Index

_

__call__() (pyabc.acceptor.Acceptor method) (pyabc.acceptor.FunctionAcceptor method) (pyabc.acceptor.ScaledPDFNorm method) (pyabc.acceptor.StochasticAcceptor method) (pyabc.acceptor.UniformAcceptor method) (pyabc.copasi.BasicoModel method) (pyabc.distance.AcceptAllDistance method) (pyabc.distance.AggregatedDistance method) (pyabc.distance.BinomialKernel method) (pyabc.distance.Distance method) (pyabc.distance.FunctionDistance method) (pyabc.distance.FunctionKernel method) (pyabc.distance.IndependentLaplaceKernel method) (pyabc.distance.IndependentNormalKernel method) (pyabc.distance.NegativeBinomialKernel method) (pyabc.distance.NoDistance method) (pyabc.distance.NormalKernel method) (pyabc.distance.PCADistance method) (pyabc.distance.PNormDistance method) (pyabc.distance.PoissonKernel method) (pyabc.distance.RangeEstimatorDistance method) (pyabc.distance.SlicedWassersteinDistance method) (pyabc.distance.WassersteinDistance method) (pyabc.distance.ZScoreDistance method) (pyabc.epsilon.AcceptanceRateScheme method) (pyabc.epsilon.ConstantEpsilon method) (pyabc.epsilon.DalyScheme method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.EssScheme method) (pyabc.epsilon.ExpDecayFixedIterScheme method) (pyabc.epsilon.ExpDecayFixedRatioScheme method) (pyabc.epsilon.FrielPettittScheme method) (pyabc.epsilon.ListEpsilon method) (pyabc.epsilon.ListTemperature method) (pyabc.epsilon.NoEpsilon method) (pyabc.epsilon.PolynomialDecayFixedIterScheme method) (pyabc.epsilon.QuantileEpsilon method) (pyabc.epsilon.SilkOptimalEpsilon method) (pyabc.epsilon.Temperature method) (pyabc.epsilon.TemperatureScheme method) (pyabc.external.ExternalDistance method) (pyabc.external.ExternalModel method) (pyabc.external.ExternalSumStat method) (pyabc.population.SampleFactory method) (pyabc.populationstrategy.AdaptivePopulationSize method) (pyabc.populationstrategy.ConstantPopulationSize method) (pyabc.populationstrategy.ListPopulationSize method) (pyabc.populationstrategy.PopulationStrategy method) (pyabc.predictor.GPKernelHandle method) (pyabc.predictor.HiddenLayerHandle method) (pyabc.sumstat.IdentitySumstat method) (pyabc.sumstat.PredictorSumstat method) (pyabc.sumstat.Sumstat method) (pyabc.util.ParTrafo method) (pyabc.util.ParTrafoBase method) __init__() (pyabc.acceptor.Acceptor method) (pyabc.acceptor.AcceptorResult method) (pyabc.acceptor.FunctionAcceptor method) (pyabc.acceptor.ScaledPDFNorm method) (pyabc.acceptor.StochasticAcceptor method) (pyabc.acceptor.UniformAcceptor method) (pyabc.copasi.BasicoModel method) (pyabc.distance.AdaptiveAggregatedDistance method) (pyabc.distance.AdaptivePNormDistance method) (pyabc.distance.AggregatedDistance method) (pyabc.distance.BinomialKernel method) (pyabc.distance.DistanceWithMeasureList method) (pyabc.distance.FunctionDistance method) (pyabc.distance.FunctionKernel method) (pyabc.distance.IndependentLaplaceKernel method) (pyabc.distance.IndependentNormalKernel method) (pyabc.distance.InfoWeightedPNormDistance method) (pyabc.distance.NegativeBinomialKernel method) (pyabc.distance.NoDistance method) (pyabc.distance.NormalKernel