bpp::RNonHomogeneousTreeLikelihood Class Reference

This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions. More...

#include <Bpp/Phyl/Legacy/Likelihood/RNonHomogeneousTreeLikelihood.h>

Inheritance diagram for bpp::RNonHomogeneousTreeLikelihood:

Collaboration diagram for bpp::RNonHomogeneousTreeLikelihood:

Public Member Functions
	RNonHomogeneousTreeLikelihood (const Tree &tree, std::shared_ptr< SubstitutionModelSet > modelSet, std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true, bool usePatterns=true, bool reparametrizeRoot=false)
	Build a new NonHomogeneousTreeLikelihood object without data. More...
	RNonHomogeneousTreeLikelihood (const Tree &tree, const AlignmentDataInterface &data, std::shared_ptr< SubstitutionModelSet > modelSet, std::shared_ptr< DiscreteDistributionInterface > rDist, bool verbose=true, bool usePatterns=true, bool reparametrizeRoot=false)
	Build a new NonHomogeneousTreeLikelihood object and compute the corresponding likelihood. More...
	RNonHomogeneousTreeLikelihood (const RNonHomogeneousTreeLikelihood &lik)
RNonHomogeneousTreeLikelihood &	operator= (const RNonHomogeneousTreeLikelihood &lik)
virtual	~RNonHomogeneousTreeLikelihood ()
RNonHomogeneousTreeLikelihood *	clone () const
void	setParameters (const ParameterList &parameters)
	Implements the Function interface. More...
double	getValue () const
DRASRTreeLikelihoodData &	likelihoodData ()
const DRASRTreeLikelihoodData &	likelihoodData () const
virtual void	computeTreeLikelihood ()
virtual double	getDLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
virtual double	getDLikelihoodForASite (size_t site) const
virtual double	getDLogLikelihoodForASite (size_t site) const
virtual double	getDLogLikelihood () const
virtual void	computeTreeDLikelihood (const std::string &variable)
virtual double	getD2LikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
virtual double	getD2LikelihoodForASite (size_t site) const
virtual double	getD2LogLikelihoodForASite (size_t site) const
virtual double	getD2LogLikelihood () const
virtual void	computeTreeD2Likelihood (const std::string &variable)
virtual void	initParameters ()
	This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree. More...
virtual void	applyParameters ()
	All parameters are stored in a parameter list. This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths. More...
virtual void	initBranchLengthsParameters (bool verbose=true)
virtual void	setMinimumBranchLength (double minimum)
virtual void	setMaximumBranchLength (double maximum)
virtual double	getMinimumBranchLength () const
virtual double	getMaximumBranchLength () const
std::shared_ptr< const TransitionModelInterface >	getModelForSite (int nodeId, size_t siteIndex) const override
	Get the substitution model associated to a given node and alignment column. More...
std::shared_ptr< TransitionModelInterface >	getModelForSite (int nodeId, size_t siteIndex) override
	Get the substitution model associated to a given node and alignment column. More...
virtual const AlignmentDataInterface &	data () const =0
	Get the dataset for which the likelihood must be evaluated. More...
virtual bool	isInitialized () const =0
virtual bool	hasLikelihoodData () const =0
virtual double	getLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the likelihood for a site and for a state. More...
virtual double	getLogLikelihoodForASiteForAState (size_t site, int state) const =0
	Get the logarithm of the likelihood for a site and for a state. More...
virtual Vdouble	getLikelihoodPerSite () const =0
	Get the likelihood for each site. More...
virtual Vdouble	getLogLikelihoodPerSite () const =0
	Get the logarithm of the likelihood for each site. More...
virtual VVdouble	getLikelihoodPerSitePerState () const =0
	Get the likelihood for each site and for each state. More...
virtual VVdouble	getLogLikelihoodPerSitePerState () const =0
	Get the logarithm of the likelihood for each site and for each state. More...
virtual const Tree &	tree () const =0
	Get the tree (topology and branch lengths). More...
virtual size_t	getNumberOfSites () const =0
	Get the number of sites in the dataset. More...
virtual std::shared_ptr< const Alphabet >	getAlphabet () const =0
	Get the alphabet associated to the dataset. More...
virtual void	enableDerivatives (bool yn)=0
	Tell if derivatives must be computed. More...
virtual ParameterList	getDerivableParameters () const =0
	All derivable parameters. More...
virtual ParameterList	getNonDerivableParameters () const =0
	All non derivable parameters. More...
virtual void	enableSecondOrderDerivatives (bool yn)=0
virtual bool	enableSecondOrderDerivatives () const=0
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 double	df (const std::string &variable, const ParameterList &parameters)
virtual double	f (const ParameterList &parameters)
virtual bool	hasParameter (const std::string &name) const=0
bool	hasParameter (const std::string &name) const override
virtual const ParameterList &	getParameters () const=0
const ParameterList &	getParameters () const override
virtual const Parameter &	parameter (const std::string &name) const=0
const Parameter &	parameter (const std::string &name) const override
virtual double	getParameterValue (const std::string &name) const=0
double	getParameterValue (const std::string &name) const override
virtual void	setAllParametersValues (const ParameterList &parameters)=0
void	setAllParametersValues (const ParameterList &parameters) override
virtual void	setParameterValue (const std::string &name, double value)=0
void	setParameterValue (const std::string &name, double value) override
virtual void	setParametersValues (const ParameterList &parameters)=0
void	setParametersValues (const ParameterList &parameters) override
virtual bool	matchParametersValues (const ParameterList &parameters)=0
bool	matchParametersValues (const ParameterList &parameters) override
virtual void	removeConstraint (const std::string &name)=0
void	removeConstraint (const std::string &name) override
virtual void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint)=0
void	setConstraint (const std::string &name, std::shared_ptr< ConstraintInterface > constraint) override
virtual size_t	getNumberOfParameters () const=0
size_t	getNumberOfParameters () const override
virtual void	setNamespace (const std::string &prefix)=0
void	setNamespace (const std::string &prefix) override
virtual std::string	getNamespace () const=0
std::string	getNamespace () const override
virtual std::string	getParameterNameWithoutNamespace (const std::string &name) const=0
std::string	getParameterNameWithoutNamespace (const std::string &name) const override
const std::shared_ptr< Parameter > &	getParameter (const std::string &name) const
The TreeLikelihood interface.
Other methods are implemented in the AbstractHomogeneousTreeLikelihood class.
void	setData (const AlignmentDataInterface &sites)
	Set the dataset for which the likelihood must be evaluated. More...
double	getLikelihood () const
	Get the likelihood for the whole dataset. More...
double	getLogLikelihood () const
