Index

A

adapt_state_size (pymob.inference.numpyro_backend.NumpyroBackend property) algortihm (pymob.sim.config.Pymoo attribute), [1], [2], [3] (pymob.sim.config.sections.Pymoo attribute), [1] all (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.Errormodel property), [1] (pymob.sim.config.Modelparameters property), [1] (pymob.sim.config.sections.Datastructure property) (pymob.sim.config.sections.Errormodel property) (pymob.sim.config.sections.Modelparameters property)

allowed_model_signature_arguments (pymob.sim.evaluator.Evaluator property) array_param_to_1d() (pymob.inference.pyabc_backend.PyabcBackend static method) atol (pymob.sim.config.Jaxsolver attribute), [1] (pymob.sim.config.sections.Jaxsolver attribute) (pymob.solvers.diffrax.JaxSolver attribute)

B

backend (pymob.sim.config.Inference attribute), [1], [2], [3] (pymob.sim.config.sections.Inference attribute), [1] batch_dimension (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.Simulation attribute), [1] (pymob.solvers.base.SolverBase attribute)

benchmark() (in module pymob.utils.misc)

C

calculate_log_likelihood() (pymob.inference.numpyro_backend.NumpyroBackend method) case_study (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] case_study_output() (in module pymob.utils.store_file) Casestudy (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) cast_to_precision() (pymob.inference.numpyro_backend.NumpyroBackend static method) catch_patterns() (in module pymob.inference.numpyro_backend) (in module pymob.utils.config) chains (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) check_dimensions() (pymob.simulation.SimulationBase method) check_distribution() (pymob.sim.config.parameters.RandomVariable class method) (pymob.sim.config.RandomVariable class method), [1] check_gradients() (pymob.inference.numpyro_backend.NumpyroBackend method) check_log_likelihood() (pymob.inference.numpyro_backend.NumpyroBackend method) check_parameters() (pymob.sim.config.parameters.RandomVariable class method) (pymob.sim.config.RandomVariable class method), [1] check_scaled_results_feasibility() (pymob.simulation.SimulationBase method) check_tolerance_and_jax_mode() (pymob.inference.numpyro_backend.NumpyroBackend method) cluster_chains() (in module pymob.utils.bayesian) combine_chains() (pymob.inference.numpyro_backend.NumpyroBackend method)

combine_legends() (in module pymob.utils.plot_helpers) compute() (pymob.simulation.SimulationBase method) Config (class in pymob.sim.config), [1] (class in pymob.sim.config.base) coordinates (pymob.solvers.base.SolverBase attribute) coordinates_indices (pymob.solvers.base.SolverBase attribute) coordinates_input_vars (pymob.simulation.SimulationBase property) (pymob.solvers.base.SolverBase attribute) copy() (pymob.simulation.SimulationBase method) cores (pymob.sim.config.Multiprocessing attribute), [1], [2], [3] (pymob.sim.config.sections.Multiprocessing attribute), [1] create_data_scaler() (pymob.simulation.SimulationBase method) create_dataset_from_dict() (in module pymob.sim.evaluator) create_dataset_from_numpy() (in module pymob.sim.evaluator) create_directory() (pymob.sim.config.base.Config method) (pymob.sim.config.Config method), [1] create_fname_date_ver() (in module pymob.utils.store_file) create_interpolated_coordinates() (pymob.simulation.SimulationBase method) create_log_likelihood() (pymob.inference.numpyro_backend.NumpyroBackend method) (pymob.inference.scipy_backend.ScipyBackend method) curve_jumps() (in module pymob.solvers.base) cvtol (pymob.sim.config.Pymoo attribute), [1] (pymob.sim.config.sections.Pymoo attribute)

D

data (pymob.sim.config.Casestudy attribute), [1] (pymob.sim.config.sections.Casestudy attribute) data_path (pymob.sim.config.Casestudy property), [1] (pymob.sim.config.sections.Casestudy property) data_structure (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] data_structure_and_dimensionality (pymob.solvers.base.SolverBase attribute) data_variables (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property) (pymob.solvers.base.SolverBase attribute) data_variables_max (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property) data_variables_min (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property) database (pymob.inference.pyabc_backend.PyabcBackend property) database_path (pymob.sim.config.Pyabc attribute), [1], [2], [3] (pymob.sim.config.sections.Pyabc attribute), [1] Datastructure (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) datavar_to_string() (in module pymob.sim.config.sections) DataVariable (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) Date2Delta (class in pymob.utils.misc) dayTicks() (in module pymob.utils.misc) dcoeff (pymob.sim.config.Jaxsolver attribute), [1] (pymob.sim.config.sections.Jaxsolver attribute) (pymob.solvers.diffrax.JaxSolver attribute) debug_report (pymob.sim.config.Report attribute), [1], [2], [3] (pymob.sim.config.sections.Report attribute), [1] default_settings_path (pymob.sim.config.Casestudy property), [1] (pymob.sim.config.sections.Casestudy property) deserialize() (in module pymob.utils.store_file) diagnostics (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) diagnostics_exclude_vars (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) diagnostics_with_batch_dim_vars (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute)

