API reference

pyABC

ABC algorithms for likelihood-free Bayesian parameter inference and model selection.

Note

pyABC allows to parallelize the sampling process via various samplers. If you want to also parallelize single model simulations, be careful that both levels of parallelization work together well. In particular, if the environment variable OMP_NUM_THREADS is not set, pyABC sets it to a default of 1. For multi-processed sampling (the default at least on linux systems), the flag PYABC_NUM_PROCS can be used to determine on how many jobs to parallelize the sampling.

• Inference
• ABCSMC
  • ABCSMC.__init__()
  • ABCSMC.check_terminate()
  • ABCSMC.initialize_components_before_run()
  • ABCSMC.load()
  • ABCSMC.new()
  • ABCSMC.run_generation()
• Distances
• AcceptAllDistance
  • AcceptAllDistance.__call__()
• AdaptiveAggregatedDistance
  • AdaptiveAggregatedDistance.__init__()
  • AdaptiveAggregatedDistance.configure_sampler()
  • AdaptiveAggregatedDistance.initialize()
  • AdaptiveAggregatedDistance.is_adaptive()
  • AdaptiveAggregatedDistance.requires_calibration()
  • AdaptiveAggregatedDistance.update()
• AdaptivePNormDistance
  • AdaptivePNormDistance.__init__()
  • AdaptivePNormDistance.configure_sampler()
  • AdaptivePNormDistance.fit_scales()
  • AdaptivePNormDistance.get_config()
  • AdaptivePNormDistance.get_weights()
  • AdaptivePNormDistance.initialize()
  • AdaptivePNormDistance.is_adaptive()
  • AdaptivePNormDistance.requires_calibration()
  • AdaptivePNormDistance.update()
• AggregatedDistance
  • AggregatedDistance.__call__()
  • AggregatedDistance.__init__()
  • AggregatedDistance.configure_sampler()
  • AggregatedDistance.format_dict()
  • AggregatedDistance.get_config()
  • AggregatedDistance.get_for_t_or_latest()
  • AggregatedDistance.initialize()
  • AggregatedDistance.is_adaptive()
  • AggregatedDistance.requires_calibration()
  • AggregatedDistance.update()
• BinomialKernel
  • BinomialKernel.__call__()
  • BinomialKernel.__init__()
  • BinomialKernel.initialize()
• Distance
  • Distance.__call__()
  • Distance.configure_sampler()
  • Distance.get_config()
  • Distance.initialize()
  • Distance.is_adaptive()
  • Distance.requires_calibration()
  • Distance.to_json()
  • Distance.update()
• DistanceWithMeasureList
  • DistanceWithMeasureList.__init__()
  • DistanceWithMeasureList.get_config()
  • DistanceWithMeasureList.initialize()
• FunctionDistance
  • FunctionDistance.__call__()
  • FunctionDistance.__init__()
  • FunctionDistance.get_config()
  • FunctionDistance.to_distance()
• FunctionKernel
  • FunctionKernel.__call__()
  • FunctionKernel.__init__()
• IndependentLaplaceKernel
  • IndependentLaplaceKernel.__call__()
  • IndependentLaplaceKernel.__init__()
  • IndependentLaplaceKernel.initialize()
• IndependentNormalKernel
  • IndependentNormalKernel.__call__()
  • IndependentNormalKernel.__init__()
  • IndependentNormalKernel.initialize()
• InfoWeightedPNormDistance
  • InfoWeightedPNormDistance.__init__()
  • InfoWeightedPNormDistance.calculate_sensis()
  • InfoWeightedPNormDistance.configure_sampler()
  • InfoWeightedPNormDistance.fit_info()
  • InfoWeightedPNormDistance.get_config()
  • InfoWeightedPNormDistance.get_weights()