method) (pyabc.distance.PCADistance method) (pyabc.distance.PNormDistance method) (pyabc.distance.PoissonKernel method) (pyabc.distance.RangeEstimatorDistance method) (pyabc.distance.SlicedWassersteinDistance method) (pyabc.distance.StochasticKernel method) (pyabc.distance.WassersteinDistance method) (pyabc.epsilon.AcceptanceRateScheme method) (pyabc.epsilon.ConstantEpsilon method) (pyabc.epsilon.DalyScheme method) (pyabc.epsilon.EssScheme method) (pyabc.epsilon.ExpDecayFixedIterScheme method) (pyabc.epsilon.ExpDecayFixedRatioScheme method) (pyabc.epsilon.ListEpsilon method) (pyabc.epsilon.ListTemperature method) (pyabc.epsilon.MedianEpsilon method) (pyabc.epsilon.PolynomialDecayFixedIterScheme method) (pyabc.epsilon.QuantileEpsilon method) (pyabc.epsilon.SilkOptimalEpsilon method) (pyabc.epsilon.Temperature method) (pyabc.external.ExternalDistance method) (pyabc.external.ExternalHandler method) (pyabc.external.ExternalModel method) (pyabc.external.ExternalSumStat method) (pyabc.external.julia.Julia method) (pyabc.external.r.R method) (pyabc.inference.ABCSMC method) (pyabc.inference_util.AnalysisVars method) (pyabc.model.FunctionModel method) (pyabc.model.Model method) (pyabc.model.ModelResult method) (pyabc.parameters.ParameterStructure method) (pyabc.population.Particle method) (pyabc.population.Population method) (pyabc.population.Sample method) (pyabc.population.SampleFactory method) (pyabc.populationstrategy.AdaptivePopulationSize method) (pyabc.populationstrategy.ConstantPopulationSize method) (pyabc.populationstrategy.ListPopulationSize method) (pyabc.populationstrategy.PopulationStrategy method) (pyabc.predictor.GPKernelHandle method) (pyabc.predictor.GPPredictor method) (pyabc.predictor.HiddenLayerHandle method) (pyabc.predictor.LassoPredictor method) (pyabc.predictor.LinearPredictor method) (pyabc.predictor.MLPPredictor method) (pyabc.predictor.ModelSelectionPredictor method) (pyabc.predictor.SimplePredictor method) (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.RV method) (pyabc.random_variables.RVDecorator method) (pyabc.sampler.ConcurrentFutureSampler method) (pyabc.sampler.DaskDistributedSampler method) (pyabc.sampler.MappingSampler method) (pyabc.sampler.RedisEvalParallelSampler method) (pyabc.sampler.RedisEvalParallelSamplerServerStarter method) (pyabc.sampler.RedisStaticSamplerServerStarter method) (pyabc.sampler.Sampler method) (pyabc.sampler.SingleCoreSampler method) (pyabc.sge.NamedPrinter method) (pyabc.sge.ProfilingContext method) (pyabc.sge.SGE method) (pyabc.storage.History method) (pyabc.sumstat.GMMSubsetter method) (pyabc.sumstat.IdentitySumstat method) (pyabc.sumstat.PredictorSumstat method) (pyabc.sumstat.Sumstat method) (pyabc.transition.AggregatedTransition method) (pyabc.transition.DiscreteJumpTransition method) (pyabc.transition.DiscreteRandomWalkTransition method) (pyabc.transition.GridSearchCV method) (pyabc.transition.LocalTransition method) (pyabc.transition.ModelPerturbationKernel method) (pyabc.transition.MultivariateNormalTransition method) (pyabc.transition.PerturbationKernel method) (pyabc.util.EventIxs method) (pyabc.util.ParTrafo method)