dict_to_string() (in module pymob.sim.config.sections) diffrax_solver (pymob.sim.config.Jaxsolver attribute), [1], [2], [3] (pymob.sim.config.sections.Jaxsolver attribute), [1] (pymob.solvers.diffrax.JaxSolver attribute) dimdict (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property) dimension_coords (pymob.simulation.SimulationBase property) dimension_sizes (pymob.solvers.base.SolverBase attribute) dimensionality (pymob.sim.evaluator.Evaluator property) dimensions (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.DataVariable attribute), [1] (pymob.sim.config.Modelparameters property), [1] (pymob.sim.config.sections.Datastructure property) (pymob.sim.config.sections.DataVariable attribute) (pymob.sim.config.sections.Modelparameters property) (pymob.solvers.base.SolverBase attribute) dimensions_evaluator (pymob.sim.config.DataVariable attribute), [1] (pymob.sim.config.sections.DataVariable attribute) dims (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) dims_input_vars (pymob.solvers.base.SolverBase attribute) dispatch() (pymob.simulation.SimulationBase method) dispatch_constructor() (pymob.simulation.SimulationBase method) dist_name (pymob.inference.numpyro_backend.NumpyroDistribution property) (pymob.inference.scipy_backend.ScipyDistribution property) distance_function_parser() (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method) distribution (pymob.inference.scipy_backend.ScipyBackend attribute) (pymob.sim.config.parameters.RandomVariable attribute) (pymob.sim.config.RandomVariable attribute), [1] distribution_map (pymob.inference.numpyro_backend.NumpyroDistribution attribute) (pymob.inference.scipy_backend.ScipyDistribution attribute) draw() (pymob.inference.pyabc_backend.Posterior method) draws (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) drop_vars_from_posterior() (pymob.inference.numpyro_backend.NumpyroBackend method) dX_dt2X() (in module pymob.utils.config)

E

enlist_attr() (in module pymob.sim.base) eps (pymob.sim.config.Inference attribute), [1], [2], [3] (pymob.sim.config.sections.Inference attribute), [1] error_model (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] Errormodel (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) ErrorModelFunction (class in pymob.inference.numpyro_backend) errormsg() (in module pymob.utils.errors) evaluate() (pymob.sim.config.Expression method), [1] (pymob.sim.config.parameters.Expression method) (pymob.simulation.SimulationBase method) Evaluator (class in pymob.sim.evaluator)

evaluator_dim_order (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property) exclude_kwargs_model (pymob.sim.config.sections.Solverbase attribute) (pymob.sim.config.Solverbase attribute), [1] (pymob.solvers.base.SolverBase attribute) exclude_kwargs_postprocessing (pymob.sim.config.sections.Solverbase attribute) (pymob.sim.config.Solverbase attribute), [1] (pymob.solvers.base.SolverBase attribute) expand_grid() (in module pymob.utils.misc) export() (pymob.simulation.SimulationBase method) Expression (class in pymob.sim.config), [1] (class in pymob.sim.config.parameters) extra_vars (pymob.sim.config.Inference attribute), [1], [2], [3] (pymob.sim.config.sections.Inference attribute), [1]

F

find_undefined_names() (pymob.sim.config.parameters.UndefinedNameFinder method) fixed (pymob.sim.config.Modelparameters property), [1] (pymob.sim.config.sections.Modelparameters property) fixed_value_dict (pymob.sim.config.Modelparameters property), [1] (pymob.sim.config.sections.Modelparameters property) forward() (pymob.inference.scipy_backend.ScipyErrorModel method) (pymob.inference.scipy_backend.ScipyPriorModel method) free (pymob.sim.config.Modelparameters property), [1] (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) (pymob.sim.config.sections.Modelparameters property)

free_value_dict (pymob.sim.config.Modelparameters property), [1] (pymob.sim.config.sections.Modelparameters property) from_directory() (pymob.simulation.SimulationBase class method) ftol (pymob.sim.config.Pymoo attribute), [1] (pymob.sim.config.sections.Pymoo attribute)

G

gaussian_base_distribution (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1], [2], [3] (pymob.sim.config.sections.Numpyro attribute), [1] generate_transform() (pymob.inference.numpyro_backend.NumpyroBackend static method) get_call_signature() (pymob.sim.evaluator.Evaluator method) get_case_study_model() (in module pymob.sim.config.casestudy_registry) get_dict() (pymob.inference.numpyro_backend.NumpyroBackend static method) get_grouped_unique_val() (in module pymob.utils.misc) get_host() (in module pymob.utils.misc)

get_limits_from_array() (in module pymob.utils.misc) get_return_arguments() (in module pymob.utils.config) get_version() (in module pymob.utils.errors) go_to_case_studies() (in module pymob.utils.store_file) goodness_of_fit (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) goodness_of_fit_nrmse_mode (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) goodness_of_fit_use_predictions (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute)