  • InfoWeightedPNormDistance.initialize()
  • InfoWeightedPNormDistance.is_adaptive()
  • InfoWeightedPNormDistance.normalize_sample()
  • InfoWeightedPNormDistance.requires_calibration()
  • InfoWeightedPNormDistance.update()
• MinMaxDistance
  • MinMaxDistance.lower()
  • MinMaxDistance.upper()
• NegativeBinomialKernel
  • NegativeBinomialKernel.__call__()
  • NegativeBinomialKernel.__init__()
  • NegativeBinomialKernel.initialize()
• NoDistance
  • NoDistance.__call__()
  • NoDistance.__init__()
• NormalKernel
  • NormalKernel.__call__()
  • NormalKernel.__init__()
  • NormalKernel.initialize()
• PCADistance
  • PCADistance.__call__()
  • PCADistance.__init__()
  • PCADistance.initialize()
  • PCADistance.requires_calibration()
• PNormDistance
  • PNormDistance.__call__()
  • PNormDistance.__init__()
  • PNormDistance.configure_sampler()
  • PNormDistance.for_t_or_latest()
  • PNormDistance.format_dict()
  • PNormDistance.get_config()
  • PNormDistance.get_weights()
  • PNormDistance.initialize()
  • PNormDistance.update()
  • PNormDistance.weights2dict()
• PercentileDistance
  • PercentileDistance.PERCENTILE
  • PercentileDistance.get_config()
  • PercentileDistance.lower()
  • PercentileDistance.upper()
• PoissonKernel
  • PoissonKernel.__call__()
  • PoissonKernel.__init__()
  • PoissonKernel.initialize()
• RangeEstimatorDistance
  • RangeEstimatorDistance.__call__()
  • RangeEstimatorDistance.__init__()
  • RangeEstimatorDistance.get_config()
  • RangeEstimatorDistance.initialize()
  • RangeEstimatorDistance.lower()
  • RangeEstimatorDistance.requires_calibration()
  • RangeEstimatorDistance.upper()
• SlicedWassersteinDistance
  • SlicedWassersteinDistance.__call__()
  • SlicedWassersteinDistance.__init__()
  • SlicedWassersteinDistance.initialize()
  • SlicedWassersteinDistance.update()
• StochasticKernel
  • StochasticKernel.__init__()
  • StochasticKernel.initialize()
• WassersteinDistance
  • WassersteinDistance.__call__()
  • WassersteinDistance.__init__()
  • WassersteinDistance.initialize()
  • WassersteinDistance.update()
• ZScoreDistance
  • ZScoreDistance.__call__()
• Acceptors
• Acceptor
  • Acceptor.__call__()
  • Acceptor.__init__()
  • Acceptor.get_epsilon_config()
  • Acceptor.initialize()
  • Acceptor.is_adaptive()
  • Acceptor.requires_calibration()
  • Acceptor.update()
• AcceptorResult
  • AcceptorResult.__init__()
• FunctionAcceptor
  • FunctionAcceptor.__call__()
  • FunctionAcceptor.__init__()
  • FunctionAcceptor.to_acceptor()
• ScaledPDFNorm
  • ScaledPDFNorm.__call__()
  • ScaledPDFNorm.__init__()
• StochasticAcceptor
  • StochasticAcceptor.__call__()
  • StochasticAcceptor.__init__()
  • StochasticAcceptor.get_epsilon_config()
  • StochasticAcceptor.initialize()
  • StochasticAcceptor.is_adaptive()
  • StochasticAcceptor.requires_calibration()
  • StochasticAcceptor.update()
• UniformAcceptor
  • UniformAcceptor.__call__()
  • UniformAcceptor.__init__()
• pdf_norm_from_kernel()
• pdf_norm_max_found()
• Models
• FunctionModel
  • FunctionModel.__init__()
  • FunctionModel.sample()
  • FunctionModel.to_model()
• IntegratedModel
  • IntegratedModel.accept()
  • IntegratedModel.integrated_simulate()
• Model
  • Model.__init__()
  • Model.accept()
  • Model.distance()