	Get the logarithm of the likelihood for the whole dataset. More...
double	getLikelihoodForASite (size_t site) const
	Get the likelihood for a site. More...
double	getLogLikelihoodForASite (size_t site) const
	Get the logarithm of the likelihood for a site. More...
size_t	getSiteIndex (size_t site) const
	Get the index (used for inner computations) of a given site (original alignment column). More...
The DiscreteRatesAcrossSites interface implementation:
double	getLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
	Get the likelihood for a site knowing its rate class. More...
double	getLogLikelihoodForASiteForARateClass (size_t site, size_t rateClass) const
	Get the logarithm of the likelihood for a site knowing its rate class. More...
double	getLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const
	Get the likelihood for a site knowing its rate class and its ancestral state. More...
double	getLogLikelihoodForASiteForARateClassForAState (size_t site, size_t rateClass, int state) const
	Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state. More...
DerivableFirstOrder interface.
double	getFirstOrderDerivative (const std::string &variable) const
DerivableSecondOrder interface.
double	getSecondOrderDerivative (const std::string &variable) const
double	getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
size_t	getNumberOfStates () const override
const std::vector< int > &	getAlphabetStates () const override
int	getAlphabetStateAsInt (size_t i) const override
std::string	getAlphabetStateAsChar (size_t i) const override
void	initialize () override
	Init the likelihood object. More...
ParameterList	getBranchLengthsParameters () const override
	Get the branch lengths parameters. More...
ParameterList	getSubstitutionModelParameters () const override
	Get the parameters associated to substitution model(s). More...
ParameterList	getRateDistributionParameters () const override
	Get the parameters associated to the rate distribution. More...
std::shared_ptr< const TransitionModelInterface >	getModelForNode (int nodeId) const override
	Get the model associated to a given node. More...
std::shared_ptr< TransitionModelInterface >	getModelForNode (int nodeId) override
	Get the substitution model associated to a given node. More...
const std::vector< double > &	getRootFrequencies (size_t siteIndex) const override
	Get the values of the frequencies for each state in the alphabet at the root node. More...
VVVdouble	getTransitionProbabilitiesPerRateClass (int nodeId, size_t siteIndex) const override
	Retrieves all Pij(t) for a particular branch, defined by the upper node. More...
ConstBranchModelIterator *	getNewBranchModelIterator (int nodeId) const override
ConstSiteModelIterator *	getNewSiteModelIterator (size_t siteIndex) const override
The NonHomogeneousTreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
std::shared_ptr< const SubstitutionModelSet >	getSubstitutionModelSet () const override
std::shared_ptr< SubstitutionModelSet >	getSubstitutionModelSet () override
const SubstitutionModelSet &	substitutionModelSet () const override
SubstitutionModelSet &	substitutionModelSet () override
void	setSubstitutionModelSet (std::shared_ptr< SubstitutionModelSet > modelSet) override
ParameterList	getRootFrequenciesParameters () const override
The TreeLikelihood interface.
const AlignmentDataInterface &	data () const
	Get the dataset for which the likelihood must be evaluated. More...
bool	isInitialized () const
bool	hasLikelihoodData () const
Vdouble	getLikelihoodPerSite () const
	Get the likelihood for each site. More...
Vdouble	getLogLikelihoodPerSite () const
	Get the logarithm of the likelihood for each site. More...
VVdouble	getLikelihoodPerSitePerState () const
	Get the likelihood for each site and for each state. More...
VVdouble	getLogLikelihoodPerSitePerState () const
	Get the logarithm of the likelihood for each site and for each state. More...
const Tree &	tree () const
	Get the tree (topology and branch lengths). More...
size_t	getNumberOfSites () const
	Get the number of sites in the dataset. More...
std::shared_ptr< const Alphabet >	getAlphabet () const
	Get the alphabet associated to the dataset. More...
void	enableDerivatives (bool yn)
	Tell if derivatives must be computed. More...
void	enableSecondOrderDerivatives (bool yn)
bool	enableSecondOrderDerivatives () const
void	enableFirstOrderDerivatives (bool yn)
bool	enableFirstOrderDerivatives () const
The TreeLikelihood interface.
Other methods are implemented in the AbstractTreeLikelihood class.
double	getLikelihoodForASiteForAState (size_t site, int state) const
	Get the likelihood for a site and for a state. More...
double	getLogLikelihoodForASiteForAState (size_t site, int state) const
	Get the logarithm of the likelihood for a site and for a state. More...
VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const
	Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More...
ParameterList	getDerivableParameters () const
	All derivable parameters. More...
ParameterList	getNonDerivableParameters () const
	All non derivable parameters. More...
Retrieve some particular parameters subsets.
virtual VVdouble	getTransitionProbabilities (int nodeId, size_t siteIndex) const =0
	Retrieves all Pij(t) for a particular branch, defined by the upper node and site. More...
The DiscreteRatesAcrossSites interface implementation:
std::shared_ptr< const DiscreteDistributionInterface >	getRateDistribution () const
	Get the rate distribution used for the computation. More...
std::shared_ptr< DiscreteDistributionInterface >	getRateDistribution ()
	Get the rate distribution used for the computation. More...
const DiscreteDistributionInterface &	rateDistribution () const
	Get the rate distribution used for the computation. More...
DiscreteDistributionInterface &	rateDistribution ()
	Get the rate distribution used for the computation. More...
size_t	getNumberOfClasses () const
	Get the number of classes. More...
VVdouble	getLikelihoodPerSitePerRateClass () const
	Get the likelihood for each site and each rate class. More...
VVdouble	getLogLikelihoodPerSitePerRateClass () const
	Get the logarithm of the likelihood for each site and each rate class. More...
VVVdouble	getLikelihoodPerSitePerRateClassPerState () const
	Get the likelihood for each site and each rate class and each state. More...
VVVdouble	getLogLikelihoodPerSitePerRateClassPerState () const
	Get the logarithm of the likelihood for each site and each rate class and each state. More...
VVdouble	getPosteriorProbabilitiesPerRate () const
	Get the posterior probability for each site of belonging to a particular rate class. More...
Vdouble	getRateWithMaxPostProbPerSite () const
	Get the posterior rate (the one with maximum posterior probability) for each site. More...
std::vector< size_t >	getRateClassWithMaxPostProbPerSite () const
	Get the posterior rate class (the one with maximum posterior probability) for each site. More...
Vdouble	getPosteriorRatePerSite () const
	Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site. More...