A

ABCSMC (class in pyabc.inference) accept() (pyabc.model.IntegratedModel method) (pyabc.model.Model method) AcceptAllDistance (class in pyabc.distance) AcceptanceRateScheme (class in pyabc.epsilon) Acceptor (class in pyabc.acceptor) AcceptorResult (class in pyabc.acceptor) act() (pyabc.util.EventIxs method) AdaptiveAggregatedDistance (class in pyabc.distance) AdaptivePNormDistance (class in pyabc.distance)

AdaptivePopulationSize (class in pyabc.populationstrategy) AggregatedDistance (class in pyabc.distance) AggregatedTransition (class in pyabc.transition) alive_models() (pyabc.storage.History method) all_runs() (pyabc.storage.History method) all_sum_stats (pyabc.population.Sample property) analysis_id (pyabc.sampler.Sampler attribute) AnalysisVars (class in pyabc.inference_util) append() (pyabc.population.Sample method) append_population() (pyabc.storage.History method) apply_parameters() (pyabc.copasi.BasicoModel method)

B

BasicoModel (class in pyabc.copasi)

BinomialKernel (class in pyabc.distance) bound_pop_size_from_env() (in module pyabc.util)

C

calculate_model_probabilities() (pyabc.population.Population method) calculate_sensis() (pyabc.distance.InfoWeightedPNormDistance static method) cdf() (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.RV method) (pyabc.random_variables.RVBase method) (pyabc.random_variables.RVDecorator method) check_analysis_variables() (pyabc.sampler.RedisEvalParallelSampler method) (pyabc.sampler.Sampler method) check_terminate() (pyabc.inference.ABCSMC method) clear_generation_t() (pyabc.sampler.RedisEvalParallelSampler method) (pyabc.sampler.RedisStaticSampler method) client_cores() (pyabc.sampler.ConcurrentFutureSampler method) (pyabc.sampler.DaskDistributedSampler method) component (pyabc.random_variables.RVDecorator attribute) ConcurrentFutureSampler (class in pyabc.sampler) configure_sampler() (pyabc.distance.AdaptiveAggregatedDistance method) (pyabc.distance.AdaptivePNormDistance method) (pyabc.distance.AggregatedDistance method) (pyabc.distance.Distance method) (pyabc.distance.InfoWeightedPNormDistance method) (pyabc.distance.PNormDistance method) (pyabc.epsilon.AcceptanceRateScheme method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.SilkOptimalEpsilon method) (pyabc.epsilon.Temperature method) (pyabc.epsilon.TemperatureScheme method) (pyabc.sumstat.PredictorSumstat method) (pyabc.sumstat.Sumstat method)

ConstantEpsilon (class in pyabc.epsilon) ConstantPopulationSize (class in pyabc.populationstrategy) copy() (pyabc.parameters.Parameter method) (pyabc.random_variables.Distribution method) (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.RV method) (pyabc.random_variables.RVBase method) (pyabc.random_variables.RVDecorator method) create_analysis_id() (in module pyabc.inference_util) create_executable() (pyabc.external.ExternalHandler method) create_loc() (pyabc.external.ExternalHandler method) create_prior_pdf() (in module pyabc.inference_util) create_sample() (pyabc.sampler.RedisEvalParallelSampler method) (pyabc.sampler.RedisStaticSampler method) create_simulate_from_prior_function() (in module pyabc.inference_util) create_simulate_function() (in module pyabc.inference_util) create_sqlite_db_id() (in module pyabc.storage) create_sum_stat() (in module pyabc.external) create_transition_pdf() (in module pyabc.inference_util) create_weight_function() (in module pyabc.inference_util)

D

DalyScheme (class in pyabc.epsilon) DaskDistributedSampler (class in pyabc.sampler) db (pyabc.storage.History attribute) db_size (pyabc.storage.History property) decorator_repr() (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.RVDecorator method) DefaultContext (class in pyabc.sge) dict2arr() (in module pyabc.util) dict2arrlabels() (in module pyabc.util) DiscreteJumpTransition (class in pyabc.transition) DiscreteRandomWalkTransition (class in pyabc.transition)

DiscreteTransition (class in pyabc.transition) display_source_ipython() (pyabc.external.julia.Julia method) (pyabc.external.r.R method) Distance (class in pyabc.distance) distance() (pyabc.external.julia.Julia method) (pyabc.external.r.R method) (pyabc.model.Model method) DistanceWithMeasureList (class in pyabc.distance) Distribution (class in pyabc.random_variables) distribution (pyabc.random_variables.RV attribute) DistributionBase (class in pyabc.random_variables) done() (pyabc.storage.History method)

E

effective_sample_size() (in module pyabc.weighted_statistics) EPS (pyabc.transition.LocalTransition attribute) eps_from_hist() (in module pyabc.inference_util) Epsilon (class in pyabc.epsilon) EssScheme (class in pyabc.epsilon) evaluate_preliminary_particle() (in module pyabc.inference_util) evaluate_proposal() (in module pyabc.inference_util)

EventIxs (class in pyabc.util) ExpDecayFixedIterScheme (class in pyabc.epsilon) ExpDecayFixedRatioScheme (class in pyabc.epsilon) ExternalDistance (class in pyabc.external) ExternalHandler (class in pyabc.external) ExternalModel (class in pyabc.external) ExternalSumStat (class in pyabc.external)

