Index A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y A algortihm (pymob.sim.config.Pymoo attribute) all (pymob.sim.config.Datastructure property) (pymob.sim.config.Errormodel property) (pymob.sim.config.Modelparameters property) all_model_parameters (pymob.simulation.SimulationBase property) allowed_model_signature_arguments (pymob.sim.evaluator.Evaluator property) array2D_to_dataset() (pymob.simulation.SimulationBase method) ArrayParam (class in pymob.sim.config) B backend (pymob.sim.config.Inference attribute) benchmark() (pymob.simulation.SimulationBase method) C case_study (pymob.sim.config.Config attribute) (pymob.simulation.SimulationBase property) case_study_output() (in module pymob.utils.store_file) case_study_path (pymob.simulation.SimulationBase property) Casestudy (class in pymob.sim.config) catch_patterns() (in module pymob.utils.config) chains (pymob.sim.config.Numpyro attribute) check_dimensions() (pymob.simulation.SimulationBase method) check_scaled_results_feasibility() (pymob.simulation.SimulationBase method) cluster_chains() (in module pymob.utils.bayesian) combine_legends() (in module pymob.utils.plot_helpers) compute() (pymob.simulation.SimulationBase method) Config (class in pymob.sim.config) coordinates (pymob.simulation.SimulationBase property) cores (pymob.sim.config.Multiprocessing attribute) create_coordinates() (pymob.simulation.SimulationBase method) 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) (pymob.simulation.SimulationBase static method) create_directory() (pymob.sim.config.Config method) create_fname_date_ver() (in module pymob.utils.store_file) create_interpolated_coordinates() (pymob.simulation.SimulationBase method) create_interpolation() (in module pymob.sim.solvetools) create_random_integers() (pymob.simulation.SimulationBase method) cvtol (pymob.sim.config.Pymoo attribute) D data (pymob.sim.config.Casestudy attribute) data_path (pymob.sim.config.Casestudy property) (pymob.simulation.SimulationBase property) data_structure (pymob.sim.config.Config attribute) (pymob.simulation.SimulationBase property) data_variable_bounds (pymob.simulation.SimulationBase property) data_variables (pymob.sim.config.Datastructure property) (pymob.simulation.SimulationBase property) data_variables_max (pymob.sim.config.Datastructure property) data_variables_min (pymob.sim.config.Datastructure property) database_path (pymob.sim.config.Pyabc attribute) dataset_to_2Darray() (pymob.simulation.SimulationBase method) Datastructure (class in pymob.sim.config) datavar_to_string() (in module pymob.sim.config) DataVariable (class in pymob.sim.config) Date2Delta (class in pymob.utils.misc) dayTicks() (in module pymob.utils.misc) default_settings_path (pymob.sim.config.Casestudy property) deserialize() (in module pymob.utils.store_file) dict_to_string() (in module pymob.sim.config) dimdict (pymob.sim.config.Datastructure property) dimensionality (pymob.sim.evaluator.Evaluator property) dimensions (pymob.sim.config.Datastructure property) (pymob.sim.config.DataVariable attribute) (pymob.simulation.SimulationBase property) dimensions_evaluator (pymob.sim.config.DataVariable attribute) dispatch() (pymob.simulation.SimulationBase method) distance_function_parser() (pymob.inference.pymoo_backend.PymooBackend method) draw_seed() (pymob.simulation.SimulationBase method) draws (pymob.sim.config.Numpyro attribute) dump() (pymob.simulation.SimulationBase method) E enlist_attr() (in module pymob.sim.base) error_model (pymob.sim.config.Config attribute) (pymob.simulation.SimulationBase property) Errormodel (class in pymob.sim.config) errormsg() (in module pymob.utils.errors) evaluate() (pymob.simulation.SimulationBase method) Evaluator (class in pymob.sim.evaluator) evaluator_dim_order (pymob.sim.config.Datastructure property) (pymob.simulation.SimulationBase property) expand_grid() (in module pymob.utils.misc) extra_vars (pymob.sim.config.Inference attribute) F fixed (pymob.sim.config.Modelparameters property) fixed_model_parameters (pymob.simulation.SimulationBase property) flatten_parameter_dict() (in module pymob.simulation) FloatParam (class in pymob.sim.config) free (pymob.sim.config.ArrayParam