Static Public Member Functions
Generic tools to deal with likelihood arrays
static void	resetLikelihoodArray (VVVdouble &likelihoodArray)
	Set all conditional likelihoods to 1. More...
static void	displayLikelihoodArray (const VVVdouble &likelihoodArray)
	Print the likelihood array to terminal (debugging tool). More...

Protected Member Functions
virtual void	computeSubtreeLikelihood (const Node *node)
	Compute the likelihood for a subtree defined by the Tree::Node node. More...
virtual void	computeDownSubtreeDLikelihood (const Node *)
virtual void	computeDownSubtreeD2Likelihood (const Node *)
void	fireParameterChanged (const ParameterList &params)
virtual void	displayLikelihood (const Node *node)
	This method is mainly for debugging purpose. More...
virtual void	computeAllTransitionProbabilities ()
	Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes. More...
virtual void	computeTransitionProbabilitiesForNode (const Node *node)
	Fill the pxy_, dpxy_ and d2pxy_ arrays for one node. More...
virtual ParameterList &	getParameters_ ()=0
ParameterList &	getParameters_ () override
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

Protected Attributes
std::shared_ptr< SubstitutionModelSet >	modelSet_
ParameterList	brLenParameters_
std::map< int, VVVdouble >	pxy_
std::map< int, VVVdouble >	dpxy_
std::map< int, VVVdouble >	d2pxy_
std::vector< double >	rootFreqs_
std::vector< Node * >	nodes_
	Pointer toward all nodes in the tree. More...
std::map< int, const Node * >	idToNode_
	An index linking nodes to their id, for faster access than the getNode() method. More...
size_t	nbSites_
size_t	nbDistinctSites_
size_t	nbClasses_
size_t	nbStates_
size_t	nbNodes_
bool	verbose_
double	minimumBrLen_
double	maximumBrLen_
std::shared_ptr< ConstraintInterface >	brLenConstraint_
bool	reparametrizeRoot_
int	root1_
int	root2_
std::shared_ptr< DiscreteDistributionInterface >	rateDistribution_
std::unique_ptr< const AlignmentDataInterface >	data_
std::shared_ptr< TreeTemplate< Node > >	tree_
bool	computeFirstOrderDerivatives_
bool	computeSecondOrderDerivatives_
bool	initialized_

Private Member Functions
void	init_ (bool usePatterns)
	Method called by constructors. More...

Private Attributes
std::shared_ptr< DRASRTreeLikelihoodData >	likelihoodData_
double	minusLogLik_
ParameterList	parameters_
std::string	prefix_

Friends
class	RNonHomogeneousMixedTreeLikelihood

Detailed Description

This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions.

A non uniform distribution of rates among the sites is allowed (ASRV models).

This class uses an instance of the DRASRTreeLikelihoodData for conditional likelihood storage.

This class can also use a simple or recursive site compression. In the simple case, computations for identical sites are not duplicated. In the recursive case, computations for identical sub-sites (site patterns ) are also not duplicated: Following N. Galtier (personal communication), we define a Pattern as a distinct site in a sub-dataset corresponding to the dataset with sequences associated to a particular subtree. The likelihood computation is the same for a given site, hence the idea is to save time from performing many times the same coputation. The network between all patterns is defined by the _patternLinks double map, initialized in the initLikelihoodsWithPatterns() method. This initialisation takes more time than the classic initTreeLikelihood one, where all likelihoods for a given site i are at the i coordinate in the likelihood tensor, but is really faster when computing the likelihood (computeLikelihoods() method). Hence, if you have to compute likelihood many times while holding the tree topology unchanged, you should use patterns. This decreases the likelihood computation time, but at a cost: some time is spent to establish the patterns relationships. Whether to use or not patterns depends on what you actllay need:

• The more you compute likelihoods without changing the data or topology, the more patterns are interesting (this divides the cost of computing patterns by the number of computation performed). Patterns are hence useful when you have a high number of computation to perform, while optimizing numerical parameters for instance).
• Patterns are more likely to occur with small alphabet (nucleotides).

Important note: The input tree will be considered as rooted, since the likelihood of non-stationary models depends on the position of the root. If the input tree is not rooted, it will be considered as a rotted tree with a root multifurcation.

Definition at line 49 of file RNonHomogeneousTreeLikelihood.h.

Constructor & Destructor Documentation

RNonHomogeneousTreeLikelihood() [1/3]

RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood	(	const Tree &	tree,
		std::shared_ptr< SubstitutionModelSet >	modelSet,
		std::shared_ptr< DiscreteDistributionInterface >	rDist,
		bool	verbose = true,
		bool	usePatterns = true,
		bool	reparametrizeRoot = false
	)

Build a new NonHomogeneousTreeLikelihood object without data.

This constructor only initialize the parameters. To compute a likelihood, you will need to call the setData() and the computeTreeLikelihood() methods.

Parameters

tree	The tree to use.
modelSet	The set of substitution models to use.
rDist	The rate across sites distribution to use. If true, any rooted tree will be unrooted before likelihood computation.
verbose	Should I display some info?
usePatterns	Tell if recursive site compression should be performed.
reparametrizeRoot	Should we reparametrize the branch lengths at root?

Exceptions

Exception

in an error occurred.

Definition at line 20 of file RNonHomogeneousTreeLikelihood.cpp.

References init_(), and bpp::AbstractTreeLikelihood::tree().

Referenced by clone().

RNonHomogeneousTreeLikelihood() [2/3]

RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood	(	const Tree &	tree,
		const AlignmentDataInterface &	data,
		std::shared_ptr< SubstitutionModelSet >	modelSet,
		std::shared_ptr< DiscreteDistributionInterface >	rDist,
		bool	verbose = true,
		bool	usePatterns = true,
		bool	reparametrizeRoot = false
	)

Build a new NonHomogeneousTreeLikelihood object and compute the corresponding likelihood.

