bpp-phyl
2.2.0
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This class implement the 'traditional' way of computing likelihood for a tree, allowing for non-homogeneous models of substitutions. More...
#include <Bpp/Phyl/Likelihood/RNonHomogeneousTreeLikelihood.h>
Public Member Functions | |
RNonHomogeneousTreeLikelihood (const Tree &tree, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose=true, bool usePatterns=true, bool reparametrizeRoot=false) throw (Exception) | |
Build a new NonHomogeneousTreeLikelihood object without data. More... | |
RNonHomogeneousTreeLikelihood (const Tree &tree, const SiteContainer &data, SubstitutionModelSet *modelSet, DiscreteDistribution *rDist, bool verbose=true, bool usePatterns=true, bool reparametrizeRoot=false) throw (Exception) | |
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 ¶meters) throw (ParameterNotFoundException, ConstraintException) |
Implements the Function interface. More... | |
double | getValue () const throw (Exception) |
DRASRTreeLikelihoodData * | getLikelihoodData () |
const DRASRTreeLikelihoodData * | getLikelihoodData () 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 () throw (Exception) |
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 () |
virtual void | setMinimumBranchLength (double minimum) throw (Exception) |
virtual void | setMaximumBranchLength (double maximum) throw (Exception) |
virtual double | getMinimumBranchLength () const |
virtual double | getMaximumBranchLength () const |
const SubstitutionModel * | getSubstitutionModel (int nodeId, size_t siteIndex) const throw (NodeNotFoundException) |
Get the substitution model associated to a given node and alignment column. More... | |
SubstitutionModel * | getSubstitutionModel (int nodeId, size_t siteIndex) throw (NodeNotFoundException) |
Get the substitution model associated to a given node and alignment column. More... | |
virtual const SiteContainer * | getData () const =0 |
Get the dataset for which the likelihood must be evaluated. More... | |
virtual bool | isInitialized () 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 | getLikelihoodForEachSite () const =0 |
Get the likelihood for each site. More... | |
virtual Vdouble | getLogLikelihoodForEachSite () const =0 |
Get the logarithm of the likelihood for each site. More... | |
virtual VVdouble | getLikelihoodForEachSiteForEachState () const =0 |
Get the likelihood for each site and for each state. More... | |
virtual VVdouble | getLogLikelihoodForEachSiteForEachState () const =0 |
Get the logarithm of the likelihood for each site and for each state. More... | |
virtual const Tree & | getTree () 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 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... | |
The TreeLikelihood interface. | |
Other methods are implemented in the AbstractHomogeneousTreeLikelihood class. | |
void | setData (const SiteContainer &sites) throw (Exception) |
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 throw (IndexOutOfBoundsException) |
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 throw (Exception) |
DerivableSecondOrder interface. | |
double | getSecondOrderDerivative (const std::string &variable) const throw (Exception) |
double | getSecondOrderDerivative (const std::string &variable1, const std::string &variable2) const throw (Exception) |
The TreeLikelihood interface. | |
Other methods are implemented in the AbstractTreeLikelihood class. | |
size_t | getNumberOfStates () const |
const std::vector< int > & | getAlphabetStates () const |
int | getAlphabetStateAsInt (size_t i) const |
std::string | getAlphabetStateAsChar (size_t i) const |
void | initialize () throw (Exception) |
Init the likelihood object. More... | |
ParameterList | getBranchLengthsParameters () const |
Get the branch lengths parameters. More... | |
ParameterList | getSubstitutionModelParameters () const |
Get the parameters associated to substitution model(s). More... | |
ParameterList | getRateDistributionParameters () const |
Get the parameters associated to the rate distirbution. More... | |
const SubstitutionModel * | getSubstitutionModelForNode (int nodeId) const throw (NodeNotFoundException) |
Get the substitution model associated to a given node. More... | |
SubstitutionModel * | getSubstitutionModelForNode (int nodeId) throw (NodeNotFoundException) |
Get the substitution model associated to a given node. More... | |
const std::vector< double > & | getRootFrequencies (size_t siteIndex) const |
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 |
Retrieves all Pij(t) for a particular branch, defined by the upper node. More... | |
ConstBranchModelIterator * | getNewBranchModelIterator (int nodeId) const |
ConstSiteModelIterator * | getNewSiteModelIterator (size_t siteIndex) const |
The NonHomogeneousTreeLikelihood interface. | |
Other methods are implemented in the AbstractTreeLikelihood class. | |
const SubstitutionModelSet * | getSubstitutionModelSet () const |
SubstitutionModelSet * | getSubstitutionModelSet () |
void | setSubstitutionModelSet (SubstitutionModelSet *modelSet) throw (Exception) |
ParameterList | getRootFrequenciesParameters () const |
The TreeLikelihood interface. | |
const SiteContainer * | getData () const |
Get the dataset for which the likelihood must be evaluated. More... | |
bool | isInitialized () const |
Vdouble | getLikelihoodForEachSite () const |
Get the likelihood for each site. More... | |
Vdouble | getLogLikelihoodForEachSite () const |
Get the logarithm of the likelihood for each site. More... | |
VVdouble | getLikelihoodForEachSiteForEachState () const |
Get the likelihood for each site and for each state. More... | |