F

fast_random_choice() (in module pyabc.random_choice) fit() (pyabc.predictor.GPPredictor method) (pyabc.predictor.LinearPredictor method) (pyabc.predictor.MLPPredictor method) (pyabc.predictor.ModelSelectionPredictor method) (pyabc.predictor.Predictor method) (pyabc.predictor.SimplePredictor method) (pyabc.transition.AggregatedTransition method) (pyabc.transition.DiscreteJumpTransition method) (pyabc.transition.DiscreteRandomWalkTransition method) (pyabc.transition.DiscreteTransition method) (pyabc.transition.GridSearchCV method) (pyabc.transition.LocalTransition method) (pyabc.transition.MultivariateNormalTransition method) (pyabc.transition.Transition method)

fit_info() (pyabc.distance.InfoWeightedPNormDistance method) fit_scales() (pyabc.distance.AdaptivePNormDistance method) for_t_or_latest() (pyabc.distance.PNormDistance static method) format_dict() (pyabc.distance.AggregatedDistance static method) (pyabc.distance.PNormDistance static method) FrielPettittScheme (class in pyabc.epsilon) from_dictionary() (pyabc.random_variables.RV class method) from_dictionary_of_dictionaries() (pyabc.random_variables.Distribution class method) from_population() (pyabc.population.Sample static method) FunctionAcceptor (class in pyabc.acceptor) FunctionDistance (class in pyabc.distance) FunctionKernel (class in pyabc.distance) FunctionModel (class in pyabc.model)

G

generate_valid_proposal() (in module pyabc.inference_util) generation_t_was_started() (pyabc.sampler.RedisEvalParallelSampler method) get_accepted_population() (pyabc.population.Sample method) get_accepted_sum_stats() (pyabc.population.Population method) get_all_populations() (pyabc.storage.History method) get_config() (pyabc.distance.AdaptivePNormDistance method) (pyabc.distance.AggregatedDistance method) (pyabc.distance.Distance method) (pyabc.distance.DistanceWithMeasureList method) (pyabc.distance.FunctionDistance method) (pyabc.distance.InfoWeightedPNormDistance method) (pyabc.distance.PercentileDistance method) (pyabc.distance.PNormDistance method) (pyabc.distance.RangeEstimatorDistance method) (pyabc.epsilon.ConstantEpsilon method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.ListEpsilon method) (pyabc.epsilon.QuantileEpsilon method) (pyabc.populationstrategy.AdaptivePopulationSize method) (pyabc.populationstrategy.ConstantPopulationSize method) (pyabc.populationstrategy.ListPopulationSize method) (pyabc.populationstrategy.PopulationStrategy method) get_distribution() (pyabc.storage.History method) get_epsilon_config() (pyabc.acceptor.Acceptor method) (pyabc.acceptor.StochasticAcceptor method) get_for_keys() (pyabc.population.Population method)

get_for_t_or_latest() (pyabc.distance.AggregatedDistance static method) get_ground_truth_parameter() (pyabc.storage.History method) get_ids() (pyabc.sumstat.IdentitySumstat method) (pyabc.sumstat.PredictorSumstat method) (pyabc.sumstat.Sumstat method) (pyabc.util.ParTrafo method) (pyabc.util.ParTrafoBase method) get_model_probabilities() (pyabc.population.Population method) (pyabc.storage.History method) get_nr_particles_per_population() (pyabc.storage.History method) get_parameter_names() (pyabc.random_variables.Distribution method) get_particles_by_model() (pyabc.population.Population method) get_population() (pyabc.storage.History method) get_population_extended() (pyabc.storage.History method) get_population_strategy() (pyabc.storage.History method) get_weighted_distances() (pyabc.population.Population method) (pyabc.storage.History method) get_weighted_sum_stats() (pyabc.population.Population method) (pyabc.storage.History method) get_weighted_sum_stats_for_model() (pyabc.storage.History method) get_weights() (pyabc.distance.AdaptivePNormDistance method) (pyabc.distance.InfoWeightedPNormDistance method) (pyabc.distance.PNormDistance method) GMMSubsetter (class in pyabc.sumstat) GPKernelHandle (class in pyabc.predictor) GPPredictor (class in pyabc.predictor) GridSearchCV (class in pyabc.transition)

H

HiddenLayerHandle (class in pyabc.predictor)

History (class in pyabc.storage)