H

history_id (pymob.sim.config.Redis attribute), [1] (pymob.sim.config.sections.Redis attribute)

hourTicks() (in module pymob.utils.misc) hyper (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute)

I

icoeff (pymob.sim.config.Jaxsolver attribute), [1] (pymob.sim.config.sections.Jaxsolver attribute) (pymob.solvers.diffrax.JaxSolver attribute) idata (pymob.inference.pymoo_backend.PymooBackend attribute) import_casestudy_modules() (pymob.sim.config.base.Config method) (pymob.sim.config.Config method), [1] import_optional_dependency() (in module pymob.utils.errors) import_package() (in module pymob.utils.store_file) import_simulation_from_case_study() (pymob.sim.config.base.Config method) (pymob.sim.config.Config method), [1] indices (pymob.sim.config.Datastructure attribute), [1] (pymob.sim.config.sections.Datastructure attribute) (pymob.solvers.base.SolverBase attribute) Inference (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) inference (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] inference_model (pymob.inference.scipy_backend.ScipyBackend attribute) inference_numpyro (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1]

inference_pyabc (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] inference_pyabc_redis (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] inference_pymoo (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] init_root (pymob.sim.config.Casestudy attribute), [1], [2], [3] (pymob.sim.config.sections.Casestudy attribute), [1] init_strategy (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) initialize() (pymob.simulation.SimulationBase method) input_file_paths (pymob.sim.config.base.Config property) (pymob.sim.config.Config property), [1] input_files (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.Simulation attribute), [1] invert_list_tuple() (in module pymob.utils.misc) is_number() (in module pymob.utils.store_file) is_stochastic (pymob.solvers.base.SolverBase attribute)

J

Jaxsolver (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) JaxSolver (class in pymob.solvers.diffrax)

jaxsolver (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] jump_interpolation() (in module pymob.solvers.base)

K

kernel (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute)

L

lambdify_expression() (in module pymob.utils.config) len_batch_coordinate (pymob.solvers.base.SolverBase attribute) linear_model() (in module pymob.examples.linear_regression) list_converter() (in module pymob.utils.store_file) list_to_string() (in module pymob.sim.config.sections) load_results() (pymob.inference.numpyro_backend.NumpyroBackend method) (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method)

logfile (pymob.sim.config.Casestudy attribute), [1] (pymob.sim.config.sections.Casestudy attribute) logging (pymob.sim.config.Casestudy attribute), [1] (pymob.sim.config.sections.Casestudy attribute) lookup() (in module pymob.utils.config) lookup_args() (in module pymob.utils.config) lookup_from() (in module pymob.utils.config)

