- r -

• RASiteSimulationResult() : bpp::RASiteSimulationResult
• RateAcrossSitesSubstitutionProcess() : bpp::RateAcrossSitesSubstitutionProcess
• rateDistribution() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood , bpp::DiscreteRatesAcrossSitesTreeLikelihoodInterface , bpp::G2001 , bpp::NonHomogeneousSequenceSimulator , bpp::NonHomogeneousSubstitutionProcess , bpp::RateAcrossSitesSubstitutionProcess , bpp::SimpleSubstitutionProcess , bpp::SubstitutionProcessCollection , bpp::SubstitutionProcessCollectionMember , bpp::SubstitutionProcessInterface
• RE08() : bpp::RE08
• RE08Codon() : bpp::RE08Codon
• RE08Nucleotide() : bpp::RE08Nucleotide
• RE08Protein() : bpp::RE08Protein
• readBranchModel() : bpp::BppOBranchModelFormat
• readDiscreteDistribution() : bpp::BppORateDistributionFormat
• readFormula() : bpp::PhyloLikelihoodFormula
• readFrequencySet() : bpp::BppOFrequencySetFormat , bpp::IFrequencySet
• readFromFile() : bpp::Coala , bpp::UserProteinSubstitutionModel
• readFromFile_() : bpp::UserFrequencySet
• readFromStream() : bpp::LegacyRewardMappingTools , bpp::LegacySubstitutionMappingTools , bpp::RewardMappingTools , bpp::SubstitutionMappingTools
• readIMultiTree() : bpp::BppOMultiTreeReaderFormat
• readITree() : bpp::BppOTreeReaderFormat
• readMixed_() : bpp::BppOTransitionModelFormat
• readOMultiTree() : bpp::BppOMultiTreeWriterFormat
• readOTree() : bpp::BppOTreeWriterFormat
• readPairedSiteLikelihoods() : bpp::IOPhymlPairedSiteLikelihoods , bpp::IOTreepuzzlePairedSiteLikelihoods
• readPhyloDAG() : bpp::AbstractIPhyloDAG , bpp::ExtendedNewick , bpp::IPhyloDAG
• readPhyloDAGs() : bpp::AbstractIMultiPhyloDAG , bpp::ExtendedNewick , bpp::IMultiPhyloDAG
• readPhyloTree() : bpp::AbstractIPhyloTree , bpp::IPhyloTree , bpp::Newick , bpp::NexusIOTree , bpp::Nhx
• readPhyloTrees() : bpp::AbstractIMultiPhyloTree , bpp::IMultiPhyloTree , bpp::Newick , bpp::NexusIOTree , bpp::Nhx
• readSubstitutionModel() : bpp::BppOSubstitutionModelFormat , bpp::ISubstitutionModel
• readTransitionModel() : bpp::BppOTransitionModelFormat
• readTree() : bpp::AbstractITree , bpp::ITree
• readTrees() : bpp::AbstractIMultiTree , bpp::IMultiTree , bpp::Newick , bpp::NexusIOTree , bpp::Nhx
• readTreeTemplate() : bpp::AbstractITree , bpp::Newick , bpp::NexusIOTree , bpp::Nhx
• readWord_() : bpp::BppOSubstitutionModelFormat
• recreate() : bpp::BackwardHmmLikelihood_DF , bpp::CategoryFromDiscreteDistribution , bpp::CombineDeltaShifted< T > , bpp::CondLikelihood , bpp::ConfiguredDistribution , bpp::ConfiguredFrequencySet , bpp::ConfiguredModel , bpp::ConfiguredParameter , bpp::ConfiguredSimplex , bpp::ConfiguredTransitionMatrix , bpp::ConstantOne< T > , bpp::ConstantZero< T > , bpp::Convert< R, F > , bpp::CWiseAdd< R, T > , bpp::CWiseAdd< R, ReductionOf< T > > , bpp::CWiseAdd< R, std::tuple< T0, T1 > > , bpp::CWiseApply< R, T, F > , bpp::CWiseCompound< R, ReductionOf< T > > , bpp::CWiseConstantPow< T > , bpp::CWiseDiv< R, std::tuple< T0, T1 > > , bpp::CWiseExp< T > , bpp::CWiseFill< R, T > , bpp::CWiseInverse< T > , bpp::CWiseLog< T > , bpp::CWiseMatching< R, ReductionOf< T > > , bpp::CWiseMean< R, ReductionOf< T >, P > , bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > > , bpp::CWiseMul< R, ReductionOf< T > > , bpp::CWiseMul< R, std::tuple< T0, T1 > > , bpp::CWiseNegate< T > , bpp::CWisePattern< R > , bpp::CWiseSub< R, std::tuple< T0, T1 > > , bpp::EquilibriumFrequenciesFromModel , bpp::EquilibriumFrequenciesFromTransitionMatrix , bpp::ForwardHmmD2Likelihood_DF , bpp::ForwardHmmDLikelihood_DF , bpp::ForwardHmmLikelihood_DF , bpp::FrequenciesFromFrequencySet , bpp::FrequenciesFromSimplex , bpp::Identity< R > , bpp::LogSumExp< R, T0, T1 > , bpp::MatrixProduct< R, T0, T1 > , bpp::Node_DF , bpp::NumericConstant< T > , bpp::NumericMutable< T > , bpp::ProbabilitiesFromDiscreteDistribution , bpp::ProbabilitiesFromMixedModel , bpp::ProbabilityFromDiscreteDistribution , bpp::ProbabilityFromMixedModel , bpp::ScalarProduct< R, T0, T1 > , bpp::Sequence_DF , bpp::ShiftDelta< T > , bpp::ShiftParameter , bpp::SumOfLogarithms< F > , bpp::TransitionFunctionFromModel , bpp::TransitionMatrixFromModel , bpp::TransitionMatrixFromTransitionMatrix , bpp::ValueFromConfiguredParameter
