Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | R | S | T | U | V | W | X | Y _ __delattr__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __dir__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __eq__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __format__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __ge__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __getattribute__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __gt__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __hash__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __init__() (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (scripts.burn_in.archive.run_tb_burn_in_South_Africa.AgeDependentTBProgression method) (scripts.burn_in.archive.run_tb_burn_in_South_Africa.GradualHIVIntervention method) (tbsim.comorbidities.hiv.hiv.HIV method) (tbsim.comorbidities.hiv.tb_hiv_cnn.TB_HIV_Connector method) (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition method) (tbsim.comorbidities.malnutrition.tb_malnut_cnn.TB_Nutrition_Connector method) (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) (tbsim.interventions.beta.BetaByYear method) (tbsim.interventions.EnhancedTBDiagnostic method) (tbsim.interventions.EnhancedTBTreatment method) (tbsim.interventions.healthseeking.HealthSeekingBehavior method) (tbsim.interventions.HealthSeekingBehavior method) (tbsim.interventions.interventions.Product method) (tbsim.interventions.interventions.TBVaccinationCampaign method) (tbsim.interventions.tb_diagnostic.EnhancedTBDiagnostic method) (tbsim.interventions.tb_diagnostic.TBDiagnostic method) (tbsim.interventions.tb_drug_types.TBDrugParameters method) (tbsim.interventions.tb_health_seeking.HealthSeekingBehavior method) (tbsim.interventions.tb_treatment.EnhancedTBTreatment method) (tbsim.interventions.TBDiagnostic method) (tbsim.interventions.TBDrugParameters method) (tbsim.interventions.TBTreatment method) (tbsim.interventions.TBVaccinationCampaign method) (tbsim.interventions.tpt.TPTInitiation method) (tbsim.interventions.TPTInitiation method) (tbsim.networks.HouseholdNet method), [1] (tbsim.networks.HouseholdNetRationsTrial method), [1] (tbsim.tb.TB method) (tbsim.utils.probabilities.Probability method) (tbsim.utils.probabilities.Range method) (tbsim.utils.probabilities.RangeDict method) __init_subclass__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __le__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __lt__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __ne__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __new__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) __reduce__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __reduce_ex__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __repr__() (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (tbsim.interventions.tb_drug_types.TBDrugParameters method) (tbsim.interventions.TBDrugParameters method) __setattr__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.tb.TB) __sizeof__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) __str__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.tb.TB) __subclasshook__() (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (in module tbsim.interventions.tb_drug_types.TBDrugTypeParameters) (in module tbsim.misc.tbterms.TermsExport) (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (in module tbsim.tb.TB) A ACTIVE_EXPTB (tbsim.tb.TBS attribute) ACTIVE_PRESYMP (tbsim.tb.TBS attribute) ACTIVE_SMNEG (tbsim.tb.TBS attribute) ACTIVE_SMPOS (tbsim.tb.TBS attribute) active_tb_state (in module tbsim.tb.TB) (tbsim.tb.TB attribute) ACUTE (tbsim.comorbidities.hiv.hiv.HIVState attribute) add() (tbsim.utils.probabilities.RangeDict method) add_hh() (tbsim.networks.HouseholdNet method), [1] (tbsim.networks.HouseholdNetRationsTrial method), [1] adherence_rate (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) administer() (tbsim.interventions.interventions.Product method) AgeDependentTBProgression (class in scripts.burn_in.archive.run_tb_burn_in_South_Africa) Agents (class in tbsim.wrappers) AIDS (tbsim.comorbidities.hiv.hiv.HIVState attribute) ALIVE_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) all() (in module tbsim.tb.TBS) (tbsim.tb.TBS method) (tbsim.tb.TBS static method) all_active() (in module tbsim.tb.TBS) (tbsim.tb.TBS method) (tbsim.tb.TBS static method) all_infected() (in module tbsim.tb.TBS) (tbsim.tb.TBS method) (tbsim.tb.TBS static method) all_latent() (in module tbsim.tb.TBS) (tbsim.tb.TBS