Index

A

add_samples() (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) adjust_iteration() (idmtools_calibra.utilities.resume_manager.ResumeManager method) adjust_iteration_step() (idmtools_calibra.utilities.resume_manager.ResumeManager method)

ALL (idmtools_calibra.resamplers.calibration_point.CalibrationPoint attribute) all_results (idmtools_calibra.plotters.base_plotter.BasePlotter property) analyze (idmtools_calibra.process_state.StatusPoint attribute) analyze_iteration() (idmtools_calibra.iteration_state.IterationState method) analyze_step() (idmtools_calibra.iteration_state.IterationState method) analyzer_list (idmtools_calibra.calib_manager.CalibManager property) assign_rep() (idmtools_calibra.algorithms.gpc.GPC method)

B

backup_calibration() (idmtools_calibra.calib_manager.CalibManager method) (idmtools_calibra.utilities.resume_manager.ResumeManager method) BaseCalibrationAnalyzer (class in idmtools_calibra.analyzers.base_calibration_analyzer) BasePlotter (class in idmtools_calibra.plotters.base_plotter) BaseResampler (class in idmtools_calibra.resamplers.base_resampler) beta_binomial() (in module idmtools_calibra.utilities.ll_calculators)

beta_binomial_pandas() (in module idmtools_calibra.utilities.ll_calculators) bin2np() (in module idmtools_calibra.utilities.parsers.bin2np) build_number() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) by_param() (idmtools_calibra.utilities.prior.MultiVariatePrior class method) by_range() (idmtools_calibra.utilities.prior.MultiVariatePrior class method)

C

cache() (idmtools_calibra.analyzers.base_calibration_analyzer.BaseCalibrationAnalyzer method) cache_calibration() (idmtools_calibra.calib_manager.CalibManager method) cached_property (class in idmtools_calibra.utilities.distro) calculate_weighted_covariance() (idmtools_calibra.algorithms.imis.IMIS method) CalibManager (class in idmtools_calibra.calib_manager) calibration_path (idmtools_calibra.calib_manager.CalibManager property) CalibrationParameter (class in idmtools_calibra.resamplers.calibration_point) CalibrationPoint (class in idmtools_calibra.resamplers.calibration_point) CalibrationPoints (class in idmtools_calibra.resamplers.calibration_points) CalibSite (class in idmtools_calibra.calib_site) cancel() (idmtools_calibra.iteration_state.IterationState method) cast_number() (in module idmtools_calibra.utilities.encoding) check_location() (idmtools_calibra.utilities.resume_manager.ResumeManager method) choose_and_clamp_hypersphere_samples_for_iteration() (idmtools_calibra.algorithms.optim_tool.OptimTool method) choose_and_clamp_samples_for_iteration() (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) choose_initial_samples() (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) choose_next_point_samples() (idmtools_calibra.algorithms.imis.IMIS method) choose_samples_via_gradient_ascent() (idmtools_calibra.algorithms.optim_tool.OptimTool method) choose_samples_via_history_matching() (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) clamp() (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) cleanup() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) (idmtools_calibra.calib_manager.CalibManager method) (idmtools_calibra.plotters.optim_tool_pbnb_plotter.OptimToolPBnBPlotter method) (idmtools_calibra.plotters.optim_tool_plotter.OptimToolPlotter method) (idmtools_calibra.plotters.optim_tool_spsa_plotter.OptimToolSPSAPlotter method) (idmtools_calibra.plotters.separatrix_bhm_plotter.SeparatrixBHMPlotter method) (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method)

cleanup_plot() (idmtools_calibra.plotters.optim_tool_plotter.OptimToolPlotter method) (idmtools_calibra.plotters.separatrix_bhm_plotter.SeparatrixBHMPlotter method) cleanup_plot_by_analyzers() (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method) cleanup_plot_for_all() (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method) cleanup_plot_for_best() (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method) codename() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) combine_by_site() (idmtools_calibra.plotters.base_plotter.BasePlotter static method) commission (idmtools_calibra.process_state.StatusPoint attribute) commission_iteration() (idmtools_calibra.iteration_state.IterationState method) commission_step() (idmtools_calibra.iteration_state.IterationState method) compare() (idmtools_calibra.analyzers.rmse_analyzer.RMSEAnalyzer method) compute_fisher_inf_matrix() (in module idmtools_calibra.algorithms.fisher_inf_matrix) constrain_sample() (in module idmtools_calibra.calib_base_app) CramerRaoResampler (class in idmtools_calibra.resamplers.cramer_rao_resampler) create_calibration() (idmtools_calibra.calib_manager.CalibManager method) create_iteration_state() (idmtools_calibra.calib_manager.CalibManager method) cSubRegion (class in idmtools_calibra.algorithms.pbnb.c_sub_region)