attribute) (pymob.sim.config.FloatParam attribute) (pymob.sim.config.Modelparameters property) free_model_parameters (pymob.simulation.SimulationBase property) free_value_dict (pymob.sim.config.Modelparameters property) ftol (pymob.sim.config.Pymoo attribute) G gaussian_base_distribution (pymob.sim.config.Numpyro attribute) get_call_signature() (pymob.sim.evaluator.Evaluator 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.simulation) get_version() (in module pymob.utils.errors) go_to_case_studies() (in module pymob.utils.store_file) H history_id (pymob.sim.config.Redis attribute) hourTicks() (in module pymob.utils.misc) I import_casestudy_modules() (pymob.sim.config.Config method) import_optional_dependency() (in module pymob.utils.errors) import_package() (in module pymob.utils.store_file) import_simulation_from_case_study() (pymob.sim.config.Config method) infer_ode_states() (pymob.simulation.SimulationBase method) Inference (class in pymob.sim.config) inference (pymob.sim.config.Config attribute) inference_numpyro (pymob.sim.config.Config attribute) inference_pyabc (pymob.sim.config.Config attribute) inference_pyabc_redis (pymob.sim.config.Config attribute) inference_pymoo (pymob.sim.config.Config attribute) init_root (pymob.sim.config.Casestudy attribute) init_strategy (pymob.sim.config.Numpyro attribute) initialize() (pymob.simulation.SimulationBase method) input_file_paths (pymob.sim.config.Config property) (pymob.simulation.SimulationBase property) input_files (pymob.sim.config.Simulation attribute) (pymob.simulation.SimulationBase property) interactive() (pymob.simulation.SimulationBase method) invert_list_tuple() (in module pymob.utils.misc) is_iterable() (in module pymob.simulation) is_number() (in module pymob.utils.store_file) K kernel (pymob.sim.config.Numpyro attribute) L lambdify_expression() (in module pymob.utils.config) list_converter() (in module pymob.utils.store_file) list_to_string() (in module pymob.sim.config) load_functions() (pymob.simulation.SimulationBase method) load_modules() (pymob.simulation.SimulationBase method) load_results() (pymob.inference.pymoo_backend.PymooBackend method) logfile (pymob.sim.config.Casestudy attribute) logging (pymob.sim.config.Casestudy attribute) lookup() (in module pymob.utils.config) lookup_args() (in module pymob.utils.config) M mappar() (in module pymob.sim.solvetools) match_columns() (in module pymob.utils.misc) max (pymob.sim.config.ArrayParam attribute) (pymob.sim.config.DataVariable attribute) (pymob.sim.config.FloatParam attribute) max_nr_populations (pymob.sim.config.Pyabc attribute) (pymob.sim.config.Pymoo attribute) min (pymob.sim.config.ArrayParam attribute) (pymob.sim.config.DataVariable attribute) (pymob.sim.config.FloatParam attribute) min_eps_diff (pymob.sim.config.Pyabc attribute) minimum_epsilon (pymob.sim.config.Pyabc attribute) model (pymob.sim.config.Simulation attribute) (pymob.simulation.SimulationBase attribute) model_config (pymob.sim.config.ArrayParam attribute) (pymob.sim.config.Casestudy attribute) (pymob.sim.config.Config attribute) (pymob.sim.config.Datastructure attribute) (pymob.sim.config.DataVariable attribute) (pymob.sim.config.Errormodel attribute) (pymob.sim.config.FloatParam attribute) (pymob.sim.config.Inference attribute) (pymob.sim.config.Modelparameters attribute) (pymob.sim.config.Multiprocessing attribute) (pymob.sim.config.Numpyro attribute) (pymob.sim.config.Pyabc attribute) (pymob.sim.config.Pymoo attribute) (pymob.sim.config.Redis attribute) (pymob.sim.config.Simulation attribute) model_fields (pymob.sim.config.ArrayParam attribute) (pymob.sim.config.Casestudy attribute) (pymob.sim.config.Config attribute) (pymob.sim.config.Datastructure attribute) (pymob.sim.config.DataVariable attribute) (pymob.sim.config.Errormodel attribute) (pymob.sim.config.FloatParam attribute) (pymob.sim.config.Inference attribute) (pymob.sim.config.Modelparameters attribute) (pymob.sim.config.Multiprocessing attribute) (pymob.sim.config.Numpyro attribute) (pymob.sim.config.Pyabc attribute) (pymob.sim.config.Pymoo attribute) (pymob.sim.config.Redis attribute) (pymob.sim.config.Simulation attribute) model_id (pymob.sim.config.Redis attribute) model_parameter_dict (pymob.simulation.SimulationBase property) model_parameter_names (pymob.simulation.SimulationBase property) model_parameter_values (pymob.simulation.SimulationBase property) model_parameters (pymob.sim.config.Config attribute) (pymob.simulation.SimulationBase property) model_post_init() (pymob.sim.config.Config method) (pymob.sim.config.Multiprocessing method) (pymob.sim.config.Redis method) Modelparameters (class in pymob.sim.config) modeltype (pymob.sim.config.Simulation attribute) module pymob pymob.infer pymob.inference pymob.inference.pymoo_backend pymob.prior_predictive_checks pymob.sim pymob.sim.base pymob.sim.config pymob.sim.evaluator pymob.sim.solvetools pymob.simulate pymob.simulation 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) Multiprocessing (class in pymob.sim.config) multiprocessing (pymob.sim.config.Config attribute) N n_cores (pymob.sim.config.Multiprocessing property) (pymob.simulation.SimulationBase property) n_free (pymob.sim.config.Modelparameters property) n_free_parameters (pymob.simulation.SimulationBase property) n_objectives (pymob.sim.config.Inference attribute) (pymob.simulation.SimulationBase property) n_ode_states (pymob.sim.config.Simulation attribute) (pymob.simulation.SimulationBase property) n_predictions (pymob.sim.config.Inference attribute) (pymob.sim.config.Redis attribute) name (pymob.sim.config.ArrayParam attribute) (pymob.sim.config.Casestudy attribute) (pymob.sim.config.FloatParam attribute) Numpyro (class in pymob.sim.config) O objective (pymob.simulation.SimulationBase property) objective_function (pymob.sim.config.Inference attribute) objective_function() (pymob.simulation.SimulationBase method) objective_names (pymob.sim.config.Inference attribute) (pymob.simulation.SimulationBase property) observations (pymob.sim.config.Casestudy attribute) (pymob.simulation.SimulationBase property) opt() (in module pymob.utils.store_file) optimize() (pymob.inference.pymoo_backend.PymooBackend method) option_as_list() (pymob.simulation.SimulationBase static method) output (pymob.sim.config.Casestudy attribute) output_path (pymob.sim.config.Casestudy property) (pymob.simulation.SimulationBase property) P package (pymob.sim.config.Casestudy attribute) param_to_string() (in module pymob.sim.config) ParameterDict (class in pymob.sim.config) parameterize() (pymob.simulation.SimulationBase static method) parse_config_section() (in module pymob.utils.store_file) parse_input() (pymob.simulation.SimulationBase method) password (pymob.sim.config.Redis attribute) pivot_xarray() (in module pymob.utils.misc) plot (pymob.sim.config.Inference attribute) plot() (pymob.simulation.SimulationBase method) plot_hist() (in module pymob.utils.plot_helpers) plot_loghist() (in module pymob.utils.plot_helpers) plot_predictions() (pymob.inference.pymoo_backend.PymooBackend method) pop_key() (in module pymob.utils.misc) population_size (pymob.sim.config.Pyabc attribute) (pymob.sim.config.Pymoo attribute) port (pymob.sim.config.Redis attribute) post_processing() (pymob.inference.pymoo_backend.PymooBackend method) post_update() (pymob.sim.config.DataVariable 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) print() (pymob.sim.config.Config method) print_scaling_info() (pymob.simulation.SimulationBase method) prior (pymob.sim.config.ArrayParam attribute) (pymob.sim.config.FloatParam attribute) prior() (pymob.simulation.SimulationBase method) Pyabc (class in pymob.sim.config) pymob module pymob.infer module pymob.inference module pymob.inference.pymoo_backend module pymob.prior_predictive_checks module pymob.sim module pymob.sim.base module pymob.sim.config module pymob.sim.evaluator module pymob.sim.solvetools module pymob.simulate module pymob.simulation 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 Pymoo (class in pymob.sim.config) PymooBackend (class in pymob.inference.pymoo_backend) R read_config() (in module pymob.utils.config) (in module pymob.utils.store_file) read_settings() (in module pymob.utils.store_file) Redis (class in pymob.sim.config) refill_consumed_seeds() (pymob.simulation.SimulationBase method) reorder_dims() (pymob.simulation.SimulationBase method) repeat_func() (in module