VVdouble | getLogLikelihoodForEachSiteForEachState () const |
Get the logarithm of the likelihood for each site and for each state. More... | |
const Tree & | getTree () const |
Get the tree (topology and branch lengths). More... | |
size_t | getNumberOfSites () const |
Get the number of sites in the dataset. More... | |
const Alphabet * | getAlphabet () const |
Get the alphabet associated to the dataset. More... | |
void | enableDerivatives (bool yn) |
Tell if derivatives must be computed. More... | |
void | enableFirstOrderDerivatives (bool yn) |
bool | enableFirstOrderDerivatives () const |
void | enableSecondOrderDerivatives (bool yn) |
bool | enableSecondOrderDerivatives () 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: | |
const DiscreteDistribution * | getRateDistribution () const |
Get the rate distribution used for the computation. More... | |
DiscreteDistribution * | getRateDistribution () |
Get the rate distribution used for the computation. More... | |
size_t | getNumberOfClasses () const |
Get the number of classes. More... | |
VVdouble | getLikelihoodForEachSiteForEachRateClass () const |
Get the likelihood for each site and each rate class. More... | |
VVdouble | getLogLikelihoodForEachSiteForEachRateClass () const |
Get the logarithm of the likelihood for each site and each rate class. More... | |
VVVdouble | getLikelihoodForEachSiteForEachRateClassForEachState () const |
Get the likelihood for each site and each rate class and each state. More... | |
VVVdouble | getLogLikelihoodForEachSiteForEachRateClassForEachState () const |
Get the logarithm of the likelihood for each site and each rate class and each state. More... | |
VVdouble | getPosteriorProbabilitiesOfEachRate () const |
Get the posterior probability for each site of belonging to a particular rate class. More... | |
Vdouble | getRateWithMaxPostProbOfEachSite () const |
Get the posterior rate (the one with maximum posterior probability) for each site. More... | |
std::vector< size_t > | getRateClassWithMaxPostProbOfEachSite () const |
Get the posterior rate class (the one with maximum posterior probability) for each site. More... | |
Vdouble | getPosteriorRateOfEachSite () 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 ¶ms) |
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... | |
Protected Attributes | |
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::auto_ptr< Constraint > | brLenConstraint_ |
bool | reparametrizeRoot_ |
int | root1_ |
int | root2_ |
DiscreteDistribution * | rateDistribution_ |
const SiteContainer * | data_ |
TreeTemplate< Node > * | tree_ |
bool | computeFirstOrderDerivatives_ |
bool | computeSecondOrderDerivatives_ |
bool | initialized_ |
Private Member Functions | |
void | init_ (bool usePatterns) throw (Exception) |
Method called by constructors. More... | |
Private Attributes | |
DRASRTreeLikelihoodData * | likelihoodData_ |
double | minusLogLik_ |
Friends | |
class | RNonHomogeneousMixedTreeLikelihood |
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 conditionnal 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:
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 86 of file RNonHomogeneousTreeLikelihood.h.
RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood | ( | const Tree & | tree, |
SubstitutionModelSet * | modelSet, | ||
DiscreteDistribution * | rDist, | ||
bool | verbose = true , |
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bool | usePatterns = true , |
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bool | reparametrizeRoot = false |
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throw | ( | Exception | |
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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.
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? |
Exception | in an error occured. |
Definition at line 56 of file RNonHomogeneousTreeLikelihood.cpp.
Referenced by clone().
RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood | ( | const Tree & | tree, |
const SiteContainer & | data, | ||
SubstitutionModelSet * | modelSet, | ||
DiscreteDistribution * | rDist, | ||
bool | verbose = true , |
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bool | usePatterns = true , |
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bool | reparametrizeRoot = false |
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throw | ( | Exception | |
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Build a new NonHomogeneousTreeLikelihood object and compute the corresponding likelihood.
This constructor initializes all parameters, data, and likelihood arrays.
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? |
Exception | in an error occured. |
Definition at line 75 of file RNonHomogeneousTreeLikelihood.cpp.
RNonHomogeneousTreeLikelihood::RNonHomogeneousTreeLikelihood | ( | const RNonHomogeneousTreeLikelihood & | lik | ) |
Definition at line 106 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::clone(), likelihoodData_, bpp::DRASRTreeLikelihoodData::setTree(), and bpp::AbstractTreeLikelihood::tree_.
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virtual |
Definition at line 131 of file RNonHomogeneousTreeLikelihood.cpp.
References likelihoodData_.
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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 314 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::initialized_, bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractNonHomogeneousTreeLikelihood::reparametrizeRoot_, bpp::AbstractNonHomogeneousTreeLikelihood::root1_, and bpp::AbstractNonHomogeneousTreeLikelihood::root2_.
Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), and bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged().
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inlinevirtual |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 149 of file RNonHomogeneousTreeLikelihood.h.
References RNonHomogeneousTreeLikelihood().
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protectedvirtualinherited |
Fill the pxy_, dpxy_ and d2pxy_ arrays for all nodes.
Definition at line 393 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::SubstitutionModelSet::getRootFrequencies(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, and bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.
Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), and bpp::AbstractNonHomogeneousTreeLikelihood::initialize().
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protectedvirtual |
Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.
Definition at line 1195 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractNonHomogeneousTreeLikelihood::pxy_.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeD2Likelihood(), and computeTreeD2Likelihood().
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protectedvirtual |
Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.
Definition at line 707 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), bpp::Node::getSon(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, and bpp::AbstractNonHomogeneousTreeLikelihood::pxy_.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeDownSubtreeDLikelihood(), and computeTreeDLikelihood().
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protectedvirtual |
Compute the likelihood for a subtree defined by the Tree::Node node.
node | The root of the subtree. |
Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.
Definition at line 1292 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), 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().
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protectedvirtualinherited |
Fill the pxy_, dpxy_ and d2pxy_ arrays for one node.
Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.
Definition at line 406 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_, bpp::AbstractNonHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::SubstitutionModel::getd2Pij_dt2(), bpp::Node::getDistanceToFather(), bpp::SubstitutionModel::getdPij_dt(), bpp::Node::getId(), bpp::SubstitutionModelSet::getModelForNode(), bpp::SubstitutionModel::getPij_t(), 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().
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virtual |
Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.
Definition at line 868 of file RNonHomogeneousTreeLikelihood.cpp.
References computeDownSubtreeD2Likelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::d2pxy_, bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), 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().
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virtual |
Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.
Definition at line 396 of file RNonHomogeneousTreeLikelihood.cpp.
References computeDownSubtreeDLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::dpxy_, bpp::DRASRTreeLikelihoodData::getArrayPositions(), bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::Node::getFather(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getNumberOfSons(), 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().
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virtual |
Definition at line 1285 of file RNonHomogeneousTreeLikelihood.cpp.
References computeSubtreeLikelihood(), and bpp::AbstractTreeLikelihood::tree_.
Referenced by fireParameterChanged(), and bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged().
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protectedvirtual |
This method is mainly for debugging purpose.
node | The node at which likelihood values must be displayed. |
Definition at line 1359 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::displayLikelihoodArray(), bpp::Node::getId(), bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::Node::getName(), and likelihoodData_.
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staticinherited |
Print the likelihood array to terminal (debugging tool).
likelihoodArray | the likelihood array. |
Definition at line 287 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
Referenced by bpp::DRHomogeneousTreeLikelihood::displayLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::displayLikelihood(), bpp::RHomogeneousTreeLikelihood::displayLikelihood(), and displayLikelihood().
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inlinevirtualinherited |
Tell if derivatives must be computed.
This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.
yn | Yes or no. |
Implements bpp::TreeLikelihood.
Definition at line 292 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.
Referenced by bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::AbstractDiscreteRatesAcrossSitesTreeLikelihood(), and bpp::DistanceEstimation::computeMatrix().
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pure virtualinherited |
Tell if derivatives must be computed.
This methods calls the enableFirstOrderDerivatives and enableSecondOrderDerivatives.
yn | Yes or no. |
Implemented in bpp::AbstractTreeLikelihood.
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inlineinherited |
Definition at line 293 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.
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inlineinherited |
Definition at line 295 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_.
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inlineinherited |
Definition at line 294 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeFirstOrderDerivatives_, and bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.
|
inlineinherited |
Definition at line 296 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::computeSecondOrderDerivatives_.
|
protected |
Definition at line 262 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeLikelihood(), getLogLikelihood(), bpp::SubstitutionModelSet::getNodeParameters(), bpp::SubstitutionModelSet::getNodesWithParameter(), bpp::SubstitutionModelSet::getRootFrequencies(), bpp::AbstractNonHomogeneousTreeLikelihood::idToNode_, minusLogLik_, bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
|
inlinevirtualinherited |
Get the alphabet associated to the dataset.
Implements bpp::TreeLikelihood.
Definition at line 285 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::data_.
|
pure virtualinherited |
Get the alphabet associated to the dataset.
Implemented in bpp::AbstractTreeLikelihood.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 183 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getAlphabetStateAsChar(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 181 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getAlphabetStateAsInt(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 179 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getAlphabetStates(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
virtualinherited |
Get the branch lengths parameters.
Implements bpp::TreeLikelihood.
Definition at line 280 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, and bpp::AbstractTreeLikelihood::initialized_.
|
virtual |
Definition at line 814 of file RNonHomogeneousTreeLikelihood.cpp.
