Reference

• tlo package
  • Subpackages
    • tlo.analysis package
      • Submodules
        • tlo.analysis.hsi_events module
          • is_valid_hsi_event_subclass()
          • get_hsi_event_classes_per_module()
          • get_details_of_defined_hsi_events()
          • sort_hsi_event_details()
          • format_hsi_event_details_as_csv()
          • format_hsi_event_details_as_table()
          • format_hsi_event_details_as_list()
          • merge_hsi_event_details()
          • get_all_defined_hsi_events_as_dataframe()
          • main()
        • tlo.analysis.life_expectancy module
          • calculate_probability_of_dying()
          • get_life_expectancy_estimates()
          • get_probability_of_premature_death()
        • tlo.analysis.utils module
          • parse_log_file()
          • merge_log_files()
          • write_log_to_excel()
          • make_calendar_period_lookup()
          • make_calendar_period_type()
          • make_age_grp_lookup()
          • make_age_grp_types()
          • to_age_group()
          • get_scenario_outputs()
          • get_scenario_info()
          • load_pickled_dataframes()
          • extract_params()
          • extract_results()
          • summarize()
          • get_grid()
          • format_gbd()
          • create_pickles_locally()
          • compare_number_of_deaths()
          • flatten_multi_index_series_into_dict_for_logging()
          • unflatten_flattened_multi_index_in_logging()
          • LogsDict
            • LogsDict.items()
            • LogsDict.keys()
            • LogsDict.values()
          • get_filtered_treatment_ids()
          • colors_in_matplotlib()
          • get_coarse_appt_type()
          • order_of_coarse_appt()
          • get_color_coarse_appt()
          • order_of_short_treatment_ids()
          • get_color_short_treatment_id()
          • order_of_cause_of_death_or_daly_label()
          • get_color_cause_of_death_or_daly_label()
          • squarify_neat()
          • get_root_path()
          • bin_hsi_event_details()
          • compute_mean_across_runs()
          • plot_stacked_bar_chart()
          • plot_clustered_stacked()
          • get_mappers_in_fullmodel()
          • get_parameters_for_status_quo()
          • get_parameters_for_standard_mode2_runs()
          • get_parameters_for_improved_healthsystem_and_healthcare_seeking()
          • mix_scenarios()
      • Module contents
    • tlo.logging package
      • Submodules
        • tlo.logging.core module
          • InconsistentLoggedColumnsWarning
          • initialise()
          • reset()
          • set_output_file()
          • disable()
          • getLogger()
          • Logger
            • Logger.HASH_LEN
            • Logger.level
            • Logger.handlers
            • Logger.addHandler()
            • Logger.isEnabledFor()
            • Logger.reset_attributes()
            • Logger.setLevel()
            • Logger.log()
            • Logger.critical()
            • Logger.debug()
            • Logger.info()
            • Logger.warning()
        • tlo.logging.encoding module
          • PandasEncoder
            • PandasEncoder.default()
        • tlo.logging.helpers module
          • set_logging_levels()
          • get_dataframe_row_as_dict_for_logging()
          • grouped_counts_with_all_combinations()
        • tlo.logging.reader module
          • LogData
            • LogData.parse_log_line()
            • LogData.get_log_dataframes()
            • LogData.parse_logged_dataframe()
      • Module contents
        • disable()
        • getLogger()
        • initialise()
        • reset()
        • set_output_file()
        • set_logging_levels()
    • tlo.methods package
      • Submodules
        • tlo.methods.alri module
          • Overview
          • Alri
            • Alri.__init__()
            • Alri.read_parameters()
            • Alri.check_params_read_in_ok()
            • Alri.define_symptoms()
            • Alri.pre_initialise_population()
            • Alri.initialise_population()
            • Alri.initialise_simulation()
            • Alri.on_birth()
            • Alri.report_daly_values()
            • Alri.over_ride_availability_of_certain_consumables()
            • Alri.look_up_consumables()
            • Alri.end_episode()
            • Alri.cancel_death_and_schedule_cure()
            • Alri.check_properties()
            • Alri.do_effects_of_treatment_and_return_outcome()
            • Alri.record_sought_care_for_alri()
            • Alri.get_imci_classification_based_on_symptoms()
            • Alri._ultimate_treatment_indicated_for_patient()
            • Alri.do_at_generic_first_appt()
            • Alri.do_at_generic_first_appt_emergency()
          • AlriPollingEvent
            • AlriPollingEvent.__init__()
            • AlriPollingEvent.get_probs_of_acquiring_pathogen()
            • AlriPollingEvent.get_persons_for_new_alri()
            • AlriPollingEvent.apply()
          • AlriIncidentCase
            • AlriIncidentCase.__init__()
            • AlriIncidentCase.determine_nature_of_the_case()
            • AlriIncidentCase.apply_characteristics_of_the_case()
            • AlriIncidentCase.apply()
          • AlriNaturalRecoveryEvent
            • AlriNaturalRecoveryEvent.__init__()
            • AlriNaturalRecoveryEvent.apply()
          • AlriCureEvent
            • AlriCureEvent.__init__()
            • AlriCureEvent.apply()
          • AlriDeathEvent
            • AlriDeathEvent.__init__()
            • AlriDeathEvent.apply()
          • HSI_Alri_Treatment
            • HSI_Alri_Treatment.__init__()
            • HSI_Alri_Treatment._as_out_patient()
            • HSI_Alri_Treatment._as_in_patient()
            • HSI_Alri_Treatment._refer_to_next_level_up()
            • HSI_Alri_Treatment._refer_to_become_inpatient()
            • HSI_Alri_Treatment._schedule_follow_up_following_treatment_failure()
            • HSI_Alri_Treatment._get_cons()
            • HSI_Alri_Treatment._get_cons_group()
            • HSI_Alri_Treatment._get_cons_with_backups()
            • HSI_Alri_Treatment._assess_and_treat()
            • HSI_Alri_Treatment._has_staph_aureus()
            • HSI_Alri_Treatment._get_imci_classification_based_on_symptoms()
            • HSI_Alri_Treatment._get_imci_classification_by_SpO2_measure()
            • HSI_Alri_Treatment._get_classification_given_by_health_worker()
            • HSI_Alri_Treatment._get_disease_classification_for_treatment_decision()
            • HSI_Alri_Treatment._do_action_given_classification()
            • HSI_Alri_Treatment._provide_bronchodilator_if_wheeze()
            • HSI_Alri_Treatment.do_on_follow_up_following_treatment_failure()
            • HSI_Alri_Treatment.apply()
            • HSI_Alri_Treatment.never_ran()
          • AlriLoggingEvent
            • AlriLoggingEvent.__init__()
            • AlriLoggingEvent.new_case()
            • AlriLoggingEvent.new_recovered_case()
            • AlriLoggingEvent.new_cured_case()
            • AlriLoggingEvent.new_death()
            • AlriLoggingEvent.new_seeking_care()
            • AlriLoggingEvent.new_treated()
            • AlriLoggingEvent.new_pulmonary_complication_case()
            • AlriLoggingEvent.new_systemic_complication_case()
            • AlriLoggingEvent.new_hypoxaemic_case()
            • AlriLoggingEvent.apply()
          • AlriCheckPropertiesEvent
            • AlriCheckPropertiesEvent.__init__()
            • AlriCheckPropertiesEvent.apply()
          • AlriIndividualLoggingEvent
            • AlriIndividualLoggingEvent.__init__()
            • AlriIndividualLoggingEvent.apply()
          • AlriPropertiesOfOtherModules
            • AlriPropertiesOfOtherModules.read_parameters()
            • AlriPropertiesOfOtherModules.initialise_population()
            • AlriPropertiesOfOtherModules.initialise_simulation()
            • AlriPropertiesOfOtherModules.on_birth()
          • AlriIncidentCase_Lethal_DangerSigns_Pneumonia
            • AlriIncidentCase_Lethal_DangerSigns_Pneumonia.__init__()
            • AlriIncidentCase_Lethal_DangerSigns_Pneumonia.apply()
          • AlriIncidentCase_NonLethal_Fast_Breathing_Pneumonia
            • AlriIncidentCase_NonLethal_Fast_Breathing_Pneumonia.__init__()
            • AlriIncidentCase_NonLethal_Fast_Breathing_Pneumonia.apply()
        • tlo.methods.bed_days module
        • tlo.methods.bladder_cancer module
          • BladderCancer
            • BladderCancer.__init__()
            • BladderCancer.read_parameters()
            • BladderCancer.initialise_population()
            • BladderCancer.initialise_simulation()
            • BladderCancer.on_birth()
            • BladderCancer.on_hsi_alert()
            • BladderCancer.report_daly_values()
            • BladderCancer.do_at_generic_first_appt()
          • BladderCancerMainPollingEvent
            • BladderCancerMainPollingEvent.__init__()
            • BladderCancerMainPollingEvent.apply()
          • HSI_BladderCancer_Investigation_Following_Blood_Urine
            • HSI_BladderCancer_Investigation_Following_Blood_Urine.__init__()
            • HSI_BladderCancer_Investigation_Following_Blood_Urine.apply()
          • HSI_BladderCancer_Investigation_Following_pelvic_pain
            • HSI_BladderCancer_Investigation_Following_pelvic_pain.__init__()
            • HSI_BladderCancer_Investigation_Following_pelvic_pain.apply()
          • HSI_BladderCancer_StartTreatment
            • HSI_BladderCancer_StartTreatment.__init__()
            • HSI_BladderCancer_StartTreatment.apply()
          • HSI_BladderCancer_PostTreatmentCheck
            • HSI_BladderCancer_PostTreatmentCheck.__init__()
            • HSI_BladderCancer_PostTreatmentCheck.apply()
          • HSI_BladderCancer_PalliativeCare
            • HSI_BladderCancer_PalliativeCare.__init__()
            • HSI_BladderCancer_PalliativeCare.apply()
          • BladderCancerLoggingEvent
            • BladderCancerLoggingEvent.__init__()
            • BladderCancerLoggingEvent.apply()
        • tlo.methods.breast_cancer module
          • BreastCancer
            • BreastCancer.__init__()
            • BreastCancer.read_parameters()
            • BreastCancer.initialise_population()
            • BreastCancer.initialise_simulation()
            • BreastCancer.on_birth()
            • BreastCancer.on_hsi_alert()
            • BreastCancer.report_daly_values()
            • BreastCancer.do_at_generic_first_appt()