method) (tbsim.tb.TBS static method) applied_years (tbsim.interventions.beta.BetaByYear attribute) ATRISK (tbsim.comorbidities.hiv.hiv.HIVState attribute) B barchar_all_state_transitions_interactive() (scripts.howto.example_enhanced_docstrings.DwtAnalyzer method) BCGProtection (class in tbsim.interventions) (class in tbsim.interventions.bcg) begin_step() (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) BetaByYear (class in tbsim.interventions.beta) build_sim() (in module scripts.interventions.run_tb_interventions) build_tbhiv_sim() (in module scripts.hiv.run_deven_sce) (in module scripts.hiv.run_tbhiv) (in module scripts.hiv.run_tbhiv_scenarios) build_tbsim() (in module scripts.basic.run_tb) (in module scripts.basic.run_tb_with_analyzer) (in module scripts.howto.comprehensive_analyzer_plots_example) (in module scripts.howto.quick_analyzer_plots_example) C calculate_calibration_score() (in module scripts.calibration.tb_calibration_south_africa) (in module scripts.calibration.tb_calibration_sweep) calculate_expected_distributions() (in module scripts.basic.run_tb_with_analyzer) calculate_tb_impact() (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) care_seeking_multiplier_invalid() (tbsim.interventions.TBDiagnosticErrors static method) CARE_SEEKING_MULTIPLIER_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) cdc_3HP (tbsim.interventions.tpt.TPTRegimes attribute) cdc_3HR (tbsim.interventions.tpt.TPTRegimes attribute) cdc_4R (tbsim.interventions.tpt.TPTRegimes attribute) cdc_6H (tbsim.interventions.tpt.TPTRegimes attribute) cdc_9H (tbsim.interventions.tpt.TPTRegimes attribute) check_eligibility() (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) compare_with_initial_results() (in module scripts.optimization.run_optimization_example) compute_age_distribution_at_year() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_age_stratified_prevalence() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) (in module scripts.calibration.tb_calibration_south_africa) compute_age_stratified_prevalence_time_series() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_annualized_infection_rate() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_annualized_tb_mortality_rate() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_case_notifications() (in module scripts.calibration.tb_calibration_south_africa) compute_hiv_positive_tb_prevalence() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_hiv_prevalence() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_hiv_prevalence_adults_15to24() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_hiv_prevalence_adults_25plus() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_hiv_tb_coinfection_rates() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_latent_prevalence() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) compute_relsus() (tbsim.comorbidities.malnutrition.tb_malnut_cnn.TB_Nutrition_Connector static method) compute_tb_hiv_risk_rr() (tbsim.comorbidities.hiv.tb_hiv_cnn.TB_HIV_Connector static method) configure() (tbsim.interventions.tb_drug_types.TBDrugParameters method) (tbsim.interventions.TBDrugParameters method) cost_per_course (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) coverage_filter_failed() (tbsim.interventions.TBDiagnosticErrors static method) coverage_filter_invalid_selection() (tbsim.interventions.TBDiagnosticErrors static method) coverage_filter_wrong_selection() (tbsim.interventions.TBDiagnosticErrors static method) coverage_invalid() (tbsim.interventions.TBDiagnosticErrors static method) create_calibration_report() (in module scripts.calibration.tb_calibration_south_africa) create_dots_improved_parameters() (tbsim.interventions.tb_drug_types.TBDrugTypeParameters static method) (tbsim.interventions.TBDrugTypeParameters static method) create_dots_improved_treatment() (in module tbsim.interventions) create_dots_parameters() (tbsim.interventions.tb_drug_types.TBDrugTypeParameters static method) (tbsim.interventions.TBDrugTypeParameters static method) create_dots_treatment() (in module tbsim.interventions) create_empiric_treatment_parameters() (tbsim.interventions.tb_drug_types.TBDrugTypeParameters static method) (tbsim.interventions.TBDrugTypeParameters static method) create_first_line_combo_parameters() (tbsim.interventions.tb_drug_types.TBDrugTypeParameters static method) (tbsim.interventions.TBDrugTypeParameters static method) create_first_line_treatment() (in module tbsim.interventions) create_histogram_kde_example() (in module