D

default() (idmtools_calibra.utilities.encoding.GeneralEncoder method) (idmtools_calibra.utilities.encoding.NumpyEncoder method) (idmtools_calibra.utilities.parsers.np2json.NumpyAwareJSONEncoder method) default_experiment_builder_function() (idmtools_calibra.calib_manager.CalibManager method) define_kernel() (idmtools_calibra.algorithms.gpc.GPC method) delete() (idmtools_calibra.calib_manager.CalibManager method) dict2json() (in module idmtools_calibra.utilities.parsers.JSON) dict2pd() (in module idmtools_calibra.utilities.parsers.dict2pd) directory (idmtools_calibra.plotters.likelihood_plotter.LikelihoodPlotter property) (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter property)

dirichlet_multinomial() (in module idmtools_calibra.utilities.ll_calculators) dirichlet_multinomial_pandas() (in module idmtools_calibra.utilities.ll_calculators) dirichlet_single() (in module idmtools_calibra.utilities.ll_calculators) distro_release_attr() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) distro_release_info() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) div0() (in module idmtools_calibra.algorithms.fisher_inf_matrix) done (idmtools_calibra.process_state.StatusPoint attribute) DYNAMIC (idmtools_calibra.resamplers.calibration_point.CalibrationPoint attribute)

E

end_condition() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method)

ep_predict() (idmtools_calibra.algorithms.gpc.GPC method) euclidean_distance() (in module idmtools_calibra.utilities.ll_calculators) euclidean_distance_pandas() (in module idmtools_calibra.utilities.ll_calculators) evaluate() (idmtools_calibra.algorithms.gpc.GPC method) expectation_propagation() (idmtools_calibra.algorithms.gpc.GPC method)

F

filter_generator() (in module idmtools_calibra.utilities.parsers.bin2np) finalize_calibration() (idmtools_calibra.calib_manager.CalibManager method) find_posterior_mode() (idmtools_calibra.algorithms.gpc.GPC method) finished() (idmtools_calibra.iteration_state.IterationState method) from_bytes() (idmtools_calibra.output.spatial_output.SpatialOutput class method) from_calibration_parameter() (idmtools_calibra.resamplers.calibration_point.CalibrationParameter class method) from_config() (idmtools_calibra.algorithms.gpc.GPC class method) from_dict() (idmtools_calibra.algorithms.gpc.GPC class method) (idmtools_calibra.resamplers.calibration_point.CalibrationParameter class method) (idmtools_calibra.resamplers.calibration_point.CalibrationPoint class method) (idmtools_calibra.utilities.parameter_set.ParameterSet class method) from_file() (idmtools_calibra.iteration_state.IterationState class method) from_range() (idmtools_calibra.utilities.prior.SampleFunctionContainer class method) from_tuple() (idmtools_calibra.utilities.prior.SampleFunctionContainer class method) fun_ci_builder() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_elite_indicator() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_generate_samples_from_df() (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method)

fun_maintaining_indicator() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_maintaining_labeler() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_order_region() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_order_subregion() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_plot2D() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_probability_branching_and_bound() (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) fun_pruning_indicator() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_pruning_labeler() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_quantile_update() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_reg_branching() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_replication_update() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_results_organizer_deterministic() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_results_organizer_noise() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_sample_points_generator_deterministic() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_sample_points_generator_noise() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) fun_worst_indicator() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions) func_wrapper() (idmtools_calibra.algorithms.gpc.GPC static method) functions (idmtools_calibra.utilities.prior.MultiVariatePrior property)

