Index A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Z A acceptance (sequince.steps.mutation.metrics.state.MutationMetricsOutput property) acceptance_by_step (sequince.steps.mutation.minipcn.MiniPCNOutput attribute) AcceptanceRatePolicy (class in sequince.steps.mutation.adaptive.policies.acceptance) AcceptanceRateRhoPolicy (class in sequince.steps.mutation.adaptive.policies.rho) accepts_evaluation() (sequince.target.Target method) adaptation_rate (sequince.steps.mutation.adaptive.policies.rho.AcceptanceRateRhoPolicy attribute) (sequince.steps.mutation.adaptive.proposal.AdaptiveGaussianProposal attribute) AdaptDEScaleWeights (class in sequince.steps.mutation.adaptive.de) AdaptiveGaussianProposal (class in sequince.steps.mutation.adaptive.proposal) AdaptiveMaskedGaussianRandomWalk (class in sequince.steps.mutation.kernels) AdaptiveMiniPCNMutation (class in sequince.steps.mutation.adaptive.minipcn) AdaptiveMutationPlot (class in sequince.callbacks) AdaptiveMutationStep (class in sequince.steps.mutation.adaptive.base) AdaptiveTemperedWeighting (class in sequince.steps.weighting) AdaptMutationSteps (class in sequince.steps.mutation.adaptive.steps) add_evaluation_counts() (sequince.steps.context.StepContext method) AffineTransform (class in sequince.transforms) after_round (sequince.steps.mutation.repeated.RepeatedMutationStep attribute) after_round_outputs (sequince.steps.mutation.repeated.RepeatedMutationStepOutput attribute) algorithm (sequince.steps.mutation.blackjax.BlackJAXOutput attribute) algorithm_name (sequince.steps.mutation.blackjax.BlackJAXMutation property) all_states (sequince.result.MetaSMCResult property) ancestors (sequince.steps.resampling.ResamplingOutput attribute) append() (sequince.state.PersistentParticleState method) append_state() (sequince.result.SMCResult method) apply() (sequince.callbacks.AdaptiveMutationPlot method) (sequince.callbacks.IntermediateParticlesPlot method) (sequince.callbacks.MutationChainPlot method) (sequince.callbacks.ParticleTransformPlot method) (sequince.callbacks.SMCCallback method) (sequince.callbacks.StatePlot method) (sequince.callbacks.TracePlot method) (sequince.steps.base.SMCStep method) (sequince.steps.constraints.LikelihoodThresholdSelection method) (sequince.steps.constraints.LikelihoodThresholdWeighting method) (sequince.steps.constraints.LogPriorMassStoppingCriterion method) (sequince.steps.constraints.ShellEvidenceStep method) (sequince.steps.control.ContinueWhile method) (sequince.steps.control.PeriodicStep method) (sequince.steps.control.RepeatStep method) (sequince.steps.control.SequentialStep method) (sequince.steps.control.StopIf method) (sequince.steps.log.LoggingStep method) (sequince.steps.meta.MetaSMCStep method) (sequince.steps.mutation.adaptive.base.AdaptiveMutationStep method) (sequince.steps.mutation.blackjax.BlackJAXMutation method) (sequince.steps.mutation.blocked.BlockedMetropolisHastingsMutation method) (sequince.steps.mutation.conditional.MutateIfResampled method) (sequince.steps.mutation.emcee.EmceeMutation method) (sequince.steps.mutation.eryn.ErynMutation method) (sequince.steps.mutation.metropolis.MetropolisHastingsMutation method) (sequince.steps.mutation.metropolis.RedBlueMetropolisHastingsMutation method) (sequince.steps.mutation.minipcn.MiniPCNMutation method) (sequince.steps.mutation.rejuvenation.ProposalRejuvenation method) (sequince.steps.mutation.repeated.RepeatedMutationStep method) (sequince.steps.persistent.PersistentAdaptiveTemperedWeighting method) (sequince.steps.persistent.PersistentTemperedWeighting method) (sequince.steps.persistent.PersistParticles method) (sequince.steps.resampling.ResamplingStep method) (sequince.steps.transformations.ExpandDimensions method) (sequince.steps.transformations.TransformationStep method) (sequince.steps.transition.ImportanceTransition method) (sequince.steps.waste_free.WasteFreeResampleMove method) (sequince.steps.weighting.AdaptiveTemperedWeighting method) (sequince.steps.weighting.BaseTemperedStep method) (sequince.steps.weighting.FixedTemperedWeighting method) (sequince.steps.weighting.IncrementalWeighting method) (sequince.steps.weighting.TemperedWeighting method) apply_functional() (sequince.steps.base.SMCStep method) (sequince.steps.constraints.LikelihoodThresholdSelection method) (sequince.steps.constraints.LikelihoodThresholdWeighting method) (sequince.steps.constraints.LogPriorMassStoppingCriterion method) (sequince.steps.constraints.ShellEvidenceStep method) (sequince.steps.control.StopIf method) (sequince.steps.mutation.adaptive.base.AdaptiveMutationStep method) (sequince.steps.mutation.minipcn.MiniPCNMutation method) (sequince.steps.mutation.rejuvenation.ProposalRejuvenation method) (sequince.steps.persistent.PersistentAdaptiveTemperedWeighting method) (sequince.steps.resampling.ResamplingStep method) (sequince.steps.weighting.AdaptiveTemperedWeighting method) (sequince.steps.weighting.FixedTemperedWeighting method) apply_functional_if() (in module sequince.steps.control) apply_weighted() (sequince.result.SMCResult method) apply_with_mutation_state() (sequince.steps.mutation.base.MutationStep method) (sequince.steps.mutation.blackjax.BlackJAXMutation method) (sequince.steps.mutation.emcee.EmceeMutation method) (sequince.steps.mutation.eryn.ErynMutation method) (sequince.steps.mutation.metropolis.MetropolisHastingsMutation method) (sequince.steps.mutation.metropolis.RedBlueMetropolisHastingsMutation method) (sequince.steps.mutation.minipcn.MiniPCNMutation method) (sequince.steps.mutation.repeated.RepeatedMutationStep method) apply_with_n_steps() (sequince.steps.base.FixedLengthMutation method) (sequince.steps.mutation.adaptive.de.AdaptDEScaleWeights method) (sequince.steps.mutation.adaptive.minipcn.AdaptiveMiniPCNMutation method) (sequince.steps.mutation.adaptive.proposal.AdaptiveGaussianProposal method) (sequince.steps.mutation.base.MutationStep method) (sequince.steps.mutation.conditional.MutateIfResampled method) (sequince.steps.mutation.repeated.RepeatedMutationStep method) Array (in module sequince.typing) array_safe_copy() (in module sequince.utils.copying) ArrayLike (in module sequince.typing) as_nested_sampling_result() (sequince.result.SMCResult method) as_scalar_log_prob() (in module sequince.steps.mutation.base) as_vector_log_prob() (in module sequince.steps.mutation.base) asarray() (in module sequince.array_api) auto_normalize (sequince.smc.SMCConfig attribute) auxiliary (sequince.steps.mutation.kernels.KernelSample attribute) B base_filename (sequince.callbacks.IntermediateParticlesPlot attribute) (sequince.callbacks.MutationChainPlot attribute) (sequince.callbacks.ParticleTransformPlot attribute) BaseTemperedStep (class in sequince.steps.weighting) batch_size (sequince.state.PersistentParticleState attribute) betas (sequince.state.PersistentParticleState attribute) BetaSchedule (in module sequince.steps.weighting) bind_evaluation() (sequince.target.Target method) bisect_monotone_decreasing() (in module sequince.utils.optimize) BlackJAXAlgorithmFactory (in module sequince.steps.mutation.blackjax) BlackJAXMutation (class in sequince.steps.mutation.blackjax) BlackJAXOutput (class in sequince.steps.mutation.blackjax) BlockedMetropolisHastingsMutation (class in sequince.steps.mutation.blocked) BoundedToUnboundedTransform (class in sequince.transforms) BoundedToUnitHypercubeTransform (class in sequince.transforms) Bounds (in module sequince.transforms) bounds (sequince.transforms.BoundedToUnitHypercubeTransform attribute) (sequince.transforms.PeriodicBoundaryTransform