scripts.howto.generate_doc_images) create_interactive_bar_example() (in module scripts.howto.generate_doc_images) create_latent_treatment_parameters() (tbsim.interventions.tb_drug_types.TBDrugTypeParameters static method) (tbsim.interventions.TBDrugTypeParameters static method) create_network_graph_example() (in module scripts.howto.generate_doc_images) create_optimization_plots() (in module scripts.optimization.run_optimization_example) create_parameters_for_type() (tbsim.interventions.tb_drug_types.TBDrugTypeParameters static method) (tbsim.interventions.TBDrugTypeParameters static method) create_reinfection_analysis_example() (in module scripts.howto.generate_doc_images) create_res_dir() (in module tbsim.config) create_sample_households() (in module scripts.plots.plot_household_networks) create_sankey_example() (in module scripts.howto.generate_doc_images) create_second_line_combo_parameters() (tbsim.interventions.tb_drug_types.TBDrugTypeParameters static method) (tbsim.interventions.TBDrugTypeParameters static method) create_south_africa_data() (in module scripts.calibration.tb_calibration_south_africa) create_third_line_combo_parameters() (tbsim.interventions.tb_drug_types.TBDrugTypeParameters static method) (tbsim.interventions.TBDrugTypeParameters static method) cumulative_negative_decreased() (tbsim.interventions.TBDiagnosticErrors static method) cumulative_positive_decreased() (tbsim.interventions.TBDiagnosticErrors static method) cumulative_update_failed() (tbsim.interventions.TBDiagnosticErrors static method) cure_rate (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) current_timestep_record_failed() (tbsim.interventions.TBDiagnosticErrors static method) D data_inconsistency() (tbsim.interventions.TBDiagnosticErrors static method) DEAD (tbsim.tb.TBS attribute) debug_hiv_results() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) debug_population() (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) demonstrate_all_analyzer_plots() (in module scripts.howto.comprehensive_analyzer_plots_example) demonstrate_essential_plots() (in module scripts.howto.quick_analyzer_plots_example) demonstrate_household_network_simulation() (in module scripts.plots.plot_household_networks) demonstrate_plotter_usage() (in module scripts.howto.quick_analyzer_plots_example) demonstrate_post_processor() (in module scripts.howto.comprehensive_analyzer_plots_example) DIAGNOSED_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) DISEASES_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) dist (tbsim.utils.probabilities.Range attribute), [1] DOTS (in module tbsim.interventions.tb_drug_types.TBDrugType) (tbsim.interventions.tb_drug_types.TBDrugType attribute), [1] (tbsim.interventions.TBDrugType attribute), [1] DOTS_IMPROVED (in module tbsim.interventions.tb_drug_types.TBDrugType) (tbsim.interventions.tb_drug_types.TBDrugType attribute), [1] (tbsim.interventions.TBDrugType attribute), [1] drug_name (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) drug_parameters (tbsim.interventions.EnhancedTBTreatment attribute) (tbsim.interventions.tb_treatment.EnhancedTBTreatment attribute) drug_type (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) drug_type_assignments (tbsim.interventions.EnhancedTBTreatment attribute) (tbsim.interventions.tb_treatment.EnhancedTBTreatment attribute) duration (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) dweight (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition attribute) dweight_loc() (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition static method) dweight_scale() (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition static method) DwtAnalyzer (class in scripts.howto.example_enhanced_docstrings) E edges (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (tbsim.networks.HouseholdNet attribute), [1] (tbsim.networks.HouseholdNetRationsTrial attribute), [1] EMPIRIC_TREATMENT (in module tbsim.interventions.tb_drug_types.TBDrugType) (tbsim.interventions.tb_drug_types.TBDrugType attribute), [1] (tbsim.interventions.TBDrugType attribute), [1] EnhancedTBDiagnostic (class in tbsim.interventions) (class in tbsim.interventions.tb_diagnostic) EnhancedTBTreatment (class in tbsim.interventions) (class in tbsim.interventions.tb_treatment) ever_infected (in module tbsim.tb.TB) (tbsim.tb.TB attribute) example_usage() (in module scripts.howto.example_enhanced_docstrings) F failures (tbsim.interventions.EnhancedTBTreatment attribute) (tbsim.interventions.tb_treatment.EnhancedTBTreatment