References getD2LikelihoodForASiteForARateClass(), bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by getD2LogLikelihoodForASite().
|
virtual |
Definition at line 799 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getD2LikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
Referenced by getD2LikelihoodForASite().
|
virtual |
Definition at line 835 of file RNonHomogeneousTreeLikelihood.cpp.
References getD2LogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.
|
virtual |
Definition at line 827 of file RNonHomogeneousTreeLikelihood.cpp.
References getD2LikelihoodForASite(), getDLikelihoodForASite(), and getLikelihoodForASite().
Referenced by getD2LogLikelihood().
|
pure virtualinherited |
Get the dataset for which the likelihood must be evaluated.
Implemented in bpp::AbstractTreeLikelihood.
|
inlinevirtualinherited |
Get the dataset for which the likelihood must be evaluated.
Implements bpp::TreeLikelihood.
Definition at line 284 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::data_.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::init().
|
virtualinherited |
All derivable parameters.
Usually, this contains all branch lengths parameters.
Implements bpp::TreeLikelihood.
Reimplemented in bpp::RHomogeneousClockTreeLikelihood.
Definition at line 73 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
All derivable parameters.
Usually, this contains all branch lengths parameters.
Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
|
virtual |
Definition at line 342 of file RNonHomogeneousTreeLikelihood.cpp.
References getDLikelihoodForASiteForARateClass(), bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by getD2LogLikelihoodForASite(), and getDLogLikelihoodForASite().
|
virtual |
Definition at line 327 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getDLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
Referenced by getDLikelihoodForASite().
|
virtual |
Definition at line 363 of file RNonHomogeneousTreeLikelihood.cpp.
References getDLogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.
|
virtual |
Definition at line 355 of file RNonHomogeneousTreeLikelihood.cpp.
References getDLikelihoodForASite(), and getLikelihoodForASite().
Referenced by getDLogLikelihood().
double RNonHomogeneousTreeLikelihood::getFirstOrderDerivative | ( | const std::string & | variable | ) | const |
throw | ( | Exception | |||
) |
Definition at line 376 of file RNonHomogeneousTreeLikelihood.cpp.
|
virtual |
Get the likelihood for the whole dataset.
Implements bpp::TreeLikelihood.
Definition at line 158 of file RNonHomogeneousTreeLikelihood.cpp.
References getLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.
|
inlinevirtual |
Implements bpp::TreeLikelihood.
Definition at line 222 of file RNonHomogeneousTreeLikelihood.h.
References likelihoodData_.
|
inlinevirtual |
Implements bpp::TreeLikelihood.
Definition at line 223 of file RNonHomogeneousTreeLikelihood.h.
References likelihoodData_.
|
virtual |
Get the likelihood for a site.
site | The site index to analyse. |
Implements bpp::TreeLikelihood.
Definition at line 188 of file RNonHomogeneousTreeLikelihood.cpp.
References getLikelihoodForASiteForARateClass(), bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by getD2LogLikelihoodForASite(), getDLogLikelihoodForASite(), and getLikelihood().
|
virtual |
Get the likelihood for a site knowing its rate class.
site | The site index. |
rateClass | The rate class index. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 214 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
Referenced by getLikelihoodForASite(), and getLogLikelihoodForASite().
|
virtual |
Get the likelihood for a site knowing its rate class and its ancestral state.
site | The site index. |
rateClass | The rate class index. |
state | The ancestral state. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 240 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), likelihoodData_, and bpp::AbstractTreeLikelihood::tree_.
|
virtualinherited |
Get the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implements bpp::TreeLikelihood.
Definition at line 111 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
Get the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState().
|
pure virtualinherited |
Get the likelihood for each site.
Implemented in bpp::AbstractTreeLikelihood.
|
virtualinherited |
Get the likelihood for each site.
Implements bpp::TreeLikelihood.
Definition at line 46 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().
|
virtualinherited |
Get the likelihood for each site and each rate class.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 93 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
virtualinherited |
Get the likelihood for each site and each rate class and each state.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 156 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
Get the likelihood for each site and for each state.
Implemented in bpp::AbstractTreeLikelihood.
|
virtualinherited |
Get the likelihood for each site and for each state.
Implements bpp::TreeLikelihood.
Definition at line 64 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().
|
virtual |
Get the logarithm of the likelihood for the whole dataset.
Implements bpp::TreeLikelihood.
Definition at line 170 of file RNonHomogeneousTreeLikelihood.cpp.
References getLogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::nbSites_.
Referenced by fireParameterChanged(), and bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged().
|
virtual |
Get the logarithm of the likelihood for a site.
site | The site index to analyse. |
Implements bpp::TreeLikelihood.
Definition at line 200 of file RNonHomogeneousTreeLikelihood.cpp.