  • Model.sample()
  • Model.summary_statistics()
• ModelResult
  • ModelResult.__init__()
• Epsilons
• AcceptanceRateScheme
  • AcceptanceRateScheme.__call__()
  • AcceptanceRateScheme.__init__()
  • AcceptanceRateScheme.configure_sampler()
• ConstantEpsilon
  • ConstantEpsilon.__call__()
  • ConstantEpsilon.__init__()
  • ConstantEpsilon.get_config()
• DalyScheme
  • DalyScheme.__call__()
  • DalyScheme.__init__()
• Epsilon
  • Epsilon.__call__()
  • Epsilon.configure_sampler()
  • Epsilon.get_config()
  • Epsilon.initialize()
  • Epsilon.is_adaptive()
  • Epsilon.requires_calibration()
  • Epsilon.to_json()
  • Epsilon.update()
• EssScheme
  • EssScheme.__call__()
  • EssScheme.__init__()
  • EssScheme.requires_distances()
• ExpDecayFixedIterScheme
  • ExpDecayFixedIterScheme.__call__()
  • ExpDecayFixedIterScheme.__init__()
• ExpDecayFixedRatioScheme
  • ExpDecayFixedRatioScheme.__call__()
  • ExpDecayFixedRatioScheme.__init__()
• FrielPettittScheme
  • FrielPettittScheme.__call__()
• ListEpsilon
  • ListEpsilon.__call__()
  • ListEpsilon.__init__()
  • ListEpsilon.get_config()
• ListTemperature
  • ListTemperature.__call__()
  • ListTemperature.__init__()
• MedianEpsilon
  • MedianEpsilon.__init__()
• NoEpsilon
  • NoEpsilon.__call__()
• PolynomialDecayFixedIterScheme
  • PolynomialDecayFixedIterScheme.__call__()
  • PolynomialDecayFixedIterScheme.__init__()
• QuantileEpsilon
  • QuantileEpsilon.__call__()
  • QuantileEpsilon.__init__()
  • QuantileEpsilon.get_config()
  • QuantileEpsilon.initialize()
  • QuantileEpsilon.is_adaptive()
  • QuantileEpsilon.requires_calibration()
  • QuantileEpsilon.update()
• SilkOptimalEpsilon
  • SilkOptimalEpsilon.__call__()
  • SilkOptimalEpsilon.__init__()
  • SilkOptimalEpsilon.configure_sampler()
  • SilkOptimalEpsilon.initialize()
  • SilkOptimalEpsilon.update()
• Temperature
  • Temperature.__call__()
  • Temperature.__init__()
  • Temperature.configure_sampler()
  • Temperature.initialize()
  • Temperature.is_adaptive()
  • Temperature.requires_calibration()
  • Temperature.update()
• TemperatureBase
• TemperatureScheme
  • TemperatureScheme.__call__()
  • TemperatureScheme.configure_sampler()
  • TemperatureScheme.requires_distances()
• Predictor
• GPKernelHandle
  • GPKernelHandle.__call__()
  • GPKernelHandle.__init__()
• GPPredictor
  • GPPredictor.__init__()
  • GPPredictor.fit()
• HiddenLayerHandle
  • HiddenLayerHandle.__call__()
  • HiddenLayerHandle.__init__()
• LassoPredictor
  • LassoPredictor.__init__()
• LinearPredictor
  • LinearPredictor.__init__()
  • LinearPredictor.fit()
• MLPPredictor
  • MLPPredictor.__init__()
  • MLPPredictor.fit()
• ModelSelectionPredictor
  • ModelSelectionPredictor.__init__()
  • ModelSelectionPredictor.fit()
  • ModelSelectionPredictor.predict()
• Predictor
  • Predictor.fit()
  • Predictor.predict()
• SimplePredictor
  • SimplePredictor.__init__()
  • SimplePredictor.fit()
  • SimplePredictor.predict()
  • SimplePredictor.set_use_ixs()
• root_mean_square_error()
• root_mean_square_relative_error()
• Summary statistics
• GMMSubsetter
  • GMMSubsetter.__init__()
  • GMMSubsetter.select()
• IdSubsetter
  • IdSubsetter.select()
• IdentitySumstat
  • IdentitySumstat.__call__()
