Index

_

__call__() (pyabc.distance_functions.AcceptAllDistance method) (pyabc.distance_functions.DistanceFunction method) (pyabc.distance_functions.IdentityFakeDistance method) (pyabc.distance_functions.NoDistance method) (pyabc.distance_functions.PCADistanceFunction method) (pyabc.distance_functions.PNormDistance method) (pyabc.distance_functions.RangeEstimatorDistanceFunction method) (pyabc.distance_functions.SimpleFunctionDistance method) (pyabc.distance_functions.ZScoreDistanceFunction method) (pyabc.epsilon.ConstantEpsilon method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.ListEpsilon method) (pyabc.epsilon.QuantileEpsilon method)

A

ABCSMC (class in pyabc.smc) accept() (pyabc.model.IntegratedModel method) (pyabc.model.Model method) AcceptAllDistance (class in pyabc.distance_functions) adapt_population_size() (pyabc.populationstrategy.AdaptivePopulationSize method) (pyabc.populationstrategy.ConstantPopulationSize method) (pyabc.populationstrategy.PopulationStrategy method)

AdaptivePopulationSize (class in pyabc.populationstrategy) alive_models() (pyabc.storage.History method) all_runs() (pyabc.storage.History method) all_summary_statistics (pyabc.sampler.Sample attribute) append() (pyabc.sampler.Sample method) append_population() (pyabc.storage.History method) assert_model() (pyabc.model.SimpleModel static method)

C

cdf() (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.RV method) (pyabc.random_variables.RVBase method) (pyabc.random_variables.RVDecorator method) component (pyabc.random_variables.RVDecorator attribute) ConcurrentFutureSampler (class in pyabc.sampler) configure_sampler() (pyabc.distance_functions.DistanceFunction method) (pyabc.distance_functions.WeightedPNormDistance 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)

D

DaskDistributedSampler (class in pyabc.sampler) db_size (pyabc.storage.History attribute) decorator_repr() (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.RVDecorator method) DefaultContext (class in pyabc.sge) display_source_ipython() (pyabc.external.R method)

distance() (pyabc.external.R method) (pyabc.model.Model method) DistanceFunction (class in pyabc.distance_functions) DistanceFunctionWithMeasureList (class in pyabc.distance_functions) Distribution (class in pyabc.random_variables) distribution (pyabc.random_variables.RV attribute) done() (pyabc.storage.History method)

E

EPS (pyabc.transition.LocalTransition attribute)

Epsilon (class in pyabc.epsilon) EuclideanDistance (class in pyabc.distance_functions)

F

fit() (pyabc.transition.GridSearchCV method) (pyabc.transition.LocalTransition method) (pyabc.transition.MultivariateNormalTransition method) (pyabc.transition.Transition method)

from_dictionary() (pyabc.random_variables.RV class method) from_dictionary_of_dictionaries() (pyabc.random_variables.Distribution class method)

G

get_accepted_population() (pyabc.sampler.Sample method) get_all_populations() (pyabc.storage.History method) get_config() (pyabc.distance_functions.DistanceFunction method) (pyabc.distance_functions.DistanceFunctionWithMeasureList method) (pyabc.distance_functions.PercentileDistanceFunction method) (pyabc.distance_functions.RangeEstimatorDistanceFunction method) (pyabc.distance_functions.SimpleFunctionDistance method) (pyabc.epsilon.ConstantEpsilon method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.ListEpsilon method) (pyabc.epsilon.QuantileEpsilon method) (pyabc.populationstrategy.AdaptivePopulationSize method) (pyabc.populationstrategy.PopulationStrategy method)

get_distribution() (pyabc.storage.History method) get_model_probabilities() (pyabc.storage.History method) get_nr_particles_per_population() (pyabc.storage.History method) get_parameter_names() (pyabc.random_variables.Distribution method) get_population_extended() (pyabc.storage.History method) get_population_strategy() (pyabc.storage.History method) get_sum_stats() (pyabc.storage.History method) get_weighted_distances() (pyabc.storage.History method) GridSearchCV (class in pyabc.transition)

H

History (class in pyabc.storage)

I

IdentityFakeDistance (class in pyabc.distance_functions) initialize() (pyabc.distance_functions.DistanceFunction method) (pyabc.distance_functions.DistanceFunctionWithMeasureList method) (pyabc.distance_functions.PCADistanceFunction method) (pyabc.distance_functions.PNormDistance method) (pyabc.distance_functions.RangeEstimatorDistanceFunction method) (pyabc.distance_functions.WeightedPNormDistance method) (pyabc.epsilon.Epsilon method) (pyabc.epsilon.QuantileEpsilon method)

integrated_simulate() (pyabc.model.IntegratedModel method) IntegratedModel (class in pyabc.model)

K

kde_1d() (in module pyabc.visualization)

kde_2d() (in module pyabc.visualization)

L

ListEpsilon (class in pyabc.epsilon) load() (pyabc.smc.ABCSMC method) LocalTransition (class in pyabc.transition)

lower() (pyabc.distance_functions.MinMaxDistanceFunction static method) (pyabc.distance_functions.PercentileDistanceFunction static method) (pyabc.distance_functions.RangeEstimatorDistanceFunction static method) LowerBoundDecorator (class in pyabc.random_variables)