M

map_parameters() (pymob.inference.pyabc_backend.PyabcBackend static method) mappar() (in module pymob.solvers.base) match_columns() (in module pymob.utils.misc) max (pymob.sim.config.DataVariable attribute), [1] (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) (pymob.sim.config.sections.DataVariable attribute) max_nr_populations (pymob.inference.pyabc_backend.PyabcBackend property) (pymob.sim.config.Pyabc attribute), [1], [2], [3] (pymob.sim.config.Pymoo attribute), [1] (pymob.sim.config.sections.Pyabc attribute), [1] (pymob.sim.config.sections.Pymoo attribute) max_steps (pymob.sim.config.Jaxsolver attribute), [1] (pymob.sim.config.sections.Jaxsolver attribute) (pymob.solvers.diffrax.JaxSolver attribute) mean() (pymob.inference.pyabc_backend.Posterior method) min (pymob.sim.config.DataVariable attribute), [1] (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) (pymob.sim.config.sections.DataVariable attribute) min_eps_diff (pymob.inference.pyabc_backend.PyabcBackend property) (pymob.sim.config.Pyabc attribute), [1] (pymob.sim.config.sections.Pyabc attribute) minimum_epsilon (pymob.inference.pyabc_backend.PyabcBackend property) (pymob.sim.config.Pyabc attribute), [1] (pymob.sim.config.sections.Pyabc attribute) model (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.Simulation attribute), [1] (pymob.solvers.base.SolverBase attribute) model() (pymob.inference.numpyro_backend.NumpyroBackend method) model_class (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.Simulation attribute), [1] model_config (pymob.sim.config.base.Config attribute) (pymob.sim.config.Casestudy attribute), [1] (pymob.sim.config.Config attribute), [1] (pymob.sim.config.Datastructure attribute), [1] (pymob.sim.config.DataVariable attribute), [1] (pymob.sim.config.Errormodel attribute), [1] (pymob.sim.config.Inference attribute), [1] (pymob.sim.config.Jaxsolver attribute), [1] (pymob.sim.config.Modelparameters attribute), [1] (pymob.sim.config.Multiprocessing attribute), [1] (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) (pymob.sim.config.parameters.RandomVariable attribute) (pymob.sim.config.Pyabc attribute), [1] (pymob.sim.config.PymobModel attribute), [1] (pymob.sim.config.Pymoo attribute), [1] (pymob.sim.config.RandomVariable attribute), [1] (pymob.sim.config.Redis attribute), [1] (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Casestudy attribute) (pymob.sim.config.sections.Datastructure attribute) (pymob.sim.config.sections.DataVariable attribute) (pymob.sim.config.sections.Errormodel attribute) (pymob.sim.config.sections.Inference attribute) (pymob.sim.config.sections.Jaxsolver attribute) (pymob.sim.config.sections.Modelparameters attribute) (pymob.sim.config.sections.Multiprocessing attribute) (pymob.sim.config.sections.Numpyro attribute) (pymob.sim.config.sections.Pyabc attribute) (pymob.sim.config.sections.PymobModel attribute) (pymob.sim.config.sections.Pymoo attribute) (pymob.sim.config.sections.Redis attribute) (pymob.sim.config.sections.Report attribute) (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.sections.Solverbase attribute) (pymob.sim.config.Simulation attribute), [1] (pymob.sim.config.Solverbase attribute), [1] model_fields (pymob.sim.config.base.Config attribute) (pymob.sim.config.Casestudy attribute), [1] (pymob.sim.config.Config attribute), [1] (pymob.sim.config.Datastructure attribute), [1] (pymob.sim.config.DataVariable attribute), [1] (pymob.sim.config.Errormodel attribute), [1] (pymob.sim.config.Inference attribute), [1] (pymob.sim.config.Jaxsolver attribute), [1] (pymob.sim.config.Modelparameters attribute), [1] (pymob.sim.config.Multiprocessing attribute), [1] (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) (pymob.sim.config.parameters.RandomVariable attribute) (pymob.sim.config.Pyabc attribute), [1] (pymob.sim.config.PymobModel attribute), [1] (pymob.sim.config.Pymoo attribute), [1] (pymob.sim.config.RandomVariable attribute), [1] (pymob.sim.config.Redis attribute), [1] (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Casestudy attribute) (pymob.sim.config.sections.Datastructure attribute) (pymob.sim.config.sections.DataVariable attribute) (pymob.sim.config.sections.Errormodel attribute) (pymob.sim.config.sections.Inference attribute) (pymob.sim.config.sections.Jaxsolver attribute) (pymob.sim.config.sections.Modelparameters attribute) (pymob.sim.config.sections.Multiprocessing attribute) (pymob.sim.config.sections.Numpyro attribute) (pymob.sim.config.sections.Pyabc attribute) (pymob.sim.config.sections.PymobModel attribute) (pymob.sim.config.sections.Pymoo attribute) (pymob.sim.config.sections.Redis attribute) (pymob.sim.config.sections.Report attribute) (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.sections.Solverbase attribute) (pymob.sim.config.Simulation attribute), [1] (pymob.sim.config.Solverbase attribute), [1]

model_id (pymob.sim.config.Redis attribute), [1] (pymob.sim.config.sections.Redis attribute) model_parameters (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] model_parser() (pymob.inference.pyabc_backend.PyabcBackend method) model_post_init() (pymob.sim.config.base.Config method) (pymob.sim.config.Config method), [1] (pymob.sim.config.Multiprocessing method), [1] (pymob.sim.config.Redis method), [1] (pymob.sim.config.sections.Multiprocessing method) (pymob.sim.config.sections.Redis method) model_ser() (pymob.sim.config.parameters.RandomVariable method) (pymob.sim.config.RandomVariable method), [1] ModelParameterDict (class in pymob.sim.config.sections) Modelparameters (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) modeltype (pymob.sim.config.sections.Simulation attribute), [1] (pymob.sim.config.Simulation attribute), [1], [2], [3] module pymob pymob.examples pymob.examples.linear_regression pymob.infer pymob.inference pymob.inference.numpyro_backend pymob.inference.pyabc_backend pymob.inference.pymoo_backend pymob.inference.scipy_backend pymob.prior_predictive_checks pymob.sim pymob.sim.base pymob.sim.config, [1] pymob.sim.config.base pymob.sim.config.casestudy_registry pymob.sim.config.parameters pymob.sim.config.sections pymob.sim.evaluator pymob.sim.solvetools pymob.simulate pymob.solvers pymob.solvers.analytic pymob.solvers.base pymob.solvers.diffrax pymob.solvers.scipy pymob.utils pymob.utils.bayesian pymob.utils.config pymob.utils.errors pymob.utils.help pymob.utils.math_helpers pymob.utils.misc pymob.utils.plot_helpers pymob.utils.store_file modules (pymob.sim.config.Casestudy attribute), [1], [2], [3] (pymob.sim.config.sections.Casestudy attribute), [1] Multiprocessing (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) multiprocessing (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1]