References getLikelihoodForASiteForARateClass(), bpp::AbstractNonHomogeneousTreeLikelihood::nbClasses_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by getLogLikelihood().
|
virtual |
Get the logarithm of the likelihood for a site knowing its rate class.
site | The site index. |
rateClass | The rate class index. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 227 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), likelihoodData_, bpp::AbstractNonHomogeneousTreeLikelihood::nbStates_, bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_, and bpp::AbstractTreeLikelihood::tree_.
|
virtual |
Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state.
site | The site index. |
rateClass | The rate class index. |
state | The ancestral state. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 247 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::getLikelihoodArray(), bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), likelihoodData_, and bpp::AbstractTreeLikelihood::tree_.
|
virtualinherited |
Get the logarithm of the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implements bpp::TreeLikelihood.
Definition at line 124 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
Get the logarithm of the likelihood for a site and for a state.
site | The site index to analyse. |
state | The state to consider. |
Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Referenced by bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState().
|
pure virtualinherited |
Get the logarithm of the likelihood for each site.
Implemented in bpp::AbstractTreeLikelihood.
|
virtualinherited |
Get the logarithm of the likelihood for each site.
Implements bpp::TreeLikelihood.
Definition at line 55 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLogLikelihoodForASite(), and bpp::AbstractTreeLikelihood::getNumberOfSites().
|
virtualinherited |
Get the logarithm of the likelihood for each site and each rate class.
V[i][j] =
likelihood of site i and rate class j. Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 138 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
virtualinherited |
Get the logarithm of the likelihood for each site and each rate class and each state.
V[i][j][k} =
likelihood of site i and rate class j and state k. Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 179 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
Get the logarithm of the likelihood for each site and for each state.
Implemented in bpp::AbstractTreeLikelihood.
|
virtualinherited |
Get the logarithm of the likelihood for each site and for each state.
Implements bpp::TreeLikelihood.
Definition at line 81 of file AbstractTreeLikelihood.cpp.
References bpp::TreeLikelihood::getLogLikelihoodForASiteForAState(), bpp::AbstractTreeLikelihood::getNumberOfSites(), and bpp::TreeLikelihood::getNumberOfStates().
|
inlinevirtualinherited |
Definition at line 279 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_.
|
inlinevirtualinherited |
Definition at line 278 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 210 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getModelForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, and bpp::AbstractNonHomogeneousTreeLikelihood::nbDistinctSites_.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 215 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
virtualinherited |
All non derivable parameters.
Usually, this contains all substitution model parameters and rate distribution.
Implements bpp::TreeLikelihood.
Reimplemented in bpp::RHomogeneousClockTreeLikelihood.
Definition at line 82 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
pure virtualinherited |
All non derivable parameters.
Usually, this contains all substitution model parameters and rate distribution.
Implemented in bpp::RHomogeneousClockTreeLikelihood, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
|
inlinevirtualinherited |
Get the number of classes.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 108 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
|
inlinevirtualinherited |
Get the number of sites in the dataset.
Implements bpp::TreeLikelihood.
Definition at line 290 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::data_.
Referenced by bpp::AbstractTreeLikelihood::getLikelihoodForEachSite(), bpp::AbstractTreeLikelihood::getLikelihoodForEachSiteForEachState(), bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSite(), and bpp::AbstractTreeLikelihood::getLogLikelihoodForEachSiteForEachState().
|
pure virtualinherited |
Get the number of sites in the dataset.
Implemented in bpp::AbstractTreeLikelihood.
Referenced by bpp::SubstitutionMappingTools::getNormalizationsPerBranch().
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 177 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getNumberOfStates(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
virtualinherited |
Get the posterior probability for each site of belonging to a particular rate class.
V[i][j] =
probablity for site i of belonging to rate class j. Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 202 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
virtualinherited |
Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities, for each site.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 220 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
virtualinherited |
Get the posterior rate class (the one with maximum posterior probability) for each site.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 239 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
inlinevirtualinherited |
Get the rate distribution used for the computation.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 106 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
|
inlinevirtualinherited |
Get the rate distribution used for the computation.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 107 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
|
inlinevirtualinherited |
Get the parameters associated to the rate distirbution.
Reimplemented from bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 191 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistributionParameters().
|
virtualinherited |
Get the posterior rate (the one with maximum posterior probability) for each site.
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 253 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
inlinevirtualinherited |
Get the values of the frequencies for each state in the alphabet at the root node.
For reversible models, these are the equilibrium frequencies. For non-reversible models, these usually are distinct parameters.
For models without site partitioning, the set of frequencies is the same for all positions. For partition models, the frequencies may differ from one site to another.
siteIndex | The index of the alignment position. |
Implements bpp::TreeLikelihood.
Definition at line 206 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::rootFreqs_.
|
inlinevirtualinherited |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 235 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getRootFrequenciesParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
double RNonHomogeneousTreeLikelihood::getSecondOrderDerivative | ( | const std::string & | variable | ) | const |
throw | ( | Exception | |||
) |
Definition at line 848 of file RNonHomogeneousTreeLikelihood.cpp.
|
inline |
Definition at line 217 of file RNonHomogeneousTreeLikelihood.h.
|
inlinevirtual |
Get the index (used for inner computations) of a given site (original alignment column).
site | An alignment position. |
Implements bpp::TreeLikelihood.