  • IdentitySumstat.__init__()
  • IdentitySumstat.get_ids()
• PredictorSumstat
  • PredictorSumstat.__call__()
  • PredictorSumstat.__init__()
  • PredictorSumstat.configure_sampler()
  • PredictorSumstat.get_ids()
  • PredictorSumstat.initialize()
  • PredictorSumstat.is_adaptive()
  • PredictorSumstat.requires_calibration()
  • PredictorSumstat.update()
• Subsetter
  • Subsetter.select()
• Sumstat
  • Sumstat.__call__()
  • Sumstat.__init__()
  • Sumstat.configure_sampler()
  • Sumstat.get_ids()
  • Sumstat.initialize()
  • Sumstat.is_adaptive()
  • Sumstat.requires_calibration()
  • Sumstat.update()
• Data store
  • Purpose of the data store
  • Initializing the database interface from a file
  • Querying the database
  • What can be stored as summary statistics
• History
  • History.db
  • History.stores_sum_stats
  • History.id
  • History.__init__()
  • History.alive_models()
  • History.all_runs()
  • History.append_population()
  • History.db_size
  • History.done()
  • History.get_all_populations()
  • History.get_distribution()
  • History.get_ground_truth_parameter()
  • History.get_model_probabilities()
  • History.get_nr_particles_per_population()
  • History.get_population()
  • History.get_population_extended()
  • History.get_population_strategy()
  • History.get_weighted_distances()
  • History.get_weighted_sum_stats()
  • History.get_weighted_sum_stats_for_model()
  • History.max_t
  • History.model_names()
  • History.n_populations
  • History.nr_of_models_alive()
  • History.observed_sum_stat()
  • History.store_initial_data()
  • History.store_pre_population()
  • History.total_nr_simulations
  • History.update_after_calibration()
• create_sqlite_db_id()
• load_dict_from_json()
• save_dict_to_json()
• Transitions kernels
• AggregatedTransition
  • AggregatedTransition.__init__()
  • AggregatedTransition.fit()
  • AggregatedTransition.pdf()
  • AggregatedTransition.rvs()
  • AggregatedTransition.rvs_single()
• DiscreteJumpTransition
  • DiscreteJumpTransition.__init__()
  • DiscreteJumpTransition.fit()
  • DiscreteJumpTransition.pdf()
  • DiscreteJumpTransition.rvs()
  • DiscreteJumpTransition.rvs_single()
• DiscreteRandomWalkTransition
  • DiscreteRandomWalkTransition.__init__()
  • DiscreteRandomWalkTransition.fit()
  • DiscreteRandomWalkTransition.pdf()
  • DiscreteRandomWalkTransition.rvs()
  • DiscreteRandomWalkTransition.rvs_single()
• DiscreteTransition
  • DiscreteTransition.fit()
  • DiscreteTransition.pdf()
  • DiscreteTransition.rvs()
  • DiscreteTransition.rvs_single()
• GridSearchCV
  • GridSearchCV.__init__()
  • GridSearchCV.fit()
• LocalTransition
  • LocalTransition.EPS
  • LocalTransition.__init__()
  • LocalTransition.fit()
  • LocalTransition.pdf()
  • LocalTransition.rvs()
  • LocalTransition.rvs_single()
• ModelPerturbationKernel
  • ModelPerturbationKernel.nr_of_models
  • ModelPerturbationKernel.probability_to_stay
  • ModelPerturbationKernel.__init__()
  • ModelPerturbationKernel.pmf()
  • ModelPerturbationKernel.rvs()
• MultivariateNormalTransition
  • MultivariateNormalTransition.__init__()
  • MultivariateNormalTransition.fit()
  • MultivariateNormalTransition.pdf()
  • MultivariateNormalTransition.rvs()
  • MultivariateNormalTransition.rvs_single()