          • BreastCancerMainPollingEvent
            • BreastCancerMainPollingEvent.__init__()
            • BreastCancerMainPollingEvent.apply()
          • HSI_BreastCancer_Investigation_Following_breast_lump_discernible
            • HSI_BreastCancer_Investigation_Following_breast_lump_discernible.__init__()
            • HSI_BreastCancer_Investigation_Following_breast_lump_discernible.apply()
          • HSI_BreastCancer_StartTreatment
            • HSI_BreastCancer_StartTreatment.__init__()
            • HSI_BreastCancer_StartTreatment.apply()
          • HSI_BreastCancer_PostTreatmentCheck
            • HSI_BreastCancer_PostTreatmentCheck.__init__()
            • HSI_BreastCancer_PostTreatmentCheck.apply()
          • HSI_BreastCancer_PalliativeCare
            • HSI_BreastCancer_PalliativeCare.__init__()
            • HSI_BreastCancer_PalliativeCare.apply()
          • BreastCancerLoggingEvent
            • BreastCancerLoggingEvent.__init__()
            • BreastCancerLoggingEvent.apply()
        • tlo.methods.cancer_consumables module
        • tlo.methods.cardio_metabolic_disorders module
          • CardioMetabolicDisorders
            • CardioMetabolicDisorders.__init__()
            • CardioMetabolicDisorders.read_parameters()
            • CardioMetabolicDisorders.initialise_population()
            • CardioMetabolicDisorders.initialise_simulation()
            • CardioMetabolicDisorders.build_linear_model()
            • CardioMetabolicDisorders.build_linear_model_symptoms()
            • CardioMetabolicDisorders.on_birth()
            • CardioMetabolicDisorders.update_risk_score()
            • CardioMetabolicDisorders.report_daly_values()
            • CardioMetabolicDisorders.on_hsi_alert()
            • CardioMetabolicDisorders.do_at_generic_first_appt()
            • CardioMetabolicDisorders.do_at_generic_first_appt_emergency()
          • CardioMetabolicDisorders_MainPollingEvent
            • CardioMetabolicDisorders_MainPollingEvent.__init__()
            • CardioMetabolicDisorders_MainPollingEvent.apply()
          • CardioMetabolicDisordersEvent
            • CardioMetabolicDisordersEvent.__init__()
            • CardioMetabolicDisordersEvent.apply()
          • CardioMetabolicDisordersDeathEvent
            • CardioMetabolicDisordersDeathEvent.__init__()
            • CardioMetabolicDisordersDeathEvent.apply()
            • CardioMetabolicDisordersDeathEvent.check_if_event_and_do_death()
          • CardioMetabolicDisordersWeightLossEvent
            • CardioMetabolicDisordersWeightLossEvent.__init__()
            • CardioMetabolicDisordersWeightLossEvent.apply()
          • CardioMetabolicDisorders_LoggingEvent
            • CardioMetabolicDisorders_LoggingEvent.__init__()
            • CardioMetabolicDisorders_LoggingEvent.apply()
          • HSI_CardioMetabolicDisorders_CommunityTestingForHypertension
            • HSI_CardioMetabolicDisorders_CommunityTestingForHypertension.__init__()
            • HSI_CardioMetabolicDisorders_CommunityTestingForHypertension.apply()
          • HSI_CardioMetabolicDisorders_Investigations
            • HSI_CardioMetabolicDisorders_Investigations.__init__()
            • HSI_CardioMetabolicDisorders_Investigations.do_for_each_condition()
            • HSI_CardioMetabolicDisorders_Investigations.apply()
          • HSI_CardioMetabolicDisorders_StartWeightLossAndMedication
            • HSI_CardioMetabolicDisorders_StartWeightLossAndMedication.__init__()
            • HSI_CardioMetabolicDisorders_StartWeightLossAndMedication.apply()
          • HSI_CardioMetabolicDisorders_Refill_Medication
            • HSI_CardioMetabolicDisorders_Refill_Medication.__init__()
            • HSI_CardioMetabolicDisorders_Refill_Medication.apply()
            • HSI_CardioMetabolicDisorders_Refill_Medication.did_not_run()
          • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment
            • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment.__init__()
            • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment.do_for_each_event_to_be_investigated()
            • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment.apply()
            • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment.did_not_run()
        • tlo.methods.care_of_women_during_pregnancy module
          • CareOfWomenDuringPregnancy
            • CareOfWomenDuringPregnancy.__init__()
            • CareOfWomenDuringPregnancy.read_parameters()
            • CareOfWomenDuringPregnancy.initialise_population()
            • CareOfWomenDuringPregnancy.get_and_store_pregnancy_item_codes()
            • CareOfWomenDuringPregnancy.initialise_simulation()
            • CareOfWomenDuringPregnancy.care_of_women_in_pregnancy_property_reset()
            • CareOfWomenDuringPregnancy.on_birth()
            • CareOfWomenDuringPregnancy.further_on_birth_care_of_women_in_pregnancy()
            • CareOfWomenDuringPregnancy.on_hsi_alert()
            • CareOfWomenDuringPregnancy.get_approx_days_of_pregnancy()
            • CareOfWomenDuringPregnancy.determine_gestational_age_for_next_contact()
            • CareOfWomenDuringPregnancy.antenatal_care_scheduler()
            • CareOfWomenDuringPregnancy.schedule_admission()
            • CareOfWomenDuringPregnancy.call_if_maternal_emergency_assessment_cant_run()
            • CareOfWomenDuringPregnancy.check_intervention_should_run_and_update_mni()
            • CareOfWomenDuringPregnancy.screening_interventions_delivered_at_every_contact()
            • CareOfWomenDuringPregnancy.iron_and_folic_acid_supplementation()
            • CareOfWomenDuringPregnancy.balance_energy_and_protein_supplementation()
            • CareOfWomenDuringPregnancy.insecticide_treated_bed_net()
            • CareOfWomenDuringPregnancy.tb_screening()
            • CareOfWomenDuringPregnancy.tetanus_vaccination()
            • CareOfWomenDuringPregnancy.calcium_supplementation()
            • CareOfWomenDuringPregnancy.point_of_care_hb_testing()
            • CareOfWomenDuringPregnancy.albendazole_administration()
            • CareOfWomenDuringPregnancy.hep_b_testing()
            • CareOfWomenDuringPregnancy.syphilis_screening_and_treatment()
            • CareOfWomenDuringPregnancy.hiv_testing()
            • CareOfWomenDuringPregnancy.iptp_administration()
            • CareOfWomenDuringPregnancy.gdm_screening()
            • CareOfWomenDuringPregnancy.interventions_delivered_each_visit_from_anc2()
            • CareOfWomenDuringPregnancy.check_anc1_can_run()
            • CareOfWomenDuringPregnancy.check_subsequent_anc_can_run()
            • CareOfWomenDuringPregnancy.full_blood_count_testing()
            • CareOfWomenDuringPregnancy.antenatal_blood_transfusion()
            • CareOfWomenDuringPregnancy.initiate_maintenance_anti_hypertensive_treatment()
            • CareOfWomenDuringPregnancy.initiate_treatment_for_severe_hypertension()
            • CareOfWomenDuringPregnancy.treatment_for_severe_pre_eclampsia_or_eclampsia()
            • CareOfWomenDuringPregnancy.antibiotics_for_prom()
            • CareOfWomenDuringPregnancy.ectopic_pregnancy_treatment_doesnt_run()
            • CareOfWomenDuringPregnancy.calculate_beddays()
          • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact
            • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact.__init__()
            • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact.apply()
            • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact.not_available()
          • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact
            • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact.__init__()
            • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact.apply()
            • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact.not_available()
          • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact
            • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact.__init__()
            • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact.apply()
            • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact.not_available()
          • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact
            • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact.__init__()
            • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact.apply()
            • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact.not_available()
          • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact
            • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact.__init__()
            • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact.apply()
            • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact.not_available()
          • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact
            • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact.__init__()
            • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact.apply()
            • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact.not_available()
          • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact
            • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact.__init__()
            • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact.apply()
            • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact.not_available()
          • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact
            • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact.__init__()
            • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact.apply()
            • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact.not_available()
          • HSI_CareOfWomenDuringPregnancy_FocusedANCVisit
            • HSI_CareOfWomenDuringPregnancy_FocusedANCVisit.__init__()
            • HSI_CareOfWomenDuringPregnancy_FocusedANCVisit.apply()
          • HSI_CareOfWomenDuringPregnancy_PresentsForInductionOfLabour
            • HSI_CareOfWomenDuringPregnancy_PresentsForInductionOfLabour.__init__()
            • HSI_CareOfWomenDuringPregnancy_PresentsForInductionOfLabour.apply()
          • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare
            • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare.__init__()
            • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare.apply()
            • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare.not_available()
          • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia
            • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia.__init__()
            • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia.apply()
            • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia.not_available()
          • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes
            • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes.__init__()
            • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes.apply()
            • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes.not_available()
          • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement
            • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement.__init__()
            • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement.apply()
            • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement.not_available()
          • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy
            • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.__init__()
            • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.apply()
            • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.never_ran()
            • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.did_not_run()
            • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.not_available()
          • CareOfWomenDuringPregnancyLoggingEvent
            • CareOfWomenDuringPregnancyLoggingEvent.__init__()
            • CareOfWomenDuringPregnancyLoggingEvent.apply()
        • tlo.methods.causes module
        • tlo.methods.chronicsyndrome module
          • ChronicSyndrome
            • ChronicSyndrome.__init__()
            • ChronicSyndrome.read_parameters()
            • ChronicSyndrome.initialise_population()
            • ChronicSyndrome.initialise_simulation()
            • ChronicSyndrome.on_birth()
            • ChronicSyndrome.on_hsi_alert()
            • ChronicSyndrome.report_daly_values()
            • ChronicSyndrome.do_at_generic_first_appt_emergency()
          • ChronicSyndromeEvent
            • ChronicSyndromeEvent.__init__()
            • ChronicSyndromeEvent.apply()
          • ChronicSyndromeDeathEvent
            • ChronicSyndromeDeathEvent.__init__()
            • ChronicSyndromeDeathEvent.apply()
          • ChronicSyndrome_LaunchOutreachEvent
            • ChronicSyndrome_LaunchOutreachEvent.__init__()
            • ChronicSyndrome_LaunchOutreachEvent.apply()
          • HSI_ChronicSyndrome_SeeksEmergencyCareAndGetsTreatment
            • HSI_ChronicSyndrome_SeeksEmergencyCareAndGetsTreatment.__init__()
            • HSI_ChronicSyndrome_SeeksEmergencyCareAndGetsTreatment.apply()
            • HSI_ChronicSyndrome_SeeksEmergencyCareAndGetsTreatment.did_not_run()
          • HSI_ChronicSyndrome_Outreach_Individual
            • HSI_ChronicSyndrome_Outreach_Individual.__init__()
            • HSI_ChronicSyndrome_Outreach_Individual.apply()
            • HSI_ChronicSyndrome_Outreach_Individual.did_not_run()
          • HSI_ChronicSyndrome_PopulationWideBehaviourChange
            • HSI_ChronicSyndrome_PopulationWideBehaviourChange.__init__()
            • HSI_ChronicSyndrome_PopulationWideBehaviourChange.apply()
          • ChronicSyndromeLoggingEvent
            • ChronicSyndromeLoggingEvent.__init__()
            • ChronicSyndromeLoggingEvent.apply()
        • tlo.methods.consumables module
        • tlo.methods.contraception module
          • Contraception
            • Contraception.__init__()
            • Contraception.read_parameters()
            • Contraception.pre_initialise_population()
            • Contraception.initialise_population()
            • Contraception.initialise_simulation()
            • Contraception.on_birth()
            • Contraception.end_pregnancy()
            • Contraception.process_params()
            • Contraception.update_params_for_interventions()
            • Contraception.select_contraceptive_following_birth()
            • Contraception.get_item_code_for_each_contraceptive()
            • Contraception.schedule_batch_of_contraceptive_changes()
            • Contraception.do_and_log_individual_contraception_change()
            • Contraception.schedule_births_for_first_9_months()
            • Contraception.on_simulation_end()
          • DirectBirth
            • DirectBirth.__init__()
            • DirectBirth.apply()
          • ContraceptionPoll
            • ContraceptionPoll.__init__()
            • ContraceptionPoll.apply()
            • ContraceptionPoll.update_contraceptive()
            • ContraceptionPoll.initiate()
            • ContraceptionPoll.discontinue_switch_or_continue()
            • ContraceptionPoll.update_pregnancy()
            • ContraceptionPoll.pregnancy_for_those_on_contraceptive()
            • ContraceptionPoll.pregnancy_for_those_not_on_contraceptive()
            • ContraceptionPoll.set_new_pregnancy()
          • ContraceptionLoggingEvent
            • ContraceptionLoggingEvent.__init__()
            • ContraceptionLoggingEvent.apply()
          • HSI_Contraception_FamilyPlanningAppt
            • HSI_Contraception_FamilyPlanningAppt.__init__()
            • HSI_Contraception_FamilyPlanningAppt.apply()
            • HSI_Contraception_FamilyPlanningAppt.post_apply_hook()
            • HSI_Contraception_FamilyPlanningAppt.reschedule()
            • HSI_Contraception_FamilyPlanningAppt.never_ran()
          • StartInterventions
            • StartInterventions.__init__()
            • StartInterventions.apply()
          • SimplifiedPregnancyAndLabour
            • SimplifiedPregnancyAndLabour.__init__()
            • SimplifiedPregnancyAndLabour.read_parameters()
            • SimplifiedPregnancyAndLabour.initialise_population()
            • SimplifiedPregnancyAndLabour.initialise_simulation()
            • SimplifiedPregnancyAndLabour.on_birth()
            • SimplifiedPregnancyAndLabour.set_date_of_labour()
          • EndOfPregnancyEvent
            • EndOfPregnancyEvent.__init__()
            • EndOfPregnancyEvent.apply()
        • tlo.methods.copd module
          • Copd
            • Copd.__init__()
            • Copd.read_parameters()
            • Copd.pre_initialise_population()
            • Copd.initialise_population()
            • Copd.initialise_simulation()
            • Copd.on_birth()
            • Copd.report_daly_values()
            • Copd.define_symptoms()
            • Copd.lookup_item_codes()
            • Copd.do_logging()
            • Copd._common_first_appt()
            • Copd.do_at_generic_first_appt()
            • Copd.do_at_generic_first_appt_emergency()
          • CopdPollEvent
            • CopdPollEvent.__init__()
            • CopdPollEvent.apply()
            • CopdPollEvent.gen_random_date_in_next_three_months()
            • CopdPollEvent.increment_category()
            • CopdPollEvent.progress_to_next_lung_function()
          • CopdExacerbationEvent
            • CopdExacerbationEvent.__init__()
            • CopdExacerbationEvent.apply()
          • CopdDeath
            • CopdDeath.__init__()
            • CopdDeath.apply()
          • HSI_Copd_TreatmentOnSevereExacerbation
            • HSI_Copd_TreatmentOnSevereExacerbation.__init__()
            • HSI_Copd_TreatmentOnSevereExacerbation.apply()
        • tlo.methods.demography module
          • Demography
            • Demography.__init__()
            • Demography.read_parameters()
            • Demography.pre_initialise_population()
            • Demography.initialise_population()
            • Demography.initialise_simulation()
            • Demography.on_birth()
            • Demography._edit_init_pop_to_prevent_persons_greater_than_max_age()
            • Demography._edit_init_pop_so_that_equal_number_in_each_district()
            • Demography.process_causes_of_death()
            • Demography.do_death()
            • Demography.create_mappers_from_causes_of_death_to_label()
            • Demography.calc_py_lived_in_last_year()
            • Demography.compute_initial_model_to_data_popsize_ratio()
          • AgeUpdateEvent
            • AgeUpdateEvent.__init__()
            • AgeUpdateEvent.apply()
          • OtherDeathPoll
            • OtherDeathPoll.__init__()
            • OtherDeathPoll.get_mort_risk_per_poll()
            • OtherDeathPoll.get_all_cause_mort_risk_per_poll()
            • OtherDeathPoll.get_proportion_of_deaths_to_represent_as_other_deaths()
            • OtherDeathPoll.apply()
          • InstantaneousDeath
            • InstantaneousDeath.__init__()
            • InstantaneousDeath.apply()
          • DemographyLoggingEvent
            • DemographyLoggingEvent.__init__()
            • DemographyLoggingEvent.apply()
        • tlo.methods.depression module
          • Depression
            • Depression.__init__()
            • Depression.read_parameters()
            • Depression.apply_linear_model()
            • Depression.initialise_population()
            • Depression.initialise_simulation()
            • Depression.on_birth()
            • Depression.on_hsi_alert()
            • Depression.report_daly_values()
            • Depression._check_for_suspected_depression()
            • Depression.do_on_presentation_to_care()
            • Depression.do_when_suspected_depression()
            • Depression.do_at_generic_first_appt()
            • Depression.do_at_generic_first_appt_emergency()
          • DepressionPollingEvent
            • DepressionPollingEvent.__init__()
            • DepressionPollingEvent.apply()
          • DepressionSelfHarmEvent
            • DepressionSelfHarmEvent.__init__()
            • DepressionSelfHarmEvent.apply()
          • DepressionSuicideEvent
            • DepressionSuicideEvent.__init__()
            • DepressionSuicideEvent.apply()
          • DepressionLoggingEvent
            • DepressionLoggingEvent.__init__()
            • DepressionLoggingEvent.apply()
          • HSI_Depression_TalkingTherapy
            • HSI_Depression_TalkingTherapy.__init__()
            • HSI_Depression_TalkingTherapy.apply()
          • HSI_Depression_Start_Antidepressant
            • HSI_Depression_Start_Antidepressant.__init__()
            • HSI_Depression_Start_Antidepressant.apply()
          • HSI_Depression_Refill_Antidepressant
            • HSI_Depression_Refill_Antidepressant.__init__()