G

gamma_poisson() (in module idmtools_calibra.utilities.ll_calculators) gamma_poisson_pandas() (in module idmtools_calibra.utilities.ll_calculators) GeneralEncoder (class in idmtools_calibra.utilities.encoding) generate_ll_all() (in module idmtools_calibra.utilities.ll_all_generator) generate_perturbed_points() (idmtools_calibra.resamplers.random_perturbation_resampler.RandomPerturbationResampler method) generate_samples_from_df() (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) generate_variables_from_data() (idmtools_calibra.algorithms.imis.IMIS method) GenericIterativeNextPoint (class in idmtools_calibra.algorithms.generic_iterative_next_point) get_analyzer_data() (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method) get_analyzers() (idmtools_calibra.calib_site.CalibSite method) (idmtools_calibra.rmse_site.RMSESiteSingleChannel method) get_attribute() (idmtools_calibra.resamplers.calibration_point.CalibrationPoint method) get_bins() (idmtools_calibra.utilities.prior.SampleRange method) get_bins_for_summary_grouping() (in module idmtools_calibra.utilities.parsers.malaria_summary) get_calib_manager() (in module idmtools_calibra.cli.utils) get_calibrated_points() (idmtools_calibra.resample_manager.ResampleManager method) get_even_spaced_samples() (idmtools_calibra.utilities.prior.SampleFunctionContainer method) get_final_samples() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) get_grouping_for_summary_channel() (in module idmtools_calibra.utilities.parsers.malaria_summary) get_iteration_directory() (idmtools_calibra.plotters.base_plotter.BasePlotter method) get_last_iteration() (idmtools_calibra.calib_manager.CalibManager method) get_next_samples_for_iteration() (idmtools_calibra.algorithms.imis.IMIS method) get_param_names() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method)

get_parameter() (idmtools_calibra.resamplers.calibration_point.CalibrationPoint method) get_parameter_sets_with_likelihoods() (idmtools_calibra.calib_manager.CalibManager method) (idmtools_calibra.iteration_state.IterationState method) get_plot_directory() (idmtools_calibra.plotters.base_plotter.BasePlotter method) get_r() (idmtools_calibra.algorithms.optim_tool.OptimTool static method) get_reference_data() (idmtools_calibra.calib_site.CalibSite method) (idmtools_calibra.rmse_site.RMSESiteSingleChannel method) get_results_to_cache() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) get_sample_function() (idmtools_calibra.utilities.prior.SampleRange method) get_samples_for_iteration() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) get_setup_functions() (idmtools_calibra.calib_site.CalibSite method) (idmtools_calibra.rmse_site.RMSESiteSingleChannel method) get_site_analyzer() (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method) get_state() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) get_xlim() (idmtools_calibra.utilities.prior.SampleRange method) go() (in module idmtools_calibra.calib_base_app) GPC (class in idmtools_calibra.algorithms.gpc)

I

id() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) idmtools_calibra module idmtools_calibra.algorithms module idmtools_calibra.algorithms.fisher_inf_matrix module idmtools_calibra.algorithms.generic_iterative_next_point module idmtools_calibra.algorithms.gpc module idmtools_calibra.algorithms.imis module idmtools_calibra.algorithms.next_point_algorithm module idmtools_calibra.algorithms.optim_tool module idmtools_calibra.algorithms.optim_tools_pspo module idmtools_calibra.algorithms.optim_tools_spsa module idmtools_calibra.algorithms.pbnb module idmtools_calibra.algorithms.pbnb.c_sub_region module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions module idmtools_calibra.algorithms.pbnb.m_intial_paramters_setting module idmtools_calibra.algorithms.pbnb.optim_tool_pbnb module idmtools_calibra.algorithms.separatrix_bhm module idmtools_calibra.analyzers module idmtools_calibra.analyzers.base_calibration_analyzer module idmtools_calibra.analyzers.rmse_analyzer module idmtools_calibra.calib_base_app module idmtools_calibra.calib_manager module idmtools_calibra.calib_site module idmtools_calibra.cli module idmtools_calibra.cli.commands module idmtools_calibra.cli.utils module idmtools_calibra.iteration_state module idmtools_calibra.output module idmtools_calibra.output.spatial_output module idmtools_calibra.plotters module idmtools_calibra.plotters.base_plotter module idmtools_calibra.plotters.likelihood_plotter module idmtools_calibra.plotters.optim_tool_pbnb_plotter module idmtools_calibra.plotters.optim_tool_plotter module idmtools_calibra.plotters.optim_tool_spsa_plotter module idmtools_calibra.plotters.separatrix_bhm_plotter module

