinherited

Definition at line 220 of file AbstractHomogeneousTreeLikelihood.h.

References bpp::AbstractHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractHomogeneousTreeLikelihood::minimumBrLen_, and bpp::TextTools::toString().

◆ setModel()

void AbstractHomogeneousTreeLikelihood::setModel ( std::shared_ptr< TransitionModelInterface > model )

virtualinherited

Returns: Set the substitution model for this instance.

Exceptions

Exception If the model could not be set (for instance, because of a wrong alphabet type).

References bpp::AbstractHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractTreeLikelihood::data_, bpp::AbstractHomogeneousTreeLikelihood::dpxy_, bpp::Node::getId(), bpp::AbstractHomogeneousTreeLikelihood::model_, bpp::AbstractHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractHomogeneousTreeLikelihood::nbStates_, bpp::AbstractHomogeneousTreeLikelihood::nodes_, bpp::AbstractHomogeneousTreeLikelihood::pxy_, and bpp::TreeLikelihoodInterface::setData().

Definition at line 135 of file AbstractHomogeneousTreeLikelihood.cpp.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::init_().

◆ setParameters()

void RHomogeneousTreeLikelihood::setParameters ( const ParameterList & parameters )

virtualinherited

Implements the Function interface.

Update the parameter list and call the applyParameters() method. Then compute the likelihoods at each node (computeLikelihood() method) and call the getLogLikelihood() method.

If a subset of the whole parameter list is passed to the function, only these parameters are updated and the other remain constant (i.e. equal to their last value).

Parameters

parameters The parameter list to pass to the function.

Implements bpp::SecondOrderDerivable.

Definition at line 218 of file RHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::setParametersValues().

◆ tree() [1/2]

const Tree& bpp::AbstractTreeLikelihood::tree ( ) const

inlinevirtualinherited

Get the tree (topology and branch lengths).

Returns: The tree of this TreeLikelihood object.