This constructor initializes all parameters, data, and likelihood arrays.

Parameters

tree	The tree to use.
data	Sequences to use.
modelSet	The set of substitution models to use.
rDist	The rate across sites distribution to use.
verbose	Should I display some info?
usePatterns	Tell if recursive site compression should be performed.
reparametrizeRoot	Should we reparametrize the branch lengths at root?

Exceptions

Exception

in an error occurred.

Definition at line 38 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::data(), init_(), setData(), and bpp::AbstractTreeLikelihood::tree().

RNonHomogeneousTreeLikelihood() [3/3]

RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood

(

const RNonHomogeneousTreeLikelihood &

lik

)

Definition at line 68 of file RNonHomogeneousTreeLikelihood.cpp.

References likelihoodData_, and bpp::AbstractTreeLikelihood::tree_.

~RNonHomogeneousTreeLikelihood()

RNonHomogeneousTreeLikelihood::~RNonHomogeneousTreeLikelihood ( )

virtual

Definition at line 92 of file RNonHomogeneousTreeLikelihood.cpp.

Member Function Documentation

applyParameters()

void AbstractNonHomogeneousTreeLikelihood::applyParameters ( )

virtualinherited

All parameters are stored in a parameter list. This function apply these parameters to the substitution model, to the rate distribution and to the branch lengths.

Definition at line 285 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::getParameters(), bpp::Parameter::getValue(), bpp::AbstractTreeLikelihood::initialized_, bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractParametrizable::parameter(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractNonHomogeneousTreeLikelihood::reparametrizeRoot_, bpp::AbstractNonHomogeneousTreeLikelihood::root1_, bpp::AbstractNonHomogeneousTreeLikelihood::root2_, and bpp::TextTools::toString().

Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), and fireParameterChanged().

clone()

RNonHomogeneousTreeLikelihood* bpp::RNonHomogeneousTreeLikelihood::clone ( ) const

inlinevirtual

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 109 of file RNonHomogeneousTreeLikelihood.h.

References RNonHomogeneousTreeLikelihood().

computeAllTransitionProbabilities()

void AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities ( )

protectedvirtualinherited

Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.

Definition at line 370 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, and bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

computeDownSubtreeD2Likelihood()

void RNonHomogeneousTreeLikelihood::computeDownSubtreeD2Likelihood ( const Node *  node )

protectedvirtual

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 1152 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::Node::getFather(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractNonHomogeneousTreeLikelihood::pxy_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeD2Likelihood(), and computeTreeD2Likelihood().

computeDownSubtreeDLikelihood()

void RNonHomogeneousTreeLikelihood::computeDownSubtreeDLikelihood ( const Node *  node )

protectedvirtual

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 665 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::Node::getFather(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractNonHomogeneousTreeLikelihood::pxy_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeDLikelihood(), and computeTreeDLikelihood().

computeSubtreeLikelihood()

void RNonHomogeneousTreeLikelihood::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 in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 1250 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), bpp::Node::isLeaf(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractNonHomogeneousTreeLikelihood::pxy_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), and computeTreeLikelihood().

computeTransitionProbabilitiesForNode()

void AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode ( const Node *  node )

protectedvirtualinherited

Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 383 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractNonHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::Node::getDistanceToFather(), bpp::Node::getId(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), and fireParameterChanged().

computeTreeD2Likelihood()

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

virtual

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 825 of file RNonHomogeneousTreeLikelihood.cpp.

References computeDownSubtreeD2Likelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::Node::getFather(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::AbstractParametrizable::getParameterValue(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, bpp::AbstractNonHomogeneousTreeLikelihood::root1_, bpp::AbstractNonHomogeneousTreeLikelihood::root2_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), and getSecondOrderDerivative().

computeTreeDLikelihood()

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

virtual

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 354 of file RNonHomogeneousTreeLikelihood.cpp.

References computeDownSubtreeDLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::Node::getFather(), bpp::Node::getId(), bpp::Node::getNumberOfSons(), bpp::AbstractParametrizable::getParameterValue(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, bpp::AbstractNonHomogeneousTreeLikelihood::root1_, bpp::AbstractNonHomogeneousTreeLikelihood::root2_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), and getFirstOrderDerivative().

computeTreeLikelihood()

void RNonHomogeneousTreeLikelihood::computeTreeLikelihood ( )

virtual

Definition at line 1243 of file RNonHomogeneousTreeLikelihood.cpp.

References computeSubtreeLikelihood(), and bpp::AbstractTreeLikelihood::tree_.

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

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 262 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

Referenced by bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood(), and RNonHomogeneousTreeLikelihood().

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 RNonHomogeneousTreeLikelihood::displayLikelihood ( const Node *  node )

protectedvirtual

This method is mainly for debugging purpose.

Parameters

node	The node at which likelihood values must be displayed.

Definition at line 1319 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(), bpp::Node::getId(), bpp::Node::getName(), and likelihoodData_.

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 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.

Implements bpp::TreeLikelihoodInterface.

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 RNonHomogeneousTreeLikelihood::fireParameterChanged ( const ParameterList &  params )

protectedvirtual

Reimplemented from bpp::AbstractParametrizable.

Definition at line 222 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeLikelihood(), bpp::ParameterList::getCommonParametersWith(), getLogLikelihood(), bpp::ParameterList::getParameterNames(), bpp::AbstractNonHomogeneousTreeLikelihood::idToNode_, minusLogLik_, bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, bpp::ParameterList::size(), bpp::AbstractTreeLikelihood::tree_, and bpp::VectorTools::vectorUnion().

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 263 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

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::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsChar ( size_t  i ) const

inlineoverridevirtualinherited

Returns

the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihoodInterface.

Definition at line 145 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

getAlphabetStateAsInt()

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

inlineoverridevirtualinherited

Returns

the alphabet state corresponding to the given model state.

Implements bpp::TreeLikelihoodInterface.

Definition at line 143 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

getAlphabetStates()

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

inlineoverridevirtualinherited

Returns

the alphabet states corresponding to all model states.

Implements bpp::TreeLikelihoodInterface.

Definition at line 141 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

getBranchLengthsParameters()

ParameterList AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters ( ) const

overridevirtualinherited

Get the branch lengths parameters.