idmtools_calibra.plotters.site_data_plotter module idmtools_calibra.process_state module idmtools_calibra.resample_manager module idmtools_calibra.resamplers module idmtools_calibra.resamplers.base_resampler module idmtools_calibra.resamplers.calibration_point module idmtools_calibra.resamplers.calibration_points module idmtools_calibra.resamplers.cramer_rao_resampler module idmtools_calibra.resamplers.random_perturbation_resampler module idmtools_calibra.rmse_site module idmtools_calibra.singularity_json_python_task module idmtools_calibra.utilities module idmtools_calibra.utilities.display module idmtools_calibra.utilities.distro module idmtools_calibra.utilities.encoding module idmtools_calibra.utilities.helper module idmtools_calibra.utilities.ll_all_generator module idmtools_calibra.utilities.ll_calculators module idmtools_calibra.utilities.mod_fn module idmtools_calibra.utilities.parameter_set module idmtools_calibra.utilities.parsers module idmtools_calibra.utilities.parsers.bin2np module idmtools_calibra.utilities.parsers.dict2pd module idmtools_calibra.utilities.parsers.JSON module idmtools_calibra.utilities.parsers.malaria_summary module idmtools_calibra.utilities.parsers.np2json module idmtools_calibra.utilities.parsers.np2pd module idmtools_calibra.utilities.parsers.pd2csv module idmtools_calibra.utilities.prior module idmtools_calibra.utilities.resume_manager module IMIS (class in idmtools_calibra.algorithms.imis) info() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) init() (in module idmtools_calibra.calib_base_app) initialize() (idmtools_calibra.utilities.resume_manager.ResumeManager method) is_int() (idmtools_calibra.utilities.prior.SampleRange method) is_log() (idmtools_calibra.utilities.prior.SampleRange method) iteration (idmtools_calibra.calib_manager.CalibManager property) iteration_directory (idmtools_calibra.iteration_state.IterationState property) iteration_directory() (idmtools_calibra.calib_manager.CalibManager method) iteration_file (idmtools_calibra.iteration_state.IterationState property) iteration_start (idmtools_calibra.process_state.StatusPoint attribute) IterationState (class in idmtools_calibra.iteration_state)

J

json2dict() (in module idmtools_calibra.utilities.parsers.JSON) json_numpy_obj_hook() (in module idmtools_calibra.utilities.encoding)

json_to_pandas() (in module idmtools_calibra.utilities.helper) (in module idmtools_calibra.utilities.parsers.malaria_summary)

K

kernel_xp() (idmtools_calibra.algorithms.gpc.GPC static method) kernel_xx() (idmtools_calibra.algorithms.gpc.GPC method)

kxp_gpu_wrapper() (idmtools_calibra.algorithms.gpc.GPC method) kxx_gpu_wrapper() (idmtools_calibra.algorithms.gpc.GPC method)

L

laplace_predict() (idmtools_calibra.algorithms.gpc.GPC method) lhs() (idmtools_calibra.utilities.prior.MultiVariatePrior method) like() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) LikelihoodPlotter (class in idmtools_calibra.plotters.likelihood_plotter) linux_distribution() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) LinuxDistribution (class in idmtools_calibra.utilities.distro)

LIST (idmtools_calibra.resamplers.calibration_point.CalibrationPoint attribute) load_config_module() (in module idmtools_calibra.cli.utils) load_restart() (idmtools_calibra.resample_manager.ResampleManager method) logging_saver() (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) lsb_release_attr() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) lsb_release_info() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro)

