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Guides

  • Model Building (liesel.model)
    • Var
      • Var.info
      • Var.inference
      • Var.auto_transform
      • Var.dist_node
      • Var.groups
      • Var.has_dist
      • Var.log_prob
      • Var.model
      • Var.name
      • Var.nodes
      • Var.observed
      • Var.parameter
      • Var.role
      • Var.strong
      • Var.value
      • Var.value_node
      • Var.var_value_node
      • Var.weak
    • Dist
      • Dist.at
      • Dist.distribution
      • Dist.log_prob
      • Dist.per_obs
      • Dist.monitor
    • Model
      • Model.auto_update
      • Model.log_lik
      • Model.log_prior
      • Model.log_prob
      • Model.node_graph
      • Model.nodes
      • Model.observed
      • Model.parameters
      • Model.state
      • Model.var_graph
      • Model.vars
    • plot_vars()
    • GraphBuilder
      • GraphBuilder.log_lik_node
      • GraphBuilder.log_prior_node
      • GraphBuilder.log_prob_node
      • GraphBuilder.nodes
      • GraphBuilder.vars
    • plot_nodes()
  • MCMC Sampling (liesel.goose)
    • LieselInterface
    • DataclassInterface
    • DictInterface
    • NamedTupleInterface
    • PyMCInterface
    • OptimResult
    • EngineBuilder
      • EngineBuilder.add_adaptation()
      • EngineBuilder.add_burnin()
      • EngineBuilder.add_kernel()
      • EngineBuilder.add_posterior()
      • EngineBuilder.add_quantity_generator()
      • EngineBuilder.append_epochs()
      • EngineBuilder.build()
      • EngineBuilder.set_duration()
      • EngineBuilder.set_duration_simple()
      • EngineBuilder.set_engine_seed()
      • EngineBuilder.set_epochs()
      • EngineBuilder.set_initial_values()
      • EngineBuilder.set_jitter_fns()
      • EngineBuilder.set_model()
      • EngineBuilder.engine_seed
      • EngineBuilder.epochs
      • EngineBuilder.jitter_fns
      • EngineBuilder.kernels
      • EngineBuilder.model_state
      • EngineBuilder.quantity_generators
      • EngineBuilder.show_progress
      • EngineBuilder.positions_included
      • EngineBuilder.positions_excluded
    • Engine
      • Engine.current_epoch
    • RWKernel
      • RWKernel.error_book
      • RWKernel.identifier
      • RWKernel.needs_history
      • RWKernel.position_keys
    • IWLSKernel
      • IWLSKernel.error_book
      • IWLSKernel.identifier
      • IWLSKernel.needs_history
      • IWLSKernel.position_keys
    • HMCKernel
      • HMCKernel.error_book
      • HMCKernel.identifier
      • HMCKernel.needs_history
      • HMCKernel.position_keys
    • NUTSKernel
      • NUTSKernel.error_book
      • NUTSKernel.identifier
      • NUTSKernel.needs_history
      • NUTSKernel.position_keys
    • GibbsKernel
      • GibbsKernel.error_book
      • GibbsKernel.identifier
      • GibbsKernel.needs_history
      • GibbsKernel.position_keys
    • SamplingResults
      • SamplingResults.positions
      • SamplingResults.transition_infos
      • SamplingResults.generated_quantities
      • SamplingResults.tuning_infos
      • SamplingResults.kernel_states
      • SamplingResults.full_model_states
      • SamplingResults.kernel_classes
      • SamplingResults.kernels_by_pos_key
    • Summary
      • Summary.per_chain
      • Summary.quantities
      • Summary.config
      • Summary.sample_info
      • Summary.error_summary
      • Summary.kernels_by_pos_key
      • Summary.liesel_version
    • plot_param()
    • plot_trace()
    • plot_density()
    • plot_pairs()
    • plot_cor()
  • Tutorials
    • Linear regression
    • Parameter transformations
    • Location-scale regression
    • GEV responses
    • Comparing samplers
    • Reproducibility