Returns

A ParameterList with all branch lengths.

Implements bpp::TreeLikelihoodInterface.

Definition at line 249 of file AbstractNonHomogeneousTreeLikelihood.cpp.

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

getD2LikelihoodForASite()

double RNonHomogeneousTreeLikelihood::getD2LikelihoodForASite ( size_t  site ) const

virtual

Definition at line 772 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by getD2LogLikelihoodForASite().

getD2LikelihoodForASiteForARateClass()

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

virtual

Definition at line 757 of file RNonHomogeneousTreeLikelihood.cpp.

References likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by getD2LikelihoodForASite().

getD2LogLikelihood()

double RNonHomogeneousTreeLikelihood::getD2LogLikelihood ( ) const

virtual

Definition at line 793 of file RNonHomogeneousTreeLikelihood.cpp.

References getD2LogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.

Referenced by getSecondOrderDerivative().

getD2LogLikelihoodForASite()

double RNonHomogeneousTreeLikelihood::getD2LogLikelihoodForASite ( size_t  site ) const

virtual

Definition at line 785 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by getD2LogLikelihood().

getDerivableParameters() [1/2]

ParameterList AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters ( ) const

virtualinherited

All derivable parameters.

Usually, this contains all branch lengths parameters.

Returns

A ParameterList.

Implements bpp::TreeLikelihoodInterface.

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 RNonHomogeneousTreeLikelihood::getDLikelihoodForASite ( size_t  site ) const

virtual

Definition at line 301 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by getD2LogLikelihoodForASite(), and getDLogLikelihoodForASite().

getDLikelihoodForASiteForARateClass()

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

virtual

Definition at line 286 of file RNonHomogeneousTreeLikelihood.cpp.

References likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by getDLikelihoodForASite().

getDLogLikelihood()

double RNonHomogeneousTreeLikelihood::getDLogLikelihood ( ) const

virtual

Definition at line 322 of file RNonHomogeneousTreeLikelihood.cpp.

References getDLogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.

Referenced by getFirstOrderDerivative().

getDLogLikelihoodForASite()

double RNonHomogeneousTreeLikelihood::getDLogLikelihoodForASite ( size_t  site ) const

virtual

Definition at line 314 of file RNonHomogeneousTreeLikelihood.cpp.

References getDLikelihoodForASite(), and getLikelihoodForASite().

Referenced by getDLogLikelihood().

getFirstOrderDerivative()

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

virtual

Implements bpp::SecondOrderDerivable.

Definition at line 335 of file RNonHomogeneousTreeLikelihood.cpp.

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

getLikelihood()

double RNonHomogeneousTreeLikelihood::getLikelihood ( ) const

virtual

Get the likelihood for the whole dataset.

Returns

The likelihood of the dataset.

Implements bpp::TreeLikelihoodInterface.

Definition at line 118 of file RNonHomogeneousTreeLikelihood.cpp.

References getLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.

getLikelihoodForASite()

double RNonHomogeneousTreeLikelihood::getLikelihoodForASite ( size_t  site ) const

virtual

Get the likelihood for a site.

Parameters

site	The site index to analyse.

Returns

The likelihood for site site.

Implements bpp::TreeLikelihoodInterface.

Definition at line 148 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by getD2LogLikelihoodForASite(), getDLogLikelihoodForASite(), and getLikelihood().

getLikelihoodForASiteForARateClass()

double RNonHomogeneousTreeLikelihood::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 175 of file RNonHomogeneousTreeLikelihood.cpp.

References likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

Referenced by getLikelihoodForASite(), and getLogLikelihoodForASite().

getLikelihoodForASiteForARateClassForAState()

double RNonHomogeneousTreeLikelihood::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 201 of file RNonHomogeneousTreeLikelihood.cpp.

References likelihoodData_, and bpp::AbstractTreeLikelihood::tree_.

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 75 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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

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.

Implements bpp::TreeLikelihoodInterface.

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.

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

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.

Implements bpp::TreeLikelihoodInterface.

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 RNonHomogeneousTreeLikelihood::getLogLikelihood ( ) const

virtual

Get the logarithm of the likelihood for the whole dataset.

Returns

The logarithm of the likelihood of the dataset.

Implements bpp::TreeLikelihoodInterface.

Definition at line 130 of file RNonHomogeneousTreeLikelihood.cpp.

References getLogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.

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

getLogLikelihoodForASite()

double RNonHomogeneousTreeLikelihood::getLogLikelihoodForASite ( size_t  site ) const

virtual

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 160 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by getLogLikelihood().

getLogLikelihoodForASiteForARateClass()

double RNonHomogeneousTreeLikelihood::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 188 of file RNonHomogeneousTreeLikelihood.cpp.

References likelihoodData_, bpp::log(), bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.

getLogLikelihoodForASiteForARateClassForAState()

double RNonHomogeneousTreeLikelihood::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 208 of file RNonHomogeneousTreeLikelihood.cpp.

References likelihoodData_, bpp::log(), and bpp::AbstractTreeLikelihood::tree_.

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 88 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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

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.

Implements bpp::TreeLikelihoodInterface.

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.

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

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.

Implements bpp::TreeLikelihoodInterface.

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::AbstractNonHomogeneousTreeLikelihood::getMaximumBranchLength ( ) const

inlinevirtualinherited

Definition at line 244 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_.

getMinimumBranchLength()

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

inlinevirtualinherited

Definition at line 243 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_.

getModelForNode() [1/2]

std::shared_ptr<const TransitionModelInterface> bpp::AbstractNonHomogeneousTreeLikelihood::getModelForNode ( int  nodeId ) const

inlineoverridevirtualinherited

Get the model associated to a given node.

Parameters

nodeId

The id of the request node.

Returns

A pointer toward the corresponding model.

Exceptions

NodeNotFoundException

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

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 158 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

getModelForNode() [2/2]

std::shared_ptr<TransitionModelInterface> bpp::AbstractNonHomogeneousTreeLikelihood::getModelForNode ( int  nodeId )

inlineoverridevirtualinherited

Get the substitution model associated to a given node.

Parameters

nodeId

The id of the request node.

Returns

A pointer toward the corresponding model.

Exceptions

NodeNotFoundException

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

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 163 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

getModelForSite() [1/2]

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

inlineoverridevirtualinherited

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 32 of file NonHomogeneousTreeLikelihood.h.