attribute) false_negative_count_invalid() (tbsim.interventions.TBDiagnosticErrors static method) false_negative_reset_failed() (tbsim.interventions.TBDiagnosticErrors static method) FILTERS (class in tbsim.utils.plots) finalize_results() (tbsim.tb.TB method) FIRST_LINE_COMBO (in module tbsim.interventions.tb_drug_types.TBDrugType) (tbsim.interventions.tb_drug_types.TBDrugType attribute), [1] (tbsim.interventions.TBDrugType attribute), [1] from_csv() (tbsim.utils.probabilities.Probability method) from_dict() (tbsim.utils.probabilities.Probability method) from_json() (tbsim.utils.probabilities.Probability method) G get_alive() (tbsim.wrappers.Agents static method) get_alive_by_age() (tbsim.wrappers.Agents static method) get_all_drug_parameters() (in module tbsim.interventions) get_all_parameter_sets() (tbsim.interventions.tb_drug_types.TBDrugTypeParameters static method) (tbsim.interventions.TBDrugTypeParameters static method) get_all_types() (tbsim.interventions.tb_drug_types.TBDrugType class method) (tbsim.interventions.TBDrugType class method) get_by_age() (tbsim.wrappers.Agents static method) get_dots_parameters() (in module tbsim.interventions) get_drug_parameters() (in module tbsim.interventions) get_effectiveness() (tbsim.interventions.tb_drug_types.TBDrugParameters method) (tbsim.interventions.TBDrugParameters method) get_extrastates() (in module tbsim.interventions.interventions) get_name() (tbsim.interventions.tb_drug_types.TBDrugType class method) (tbsim.interventions.TBDrugType class method) get_output_path() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) get_scenarios() (in module scripts.hiv.run_deven_sce) (in module scripts.interventions.run_tb_interventions) get_summary_stats() (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) GradualHIVIntervention (class in scripts.burn_in.archive.run_tb_burn_in_South_Africa) graph_state_transitions_curved() (scripts.howto.example_enhanced_docstrings.DwtAnalyzer method) H HealthSeeking (in module tbsim.interventions) HealthSeekingBehavior (class in tbsim.interventions) (class in tbsim.interventions.healthseeking) (class in tbsim.interventions.tb_health_seeking) height() (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition method) hhs (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (tbsim.networks.HouseholdNet attribute), [1] (tbsim.networks.HouseholdNetRationsTrial attribute), [1] histogram_with_kde() (scripts.howto.example_enhanced_docstrings.DwtAnalyzer method) HIV (class in tbsim.comorbidities.hiv.hiv) HIVState (class in tbsim.comorbidities.hiv.hiv) HouseholdNet (class in tbsim.networks), [1] HouseholdNetRationsTrial (class in tbsim.networks), [1] I important_metrics (tbsim.utils.plots.FILTERS attribute) inactivation_rate (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) infectious (tbsim.tb.TB property) init_post() (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) init_pre() (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) (tbsim.interventions.interventions.Product method) (tbsim.interventions.interventions.TBVaccinationCampaign method) (tbsim.interventions.TBVaccinationCampaign method) (tbsim.networks.HouseholdNet method), [1] (tbsim.networks.HouseholdNetRationsTrial method), [1] init_results() (tbsim.comorbidities.hiv.hiv.HIV method) (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition method) (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) (tbsim.interventions.EnhancedTBDiagnostic method) (tbsim.interventions.EnhancedTBTreatment method) (tbsim.interventions.healthseeking.HealthSeekingBehavior method) (tbsim.interventions.HealthSeekingBehavior method) (tbsim.interventions.tb_diagnostic.EnhancedTBDiagnostic method) (tbsim.interventions.tb_diagnostic.TBDiagnostic method) (tbsim.interventions.tb_health_seeking.HealthSeekingBehavior method) (tbsim.interventions.tb_treatment.EnhancedTBTreatment method) (tbsim.interventions.TBDiagnostic method) (tbsim.interventions.TBTreatment method) (tbsim.interventions.tpt.TPTInitiation method) (tbsim.interventions.TPTInitiation method) (tbsim.tb.TB method) is_protected() (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) items() (tbsim.utils.probabilities.RangeDict method) K keys() (tbsim.utils.probabilities.RangeDict method) L LATENT (tbsim.comorbidities.hiv.hiv.HIVState attribute) LATENT_FAST (tbsim.tb.TBS attribute) LATENT_SLOW (tbsim.tb.TBS attribute) latent_tb_state (in module tbsim.tb.TB) (tbsim.tb.TB attribute) LATENT_TREATMENT (in module