    • PyMC and Liesel: Spike and Slab

API Reference

  • liesel.model
    • dist_reg_mcmc()
    • tau2_gibbs_kernel()
    • PIT()
    • Addition()
    • Bijector()
    • ColumnStack()
    • DesignMatrix()
    • Hyperparameter()
    • InverseLink()
    • Parameter()
    • Predictor()
    • RegressionCoef()
    • Response()
    • Smooth()
    • SmoothingParam()
    • load_model()
    • save_model()
    • plot_nodes()
    • plot_vars()
    • DistRegBuilder
      • DistRegBuilder.add()
      • DistRegBuilder.add_groups()
      • DistRegBuilder.add_np_smooth()
      • DistRegBuilder.add_p_smooth()
      • DistRegBuilder.add_predictor()
      • DistRegBuilder.add_response()
      • DistRegBuilder.build_model()
      • DistRegBuilder.convert_dtype()
      • DistRegBuilder.copy()
      • DistRegBuilder.count_node_names()
      • DistRegBuilder.count_var_names()
      • DistRegBuilder.groups()
      • DistRegBuilder.plot_nodes()
      • DistRegBuilder.plot_vars()
      • DistRegBuilder.rename()
      • DistRegBuilder.rename_nodes()
      • DistRegBuilder.rename_vars()
      • DistRegBuilder.replace_node()
      • DistRegBuilder.replace_var()
      • DistRegBuilder.update()
      • DistRegBuilder.log_lik_node
      • DistRegBuilder.log_prior_node
      • DistRegBuilder.log_prob_node
      • DistRegBuilder.response
      • DistRegBuilder.nodes
      • DistRegBuilder.vars
    • GraphBuilder
      • GraphBuilder.add()
      • GraphBuilder.add_groups()
      • GraphBuilder.build_model()
      • GraphBuilder.convert_dtype()
      • GraphBuilder.copy()
      • GraphBuilder.count_node_names()
      • GraphBuilder.count_var_names()
      • GraphBuilder.groups()
      • GraphBuilder.plot_nodes()
      • GraphBuilder.plot_vars()
      • GraphBuilder.rename()
      • GraphBuilder.rename_nodes()
      • GraphBuilder.rename_vars()
      • GraphBuilder.replace_node()
      • GraphBuilder.replace_var()
      • GraphBuilder.update()
      • GraphBuilder.log_lik_node
      • GraphBuilder.log_prior_node
      • GraphBuilder.log_prob_node
      • GraphBuilder.nodes
      • GraphBuilder.vars
    • Model
      • Model.copy_nodes_and_vars()
      • Model.extract_position()
      • Model.groups()
      • Model.node_parental_subgraph()
      • Model.parental_submodel()
      • Model.plot_nodes()
      • Model.plot_vars()
      • Model.pop_nodes_and_vars()
      • Model.predict()
      • Model.sample()
      • Model.set_seed()
      • Model.simulate()
      • Model.update()
      • Model.update_state()
      • Model.var_parental_subgraph()
      • Model.auto_update
      • Model.log_lik
      • Model.log_prior
      • Model.log_prob
      • Model.node_graph
      • Model.nodes
      • Model.observed
      • Model.parameters
      • Model.state
      • Model.var_graph
      • Model.vars
    • Calc
      • Calc.add_inputs()
      • Calc.all_input_nodes()
      • Calc.all_output_nodes()
      • Calc.clear_state()
      • Calc.flag_outdated()
      • Calc.set_inputs()
      • Calc.update()
      • Calc.function
      • Calc.groups
      • Calc.inputs
      • Calc.kwinputs
      • Calc.model
      • Calc.name
      • Calc.needs_seed
      • Calc.outdated
      • Calc.outputs
      • Calc.state
      • Calc.value
      • Calc.var
      • Calc.monitor
    • Data
      • Data.add_inputs()
      • Data.all_input_nodes()
      • Data.all_output_nodes()
      • Data.clear_state()
      • Data.flag_outdated()
      • Data.set_inputs()
      • Data.update()
      • Data.groups
      • Data.inputs
      • Data.kwinputs
      • Data.model
      • Data.name
      • Data.needs_seed
      • Data.outdated
      • Data.outputs
      • Data.state
      • Data.value
      • Data.var