            • HSI_Depression_Refill_Antidepressant.apply()
            • HSI_Depression_Refill_Antidepressant.did_not_run()
        • tlo.methods.diarrhoea module
          • Overview
          • Diarrhoea
            • Diarrhoea.__init__()
            • Diarrhoea.read_parameters()
            • Diarrhoea.initialise_population()
            • Diarrhoea.initialise_simulation()
            • Diarrhoea.on_birth()
            • Diarrhoea.on_hsi_alert()
            • Diarrhoea.report_daly_values()
            • Diarrhoea.look_up_consumables()
            • Diarrhoea.do_treatment()
            • Diarrhoea.cancel_death_date()
            • Diarrhoea.end_episode()
            • Diarrhoea.check_properties()
            • Diarrhoea.do_at_generic_first_appt()
          • DiarrhoeaPollingEvent
            • DiarrhoeaPollingEvent.__init__()
            • DiarrhoeaPollingEvent.compute_fraction_of_year_between_polling_event()
            • DiarrhoeaPollingEvent.apply()
          • DiarrhoeaIncidentCase
            • DiarrhoeaIncidentCase.__init__()
            • DiarrhoeaIncidentCase.apply()
          • DiarrhoeaNaturalRecoveryEvent
            • DiarrhoeaNaturalRecoveryEvent.__init__()
            • DiarrhoeaNaturalRecoveryEvent.apply()
          • DiarrhoeaDeathEvent
            • DiarrhoeaDeathEvent.__init__()
            • DiarrhoeaDeathEvent.apply()
          • DiarrhoeaCureEvent
            • DiarrhoeaCureEvent.__init__()
            • DiarrhoeaCureEvent.apply()
          • HSI_Diarrhoea_Treatment_Outpatient
            • HSI_Diarrhoea_Treatment_Outpatient.__init__()
            • HSI_Diarrhoea_Treatment_Outpatient.apply()
          • HSI_Diarrhoea_Treatment_Inpatient
            • HSI_Diarrhoea_Treatment_Inpatient.__init__()
            • HSI_Diarrhoea_Treatment_Inpatient.apply()
          • DiarrhoeaPropertiesOfOtherModules
            • DiarrhoeaPropertiesOfOtherModules.__init__()
            • DiarrhoeaPropertiesOfOtherModules.read_parameters()
            • DiarrhoeaPropertiesOfOtherModules.initialise_population()
            • DiarrhoeaPropertiesOfOtherModules.initialise_simulation()
            • DiarrhoeaPropertiesOfOtherModules.on_birth()
          • DiarrhoeaCheckPropertiesEvent
            • DiarrhoeaCheckPropertiesEvent.__init__()
            • DiarrhoeaCheckPropertiesEvent.apply()
        • tlo.methods.dxmanager module
        • tlo.methods.enhanced_lifestyle module
          • Lifestyle
            • Lifestyle.__init__()
            • Lifestyle.read_parameters()
            • Lifestyle.pre_initialise_population()
            • Lifestyle.initialise_population()
            • Lifestyle.initialise_simulation()
            • Lifestyle.on_birth()
          • LifestyleEvent
            • LifestyleEvent.__init__()
            • LifestyleEvent.apply()
          • LifestylesLoggingEvent
            • LifestylesLoggingEvent.__init__()
            • LifestylesLoggingEvent.apply()
        • tlo.methods.epi module
          • Epi
            • Epi.__init__()
            • Epi.read_parameters()
            • Epi.initialise_population()
            • Epi.initialise_simulation()
            • Epi.on_birth()
            • Epi.report_daly_values()
            • Epi.increment_dose()
            • Epi.get_item_codes()
          • HpvScheduleEvent
            • HpvScheduleEvent.__init__()
            • HpvScheduleEvent.apply()
          • HsiBaseVaccine
            • HsiBaseVaccine.__init__()
            • HsiBaseVaccine.treatment_id()
            • HsiBaseVaccine.apply()
          • HSI_BcgVaccine
            • HSI_BcgVaccine.treatment_id()
            • HSI_BcgVaccine.apply()
          • HSI_opv
            • HSI_opv.treatment_id()
            • HSI_opv.apply()
          • HSI_DtpHibHepVaccine
            • HSI_DtpHibHepVaccine.treatment_id()
            • HSI_DtpHibHepVaccine.apply()
          • HSI_RotaVaccine
            • HSI_RotaVaccine.treatment_id()
            • HSI_RotaVaccine.apply()
          • HSI_PneumoVaccine
            • HSI_PneumoVaccine.treatment_id()
            • HSI_PneumoVaccine.apply()
          • HSI_MeaslesRubellaVaccine
            • HSI_MeaslesRubellaVaccine.treatment_id()
            • HSI_MeaslesRubellaVaccine.apply()
          • HSI_HpvVaccine
            • HSI_HpvVaccine.treatment_id()
            • HSI_HpvVaccine.apply()
          • HSI_TdVaccine
            • HSI_TdVaccine.treatment_id()
            • HSI_TdVaccine.apply()
          • EpiLoggingEvent
            • EpiLoggingEvent.__init__()
            • EpiLoggingEvent.apply()
        • tlo.methods.epilepsy module
          • Epilepsy
            • Epilepsy.__init__()
            • Epilepsy.read_parameters()
            • Epilepsy.initialise_population()
            • Epilepsy.initialise_simulation()
            • Epilepsy.on_birth()
            • Epilepsy.report_daly_values()
            • Epilepsy.transition_seizure_stat()
            • Epilepsy.stop_antiep()
            • Epilepsy.get_best_available_medicine()
            • Epilepsy.do_at_generic_first_appt_emergency()
          • EpilepsyEvent
            • EpilepsyEvent.__init__()
            • EpilepsyEvent.apply()
          • EpilepsyLoggingEvent
            • EpilepsyLoggingEvent.__init__()
            • EpilepsyLoggingEvent.apply()
          • HSI_Epilepsy_Start_Anti_Epileptic
            • HSI_Epilepsy_Start_Anti_Epileptic.__init__()
            • HSI_Epilepsy_Start_Anti_Epileptic.apply()
          • HSI_Epilepsy_Follow_Up
            • HSI_Epilepsy_Follow_Up.__init__()
            • HSI_Epilepsy_Follow_Up.apply()
        • tlo.methods.equipment module
        • tlo.methods.fullmodel module
        • tlo.methods.healthburden module
          • HealthBurden
            • HealthBurden.__init__()
            • HealthBurden.read_parameters()
            • HealthBurden.initialise_population()
            • HealthBurden.initialise_simulation()
            • HealthBurden.process_causes_of_disability()
            • HealthBurden.process_causes_of_dalys()
            • HealthBurden.on_birth()
            • HealthBurden.on_simulation_end()
            • HealthBurden.get_dalys()
            • HealthBurden.get_daly_weight()
            • HealthBurden.report_live_years_lost()
            • HealthBurden.decompose_yll_by_age_and_time()
            • HealthBurden.write_to_log()
            • HealthBurden.check_multi_index()
          • Get_Current_DALYS
            • Get_Current_DALYS.__init__()
            • Get_Current_DALYS.apply()
          • Healthburden_WriteToLog
            • Healthburden_WriteToLog.__init__()
            • Healthburden_WriteToLog.apply()
        • tlo.methods.healthseekingbehaviour module
          • HealthSeekingBehaviour
            • HealthSeekingBehaviour.__init__()
            • HealthSeekingBehaviour.read_parameters()
            • HealthSeekingBehaviour.initialise_population()
            • HealthSeekingBehaviour.initialise_simulation()
            • HealthSeekingBehaviour.on_birth()
            • HealthSeekingBehaviour.define_linear_models()
            • HealthSeekingBehaviour.do_at_generic_first_appt_emergency()
          • HealthSeekingBehaviourPoll
            • HealthSeekingBehaviourPoll.__init__()
            • HealthSeekingBehaviourPoll._has_any_symptoms()
            • HealthSeekingBehaviourPoll.apply()
        • tlo.methods.healthsystem module
          • HealthSystem
            • HealthSystem.__init__()
            • HealthSystem.read_parameters()
            • HealthSystem.pre_initialise_population()
            • HealthSystem.initialise_population()
            • HealthSystem.initialise_simulation()
            • HealthSystem.on_birth()
            • HealthSystem.on_simulation_end()
            • HealthSystem.setup_priority_policy()
            • HealthSystem.process_healthsystem_organisation_files()
            • HealthSystem.setup_daily_capabilities()
            • HealthSystem.format_daily_capabilities()
            • HealthSystem._rescale_capabilities_to_capture_effective_capability()
            • HealthSystem.update_consumables_availability_to_represent_merging_of_levels_1b_and_2()
            • HealthSystem.get_service_availability()
            • HealthSystem.get_cons_availability()
            • HealthSystem.get_beds_availability()
            • HealthSystem.get_equip_availability()
            • HealthSystem.schedule_to_call_never_ran_on_date()
            • HealthSystem.get_mode_appt_constraints()
            • HealthSystem.get_priority_policy_initial()
            • HealthSystem.load_priority_policy()
            • HealthSystem.schedule_hsi_event()
            • HealthSystem._add_hsi_event_queue_item_to_hsi_event_queue()
            • HealthSystem.enforce_priority_policy()
            • HealthSystem.check_hsi_event_is_valid()
            • HealthSystem.is_treatment_id_allowed()
            • HealthSystem.schedule_batch_of_individual_hsi_events()
            • HealthSystem.appt_footprint_is_valid()
            • HealthSystem.get_blank_appt_footprint()
            • HealthSystem.get_facility_info()
            • HealthSystem.get_appt_footprint_as_time_request()
            • HealthSystem.get_squeeze_factors()
            • HealthSystem.record_hsi_event()
            • HealthSystem.write_to_hsi_log()
            • HealthSystem.call_and_record_never_ran_hsi_event()
            • HealthSystem.write_to_never_ran_hsi_log()
            • HealthSystem.log_current_capabilities_and_usage()
            • HealthSystem.remove_beddays_footprint()
            • HealthSystem.find_events_for_person()
            • HealthSystem.reset_queue()
            • HealthSystem.get_item_codes_from_package_name()
            • HealthSystem.get_item_code_from_item_name()
            • HealthSystem.override_availability_of_consumables()
            • HealthSystem._write_hsi_event_counts_to_log_and_reset()
            • HealthSystem._write_never_ran_hsi_event_counts_to_log_and_reset()
            • HealthSystem.on_end_of_day()
            • HealthSystem.on_end_of_month()
            • HealthSystem.on_end_of_year()
            • HealthSystem.run_population_level_events()
            • HealthSystem.run_individual_level_events_in_mode_0_or_1()
          • HealthSystemScheduler
            • HealthSystemScheduler.__init__()
            • HealthSystemScheduler._is_last_day_of_the_year()
            • HealthSystemScheduler._is_last_day_of_the_month()
            • HealthSystemScheduler._get_events_due_today()
