Index

A

allowed_model_signature_arguments (pymob.sim.evaluator.Evaluator property)

array2D_to_dataset() (pymob.simulation.SimulationBase method) array_param_to_1d() (pymob.inference.pyabc_backend.PyabcBackend static method)

B

benchmark() (pymob.simulation.SimulationBase method)

C

case_study (pymob.simulation.SimulationBase property) case_study_output() (in module pymob.utils.store_file) case_study_path (pymob.simulation.SimulationBase property) catch_patterns() (in module pymob.utils.config) 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)

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_dim_index() (pymob.simulation.SimulationBase method) create_fname_date_ver() (in module pymob.utils.store_file) create_interpolation() (in module pymob.sim.solvetools) create_random_integers() (pymob.simulation.SimulationBase method) cvtol (pymob.inference.pymoo_backend.PymooBackend property)

D

data_path (pymob.simulation.SimulationBase property) data_structure (pymob.simulation.SimulationBase property) data_variable_bounds (pymob.simulation.SimulationBase property) data_variables (pymob.simulation.SimulationBase property) database (pymob.inference.pyabc_backend.PyabcBackend property) dataset_to_2Darray() (pymob.simulation.SimulationBase method) Date2Delta (class in pymob.utils.misc) dayTicks() (in module pymob.utils.misc)

deserialize() (in module pymob.utils.store_file) dimensionality (pymob.sim.evaluator.Evaluator property) dimensions (pymob.simulation.SimulationBase property) dispatch() (pymob.simulation.SimulationBase method) distance_function_parser() (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method) draw() (pymob.inference.pyabc_backend.Posterior method) draw_seed() (pymob.simulation.SimulationBase method) dump() (pymob.simulation.SimulationBase method)

E

enlist_attr() (in module pymob.sim.base) error_model (pymob.simulation.SimulationBase property) errormsg() (in module pymob.utils.errors) evaluate() (pymob.simulation.SimulationBase method)

Evaluator (class in pymob.sim.evaluator) evaluator_dim_order (pymob.simulation.SimulationBase property) expand_grid() (in module pymob.utils.misc) extra_vars (pymob.inference.pyabc_backend.PyabcBackend property)

F

fixed_model_parameters (pymob.simulation.SimulationBase property)

flatten_parameter_dict() (in module pymob.simulation) ftol (pymob.inference.pymoo_backend.PymooBackend property)

G

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.inference.pyabc_backend.PyabcBackend property)

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

I

import_optional_dependency() (in module pymob.utils.errors) import_package() (in module pymob.utils.store_file) infer_ode_states() (pymob.simulation.SimulationBase method) initialize() (pymob.simulation.SimulationBase method) input_file_paths (pymob.simulation.SimulationBase property)

input_files (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)

L

lambdify_expression() (in module pymob.utils.config) load_functions() (pymob.simulation.SimulationBase method) load_results() (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)

M

map_parameters() (pymob.inference.pyabc_backend.PyabcBackend static method) mappar() (in module pymob.sim.solvetools) match_columns() (in module pymob.utils.misc) max_nr_populations (pymob.inference.pyabc_backend.PyabcBackend property) (pymob.inference.pymoo_backend.PymooBackend property) 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.simulation.SimulationBase attribute) model_id (pymob.inference.pyabc_backend.PyabcBackend property) model_parameter_dict (pymob.simulation.SimulationBase property) model_parameter_names (pymob.simulation.SimulationBase property) model_parameter_values (pymob.simulation.SimulationBase property) model_parser() (pymob.inference.pyabc_backend.PyabcBackend method) module pymob pymob.infer pymob.inference pymob.inference.pyabc_backend pymob.inference.pymoo_backend pymob.prior_predictive_checks pymob.sim pymob.sim.base 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