      • Data.monitor
    • Dist
      • Dist.add_inputs()
      • Dist.all_input_nodes()
      • Dist.all_output_nodes()
      • Dist.clear_state()
      • Dist.flag_outdated()
      • Dist.init_dist()
      • Dist.set_inputs()
      • Dist.update()
      • Dist.at
      • Dist.distribution
      • Dist.groups
      • Dist.inputs
      • Dist.kwinputs
      • Dist.log_prob
      • Dist.model
      • Dist.name
      • Dist.needs_seed
      • Dist.outdated
      • Dist.outputs
      • Dist.per_obs
      • Dist.state
      • Dist.value
      • Dist.var
      • Dist.monitor
    • Group
      • Group.value_from()
      • Group.name
      • Group.nodes
      • Group.nodes_and_vars
      • Group.vars
    • InputGroup
      • InputGroup.add_inputs()
      • InputGroup.all_input_nodes()
      • InputGroup.all_output_nodes()
      • InputGroup.clear_state()
      • InputGroup.flag_outdated()
      • InputGroup.set_inputs()
      • InputGroup.update()
      • InputGroup.groups
      • InputGroup.inputs
      • InputGroup.kwinputs
      • InputGroup.model
      • InputGroup.name
      • InputGroup.needs_seed
      • InputGroup.outdated
      • InputGroup.outputs
      • InputGroup.state
      • InputGroup.value
      • InputGroup.var
      • InputGroup.monitor
    • Node
      • Node.add_inputs()
      • Node.all_input_nodes()
      • Node.all_output_nodes()
      • Node.clear_state()
      • Node.flag_outdated()
      • Node.set_inputs()
      • Node.update()
      • Node.groups
      • Node.inputs
      • Node.kwinputs
      • Node.model
      • Node.name
      • Node.needs_seed
      • Node.outdated
      • Node.outputs
      • Node.state
      • Node.value
      • Node.var
      • Node.monitor
    • NodeState
      • NodeState.count()
      • NodeState.index()
      • NodeState.extra
      • NodeState.outdated
      • NodeState.value
    • TransientCalc
      • TransientCalc.add_inputs()
      • TransientCalc.all_input_nodes()
      • TransientCalc.all_output_nodes()
      • TransientCalc.clear_state()
      • TransientCalc.flag_outdated()
      • TransientCalc.set_inputs()
      • TransientCalc.update()
      • TransientCalc.function
      • TransientCalc.groups
      • TransientCalc.inputs
      • TransientCalc.kwinputs
      • TransientCalc.model
      • TransientCalc.name
      • TransientCalc.needs_seed
      • TransientCalc.outdated
      • TransientCalc.outputs
      • TransientCalc.state
      • TransientCalc.value
      • TransientCalc.var
      • TransientCalc.monitor
    • TransientDist
      • TransientDist.add_inputs()
      • TransientDist.all_input_nodes()
      • TransientDist.all_output_nodes()
      • TransientDist.clear_state()
      • TransientDist.flag_outdated()
      • TransientDist.init_dist()
      • TransientDist.set_inputs()
      • TransientDist.update()
      • TransientDist.at
      • TransientDist.distribution
      • TransientDist.groups
      • TransientDist.inputs
      • TransientDist.kwinputs
      • TransientDist.log_prob
      • TransientDist.model
      • TransientDist.name
      • TransientDist.needs_seed
      • TransientDist.outdated
      • TransientDist.outputs
      • TransientDist.per_obs
      • TransientDist.state
      • TransientDist.value
      • TransientDist.var
      • TransientDist.monitor
    • TransientIdentity
      • TransientIdentity.add_inputs()
      • TransientIdentity.all_input_nodes()
      • TransientIdentity.all_output_nodes()
      • TransientIdentity.clear_state()
      • TransientIdentity.flag_outdated()
      • TransientIdentity.set_inputs()
      • TransientIdentity.update()
      • TransientIdentity.function
      • TransientIdentity.groups
