Index

A

align_params_to_qois() (in module uq_physicell.model_analysis.utils) analyze_convergence() (uq_physicell.bo.bo_context.CalibrationContext method)

apply_autoencoder_to_qois() (in module uq_physicell.model_analysis.utils) apply_pca_to_qois() (in module uq_physicell.model_analysis.utils)

C

calculate_qoi_from_db_file() (in module uq_physicell.model_analysis.utils) calculate_qoi_statistics() (in module uq_physicell.model_analysis.utils) CalibrationContext (class in uq_physicell.abc.abc_context) (class in uq_physicell.bo.bo_context) cancelled() (uq_physicell.model_analysis.ma_context.ModelAnalysisContext method) Chebyshev() (in module uq_physicell.utils.distances)

check_convergence() (uq_physicell.abc.abc_context.CalibrationContext method) check_db_consistency() (in module uq_physicell.database.ma_db) check_simulations_db() (in module uq_physicell.database.ma_db) create_model_wrapper() (uq_physicell.abc.abc_context.CalibrationContext method) create_structure() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db)

D

default_aggregation_func() (uq_physicell.bo.bo_context.CalibrationContext method)

default_run_single_replicate() (uq_physicell.bo.bo_context.CalibrationContext method)

E

evaluate_params() (uq_physicell.bo.bo_context.CalibrationContext method)

F

find_optimal_qoi_set() (in module uq_physicell.model_analysis.utils)

G

generate_and_evaluate_samples() (uq_physicell.bo.bo_context.CalibrationContext method) generate_initial_samples_from_db() (uq_physicell.bo.bo_context.CalibrationContext method) generate_samples() (uq_physicell.model_analysis.ma_context.ModelAnalysisContext method) get_active_processes_info() (uq_physicell.PhysiCell_Model method) get_database_type() (in module uq_physicell.database.ma_db) get_global_SA_parameters() (in module uq_physicell.model_analysis.sensitivity_analysis)

get_local_SA_parameters() (in module uq_physicell.model_analysis.sensitivity_analysis) get_mean_std_qois() (in module uq_physicell.model_analysis.utils) get_qoi_from_db_file() (in module uq_physicell.model_analysis.utils) get_relative_mcse_qois() (in module uq_physicell.model_analysis.utils) get_sa_results() (in module uq_physicell.model_analysis.sensitivity_analysis) get_summary_statistics_qois() (in module uq_physicell.model_analysis.utils)

I

include_additional_metadata() (uq_physicell.abc.abc_context.CalibrationContext method) info() (uq_physicell.PhysiCell_Model method) insert_gp_models() (in module uq_physicell.database.bo_db) insert_metadata() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db) insert_output() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db)

insert_param_space() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db) insert_qois() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db) insert_samples() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db)

L

load_data_unserialized() (in module uq_physicell.database.ma_db) load_existing_data() (uq_physicell.bo.bo_context.CalibrationContext method) load_gp_models() (in module uq_physicell.database.bo_db) load_metadata() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db) load_or_create_database() (uq_physicell.abc.abc_context.CalibrationContext method) load_output() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db)

load_parameter_space() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db) load_qois() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db) load_samples() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db) load_structure() (in module uq_physicell.database.bo_db) (in module uq_physicell.database.ma_db)

M

Manhattan() (in module uq_physicell.utils.distances) mcds_list_to_qoi_df_for_calib() (in module uq_physicell.model_analysis.utils) mcds_list_to_qoi_df_for_sa() (in module uq_physicell.model_analysis.utils) mcds_list_to_qoi_df_long() (in module uq_physicell.model_analysis.utils) ModelAnalysisContext (class in uq_physicell.model_analysis.ma_context) module uq_physicell uq_physicell.abc.abc_context uq_physicell.bo.bo_context uq_physicell.bo.plots uq_physicell.database.bo_db uq_physicell.database.ma_db uq_physicell.model_analysis.ma_context uq_physicell.model_analysis.samplers uq_physicell.model_analysis.sensitivity_analysis uq_physicell.model_analysis.utils uq_physicell.utils.distances uq_physicell.utils.model_wrapper uq_physicell.utils.sumstats

multi_objective_bayesian_optimization() (in module uq_physicell.bo.bo_context)