I

id (pyabc.storage.History attribute) IdentitySumstat (class in pyabc.sumstat) IdSubsetter (class in pyabc.sumstat) IndependentLaplaceKernel (class in pyabc.distance) IndependentNormalKernel (class in pyabc.distance) InfoWeightedPNormDistance (class in pyabc.distance) initialize() (pyabc.acceptor.Acceptor method) (pyabc.acceptor.StochasticAcceptor method) (pyabc.distance.AdaptiveAggregatedDistance method) (pyabc.distance.AdaptivePNormDistance method) (pyabc.distance.AggregatedDistance method) (pyabc.distance.BinomialKernel method) (pyabc.distance.Distance method) (pyabc.distance.DistanceWithMeasureList method) (pyabc.distance.IndependentLaplaceKernel method) (pyabc.distance.IndependentNormalKernel method) (pyabc.distance.InfoWeightedPNormDistance method) (pyabc.distance.NegativeBinomialKernel method) (pyabc.distance.NormalKernel method) (pyabc.distance.PCADistance method) (pyabc.distance.PNormDistance method) (pyabc.distance.PoissonKernel method) (pyabc.distance.RangeEstimatorDistance method) (pyabc.distance.SlicedWassersteinDistance method) (pyabc.distance.StochasticKernel method) (pyabc.distance.WassersteinDistance method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.QuantileEpsilon method) (pyabc.epsilon.SilkOptimalEpsilon method) (pyabc.epsilon.Temperature method) (pyabc.sumstat.PredictorSumstat method) (pyabc.sumstat.Sumstat method) (pyabc.util.ParTrafo method) (pyabc.util.ParTrafoBase method)

initialize_components_before_run() (pyabc.inference.ABCSMC method) integrated_simulate() (pyabc.model.IntegratedModel method) IntegratedModel (class in pyabc.model) io_dict2arr() (in module pyabc.util) is_adaptive() (pyabc.acceptor.Acceptor method) (pyabc.acceptor.StochasticAcceptor method) (pyabc.distance.AdaptiveAggregatedDistance method) (pyabc.distance.AdaptivePNormDistance method) (pyabc.distance.AggregatedDistance method) (pyabc.distance.Distance method) (pyabc.distance.InfoWeightedPNormDistance method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.QuantileEpsilon method) (pyabc.epsilon.Temperature method) (pyabc.sumstat.PredictorSumstat method) (pyabc.sumstat.Sumstat method)

J

Julia (class in pyabc.external.julia)

L

LassoPredictor (class in pyabc.predictor) LinearPredictor (class in pyabc.predictor) ListEpsilon (class in pyabc.epsilon) ListPopulationSize (class in pyabc.populationstrategy) ListTemperature (class in pyabc.epsilon) load() (pyabc.inference.ABCSMC method)

load_dict_from_json() (in module pyabc.storage) LocalTransition (class in pyabc.transition) log_samples() (in module pyabc.util) lower() (pyabc.distance.MinMaxDistance static method) (pyabc.distance.PercentileDistance static method) (pyabc.distance.RangeEstimatorDistance static method) LowerBoundDecorator (class in pyabc.random_variables)

M

map() (pyabc.sge.SGE method) MappingSampler (class in pyabc.sampler) max_t (pyabc.storage.History property) maybe_start_next_generation() (pyabc.sampler.RedisEvalParallelSampler method) mean_cv() (pyabc.transition.Transition method) MedianEpsilon (class in pyabc.epsilon) MinMaxDistance (class in pyabc.distance) MLPPredictor (class in pyabc.predictor) Model (class in pyabc.model) model() (pyabc.external.julia.Julia method) (pyabc.external.r.R method) model_names() (pyabc.storage.History method) ModelPerturbationKernel (class in pyabc.transition) ModelResult (class in pyabc.model) ModelSelectionPredictor (class in pyabc.predictor) module pyabc.acceptor pyabc.copasi pyabc.distance pyabc.epsilon pyabc.external pyabc.external.julia pyabc.external.r pyabc.inference pyabc.inference_util pyabc.model pyabc.parameters pyabc.population pyabc.populationstrategy pyabc.predictor pyabc.random_choice pyabc.random_variables pyabc.sampler pyabc.settings pyabc.sge pyabc.storage pyabc.sumstat pyabc.transition pyabc.util pyabc.visserver pyabc.visualization pyabc.weighted_statistics

MulticoreEvalParallelSampler (class in pyabc.sampler) MulticoreParticleParallelSampler (class in pyabc.sampler) MultivariateNormalTransition (class in pyabc.transition)