      • TransientIdentity.inputs
      • TransientIdentity.kwinputs
      • TransientIdentity.model
      • TransientIdentity.name
      • TransientIdentity.needs_seed
      • TransientIdentity.outdated
      • TransientIdentity.outputs
      • TransientIdentity.state
      • TransientIdentity.value
      • TransientIdentity.var
      • TransientIdentity.monitor
    • TransientNode
      • TransientNode.add_inputs()
      • TransientNode.all_input_nodes()
      • TransientNode.all_output_nodes()
      • TransientNode.clear_state()
      • TransientNode.flag_outdated()
      • TransientNode.set_inputs()
      • TransientNode.update()
      • TransientNode.groups
      • TransientNode.inputs
      • TransientNode.kwinputs
      • TransientNode.model
      • TransientNode.name
      • TransientNode.needs_seed
      • TransientNode.outdated
      • TransientNode.outputs
      • TransientNode.state
      • TransientNode.value
      • TransientNode.var
      • TransientNode.monitor
    • Value
      • Value.add_inputs()
      • Value.all_input_nodes()
      • Value.all_output_nodes()
      • Value.clear_state()
      • Value.flag_outdated()
      • Value.set_inputs()
      • Value.update()
      • Value.groups
      • Value.inputs
      • Value.kwinputs
      • Value.model
      • Value.name
      • Value.needs_seed
      • Value.outdated
      • Value.outputs
      • Value.state
      • Value.value
      • Value.var
      • Value.monitor
    • Var
      • Var.all_input_nodes()
      • Var.all_input_vars()
      • Var.all_output_nodes()
      • Var.all_output_vars()
      • Var.get_inference()
      • Var.new_calc()
      • Var.new_obs()
      • Var.new_param()
      • Var.new_value()
      • Var.plot_nodes()
      • Var.plot_vars()
      • Var.predict()
      • Var.sample()
      • Var.transform()
      • Var.update()
      • Var.info
      • Var.inference
      • Var.auto_transform
      • Var.dist_node
      • Var.groups
      • Var.has_dist
      • Var.log_prob
      • Var.model
      • Var.name
      • Var.nodes
      • Var.observed
      • Var.parameter
      • Var.role
      • Var.strong
      • Var.value
      • Var.value_node
      • Var.var_value_node
      • Var.weak
  • liesel.goose
    • history_to_df()
    • plot_cor()
    • plot_density()
    • plot_param()
    • plot_trace()
    • plot_scatter()
    • plot_pairs()
    • stan_epochs()
    • optim_flat()
    • DictInterface
      • DictInterface.extract_position()
      • DictInterface.log_prob()
      • DictInterface.update_state()
    • DataclassInterface
      • DataclassInterface.extract_position()
      • DataclassInterface.log_prob()
      • DataclassInterface.update_state()
    • LieselInterface
      • LieselInterface.extract_position()
      • LieselInterface.log_prob()
      • LieselInterface.update_state()
    • Engine
      • Engine.append_epoch()
      • Engine.get_results()
      • Engine.is_sampling_done()
      • Engine.sample_all_epochs()
      • Engine.sample_next_epoch()
      • Engine.current_epoch
    • EngineBuilder
      • EngineBuilder.add_adaptation()
      • EngineBuilder.add_burnin()
      • EngineBuilder.add_kernel()
      • EngineBuilder.add_posterior()
      • EngineBuilder.add_quantity_generator()
      • EngineBuilder.append_epochs()
      • EngineBuilder.build()
      • EngineBuilder.set_duration()
      • EngineBuilder.set_duration_simple()
      • EngineBuilder.set_engine_seed()
      • EngineBuilder.set_epochs()
      • EngineBuilder.set_initial_values()
      • EngineBuilder.set_jitter_fns()
      • EngineBuilder.set_model()
      • EngineBuilder.engine_seed
      • EngineBuilder.epochs
      • EngineBuilder.jitter_fns
      • EngineBuilder.kernels