M

main() (in module idmtools_calibra.utilities.distro) major_version() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) make_prediction_grid() (idmtools_calibra.plotters.separatrix_bhm_plotter.SeparatrixBHMPlotter method) map() (idmtools_calibra.analyzers.rmse_analyzer.RMSEAnalyzer method) map_sample_to_model_input() (in module idmtools_calibra.calib_base_app) minor_version() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) ModFn (class in idmtools_calibra.utilities.mod_fn) module idmtools_calibra idmtools_calibra.algorithms idmtools_calibra.algorithms.fisher_inf_matrix idmtools_calibra.algorithms.generic_iterative_next_point idmtools_calibra.algorithms.gpc idmtools_calibra.algorithms.imis idmtools_calibra.algorithms.next_point_algorithm idmtools_calibra.algorithms.optim_tool idmtools_calibra.algorithms.optim_tools_pspo idmtools_calibra.algorithms.optim_tools_spsa idmtools_calibra.algorithms.pbnb idmtools_calibra.algorithms.pbnb.c_sub_region idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions idmtools_calibra.algorithms.pbnb.m_intial_paramters_setting idmtools_calibra.algorithms.pbnb.optim_tool_pbnb idmtools_calibra.algorithms.separatrix_bhm idmtools_calibra.analyzers idmtools_calibra.analyzers.base_calibration_analyzer idmtools_calibra.analyzers.rmse_analyzer idmtools_calibra.calib_base_app idmtools_calibra.calib_manager idmtools_calibra.calib_site idmtools_calibra.cli idmtools_calibra.cli.commands idmtools_calibra.cli.utils idmtools_calibra.iteration_state idmtools_calibra.output idmtools_calibra.output.spatial_output idmtools_calibra.plotters idmtools_calibra.plotters.base_plotter idmtools_calibra.plotters.likelihood_plotter idmtools_calibra.plotters.optim_tool_pbnb_plotter idmtools_calibra.plotters.optim_tool_plotter idmtools_calibra.plotters.optim_tool_spsa_plotter idmtools_calibra.plotters.separatrix_bhm_plotter idmtools_calibra.plotters.site_data_plotter idmtools_calibra.process_state idmtools_calibra.resample_manager idmtools_calibra.resamplers idmtools_calibra.resamplers.base_resampler idmtools_calibra.resamplers.calibration_point idmtools_calibra.resamplers.calibration_points idmtools_calibra.resamplers.cramer_rao_resampler idmtools_calibra.resamplers.random_perturbation_resampler idmtools_calibra.rmse_site idmtools_calibra.singularity_json_python_task idmtools_calibra.utilities idmtools_calibra.utilities.display idmtools_calibra.utilities.distro idmtools_calibra.utilities.encoding idmtools_calibra.utilities.helper idmtools_calibra.utilities.ll_all_generator idmtools_calibra.utilities.ll_calculators idmtools_calibra.utilities.mod_fn idmtools_calibra.utilities.parameter_set idmtools_calibra.utilities.parsers idmtools_calibra.utilities.parsers.bin2np idmtools_calibra.utilities.parsers.dict2pd idmtools_calibra.utilities.parsers.JSON idmtools_calibra.utilities.parsers.malaria_summary idmtools_calibra.utilities.parsers.np2json idmtools_calibra.utilities.parsers.np2pd idmtools_calibra.utilities.parsers.pd2csv idmtools_calibra.utilities.prior idmtools_calibra.utilities.resume_manager

MultiVariatePrior (class in idmtools_calibra.utilities.prior)

N

name() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) NaNDetectedError ndim (idmtools_calibra.utilities.prior.MultiVariatePrior property) near_pd() (in module idmtools_calibra.algorithms.fisher_inf_matrix) negative_log_marginal_likelihood() (idmtools_calibra.algorithms.gpc.GPC method) negative_log_marginal_likelihood_and_gradient() (idmtools_calibra.algorithms.gpc.GPC method) next_point (idmtools_calibra.process_state.StatusPoint attribute) next_point_fn() (idmtools_calibra.algorithms.imis.IMIS method)

next_point_step() (idmtools_calibra.iteration_state.IterationState method) NextPointAlgorithm (class in idmtools_calibra.algorithms.next_point_algorithm) NORMALIZED_DISTRO_ID (in module idmtools_calibra.utilities.distro) NORMALIZED_LSB_ID (in module idmtools_calibra.utilities.distro) NORMALIZED_OS_ID (in module idmtools_calibra.utilities.distro) np2json() (in module idmtools_calibra.utilities.parsers.np2json) np2pd() (in module idmtools_calibra.utilities.parsers.np2pd) NUMPY (idmtools_calibra.resamplers.calibration_point.CalibrationPoint attribute) NumpyAwareJSONEncoder (class in idmtools_calibra.utilities.parsers.np2json) NumpyEncoder (class in idmtools_calibra.utilities.encoding)

O

on_off() (in module idmtools_calibra.utilities.display) open_for_reading() (idmtools_calibra.calib_manager.CalibManager class method) optimize_hyperparameters() (idmtools_calibra.algorithms.gpc.GPC method) OptimTool (class in idmtools_calibra.algorithms.optim_tool) OptimToolPBnB (class in idmtools_calibra.algorithms.pbnb.optim_tool_pbnb) OptimToolPBnBPlotter (class in idmtools_calibra.plotters.optim_tool_pbnb_plotter) OptimToolPlotter (class in idmtools_calibra.plotters.optim_tool_plotter)

OptimToolPSPO (class in idmtools_calibra.algorithms.optim_tools_pspo) OptimToolSPSA (class in idmtools_calibra.algorithms.optim_tools_spsa) OptimToolSPSAPlotter (class in idmtools_calibra.plotters.optim_tool_spsa_plotter) os_release_attr() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) os_release_info() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro)