N

n_cores (pymob.sim.config.Multiprocessing property), [1] (pymob.sim.config.sections.Multiprocessing property) n_free (pymob.sim.config.Modelparameters property), [1] (pymob.sim.config.sections.Modelparameters property) n_objectives (pymob.sim.config.Inference attribute), [1], [2], [3] (pymob.sim.config.sections.Inference attribute), [1] n_ode_states (pymob.sim.config.sections.Simulation attribute), [1] (pymob.sim.config.Simulation attribute), [1], [2], [3] (pymob.solvers.base.SolverBase attribute) n_predictions (pymob.sim.config.Inference attribute), [1], [2], [3] (pymob.sim.config.Redis attribute), [1] (pymob.sim.config.sections.Inference attribute), [1] (pymob.sim.config.sections.Redis attribute) name (pymob.sim.config.Casestudy attribute), [1], [2], [3] (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) (pymob.sim.config.sections.Casestudy attribute), [1] nested_dict_to_string() (in module pymob.sim.config.sections)

Numpyro (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) NumpyroBackend (class in pymob.inference.numpyro_backend) NumpyroDistribution (class in pymob.inference.numpyro_backend) nuts_adapt_mass_matrix (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) nuts_adapt_step_size (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) nuts_dense_mass (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) nuts_draws (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) nuts_max_tree_depth (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) nuts_posterior() (pymob.inference.numpyro_backend.NumpyroBackend method) nuts_step_size (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) nuts_target_accept_prob (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute)

O

objective_function (pymob.sim.config.Inference attribute), [1], [2], [3] (pymob.sim.config.sections.Inference attribute), [1] objective_names (pymob.sim.config.Inference attribute), [1], [2], [3] (pymob.sim.config.sections.Inference attribute), [1] obs (pymob.sim.config.parameters.RandomVariable attribute) (pymob.sim.config.RandomVariable attribute), [1] obs_inv (pymob.sim.config.parameters.RandomVariable attribute) (pymob.sim.config.RandomVariable attribute), [1] observation_parser() (pymob.inference.numpyro_backend.NumpyroBackend method) observations (pymob.sim.config.Casestudy attribute), [1] (pymob.sim.config.sections.Casestudy attribute) observed (pymob.sim.config.DataVariable attribute), [1] (pymob.sim.config.sections.DataVariable attribute) observed_data_variables (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property)

observed_data_variables_max (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property) observed_data_variables_min (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property) observed_dimdict (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property) odesolve() (pymob.solvers.diffrax.JaxSolver method) odesolve_splitargs() (pymob.solvers.diffrax.JaxSolver method) opt() (in module pymob.utils.store_file) OptimizationProblem (class in pymob.inference.pymoo_backend) optimize() (pymob.inference.pymoo_backend.PymooBackend method) output (pymob.sim.config.Casestudy attribute), [1] (pymob.sim.config.sections.Casestudy attribute) output_path (pymob.sim.config.Casestudy property), [1] (pymob.sim.config.sections.Casestudy property)