tbsim.interventions.tb_drug_types.TBDrugType) (tbsim.interventions.tb_drug_types.TBDrugType attribute), [1] (tbsim.interventions.TBDrugType attribute), [1] lms() (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition method) LMS_data (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition attribute) load_age_data() (in module scripts.common_functions) (in module tbsim.utils.demographics) lonnroth_bmi_rr() (tbsim.comorbidities.malnutrition.tb_malnut_cnn.TB_Nutrition_Connector static method) M main() (in module scripts.calibration.tb_calibration_south_africa) (in module scripts.calibration.tb_calibration_sweep) (in module scripts.hiv.run_deven_sce) (in module scripts.howto.generate_doc_images) (in module scripts.optimization.run_optimization_example) (in module scripts.plots.plot_household_networks) make_births() (in module scripts.common_functions) make_cnn() (in module scripts.common_functions) make_deaths() (in module scripts.common_functions) make_demographics() (in module scripts.common_functions) (in module scripts.hiv.shared_functions) make_hiv() (in module scripts.common_functions) (in module scripts.hiv.shared_functions) make_hiv_comorbidity() (in module scripts.common_functions) make_hiv_interventions() (in module scripts.common_functions) (in module scripts.hiv.shared_functions) make_intervention() (in module scripts.common_functions) make_malnutrition() (in module scripts.basic.run_malnutrition) make_net() (in module scripts.common_functions) make_people() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) make_pop() (in module scripts.common_functions) make_tb() (in module scripts.common_functions) (in module scripts.hiv.shared_functions) make_tb_comorbidity() (in module scripts.common_functions) make_tb_hiv_connector() (in module scripts.common_functions) (in module scripts.hiv.shared_functions) make_tb_nut() (in module scripts.basic.run_tb_and_malnutrition) make_tb_nut_02() (in module scripts.basic.run_tb_and_malnutrition) Malnutrition (class in tbsim.comorbidities.malnutrition.malnutrition) max (tbsim.utils.probabilities.Range attribute), [1] min (tbsim.utils.probabilities.Range attribute), [1] module scripts.basic.run_malnutrition scripts.basic.run_scenarios scripts.basic.run_tb scripts.basic.run_tb_and_malnutrition scripts.basic.run_tb_with_analyzer scripts.burn_in.archive.run_tb_burn_in_South_Africa scripts.calibration.tb_calibration_south_africa scripts.calibration.tb_calibration_sweep scripts.common_functions scripts.hiv.run_deven_sce scripts.hiv.run_hiv scripts.hiv.run_tbhiv scripts.hiv.run_tbhiv_scenarios scripts.hiv.shared_functions scripts.howto.comprehensive_analyzer_plots_example scripts.howto.example_enhanced_docstrings scripts.howto.generate_doc_images scripts.howto.quick_analyzer_plots_example scripts.interventions.run_tb_interventions scripts.optimization.run_optimization_example scripts.plots.plot_household_networks tbsim.comorbidities tbsim.comorbidities.hiv.hiv tbsim.comorbidities.hiv.hiv.HIVState tbsim.comorbidities.hiv.tb_hiv_cnn tbsim.comorbidities.malnutrition.malnutrition tbsim.comorbidities.malnutrition.tb_malnut_cnn tbsim.config tbsim.interventions tbsim.interventions.bcg tbsim.interventions.beta tbsim.interventions.healthseeking tbsim.interventions.interventions tbsim.interventions.tb_diagnostic tbsim.interventions.tb_drug_types tbsim.interventions.tb_drug_types.TBDrugParameters tbsim.interventions.tb_drug_types.TBDrugType tbsim.interventions.tb_drug_types.TBDrugTypeParameters tbsim.interventions.tb_health_seeking tbsim.interventions.tb_treatment tbsim.interventions.tpt tbsim.misc tbsim.misc.tbterms.TBTerms tbsim.misc.tbterms.TermsExport tbsim.networks, [1] tbsim.networks.HouseholdNet tbsim.networks.HouseholdNetRationsTrial tbsim.tb tbsim.tb.TB tbsim.tb.TBS tbsim.utils tbsim.utils.demographics tbsim.utils.plots tbsim.utils.probabilities tbsim.version tbsim.wrappers mortality_rate (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) multiplier_application_failed() (tbsim.interventions.TBDiagnosticErrors static method) MULTIPLIER_APPLIED_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) multiplier_filter_failed() (tbsim.interventions.TBDiagnosticErrors static method) N N_TIMES_TESTED_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) negative_negative_count() (tbsim.interventions.TBDiagnosticErrors static method) negative_positive_count() (tbsim.interventions.TBDiagnosticErrors static method) negative_tested_count() (tbsim.interventions.TBDiagnosticErrors static method) new_treated (tbsim.interventions.EnhancedTBTreatment