Definition at line 172 of file RNonHomogeneousTreeLikelihood.h.
References bpp::DRASRTreeLikelihoodData::getRootArrayPosition(), and likelihoodData_.
|
inlinevirtualinherited |
Get the substitution model associated to a given node and alignment column.
nodeId | The id of the request node. |
siteIndex | The index of the alignment position. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implements bpp::TreeLikelihood.
Definition at line 69 of file NonHomogeneousTreeLikelihood.h.
References bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelForNode().
|
inlinevirtualinherited |
Get the substitution model associated to a given node and alignment column.
nodeId | The id of the request node. |
siteIndex | The index of the alignment position. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implements bpp::TreeLikelihood.
Definition at line 74 of file NonHomogeneousTreeLikelihood.h.
References bpp::NonHomogeneousTreeLikelihood::getSubstitutionModelForNode().
|
inlinevirtualinherited |
Get the substitution model associated to a given node.
nodeId | The id of the request node. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 196 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getModelForNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Get the substitution model associated to a given node.
nodeId | The id of the request node. |
NodeNotFoundException | This exception may be thrown if the node is not found (depending on the implementation). |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 201 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::SubstitutionModelSet::getModelForNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
virtualinherited |
Get the parameters associated to substitution model(s).
Implements bpp::TreeLikelihood.
Definition at line 288 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 229 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
inlinevirtualinherited |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 231 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_.
|
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.
nodeId | The node defining the branch of interest. |
siteIndex | The index of the alignment position. |
Implements bpp::TreeLikelihood.
Definition at line 311 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.cpp.
|
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.
nodeId | The node defining the branch of interest. |
siteIndex | The index of the alignment position. |
Implemented in bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood.
|
inlinevirtualinherited |
Retrieves all Pij(t) for a particular branch, defined by the upper node.
These intermediate results may be used by other methods.
nodeId | The node defining the branch of interest. |
siteIndex | The position in the alignment. |
Implements bpp::DiscreteRatesAcrossSitesTreeLikelihood.
Definition at line 208 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::pxy_.
|
inlinevirtualinherited |
Get the tree (topology and branch lengths).
Implements bpp::TreeLikelihood.
Definition at line 291 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::tree_.
Referenced by bpp::NNIHomogeneousTreeLikelihood::getTopology(), and bpp::RNonHomogeneousMixedTreeLikelihood::init().
|
pure virtualinherited |
Get the tree (topology and branch lengths).
Implemented in bpp::AbstractTreeLikelihood.
Referenced by bpp::GlobalClockTreeLikelihoodFunctionWrapper::fireParameterChanged(), bpp::SubstitutionMappingTools::getNormalizedCountsPerBranch(), bpp::DRTreeLikelihoodTools::getPosteriorProbabilitiesForEachStateForEachRate(), and bpp::GlobalClockTreeLikelihoodFunctionWrapper::initParameters_().
double RNonHomogeneousTreeLikelihood::getValue | ( | ) | const | |
throw | ( | Exception | ||
) |
Definition at line 316 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractTreeLikelihood::isInitialized(), and minusLogLik_.
|
private |
Method called by constructors.
Definition at line 96 of file RNonHomogeneousTreeLikelihood.cpp.
|
virtualinherited |
Definition at line 348 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_, bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_, bpp::AbstractNonHomogeneousTreeLikelihood::nbNodes_, bpp::AbstractNonHomogeneousTreeLikelihood::nodes_, bpp::AbstractNonHomogeneousTreeLikelihood::reparametrizeRoot_, bpp::AbstractNonHomogeneousTreeLikelihood::root1_, and bpp::AbstractNonHomogeneousTreeLikelihood::root2_.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().
|
virtualinherited |
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.
Exception | if something bad happened, for instance if no data are associated to the likelihood function. |
Implements bpp::TreeLikelihood.
Reimplemented in bpp::RNonHomogeneousMixedTreeLikelihood.
Definition at line 268 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::AbstractTreeLikelihood::data_, bpp::AbstractTreeLikelihood::initialized_, and bpp::AbstractNonHomogeneousTreeLikelihood::initParameters().
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::initialize().
|
virtualinherited |
This builds the parameters list from all parametrizable objects, i.e. substitution model, rate distribution and tree.
Definition at line 296 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::AbstractNonHomogeneousTreeLikelihood::brLenParameters_, bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::modelSet_, and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::rateDistribution_.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), and bpp::RNonHomogeneousMixedTreeLikelihood::initialize().
|
pure virtualinherited |
Implemented in bpp::AbstractTreeLikelihood.
|
inlinevirtualinherited |
Implements bpp::TreeLikelihood.
Definition at line 297 of file AbstractTreeLikelihood.h.
References bpp::AbstractTreeLikelihood::initialized_.