P

package (pymob.sim.config.Casestudy attribute), [1], [2], [3] (pymob.sim.config.sections.Casestudy attribute), [1] pandoc_output_format (pymob.sim.config.Report attribute), [1], [2], [3] (pymob.sim.config.sections.Report attribute), [1] Param (class in pymob.sim.config), [1] (class in pymob.sim.config.parameters) param_to_prior() (pymob.inference.pyabc_backend.PyabcBackend static method) param_to_string() (in module pymob.sim.config.sections) parameter_converter() (pymob.inference.numpyro_backend.NumpyroDistribution static method) (pymob.inference.scipy_backend.ScipyDistribution static method) parameter_dims (pymob.solvers.base.SolverBase attribute) ParameterDict (class in pymob.sim.config.sections) parameterize() (pymob.simulation.SimulationBase static method) parameters (pymob.sim.config.parameters.RandomVariable attribute) (pymob.sim.config.RandomVariable attribute), [1] (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.ModelParameterDict attribute), [1] (pymob.sim.config.sections.Report attribute) (pymob.sim.evaluator.Evaluator property) parameters_format (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) parse_config_section() (in module pymob.utils.store_file) parse_deterministic_model() (pymob.inference.numpyro_backend.NumpyroBackend method) (pymob.inference.scipy_backend.ScipyBackend method) parse_input() (pymob.simulation.SimulationBase method) parse_probabilistic_model() (pymob.inference.numpyro_backend.NumpyroBackend method) (pymob.inference.scipy_backend.ScipyBackend method) password (pymob.sim.config.Redis attribute), [1], [2], [3] (pymob.sim.config.sections.Redis attribute), [1] pcoeff (pymob.sim.config.Jaxsolver attribute), [1] (pymob.sim.config.sections.Jaxsolver attribute) (pymob.solvers.diffrax.JaxSolver attribute) pivot_xarray() (in module pymob.utils.misc) plot (pymob.sim.config.Inference attribute), [1], [2], [3] (pymob.sim.config.sections.Inference attribute), [1] plot() (pymob.inference.pyabc_backend.PyabcBackend method) plot_chains() (pymob.inference.pyabc_backend.PyabcBackend method) plot_hist() (in module pymob.utils.plot_helpers) plot_loghist() (in module pymob.utils.plot_helpers) plot_parameter_pairs (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) plot_predictions() (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method) plot_trace (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) pop_key() (in module pymob.utils.misc) population_size (pymob.inference.pyabc_backend.PyabcBackend property) (pymob.sim.config.Pyabc attribute), [1], [2], [3] (pymob.sim.config.Pymoo attribute), [1] (pymob.sim.config.sections.Pyabc attribute), [1] (pymob.sim.config.sections.Pymoo attribute) port (pymob.sim.config.Redis attribute), [1], [2], [3] (pymob.sim.config.sections.Redis attribute), [1] post_processing (pymob.solvers.base.SolverBase attribute) post_processing() (pymob.inference.pymoo_backend.PymooBackend method) post_update() (pymob.sim.config.DataVariable method), [1] (pymob.sim.config.Param method), [1] (pymob.sim.config.parameters.Param method) (pymob.sim.config.sections.DataVariable method) Posterior (class in pymob.inference.pyabc_backend) posterior (pymob.inference.numpyro_backend.NumpyroBackend property) posterior() (pymob.simulation.SimulationBase.Report method) posterior_coordinates (pymob.inference.pyabc_backend.PyabcBackend property) posterior_data_structure (pymob.inference.pyabc_backend.PyabcBackend property) posterior_draws_from_svi() (pymob.inference.numpyro_backend.NumpyroBackend method) posterior_predictions() (pymob.inference.numpyro_backend.NumpyroBackend method) (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.scipy_backend.ScipyBackend method) posterior_predictive_checks() (pymob.simulation.SimulationBase method) predict_observations() (pymob.inference.numpyro_backend.NumpyroBackend method) prepare_casestudy() (in module pymob.utils.store_file) prepare_casestudy_sbi() (in module pymob.utils.store_file) prepare_sbi() (in module pymob.utils.store_file) prepare_scenario() (in module pymob.utils.store_file) preprocess_parameters() (pymob.solvers.base.SolverBase method) (pymob.solvers.diffrax.JaxSolver method) preprocess_x_in() (pymob.solvers.base.SolverBase method) (pymob.solvers.diffrax.JaxSolver method) preprocess_y_0() (pymob.solvers.base.SolverBase method) (pymob.solvers.diffrax.JaxSolver method) preprocessing() (pymob.inference.numpyro_backend.NumpyroBackend static method) print() (pymob.sim.config.base.Config method) (pymob.sim.config.Config method), [1] prior (pymob.inference.numpyro_backend.NumpyroBackend attribute) (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute)

prior_parser() (pymob.inference.pyabc_backend.PyabcBackend method) prior_predictions() (pymob.inference.numpyro_backend.NumpyroBackend method) (pymob.inference.scipy_backend.ScipyBackend method) prior_predictive_checks() (pymob.simulation.SimulationBase method) ProbabilisticModel (class in pymob.inference.scipy_backend) Pyabc (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) PyabcBackend (class in pymob.inference.pyabc_backend) pymob module pymob.examples module pymob.examples.linear_regression module pymob.infer module pymob.inference module pymob.inference.numpyro_backend module pymob.inference.pyabc_backend module pymob.inference.pymoo_backend module pymob.inference.scipy_backend module pymob.prior_predictive_checks module pymob.sim module pymob.sim.base module pymob.sim.config module, [1] pymob.sim.config.base module pymob.sim.config.casestudy_registry module pymob.sim.config.parameters module pymob.sim.config.sections module pymob.sim.evaluator module pymob.sim.solvetools module pymob.simulate module pymob.solvers module pymob.solvers.analytic module pymob.solvers.base module pymob.solvers.diffrax module pymob.solvers.scipy module pymob.utils module pymob.utils.bayesian module pymob.utils.config module pymob.utils.errors module pymob.utils.help module pymob.utils.math_helpers module pymob.utils.misc module pymob.utils.plot_helpers module pymob.utils.store_file module pymob_version (pymob.sim.config.Casestudy attribute), [1], [2], [3] (pymob.sim.config.sections.Casestudy attribute), [1] PymobError PymobModel (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) Pymoo (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) PymooBackend (class in pymob.inference.pymoo_backend)

