Here is a list of all class members with links to the classes they belong to:
- r -
- R_ : bpp::CoalaCore
- r_ : bpp::F81, bpp::F84, bpp::HKY85, bpp::K80, bpp::LegacyMarginalAncestralStateReconstruction, bpp::T92, bpp::TN93
- radix : bpp::ExtendedFloat
- RASiteSimulationResult() : bpp::RASiteSimulationResult
- rate_ : bpp::AbstractTransitionModel, bpp::NonHomogeneousSequenceSimulator, 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
- 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
- RE08() : bpp::RE08
- RE08Codon() : bpp::RE08Codon
- RE08Nucleotide() : bpp::RE08Nucleotide
- RE08Protein() : bpp::RE08Protein
- readBranchModel() : bpp::BppOBranchModelFormat
- ReadCost : Eigen::NumTraits< bpp::ExtendedFloat >
- 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
- Real : Eigen::NumTraits< bpp::ExtendedFloat >
- RealScalar : bpp::ExtendedFloatEigenBase< Derived >
- 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
- ref : bpp::Context::CachedNodeRef
- RefMatType : bpp::ExtendedFloatEigen< R, C, EigenType >
- register_ : bpp::AbstractSubstitutionCount
- registeredTreeDrawings_ : bpp::TreeDrawingDisplayControler
- registerName_ : bpp::OneChangeRegisterTransitionModel, bpp::RegisterRatesSubstitutionModel
- 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
- reparametrization : bpp::OptimizationTools::OptimizationOptions
- reparametrization_ : bpp::NNITopologyListener2, bpp::NNITopologyListener
- reparametrizeRoot_ : bpp::AbstractNonHomogeneousTreeLikelihood
- repartition_ : bpp::AbstractMutationProcess
- replaceFrequencies() : bpp::SubstitutionProcessCollection
- replaceModel() : bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollection
- replaceParametrizable() : bpp::SubstitutionProcessCollection
- replaceTree() : bpp::SubstitutionProcessCollection
- RequireInitialization : Eigen::NumTraits< bpp::ExtendedFloat >
- 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 >
- result_ : bpp::ConstantTransitionFunction
- ReturnType : Eigen::ScalarBinaryOpTraits< bpp::ExtendedFloat, double, BinaryOp >, Eigen::ScalarBinaryOpTraits< double, bpp::ExtendedFloat, BinaryOp >
- ReversibleSubstitutionModelInterface() : bpp::ReversibleSubstitutionModelInterface
- revIndex_ : bpp::CategorySubstitutionRegister
- Reward() : bpp::Reward
- reward_ : bpp::LegacyProbabilisticRewardMapping
- RewardMappingInterface() : bpp::RewardMappingInterface
- RewardMappingTools() : bpp::RewardMappingTools
- rewards_ : bpp::DecompositionReward, bpp::PhyloBranchReward
- rFreqs_ : bpp::BackwardLikelihoodTree, bpp::LikelihoodCalculationSingleProcess
- rho_ : bpp::AbstractCodonCpGSubstitutionModel
- RHomogeneousMixedTreeLikelihood() : bpp::RHomogeneousMixedTreeLikelihood, bpp::RHomogeneousTreeLikelihood
- RHomogeneousTreeLikelihood() : bpp::RHomogeneousTreeLikelihood
- rightEigenVectors_ : bpp::AbstractSubstitutionModel, bpp::DecompositionMethods, bpp::MarkovModulatedSubstitutionModel
- rightIEigenVectors_ : bpp::DecompositionMethods
- RN95() : bpp::RN95
- RN95s() : bpp::RN95s
- RNA : bpp::BppOFrequencySetFormat, bpp::BppOSubstitutionModelFormat
- RNonHomogeneousMixedTreeLikelihood() : bpp::RNonHomogeneousMixedTreeLikelihood, bpp::RNonHomogeneousTreeLikelihood
- RNonHomogeneousTreeLikelihood() : bpp::RNonHomogeneousTreeLikelihood
- robinsonFouldsDistance() : bpp::TreeTools
- root1_ : bpp::AbstractNonHomogeneousTreeLikelihood
- root2_ : bpp::AbstractNonHomogeneousTreeLikelihood
- root_ : bpp::TreeTemplate< N >
- rootArray_ : bpp::DRHomogeneousMixedTreeLikelihood
- rootAt() : bpp::Tree, bpp::TreeTemplate< N >
- rootBitsets_ : bpp::DRTreeParsimonyData
- rootFreqs_ : bpp::AbstractHomogeneousTreeLikelihood, bpp::AbstractNonHomogeneousTreeLikelihood
- rootFreqsNode_ : bpp::LikelihoodCalculationSingleProcess::ProcessNodes
- rootFrequencies_ : bpp::AbstractAutonomousSubstitutionProcess, bpp::SubstitutionModelSet
- rootFrequencySet() : bpp::AbstractAutonomousSubstitutionProcess, bpp::SubstitutionModelSet, bpp::SubstitutionProcessCollectionMember, bpp::SubstitutionProcessInterface
- rootLikelihoods_ : bpp::DRASDRTreeLikelihoodData
- rootLikelihoodsS_ : bpp::DRASDRTreeLikelihoodData
- rootLikelihoodsSR_ : bpp::DRASDRTreeLikelihoodData
- rootNode() : bpp::TreeTemplate< N >
- 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
- row() : bpp::ExtendedFloatEigen< R, C, EigenType >
- rowCoords_ : bpp::MvaFrequencySet
- rows() : bpp::ExtendedFloatEigen< R, C, EigenType >, bpp::MatrixDimension
- RowVectorDimension() : bpp::RowVectorDimension
- rowwise() : bpp::ExtendedFloatEigen< R, C, EigenType >