Referenced by bpp::DRHomogeneousTreeLikelihood::getValue(), bpp::DRNonHomogeneousTreeLikelihood::getValue(), bpp::RHomogeneousTreeLikelihood::getValue(), and getValue().
RNonHomogeneousTreeLikelihood & RNonHomogeneousTreeLikelihood::operator= | ( | const RNonHomogeneousTreeLikelihood & | lik | ) |
Definition at line 118 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::DRASRTreeLikelihoodData::clone(), likelihoodData_, minusLogLik_, bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::DRASRTreeLikelihoodData::setTree(), and bpp::AbstractTreeLikelihood::tree_.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::operator=().
|
staticinherited |
Set all conditional likelihoods to 1.
likelihoodArray | the likelihood array. |
Definition at line 267 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(), and bpp::DRNonHomogeneousTreeLikelihood::resetLikelihoodArrays().
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virtual |
Set the dataset for which the likelihood must be evaluated.
sites | The data set to use. |
Implements bpp::TreeLikelihood.
Definition at line 138 of file RNonHomogeneousTreeLikelihood.cpp.
References bpp::PatternTools::getSequenceSubset().
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::setData().
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inlinevirtualinherited |
Definition at line 268 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_, and bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_.
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Definition at line 258 of file AbstractNonHomogeneousTreeLikelihood.h.
References bpp::AbstractNonHomogeneousTreeLikelihood::brLenConstraint_, bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::maximumBrLen_, and bpp::AbstractNonHomogeneousTreeLikelihood::minimumBrLen_.
void RNonHomogeneousTreeLikelihood::setParameters | ( | const ParameterList & | parameters | ) | |
throw | ( | ParameterNotFoundException, | |||
ConstraintException | |||||
) |
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 | The parameter list to pass to the function. |
Definition at line 254 of file RNonHomogeneousTreeLikelihood.cpp.
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virtualinherited |
Exception | If the model could not be set (for instance, because of a wrong alphabet type). |
Implements bpp::NonHomogeneousTreeLikelihood.
Definition at line 195 of file AbstractNonHomogeneousTreeLikelihood.cpp.
References bpp::Node::getId().
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friend |
Definition at line 271 of file RNonHomogeneousTreeLikelihood.h.
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protectedinherited |
Definition at line 127 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().
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Definition at line 93 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::RNonHomogeneousMixedTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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Definition at line 227 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableFirstOrderDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().
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Definition at line 228 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractTreeLikelihood::enableDerivatives(), bpp::AbstractTreeLikelihood::enableSecondOrderDerivatives(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), and bpp::AbstractTreeLikelihood::operator=().
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mutableprotectedinherited |
Definition at line 99 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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Definition at line 225 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::AbstractTreeLikelihood::getAlphabet(), bpp::AbstractTreeLikelihood::getData(), bpp::AbstractTreeLikelihood::getNumberOfSites(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::operator=(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().
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mutableprotectedinherited |
Definition at line 97 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihood(), computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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mutableprotectedinherited |
An index linking nodes to their id, for faster access than the getNode() method.
Definition at line 114 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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Definition at line 229 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getBranchLengthsParameters(), bpp::TwoTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::TwoTreeLikelihood::initialize(), bpp::AbstractHomogeneousTreeLikelihood::initialize(), bpp::AbstractNonHomogeneousTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::initialize(), bpp::AbstractTreeLikelihood::isInitialized(), and bpp::AbstractTreeLikelihood::operator=().
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Definition at line 91 of file RNonHomogeneousTreeLikelihood.h.
Referenced by computeDownSubtreeD2Likelihood(), computeDownSubtreeDLikelihood(), computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), displayLikelihood(), getD2LikelihoodForASiteForARateClass(), getDLikelihoodForASiteForARateClass(), getLikelihoodData(), getLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClassForAState(), getLogLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClassForAState(), getSiteIndex(), operator=(), RNonHomogeneousTreeLikelihood(), and ~RNonHomogeneousTreeLikelihood().
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protectedinherited |
Definition at line 126 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getMaximumBranchLength(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().
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protectedinherited |
Definition at line 125 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::getMinimumBranchLength(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::setMaximumBranchLength(), and bpp::AbstractNonHomogeneousTreeLikelihood::setMinimumBranchLength().
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private |
Definition at line 92 of file RNonHomogeneousTreeLikelihood.h.
Referenced by fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), getValue(), and operator=().