M

map() (pyabc.sge.SGE method) MappingSampler (class in pyabc.sampler) max_t (pyabc.storage.History attribute) mean_cv() (pyabc.transition.Transition method) measures_to_use (pyabc.distance_functions.DistanceFunctionWithMeasureList attribute) median_absolute_deviation() (in module pyabc.distance_functions) MedianEpsilon (class in pyabc.epsilon)

MinMaxDistanceFunction (class in pyabc.distance_functions) Model (class in pyabc.model) model() (pyabc.external.R method) ModelPerturbationKernel (class in pyabc.random_variables) ModelResult (class in pyabc.model) MulticoreEvalParallelSampler (class in pyabc.sampler) MulticoreParticleParallelSampler (class in pyabc.sampler) MultivariateNormalTransition (class in pyabc.transition)

N

n_populations (pyabc.storage.History attribute) n_worker() (pyabc.sampler.RedisEvalParallelSampler method) NamedPrinter (class in pyabc.sge) new() (pyabc.smc.ABCSMC method)

NoDistance (class in pyabc.distance_functions) NotEnoughParticles nr_cores_available() (in module pyabc.sge) nr_of_models_alive() (pyabc.storage.History method)

O

observation() (pyabc.external.R method)

P

Parameter (class in pyabc.parameters) PCADistanceFunction (class in pyabc.distance_functions) pdf() (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) (pyabc.transition.LocalTransition method) (pyabc.transition.MultivariateNormalTransition method) (pyabc.transition.Transition method) PERCENTILE (pyabc.distance_functions.PercentileDistanceFunction attribute) PercentileDistanceFunction (class in pyabc.distance_functions) plot_kde_1d() (in module pyabc.visualization) plot_kde_2d() (in module pyabc.visualization) plot_kde_matrix() (in module pyabc.visualization) pmf() (pyabc.random_variables.LowerBoundDecorator method) (pyabc.random_variables.ModelPerturbationKernel method) (pyabc.random_variables.RV method) (pyabc.random_variables.RVBase method) (pyabc.random_variables.RVDecorator method)

PNormDistance (class in pyabc.distance_functions) PopulationStrategy (class in pyabc.populationstrategy) ProfilingContext (class in pyabc.sge) pyabc.distance_functions (module) pyabc.epsilon (module) pyabc.external (module) pyabc.model (module) pyabc.parameters (module) pyabc.populationstrategy (module) pyabc.random_variables (module) pyabc.sampler (module) pyabc.sge (module) pyabc.smc (module) pyabc.storage (module) pyabc.transition (module) pyabc.visualization (module)

Q

QuantileEpsilon (class in pyabc.epsilon)

R

R (class in pyabc.external) RangeEstimatorDistanceFunction (class in pyabc.distance_functions) RedisEvalParallelSampler (class in pyabc.sampler) RedisEvalParallelSamplerServerStarter (class in pyabc.sampler) run() (pyabc.smc.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.LowerBoundDecorator method) (pyabc.random_variables.ModelPerturbationKernel method) (pyabc.random_variables.RV method) (pyabc.random_variables.RVBase method) (pyabc.random_variables.RVDecorator method) (pyabc.transition.Transition method)

rvs_single() (pyabc.transition.LocalTransition method) (pyabc.transition.MultivariateNormalTransition method) (pyabc.transition.Transition method)

S

Sample (class in pyabc.sampler) sample() (pyabc.model.Model method) (pyabc.model.SimpleModel method) sample_until_n_accepted() (pyabc.sampler.MappingSampler method) (pyabc.sampler.MulticoreEvalParallelSampler method) (pyabc.sampler.MulticoreParticleParallelSampler method) (pyabc.sampler.RedisEvalParallelSampler method) (pyabc.sampler.Sampler method) (pyabc.sampler.SingleCoreSampler method) Sampler (class in pyabc.sampler) scott_rule_of_thumb() (in module pyabc.transition) set_data() (pyabc.smc.ABCSMC method)

SGE (class in pyabc.sge) sge_available() (in module pyabc.sge) silverman_rule_of_thumb() (in module pyabc.transition) SimpleFunctionDistance (class in pyabc.distance_functions) SimpleModel (class in pyabc.model) SingleCoreSampler (class in pyabc.sampler) standard_deviation() (in module pyabc.distance_functions) stop_if_only_single_model_alive (pyabc.smc.ABCSMC attribute) store_initial_data() (pyabc.storage.History method) summary_statistics() (pyabc.external.R method) (pyabc.model.IntegratedModel method) (pyabc.model.Model method)

T

to_distance() (in module pyabc.distance_functions) to_json() (pyabc.distance_functions.DistanceFunction method) (pyabc.epsilon.Epsilon method) (pyabc.populationstrategy.PopulationStrategy method)

total_nr_simulations (pyabc.storage.History attribute) Transition (class in pyabc.transition)

U

update() (pyabc.distance_functions.DistanceFunction method) (pyabc.distance_functions.WeightedPNormDistance method) update_random_variables() (pyabc.random_variables.Distribution method)

upper() (pyabc.distance_functions.MinMaxDistanceFunction static method) (pyabc.distance_functions.PercentileDistanceFunction static method) (pyabc.distance_functions.RangeEstimatorDistanceFunction static method)

W

WeightedEuclideanDistance (class in pyabc.distance_functions)

WeightedPNormDistance (class in pyabc.distance_functions)

Z

ZScoreDistanceFunction (class in pyabc.distance_functions)