- 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