References bpp::NonHomogeneousTreeLikelihood::getModelForNode().

getModelForSite() [2/2]

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

inlineoverridevirtualinherited

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).

Implements bpp::TreeLikelihoodInterface.

Definition at line 37 of file NonHomogeneousTreeLikelihood.h.

References bpp::NonHomogeneousTreeLikelihood::getModelForNode().

getNewBranchModelIterator()

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

inlineoverridevirtualinherited

Implements bpp::TreeLikelihoodInterface.

Definition at line 172 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, and bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_.

getNewSiteModelIterator()

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

inlineoverridevirtualinherited

Implements bpp::TreeLikelihoodInterface.

Definition at line 177 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 46 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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

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_.

Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities().

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 268 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

Referenced by bpp::AbstractTreeLikelihood::getLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodPerSitePerRateClassPerState(), bpp::AbstractTreeLikelihood::getLikelihoodPerSitePerState(), bpp::AbstractTreeLikelihood::getLogLikelihoodPerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClass(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodPerSitePerRateClassPerState(), bpp::AbstractTreeLikelihood::getLogLikelihoodPerSitePerState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateClassWithMaxPostProbPerSite(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite().

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::AbstractNonHomogeneousTreeLikelihood::getNumberOfStates ( ) const

inlineoverridevirtualinherited

Returns

the number of model states of the underlying Markov chain.

Implements bpp::TreeLikelihoodInterface.

Definition at line 139 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

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.

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

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::AbstractNonHomogeneousTreeLikelihood::getRateDistributionParameters ( ) const

inlineoverridevirtualinherited

Get the parameters associated to the rate distribution.

Returns

A ParameterList object with all rate distribution parameters.

Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.

Definition at line 153 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters().

Referenced by bpp::DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), getFirstOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), and 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::AbstractNonHomogeneousTreeLikelihood::getRootFrequencies ( size_t  siteIndex ) const

inlineoverridevirtualinherited

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;

Implements bpp::TreeLikelihoodInterface.

Definition at line 168 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.

getRootFrequenciesParameters()

ParameterList bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequenciesParameters ( ) const

inlineoverridevirtualinherited

Returns

The parameters on which the root frequencies depend.

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 201 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

getSecondOrderDerivative() [1/2]

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

virtual

Implements bpp::SecondOrderDerivable.

Definition at line 806 of file RNonHomogeneousTreeLikelihood.cpp.

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

getSecondOrderDerivative() [2/2]

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

inlinevirtual

Implements bpp::SecondOrderDerivable.

Definition at line 175 of file RNonHomogeneousTreeLikelihood.h.

getSiteIndex()

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

inlinevirtual

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 130 of file RNonHomogeneousTreeLikelihood.h.

References likelihoodData_.

getSubstitutionModelParameters()

ParameterList AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters ( ) const

overridevirtualinherited

Get the parameters associated to substitution model(s).

Returns

A ParameterList.

Implements bpp::TreeLikelihoodInterface.

Definition at line 258 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), getFirstOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), and getSecondOrderDerivative().

getSubstitutionModelSet() [1/2]

std::shared_ptr<const SubstitutionModelSet> bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelSet ( ) const

inlineoverridevirtualinherited

Returns

The set of substitution models associated to this instance.

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 191 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

getSubstitutionModelSet() [2/2]

std::shared_ptr<SubstitutionModelSet> bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelSet ( )

inlineoverridevirtualinherited

Returns

The set of substitution models associated to this instance.

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 195 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

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.

Implements bpp::TreeLikelihoodInterface.

Definition at line 275 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.

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

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::AbstractNonHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass ( int  nodeId, size_t  siteIndex  ) const

inlineoverridevirtualinherited

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 170 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::pxy_.

getValue()

double RNonHomogeneousTreeLikelihood::getValue ( ) const

virtual

Implements bpp::SecondOrderDerivable.

Definition at line 276 of file RNonHomogeneousTreeLikelihood.cpp.

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

hasLikelihoodData() [1/2]

bool bpp::AbstractTreeLikelihood::hasLikelihoodData ( ) const

inlinevirtualinherited

Returns

True if the TreeLikelihood object has a LikelihoodData.

Implements bpp::TreeLikelihoodInterface.

Definition at line 261 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::data_.

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 RNonHomogeneousTreeLikelihood::init_ ( bool  usePatterns )

private

Method called by constructors.

Definition at line 58 of file RNonHomogeneousTreeLikelihood.cpp.

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

Referenced by RNonHomogeneousTreeLikelihood().

initBranchLengthsParameters()

void AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters ( bool  verbose = true )

virtualinherited

Definition at line 321 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::ParameterList::addParameter(), bpp::AbstractNonHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::ApplicationTools::displayWarning(), bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::Parameter::PROP_CONSTRAINT_EX, bpp::AbstractNonHomogeneousTreeLikelihood::reparametrizeRoot_, bpp::ParameterList::reset(), bpp::AbstractNonHomogeneousTreeLikelihood::root1_, bpp::AbstractNonHomogeneousTreeLikelihood::root2_, and bpp::TextTools::toString().

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().

initialize()

void AbstractNonHomogeneousTreeLikelihood::initialize ( )

overridevirtualinherited

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.

Implements bpp::TreeLikelihoodInterface.

Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.

Definition at line 234 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractTreeLikelihood::data_, bpp::AbstractParametrizable::fireParameterChanged(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractNonHomogeneousTreeLikelihood::initParameters().

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

initParameters()

void AbstractNonHomogeneousTreeLikelihood::initParameters ( )

virtualinherited

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

Definition at line 267 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::addParameters_(), bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, and bpp::AbstractParametrizable::resetParameters_().

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

isInitialized() [1/2]

bool bpp::AbstractTreeLikelihood::isInitialized ( ) const

inlinevirtualinherited

Returns

'true' is the likelihood function has been initialized.

Implements bpp::TreeLikelihoodInterface.

Definition at line 275 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::initialized_.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::getValue(), bpp::RHomogeneousTreeLikelihood::getValue(), 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::RNonHomogeneousTreeLikelihood::likelihoodData ( )

inlinevirtual

Returns

The underlying likelihood data structure.

Implements bpp::TreeLikelihoodInterface.