O

OAT_analyze() (in module uq_physicell.model_analysis.sensitivity_analysis)

P

PhysiCell_Model (class in uq_physicell) plot_parameter_space() (in module uq_physicell.bo.plots) plot_parameter_space_db() (in module uq_physicell.bo.plots) plot_parameter_vs_fitness() (in module uq_physicell.bo.plots)

plot_parameter_vs_fitness_db() (in module uq_physicell.bo.plots) plot_pareto_front() (in module uq_physicell.bo.plots) plot_qoi_param() (in module uq_physicell.bo.plots) plot_qoi_param_db() (in module uq_physicell.bo.plots)

Q

qoi_func_persistent_homology() (in module uq_physicell.utils.sumstats)

qoi_func_radial_density_summary() (in module uq_physicell.utils.sumstats) qoi_func_relational_ph() (in module uq_physicell.utils.sumstats)

R

recreate_qoi_functions() (in module uq_physicell.utils.sumstats) recursive_feature_elimination() (in module uq_physicell.model_analysis.utils) regression_accuracy_parameters() (in module uq_physicell.model_analysis.utils) remove_io_folders() (uq_physicell.PhysiCell_Model method) request_cancellation() (uq_physicell.model_analysis.ma_context.ModelAnalysisContext method) run() (uq_physicell.model_analysis.ma_context.ModelAnalysisContext method) run_abc_calibration() (in module uq_physicell.abc.abc_context) run_bayesian_optimization() (in module uq_physicell.bo.bo_context) run_calibration() (uq_physicell.abc.abc_context.CalibrationContext method)

run_global_sa() (in module uq_physicell.model_analysis.sensitivity_analysis) run_global_sampler() (in module uq_physicell.model_analysis.samplers) run_local_sa() (in module uq_physicell.model_analysis.sensitivity_analysis) run_local_sampler() (in module uq_physicell.model_analysis.samplers) run_replicate() (in module uq_physicell.utils.model_wrapper) run_replicate_serializable() (in module uq_physicell.utils.model_wrapper) run_simulation_subprocess() (uq_physicell.PhysiCell_Model method) run_simulations() (in module uq_physicell.model_analysis.ma_context) RunModel() (uq_physicell.PhysiCell_Model method)

S

safe_call_qoi_function() (in module uq_physicell.utils.sumstats) save_results_to_db() (uq_physicell.bo.bo_context.CalibrationContext method) set_samples() (uq_physicell.model_analysis.ma_context.ModelAnalysisContext method) setup_abc_smc() (uq_physicell.abc.abc_context.CalibrationContext method) setup_distance_function() (uq_physicell.abc.abc_context.CalibrationContext method) setup_epsilon_function() (uq_physicell.abc.abc_context.CalibrationContext method) setup_population_strategy() (uq_physicell.abc.abc_context.CalibrationContext method)

setup_sampler() (uq_physicell.abc.abc_context.CalibrationContext method) setup_transition_function() (uq_physicell.abc.abc_context.CalibrationContext method) single_objective_bayesian_optimization() (in module uq_physicell.bo.bo_context) summ_func_FinalPopLiveDead() (in module uq_physicell.utils.sumstats) summ_func_TimeSeriesPopLiveDead() (in module uq_physicell.utils.sumstats) summary_function() (in module uq_physicell.utils.sumstats) SumSquaredDifferences() (in module uq_physicell.utils.distances)

T

terminate_all_simulations() (uq_physicell.PhysiCell_Model method)

U

update_bo_iterations() (uq_physicell.bo.bo_context.CalibrationContext method) uq_physicell module uq_physicell.abc.abc_context module uq_physicell.bo.bo_context module uq_physicell.bo.plots module uq_physicell.database.bo_db module uq_physicell.database.ma_db module

uq_physicell.model_analysis.ma_context module uq_physicell.model_analysis.samplers module uq_physicell.model_analysis.sensitivity_analysis module uq_physicell.model_analysis.utils module uq_physicell.utils.distances module uq_physicell.utils.model_wrapper module uq_physicell.utils.sumstats module