            • HealthSystemScheduler.process_events_mode_0_and_1()
            • HealthSystemScheduler.process_events_mode_2()
            • HealthSystemScheduler.apply()
          • HealthSystemChangeParameters
            • HealthSystemChangeParameters.__init__()
            • HealthSystemChangeParameters.apply()
          • DynamicRescalingHRCapabilities
            • DynamicRescalingHRCapabilities.__init__()
            • DynamicRescalingHRCapabilities._get_most_recent_year_specified_for_a_change_in_configuration()
            • DynamicRescalingHRCapabilities.apply()
          • ConstantRescalingHRCapabilities
            • ConstantRescalingHRCapabilities.__init__()
            • ConstantRescalingHRCapabilities.apply()
          • RescaleHRCapabilities_ByDistrict
            • RescaleHRCapabilities_ByDistrict.__init__()
            • RescaleHRCapabilities_ByDistrict.apply()
          • HealthSystemChangeMode
            • HealthSystemChangeMode.__init__()
            • HealthSystemChangeMode.apply()
        • tlo.methods.hiv module
          • Hiv
            • Hiv.__init__()
            • Hiv.read_parameters()
            • Hiv.pre_initialise_population()
            • Hiv._build_linear_models()
            • Hiv.initialise_population()
            • Hiv.initialise_baseline_prevalence()
            • Hiv.initialise_baseline_art()
            • Hiv.initialise_baseline_tested()
            • Hiv.initialise_simulation()
            • Hiv.update_parameters_for_program_scaleup()
            • Hiv.on_birth()
            • Hiv.report_daly_values()
            • Hiv.mtct_during_breastfeeding()
            • Hiv.do_new_infection()
            • Hiv.sample_time_from_infection_to_aids_given_parameters()
            • Hiv.get_time_from_infection_to_aids_distribution_parameters()
            • Hiv.get_time_from_aids_to_death()
            • Hiv.do_when_hiv_diagnosed()
            • Hiv.prob_art_start_after_test()
            • Hiv.prob_viral_suppression()
            • Hiv.stops_treatment()
            • Hiv.per_capita_testing_rate()
            • Hiv.decide_whether_hiv_test_for_mother()
            • Hiv.decide_whether_hiv_test_for_infant()
            • Hiv.check_config_of_properties()
            • Hiv.do_at_generic_first_appt()
          • HivRegularPollingEvent
            • HivRegularPollingEvent.__init__()
            • HivRegularPollingEvent.apply()
          • HivInfectionEvent
            • HivInfectionEvent.__init__()
            • HivInfectionEvent.apply()
          • HivInfectionDuringBreastFeedingEvent
            • HivInfectionDuringBreastFeedingEvent.__init__()
            • HivInfectionDuringBreastFeedingEvent.apply()
          • HivAidsOnsetEvent
            • HivAidsOnsetEvent.__init__()
            • HivAidsOnsetEvent.apply()
          • HivAidsDeathEvent
            • HivAidsDeathEvent.__init__()
            • HivAidsDeathEvent.apply()
          • HivAidsTbDeathEvent
            • HivAidsTbDeathEvent.__init__()
            • HivAidsTbDeathEvent.apply()
          • Hiv_DecisionToContinueOnPrEP
            • Hiv_DecisionToContinueOnPrEP.__init__()
            • Hiv_DecisionToContinueOnPrEP.apply()
          • Hiv_DecisionToContinueTreatment
            • Hiv_DecisionToContinueTreatment.__init__()
            • Hiv_DecisionToContinueTreatment.apply()
          • HivScaleUpEvent
            • HivScaleUpEvent.__init__()
            • HivScaleUpEvent.apply()
          • HSI_Hiv_TestAndRefer
            • HSI_Hiv_TestAndRefer.__init__()
            • HSI_Hiv_TestAndRefer.apply()
          • HSI_Hiv_Circ
            • HSI_Hiv_Circ.__init__()
            • HSI_Hiv_Circ.apply()
          • HSI_Hiv_StartInfantProphylaxis
            • HSI_Hiv_StartInfantProphylaxis.__init__()
            • HSI_Hiv_StartInfantProphylaxis.apply()
            • HSI_Hiv_StartInfantProphylaxis.never_ran()
          • HSI_Hiv_StartOrContinueOnPrep
            • HSI_Hiv_StartOrContinueOnPrep.__init__()
            • HSI_Hiv_StartOrContinueOnPrep.apply()
            • HSI_Hiv_StartOrContinueOnPrep.never_ran()
          • HSI_Hiv_StartOrContinueTreatment
            • HSI_Hiv_StartOrContinueTreatment.__init__()
            • HSI_Hiv_StartOrContinueTreatment.apply()
            • HSI_Hiv_StartOrContinueTreatment.do_at_initiation()
            • HSI_Hiv_StartOrContinueTreatment.do_at_continuation()
            • HSI_Hiv_StartOrContinueTreatment.determine_vl_status()
            • HSI_Hiv_StartOrContinueTreatment.get_drugs()
            • HSI_Hiv_StartOrContinueTreatment.consider_tb()
            • HSI_Hiv_StartOrContinueTreatment.never_ran()
          • HSI_Hiv_EndOfLifeCare
            • HSI_Hiv_EndOfLifeCare.__init__()
            • HSI_Hiv_EndOfLifeCare.apply()
          • HivLoggingEvent
            • HivLoggingEvent.__init__()
            • HivLoggingEvent.apply()
          • HivCheckPropertiesEvent
            • HivCheckPropertiesEvent.__init__()
            • HivCheckPropertiesEvent.apply()
          • DummyHivModule
            • DummyHivModule.__init__()
            • DummyHivModule.read_parameters()
            • DummyHivModule.initialise_population()
            • DummyHivModule.initialise_simulation()
            • DummyHivModule.on_birth()
        • tlo.methods.hiv_tb_calibration module
          • Deviance
            • Deviance.__init__()
            • Deviance.read_parameters()
            • Deviance.initialise_population()
            • Deviance.initialise_simulation()
            • Deviance.on_birth()
            • Deviance.read_data_files()
            • Deviance.read_model_outputs()
            • Deviance.weighted_mean()
            • Deviance.record_death()
            • Deviance.on_simulation_end()
        • tlo.methods.hsi_event module
          • HSI_Event
            • HSI_Event.__init__()
            • HSI_Event._adjust_facility_level_to_merge_1b_and_2()
            • HSI_Event.apply()
            • HSI_Event.did_not_run()
            • HSI_Event.never_ran()
            • HSI_Event.post_apply_hook()
            • HSI_Event._run_after_hsi_event()
            • HSI_Event.run()
            • HSI_Event.get_consumables()
            • HSI_Event.make_beddays_footprint()
            • HSI_Event.is_all_beddays_allocated()
            • HSI_Event.make_appt_footprint()
            • HSI_Event.add_equipment()
            • HSI_Event.probability_all_equipment_available()
            • HSI_Event.initialise()
            • HSI_Event._check_if_appt_footprint_can_run()
            • HSI_Event._return_item_codes_in_dict()
            • HSI_Event.as_namedtuple()
          • HSIEventWrapper
            • HSIEventWrapper.__init__()
            • HSIEventWrapper.run()
        • tlo.methods.hsi_generic_first_appts module
          • _BaseHSIGenericFirstAppt
            • _BaseHSIGenericFirstAppt.__init__()
            • _BaseHSIGenericFirstAppt._diagnosis_function()
            • _BaseHSIGenericFirstAppt._do_at_generic_first_appt_for_module()
            • _BaseHSIGenericFirstAppt.apply()
          • HSI_GenericNonEmergencyFirstAppt
            • HSI_GenericNonEmergencyFirstAppt.__init__()
            • HSI_GenericNonEmergencyFirstAppt._do_at_generic_first_appt_for_module()
          • HSI_GenericEmergencyFirstAppt
            • HSI_GenericEmergencyFirstAppt.__init__()
            • HSI_GenericEmergencyFirstAppt._do_at_generic_first_appt_for_module()
          • HSI_EmergencyCare_SpuriousSymptom
            • HSI_EmergencyCare_SpuriousSymptom.__init__()
            • HSI_EmergencyCare_SpuriousSymptom.apply()
        • tlo.methods.labour module
          • Labour
            • Labour.__init__()
            • Labour.read_parameters()
            • Labour.initialise_population()
            • Labour.get_and_store_labour_item_codes()
            • Labour.initialise_simulation()
            • Labour.on_birth()
            • Labour.further_on_birth_labour()
            • Labour.on_hsi_alert()
            • Labour.report_daly_values()
            • Labour.set_date_of_labour()
            • Labour.predict()
            • Labour.reset_due_date()
            • Labour.check_labour_can_proceed()
            • Labour.set_intrapartum_complications()
            • Labour.set_postpartum_complications()
            • Labour.progression_of_hypertensive_disorders()
            • Labour.apply_risk_of_early_postpartum_death()
            • Labour.labour_characteristics_checker()
            • Labour.postpartum_characteristics_checker()
            • Labour.prophylactic_labour_interventions()
            • Labour.determine_delivery_mode_in_spe_or_ec()
            • Labour.assessment_and_treatment_of_severe_pre_eclampsia_mgso4()
            • Labour.assessment_and_treatment_of_hypertension()
            • Labour.assessment_and_treatment_of_eclampsia()
            • Labour.assessment_for_assisted_vaginal_delivery()
            • Labour.assessment_and_treatment_of_maternal_sepsis()
            • Labour.assessment_and_plan_for_antepartum_haemorrhage()
            • Labour.assessment_for_referral_uterine_rupture()
            • Labour.active_management_of_the_third_stage_of_labour()
            • Labour.assessment_and_treatment_of_pph_uterine_atony()
            • Labour.assessment_and_treatment_of_pph_retained_placenta()
            • Labour.surgical_management_of_pph()
            • Labour.blood_transfusion()
            • Labour.assessment_and_treatment_of_anaemia()
            • Labour.assessment_for_depression()
            • Labour.interventions_delivered_pre_discharge()
            • Labour.run_if_receives_skilled_birth_attendance_cant_run()
            • Labour.run_if_receives_postnatal_check_cant_run()
            • Labour.run_if_receives_comprehensive_emergency_obstetric_care_cant_run()
            • Labour.do_at_generic_first_appt_emergency()
          • LabourOnsetEvent
            • LabourOnsetEvent.__init__()
            • LabourOnsetEvent.apply()
          • LabourAtHomeEvent
            • LabourAtHomeEvent.__init__()
            • LabourAtHomeEvent.apply()
          • LabourDeathAndStillBirthEvent
            • LabourDeathAndStillBirthEvent.__init__()
            • LabourDeathAndStillBirthEvent.apply()
          • BirthAndPostnatalOutcomesEvent
            • BirthAndPostnatalOutcomesEvent.__init__()
            • BirthAndPostnatalOutcomesEvent.apply()
          • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour
            • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.__init__()
            • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.apply()
            • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.never_ran()
            • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.did_not_run()
            • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.not_available()
          • HSI_Labour_ReceivesPostnatalCheck
            • HSI_Labour_ReceivesPostnatalCheck.__init__()
            • HSI_Labour_ReceivesPostnatalCheck.apply()
            • HSI_Labour_ReceivesPostnatalCheck.never_ran()
            • HSI_Labour_ReceivesPostnatalCheck.did_not_run()
            • HSI_Labour_ReceivesPostnatalCheck.not_available()
            • HSI_Labour_ReceivesPostnatalCheck._get_facility_level_for_pnc()
          • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare
            • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.__init__()
            • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.apply()
            • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.never_ran()
            • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.did_not_run()
            • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.not_available()
          • HSI_Labour_PostnatalWardInpatientCare
            • HSI_Labour_PostnatalWardInpatientCare.__init__()
            • HSI_Labour_PostnatalWardInpatientCare.apply()
            • HSI_Labour_PostnatalWardInpatientCare.did_not_run()
            • HSI_Labour_PostnatalWardInpatientCare.not_available()
          • LabourAndPostnatalCareAnalysisEvent
            • LabourAndPostnatalCareAnalysisEvent.__init__()
            • LabourAndPostnatalCareAnalysisEvent.apply()
          • LabourLoggingEvent
            • LabourLoggingEvent.__init__()
            • LabourLoggingEvent.apply()
        • tlo.methods.labour_lm module
        • tlo.methods.malaria module
          • Malaria
            • Malaria.__init__()
            • Malaria.read_parameters()
            • Malaria.pre_initialise_population()
            • Malaria._build_linear_models()
            • Malaria.initialise_population()
            • Malaria.malaria_poll2()
            • Malaria.general_population_rdt_scheduler()
            • Malaria.initialise_simulation()
            • Malaria.update_parameters_for_program_scaleup()
            • Malaria.on_birth()
            • Malaria.report_daly_values()
            • Malaria.check_if_fever_is_caused_by_malaria()
            • Malaria.do_at_generic_first_appt()
            • Malaria.do_at_generic_first_appt_emergency()
          • MalariaPollingEventDistrict
            • MalariaPollingEventDistrict.__init__()
            • MalariaPollingEventDistrict.apply()
          • MalariaScaleUpEvent
            • MalariaScaleUpEvent.__init__()
            • MalariaScaleUpEvent.apply()
          • MalariaIPTp
            • MalariaIPTp.__init__()
            • MalariaIPTp.apply()
          • MalariaEndIPTpProtection
            • MalariaEndIPTpProtection.__init__()
            • MalariaEndIPTpProtection.apply()
          • MalariaDeathEvent
            • MalariaDeathEvent.__init__()
            • MalariaDeathEvent.apply()
          • HSI_Malaria_rdt
            • HSI_Malaria_rdt.__init__()
            • HSI_Malaria_rdt.apply()
          • HSI_Malaria_rdt_community
            • HSI_Malaria_rdt_community.__init__()
            • HSI_Malaria_rdt_community.apply()
          • HSI_Malaria_Treatment
            • HSI_Malaria_Treatment.__init__()
            • HSI_Malaria_Treatment.apply()
            • HSI_Malaria_Treatment.get_drugs()
            • HSI_Malaria_Treatment.did_not_run()
          • HSI_Malaria_Treatment_Complicated
            • HSI_Malaria_Treatment_Complicated.__init__()
            • HSI_Malaria_Treatment_Complicated.apply()
            • HSI_Malaria_Treatment_Complicated.did_not_run()
          • HSI_MalariaIPTp
            • HSI_MalariaIPTp.__init__()
            • HSI_MalariaIPTp.apply()
            • HSI_MalariaIPTp.did_not_run()
          • MalariaUpdateEvent
            • MalariaUpdateEvent.__init__()
            • MalariaUpdateEvent.apply()
          • MalariaParasiteClearanceEvent
            • MalariaParasiteClearanceEvent.__init__()
            • MalariaParasiteClearanceEvent.apply()
          • MalariaLoggingEvent
            • MalariaLoggingEvent.__init__()
            • MalariaLoggingEvent.apply()
          • MalariaTxLoggingEvent
            • MalariaTxLoggingEvent.__init__()
            • MalariaTxLoggingEvent.apply()
          • MalariaPrevDistrictLoggingEvent
            • MalariaPrevDistrictLoggingEvent.__init__()
            • MalariaPrevDistrictLoggingEvent.apply()
        • tlo.methods.measles module
          • Measles
            • Measles.__init__()
            • Measles.read_parameters()
            • Measles.pre_initialise_population()
            • Measles.initialise_population()
            • Measles.initialise_simulation()
            • Measles.on_birth()
            • Measles.report_daly_values()
            • Measles.process_parameters()
            • Measles.do_at_generic_first_appt()
          • MeaslesEvent
            • MeaslesEvent.__init__()
            • MeaslesEvent.apply()
          • MeaslesOnsetEvent
            • MeaslesOnsetEvent.__init__()
            • MeaslesOnsetEvent.apply()
            • MeaslesOnsetEvent.assign_symptoms()
            • MeaslesOnsetEvent.get_prob_death()
          • MeaslesSymptomResolveEvent
            • MeaslesSymptomResolveEvent.__init__()
            • MeaslesSymptomResolveEvent.apply()
          • MeaslesDeathEvent
            • MeaslesDeathEvent.__init__()
            • MeaslesDeathEvent.apply()
          • HSI_Measles_Treatment
            • HSI_Measles_Treatment.__init__()
            • HSI_Measles_Treatment.apply()
            • HSI_Measles_Treatment.did_not_run()
          • MeaslesLoggingEvent
            • MeaslesLoggingEvent.__init__()
            • MeaslesLoggingEvent.apply()
          • MeaslesLoggingFortnightEvent
            • MeaslesLoggingFortnightEvent.__init__()
            • MeaslesLoggingFortnightEvent.apply()
          • MeaslesLoggingAnnualEvent
            • MeaslesLoggingAnnualEvent.__init__()
            • MeaslesLoggingAnnualEvent.apply()
        • tlo.methods.mockitis module
          • Mockitis
            • Mockitis.__init__()
            • Mockitis.read_parameters()
            • Mockitis.initialise_population()
            • Mockitis.initialise_simulation()
            • Mockitis.on_birth()
            • Mockitis.on_hsi_alert()
            • Mockitis.report_daly_values()
            • Mockitis.do_at_generic_first_appt_emergency()
          • MockitisEvent
            • MockitisEvent.__init__()
            • MockitisEvent.apply()
          • MockitisDeathEvent
            • MockitisDeathEvent.__init__()
            • MockitisDeathEvent.apply()
          • HSI_Mockitis_PresentsForCareWithSevereSymptoms
            • HSI_Mockitis_PresentsForCareWithSevereSymptoms.__init__()
            • HSI_Mockitis_PresentsForCareWithSevereSymptoms.apply()
            • HSI_Mockitis_PresentsForCareWithSevereSymptoms.did_not_run()
          • HSI_Mockitis_StartTreatment
            • HSI_Mockitis_StartTreatment.__init__()
            • HSI_Mockitis_StartTreatment.apply()
            • HSI_Mockitis_StartTreatment.did_not_run()
          • HSI_Mockitis_TreatmentMonitoring
            • HSI_Mockitis_TreatmentMonitoring.__init__()
            • HSI_Mockitis_TreatmentMonitoring.apply()
            • HSI_Mockitis_TreatmentMonitoring.did_not_run()
          • MockitisLoggingEvent
            • MockitisLoggingEvent.__init__()
            • MockitisLoggingEvent.apply()
        • tlo.methods.newborn_outcomes module
          • NewbornOutcomes
            • NewbornOutcomes.__init__()
            • NewbornOutcomes.read_parameters()
            • NewbornOutcomes.initialise_population()
            • NewbornOutcomes.get_and_store_newborn_item_codes()
            • NewbornOutcomes.initialise_simulation()
            • NewbornOutcomes.eval()
            • NewbornOutcomes.apply_risk_of_congenital_anomaly()
            • NewbornOutcomes.apply_risk_of_neonatal_infection_and_sepsis()
            • NewbornOutcomes.apply_risk_of_encephalopathy()
            • NewbornOutcomes.apply_risk_of_preterm_respiratory_distress_syndrome()
            • NewbornOutcomes.apply_risk_of_not_breathing_at_birth()
            • NewbornOutcomes.scheduled_week_one_postnatal_event()
            • NewbornOutcomes.set_death_status()
            • NewbornOutcomes.set_disability_status()
            • NewbornOutcomes.essential_newborn_care()
            • NewbornOutcomes.breast_feeding()
            • NewbornOutcomes.kangaroo_mother_care()
            • NewbornOutcomes.hiv_screening_for_at_risk_newborns()
            • NewbornOutcomes.apply_effect_of_neonatal_resus()
            • NewbornOutcomes.assessment_and_treatment_newborn_sepsis()
            • NewbornOutcomes.link_twins()
            • NewbornOutcomes.schedule_pnc()
            • NewbornOutcomes.on_birth()
            • NewbornOutcomes.on_hsi_alert()
            • NewbornOutcomes.report_daly_values()
            • NewbornOutcomes.run_if_care_of_the_receives_postnatal_check_cant_run()
          • HSI_NewbornOutcomes_ReceivesPostnatalCheck
            • HSI_NewbornOutcomes_ReceivesPostnatalCheck.__init__()
            • HSI_NewbornOutcomes_ReceivesPostnatalCheck.apply()
            • HSI_NewbornOutcomes_ReceivesPostnatalCheck.never_ran()
            • HSI_NewbornOutcomes_ReceivesPostnatalCheck.did_not_run()
            • HSI_NewbornOutcomes_ReceivesPostnatalCheck.not_available()
            • HSI_NewbornOutcomes_ReceivesPostnatalCheck._get_facility_level_for_pnc()
          • HSI_NewbornOutcomes_NeonatalWardInpatientCare
            • HSI_NewbornOutcomes_NeonatalWardInpatientCare.__init__()
            • HSI_NewbornOutcomes_NeonatalWardInpatientCare.apply()
            • HSI_NewbornOutcomes_NeonatalWardInpatientCare.did_not_run()
            • HSI_NewbornOutcomes_NeonatalWardInpatientCare.not_available()
          • BreastfeedingStatusUpdateEventSixMonths
            • BreastfeedingStatusUpdateEventSixMonths.__init__()
            • BreastfeedingStatusUpdateEventSixMonths.apply()
          • BreastfeedingStatusUpdateEventTwoYears
            • BreastfeedingStatusUpdateEventTwoYears.__init__()
            • BreastfeedingStatusUpdateEventTwoYears.apply()
        • tlo.methods.newborn_outcomes_lm module