attribute) C call_log_prob() (in module sequince.steps.mutation.base) call_with_optional_context() (in module sequince.utils.callables) CallableMutationKernel (class in sequince.steps.mutation.kernels) callbacks (sequince.smc.SMCConfig attribute) capture_step_states() (in module sequince.checkpoint) CauchitMapping (class in sequince.transforms) centering (sequince.transforms.PeriodicBoundaryTransform attribute) cess_ratio_from_log_weights_and_increments() (in module sequince.stats) chain (sequince.mcmc.MCMCResult property) (sequince.steps.mutation.blackjax.BlackJAXOutput attribute) (sequince.steps.mutation.minipcn.MiniPCNOutput attribute) CHECKPOINT_VERSION (in module sequince.checkpoint) checkpoint_writers (sequince.smc.SMCConfig attribute) CheckpointWriter (class in sequince.checkpoint) child_output (sequince.steps.control.ConditionalStepOutput attribute) clear_stop_request() (sequince.steps.context.StepContext method) clone() (sequince.proposals.FlowProposal method) (sequince.transforms.CompositeTransform method) (sequince.transforms.FlowTransform method) (sequince.transforms.ParticleTransform method) clone_flow() (in module sequince.flows) columns (sequince.transforms.AffineTransform attribute) compile_functional_iteration() (in module sequince.jax) COMPLEMENTARY_ENSEMBLE_KERNELS (in module sequince.steps.mutation.kernels) ComplementaryEnsembleKernel (class in sequince.steps.mutation.kernels) complete (sequince.result.NestedSamplingSMCResult property) components (sequince.target.TargetEvaluation attribute) CompositeTransform (class in sequince.transforms) concatenate() (sequince.target.TargetEvaluation class method) ConditionalStepOutput (class in sequince.steps.control) config (sequince.smc.SequentialMonteCarlo property) configure_logging() (in module sequince.log) context (sequince.mcmc.MCMCResult attribute) (sequince.result.NestedSamplingSMCResult property) (sequince.result.SMCResult attribute) context_metadata_fn (sequince.steps.transformations.MetadataTransformation attribute) ContinueWhile (class in sequince.steps.control) copy() (in module sequince.array_api) (sequince.state.ParticleState method) (sequince.state.PersistentParticleState method) (sequince.target.TargetEvaluation method) covariance (sequince.steps.mutation.kernels.MaskedGaussianRandomWalk attribute) current_n_steps (sequince.steps.mutation.adaptive.steps.AdaptMutationSteps property) current_rho (sequince.steps.mutation.adaptive.minipcn.AdaptiveMiniPCNMutation property) current_weights (sequince.steps.mutation.adaptive.de.AdaptDEScaleWeights property) D DEFAULT_FORMAT (in module sequince.log) DegenerateWeightsError DensityMutationKernel (class in sequince.steps.mutation.kernels) DEScaleMetrics (class in sequince.steps.mutation.metrics.de) DEScaleWeightPolicy (class in sequince.steps.mutation.adaptive.policies.de) determine_backend_name() (in module sequince.array_api) diagnostics (sequince.mcmc.MCMCResult property) DifferentialEvolutionKernel (class in sequince.steps.mutation.kernels) DifferentialEvolutionMutation (class in sequince.steps.mutation.metropolis) displacement (sequince.steps.mutation.metrics.state.MutationTransition attribute) distinct_ancestors (sequince.result.FixedLagLeeWhiteleyDiagnostics attribute) divergence (sequince.steps.mutation.blackjax.BlackJAXOutput attribute) draw_additional_samples() (in module sequince.posterior) draw_initial_state() (in module sequince.proposals) draw_mcmc_initial_state() (in module sequince.proposals) dsetname (sequince.checkpoint.HDF5CheckpointWriter attribute) E effective_sample_size() (sequince.state.ParticleState method) effective_sample_size_ratios() (sequince.result.SMCResult method) effective_sample_sizes() (sequince.result.SMCResult method) EMCEE_MOVES (in module sequince.steps.mutation.emcee) EmceeMutation (class in sequince.steps.mutation.emcee) enable_scipy_array_api() (in module sequince.array_api) encode_for_hdf5() (sequince.mcmc.MCMCResult method) (sequince.result.MetaSMCResult method) (sequince.result.SMCResult method) (sequince.state.ParticleState method) (sequince.state.PersistentParticleState method) (sequince.target.TargetEvaluation method) eps (sequince.transforms.AffineTransform attribute) (sequince.transforms.CauchitMapping attribute) (sequince.transforms.LogitMapping attribute) (sequince.transforms.ProbitMapping attribute) (sequince.transforms.WhiteningTransform attribute) ErynMutation (class in sequince.steps.mutation.eryn) ESJDMetric (class in sequince.steps.mutation.metrics.esjd) ESJDScaleWeightPolicy (class in sequince.steps.mutation.adaptive.policies.de) ess (sequince.steps.resampling.ResamplingOutput attribute) ess_from_log_weights() (in module sequince.stats) ess_ratio_from_log_weights() (in module sequince.stats) evaluate() (sequince.posterior.TemperedPosterior method) (sequince.steps.constraints.LikelihoodConstrainedPrior method) (sequince.target.Target method) evaluate_log_increment() (sequince.steps.weighting.BaseTemperedStep method) evaluate_log_transition_ratio() (in module sequince.steps.mutation.kernels) evaluation (sequince.state.ParticleState attribute) evaluation_components() (sequince.density.SequentialDensity method) (sequince.posterior.TemperedPosterior method) (sequince.steps.constraints.LikelihoodConstrainedPrior method) (sequince.target.Target method) evaluation_counts (sequince.checkpoint.SMCCheckpoint attribute) (sequince.result.SMCResult property) (sequince.smc.SMCRuntime attribute) (sequince.steps.context.StepContext attribute) EVALUATION_COUNTS_KEY (in module sequince.steps.context) evaluation_id (sequince.target.Target property) evaluation_key (sequince.target.TargetEvaluation attribute) evaluation_key() (sequince.target.Target method) EvaluationCounts (class in sequince.target) every (sequince.callbacks.SMCCallback attribute) (sequince.checkpoint.CheckpointWriter attribute) evidence_tolerance (sequince.steps.constraints.LikelihoodThresholdSelection attribute) evolving_target_ess_ratio() (in module sequince.steps.weighting) executed (sequince.steps.control.ConditionalStepOutput attribute) ExpandDimensions (class in sequince.steps.transformations) expected_unique_count() (in module sequince.steps.persistent) exploration_probability (sequince.steps.mutation.adaptive.policies.de.ESJDScaleWeightPolicy attribute) F factor (sequince.steps.mutation.adaptive.policies.rjd.RelativeJumpDistancePolicy attribute) family_ess (sequince.result.FixedLagLeeWhiteleyDiagnostics attribute) file_path (sequince.checkpoint.HDF5CheckpointWriter attribute) (sequince.checkpoint.PickleCheckpointWriter attribute) filename (sequince.callbacks.PlotCallback attribute) final_result (sequince.result.MetaSMCResult property) final_state (sequince.mcmc.MCMCResult property) (sequince.result.MetaSMCResult property) (sequince.result.NestedSamplingSMCResult property) (sequince.result.SMCResult property) fit() (sequince.flows.NormalizingFlow method) (sequince.proposals.FlowProposal method) (sequince.proposals.TrainableProposal method) (sequince.steps.mutation.rejuvenation.GenerativeProposal method) (sequince.transforms.AffineTransform method) (sequince.transforms.CompositeTransform method) (sequince.transforms.FlowTransform method) (sequince.transforms.ParticleTransform method) (sequince.transforms.PeriodicBoundaryTransform method) (sequince.transforms.WhiteningTransform method) fit_kwargs (sequince.transforms.FlowTransform attribute) fixed_lag_lee_whiteley_diagnostics() (sequince.result.SMCResult method) FixedLagLeeWhiteleyDiagnostics (class in sequince.result) FixedLengthMutation (class in sequince.steps.base) FixedLikelihoodThresholdSchedule (class in sequince.steps.constraints) FixedMutationStepPolicy (class in sequince.steps.mutation.adaptive.policies.fixed) FixedTemperedWeighting (class in sequince.steps.weighting) flow (sequince.proposals.FlowProposal property) (sequince.transforms.FlowTransform attribute) flow_asarray() (in module sequince.flows) flow_state_dict() (in module sequince.flows) FlowProposal (class in sequince.proposals) FlowTransform (class in sequince.transforms) forward() (sequince.flows.NormalizingFlow method) (sequince.steps.transformations.SMCTransformation method) (sequince.transforms.AffineTransform method) (sequince.transforms.BoundedToUnboundedTransform method) (sequince.transforms.BoundedToUnitHypercubeTransform method) (sequince.transforms.CauchitMapping method) (sequince.transforms.CompositeTransform method) (sequince.transforms.FlowTransform method) (sequince.transforms.LogitMapping method) (sequince.transforms.ParticleTransform method) (sequince.transforms.PeriodicBoundaryTransform method) (sequince.transforms.ProbitMapping method) (sequince.transforms.UnitIntervalMapping method) (sequince.transforms.WhiteningTransform method) forward_with_context() (sequince.steps.transformations.MetadataTransformation method) (sequince.steps.transformations.SMCTransformation method) freeze_log_prob() (sequince.posterior.TemperedPosterior method) from_config() (sequince.smc.SequentialMonteCarlo class method) from_dict() (sequince.checkpoint.SMCCheckpoint class method) (sequince.checkpoint.StepState class method) (sequince.state.ParticleState class method) (sequince.state.PersistentParticleState class method) (sequince.target.TargetEvaluation class method) from_runtime() (sequince.checkpoint.SMCCheckpoint class method) from_smc_result() (sequince.mcmc.MCMCResult class method) from_state() (sequince.state.PersistentParticleState class method) from_step() (sequince.checkpoint.StepState class method) full_path (sequince.callbacks.PlotCallback attribute) functional_iteration() (sequince.smc.SequentialMonteCarlo method) G gamma (sequince.steps.mutation.kernels.DifferentialEvolutionKernel attribute) gamma_one_probability (sequince.steps.mutation.kernels.DifferentialEvolutionKernel attribute) gamma_randomization (sequince.steps.mutation.kernels.DifferentialEvolutionKernel attribute) GammaRandomization (in module sequince.steps.mutation.kernels) GaussianRandomWalk (class in sequince.steps.mutation.kernels) GenerativeProposal (class in sequince.steps.mutation.rejuvenation) get_complementary_ensemble_kernel() (in module sequince.steps.mutation.kernels) get_emcee_move() (in module sequince.steps.mutation.emcee) get_meta_results() (sequince.result.SMCResult method) get_mutation_kernel() (in module sequince.steps.mutation.kernels) get_mutation_step() (in module sequince.steps.mutation.factory) get_prebuilt_transform() (in module sequince.transforms) get_unit_interval_mapping() (in module sequince.transforms) H has_particle_aligned_auxiliary() (in module sequince.transforms) HDF5CheckpointWriter (class in sequince.checkpoint) I IdentityTransform (class in sequince.transforms) ImportanceKernel (class in sequince.filtering.kernel) ImportanceTransition (class in sequince.steps.transition) in_bounds() (in module sequince.utils.bounds) inclusive (sequince.steps.constraints.LikelihoodConstrainedPrior attribute) IncrementalWeighting (class in sequince.steps.weighting) IncrementFn (in module sequince.steps.weighting) index (sequince.checkpoint.StepState attribute) indices (sequince.steps.mutation.kernels.AdaptiveMaskedGaussianRandomWalk attribute) (sequince.steps.mutation.kernels.MaskedGaussianRandomWalk attribute) initial_ancestor_indices (sequince.state.ParticleState attribute) initial_rho (sequince.steps.mutation.adaptive.minipcn.AdaptiveMiniPCNMutation attribute) initial_scale (sequince.steps.mutation.adaptive.proposal.AdaptiveGaussianProposal attribute) initial_state (sequince.checkpoint.SMCCheckpoint attribute) (sequince.result.SMCResult attribute) (sequince.smc.SMCRuntime attribute) initialise() (sequince.steps.mutation.adaptive.policies.acceptance.AcceptanceRatePolicy method) (sequince.steps.mutation.adaptive.policies.base.MutationStepPolicy method) (sequince.steps.mutation.adaptive.policies.de.DEScaleWeightPolicy method) (sequince.steps.mutation.adaptive.policies.de.ESJDScaleWeightPolicy method) (sequince.steps.mutation.adaptive.policies.fixed.FixedMutationStepPolicy method) (sequince.steps.mutation.adaptive.policies.rho.AcceptanceRateRhoPolicy method) (sequince.steps.mutation.adaptive.policies.rho.MiniPCNRhoPolicy method) (sequince.steps.mutation.adaptive.policies.rjd.RelativeJumpDistancePolicy method) initialize() (sequince.steps.mutation.metrics.base.MutationMetric method) (sequince.steps.mutation.metrics.base.MutationMetrics method) (sequince.steps.mutation.metrics.de.DEScaleMetrics method) (sequince.steps.mutation.metrics.esjd.ESJDMetric method) (sequince.steps.mutation.metrics.rjd.RelativeJumpDistanceMetric method) initialize_functional() (sequince.smc.SequentialMonteCarlo method) initialize_functional_metadata() (sequince.steps.base.SMCStep method) (sequince.steps.constraints.LikelihoodThresholdSelection method) (sequince.steps.mutation.metropolis.RedBlueMetropolisHastingsMutation method) (sequince.steps.resampling.ResamplingStep method) (sequince.steps.weighting.AdaptiveTemperedWeighting method) (sequince.steps.weighting.BaseTemperedStep method) initialize_functional_state_and_context() (sequince.steps.base.SMCStep method) (sequince.steps.constraints.LikelihoodThresholdSelection method) (sequince.steps.mutation.base.MutationStep method) (sequince.steps.mutation.repeated.RepeatedMutationStep method) (sequince.steps.weighting.BaseTemperedStep method) (sequince.steps.weighting.IncrementalWeighting method) initialize_metadata() (sequince.steps.weighting.BaseTemperedStep method) IntermediateParticlesPlot (class in sequince.callbacks) inverse() (sequince.flows.NormalizingFlow method) (sequince.steps.transformations.SMCTransformation method) (sequince.transforms.AffineTransform method) (sequince.transforms.BoundedToUnboundedTransform method) (sequince.transforms.BoundedToUnitHypercubeTransform method) (sequince.transforms.CauchitMapping method) (sequince.transforms.CompositeTransform method) (sequince.transforms.FlowTransform method) (sequince.transforms.LogitMapping method) (sequince.transforms.ParticleTransform method) (sequince.transforms.PeriodicBoundaryTransform method) (sequince.transforms.ProbitMapping method) (sequince.transforms.UnitIntervalMapping method) (sequince.transforms.WhiteningTransform method) is_due() (sequince.checkpoint.CheckpointWriter method) is_terminal (sequince.steps.constraints.NestedSamplingLevel attribute) iteration (sequince.steps.constraints.NestedSamplingLevel attribute) (sequince.steps.context.StepContext property) iteration() (sequince.smc.SequentialMonteCarlo method) IterationCallable (in module sequince.smc) J JointLogDensityFn (in module sequince.posterior) K kernel (sequince.steps.mutation.blocked.MetropolisBlock attribute) (sequince.steps.mutation.metropolis.RedBlueMetropolisHastingsMutation property) (sequince.steps.transition.ImportanceTransition property) kernel_auxiliary (sequince.steps.mutation.metrics.state.MutationTransition attribute) kernels (sequince.steps.mutation.kernels.MixtureMutationKernel attribute) KernelSample (class in sequince.steps.mutation.kernels) KIND_KEY (in module sequince.utils.hdf5) L learning_rate (sequince.steps.mutation.adaptive.policies.de.ESJDScaleWeightPolicy attribute) levels() (sequince.result.NestedSamplingSMCResult method) LikelihoodConstrainedPrior (class in sequince.steps.constraints) LikelihoodThresholdSchedule (in module sequince.steps.constraints) LikelihoodThresholdSelection (class in sequince.steps.constraints) LikelihoodThresholdWeighting (class in sequince.steps.constraints) load() (sequince.mcmc.MCMCResult class method) (sequince.result.MetaSMCResult class method) (sequince.result.SMCResult class method) (sequince.state.ParticleState class method) (sequince.target.TargetEvaluation class method) load_flow_state_dict() (in module sequince.flows) load_from_file() (sequince.result.SMCResult class method) load_from_h5_file() (in module sequince.utils.hdf5) load_hdf5() (sequince.checkpoint.SMCCheckpoint class method) load_pickle() (sequince.checkpoint.SMCCheckpoint class method) load_state_dict() (sequince.proposals.FlowProposal method) (sequince.smc.SequentialMonteCarlo method) (sequince.steps.base.SMCStep method) (sequince.steps.control.PeriodicStep method) (sequince.steps.control.RepeatStep method) (sequince.steps.control.SequentialStep method) (sequince.steps.meta.MetaSMCStep method) (sequince.steps.mutation.adaptive.base.AdaptiveMutationStep method) (sequince.steps.mutation.adaptive.de.AdaptDEScaleWeights method) (sequince.steps.mutation.adaptive.minipcn.AdaptiveMiniPCNMutation method) (sequince.steps.mutation.adaptive.policies.rho.AcceptanceRateRhoPolicy method) (sequince.steps.mutation.adaptive.steps.AdaptMutationSteps method) (sequince.steps.mutation.base.MutationStep method) (sequince.steps.mutation.rejuvenation.ProposalRejuvenation method) (sequince.steps.mutation.repeated.RepeatedMutationStep method) (sequince.steps.persistent.PersistentAdaptiveTemperedWeighting method) (sequince.steps.persistent.PersistParticles method) (sequince.steps.waste_free.WasteFreeResampleMove method) (sequince.transforms.FlowTransform method) log_auxiliary_density() (sequince.steps.transformations.SMCTransformation method) log_density() (sequince.steps.mutation.kernels.DensityMutationKernel method) (sequince.steps.mutation.kernels.GaussianRandomWalk method) log_density_fn (sequince.steps.mutation.kernels.CallableMutationKernel attribute) log_density_ratio (sequince.posterior.TemperedPosterior attribute) log_evidence (sequince.result.NestedSamplingSMCResult property) (sequince.state.ParticleState property) (sequince.state.PersistentParticleState property) (sequince.steps.constraints.NestedSamplingLevel attribute) log_evidence() (sequince.result.SMCResult method) log_evidence_error() (sequince.result.SMCResult method) log_evidence_history() (sequince.result.MetaSMCResult method) (sequince.result.NestedSamplingSMCResult method) (sequince.result.SMCResult method) log_evidence_increment (sequince.steps.constraints.NestedSamplingLevel attribute) log_evidence_increment_history() (sequince.result.NestedSamplingSMCResult method) log_evidence_variance() (sequince.result.SMCResult method) log_evidences (sequince.state.PersistentParticleState property) log_increment() (sequince.density.SequentialDensity method) (sequince.density.TemperedDensity method) (sequince.filtering.kernel.ImportanceKernel method) (sequince.posterior.TemperedPosterior method) (sequince.target.SequentialTarget method) (sequince.target.TemperedTarget method) log_increment_evaluations (sequince.target.EvaluationCounts attribute) log_initial() (sequince.density.TemperedDensity method) (sequince.posterior.TemperedPosterior method) (sequince.target.TemperedTarget method) log_jacobian() (sequince.steps.transformations.SMCTransformation method) log_likelihood (sequince.posterior.TemperedPosterior attribute) log_likelihood_and_proposal (sequince.posterior.TemperedPosterior attribute) log_likelihood_evaluations (sequince.target.EvaluationCounts attribute) log_likelihood_upper_bound (sequince.steps.constraints.LikelihoodThresholdSelection attribute) log_normalizer (sequince.exceptions.DegenerateWeightsError attribute) log_normalizing_constant (sequince.state.ParticleState attribute) log_normalizing_constant() (sequince.result.SMCResult method) log_normalizing_constant_error() (sequince.result.SMCResult method) log_normalizing_constant_history() (sequince.result.MetaSMCResult method) (sequince.result.SMCResult method) log_normalizing_constant_variance() (sequince.result.SMCResult method) log_normalizing_constants (sequince.state.PersistentParticleState attribute) log_prior (sequince.posterior.TemperedPosterior attribute) log_prior_volume (sequince.steps.constraints.NestedSamplingLevel attribute) log_prior_volume_history() (sequince.result.NestedSamplingSMCResult method) log_prior_volume_increment_history() (sequince.result.NestedSamplingSMCResult method) log_prob() (sequince.density.SequentialDensity method) (sequince.density.TemperedDensity method) (sequince.flows.NormalizingFlow method) (sequince.posterior.TemperedPosterior method) (sequince.proposals.FlowProposal method) (sequince.proposals.ProposalDistribution method) (sequince.steps.constraints.LikelihoodConstrainedPrior method) (sequince.target.Target method) (sequince.target.TemperedTarget method) log_proposal (sequince.posterior.TemperedPosterior attribute) log_proposal_evaluations (sequince.target.EvaluationCounts attribute) LOG_PROPOSAL_OVERRIDE_KEY (in module sequince.steps.context) log_proposal_override_key (sequince.posterior.TemperedPosterior attribute) log_shell_expectation (sequince.steps.constraints.NestedSamplingLevel attribute) log_target_evaluations (sequince.target.EvaluationCounts attribute) log_terminal() (sequince.density.TemperedDensity method) (sequince.posterior.TemperedPosterior method) (sequince.target.TemperedTarget method) log_transition_ratio() (sequince.steps.mutation.kernels.CallableMutationKernel method) (sequince.steps.mutation.kernels.ComplementaryEnsembleKernel method) (sequince.steps.mutation.kernels.SymmetricComplementaryEnsembleKernel method) (sequince.steps.mutation.kernels.SymmetricMutationKernel method) (sequince.steps.mutation.kernels.TransitionRatioKernel method) log_transition_ratio_fn (sequince.steps.mutation.kernels.CallableMutationKernel attribute) log_transition_ratio_from_sample() (sequince.steps.mutation.kernels.MixtureMutationKernel method) (sequince.steps.mutation.kernels.SampleAwareMutationKernel method) log_weights (sequince.state.ParticleState attribute) LogDensityFn (in module sequince.steps.mutation.kernels) logger (in module sequince.callbacks) (in module sequince.jax) (in module sequince.proposals) (in module sequince.smc) (in module sequince.steps.control) (in module sequince.steps.log) (in module sequince.steps.mutation.blackjax) (in module sequince.steps.mutation.conditional) (in module sequince.steps.mutation.emcee) (in module sequince.steps.mutation.eryn) (in module sequince.steps.mutation.metropolis) (in module sequince.steps.mutation.minipcn) (in module sequince.steps.resampling) (in module sequince.steps.transformations) (in module sequince.steps.weighting) (in module sequince.target) (in module sequince.transforms) LOGGER_NAME (in module sequince.log) LoggingStep (class in sequince.steps.log) LogitMapping (class in sequince.transforms) LogLikelihoodWeighting (class in sequince.steps.weighting) LogPriorMassStoppingCriterion (class in sequince.steps.constraints) LogProbFn (in module sequince.steps.mutation.base) LogProposalLike (in module sequince.posterior) logsumexp() (in module sequince.array_api) LogTransitionRatioFn (in module sequince.steps.mutation.kernels) M