Definition at line 181 of file RNonHomogeneousTreeLikelihood.h.

References likelihoodData_.

likelihoodData() [2/2]

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

inlinevirtual

Returns

The underlying likelihood data structure.

Implements bpp::TreeLikelihoodInterface.

Definition at line 183 of file RNonHomogeneousTreeLikelihood.h.

References likelihoodData_.

operator=()

RNonHomogeneousTreeLikelihood & RNonHomogeneousTreeLikelihood::operator=

(

const RNonHomogeneousTreeLikelihood &

lik

)

Definition at line 80 of file RNonHomogeneousTreeLikelihood.cpp.

References likelihoodData_, minusLogLik_, bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), and bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::operator=().

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.

Referenced by bpp::DRHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodFromArrays(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRHomogeneousTreeLikelihood::resetLikelihoodArrays(), bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().

setData()

void RNonHomogeneousTreeLikelihood::setData ( const AlignmentDataInterface &  sites )

virtual

Set the dataset for which the likelihood must be evaluated.

Parameters

sites

The data set to use.

Implements bpp::TreeLikelihoodInterface.

Definition at line 96 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractTreeLikelihood::data_, bpp::ApplicationTools::displayResult(), bpp::ApplicationTools::displayTask(), bpp::ApplicationTools::displayTaskDone(), bpp::PatternTools::getSequenceSubset(), bpp::AbstractTreeLikelihood::initialized_, likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_, bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::TextTools::toString(), bpp::AbstractTreeLikelihood::tree_, and bpp::AbstractNonHomogeneousTreeLikelihood::verbose_.

Referenced by RNonHomogeneousTreeLikelihood(), and bpp::RNonHomogeneousMixedTreeLikelihood::setData().

setMaximumBranchLength()

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

inlinevirtualinherited

Definition at line 234 of file AbstractNonHomogeneousTreeLikelihood.h.

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

setMinimumBranchLength()

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

inlinevirtualinherited

Definition at line 225 of file AbstractNonHomogeneousTreeLikelihood.h.

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

setParameters()

void RNonHomogeneousTreeLikelihood::setParameters ( const ParameterList &  parameters )

virtual

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 215 of file RNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractParametrizable::setParametersValues().

setSubstitutionModelSet()

void AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet ( std::shared_ptr< SubstitutionModelSet >  model )

overridevirtualinherited

Returns

Set the substitution models for this instance.

Exceptions

Exception

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

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 159 of file AbstractNonHomogeneousTreeLikelihood.cpp.

References bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractNonHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractTreeLikelihood::data_, bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::AbstractParametrizable::fireParameterChanged(), bpp::Node::getId(), bpp::AbstractParametrizable::getParameters(), bpp::AbstractTreeLikelihood::initialized_, bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractNonHomogeneousTreeLikelihood::pxy_, and bpp::TreeLikelihoodInterface::setData().

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

substitutionModelSet() [1/2]

const SubstitutionModelSet& bpp::AbstractNonHomogeneousTreeLikelihood::substitutionModelSet ( ) const

inlineoverridevirtualinherited

Returns

The set of substitution models associated to this instance.

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 193 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

substitutionModelSet() [2/2]

SubstitutionModelSet& bpp::AbstractNonHomogeneousTreeLikelihood::substitutionModelSet ( )

inlineoverridevirtualinherited

Returns

The set of substitution models associated to this instance.

Implements bpp::NonHomogeneousTreeLikelihood.

Definition at line 197 of file AbstractNonHomogeneousTreeLikelihood.h.

References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.

tree() [1/2]

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

inlinevirtualinherited

Get the tree (topology and branch lengths).

Returns

The tree of this TreeLikelihood object.

Implements bpp::TreeLikelihoodInterface.

Definition at line 269 of file AbstractTreeLikelihood.h.

References bpp::AbstractTreeLikelihood::tree_.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::DRHomogeneousMixedTreeLikelihood::DRHomogeneousMixedTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousMixedTreeLikelihood::RHomogeneousMixedTreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood(), RNonHomogeneousTreeLikelihood(), and bpp::NNIHomogeneousTreeLikelihood::topology().

tree() [2/2]

virtual const Tree& bpp::TreeLikelihoodInterface::tree ( ) const

pure virtualinherited

Get the tree (topology and branch lengths).

Returns

The tree of this TreeLikelihood object.

Implemented in bpp::AbstractTreeLikelihood.

Referenced by bpp::PairedSiteLikelihoods::appendModel(), bpp::TreeLikelihoodTools::getAncestralFrequencies(), bpp::TreeLikelihoodTools::getAncestralFrequencies_(), and bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesPerStatePerRate().

Friends And Related Function Documentation

RNonHomogeneousMixedTreeLikelihood

friend class RNonHomogeneousMixedTreeLikelihood

friend

Definition at line 229 of file RNonHomogeneousTreeLikelihood.h.

Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::clone(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), and bpp::RNonHomogeneousMixedTreeLikelihood::RNonHomogeneousMixedTreeLikelihood().

Member Data Documentation

brLenConstraint_

std::shared_ptr<ConstraintInterface> bpp::AbstractNonHomogeneousTreeLikelihood::brLenConstraint_

protectedinherited

Definition at line 92 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().

brLenParameters_

ParameterList bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_

protectedinherited

Definition at line 58 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::RNonHomogeneousMixedTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

computeFirstOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_

protectedinherited

Definition at line 210 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().

computeSecondOrderDerivatives_

bool bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_

protectedinherited

Definition at line 211 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().

d2pxy_

std::map<int, VVVdouble> bpp::AbstractNonHomogeneousTreeLikelihood::d2pxy_

mutableprotectedinherited

Definition at line 64 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

data_

std::unique_ptr<const AlignmentDataInterface> bpp::AbstractTreeLikelihood::data_

protectedinherited

Definition at line 208 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::AbstractTreeLikelihood::data(), bpp::AbstractTreeLikelihood::getAlphabet(), bpp::AbstractTreeLikelihood::getNumberOfSites(), bpp::AbstractTreeLikelihood::hasLikelihoodData(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), setData(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::AbstractHomogeneousTreeLikelihood::setModel(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

dpxy_

std::map<int, VVVdouble> bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_

mutableprotectedinherited

Definition at line 62 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihood(), computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

idToNode_

std::map<int, const Node*> bpp::AbstractNonHomogeneousTreeLikelihood::idToNode_

mutableprotectedinherited

An index linking nodes to their id, for faster access than the getNode() method.