      • EngineBuilder.model_state
      • EngineBuilder.quantity_generators
      • EngineBuilder.show_progress
      • EngineBuilder.positions_included
      • EngineBuilder.positions_excluded
    • MCMCSpec
      • MCMCSpec.apply_jitter()
      • MCMCSpec.jitter_dist
      • MCMCSpec.jitter_method
      • MCMCSpec.kernel_group
      • MCMCSpec.kernel
      • MCMCSpec.kernel_kwargs
    • LieselMCMC
      • LieselMCMC.get_engine_builder()
      • LieselMCMC.get_jitter_functions()
      • LieselMCMC.get_kernel_groups()
      • LieselMCMC.get_kernel_list()
      • LieselMCMC.get_spec()
      • LieselMCMC.which
      • LieselMCMC.model
    • EpochConfig
      • EpochConfig.to_state()
      • EpochConfig.type
      • EpochConfig.duration
      • EpochConfig.thinning
      • EpochConfig.optional
    • EpochType
      • EpochType.conjugate()
      • EpochType.bit_length()
      • EpochType.bit_count()
      • EpochType.to_bytes()
      • EpochType.from_bytes()
      • EpochType.as_integer_ratio()
      • EpochType.is_integer()
      • EpochType.is_adaptation()
      • EpochType.is_warmup()
      • EpochType.real
      • EpochType.imag
      • EpochType.numerator
      • EpochType.denominator
      • EpochType.INITIAL_VALUES
      • EpochType.FAST_ADAPTATION
      • EpochType.SLOW_ADAPTATION
      • EpochType.BURNIN
      • EpochType.POSTERIOR
    • GibbsKernel
      • GibbsKernel.end_epoch()
      • GibbsKernel.end_warmup()
      • GibbsKernel.has_model()
      • GibbsKernel.init_state()
      • GibbsKernel.log_prob_fn()
      • GibbsKernel.position()
      • GibbsKernel.set_model()
      • GibbsKernel.start_epoch()
      • GibbsKernel.transition()
      • GibbsKernel.tune()
      • GibbsKernel.error_book
      • GibbsKernel.identifier
      • GibbsKernel.model
      • GibbsKernel.needs_history
      • GibbsKernel.position_keys
    • HMCKernel
      • HMCKernel.end_epoch()
      • HMCKernel.end_warmup()
      • HMCKernel.has_model()
      • HMCKernel.init_state()
      • HMCKernel.log_prob_fn()
      • HMCKernel.position()
      • HMCKernel.set_model()
      • HMCKernel.start_epoch()
      • HMCKernel.transition()
      • HMCKernel.tune()
      • HMCKernel.error_book
      • HMCKernel.identifier
      • HMCKernel.model
      • HMCKernel.needs_history
      • HMCKernel.position_keys
    • IWLSKernel
      • IWLSKernel.end_epoch()
      • IWLSKernel.end_warmup()
      • IWLSKernel.has_model()
      • IWLSKernel.init_state()
      • IWLSKernel.log_prob_fn()
      • IWLSKernel.position()
      • IWLSKernel.set_model()
      • IWLSKernel.start_epoch()
      • IWLSKernel.transition()
      • IWLSKernel.tune()
      • IWLSKernel.untuned()
      • IWLSKernel.error_book
      • IWLSKernel.identifier
      • IWLSKernel.model
      • IWLSKernel.needs_history
      • IWLSKernel.position_keys
    • MHKernel
      • MHKernel.end_epoch()
      • MHKernel.end_warmup()
      • MHKernel.has_model()
      • MHKernel.init_state()
      • MHKernel.log_prob_fn()
      • MHKernel.position()
      • MHKernel.set_model()
      • MHKernel.start_epoch()
      • MHKernel.transition()
      • MHKernel.tune()
      • MHKernel.error_book
      • MHKernel.identifier
      • MHKernel.model
      • MHKernel.needs_history
      • MHKernel.position_keys
    • MHProposal
      • MHProposal.count()
      • MHProposal.index()
      • MHProposal.log_correction
      • MHProposal.position
    • ModelInterface
      • ModelInterface.extract_position()
      • ModelInterface.log_prob()
      • ModelInterface.update_state()
    • NamedTupleInterface
      • NamedTupleInterface.extract_position()
      • NamedTupleInterface.log_prob()