attribute) (tbsim.interventions.tb_treatment.EnhancedTBTreatment attribute) NONE (tbsim.tb.TBS attribute) O of_age() (tbsim.wrappers.Agents static method) on_treatment (in module tbsim.tb.TB) (tbsim.tb.TB attribute) ones_rr() (tbsim.comorbidities.malnutrition.tb_malnut_cnn.TB_Nutrition_Connector static method) out_to() (in module tbsim.utils.plots) over_5() (tbsim.wrappers.Agents static method) P p_active_to_clear() (tbsim.tb.TB method) p_active_to_death() (tbsim.tb.TB method) p_care_seeking() (tbsim.interventions.HealthSeekingBehavior method) (tbsim.interventions.tb_health_seeking.HealthSeekingBehavior method) p_latent_to_presym() (tbsim.tb.TB method) p_presym_to_active() (tbsim.tb.TB method) p_presym_to_clear() (tbsim.tb.TB method) pars (in module tbsim.networks.HouseholdNet) (in module tbsim.networks.HouseholdNetRationsTrial) (tbsim.comorbidities.malnutrition.tb_malnut_cnn.TB_Nutrition_Connector attribute) (tbsim.networks.HouseholdNet attribute), [1] (tbsim.networks.HouseholdNetRationsTrial attribute), [1] person_state_update_failed() (tbsim.interventions.TBDiagnosticErrors static method) plot() (tbsim.tb.TB method) plot_active_tb_sweep_with_data() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_age_prevalence_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_annualized_infection_rate_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_calibration_comparison() (in module scripts.calibration.tb_calibration_south_africa) plot_case_notification_rate_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_combined() (in module tbsim.utils.plots) plot_cumulative_diagnostic_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_cumulative_treatment_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_diagnostic_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_health_seeking_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_hiv_metrics_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_hiv_tb_coinfection_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_household_network_advanced() (in module scripts.plots.plot_household_networks) plot_household_network_basic() (in module scripts.plots.plot_household_networks) plot_household_structure() (in module tbsim.networks), [1] plot_latent_tb_sweep_with_data() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_population_pyramid_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_results() (in module scripts.common_functions) (in module scripts.hiv.run_tbhiv_scenarios) (in module scripts.hiv.shared_functions) (in module tbsim.utils.plots) plot_sweep_results() (in module scripts.calibration.tb_calibration_sweep) plot_tb_mortality_rate_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_tb_sweep_with_data() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_total_population_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) plot_treatment_grid() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) primary_decay_time_constant (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) Probability (class in tbsim.utils.probabilities) Product (class in tbsim.interventions.interventions) PROTECTED (tbsim.tb.TBS attribute) R Range (class in tbsim.utils.probabilities) RangeDict (class in tbsim.utils.probabilities) refined_sweep() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) reinfections_percents_bars_interactive() (scripts.howto.example_enhanced_docstrings.DwtAnalyzer method) relapse_rate (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) reltrans_het (in module tbsim.tb.TB) (tbsim.tb.TB attribute) resistance_rate (in module tbsim.interventions.tb_drug_types.TBDrugParameters) (tbsim.interventions.tb_drug_types.TBDrugParameters attribute) (tbsim.interventions.TBDrugParameters attribute) result_calculation_failed() (tbsim.interventions.TBDiagnosticErrors static method) result_count_mismatch() (tbsim.interventions.TBDiagnosticErrors static method) result_missing() (tbsim.interventions.TBDiagnosticErrors static method) RESULTS_ATTR_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) results_init_failed() (tbsim.interventions.TBDiagnosticErrors static method) RESULTS_NOT_INITIALIZED (tbsim.interventions.TBDiagnosticErrors attribute) rr_activation (in module tbsim.tb.TB) (tbsim.tb.TB attribute) rr_clearance (in module tbsim.tb.TB) (tbsim.tb.TB attribute) rr_death (in module tbsim.tb.TB) (tbsim.tb.TB attribute) run_calibration_simulation() (in module scripts.calibration.tb_calibration_south_africa) run_calibration_sweep() (in module