N

n_accepted (pyabc.population.Sample property) n_populations (pyabc.storage.History property) NamedPrinter (class in pyabc.sge) NegativeBinomialKernel (class in pyabc.distance) new() (pyabc.inference.ABCSMC method) NoDistance (class in pyabc.distance) NoEpsilon (class in pyabc.epsilon) normalize_sample() (pyabc.distance.InfoWeightedPNormDistance static method)

normalize_weights() (pyabc.population.Sample method) NormalKernel (class in pyabc.distance) NotEnoughParticles nr_cores_available() (in module pyabc.sampler) (in module pyabc.sge) nr_evaluations_ (pyabc.sampler.Sampler attribute) nr_of_models (pyabc.transition.ModelPerturbationKernel attribute) nr_of_models_alive() (pyabc.storage.History method)

O

observation() (pyabc.external.julia.Julia method) (pyabc.external.r.R method)

observed_sum_stat() (pyabc.storage.History method) only_simulate_data_for_proposal() (in module pyabc.inference_util)

P

Parameter (class in pyabc.parameters) ParameterStructure (class in pyabc.parameters) Particle (class in pyabc.population) ParTrafo (class in pyabc.util) ParTrafoBase (class in pyabc.util) PCADistance (class in pyabc.distance) pdf() (pyabc.random_variables.Distribution method) (pyabc.random_variables.DistributionBase method) (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.RV method) (pyabc.random_variables.RVBase method) (pyabc.random_variables.RVDecorator method) (pyabc.transition.AggregatedTransition method) (pyabc.transition.DiscreteJumpTransition method) (pyabc.transition.DiscreteRandomWalkTransition method) (pyabc.transition.DiscreteTransition method) (pyabc.transition.LocalTransition method) (pyabc.transition.MultivariateNormalTransition method) (pyabc.transition.PerturbationKernel method) (pyabc.transition.Transition method) pdf_norm_from_kernel() (in module pyabc.acceptor) pdf_norm_max_found() (in module pyabc.acceptor) PERCENTILE (pyabc.distance.PercentileDistance attribute) PercentileDistance (class in pyabc.distance) PerturbationKernel (class in pyabc.transition) plot_acceptance_rates_trajectory() (in module pyabc.visualization) plot_contour_2d() (in module pyabc.visualization) plot_contour_2d_lowlevel() (in module pyabc.visualization) plot_contour_matrix() (in module pyabc.visualization) plot_contour_matrix_lowlevel() (in module pyabc.visualization) plot_credible_intervals() (in module pyabc.visualization) plot_credible_intervals_for_time() (in module pyabc.visualization) plot_data_callback() (in module pyabc.visualization) plot_data_default() (in module pyabc.visualization) plot_distance_weights() (in module pyabc.visualization) plot_effective_sample_sizes() (in module pyabc.visualization) plot_eps_walltime() (in module pyabc.visualization) plot_eps_walltime_lowlevel() (in module pyabc.visualization) plot_epsilons() (in module pyabc.visualization) plot_histogram_1d() (in module pyabc.visualization) plot_histogram_1d_lowlevel() (in module pyabc.visualization) plot_histogram_2d() (in module pyabc.visualization) plot_histogram_2d_lowlevel() (in module pyabc.visualization) plot_histogram_matrix() (in module pyabc.visualization) plot_histogram_matrix_lowlevel() (in module pyabc.visualization) plot_kde_1d() (in module pyabc.visualization) plot_kde_1d_highlevel() (in module pyabc.visualization) plot_kde_2d() (in module pyabc.visualization) plot_kde_2d_highlevel() (in module pyabc.visualization) plot_kde_matrix() (in module pyabc.visualization) plot_kde_matrix_highlevel() (in module pyabc.visualization) plot_lookahead_acceptance_rates() (in module pyabc.visualization) plot_lookahead_evaluations() (in module pyabc.visualization) plot_lookahead_final_acceptance_fractions() (in module pyabc.visualization) plot_model_probabilities() (in module pyabc.visualization) plot_sample_numbers() (in module pyabc.visualization) plot_sample_numbers_trajectory() (in module pyabc.visualization) plot_sensitivity_sankey() (in module pyabc.visualization) plot_total_sample_numbers() (in module pyabc.visualization) plot_total_walltime() (in module pyabc.visualization) plot_walltime() (in module pyabc.visualization) plot_walltime_lowlevel() (in module pyabc.visualization) pmf() (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.RV method) (pyabc.random_variables.RVBase method) (pyabc.random_variables.RVDecorator method) (pyabc.transition.ModelPerturbationKernel method)

