Index

A

adapt_state_size (pymob.inference.numpyro_backend.NumpyroBackend property) allowed_model_signature_arguments (pymob.sim.evaluator.Evaluator property)

array_param_to_1d() (pymob.inference.pyabc_backend.PyabcBackend static method) atol (pymob.solvers.diffrax.JaxSolver attribute)

B

batch_dimension (pymob.solvers.base.SolverBase attribute)

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

C

calculate_log_likelihood() (pymob.inference.numpyro_backend.NumpyroBackend method) case_study_output() (in module pymob.utils.store_file) 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) check_dimensions() (pymob.simulation.SimulationBase method) check_gradients() (pymob.inference.numpyro_backend.NumpyroBackend method) check_log_likelihood() (pymob.inference.numpyro_backend.NumpyroBackend method) 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) 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) 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_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)

D

data_structure_and_dimensionality (pymob.solvers.base.SolverBase attribute) data_variables (pymob.solvers.base.SolverBase attribute) database (pymob.inference.pyabc_backend.PyabcBackend property) Date2Delta (class in pymob.utils.misc) dayTicks() (in module pymob.utils.misc) dcoeff (pymob.solvers.diffrax.JaxSolver attribute) deserialize() (in module pymob.utils.store_file) diffrax_solver (pymob.solvers.diffrax.JaxSolver attribute) dimension_coords (pymob.simulation.SimulationBase property) dimension_sizes (pymob.solvers.base.SolverBase attribute) dimensionality (pymob.sim.evaluator.Evaluator property) dimensions (pymob.solvers.base.SolverBase 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) 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) 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) ErrorModelFunction (class in pymob.inference.numpyro_backend) errormsg() (in module pymob.utils.errors) evaluate() (pymob.simulation.SimulationBase method)

Evaluator (class in pymob.sim.evaluator) exclude_kwargs_model (pymob.solvers.base.SolverBase attribute) exclude_kwargs_postprocessing (pymob.solvers.base.SolverBase attribute) expand_grid() (in module pymob.utils.misc) export() (pymob.simulation.SimulationBase method)

F

forward() (pymob.inference.scipy_backend.ScipyErrorModel method) (pymob.inference.scipy_backend.ScipyPriorModel method)

from_directory() (pymob.simulation.SimulationBase class method)

G

gaussian_base_distribution (pymob.inference.numpyro_backend.NumpyroBackend property) generate_transform() (pymob.inference.numpyro_backend.NumpyroBackend static method) get_call_signature() (pymob.sim.evaluator.Evaluator method) 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)

H

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

I

icoeff (pymob.solvers.diffrax.JaxSolver attribute) idata (pymob.inference.pymoo_backend.PymooBackend attribute) import_optional_dependency() (in module pymob.utils.errors) import_package() (in module pymob.utils.store_file) indices (pymob.solvers.base.SolverBase attribute)

inference_model (pymob.inference.scipy_backend.ScipyBackend attribute) init_strategy (pymob.inference.numpyro_backend.NumpyroBackend property) initialize() (pymob.simulation.SimulationBase method) 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.solvers.diffrax)

jump_interpolation() (in module pymob.solvers.base)

K

kernel (pymob.inference.numpyro_backend.NumpyroBackend property)

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) load_results() (pymob.inference.numpyro_backend.NumpyroBackend method) (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method)

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_nr_populations (pymob.inference.pyabc_backend.PyabcBackend property) max_steps (pymob.solvers.diffrax.JaxSolver attribute) mean() (pymob.inference.pyabc_backend.Posterior method) min_eps_diff (pymob.inference.pyabc_backend.PyabcBackend property) minimum_epsilon (pymob.inference.pyabc_backend.PyabcBackend property) model (pymob.solvers.base.SolverBase attribute) model() (pymob.inference.numpyro_backend.NumpyroBackend method) model_parser() (pymob.inference.pyabc_backend.PyabcBackend method) 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 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