scripts.calibration.tb_calibration_sweep) run_focused_optimization() (in module scripts.optimization.run_optimization_example) run_scenarios() (in module scripts.basic.run_scenarios) (in module scripts.hiv.run_tbhiv_scenarios) (in module scripts.interventions.run_tb_interventions) run_sim() (in module scripts.basic.run_scenarios) (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) S sample() (tbsim.utils.probabilities.Probability method) (tbsim.utils.probabilities.Range method) sankey_agents() (scripts.howto.example_enhanced_docstrings.DwtAnalyzer method) scripts.basic.run_malnutrition module scripts.basic.run_scenarios module scripts.basic.run_tb module scripts.basic.run_tb_and_malnutrition module scripts.basic.run_tb_with_analyzer module scripts.burn_in.archive.run_tb_burn_in_South_Africa module scripts.calibration.tb_calibration_south_africa module scripts.calibration.tb_calibration_sweep module scripts.common_functions module scripts.hiv.run_deven_sce module scripts.hiv.run_hiv module scripts.hiv.run_tbhiv module scripts.hiv.run_tbhiv_scenarios module scripts.hiv.shared_functions module scripts.howto.comprehensive_analyzer_plots_example module scripts.howto.example_enhanced_docstrings module scripts.howto.generate_doc_images module scripts.howto.quick_analyzer_plots_example module scripts.interventions.run_tb_interventions module scripts.optimization.run_optimization_example module scripts.plots.plot_household_networks module SECOND_LINE_COMBO (in module tbsim.interventions.tb_drug_types.TBDrugType) (tbsim.interventions.tb_drug_types.TBDrugType attribute), [1] (tbsim.interventions.TBDrugType attribute), [1] sensitivity_invalid() (tbsim.interventions.TBDiagnosticErrors static method) sensitivity_test_failed() (tbsim.interventions.TBDiagnosticErrors static method) set_initial_states() (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition method) set_prognoses() (tbsim.comorbidities.hiv.hiv.HIV method) (tbsim.tb.TB method) sim (tbsim.comorbidities.malnutrition.tb_malnut_cnn.TB_Nutrition_Connector attribute) sim_setup() (in module scripts.hiv.run_hiv) SOUGHT_CARE_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) sought_care_reset_failed() (tbsim.interventions.TBDiagnosticErrors static method) specificity_invalid() (tbsim.interventions.TBDiagnosticErrors static method) specificity_test_failed() (tbsim.interventions.TBDiagnosticErrors static method) start_treatment() (tbsim.tb.TB method) state (in module tbsim.tb.TB) (tbsim.tb.TB attribute) step() (scripts.burn_in.archive.run_tb_burn_in_South_Africa.AgeDependentTBProgression method) (scripts.burn_in.archive.run_tb_burn_in_South_Africa.GradualHIVIntervention method) (tbsim.comorbidities.hiv.hiv.HIV method) (tbsim.comorbidities.hiv.tb_hiv_cnn.TB_HIV_Connector method) (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition method) (tbsim.comorbidities.malnutrition.tb_malnut_cnn.TB_Nutrition_Connector method) (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) (tbsim.interventions.beta.BetaByYear method) (tbsim.interventions.EnhancedTBDiagnostic method) (tbsim.interventions.EnhancedTBTreatment method) (tbsim.interventions.healthseeking.HealthSeekingBehavior method) (tbsim.interventions.HealthSeekingBehavior method) (tbsim.interventions.tb_diagnostic.EnhancedTBDiagnostic method) (tbsim.interventions.tb_diagnostic.TBDiagnostic method) (tbsim.interventions.tb_health_seeking.HealthSeekingBehavior method) (tbsim.interventions.tb_treatment.EnhancedTBTreatment method) (tbsim.interventions.TBDiagnostic method) (tbsim.interventions.TBTreatment method) (tbsim.interventions.tpt.TPTInitiation method) (tbsim.interventions.TPTInitiation method) (tbsim.networks.HouseholdNet method), [1] (tbsim.networks.HouseholdNetRationsTrial method), [1] (tbsim.tb.TB method) step_die() (tbsim.tb.TB method) successes (tbsim.interventions.EnhancedTBTreatment attribute) (tbsim.interventions.tb_treatment.EnhancedTBTreatment attribute) supplementation_rr() (tbsim.comorbidities.malnutrition.tb_malnut_cnn.TB_Nutrition_Connector static method) T TB (class in tbsim.tb) TB_DISEASE_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) TB_HIV_Connector (class in tbsim.comorbidities.hiv.tb_hiv_cnn) TB_Nutrition_Connector (class in tbsim.comorbidities.malnutrition.tb_malnut_cnn) tb_state_length_mismatch() (tbsim.interventions.TBDiagnosticErrors static method) TB_STATE_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) tb_status_failed() (tbsim.interventions.TBDiagnosticErrors static method) TBDiagnostic (class in tbsim.interventions) (class