PNormDistance (class in pyabc.distance) PoissonKernel (class in pyabc.distance) PolynomialDecayFixedIterScheme (class in pyabc.epsilon) Population (class in pyabc.population) PopulationStrategy (class in pyabc.populationstrategy) predict() (pyabc.predictor.ModelSelectionPredictor method) (pyabc.predictor.Predictor method) (pyabc.predictor.SimplePredictor method) Predictor (class in pyabc.predictor) PredictorSumstat (class in pyabc.sumstat) probability_to_stay (pyabc.transition.ModelPerturbationKernel attribute) probably_has_late_events() (pyabc.util.EventIxs method) ProfilingContext (class in pyabc.sge) pyabc.acceptor module pyabc.copasi module pyabc.distance module pyabc.epsilon module pyabc.external module pyabc.external.julia module pyabc.external.r module pyabc.inference module pyabc.inference_util module pyabc.model module pyabc.parameters module pyabc.population module pyabc.populationstrategy module pyabc.predictor module pyabc.random_choice module pyabc.random_variables module pyabc.sampler module pyabc.settings module pyabc.sge module pyabc.storage module pyabc.sumstat module pyabc.transition module pyabc.util module pyabc.visserver module pyabc.visualization module pyabc.weighted_statistics module

Q

QuantileEpsilon (class in pyabc.epsilon)

R

R (class in pyabc.external.r) RangeEstimatorDistance (class in pyabc.distance) read_sample() (in module pyabc.util) record_rejected() (pyabc.population.SampleFactory method) RedisEvalParallelSampler (class in pyabc.sampler) RedisEvalParallelSamplerServerStarter (class in pyabc.sampler) RedisStaticSampler (class in pyabc.sampler) RedisStaticSamplerServerStarter (class in pyabc.sampler) requires_calibration() (pyabc.acceptor.Acceptor method) (pyabc.acceptor.StochasticAcceptor method) (pyabc.distance.AdaptiveAggregatedDistance method) (pyabc.distance.AdaptivePNormDistance method) (pyabc.distance.AggregatedDistance method) (pyabc.distance.Distance method) (pyabc.distance.InfoWeightedPNormDistance method) (pyabc.distance.PCADistance method) (pyabc.distance.RangeEstimatorDistance method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.QuantileEpsilon method) (pyabc.epsilon.Temperature method) (pyabc.sumstat.PredictorSumstat method) (pyabc.sumstat.Sumstat method) (pyabc.util.EventIxs method) requires_distances() (pyabc.epsilon.EssScheme method) (pyabc.epsilon.TemperatureScheme method) resample() (in module pyabc.weighted_statistics) resample_deterministic() (in module pyabc.weighted_statistics) root_mean_square_error() (in module pyabc.predictor)

root_mean_square_relative_error() (in module pyabc.predictor) run() (pyabc.external.ExternalHandler method) run_generation() (pyabc.inference.ABCSMC method) RV (class in pyabc.random_variables) RVBase (class in pyabc.random_variables) RVDecorator (class in pyabc.random_variables) rvs() (pyabc.random_variables.Distribution method) (pyabc.random_variables.DistributionBase method) (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.RV method) (pyabc.random_variables.RVBase method) (pyabc.random_variables.RVDecorator method) (pyabc.transition.AggregatedTransition method) (pyabc.transition.DiscreteJumpTransition method) (pyabc.transition.DiscreteRandomWalkTransition method) (pyabc.transition.DiscreteTransition method) (pyabc.transition.LocalTransition method) (pyabc.transition.ModelPerturbationKernel method) (pyabc.transition.MultivariateNormalTransition method) (pyabc.transition.PerturbationKernel method) (pyabc.transition.Transition method) rvs_single() (pyabc.transition.AggregatedTransition method) (pyabc.transition.DiscreteJumpTransition method) (pyabc.transition.DiscreteRandomWalkTransition method) (pyabc.transition.DiscreteTransition method) (pyabc.transition.LocalTransition method) (pyabc.transition.MultivariateNormalTransition method) (pyabc.transition.Transition method)