• NotEnoughParticles
• PerturbationKernel
  • PerturbationKernel.__init__()
  • PerturbationKernel.pdf()
  • PerturbationKernel.rvs()
• Transition
  • Transition.fit()
  • Transition.mean_cv()
  • Transition.pdf()
  • Transition.rvs()
  • Transition.rvs_single()
• scott_rule_of_thumb()
• silverman_rule_of_thumb()
• Population strategies
• AdaptivePopulationSize
  • AdaptivePopulationSize.__call__()
  • AdaptivePopulationSize.__init__()
  • AdaptivePopulationSize.get_config()
  • AdaptivePopulationSize.update()
• ConstantPopulationSize
  • ConstantPopulationSize.__call__()
  • ConstantPopulationSize.__init__()
  • ConstantPopulationSize.get_config()
• ListPopulationSize
  • ListPopulationSize.__call__()
  • ListPopulationSize.__init__()
  • ListPopulationSize.get_config()
• PopulationStrategy
  • PopulationStrategy.__call__()
  • PopulationStrategy.__init__()
  • PopulationStrategy.get_config()
  • PopulationStrategy.to_json()
  • PopulationStrategy.update()
• dec_bound_pop_size_from_env()
• Parallel sampling
• ConcurrentFutureSampler
  • ConcurrentFutureSampler.__init__()
  • ConcurrentFutureSampler.client_cores()
• DaskDistributedSampler
  • DaskDistributedSampler.__init__()
  • DaskDistributedSampler.client_cores()
  • DaskDistributedSampler.shutdown()
• MappingSampler
  • MappingSampler.__init__()
• MulticoreEvalParallelSampler
• MulticoreParticleParallelSampler
• RedisEvalParallelSampler
  • RedisEvalParallelSampler.__init__()
  • RedisEvalParallelSampler.check_analysis_variables()
  • RedisEvalParallelSampler.clear_generation_t()
  • RedisEvalParallelSampler.create_sample()
  • RedisEvalParallelSampler.generation_t_was_started()
  • RedisEvalParallelSampler.maybe_start_next_generation()
  • RedisEvalParallelSampler.start_generation_t()
• RedisEvalParallelSamplerServerStarter
  • RedisEvalParallelSamplerServerStarter.__init__()
• RedisStaticSampler
  • RedisStaticSampler.clear_generation_t()
  • RedisStaticSampler.create_sample()
  • RedisStaticSampler.start_generation_t()
• RedisStaticSamplerServerStarter
  • RedisStaticSamplerServerStarter.__init__()
• Sampler
  • Sampler.nr_evaluations_
  • Sampler.sample_factory
  • Sampler.show_progress
  • Sampler.analysis_id
  • Sampler.__init__()
  • Sampler.check_analysis_variables()
  • Sampler.set_analysis_id()
  • Sampler.stop()
• SingleCoreSampler
  • SingleCoreSampler.__init__()
• nr_cores_available()
• Model parameters
• Parameter
  • Parameter.copy()
• ParameterStructure
  • ParameterStructure.__init__()
• Particles and Populations
• Particle
  • Particle.__init__()
• Population
  • Population.__init__()
  • Population.calculate_model_probabilities()
  • Population.get_accepted_sum_stats()
  • Population.get_for_keys()
  • Population.get_model_probabilities()
  • Population.get_particles_by_model()
  • Population.get_weighted_distances()
  • Population.get_weighted_sum_stats()
  • Population.update_distances()
• Sample
  • Sample.__init__()
  • Sample.all_sum_stats
  • Sample.append()
  • Sample.from_population()
  • Sample.get_accepted_population()
  • Sample.n_accepted
  • Sample.normalize_weights()
• SampleFactory
  • SampleFactory.__call__()
  • SampleFactory.__init__()
  • SampleFactory.record_rejected()
• Random variables