make_log_proposal() (sequince.steps.transformations.SMCTransformation method) make_mcmc() (in module sequince.mcmc) make_nested_sampling_smc() (in module sequince.prebuilt_samplers) make_persistent_bayesian_smc() (in module sequince.prebuilt_samplers) make_standard_bayesian_smc() (in module sequince.prebuilt_samplers) mapping (sequince.transforms.BoundedToUnboundedTransform attribute) MarkovChainMonteCarlo (class in sequince.mcmc) MaskedGaussianRandomWalk (class in sequince.steps.mutation.kernels) max_rho (sequince.steps.mutation.adaptive.policies.rho.AcceptanceRateRhoPolicy attribute) max_scale (sequince.steps.mutation.adaptive.proposal.AdaptiveGaussianProposal attribute) max_steps (sequince.steps.mutation.adaptive.policies.acceptance.AcceptanceRatePolicy attribute) MCMCResult (class in sequince.mcmc) mean_acceptance_probability (sequince.steps.mutation.blackjax.BlackJAXOutput attribute) META_SMC_OUTPUT_KEY (in module sequince.steps.meta) metadata (sequince.checkpoint.SMCCheckpoint attribute) (sequince.smc.SMCRuntime attribute) (sequince.state.ParticleState attribute) (sequince.steps.context.StepContext attribute) metadata_history() (sequince.result.SMCResult method) metadata_key (sequince.callbacks.ParticleTransformPlot attribute) (sequince.callbacks.TransformedMutationChainPlot attribute) metadata_keys (sequince.callbacks.StatePlot attribute) MetadataTransformation (class in sequince.steps.transformations) MetadataUpdateFn (in module sequince.steps.transformations) MetaSMCResult (class in sequince.result) MetaSMCStep (class in sequince.steps.meta) metric_name (sequince.steps.mutation.adaptive.policies.rjd.RelativeJumpDistancePolicy attribute) metrics (sequince.steps.mutation.base.MutationStep attribute) (sequince.steps.mutation.blackjax.BlackJAXOutput attribute) (sequince.steps.mutation.blocked.BlockedMetropolisHastingsMutation attribute) (sequince.steps.mutation.minipcn.MiniPCNOutput attribute) (sequince.steps.mutation.repeated.RepeatedMutationStep property) (sequince.steps.mutation.repeated.RepeatedMutationStepOutput attribute) MetropolisBlock (class in sequince.steps.mutation.blocked) MetropolisHastingsMutation (class in sequince.steps.mutation.metropolis) min_acceptance (sequince.steps.mutation.adaptive.policies.acceptance.AcceptanceRatePolicy attribute) min_attempts (sequince.steps.mutation.adaptive.policies.de.ESJDScaleWeightPolicy attribute) min_rho (sequince.steps.mutation.adaptive.policies.rho.AcceptanceRateRhoPolicy attribute) min_scale (sequince.steps.mutation.adaptive.proposal.AdaptiveGaussianProposal attribute) min_steps (sequince.steps.mutation.adaptive.policies.acceptance.AcceptanceRatePolicy attribute) minimum (sequince.steps.constraints.LogPriorMassStoppingCriterion attribute) MiniPCNMutation (class in sequince.steps.mutation.minipcn) MiniPCNOutput (class in sequince.steps.mutation.minipcn) MiniPCNRhoPolicy (class in sequince.steps.mutation.adaptive.policies.rho) MixtureMutationKernel (class in sequince.steps.mutation.kernels) module sequince sequince.array_api sequince.callbacks sequince.checkpoint sequince.density sequince.exceptions sequince.filtering sequince.filtering.kernel sequince.flows sequince.jax sequince.log sequince.mcmc sequince.plot sequince.posterior sequince.prebuilt_samplers sequince.proposals sequince.result sequince.smc sequince.state sequince.stats sequince.steps sequince.steps.base sequince.steps.constraints sequince.steps.context sequince.steps.control sequince.steps.log sequince.steps.meta sequince.steps.mutation sequince.steps.mutation.adaptive sequince.steps.mutation.adaptive.base sequince.steps.mutation.adaptive.de sequince.steps.mutation.adaptive.minipcn sequince.steps.mutation.adaptive.policies sequince.steps.mutation.adaptive.policies.acceptance sequince.steps.mutation.adaptive.policies.base sequince.steps.mutation.adaptive.policies.de sequince.steps.mutation.adaptive.policies.fixed sequince.steps.mutation.adaptive.policies.rho sequince.steps.mutation.adaptive.policies.rjd sequince.steps.mutation.adaptive.proposal sequince.steps.mutation.adaptive.steps sequince.steps.mutation.base sequince.steps.mutation.blackjax sequince.steps.mutation.blocked sequince.steps.mutation.conditional sequince.steps.mutation.emcee sequince.steps.mutation.eryn sequince.steps.mutation.factory sequince.steps.mutation.kernels sequince.steps.mutation.metrics sequince.steps.mutation.metrics.base sequince.steps.mutation.metrics.de sequince.steps.mutation.metrics.esjd sequince.steps.mutation.metrics.rjd sequince.steps.mutation.metrics.state sequince.steps.mutation.metropolis sequince.steps.mutation.minipcn sequince.steps.mutation.rejuvenation sequince.steps.mutation.repeated sequince.steps.persistent sequince.steps.resampling sequince.steps.transformations sequince.steps.transition sequince.steps.waste_free sequince.steps.weighting sequince.target sequince.transforms sequince.typing sequince.utils sequince.utils.bounds sequince.utils.callables sequince.utils.copying sequince.utils.hdf5 sequince.utils.optimize sequince.utils.pytrees sequince.utils.random module (sequince.checkpoint.StepState attribute) MultinomialResampling (class in sequince.steps.resampling) multipliers (sequince.steps.mutation.metrics.de.DEScaleMetrics attribute) MutateIfResampled (class in sequince.steps.mutation.conditional) mutation (sequince.mcmc.MarkovChainMonteCarlo attribute) (sequince.steps.mutation.adaptive.base.AdaptiveMutationStep attribute) (sequince.steps.mutation.adaptive.proposal.AdaptiveGaussianProposal attribute) (sequince.steps.mutation.conditional.MutateIfResampled attribute) (sequince.steps.mutation.repeated.RepeatedMutationStep attribute) (sequince.steps.waste_free.WasteFreeResampleMove attribute) MUTATION_KERNELS (in module sequince.steps.mutation.kernels) MutationChainPlot (class in sequince.callbacks) MutationKernel (in module sequince.steps.mutation.kernels) MutationKernelFactory (in module sequince.steps.mutation.metropolis) MutationMetric (class in sequince.steps.mutation.metrics.base) MutationMetrics (class in sequince.steps.mutation.metrics.base) MutationMetricsOutput (class in sequince.steps.mutation.metrics.state) MutationStep (class in sequince.steps.mutation.base) MutationStepPolicy (class in sequince.steps.mutation.adaptive.policies.base) MutationStepState (class in sequince.steps.mutation.metrics.state) MutationTransition (class in sequince.steps.mutation.metrics.state) N n (sequince.steps.control.PeriodicStep attribute) (sequince.steps.control.RepeatStep attribute) n_accepted (sequince.steps.mutation.metrics.state.MutationMetricsOutput attribute) (sequince.steps.mutation.metrics.state.MutationStepState attribute) n_attempted (sequince.steps.mutation.metrics.state.MutationMetricsOutput attribute) (sequince.steps.mutation.metrics.state.MutationStepState attribute) n_batches (sequince.state.PersistentParticleState property) n_pairs (sequince.steps.mutation.metrics.rjd.RelativeJumpDistanceMetric attribute) n_particles (sequince.state.PersistentParticleState property) (sequince.target.TargetEvaluation property) n_rounds (sequince.steps.mutation.repeated.RepeatedMutationStep attribute) n_steps (sequince.steps.mutation.base.MutationStep property) (sequince.steps.mutation.blocked.MetropolisBlock attribute) (sequince.steps.mutation.metrics.state.MutationMetricsOutput attribute) (sequince.steps.mutation.metrics.state.MutationStepState attribute) (sequince.steps.mutation.repeated.RepeatedMutationStep property) n_surviving (sequince.steps.constraints.NestedSamplingLevel attribute) name (sequince.steps.mutation.blocked.MetropolisBlock attribute) (sequince.steps.mutation.metrics.base.MutationMetric property) (sequince.steps.mutation.metrics.de.DEScaleMetrics attribute) (sequince.steps.mutation.metrics.esjd.ESJDMetric attribute) (sequince.steps.mutation.metrics.rjd.RelativeJumpDistanceMetric attribute) namespace() (in module sequince.array_api) needs_transition (sequince.steps.mutation.metrics.base.MutationMetrics attribute) (sequince.steps.mutation.metrics.de.DEScaleMetrics attribute) nested() (in module sequince.utils.hdf5) NestedSamplingLevel (class in sequince.steps.constraints) NestedSamplingSMCResult (class in sequince.result) next_iteration (sequince.checkpoint.SMCCheckpoint attribute) next_n_steps (sequince.steps.mutation.adaptive.steps.AdaptMutationSteps property) next_observation_index (sequince.checkpoint.SMCCheckpoint attribute) (sequince.smc.SMCRuntime attribute) (sequince.steps.context.StepContext attribute) next_rho (sequince.steps.mutation.adaptive.minipcn.AdaptiveMiniPCNMutation property) next_weights (sequince.steps.mutation.adaptive.de.AdaptDEScaleWeights property) normalize() (sequince.state.ParticleState method) normalize_log_weights() (in module sequince.state) NormalizingConstantVarianceMethod (in module sequince.result) NormalizingFlow (class in sequince.flows) num_integration_steps (sequince.steps.mutation.blackjax.BlackJAXOutput attribute) O observation (sequince.checkpoint.SMCCheckpoint attribute) (sequince.steps.context.StepContext attribute) offset (sequince.steps.control.PeriodicStep attribute) OPTREE_NAMESPACE (in module sequince.utils.pytrees) outdir (sequince.callbacks.PlotCallback attribute) output_key (sequince.callbacks.MutationChainPlot attribute) (sequince.steps.constraints.NestedSamplingLevel attribute) (sequince.steps.meta.MetaSMCStep attribute) outputs (sequince.checkpoint.SMCCheckpoint attribute) (sequince.mcmc.MCMCResult attribute) (sequince.result.SMCResult attribute) (sequince.smc.SMCRuntime attribute) P parameter_inds (sequince.callbacks.IntermediateParticlesPlot attribute) (sequince.callbacks.MutationChainPlot attribute) (sequince.callbacks.ParticleTransformPlot attribute) (sequince.callbacks.TracePlot attribute) parameter_labels (sequince.callbacks.IntermediateParticlesPlot attribute) (sequince.callbacks.MutationChainPlot attribute) (sequince.callbacks.ParticleTransformPlot attribute) (sequince.callbacks.TracePlot attribute) PARTICLE_TRANSFORM_KEY (in module sequince.steps.mutation.base) particles (sequince.state.ParticleState attribute) (sequince.steps.mutation.kernels.KernelSample attribute) ParticleState (class in sequince.state) ParticleTransform (class in sequince.transforms) ParticleTransformPlot (class in sequince.callbacks) path (sequince.checkpoint.HDF5CheckpointWriter attribute) PeriodicBoundaryTransform (class in sequince.transforms) PeriodicStep (class in sequince.steps.control) persistent_log_mixture_denominator() (in module sequince.steps.persistent) persistent_log_weights() (in module sequince.steps.persistent) persistent_state (sequince.steps.persistent.PersistParticles attribute) PersistentAdaptiveTemperedWeighting (class in sequince.steps.persistent) PersistentParticleState (class in sequince.state) PersistentTemperedWeighting (class in sequince.steps.persistent) PersistParticles (class in sequince.steps.persistent) PickleCheckpointWriter (class in sequince.checkpoint) plot_chains() (in module sequince.plot) plot_corner() (in module sequince.plot) (sequince.result.SMCResult method) plot_effective_sample_size() (sequince.result.SMCResult method) plot_kwargs (sequince.callbacks.PlotCallback attribute) plot_log_evidence() (sequince.result.MetaSMCResult method) (sequince.result.SMCResult method) plot_log_normalizing_constant() (sequince.result.MetaSMCResult method) (sequince.result.SMCResult method) plot_metadata_history() (sequince.result.MetaSMCResult method) (sequince.result.SMCResult method) plot_trace() (sequince.result.SMCResult method) PlotCallback (class in sequince.callbacks) policy (sequince.steps.mutation.adaptive.de.AdaptDEScaleWeights attribute) (sequince.steps.mutation.adaptive.minipcn.AdaptiveMiniPCNMutation attribute) (sequince.steps.mutation.adaptive.steps.AdaptMutationSteps attribute) posterior (sequince.steps.meta.MetaSMCStep attribute) posterior_samples() (sequince.result.NestedSamplingSMCResult method) (sequince.result.SMCResult method) prepare() (sequince.steps.mutation.metrics.base.MutationMetrics method) (sequince.steps.mutation.metrics.esjd.ESJDMetric method) (sequince.steps.mutation.metrics.rjd.RelativeJumpDistanceMetric method) prepare_evaluation() (sequince.target.Target method) ProbitMapping (class in sequince.transforms) produced_states (sequince.smc.SMCRuntime attribute) proposal (sequince.steps.mutation.rejuvenation.ProposalRejuvenation property) proposal_fn (sequince.steps.mutation.kernels.CallableMutationKernel attribute) ProposalDistribution (class in sequince.proposals) ProposalFn (in module sequince.steps.mutation.kernels) ProposalRejuvenation (class in sequince.steps.mutation.rejuvenation) protocol (sequince.checkpoint.PickleCheckpointWriter attribute) pytree_dataclass() (in module sequince.utils.pytrees) Q qualname (sequince.checkpoint.StepState attribute) quantile (sequince.steps.constraints.QuantileLikelihoodThresholdSchedule attribute) QuantileLikelihoodThresholdSchedule (class in sequince.steps.constraints) R record_outputs (sequince.steps.meta.MetaSMCStep attribute) recursively_save_to_h5_file() (in module sequince.utils.hdf5) RedBlueMetropolisHastingsMutation (class in sequince.steps.mutation.metropolis) reference_radius (sequince.steps.mutation.metrics.rjd.RelativeJumpDistanceMetric attribute) refresh() (sequince.target.Target method) regularization (sequince.steps.mutation.kernels.AdaptiveMaskedGaussianRandomWalk attribute) RelativeJumpDistanceMetric (class in sequince.steps.mutation.metrics.rjd) RelativeJumpDistancePolicy (class in sequince.steps.mutation.adaptive.policies.rjd) RepeatedMutationStep (class in sequince.steps.mutation.repeated) RepeatedMutationStepOutput (class in sequince.steps.mutation.repeated) RepeatStep (class in sequince.steps.control) replace() (sequince.target.TargetEvaluation method) replace_particles() (sequince.state.ParticleState method) request_stop() (sequince.steps.context.StepContext method) request_stop_immediately() (sequince.steps.context.StepContext method) requested_lag (sequince.result.FixedLagLeeWhiteleyDiagnostics attribute) requires_detached_checkpoint (sequince.checkpoint.CheckpointWriter attribute) (sequince.checkpoint.HDF5CheckpointWriter attribute) (sequince.checkpoint.PickleCheckpointWriter attribute) resample() (sequince.state.ParticleState method) resampled (sequince.steps.resampling.ResamplingOutput attribute) resampling_scheme (sequince.steps.resampling.MultinomialResampling attribute) (sequince.steps.resampling.ResamplingOutput attribute) (sequince.steps.resampling.ResamplingStep attribute) (sequince.steps.resampling.StratifiedResampling attribute) (sequince.steps.resampling.SystematicResampling attribute) ResamplingOutput (class in sequince.steps.resampling) ResamplingStep (class in sequince.steps.resampling) resolve_dtype() (in module sequince.array_api) resolve_emcee_moves() (in module sequince.steps.mutation.emcee) resolve_log_proposal() (sequince.posterior.TemperedPosterior method) resolve_rng() (in module sequince.utils.random) restore_rng() (sequince.checkpoint.SMCCheckpoint method) restore_steps() (in module sequince.checkpoint) result (sequince.result.NestedSamplingSMCResult attribute) result() (sequince.checkpoint.SMCCheckpoint method) (sequince.steps.mutation.metrics.base.MutationMetric method) (sequince.steps.mutation.metrics.base.MutationMetrics method) (sequince.steps.mutation.metrics.de.DEScaleMetrics method) (sequince.steps.mutation.metrics.esjd.ESJDMetric method) (sequince.steps.mutation.metrics.rjd.RelativeJumpDistanceMetric method) RESULT_HDF5_OMITTED_METADATA_KEYS (in module sequince.steps.context) results (sequince.result.MetaSMCResult attribute) resume_from() (sequince.mcmc.MarkovChainMonteCarlo method) (sequince.smc.SequentialMonteCarlo method) resume_functional_from() (sequince.smc.SequentialMonteCarlo method) rng (sequince.smc.SMCRuntime attribute) rng_state (sequince.checkpoint.SMCCheckpoint attribute) RNGLike (in module sequince.utils.random) round_outputs (sequince.steps.mutation.repeated.RepeatedMutationStepOutput attribute) run() (sequince.mcmc.MarkovChainMonteCarlo method) (sequince.smc.SequentialMonteCarlo method) run_functional() (sequince.smc.SequentialMonteCarlo method) run_kwargs (sequince.steps.meta.MetaSMCStep attribute) runner (sequince.steps.meta.MetaSMCStep attribute) S sample() (sequince.filtering.kernel.ImportanceKernel method) (sequince.flows.NormalizingFlow method) (sequince.proposals.FlowProposal method) (sequince.proposals.ProposalDistribution method) (sequince.steps.mutation.kernels.CallableMutationKernel method) (sequince.steps.mutation.kernels.ComplementaryEnsembleKernel method) (sequince.steps.mutation.kernels.DifferentialEvolutionKernel method) (sequince.steps.mutation.kernels.GaussianRandomWalk method) (sequince.steps.mutation.kernels.MaskedGaussianRandomWalk method) (sequince.steps.mutation.kernels.MixtureMutationKernel method) (sequince.steps.mutation.rejuvenation.GenerativeProposal method) sample_and_log_prob() (sequince.proposals.FlowProposal method) (sequince.proposals.ProposalDistribution method) SampleAwareMutationKernel (class in sequince.steps.mutation.kernels) samples() (sequince.mcmc.MCMCResult method) save() (sequince.mcmc.MCMCResult method) (sequince.result.MetaSMCResult method) (sequince.result.SMCResult method) (sequince.state.ParticleState method) (sequince.target.TargetEvaluation method) save_hdf5() (sequince.checkpoint.SMCCheckpoint method) save_pickle() (sequince.checkpoint.SMCCheckpoint method) save_rng (sequince.checkpoint.CheckpointWriter attribute) save_to_file() (sequince.result.SMCResult method) scale (sequince.steps.mutation.kernels.AdaptiveMaskedGaussianRandomWalk attribute) (sequince.steps.mutation.kernels.GaussianRandomWalk attribute) (sequince.steps.mutation.kernels.MaskedGaussianRandomWalk attribute) scale_key (sequince.steps.mutation.adaptive.proposal.AdaptiveGaussianProposal attribute) scale_multipliers (sequince.steps.mutation.kernels.DifferentialEvolutionKernel attribute) scale_weights (sequince.steps.mutation.kernels.DifferentialEvolutionKernel attribute) schedule (sequince.steps.constraints.LikelihoodThresholdSelection attribute) schema_header() (in module sequince.utils.hdf5) SCHEMA_KEY (in module sequince.utils.hdf5) SCHEMA_VERSION (in module sequince.utils.hdf5) seed (sequince.steps.mutation.metrics.rjd.RelativeJumpDistanceMetric attribute) select() (sequince.target.TargetEvaluation method) select_transform_auxiliary() (in module sequince.transforms) SequentialDensity (class in sequince.density) SequentialMonteCarlo (class in sequince.smc) SequentialStep (class in sequince.steps.control) SequentialTarget (class in sequince.target) sequince module sequince.array_api module sequince.callbacks module sequince.checkpoint module sequince.density module sequince.exceptions module sequince.filtering module sequince.filtering.kernel module sequince.flows module sequince.jax module sequince.log module sequince.mcmc module sequince.plot module sequince.posterior module sequince.prebuilt_samplers module sequince.proposals module sequince.result module sequince.smc module sequince.state module sequince.stats module sequince.steps module sequince.steps.base module sequince.steps.constraints module sequince.steps.context module sequince.steps.control module sequince.steps.log module sequince.steps.meta module sequince.steps.mutation module sequince.steps.mutation.adaptive module sequince.steps.mutation.adaptive.base module sequince.steps.mutation.adaptive.de module sequince.steps.mutation.adaptive.minipcn module sequince.steps.mutation.adaptive.policies module sequince.steps.mutation.adaptive.policies.acceptance module sequince.steps.mutation.adaptive.policies.base module sequince.steps.mutation.adaptive.policies.de module sequince.steps.mutation.adaptive.policies.fixed module sequince.steps.mutation.adaptive.policies.rho module sequince.steps.mutation.adaptive.policies.rjd module sequince.steps.mutation.adaptive.proposal module sequince.steps.mutation.adaptive.steps module sequince.steps.mutation.base module sequince.steps.mutation.blackjax module sequince.steps.mutation.blocked module sequince.steps.mutation.conditional module sequince.steps.mutation.emcee module sequince.steps.mutation.eryn module sequince.steps.mutation.factory module sequince.steps.mutation.kernels module sequince.steps.mutation.metrics module sequince.steps.mutation.metrics.base module sequince.steps.mutation.metrics.de module sequince.steps.mutation.metrics.esjd module sequince.steps.mutation.metrics.rjd module sequince.steps.mutation.metrics.state module sequince.steps.mutation.metropolis module sequince.steps.mutation.minipcn module sequince.steps.mutation.rejuvenation module sequince.steps.mutation.repeated module sequince.steps.persistent module sequince.steps.resampling module sequince.steps.transformations module sequince.steps.transition module sequince.steps.waste_free module sequince.steps.weighting module sequince.target module sequince.transforms module sequince.typing module sequince.utils module sequince.utils.bounds module sequince.utils.callables module sequince.utils.copying module sequince.utils.hdf5 module sequince.utils.optimize module sequince.utils.pytrees module sequince.utils.random module shared (sequince.steps.context.StepContext attribute) shared_context (sequince.smc.SMCRuntime attribute) shell (sequince.steps.constraints.LogPriorMassStoppingCriterion attribute) shell_lower_threshold (sequince.steps.constraints.NestedSamplingLevel attribute) shell_lower_threshold_history() (sequince.result.NestedSamplingSMCResult method) shell_upper_threshold (sequince.steps.constraints.NestedSamplingLevel attribute) shell_upper_threshold_history() (sequince.result.NestedSamplingSMCResult method) ShellEvidenceStep (class in sequince.steps.constraints) SMC_TRANSFORMATION_KEY (in module sequince.steps.context) SMCCallback (class in sequince.callbacks) SMCCheckpoint (class in sequince.checkpoint) SMCConfig (class in sequince.smc) SMCResult (class in sequince.result) SMCRuntime (class in sequince.smc) SMCStep (class in sequince.steps.base) SMCTransformation (class in sequince.steps.transformations) state (sequince.checkpoint.SMCCheckpoint property) (sequince.checkpoint.StepState attribute) (sequince.smc.SMCRuntime attribute) state_dict() (sequince.proposals.FlowProposal method) (sequince.smc.SequentialMonteCarlo method) (sequince.steps.base.SMCStep method) (sequince.steps.control.PeriodicStep method) (sequince.steps.control.RepeatStep method) (sequince.steps.control.SequentialStep method) (sequince.steps.meta.MetaSMCStep method) (sequince.steps.mutation.adaptive.base.AdaptiveMutationStep