in tbsim.interventions.tb_diagnostic) TBDiagnosticErrors (class in tbsim.interventions) TBDrugParameters (class in tbsim.interventions) (class in tbsim.interventions.tb_drug_types) TBDrugType (class in tbsim.interventions) (class in tbsim.interventions.tb_drug_types) TBDrugTypeParameters (class in tbsim.interventions) (class in tbsim.interventions.tb_drug_types) TBS (class in tbsim.tb) tbsim.comorbidities module tbsim.comorbidities.hiv.hiv module tbsim.comorbidities.hiv.hiv.HIVState module tbsim.comorbidities.hiv.tb_hiv_cnn module tbsim.comorbidities.malnutrition.malnutrition module tbsim.comorbidities.malnutrition.tb_malnut_cnn module tbsim.config module tbsim.interventions module tbsim.interventions.bcg module tbsim.interventions.beta module tbsim.interventions.healthseeking module tbsim.interventions.interventions module tbsim.interventions.tb_diagnostic module tbsim.interventions.tb_drug_types module tbsim.interventions.tb_drug_types.TBDrugParameters module tbsim.interventions.tb_drug_types.TBDrugType module tbsim.interventions.tb_drug_types.TBDrugTypeParameters module tbsim.interventions.tb_health_seeking module tbsim.interventions.tb_treatment module tbsim.interventions.tpt module tbsim.misc module tbsim.misc.tbterms.TBTerms module tbsim.misc.tbterms.TermsExport module tbsim.networks module, [1] tbsim.networks.HouseholdNet module tbsim.networks.HouseholdNetRationsTrial module tbsim.tb module tbsim.tb.TB module tbsim.tb.TBS module tbsim.utils module tbsim.utils.demographics module tbsim.utils.plots module tbsim.utils.probabilities module tbsim.version module tbsim.wrappers module TBTreatment (class in tbsim.interventions) TBVaccinationCampaign (class in tbsim.interventions) (class in tbsim.interventions.interventions) test_health_seeking_diagnostic_integration() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) test_hiv_integration() (in module scripts.burn_in.archive.run_tb_burn_in_South_Africa) test_result_length_mismatch() (tbsim.interventions.TBDiagnosticErrors static method) TEST_RESULT_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) TEST_RESULT_THIS_STEP_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) test_result_wrong_type() (tbsim.interventions.TBDiagnosticErrors static method) TESTED_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) TESTED_THIS_STEP_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) THIRD_LINE_COMBO (in module tbsim.interventions.tb_drug_types.TBDrugType) (tbsim.interventions.tb_drug_types.TBDrugType attribute), [1] (tbsim.interventions.TBDrugType attribute), [1] TI_MISSING (tbsim.interventions.TBDiagnosticErrors attribute) to_csv() (tbsim.utils.probabilities.Probability method) to_dict() (tbsim.utils.probabilities.RangeDict method) to_json() (tbsim.utils.probabilities.Probability method) TPTInitiation (class in tbsim.interventions) (class in tbsim.interventions.tpt) TPTRegimes (class in tbsim.interventions.tpt) U unboosted_count_invalid() (tbsim.interventions.TBDiagnosticErrors static method) uncertainty_plot() (in module scripts.common_functions) uncertanty_plot() (in module scripts.hiv.shared_functions) under_5() (tbsim.wrappers.Agents static method) update() (tbsim.interventions.interventions.TBVaccinationCampaign method) (tbsim.interventions.TBVaccinationCampaign method) update_results() (tbsim.comorbidities.hiv.hiv.HIV method) (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition method) (tbsim.interventions.bcg.BCGProtection method) (tbsim.interventions.BCGProtection method) (tbsim.interventions.EnhancedTBDiagnostic method) (tbsim.interventions.EnhancedTBTreatment method) (tbsim.interventions.healthseeking.HealthSeekingBehavior method) (tbsim.interventions.HealthSeekingBehavior method) (tbsim.interventions.tb_diagnostic.EnhancedTBDiagnostic method) (tbsim.interventions.tb_diagnostic.TBDiagnostic method) (tbsim.interventions.tb_health_seeking.HealthSeekingBehavior method) (tbsim.interventions.tb_treatment.EnhancedTBTreatment method) (tbsim.interventions.TBDiagnostic method) (tbsim.interventions.TBTreatment method) (tbsim.interventions.tpt.TPTInitiation method) (tbsim.interventions.TPTInitiation method) (tbsim.tb.TB method) V validate() (tbsim.utils.probabilities.Range method) values() (tbsim.utils.probabilities.RangeDict method) W weight() (tbsim.comorbidities.malnutrition.malnutrition.Malnutrition method) where() (tbsim.wrappers.Agents static method) X x_beta (tbsim.interventions.beta.BetaByYear attribute) Y years (tbsim.interventions.beta.BetaByYear attribute)