P

param_names (idmtools_calibra.iteration_state.IterationState property) (idmtools_calibra.plotters.likelihood_plotter.LikelihoodPlotter property) param_names() (idmtools_calibra.calib_manager.CalibManager method) parameter_names (idmtools_calibra.resamplers.calibration_point.CalibrationPoint property) PARAMETER_TYPES (idmtools_calibra.resamplers.calibration_point.CalibrationPoint attribute) ParameterSet (class in idmtools_calibra.utilities.parameter_set) params (idmtools_calibra.utilities.prior.MultiVariatePrior property) parse() (in module idmtools_calibra.utilities.parsers.JSON) pd2csv() (in module idmtools_calibra.utilities.parsers.pd2csv) pdf() (idmtools_calibra.utilities.prior.MultiVariatePrior method) (idmtools_calibra.utilities.prior.SampleFunctionContainer method) perturbed_points() (in module idmtools_calibra.algorithms.fisher_inf_matrix) plot (idmtools_calibra.process_state.StatusPoint attribute) plot() (idmtools_calibra.algorithms.gpc.GPC method) plot1d_by_iteration() (idmtools_calibra.plotters.likelihood_plotter.LikelihoodPlotter static method) plot_all() (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method) plot_analyzers() (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method) plot_best() (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method) plot_by_parameter() (idmtools_calibra.plotters.likelihood_plotter.LikelihoodPlotter method) plot_by_parameter_and_site() (idmtools_calibra.plotters.likelihood_plotter.LikelihoodPlotter method) plot_data() (idmtools_calibra.algorithms.gpc.GPC method)

plot_errors() (idmtools_calibra.algorithms.gpc.GPC method) plot_histogram() (idmtools_calibra.algorithms.gpc.GPC method) plot_iteration() (idmtools_calibra.iteration_state.IterationState method) plot_state_evolution() (idmtools_calibra.plotters.optim_tool_pbnb_plotter.OptimToolPBnBPlotter static method) (idmtools_calibra.plotters.optim_tool_plotter.OptimToolPlotter method) (idmtools_calibra.plotters.optim_tool_spsa_plotter.OptimToolSPSAPlotter method) plotting_step() (idmtools_calibra.iteration_state.IterationState method) pluralize() (in module idmtools_calibra.utilities.display) post_analysis() (idmtools_calibra.resamplers.base_resampler.BaseResampler method) (idmtools_calibra.resamplers.cramer_rao_resampler.CramerRaoResampler method) (idmtools_calibra.resamplers.random_perturbation_resampler.RandomPerturbationResampler method) post_iteration() (idmtools_calibra.calib_manager.CalibManager method) pre_creation() (idmtools_calibra.singularity_json_python_task.SingularityJSONConfiguredPythonTask method) prep_for_dict() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) print_results_for_iteration() (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) prior_fn (idmtools_calibra.plotters.likelihood_plotter.LikelihoodPlotter property) provided_command (idmtools_calibra.singularity_json_python_task.SingularityJSONConfiguredPythonTask attribute)

R

RandomPerturbationResampler (class in idmtools_calibra.resamplers.random_perturbation_resampler) read() (idmtools_calibra.resamplers.calibration_points.CalibrationPoints class method) read_calib_data() (idmtools_calibra.calib_manager.CalibManager method) (in module idmtools_calibra.cli.utils) reduce() (idmtools_calibra.analyzers.rmse_analyzer.RMSEAnalyzer method) required_components (idmtools_calibra.calib_manager.CalibManager property) resample() (idmtools_calibra.resamplers.base_resampler.BaseResampler method) (idmtools_calibra.resamplers.cramer_rao_resampler.CramerRaoResampler method) (idmtools_calibra.resamplers.random_perturbation_resampler.RandomPerturbationResampler method) resample_and_run() (idmtools_calibra.resample_manager.ResampleManager method) (idmtools_calibra.resamplers.base_resampler.BaseResampler method) ResampleManager (class in idmtools_calibra.resample_manager) resolve_args() (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) restore() (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method)