N

n_cores (pymob.simulation.SimulationBase property) n_free_parameters (pymob.simulation.SimulationBase property) n_objectives (pymob.simulation.SimulationBase property)

n_ode_states (pymob.simulation.SimulationBase property) n_predictions (pymob.inference.pyabc_backend.PyabcBackend property) n_threads (pymob.simulation.SimulationBase property)

O

objective (pymob.simulation.SimulationBase property) objective_function() (pymob.simulation.SimulationBase method) objective_names (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_path (pymob.simulation.SimulationBase property)

P

param_to_prior() (pymob.inference.pyabc_backend.PyabcBackend static method) parameterize() (pymob.simulation.SimulationBase static method) parse_config_section() (in module pymob.utils.store_file) parse_input() (pymob.simulation.SimulationBase method) pivot_xarray() (in module pymob.utils.misc) plot() (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.simulation.SimulationBase method) plot_chains() (pymob.inference.pyabc_backend.PyabcBackend method) plot_function (pymob.inference.pyabc_backend.PyabcBackend property) 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) (pymob.inference.pymoo_backend.PymooBackend property) post_processing() (pymob.inference.pymoo_backend.PymooBackend method) Posterior (class in pymob.inference.pyabc_backend) posterior_coordinates (pymob.inference.pyabc_backend.PyabcBackend property) posterior_data_structure (pymob.inference.pyabc_backend.PyabcBackend property) posterior_predictions() (pymob.inference.pyabc_backend.PyabcBackend 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_config() (pymob.simulation.SimulationBase method) print_scaling_info() (pymob.simulation.SimulationBase method) prior() (pymob.simulation.SimulationBase method) prior_parser() (pymob.inference.pyabc_backend.PyabcBackend method) PyabcBackend (class in pymob.inference.pyabc_backend) pymob module pymob.infer module pymob.inference module

pymob.inference.pyabc_backend module pymob.inference.pymoo_backend module pymob.prior_predictive_checks module pymob.sim module pymob.sim.base 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 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_password (pymob.inference.pyabc_backend.PyabcBackend property) redis_port (pymob.inference.pyabc_backend.PyabcBackend property) 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) 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) (pymob.simulation.SimulationBase property) results_scaled (pymob.simulation.SimulationBase property) results_to_df() (pymob.simulation.SimulationBase method) 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.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method) (pymob.simulation.SimulationBase method)

S

sampler (pymob.inference.pyabc_backend.PyabcBackend property) scale_() (pymob.simulation.SimulationBase method) scale_results() (pymob.simulation.SimulationBase method) scenario (pymob.simulation.SimulationBase property) scenario_file() (in module pymob.utils.store_file) scenario_path (pymob.simulation.SimulationBase property) seed (pymob.inference.pymoo_backend.PymooBackend property) (pymob.simulation.SimulationBase property) sequential_filename_iterator() (in module pymob.utils.store_file) serialize() (in module pymob.utils.store_file)

set_free_model_parameters() (pymob.simulation.SimulationBase method) set_inferer() (pymob.simulation.SimulationBase method) simulation_io_adapter() (in module pymob.utils.config) SimulationBase (class in pymob.simulation) solve() (pymob.sim.solvetools.SolverBase static method) solver_post_processing (pymob.simulation.SimulationBase property) SolverBase (class in pymob.sim.solvetools) stack_variables() (in module pymob.sim.base) store_results() (pymob.inference.pyabc_backend.PyabcBackend method) (pymob.inference.pymoo_backend.PymooBackend method) store_sbi_simulations() (in module pymob.utils.store_file)

T

take_mean() (in module pymob.utils.math_helpers) to_dict() (pymob.inference.pyabc_backend.Posterior method)

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_parameters_dict() (in module pymob.simulation)

V

validate() (pymob.simulation.SimulationBase method) variable_mapper() (pymob.inference.pymoo_backend.PymooBackend method)

variable_parser() (pymob.inference.pymoo_backend.PymooBackend method) verbose (pymob.inference.pymoo_backend.PymooBackend property)

X

xtol (pymob.inference.pymoo_backend.PymooBackend property)