method) (sequince.steps.mutation.adaptive.de.AdaptDEScaleWeights method) (sequince.steps.mutation.adaptive.minipcn.AdaptiveMiniPCNMutation method) (sequince.steps.mutation.adaptive.policies.rho.AcceptanceRateRhoPolicy method) (sequince.steps.mutation.adaptive.steps.AdaptMutationSteps method) (sequince.steps.mutation.base.MutationStep method) (sequince.steps.mutation.rejuvenation.ProposalRejuvenation method) (sequince.steps.mutation.repeated.RepeatedMutationStep method) (sequince.steps.persistent.PersistentAdaptiveTemperedWeighting method) (sequince.steps.persistent.PersistParticles method) (sequince.steps.waste_free.WasteFreeResampleMove method) (sequince.transforms.FlowTransform method) state_metadata_fn (sequince.steps.transformations.MetadataTransformation attribute) StatePlot (class in sequince.callbacks) states (sequince.checkpoint.SMCCheckpoint attribute) (sequince.mcmc.MCMCResult attribute) (sequince.result.NestedSamplingSMCResult property) (sequince.result.SMCResult attribute) (sequince.steps.mutation.metrics.state.MutationStepState attribute) step (sequince.steps.control.PeriodicStep attribute) (sequince.steps.control.RepeatStep attribute) step_fn (sequince.steps.mutation.minipcn.MiniPCNOutput attribute) step_index (sequince.callbacks.AdaptiveMutationPlot attribute) (sequince.callbacks.MutationChainPlot attribute) step_states (sequince.checkpoint.SMCCheckpoint attribute) StepCallable (in module sequince.smc) StepContext (class in sequince.steps.context) steps (sequince.smc.SMCConfig attribute) (sequince.steps.control.SequentialStep attribute) (sequince.steps.mutation.blackjax.BlackJAXOutput attribute) (sequince.steps.mutation.minipcn.MiniPCNOutput attribute) StepState (class in sequince.checkpoint) stop_immediately (sequince.steps.context.StepContext attribute) stop_reason (sequince.result.NestedSamplingSMCResult property) stop_requested (sequince.steps.context.StepContext attribute) StopIf (class in sequince.steps.control) store_chains (sequince.steps.mutation.base.MutationStep property) store_shell_particles (sequince.steps.constraints.ShellEvidenceStep attribute) StratifiedResampling (class in sequince.steps.resampling) summary() (sequince.result.MetaSMCResult method) (sequince.result.NestedSamplingSMCResult method) (sequince.result.SMCResult method) survival_fraction (sequince.steps.constraints.NestedSamplingLevel attribute) survival_fraction_history() (sequince.result.NestedSamplingSMCResult method) surviving_particles_history() (sequince.result.NestedSamplingSMCResult method) symmetric (sequince.steps.mutation.kernels.CallableMutationKernel attribute) SymmetricComplementaryEnsembleKernel (class in sequince.steps.mutation.kernels) SymmetricMutationKernel (class in sequince.steps.mutation.kernels) SystematicResampling (class in sequince.steps.resampling) T t (sequince.smc.SMCRuntime attribute) (sequince.steps.context.StepContext attribute) take() (sequince.target.TargetEvaluation method) Target (class in sequince.target) target (sequince.steps.constraints.LikelihoodThresholdSelection attribute) (sequince.steps.constraints.LikelihoodThresholdWeighting attribute) (sequince.steps.constraints.ShellEvidenceStep attribute) target_acceptance (sequince.steps.mutation.adaptive.policies.rho.AcceptanceRateRhoPolicy attribute) (sequince.steps.mutation.adaptive.proposal.AdaptiveGaussianProposal attribute) target_fraction (sequince.steps.mutation.adaptive.policies.rjd.RelativeJumpDistancePolicy attribute) target_id (sequince.target.TargetEvaluation attribute) target_steps (sequince.callbacks.AdaptiveMutationPlot attribute) (sequince.steps.mutation.adaptive.policies.acceptance.AcceptanceRatePolicy attribute) TargetComponentFn (in module sequince.target) TargetESSRatio (in module sequince.steps.weighting) TargetEvaluation (class in sequince.target) TemperedDensity (class in sequince.density) TemperedPosterior (class in sequince.posterior) TemperedTarget (class in sequince.target) TemperedWeighting (class in sequince.steps.weighting) threshold_history() (sequince.result.NestedSamplingSMCResult method) thresholds (sequince.steps.constraints.FixedLikelihoodThresholdSchedule attribute) to_dict() (sequince.checkpoint.SMCCheckpoint method) (sequince.checkpoint.StepState method) (sequince.state.ParticleState method) (sequince.state.PersistentParticleState method) (sequince.target.TargetEvaluation method) to_numpy() (in module sequince.array_api) total_resampling_events (sequince.result.FixedLagLeeWhiteleyDiagnostics attribute) traced_resampling_events (sequince.result.FixedLagLeeWhiteleyDiagnostics attribute) TracePlot (class in sequince.callbacks) TrainableProposal (class in sequince.proposals) TransformationStep (class in sequince.steps.transformations) TransformedMutationChainPlot (class in sequince.callbacks) TransformRefit (in module sequince.steps.mutation.base) transforms (sequince.transforms.CompositeTransform attribute) TransitionRatioKernel (class in sequince.steps.mutation.kernels) U UnitIntervalMapping (class in sequince.transforms) update() (sequince.steps.mutation.adaptive.policies.acceptance.AcceptanceRatePolicy method) (sequince.steps.mutation.adaptive.policies.base.MutationStepPolicy method) (sequince.steps.mutation.adaptive.policies.de.DEScaleWeightPolicy method) (sequince.steps.mutation.adaptive.policies.de.ESJDScaleWeightPolicy method) (sequince.steps.mutation.adaptive.policies.fixed.FixedMutationStepPolicy method) (sequince.steps.mutation.adaptive.policies.rho.AcceptanceRateRhoPolicy method) (sequince.steps.mutation.adaptive.policies.rho.MiniPCNRhoPolicy method) (sequince.steps.mutation.adaptive.policies.rjd.RelativeJumpDistancePolicy method) (sequince.steps.mutation.metrics.base.MutationMetric method) (sequince.steps.mutation.metrics.base.MutationMetrics method) (sequince.steps.mutation.metrics.de.DEScaleMetrics method) (sequince.steps.mutation.metrics.esjd.ESJDMetric method) (sequince.steps.mutation.metrics.rjd.RelativeJumpDistanceMetric method) upper_target_fraction (sequince.steps.mutation.adaptive.policies.rjd.RelativeJumpDistancePolicy attribute) V validate_evaluation() (sequince.target.Target method) validate_for() (sequince.target.TargetEvaluation method) validate_functional_configuration() (sequince.steps.base.SMCStep method) (sequince.steps.constraints.LikelihoodThresholdSelection method) validate_functional_state_and_context() (sequince.steps.constraints.LikelihoodThresholdSelection method) validate_n_steps() (in module sequince.steps.base) validate_schema() (in module sequince.utils.hdf5) values (sequince.steps.mutation.metrics.state.MutationMetricsOutput attribute) version (sequince.checkpoint.SMCCheckpoint attribute) VERSION_KEY (in module sequince.utils.hdf5) W WasteFreeResampleMove (class in sequince.steps.waste_free) weighted_covariance() (sequince.result.SMCResult method) weighted_mean() (sequince.result.SMCResult method) weights (sequince.state.ParticleState property) (sequince.steps.mutation.kernels.MixtureMutationKernel attribute) WhiteningTransform (class in sequince.transforms) with_metadata() (sequince.steps.context.StepContext method) with_target() (sequince.target.TargetEvaluation method) with_updates() (sequince.state.ParticleState method) (sequince.state.PersistentParticleState method) without_metadata() (sequince.steps.context.StepContext method) WorstParticleLikelihoodThresholdSchedule (class in sequince.steps.constraints) write() (sequince.checkpoint.CheckpointWriter method) X xp (sequince.flows.NormalizingFlow attribute) Z zeros() (sequince.target.EvaluationCounts class method)