• recursiveMarginalAncestralStates() : bpp::LegacyMarginalAncestralStateReconstruction , bpp::MarginalAncestralReconstruction
• recursivePlot_() : bpp::CladogramPlot , bpp::PhylogramPlot
• registerNode() : bpp::Node_DF
• registerProperty() : bpp::Nhx
• RegisterRatesSubstitutionModel() : bpp::RegisterRatesSubstitutionModel
• registerTreeDrawing() : bpp::TreeDrawingDisplayControler
• reInit() : bpp::DRASDRTreeLikelihoodData , bpp::DRTreeParsimonyData
• reInit_() : bpp::DRTreeParsimonyData
• RELAX() : bpp::RELAX
• removeBranchProperties() : bpp::Node
• removeBranchProperty() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• removeFather() : bpp::AwareNode , bpp::Node , bpp::NodeTemplate< NodeInfos >
• removeModel() : bpp::ModelPath
• removeN() : bpp::ModelPath::PathNode
• removeNodeProperties() : bpp::Node
• removeNodeProperty() : bpp::Node , bpp::Tree , bpp::TreeTemplate< N >
• removeProperties() : bpp::PhyloBranch , bpp::PhyloNode
• removeProperty() : bpp::PhyloBranch , bpp::PhyloNode
• removeRedundantBipartitions() : bpp::BipartitionList
• removeSon() : bpp::AwareNode , bpp::Node
• removeSons() : bpp::AwareNode , bpp::Node
• removeTreeDrawingListener() : bpp::AbstractTreeDrawing , bpp::TreeDrawing
• removeTrivialBipartitions() : bpp::BipartitionList
• replaceFrequencies() : bpp::SubstitutionProcessCollection
• replaceModel() : bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollection
• replaceParametrizable() : bpp::SubstitutionProcessCollection
• replaceTree() : bpp::SubstitutionProcessCollection
• resetAdditionalParameters() : bpp::DistanceEstimation
• resetBMatrices_() : bpp::UniformizationSubstitutionCount
• resetDependencies() : bpp::ConfiguredParameter
• resetDependencies_() : bpp::Node_DF
• resetLikelihoodArray() : bpp::AbstractDiscreteRatesAcrossSitesTreeLikelihood
• resetLikelihoodArrays() : bpp::DRHomogeneousMixedTreeLikelihood , bpp::DRHomogeneousTreeLikelihood , bpp::DRNonHomogeneousTreeLikelihood
• resetLikelihoods() : bpp::BranchLikelihood
• resetModelToNodeIds() : bpp::SubstitutionModelSet
• resetNodesId() : bpp::PhyloTree , bpp::Tree , bpp::TreeTemplate< N >
• resetOptimizer() : bpp::DistanceEstimation
• resetSiteSimulators() : bpp::EvolutionSequenceSimulator
• resize() : bpp::ExtendedFloatEigen< R, C, EigenType >
• ReversibleSubstitutionModelInterface() : bpp::ReversibleSubstitutionModelInterface
• Reward() : bpp::Reward
• RewardMappingInterface() : bpp::RewardMappingInterface
• RewardMappingTools() : bpp::RewardMappingTools
• RHomogeneousMixedTreeLikelihood() : bpp::RHomogeneousMixedTreeLikelihood
• RHomogeneousTreeLikelihood() : bpp::RHomogeneousTreeLikelihood
• RN95() : bpp::RN95
• RN95s() : bpp::RN95s
• RNonHomogeneousMixedTreeLikelihood() : bpp::RNonHomogeneousMixedTreeLikelihood
• RNonHomogeneousTreeLikelihood() : bpp::RNonHomogeneousTreeLikelihood
• robinsonFouldsDistance() : bpp::TreeTools
• rootAt() : bpp::Tree , bpp::TreeTemplate< N >
• rootFrequencySet() : bpp::AbstractAutonomousSubstitutionProcess , bpp::SubstitutionModelSet , bpp::SubstitutionProcessCollectionMember , bpp::SubstitutionProcessInterface
• row() : bpp::ExtendedFloatEigen< R, C, EigenType >
• rows() : bpp::ExtendedFloatEigen< R, C, EigenType >
• RowVectorDimension() : bpp::RowVectorDimension
• rowwise() : bpp::ExtendedFloatEigen< R, C, EigenType >