pymob.utils.misc) replace_na() (in module pymob.utils.misc) replicated (pymob.sim.config.Simulation attribute) reroute_output_to_base() (in module pymob.utils.store_file) reset_all_coordinates() (pymob.simulation.SimulationBase method) reset_coordinate() (pymob.simulation.SimulationBase method) reset_data_variable() (pymob.simulation.SimulationBase method) reshape_observations() (pymob.simulation.SimulationBase method) result (pymob.sim.evaluator.Evaluator attribute) results (pymob.sim.evaluator.Evaluator property) (pymob.simulation.SimulationBase property) results_scaled (pymob.simulation.SimulationBase property) results_to_df() (pymob.simulation.SimulationBase method) root (pymob.sim.config.Casestudy attribute) root_path (pymob.simulation.SimulationBase property) round_decimals_down() (in module pymob.utils.misc) round_to_nearest_multiple_of_y() (in module pymob.utils.math_helpers) run() (pymob.inference.pymoo_backend.PymooBackend method) (pymob.simulation.SimulationBase method) S sa_adapt_state_size (pymob.sim.config.Numpyro attribute) sampler (pymob.sim.config.Pyabc attribute) save() (pymob.sim.config.Config method) scale_() (pymob.simulation.SimulationBase method) scale_results() (pymob.simulation.SimulationBase method) scenario (pymob.sim.config.Casestudy attribute) (pymob.simulation.SimulationBase property) scenario_file() (in module pymob.utils.store_file) scenario_path (pymob.sim.config.Casestudy property) (pymob.simulation.SimulationBase property) seed (pymob.sim.config.Simulation attribute) sequential_filename_iterator() (in module pymob.utils.store_file) serialize() (in module pymob.utils.store_file) set_coordinates() (pymob.simulation.SimulationBase method) set_data_variable_bounds() (pymob.sim.config.DataVariable class method) set_inferer() (pymob.simulation.SimulationBase method) set_root() (pymob.sim.config.Casestudy class method) setup() (pymob.simulation.SimulationBase method) Simulation (class in pymob.sim.config) simulation (pymob.sim.config.Casestudy attribute) (pymob.sim.config.Config attribute) simulation_io_adapter() (in module pymob.utils.config) SimulationBase (class in pymob.simulation) solve() (pymob.sim.solvetools.SolverBase static method) solve_analytic_1d() (in module pymob.sim.solvetools) solve_ivp_1d() (in module pymob.sim.solvetools) solver (pymob.sim.config.Simulation attribute) (pymob.simulation.SimulationBase attribute) solver_post_processing (pymob.sim.config.Simulation attribute) (pymob.simulation.SimulationBase property) SolverBase (class in pymob.sim.solvetools) stack_variables() (in module pymob.sim.base) step (pymob.sim.config.ArrayParam attribute) (pymob.sim.config.FloatParam attribute) store_results() (pymob.inference.pymoo_backend.PymooBackend method) store_sbi_simulations() (in module pymob.utils.store_file) string_to_datavar() (in module pymob.sim.config) string_to_dict() (in module pymob.sim.config) string_to_list() (in module pymob.sim.config) string_to_param() (in module pymob.sim.config) svi_iterations (pymob.sim.config.Numpyro attribute) svi_learning_rate (pymob.sim.config.Numpyro attribute) T take_mean() (in module pymob.utils.math_helpers) thinning (pymob.sim.config.Numpyro attribute) to_xarray_dataset() (in module pymob.utils.misc) total_average() (pymob.simulation.SimulationBase method) U 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.ParameterDict method) update_parameters_dict() (in module pymob.simulation) user_defined_preprocessing (pymob.sim.config.Numpyro attribute) user_defined_probability_model (pymob.sim.config.Numpyro attribute) V validate() (pymob.simulation.SimulationBase method) value (pymob.sim.config.ArrayParam attribute) (pymob.sim.config.FloatParam attribute) value_dict (pymob.sim.config.Modelparameters property) var_dim_mapper (pymob.sim.config.Datastructure property) (pymob.simulation.SimulationBase property) variable_mapper() (pymob.inference.pymoo_backend.PymooBackend method) variable_parser() (pymob.inference.pymoo_backend.PymooBackend method) verbose (pymob.sim.config.Pymoo attribute) W warmup (pymob.sim.config.Numpyro attribute) X x_in (pymob.sim.config.Simulation attribute) xtol (pymob.sim.config.Pymoo attribute) Y y0 (pymob.sim.config.Simulation attribute)