      • NamedTupleInterface.update_state()
    • NUTSKernel
      • NUTSKernel.end_epoch()
      • NUTSKernel.end_warmup()
      • NUTSKernel.has_model()
      • NUTSKernel.init_state()
      • NUTSKernel.log_prob_fn()
      • NUTSKernel.position()
      • NUTSKernel.set_model()
      • NUTSKernel.start_epoch()
      • NUTSKernel.transition()
      • NUTSKernel.tune()
      • NUTSKernel.error_book
      • NUTSKernel.identifier
      • NUTSKernel.model
      • NUTSKernel.needs_history
      • NUTSKernel.position_keys
    • Stopper
      • Stopper.continue_()
      • Stopper.stop_early()
      • Stopper.stop_now()
      • Stopper.which_best_in_recent_history()
      • Stopper.atol
      • Stopper.rtol
      • Stopper.max_iter
      • Stopper.patience
    • RWKernel
      • RWKernel.end_epoch()
      • RWKernel.end_warmup()
      • RWKernel.has_model()
      • RWKernel.init_state()
      • RWKernel.log_prob_fn()
      • RWKernel.position()
      • RWKernel.set_model()
      • RWKernel.start_epoch()
      • RWKernel.transition()
      • RWKernel.tune()
      • RWKernel.error_book
      • RWKernel.identifier
      • RWKernel.model
      • RWKernel.needs_history
      • RWKernel.position_keys
    • Summary
      • Summary.error_df()
      • Summary.to_dataframe()
      • Summary.per_chain
      • Summary.quantities
      • Summary.config
      • Summary.sample_info
      • Summary.error_summary
      • Summary.kernels_by_pos_key
      • Summary.liesel_version
    • SamplesSummary
      • SamplesSummary.from_array()
      • SamplesSummary.to_dataframe()
      • SamplesSummary.config
    • SamplingResults
      • SamplingResults.get_adaptation_samples()
      • SamplingResults.get_error_log()
      • SamplingResults.get_kernels_by_pos_key()
      • SamplingResults.get_posterior_samples()
      • SamplingResults.get_posterior_transition_infos()
      • SamplingResults.get_samples()
      • SamplingResults.get_tuning_times()
      • SamplingResults.get_warmup_samples()
      • SamplingResults.pkl_load()
      • SamplingResults.pkl_save()
      • SamplingResults.positions
      • SamplingResults.transition_infos
      • SamplingResults.generated_quantities
      • SamplingResults.tuning_infos
      • SamplingResults.kernel_states
      • SamplingResults.full_model_states
      • SamplingResults.kernel_classes
      • SamplingResults.kernels_by_pos_key
    • OptimResult
      • OptimResult.model_state
      • OptimResult.position
      • OptimResult.iteration
      • OptimResult.iteration_best
      • OptimResult.history
      • OptimResult.max_iter
      • OptimResult.n_train
      • OptimResult.n_validation
  • liesel.contrib
    • liesel.contrib.splines
      • basis_matrix()
      • equidistant_knots()
      • pspline_penalty()
  • liesel.distributions
    • GaussianCopula
    • MultivariateNormalDegenerate
      • MultivariateNormalDegenerate.from_penalty()
      • MultivariateNormalDegenerate.from_penalty_smooth()
      • MultivariateNormalDegenerate.eig
      • MultivariateNormalDegenerate.loc
      • MultivariateNormalDegenerate.log_pdet
      • MultivariateNormalDegenerate.prec
      • MultivariateNormalDegenerate.rank
  • liesel.bijectors
    • AlgebraicSigmoid

Experimental API

  • liesel.experimental
    • liesel.experimental.arviz
      • to_arviz_inference_data()
    • liesel.experimental.pymc
      • PyMCInterface

Python Module Index

l
 
l
- liesel
    liesel.bijectors
    liesel.contrib
    liesel.contrib.splines
    liesel.distributions
    liesel.experimental
    liesel.experimental.arviz
    liesel.experimental.pymc
    liesel.goose
    liesel.model

By Hannes Riebl & Paul Wiemann

© Copyright 2022, Hannes Riebl & Paul Wiemann.