- 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::PhyloDAG, 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
• rootNode() : bpp::TreeTemplate< N >
• row() : bpp::ExtendedFloatEigen< R, C, EigenType >
• rows() : bpp::ExtendedFloatEigen< R, C, EigenType >
• RowVectorDimension() : bpp::RowVectorDimension
• rowwise() : bpp::ExtendedFloatEigen< R, C, EigenType >