        • tlo.methods.oesophagealcancer module
          • OesophagealCancer
            • OesophagealCancer.__init__()
            • OesophagealCancer.read_parameters()
            • OesophagealCancer.initialise_population()
            • OesophagealCancer.initialise_simulation()
            • OesophagealCancer.on_birth()
            • OesophagealCancer.on_hsi_alert()
            • OesophagealCancer.report_daly_values()
            • OesophagealCancer.do_at_generic_first_appt()
          • OesCancerMainPollingEvent
            • OesCancerMainPollingEvent.__init__()
            • OesCancerMainPollingEvent.apply()
          • HSI_OesophagealCancer_Investigation_Following_Dysphagia
            • HSI_OesophagealCancer_Investigation_Following_Dysphagia.__init__()
            • HSI_OesophagealCancer_Investigation_Following_Dysphagia.apply()
          • HSI_OesophagealCancer_StartTreatment
            • HSI_OesophagealCancer_StartTreatment.__init__()
            • HSI_OesophagealCancer_StartTreatment.apply()
          • HSI_OesophagealCancer_PostTreatmentCheck
            • HSI_OesophagealCancer_PostTreatmentCheck.__init__()
            • HSI_OesophagealCancer_PostTreatmentCheck.apply()
          • HSI_OesophagealCancer_PalliativeCare
            • HSI_OesophagealCancer_PalliativeCare.__init__()
            • HSI_OesophagealCancer_PalliativeCare.apply()
          • OesCancerLoggingEvent
            • OesCancerLoggingEvent.__init__()
            • OesCancerLoggingEvent.apply()
        • tlo.methods.other_adult_cancers module
          • OtherAdultCancer
            • OtherAdultCancer.__init__()
            • OtherAdultCancer.read_parameters()
            • OtherAdultCancer.initialise_population()
            • OtherAdultCancer.initialise_simulation()
            • OtherAdultCancer.on_birth()
            • OtherAdultCancer.on_hsi_alert()
            • OtherAdultCancer.report_daly_values()
            • OtherAdultCancer.do_at_generic_first_appt()
          • OtherAdultCancerMainPollingEvent
            • OtherAdultCancerMainPollingEvent.__init__()
            • OtherAdultCancerMainPollingEvent.apply()
          • HSI_OtherAdultCancer_Investigation_Following_early_other_adult_ca_symptom
            • HSI_OtherAdultCancer_Investigation_Following_early_other_adult_ca_symptom.__init__()
            • HSI_OtherAdultCancer_Investigation_Following_early_other_adult_ca_symptom.apply()
          • HSI_OtherAdultCancer_StartTreatment
            • HSI_OtherAdultCancer_StartTreatment.__init__()
            • HSI_OtherAdultCancer_StartTreatment.apply()
            • HSI_OtherAdultCancer_StartTreatment.did_not_run()
          • HSI_OtherAdultCancer_PostTreatmentCheck
            • HSI_OtherAdultCancer_PostTreatmentCheck.__init__()
            • HSI_OtherAdultCancer_PostTreatmentCheck.apply()
            • HSI_OtherAdultCancer_PostTreatmentCheck.did_not_run()
          • HSI_OtherAdultCancer_PalliativeCare
            • HSI_OtherAdultCancer_PalliativeCare.__init__()
            • HSI_OtherAdultCancer_PalliativeCare.apply()
            • HSI_OtherAdultCancer_PalliativeCare.did_not_run()
          • OtherAdultCancerLoggingEvent
            • OtherAdultCancerLoggingEvent.__init__()
            • OtherAdultCancerLoggingEvent.apply()
        • tlo.methods.postnatal_supervisor module
          • PostnatalSupervisor
            • PostnatalSupervisor.__init__()
            • PostnatalSupervisor.read_parameters()
            • PostnatalSupervisor.initialise_population()
            • PostnatalSupervisor.initialise_simulation()
            • PostnatalSupervisor.on_birth()
            • PostnatalSupervisor.further_on_birth_postnatal_supervisor()
            • PostnatalSupervisor.on_hsi_alert()
            • PostnatalSupervisor.report_daly_values()
            • PostnatalSupervisor.apply_linear_model()
            • PostnatalSupervisor.set_postnatal_complications_mothers()
            • PostnatalSupervisor.apply_risk_of_neonatal_complications_in_week_one()
            • PostnatalSupervisor.set_postnatal_complications_neonates()
            • PostnatalSupervisor.apply_risk_of_maternal_or_neonatal_death_postnatal()
          • PostnatalSupervisorEvent
            • PostnatalSupervisorEvent.__init__()
            • PostnatalSupervisorEvent.apply()
          • PostnatalWeekOneMaternalEvent
            • PostnatalWeekOneMaternalEvent.__init__()
            • PostnatalWeekOneMaternalEvent.apply()
          • PostnatalWeekOneNeonatalEvent
            • PostnatalWeekOneNeonatalEvent.__init__()
            • PostnatalWeekOneNeonatalEvent.apply()
          • HSI_PostnatalSupervisor_TreatmentForObstetricFistula
            • HSI_PostnatalSupervisor_TreatmentForObstetricFistula.__init__()
            • HSI_PostnatalSupervisor_TreatmentForObstetricFistula.apply()
        • tlo.methods.postnatal_supervisor_lm module
        • tlo.methods.pregnancy_helper_functions module
        • tlo.methods.pregnancy_supervisor module
          • PregnancySupervisor
            • PregnancySupervisor.__init__()
            • PregnancySupervisor.read_parameters()
            • PregnancySupervisor.initialise_population()
            • PregnancySupervisor.initialise_simulation()
            • PregnancySupervisor.on_birth()
            • PregnancySupervisor.further_on_birth_pregnancy_supervisor()
            • PregnancySupervisor.on_hsi_alert()
            • PregnancySupervisor.report_daly_values()
            • PregnancySupervisor.pregnancy_supervisor_property_reset()
            • PregnancySupervisor.apply_linear_model()
            • PregnancySupervisor.schedule_anc_one()
            • PregnancySupervisor.apply_risk_of_spontaneous_abortion()
            • PregnancySupervisor.apply_risk_of_induced_abortion()
            • PregnancySupervisor.do_after_abortion()
            • PregnancySupervisor.apply_risk_of_abortion_complications()
            • PregnancySupervisor.apply_risk_of_anaemia()
            • PregnancySupervisor.apply_risk_of_gestational_diabetes()
            • PregnancySupervisor.apply_risk_of_hypertensive_disorders()
            • PregnancySupervisor.apply_risk_of_progression_of_hypertension()
            • PregnancySupervisor.apply_risk_of_death_from_hypertension()
            • PregnancySupervisor.apply_risk_of_placental_abruption()
            • PregnancySupervisor.apply_risk_of_antepartum_haemorrhage()
            • PregnancySupervisor.apply_risk_of_premature_rupture_of_membranes_and_chorioamnionitis()
            • PregnancySupervisor.apply_risk_of_preterm_labour()
            • PregnancySupervisor.update_variables_post_still_birth_for_data_frame()
            • PregnancySupervisor.update_variables_post_still_birth_for_individual()
            • PregnancySupervisor.apply_risk_of_still_birth()
            • PregnancySupervisor.induction_care_seeking_and_still_birth_risk()
            • PregnancySupervisor.care_seeking_pregnancy_loss_complications()
            • PregnancySupervisor.apply_risk_of_death_from_monthly_complications()
            • PregnancySupervisor.schedule_first_anc_contact_for_new_pregnancy()
            • PregnancySupervisor.do_at_generic_first_appt_emergency()
          • PregnancySupervisorEvent
            • PregnancySupervisorEvent.__init__()
            • PregnancySupervisorEvent.apply()
          • EctopicPregnancyEvent
            • EctopicPregnancyEvent.__init__()
            • EctopicPregnancyEvent.apply()
          • EctopicPregnancyRuptureEvent
            • EctopicPregnancyRuptureEvent.__init__()
            • EctopicPregnancyRuptureEvent.apply()
          • EarlyPregnancyLossDeathEvent
            • EarlyPregnancyLossDeathEvent.__init__()
            • EarlyPregnancyLossDeathEvent.apply()
          • GestationalDiabetesGlycaemicControlEvent
            • GestationalDiabetesGlycaemicControlEvent.__init__()
            • GestationalDiabetesGlycaemicControlEvent.apply()
          • SyphilisInPregnancyEvent
            • SyphilisInPregnancyEvent.__init__()
            • SyphilisInPregnancyEvent.apply()
          • ParameterUpdateEvent
            • ParameterUpdateEvent.__init__()
            • ParameterUpdateEvent.apply()
          • PregnancyAnalysisEvent
            • PregnancyAnalysisEvent.__init__()
            • PregnancyAnalysisEvent.apply()
          • PregnancyLoggingEvent
            • PregnancyLoggingEvent.__init__()
            • PregnancyLoggingEvent.apply()
        • tlo.methods.pregnancy_supervisor_lm module
        • tlo.methods.prostate_cancer module
          • ProstateCancer
            • ProstateCancer.__init__()
            • ProstateCancer.read_parameters()
            • ProstateCancer.initialise_population()
            • ProstateCancer.initialise_simulation()
            • ProstateCancer.on_birth()
            • ProstateCancer.on_hsi_alert()
            • ProstateCancer.report_daly_values()
            • ProstateCancer.do_at_generic_first_appt()
          • ProstateCancerMainPollingEvent
            • ProstateCancerMainPollingEvent.__init__()
            • ProstateCancerMainPollingEvent.apply()
          • HSI_ProstateCancer_Investigation_Following_Urinary_Symptoms
            • HSI_ProstateCancer_Investigation_Following_Urinary_Symptoms.__init__()
            • HSI_ProstateCancer_Investigation_Following_Urinary_Symptoms.apply()
          • HSI_ProstateCancer_Investigation_Following_Pelvic_Pain
            • HSI_ProstateCancer_Investigation_Following_Pelvic_Pain.__init__()
            • HSI_ProstateCancer_Investigation_Following_Pelvic_Pain.apply()
          • HSI_ProstateCancer_Investigation_Following_psa_positive
            • HSI_ProstateCancer_Investigation_Following_psa_positive.__init__()
            • HSI_ProstateCancer_Investigation_Following_psa_positive.apply()
          • HSI_ProstateCancer_StartTreatment
            • HSI_ProstateCancer_StartTreatment.__init__()
            • HSI_ProstateCancer_StartTreatment.apply()
          • HSI_ProstateCancer_PostTreatmentCheck
            • HSI_ProstateCancer_PostTreatmentCheck.__init__()
            • HSI_ProstateCancer_PostTreatmentCheck.apply()
          • HSI_ProstateCancer_PalliativeCare
            • HSI_ProstateCancer_PalliativeCare.__init__()
            • HSI_ProstateCancer_PalliativeCare.apply()
          • ProstateCancerLoggingEvent
            • ProstateCancerLoggingEvent.__init__()
            • ProstateCancerLoggingEvent.apply()
        • tlo.methods.rti module
          • RTI
            • RTI.__init__()
