40 #ifndef _DISCRETERATESACROSSSITESTREELIKELIHOOD_H_ 41 #define _DISCRETERATESACROSSSITESTREELIKELIHOOD_H_ 45 #include <Bpp/Numeric/Prob/DiscreteDistribution.h> 46 #include <Bpp/Numeric/ParameterList.h> 209 #endif //_DISCRETERATESACROSSSITESTREELIKELIHOOD_H_ DiscreteRatesAcrossSitesTreeLikelihood()
virtual VVdouble getLikelihoodForEachSiteForEachRateClass() const =0
Get the likelihood for each site and each rate class.
The TreeLikelihood interface.
virtual size_t getNumberOfClasses() const =0
Get the number of classes.
virtual double getLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0
Get the likelihood for a site knowing its rate class and its ancestral state.
virtual double getLogLikelihoodForASiteForARateClassForAState(size_t site, size_t rateClass, int state) const =0
Get the logarithm of the likelihood for a site knowing its rate class and its ancestral state...
virtual VVdouble getPosteriorProbabilitiesOfEachRate() const =0
Get the posterior probability for each site of belonging to a particular rate class.
virtual double getLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0
Get the likelihood for a site knowing its rate class.
virtual VVVdouble getLogLikelihoodForEachSiteForEachRateClassForEachState() const =0
Get the logarithm of the likelihood for each site and each rate class and each state.
virtual std::vector< size_t > getRateClassWithMaxPostProbOfEachSite() const =0
Get the posterior rate class (the one with maximum posterior probability) for each site...
virtual ParameterList getRateDistributionParameters() const =0
Get the parameters associated to the rate distirbution.
virtual Vdouble getRateWithMaxPostProbOfEachSite() const =0
Get the posterior rate (the one with maximum posterior probability) for each site.
Interface for rate across sites (RAS) implementation.
virtual VVdouble getLogLikelihoodForEachSiteForEachRateClass() const =0
Get the logarithm of the likelihood for each site and each rate class.
virtual ~DiscreteRatesAcrossSitesTreeLikelihood()
virtual double getLogLikelihoodForASiteForARateClass(size_t site, size_t rateClass) const =0
Get the logarithm of the likelihood for a site knowing its rate class.
virtual VVVdouble getLikelihoodForEachSiteForEachRateClassForEachState() const =0
Get the likelihood for each site and each rate class and each state.
virtual const DiscreteDistribution * getRateDistribution() const =0
Get the rate distribution used for the computation.
virtual Vdouble getPosteriorRateOfEachSite() const =0
Get the posterior rate, i.e. averaged over all classes and weighted with posterior probabilities...
virtual VVVdouble getTransitionProbabilitiesPerRateClass(int nodeId, size_t siteIndex) const =0
Retrieves all Pij(t) for a particular branch, defined by the upper node.