N

n_ode_states (pymob.solvers.base.SolverBase attribute) NumpyroBackend (class in pymob.inference.numpyro_backend)

NumpyroDistribution (class in pymob.inference.numpyro_backend) nuts_posterior() (pymob.inference.numpyro_backend.NumpyroBackend method)

O

observation_parser() (pymob.inference.numpyro_backend.NumpyroBackend method) 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)

P

param_to_prior() (pymob.inference.pyabc_backend.PyabcBackend static method) parameter_converter() (pymob.inference.numpyro_backend.NumpyroDistribution static method) (pymob.inference.scipy_backend.ScipyDistribution static method) parameter_dims (pymob.solvers.base.SolverBase attribute) parameterize() (pymob.simulation.SimulationBase static method) parameters (pymob.sim.evaluator.Evaluator property) 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) pcoeff (pymob.solvers.diffrax.JaxSolver attribute) pivot_xarray() (in module pymob.utils.misc) 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_predictions() (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method) pop_key() (in module pymob.utils.misc) population_size (pymob.inference.pyabc_backend.PyabcBackend property) post_processing (pymob.solvers.base.SolverBase attribute) post_processing() (pymob.inference.pymoo_backend.PymooBackend 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) prior (pymob.inference.numpyro_backend.NumpyroBackend 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) 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 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 PymobError PymooBackend (class in pymob.inference.pymoo_backend)

R

radius_interpolation() (in module pymob.solvers.base) random_state (pymob.inference.scipy_backend.ScipyBackend attribute) 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) repeat_func() (in module pymob.utils.misc) replace_na() (in module pymob.utils.misc) 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) round_decimals_down() (in module pymob.utils.misc) round_to_nearest_multiple_of_y() (in module pymob.utils.math_helpers) rtol (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

sample_distribution() (pymob.inference.scipy_backend.ScipyBackend method) sampler (pymob.inference.pyabc_backend.PyabcBackend property) save_observations() (pymob.simulation.SimulationBase method) scenario_file() (in module pymob.utils.store_file) 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) 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) 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_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_kwargs (pymob.solvers.base.SolverBase attribute) SolverBase (class in pymob.solvers.base) spawn() (pymob.sim.evaluator.Evaluator method) stack_variables() (in module pymob.sim.base) 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) subset_by_batch_dimension() (pymob.simulation.SimulationBase method) svi_iterations (pymob.inference.numpyro_backend.NumpyroBackend property) svi_learning_rate (pymob.inference.numpyro_backend.NumpyroBackend property) svi_posterior() (pymob.inference.numpyro_backend.NumpyroBackend method)

T

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)

throw_exception (pymob.solvers.diffrax.JaxSolver attribute) to_arviz_idata() (pymob.inference.numpyro_backend.NumpyroBackend method) to_dict() (pymob.inference.pyabc_backend.Posterior 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

unixify_path() (in module pymob.utils.store_file) unlist_attrs() (in module pymob.sim.base) unnest() (in module pymob.utils.store_file)

user_defined_error_model (pymob.inference.numpyro_backend.NumpyroBackend property) user_defined_preprocessing (pymob.inference.numpyro_backend.NumpyroBackend property) user_defined_probability_model (pymob.inference.numpyro_backend.NumpyroBackend property)

V

validate_model_input() (pymob.simulation.SimulationBase static method)

variable_mapper() (pymob.inference.pymoo_backend.PymooBackend method) variable_parser() (pymob.inference.pymoo_backend.PymooBackend method)

W

warmup (pymob.inference.numpyro_backend.NumpyroBackend property)

X

x (pymob.solvers.base.SolverBase attribute) x_dim (pymob.solvers.base.SolverBase attribute)

x_in_jumps (pymob.solvers.diffrax.JaxSolver attribute) x_shape_batched (pymob.solvers.base.SolverBase attribute)