Definition at line 79 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

initialized_

bool bpp::AbstractTreeLikelihood::initialized_

protectedinherited

Definition at line 212 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getDerivableParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNonDerivableParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::isInitialized(), bpp::AbstractTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), setData(), bpp::DRHomogeneousTreeLikelihood::setData(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

likelihoodData_

std::shared_ptr<DRASRTreeLikelihoodData> bpp::RNonHomogeneousTreeLikelihood::likelihoodData_

mutableprivate

Definition at line 53 of file RNonHomogeneousTreeLikelihood.h.

Referenced by computeDownSubtreeD2Likelihood(), computeDownSubtreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihood(), displayLikelihood(), getD2LikelihoodForASiteForARateClass(), getDLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClassForAState(), getLogLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClassForAState(), getSiteIndex(), init_(), likelihoodData(), operator=(), RNonHomogeneousTreeLikelihood(), and setData().

maximumBrLen_

double bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_

protectedinherited

Definition at line 91 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getMaximumBranchLength(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().

minimumBrLen_

double bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_

protectedinherited

Definition at line 90 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getMinimumBranchLength(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().

minusLogLik_

double bpp::RNonHomogeneousTreeLikelihood::minusLogLik_

private

Definition at line 54 of file RNonHomogeneousTreeLikelihood.h.

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

modelSet_

std::shared_ptr<SubstitutionModelSet> bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_

protectedinherited

Definition at line 57 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStates(), bpp::AbstractNonHomogeneousTreeLikelihood::getModelForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewBranchModelIterator(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractNonHomogeneousTreeLikelihood::getNumberOfStates(), bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequenciesParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelSet(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), setData(), bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet(), and bpp::AbstractNonHomogeneousTreeLikelihood::substitutionModelSet().

nbClasses_

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_

protectedinherited

Definition at line 84 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by computeDownSubtreeD2Likelihood(), computeDownSubtreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), computeSubtreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), getD2LikelihoodForASite(), getDLikelihoodForASite(), getLikelihoodForASite(), getLogLikelihoodForASite(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

nbDistinctSites_

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_

protectedinherited

Definition at line 83 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewBranchModelIterator(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), and setData().

nbNodes_

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_

protectedinherited

Definition at line 86 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

nbSites_

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_

protectedinherited

Definition at line 82 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by getD2LogLikelihood(), getDLogLikelihood(), getLikelihood(), getLogLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), and setData().

nbStates_

size_t bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_

protectedinherited

Definition at line 85 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by computeDownSubtreeD2Likelihood(), computeDownSubtreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), computeSubtreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), getD2LikelihoodForASiteForARateClass(), getDLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClass(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), setData(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

nodes_

std::vector<Node*> bpp::AbstractNonHomogeneousTreeLikelihood::nodes_

protectedinherited

Pointer toward all nodes in the tree.

The position in the array is the number used in the parameter name. This may be different from the node id, unless you used the resetNodeId method on the input tree.

Definition at line 74 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

pxy_

std::map<int, VVVdouble> bpp::AbstractNonHomogeneousTreeLikelihood::pxy_

mutableprotectedinherited

Definition at line 60 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by computeDownSubtreeD2Likelihood(), computeDownSubtreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), computeSubtreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractNonHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), and bpp::AbstractNonHomogeneousTreeLikelihood::setSubstitutionModelSet().

rateDistribution_

std::shared_ptr<DiscreteDistributionInterface> bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_

protectedinherited

Definition at line 26 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), getLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLikelihoodForASiteForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), getLogLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getLogLikelihoodForASiteForAState(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorProbabilitiesPerRate(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getPosteriorRatePerSite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateWithMaxPostProbPerSite(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getTransitionProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::DRHomogeneousTreeLikelihood::init_(), bpp::DRNonHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousTreeLikelihood::init_(), init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution(), and bpp::NNIHomogeneousTreeLikelihood::testNNI().

reparametrizeRoot_

bool bpp::AbstractNonHomogeneousTreeLikelihood::reparametrizeRoot_

protectedinherited

Definition at line 94 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

root1_

int bpp::AbstractNonHomogeneousTreeLikelihood::root1_

protectedinherited

Definition at line 95 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), computeTreeD2Likelihood(), computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

root2_

int bpp::AbstractNonHomogeneousTreeLikelihood::root2_

protectedinherited

Definition at line 95 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), computeTreeD2Likelihood(), computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::getFirstOrderDerivative(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

rootFreqs_

std::vector<double> bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_

protectedinherited

Definition at line 66 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), getD2LikelihoodForASiteForARateClass(), getDLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClass(), bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequencies(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().

tree_

std::shared_ptr< TreeTemplate<Node> > bpp::AbstractTreeLikelihood::tree_

mutableprotectedinherited

Definition at line 209 of file AbstractTreeLikelihood.h.

Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood(), computeTreeLikelihood(), bpp::NNIHomogeneousTreeLikelihood::doNNI(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), getLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::DRNonHomogeneousTreeLikelihood::getSecondOrderDerivative(), bpp::DRHomogeneousTreeLikelihood::init_(), bpp::DRNonHomogeneousTreeLikelihood::init_(), bpp::RHomogeneousTreeLikelihood::init_(), init_(), bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::init_(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractTreeLikelihood::operator=(), bpp::DRHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::operator=(), operator=(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), RNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::setData(), bpp::RHomogeneousTreeLikelihood::setData(), setData(), bpp::DRHomogeneousTreeLikelihood::setData(), bpp::NNIHomogeneousTreeLikelihood::testNNI(), and bpp::AbstractTreeLikelihood::tree().

verbose_

bool bpp::AbstractNonHomogeneousTreeLikelihood::verbose_

protectedinherited

Definition at line 88 of file AbstractNonHomogeneousTreeLikelihood.h.

Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::init_(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::setData(), and setData().

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

• Bpp/Phyl/Legacy/Likelihood/RNonHomogeneousTreeLikelihood.h
• Bpp/Phyl/Legacy/Likelihood/RNonHomogeneousTreeLikelihood.cpp