• Distribution
  • Distribution.copy()
  • Distribution.from_dictionary_of_dictionaries()
  • Distribution.get_parameter_names()
  • Distribution.pdf()
  • Distribution.rvs()
  • Distribution.update_random_variables()
• DistributionBase
  • DistributionBase.pdf()
  • DistributionBase.rvs()
• LowerBoundDecorator
  • LowerBoundDecorator.__init__()
  • LowerBoundDecorator.cdf()
  • LowerBoundDecorator.copy()
  • LowerBoundDecorator.decorator_repr()
  • LowerBoundDecorator.pdf()
  • LowerBoundDecorator.pmf()
  • LowerBoundDecorator.rvs()
• RV
  • RV.__init__()
  • RV.cdf()
  • RV.copy()
  • RV.distribution
  • RV.from_dictionary()
  • RV.pdf()
  • RV.pmf()
  • RV.rvs()
• RVBase
  • RVBase.cdf()
  • RVBase.copy()
  • RVBase.pdf()
  • RVBase.pmf()
  • RVBase.rvs()
• RVDecorator
  • RVDecorator.__init__()
  • RVDecorator.cdf()
  • RVDecorator.component
  • RVDecorator.copy()
  • RVDecorator.decorator_repr()
  • RVDecorator.pdf()
  • RVDecorator.pmf()
  • RVDecorator.rvs()
• SGE
• SGE
  • SGE.__init__()
  • SGE.map()
• sge_available()
• nr_cores_available()
• NamedPrinter
  • NamedPrinter.__init__()
• DefaultContext
• ProfilingContext
  • ProfilingContext.__init__()
• External simulators
• ExternalDistance
  • ExternalDistance.__call__()
  • ExternalDistance.__init__()
• ExternalHandler
  • ExternalHandler.__init__()
  • ExternalHandler.create_executable()
  • ExternalHandler.create_loc()
  • ExternalHandler.run()
• ExternalModel
  • ExternalModel.__call__()
  • ExternalModel.__init__()
  • ExternalModel.sample()
• ExternalSumStat
  • ExternalSumStat.__call__()
  • ExternalSumStat.__init__()
• create_sum_stat()
• R interface via rpy2
• R
  • R.__init__()
  • R.display_source_ipython()
  • R.distance()
  • R.model()
  • R.observation()
  • R.summary_statistics()
• Julia interface via PyJulia
• Julia
  • Julia.__init__()
  • Julia.display_source_ipython()
  • Julia.distance()
  • Julia.model()
  • Julia.observation()
• Copasi
• BasicoModel
  • BasicoModel.__call__()
  • BasicoModel.__init__()
  • BasicoModel.apply_parameters()
  • BasicoModel.sample()
• Visualization
• plot_acceptance_rates_trajectory()
• plot_credible_intervals()
• plot_credible_intervals_for_time()
• plot_data_callback()
• plot_data_default()
• plot_distance_weights()
• plot_effective_sample_sizes()
• plot_eps_walltime()
• plot_eps_walltime_lowlevel()
• plot_epsilons()
• plot_histogram_1d()
• plot_histogram_1d_lowlevel()
• plot_histogram_2d()
• plot_histogram_2d_lowlevel()
• plot_histogram_matrix()
• plot_histogram_matrix_lowlevel()
• plot_kde_1d()
• plot_kde_1d_highlevel()
• plot_kde_2d()
• plot_kde_2d_highlevel()
• plot_kde_matrix()
• plot_kde_matrix_highlevel()
• plot_lookahead_acceptance_rates()
• plot_lookahead_evaluations()
• plot_lookahead_final_acceptance_fractions()
• plot_model_probabilities()
• plot_sample_numbers()
• plot_sample_numbers_trajectory()
• plot_sensitivity_sankey()
• plot_total_sample_numbers()
• plot_total_walltime()
• plot_walltime()
• plot_walltime_lowlevel()
• Weighted statistics
• effective_sample_size()
• resample()
• resample_deterministic()
• weight_checked()
• weighted_mean()
• weighted_median()
• weighted_mse()
• weighted_quantile()
• weighted_rmse()
• weighted_std()
• weighted_var()