- r -

• R_ : bpp::CoalaCore
• r_ : bpp::F81, bpp::F84, bpp::HKY85, bpp::K80, bpp::LegacyMarginalAncestralStateReconstruction, bpp::T92, bpp::TN93
• radix : bpp::ExtendedFloat
• rate_ : bpp::AbstractTransitionModel, bpp::NonHomogeneousSequenceSimulator, bpp::RASiteSimulationResult
• rateDistribution_ : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
• rateFreqs_ : bpp::MarkovModulatedFrequencySet
• rates_ : bpp::MarkovModulatedSubstitutionModel
• ratesExchangeability_ : bpp::MarkovModulatedSubstitutionModel
• ratesFreq_ : bpp::MarkovModulatedSubstitutionModel
• ratesGenerator_ : bpp::MarkovModulatedSubstitutionModel
• ratesNode_ : bpp::LikelihoodCalculationSingleProcess::ProcessNodes
• rDist_ : bpp::BranchLikelihood, bpp::G2001, bpp::NonHomogeneousSubstitutionProcess, bpp::RateAcrossSitesSubstitutionProcess
• ref : bpp::Context::CachedNodeRef
• register_ : bpp::AbstractSubstitutionCount
• registeredTreeDrawings_ : bpp::TreeDrawingDisplayControler
• registerName_ : bpp::OneChangeRegisterTransitionModel, bpp::RegisterRatesSubstitutionModel
• reparametrization : bpp::OptimizationTools::OptimizationOptions
• reparametrization_ : bpp::NNITopologyListener2, bpp::NNITopologyListener
• reparametrizeRoot_ : bpp::AbstractNonHomogeneousTreeLikelihood
• repartition_ : bpp::AbstractMutationProcess
• result_ : bpp::ConstantTransitionFunction
• revIndex_ : bpp::CategorySubstitutionRegister
• reward_ : bpp::LegacyProbabilisticRewardMapping
• rewards_ : bpp::DecompositionReward, bpp::PhyloBranchReward
• rFreqs_ : bpp::BackwardLikelihoodTree, bpp::LikelihoodCalculationSingleProcess
• rho_ : bpp::AbstractCodonCpGSubstitutionModel
• rightEigenVectors_ : bpp::AbstractSubstitutionModel, bpp::DecompositionMethods, bpp::MarkovModulatedSubstitutionModel
• rightIEigenVectors_ : bpp::DecompositionMethods
• RNA : bpp::BppOFrequencySetFormat, bpp::BppOSubstitutionModelFormat
• root1_ : bpp::AbstractNonHomogeneousTreeLikelihood
• root2_ : bpp::AbstractNonHomogeneousTreeLikelihood
• root_ : bpp::TreeTemplate< N >
• rootArray_ : bpp::DRHomogeneousMixedTreeLikelihood
• rootBitsets_ : bpp::DRTreeParsimonyData
• rootFreqs_ : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood
• rootFreqsNode_ : bpp::LikelihoodCalculationSingleProcess::ProcessNodes
• rootFrequencies_ : bpp::AbstractAutonomousSubstitutionProcess, bpp::SubstitutionModelSet
• rootLikelihoods_ : bpp::DRASDRTreeLikelihoodData
• rootLikelihoodsS_ : bpp::DRASDRTreeLikelihoodData
• rootLikelihoodsSR_ : bpp::DRASDRTreeLikelihoodData
• rootPatternLinks_ : bpp::AbstractTreeLikelihoodData, bpp::AbstractTreeParsimonyData, bpp::LegacyMarginalAncestralStateReconstruction, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess, bpp::MarginalAncestralReconstruction, bpp::ProbabilisticRewardMapping, bpp::ProbabilisticSubstitutionMapping
• rootScores_ : bpp::DRTreeParsimonyData
• rootTree_ : bpp::AbstractAgglomerativeDistanceMethod
• rootWeights_ : bpp::AbstractTreeLikelihoodData, bpp::AbstractTreeParsimonyData, bpp::LikelihoodCalculationOnABranch, bpp::LikelihoodCalculationSingleProcess
• rowCoords_ : bpp::MvaFrequencySet
• rows : bpp::MatrixDimension