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Definition at line 92 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsChar(), bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStateAsInt(), bpp::AbstractNonHomogeneousTreeLikelihood::getAlphabetStates(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewBranchModelIterator(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractNonHomogeneousTreeLikelihood::getNumberOfStates(), bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequenciesParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::getSubstitutionModelSet(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by computeDownSubtreeD2Likelihood(), computeDownSubtreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), getD2LikelihoodForASite(), getDLikelihoodForASite(), getLikelihoodForASite(), getLogLikelihoodForASite(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 117 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::getLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::getLogLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::getNewBranchModelIterator(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by getD2LogLikelihood(), getDLogLikelihood(), getLikelihood(), getLogLikelihood(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 117 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by computeDownSubtreeD2Likelihood(), computeDownSubtreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), computeSubtreeLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeSubtreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), getD2LikelihoodForASiteForARateClass(), getDLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClass(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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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 109 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2Likelihoods(), computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoods(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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mutableprotectedinherited |
Definition at line 95 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by computeDownSubtreeD2Likelihood(), computeDownSubtreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), computeSubtreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPostfix(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), computeTreeD2Likelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), computeTreeDLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::AbstractNonHomogeneousTreeLikelihood::getTransitionProbabilitiesPerRateClass(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 61 of file AbstractDiscreteRatesAcrossSitesTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::applyParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::TwoTreeLikelihood::applyParameters(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::AbstractHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::AbstractNonHomogeneousTreeLikelihood::computeTransitionProbabilitiesForNode(), bpp::TwoTreeLikelihood::computeTreeD2Likelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeD2LikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeDLikelihoodAtNode(), bpp::TwoTreeLikelihood::computeTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::fireParameterChanged(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), bpp::RHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::TwoTreeLikelihood::fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), getD2LikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASite(), getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASite(), getLikelihoodForASite(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASite(), getLogLikelihoodForASite(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getNumberOfClasses(), bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::getRateDistribution(), bpp::RNonHomogeneousMixedTreeLikelihood::init(), bpp::AbstractHomogeneousTreeLikelihood::initParameters(), bpp::AbstractNonHomogeneousTreeLikelihood::initParameters(), bpp::TwoTreeLikelihood::initParameters(), and bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood::operator=().
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protectedinherited |
Definition at line 129 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 130 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), computeTreeD2Likelihood(), computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 130 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::applyParameters(), computeTreeD2Likelihood(), computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), bpp::AbstractNonHomogeneousTreeLikelihood::initBranchLengthsParameters(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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protectedinherited |
Definition at line 101 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::computeAllTransitionProbabilities(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode_(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeSubtreeLikelihoodPrefix(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), getD2LikelihoodForASiteForARateClass(), getDLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClass(), bpp::AbstractNonHomogeneousTreeLikelihood::getRootFrequencies(), and bpp::AbstractNonHomogeneousTreeLikelihood::operator=().
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mutableprotectedinherited |
Definition at line 226 of file AbstractTreeLikelihood.h.
Referenced by bpp::AbstractHomogeneousTreeLikelihood::AbstractHomogeneousTreeLikelihood(), bpp::AbstractNonHomogeneousTreeLikelihood::AbstractNonHomogeneousTreeLikelihood(), bpp::AbstractTreeLikelihood::AbstractTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRNonHomogeneousTreeLikelihood::computeLikelihoodAtNode(), bpp::DRHomogeneousTreeLikelihood::computeRootLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeRootLikelihood(), computeTreeD2Likelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeD2Likelihood(), computeTreeDLikelihood(), bpp::RNonHomogeneousMixedTreeLikelihood::computeTreeDLikelihood(), bpp::DRHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::computeTreeLikelihood(), computeTreeLikelihood(), bpp::RHomogeneousTreeLikelihood::computeTreeLikelihood(), bpp::DRHomogeneousTreeLikelihood::DRHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::DRNonHomogeneousTreeLikelihood(), bpp::DRNonHomogeneousTreeLikelihood::fireParameterChanged(), fireParameterChanged(), bpp::RNonHomogeneousMixedTreeLikelihood::fireParameterChanged(), getD2LikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getD2LikelihoodForASiteForARateClass(), getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getDLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClass(), getLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLikelihoodForASiteForARateClassForAState(), getLikelihoodForASiteForARateClassForAState(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClass(), getLogLikelihoodForASiteForARateClass(), bpp::RHomogeneousTreeLikelihood::getLogLikelihoodForASiteForARateClassForAState(), getLogLikelihoodForASiteForARateClassForAState(), bpp::AbstractHomogeneousTreeLikelihood::getNewSiteModelIterator(), bpp::AbstractTreeLikelihood::getTree(), bpp::DRHomogeneousTreeLikelihood::operator=(), bpp::DRNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractHomogeneousTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::operator=(), operator=(), bpp::AbstractNonHomogeneousTreeLikelihood::operator=(), bpp::AbstractTreeLikelihood::operator=(), bpp::RHomogeneousTreeLikelihood::RHomogeneousTreeLikelihood(), RNonHomogeneousTreeLikelihood(), and bpp::AbstractTreeLikelihood::~AbstractTreeLikelihood().
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protectedinherited |
Definition at line 123 of file AbstractNonHomogeneousTreeLikelihood.h.
Referenced by bpp::AbstractNonHomogeneousTreeLikelihood::operator=().