restore_calib_manager() (idmtools_calibra.utilities.resume_manager.ResumeManager method) restore_iteration_state() (idmtools_calibra.utilities.resume_manager.ResumeManager method) restore_ll_all() (idmtools_calibra.utilities.resume_manager.ResumeManager method) restore_results() (idmtools_calibra.iteration_state.IterationState method) restore_state() (idmtools_calibra.iteration_state.IterationState class method) resume() (idmtools_calibra.utilities.resume_manager.ResumeManager method) resume_calibration() (idmtools_calibra.calib_manager.CalibManager method) ResumeManager (class in idmtools_calibra.utilities.resume_manager) rmse() (idmtools_calibra.analyzers.rmse_analyzer.RMSEAnalyzer method) RMSEAnalyzer (class in idmtools_calibra.analyzers.rmse_analyzer) RMSESiteSingleChannel (class in idmtools_calibra.rmse_site) run() (idmtools_calibra.iteration_state.IterationState method) run_calibration() (idmtools_calibra.calib_manager.CalibManager method) run_iterations() (idmtools_calibra.calib_manager.CalibManager method) running (idmtools_calibra.process_state.StatusPoint attribute) rvs() (idmtools_calibra.utilities.prior.MultiVariatePrior method)

S

sample_cov_ellipse() (in module idmtools_calibra.algorithms.fisher_inf_matrix) sample_from_function() (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm static method) sample_hypersphere() (idmtools_calibra.algorithms.optim_tool.OptimTool method) sample_simultaneous_perturbation() (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) SampleFunctionContainer (class in idmtools_calibra.utilities.prior) SampleIndexWrapper (class in idmtools_calibra.calib_manager) SampleRange (class in idmtools_calibra.utilities.prior) save() (idmtools_calibra.algorithms.gpc.GPC method) (idmtools_calibra.iteration_state.IterationState method) SeparatrixBHM (class in idmtools_calibra.algorithms.separatrix_bhm) SeparatrixBHMPlotter (class in idmtools_calibra.plotters.separatrix_bhm_plotter) serialize_results() (idmtools_calibra.calib_manager.CalibManager method) SERIES (idmtools_calibra.resamplers.calibration_point.CalibrationPoint attribute) set_calibration_manager() (idmtools_calibra.resamplers.base_resampler.BaseResampler method) set_calibration_site() (idmtools_calibra.calib_site.SiteFunctions method) set_custom_cost_fn() (idmtools_calibra.analyzers.rmse_analyzer.RMSEAnalyzer static method) set_experiment_builder_function() (idmtools_calibra.calib_manager.CalibManager method) set_gpc_vec() (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) set_initial_samples() (idmtools_calibra.algorithms.imis.IMIS method) set_map_replicates_callback() (idmtools_calibra.calib_manager.CalibManager method) set_param_partial() (idmtools_calibra.singularity_json_python_task.SingularityJSONConfiguredPythonTask class method) set_parameter_sweep_callback() (idmtools_calibra.singularity_json_python_task.SingularityJSONConfiguredPythonTask static method) (in module idmtools_calibra.calib_manager) set_results_for_iteration() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method)

set_samples_for_iteration() (idmtools_calibra.iteration_state.IterationState method) set_state() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.optim_tool.OptimTool method) (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method) (idmtools_calibra.algorithms.separatrix_bhm.SeparatrixBHM method) set_training_data() (idmtools_calibra.algorithms.gpc.GPC method) SingularityJSONConfiguredPythonTask (class in idmtools_calibra.singularity_json_python_task) site_analyzer_names() (idmtools_calibra.calib_manager.CalibManager method) SiteDataPlotter (class in idmtools_calibra.plotters.site_data_plotter) SiteFunctions (class in idmtools_calibra.calib_site) SpatialOutput (class in idmtools_calibra.output.spatial_output) starting_step() (idmtools_calibra.iteration_state.IterationState method) state_for_iteration() (idmtools_calibra.calib_manager.CalibManager method) STATIC (idmtools_calibra.resamplers.calibration_point.CalibrationPoint attribute) status (idmtools_calibra.iteration_state.IterationState property) status_to_iter_step() (in module idmtools_calibra.utilities.resume_manager) StatusPoint (class in idmtools_calibra.process_state) stochastic_newton_raphson() (idmtools_calibra.algorithms.optim_tools_pspo.OptimToolPSPO method) (idmtools_calibra.algorithms.optim_tools_spsa.OptimToolSPSA method) strip() (in module idmtools_calibra.utilities.parsers.JSON) suite_id (idmtools_calibra.calib_manager.CalibManager property) summary_channel_to_pandas() (in module idmtools_calibra.utilities.parsers.malaria_summary)