R

radius_interpolation() (in module pymob.solvers.base) random_state (pymob.inference.scipy_backend.ScipyBackend attribute) RandomVariable (class in pymob.sim.config), [1] (class in pymob.sim.config.parameters) read_config() (in module pymob.utils.config) (in module pymob.utils.store_file) read_settings() (in module pymob.utils.store_file) rect_interpolation() (in module pymob.solvers.base) Redis (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) register_case_study_config() (in module pymob.sim.config), [1] (in module pymob.sim.config.casestudy_registry) remove() (pymob.sim.config.Datastructure method), [1] (pymob.sim.config.Modelparameters method), [1] (pymob.sim.config.sections.Datastructure method) (pymob.sim.config.sections.Modelparameters method) reorder() (pymob.sim.config.Modelparameters method), [1] (pymob.sim.config.sections.Modelparameters method) repeat_func() (in module pymob.utils.misc) replace_na() (in module pymob.utils.misc) Report (class in pymob.sim.config), [1] (class in pymob.sim.config.sections)

report (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] report() (pymob.simulation.SimulationBase method) reroute_output_to_base() (in module pymob.utils.store_file) reshape_observations() (pymob.simulation.SimulationBase method) result (pymob.sim.evaluator.Evaluator attribute) results (pymob.sim.evaluator.Evaluator property) reverse() (pymob.inference.scipy_backend.ScipyErrorModel method) (pymob.inference.scipy_backend.ScipyPriorModel method) root (pymob.sim.config.Casestudy attribute), [1], [2], [3] (pymob.sim.config.sections.Casestudy attribute), [1] round_decimals_down() (in module pymob.utils.misc) round_to_nearest_multiple_of_y() (in module pymob.utils.math_helpers) rtol (pymob.sim.config.Jaxsolver attribute), [1] (pymob.sim.config.sections.Jaxsolver attribute) (pymob.solvers.diffrax.JaxSolver attribute) run() (pymob.inference.numpyro_backend.NumpyroBackend method) (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method) (pymob.inference.scipy_backend.ScipyBackend method) (pymob.simulation.SimulationBase method) run_mcmc() (pymob.inference.numpyro_backend.NumpyroBackend method) run_svi() (pymob.inference.numpyro_backend.NumpyroBackend static method)

S

sa_adapt_state_size (pymob.sim.config.Numpyro attribute), [1], [2], [3] (pymob.sim.config.sections.Numpyro attribute), [1] sample_distribution() (pymob.inference.scipy_backend.ScipyBackend method) sampler (pymob.inference.pyabc_backend.PyabcBackend property) (pymob.sim.config.Pyabc attribute), [1], [2], [3] (pymob.sim.config.sections.Pyabc attribute), [1] save() (pymob.sim.config.base.Config method) (pymob.sim.config.Config method), [1] save_observations() (pymob.simulation.SimulationBase method) scenario (pymob.sim.config.Casestudy attribute), [1], [2], [3] (pymob.sim.config.sections.Casestudy attribute), [1] scenario_file() (in module pymob.utils.store_file) scenario_path (pymob.sim.config.Casestudy property), [1] (pymob.sim.config.sections.Casestudy property) scenario_path_override (pymob.sim.config.Casestudy attribute), [1] (pymob.sim.config.sections.Casestudy attribute) ScipyBackend (class in pymob.inference.scipy_backend) ScipyDistribution (class in pymob.inference.scipy_backend) ScipyErrorModel (class in pymob.inference.scipy_backend) ScipyPriorModel (class in pymob.inference.scipy_backend) ScipyTransModel (class in pymob.inference.scipy_backend) seed (pymob.sim.config.sections.Simulation attribute), [1] (pymob.sim.config.Simulation attribute), [1], [2], [3] select_cluster() (pymob.inference.numpyro_backend.NumpyroBackend static method) sequential_filename_iterator() (in module pymob.utils.store_file) serialize() (in module pymob.utils.store_file) set_data_variable_bounds() (pymob.sim.config.DataVariable class method), [1] (pymob.sim.config.sections.DataVariable class method) set_option() (pymob.sim.config.base.Config method) (pymob.sim.config.Config method), [1] set_root() (pymob.sim.config.Casestudy class method), [1] (pymob.sim.config.sections.Casestudy class method) setup() (pymob.simulation.SimulationBase method) shapes_coordinates (pymob.solvers.base.SolverBase attribute) shapes_input_vars_coordinates (pymob.solvers.base.SolverBase attribute) shapes_parameter_coordinates (pymob.solvers.base.SolverBase attribute) Simulation (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) simulation (pymob.sim.config.base.Config attribute) (pymob.sim.config.Casestudy attribute), [1], [2], [3] (pymob.sim.config.Config attribute), [1] (pymob.sim.config.sections.Casestudy attribute), [1]

simulation_io_adapter() (in module pymob.utils.config) SimulationBase (class in pymob.simulation) SimulationBase.Report (class in pymob.simulation) smoothed_interpolation() (in module pymob.solvers.base) solve() (pymob.solvers.base.SolverBase method) (pymob.solvers.diffrax.JaxSolver method) solve_analytic_1d() (in module pymob.solvers.analytic) solve_ivp_1d() (in module pymob.solvers.scipy) solver (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.Simulation attribute), [1] solver_kwargs (pymob.solvers.base.SolverBase attribute) solver_post_processing (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.Simulation attribute), [1] Solverbase (class in pymob.sim.config), [1] (class in pymob.sim.config.sections) SolverBase (class in pymob.solvers.base) solverbase (pymob.sim.config.base.Config attribute) (pymob.sim.config.Config attribute), [1] spawn() (pymob.sim.evaluator.Evaluator method) stack_variables() (in module pymob.sim.base) step (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) store_results() (pymob.inference.numpyro_backend.NumpyroBackend method) (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method) store_sbi_simulations() (in module pymob.utils.store_file) string_to_datavar() (in module pymob.sim.config.sections) string_to_dict() (in module pymob.sim.config.sections) string_to_list() (in module pymob.sim.config.sections) string_to_param() (in module pymob.sim.config.sections) string_to_prior_dict() (in module pymob.sim.config.parameters) string_to_tuple() (in module pymob.sim.config.sections) subset_by_batch_dimension() (pymob.simulation.SimulationBase method) svi_iterations (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) svi_learning_rate (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) svi_posterior() (pymob.inference.numpyro_backend.NumpyroBackend method)