S

Sample (class in pyabc.population) sample() (pyabc.copasi.BasicoModel method) (pyabc.external.ExternalModel method) (pyabc.model.FunctionModel method) (pyabc.model.Model method) sample_factory (pyabc.sampler.Sampler attribute) SampleFactory (class in pyabc.population) Sampler (class in pyabc.sampler) save_dict_to_json() (in module pyabc.storage) ScaledPDFNorm (class in pyabc.acceptor) scott_rule_of_thumb() (in module pyabc.transition) select() (pyabc.sumstat.GMMSubsetter method) (pyabc.sumstat.IdSubsetter method) (pyabc.sumstat.Subsetter method) set_analysis_id() (pyabc.sampler.Sampler method) set_figure_params() (in module pyabc.settings) set_use_ixs() (pyabc.predictor.SimplePredictor method) SGE (class in pyabc.sge) sge_available() (in module pyabc.sge)

show_progress (pyabc.sampler.Sampler attribute) shutdown() (pyabc.sampler.DaskDistributedSampler method) SilkOptimalEpsilon (class in pyabc.epsilon) silverman_rule_of_thumb() (in module pyabc.transition) SimplePredictor (class in pyabc.predictor) SingleCoreSampler (class in pyabc.sampler) SlicedWassersteinDistance (class in pyabc.distance) start_generation_t() (pyabc.sampler.RedisEvalParallelSampler method) (pyabc.sampler.RedisStaticSampler method) StochasticAcceptor (class in pyabc.acceptor) StochasticKernel (class in pyabc.distance) stop() (pyabc.sampler.Sampler method) store_initial_data() (pyabc.storage.History method) store_pre_population() (pyabc.storage.History method) stores_sum_stats (pyabc.storage.History attribute) Subsetter (class in pyabc.sumstat) summary_statistics() (pyabc.external.r.R method) (pyabc.model.Model method) Sumstat (class in pyabc.sumstat)

T

Temperature (class in pyabc.epsilon) TemperatureBase (class in pyabc.epsilon) TemperatureScheme (class in pyabc.epsilon) termination_criteria_fulfilled() (in module pyabc.inference_util) to_acceptor() (pyabc.acceptor.FunctionAcceptor static method) to_distance() (pyabc.distance.FunctionDistance static method)

to_instance() (pyabc.util.EventIxs static method) to_json() (pyabc.distance.Distance method) (pyabc.epsilon.Epsilon method) (pyabc.populationstrategy.PopulationStrategy method) to_model() (pyabc.model.FunctionModel static method) total_nr_simulations (pyabc.storage.History property) Transition (class in pyabc.transition)

U

UniformAcceptor (class in pyabc.acceptor) update() (pyabc.acceptor.Acceptor method) (pyabc.acceptor.StochasticAcceptor method) (pyabc.distance.AdaptiveAggregatedDistance method) (pyabc.distance.AdaptivePNormDistance method) (pyabc.distance.AggregatedDistance method) (pyabc.distance.Distance method) (pyabc.distance.InfoWeightedPNormDistance method) (pyabc.distance.PNormDistance method) (pyabc.distance.SlicedWassersteinDistance method) (pyabc.distance.WassersteinDistance method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.QuantileEpsilon method) (pyabc.epsilon.SilkOptimalEpsilon method) (pyabc.epsilon.Temperature method) (pyabc.populationstrategy.AdaptivePopulationSize method) (pyabc.populationstrategy.PopulationStrategy method) (pyabc.sumstat.PredictorSumstat method) (pyabc.sumstat.Sumstat method)

update_after_calibration() (pyabc.storage.History method) update_distances() (pyabc.population.Population method) update_random_variables() (pyabc.random_variables.Distribution method) upper() (pyabc.distance.MinMaxDistance static method) (pyabc.distance.PercentileDistance static method) (pyabc.distance.RangeEstimatorDistance static method)

W

WassersteinDistance (class in pyabc.distance) weighted_mean() (in module pyabc.weighted_statistics) weighted_median() (in module pyabc.weighted_statistics) weighted_mse() (in module pyabc.weighted_statistics)

weighted_quantile() (in module pyabc.weighted_statistics) weighted_rmse() (in module pyabc.weighted_statistics) weighted_std() (in module pyabc.weighted_statistics) weighted_var() (in module pyabc.weighted_statistics) weights2dict() (pyabc.distance.PNormDistance method)

Z

ZScoreDistance (class in pyabc.distance)