T

test() (in module idmtools_calibra.utilities.distro) to_dataframe() (idmtools_calibra.resamplers.calibration_point.CalibrationParameter method) (idmtools_calibra.resamplers.calibration_point.CalibrationPoint method) (idmtools_calibra.utilities.prior.MultiVariatePrior method) to_dict() (idmtools_calibra.output.spatial_output.SpatialOutput method) (idmtools_calibra.resamplers.calibration_point.CalibrationParameter method) (idmtools_calibra.resamplers.calibration_point.CalibrationPoint method) (idmtools_calibra.utilities.parameter_set.ParameterSet method) (idmtools_calibra.utilities.prior.MultiVariatePrior method)

to_file() (idmtools_calibra.iteration_state.IterationState method) to_value_dict() (idmtools_calibra.resamplers.calibration_point.CalibrationPoint method) trunc_gauss() (in module idmtools_calibra.algorithms.fisher_inf_matrix) turn_to_power() (in module idmtools_calibra.algorithms.pbnb.fun_pbnb_support_functions)

U

uname_attr() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) uname_info() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) update() (idmtools_calibra.iteration_state.IterationState method) update_gaussian() (idmtools_calibra.algorithms.imis.IMIS method) update_gaussian_center() (idmtools_calibra.algorithms.imis.IMIS method) update_gaussian_covariance() (idmtools_calibra.algorithms.imis.IMIS method)

update_gaussian_probabilities() (idmtools_calibra.algorithms.imis.IMIS method) update_iteration() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.imis.IMIS method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) update_state() (idmtools_calibra.algorithms.imis.IMIS method) update_summary_table() (idmtools_calibra.algorithms.generic_iterative_next_point.GenericIterativeNextPoint method) (idmtools_calibra.algorithms.next_point_algorithm.NextPointAlgorithm method) (idmtools_calibra.algorithms.pbnb.optim_tool_pbnb.OptimToolPBnB method)

V

validate_exp_name() (in module idmtools_calibra.utilities.helper) validate_parameters() (idmtools_calibra.algorithms.imis.IMIS method) verbose_timedelta() (in module idmtools_calibra.utilities.display) verify_param() (idmtools_calibra.algorithms.optim_tool.OptimTool method) verify_valid_samples() (idmtools_calibra.algorithms.imis.IMIS method) version() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) version_parts() (idmtools_calibra.utilities.distro.LinuxDistribution method) (in module idmtools_calibra.utilities.distro) visualize() (idmtools_calibra.plotters.base_plotter.BasePlotter method) (idmtools_calibra.plotters.likelihood_plotter.LikelihoodPlotter method) (idmtools_calibra.plotters.optim_tool_pbnb_plotter.OptimToolPBnBPlotter method) (idmtools_calibra.plotters.optim_tool_plotter.OptimToolPlotter method) (idmtools_calibra.plotters.optim_tool_spsa_plotter.OptimToolSPSAPlotter method) (idmtools_calibra.plotters.separatrix_bhm_plotter.SeparatrixBHMPlotter method) (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method)

visualize_at_end_of_iteration() (idmtools_calibra.plotters.separatrix_bhm_plotter.SeparatrixBHMPlotter method) visualize_at_start_of_iteration() (idmtools_calibra.plotters.separatrix_bhm_plotter.SeparatrixBHMPlotter method) visualize_optimtool_diagnoistics() (idmtools_calibra.plotters.optim_tool_plotter.OptimToolPlotter method) (idmtools_calibra.plotters.optim_tool_spsa_plotter.OptimToolSPSAPlotter method) visualize_results() (idmtools_calibra.plotters.optim_tool_pbnb_plotter.OptimToolPBnBPlotter method) (idmtools_calibra.plotters.optim_tool_plotter.OptimToolPlotter method) (idmtools_calibra.plotters.optim_tool_spsa_plotter.OptimToolSPSAPlotter method)

W

wait_for_finished() (idmtools_calibra.iteration_state.IterationState method) weighted_distances_from_center() (idmtools_calibra.algorithms.imis.IMIS method) weighted_squares() (in module idmtools_calibra.utilities.ll_calculators)

write() (idmtools_calibra.resamplers.calibration_points.CalibrationPoints method) write_LL_csv() (idmtools_calibra.plotters.site_data_plotter.SiteDataPlotter method) write_point() (idmtools_calibra.resamplers.calibration_point.CalibrationPoint method) write_restart() (idmtools_calibra.resample_manager.ResampleManager method)