T

table_parameter_estimates (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) table_parameter_estimates_error_metric (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) table_parameter_estimates_exclude_vars (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) table_parameter_estimates_format (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) table_parameter_estimates_override_names (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) table_parameter_estimates_parameters_as_rows (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) table_parameter_estimates_significant_figures (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) table_parameter_estimates_with_batch_dim_vars (pymob.sim.config.Report attribute), [1] (pymob.sim.config.sections.Report attribute) take_mean() (in module pymob.utils.math_helpers)

test_batch_dim_consistency() (pymob.solvers.base.SolverBase method) test_matching_batch_dims() (pymob.solvers.base.SolverBase method) test_x_coordinates() (pymob.solvers.base.SolverBase method) thinning (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) throw_exception (pymob.sim.config.Jaxsolver attribute), [1], [2], [3] (pymob.sim.config.sections.Jaxsolver attribute), [1] (pymob.solvers.diffrax.JaxSolver attribute) to_arviz_idata() (pymob.inference.numpyro_backend.NumpyroBackend method) to_dict() (pymob.inference.pyabc_backend.Posterior method) to_nested_dict() (in module pymob.sim.config.sections) to_rv() (in module pymob.sim.config.parameters) to_xarray() (pymob.sim.config.Param method), [1] (pymob.sim.config.parameters.Param method) to_xarray_dataset() (in module pymob.utils.misc) total_average() (pymob.simulation.SimulationBase method) transform_prior_to_error_model() (pymob.inference.scipy_backend.ScipyTransModel method)

U

UndefinedNameFinder (class in pymob.sim.config.parameters) unit (pymob.sim.config.DataVariable attribute), [1] (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) (pymob.sim.config.sections.DataVariable attribute) unixify_path() (in module pymob.utils.store_file) unlist_attrs() (in module pymob.sim.base) unnest() (in module pymob.utils.store_file) update() (pymob.sim.config.sections.ParameterDict method)

user_defined_error_model (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute) user_defined_preprocessing (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1], [2], [3] (pymob.sim.config.sections.Numpyro attribute), [1] user_defined_probability_model (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute)

V

validate_model_input() (pymob.simulation.SimulationBase static method) value (pymob.sim.config.Param attribute), [1] (pymob.sim.config.parameters.Param attribute) value_dict (pymob.sim.config.Modelparameters property), [1] (pymob.sim.config.sections.Modelparameters property) var_dim_mapper (pymob.sim.config.Datastructure property), [1] (pymob.sim.config.sections.Datastructure property)

variable_mapper() (pymob.inference.pymoo_backend.PymooBackend method) variable_parser() (pymob.inference.pymoo_backend.PymooBackend method) verbose (pymob.sim.config.Pymoo attribute), [1], [2], [3] (pymob.sim.config.sections.Pymoo attribute), [1] version (pymob.sim.config.Casestudy attribute), [1], [2], [3] (pymob.sim.config.sections.Casestudy attribute), [1] visit_FunctionDef() (pymob.sim.config.parameters.UndefinedNameFinder method) visit_Name() (pymob.sim.config.parameters.UndefinedNameFinder method)

W

warmup (pymob.inference.numpyro_backend.NumpyroBackend property) (pymob.sim.config.Numpyro attribute), [1] (pymob.sim.config.sections.Numpyro attribute)

X

x (pymob.solvers.base.SolverBase attribute) x_dim (pymob.sim.config.sections.Solverbase attribute), [1] (pymob.sim.config.Solverbase attribute), [1], [2], [3] (pymob.solvers.base.SolverBase attribute) x_dimension (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.Simulation attribute), [1]

x_in (pymob.sim.config.sections.ModelParameterDict attribute), [1] (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.Simulation attribute), [1] x_in_jumps (pymob.solvers.diffrax.JaxSolver attribute) x_shape_batched (pymob.solvers.base.SolverBase attribute) xtol (pymob.sim.config.Pymoo attribute), [1] (pymob.sim.config.sections.Pymoo attribute)

Y

y0 (pymob.sim.config.sections.ModelParameterDict attribute), [1] (pymob.sim.config.sections.Simulation attribute) (pymob.sim.config.Simulation attribute), [1]