            • RTI.read_parameters()
            • RTI.rti_injury_diagnosis()
            • RTI.initialise_population()
            • RTI.initialise_simulation()
            • RTI.rti_do_when_diagnosed()
            • RTI.rti_do_for_major_surgeries()
            • RTI.rti_do_for_minor_surgeries()
            • RTI.rti_acute_pain_management()
            • RTI.rti_ask_for_suture_kit()
            • RTI.rti_ask_for_shock_treatment()
            • RTI.rti_ask_for_burn_treatment()
            • RTI.rti_ask_for_fracture_casts()
            • RTI.rti_ask_for_open_fracture_treatment()
            • RTI.rti_ask_for_tetanus()
            • RTI.schedule_hsi_event_for_tomorrow()
            • RTI.rti_find_injury_column()
            • RTI.rti_find_all_columns_of_treated_injuries()
            • RTI.rti_assign_daly_weights()
            • RTI.rti_alter_daly_post_treatment()
            • RTI.rti_swap_injury_daly_upon_treatment()
            • RTI.rti_determine_LOS()
            • RTI.rti_find_and_count_injuries()
            • RTI.rti_treated_injuries()
            • RTI.on_birth()
            • RTI.look_up_consumable_item_codes()
            • RTI.on_hsi_alert()
            • RTI.report_daly_values()
            • RTI.rti_assign_injuries()
            • RTI._common_first_appt_steps()
            • RTI.do_at_generic_first_appt()
            • RTI.do_at_generic_first_appt_emergency()
          • RTIPollingEvent
            • RTIPollingEvent.__init__()
            • RTIPollingEvent.apply()
          • RTI_Check_Death_No_Med
            • RTI_Check_Death_No_Med.__init__()
            • RTI_Check_Death_No_Med.apply()
          • RTI_Recovery_Event
            • RTI_Recovery_Event.__init__()
            • RTI_Recovery_Event.apply()
          • HSI_RTI_Imaging_Event
            • HSI_RTI_Imaging_Event.__init__()
            • HSI_RTI_Imaging_Event.apply()
            • HSI_RTI_Imaging_Event.did_not_run()
          • HSI_RTI_Medical_Intervention
            • HSI_RTI_Medical_Intervention.__init__()
            • HSI_RTI_Medical_Intervention.apply()
            • HSI_RTI_Medical_Intervention.did_not_run()
          • HSI_RTI_Shock_Treatment
            • HSI_RTI_Shock_Treatment.__init__()
            • HSI_RTI_Shock_Treatment.apply()
            • HSI_RTI_Shock_Treatment.did_not_run()
          • HSI_RTI_Fracture_Cast
            • HSI_RTI_Fracture_Cast.__init__()
            • HSI_RTI_Fracture_Cast.apply()
            • HSI_RTI_Fracture_Cast.did_not_run()
          • HSI_RTI_Open_Fracture_Treatment
            • HSI_RTI_Open_Fracture_Treatment.__init__()
            • HSI_RTI_Open_Fracture_Treatment.apply()
            • HSI_RTI_Open_Fracture_Treatment.did_not_run()
          • HSI_RTI_Suture
            • HSI_RTI_Suture.__init__()
            • HSI_RTI_Suture.apply()
            • HSI_RTI_Suture.did_not_run()
          • HSI_RTI_Burn_Management
            • HSI_RTI_Burn_Management.__init__()
            • HSI_RTI_Burn_Management.apply()
            • HSI_RTI_Burn_Management.did_not_run()
          • HSI_RTI_Tetanus_Vaccine
            • HSI_RTI_Tetanus_Vaccine.__init__()
            • HSI_RTI_Tetanus_Vaccine.apply()
            • HSI_RTI_Tetanus_Vaccine.did_not_run()
          • HSI_RTI_Acute_Pain_Management
            • HSI_RTI_Acute_Pain_Management.__init__()
            • HSI_RTI_Acute_Pain_Management.apply()
            • HSI_RTI_Acute_Pain_Management.did_not_run()
          • HSI_RTI_Major_Surgeries
            • HSI_RTI_Major_Surgeries.__init__()
            • HSI_RTI_Major_Surgeries.apply()
            • HSI_RTI_Major_Surgeries.did_not_run()
          • HSI_RTI_Minor_Surgeries
            • HSI_RTI_Minor_Surgeries.__init__()
            • HSI_RTI_Minor_Surgeries.apply()
            • HSI_RTI_Minor_Surgeries.did_not_run()
          • RTI_Medical_Intervention_Death_Event
            • RTI_Medical_Intervention_Death_Event.__init__()
            • RTI_Medical_Intervention_Death_Event.apply()
          • RTI_No_Lifesaving_Medical_Intervention_Death_Event
            • RTI_No_Lifesaving_Medical_Intervention_Death_Event.__init__()
            • RTI_No_Lifesaving_Medical_Intervention_Death_Event.apply()
          • RTI_Logging_Event
            • RTI_Logging_Event.__init__()
            • RTI_Logging_Event.apply()
        • tlo.methods.scenario_switcher module
          • ImprovedHealthSystemAndCareSeekingScenarioSwitcher
            • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.__init__()
            • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.read_parameters()
            • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.pre_initialise_population()
            • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.update_parameters()
            • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.initialise_population()
            • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.initialise_simulation()
            • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.on_birth()
          • ScenarioSwitchEvent
            • ScenarioSwitchEvent.__init__()
            • ScenarioSwitchEvent.apply()
        • tlo.methods.schisto module
          • Schisto
            • Schisto.__init__()
            • Schisto.read_parameters()
            • Schisto.pre_initialise_population()
            • Schisto.initialise_population()
            • Schisto.initialise_simulation()
            • Schisto.on_birth()
            • Schisto.report_daly_values()
            • Schisto.do_effect_of_treatment()
            • Schisto._load_parameters_from_workbook()
            • Schisto._register_symptoms()
            • Schisto._get_disability_weight()
            • Schisto._get_item_code_for_praziquantel()
            • Schisto._schedule_mda_events()
            • Schisto.do_at_generic_first_appt()
          • SchistoInfectionWormBurdenEvent
            • SchistoInfectionWormBurdenEvent.__init__()
            • SchistoInfectionWormBurdenEvent.apply()
          • SchistoMatureWorms
            • SchistoMatureWorms.__init__()
            • SchistoMatureWorms.apply()
          • SchistoWormsNatDeath
            • SchistoWormsNatDeath.__init__()
            • SchistoWormsNatDeath.apply()
          • SchistoMDAEvent
            • SchistoMDAEvent.__init__()
            • SchistoMDAEvent.apply()
            • SchistoMDAEvent._select_recipients()
          • HSI_Schisto_TestingFollowingSymptoms
            • HSI_Schisto_TestingFollowingSymptoms.__init__()
            • HSI_Schisto_TestingFollowingSymptoms.apply()
          • HSI_Schisto_TreatmentFollowingDiagnosis
            • HSI_Schisto_TreatmentFollowingDiagnosis.__init__()
            • HSI_Schisto_TreatmentFollowingDiagnosis.apply()
          • HSI_Schisto_MDA
            • HSI_Schisto_MDA.__init__()
            • HSI_Schisto_MDA.apply()
          • SchistoLoggingEvent
            • SchistoLoggingEvent.__init__()
            • SchistoLoggingEvent.apply()
        • tlo.methods.simplified_births module
          • SimplifiedBirths
            • SimplifiedBirths.__init__()
            • SimplifiedBirths.read_parameters()
            • SimplifiedBirths.initialise_population()
            • SimplifiedBirths.initialise_simulation()
            • SimplifiedBirths.on_birth()
          • SimplifiedBirthsPoll
            • SimplifiedBirthsPoll.__init__()
            • SimplifiedBirthsPoll.apply()
            • SimplifiedBirthsPoll.set_new_pregnancies()
            • SimplifiedBirthsPoll.do_deliveries()
            • SimplifiedBirthsPoll.update_breastfed_status()
        • tlo.methods.skeleton module
          • Skeleton
            • Skeleton.__init__()
            • Skeleton.read_parameters()
            • Skeleton.initialise_population()
            • Skeleton.initialise_simulation()
            • Skeleton.on_birth()
            • Skeleton.report_daly_values()
            • Skeleton.on_hsi_alert()
          • Skeleton_Event
            • Skeleton_Event.__init__()
            • Skeleton_Event.apply()
          • Skeleton_LoggingEvent
            • Skeleton_LoggingEvent.__init__()
            • Skeleton_LoggingEvent.apply()
          • HSI_Skeleton_Example_Interaction
            • HSI_Skeleton_Example_Interaction.__init__()
            • HSI_Skeleton_Example_Interaction.apply()
            • HSI_Skeleton_Example_Interaction.did_not_run()
            • HSI_Skeleton_Example_Interaction.never_ran()
        • tlo.methods.stunting module
          • Overview
          • Stunting
            • Stunting.__init__()
            • Stunting.read_parameters()
            • Stunting.initialise_population()
            • Stunting.initialise_simulation()
            • Stunting.on_birth()
            • Stunting.look_up_consumable_item_codes()
            • Stunting.do_onset()
            • Stunting.do_progression()
            • Stunting.do_recovery()
            • Stunting.do_treatment()
            • Stunting.do_at_generic_first_appt()
          • StuntingPollingEvent
            • StuntingPollingEvent.__init__()
            • StuntingPollingEvent.apply()
            • StuntingPollingEvent.apply_model()
          • StuntingLoggingEvent
            • StuntingLoggingEvent.__init__()
            • StuntingLoggingEvent.apply()
          • HSI_Stunting_ComplementaryFeeding
            • HSI_Stunting_ComplementaryFeeding.__init__()
            • HSI_Stunting_ComplementaryFeeding.apply()
          • StuntingPropertiesOfOtherModules
            • StuntingPropertiesOfOtherModules.__init__()
            • StuntingPropertiesOfOtherModules.read_parameters()
            • StuntingPropertiesOfOtherModules.initialise_population()
            • StuntingPropertiesOfOtherModules.initialise_simulation()
            • StuntingPropertiesOfOtherModules.on_birth()
        • tlo.methods.symptommanager module
          • SymptomManager
            • SymptomManager.__init__()
            • SymptomManager.get_column_name_for_symptom()
            • SymptomManager.read_parameters()
            • SymptomManager.register_symptom()
            • SymptomManager.register_generic_symptoms()
            • SymptomManager.pre_initialise_population()
            • SymptomManager.initialise_population()
            • SymptomManager.initialise_simulation()
            • SymptomManager.on_birth()
            • SymptomManager.change_symptom()
            • SymptomManager.who_has()
            • SymptomManager.who_not_have()
            • SymptomManager.has_what()
            • SymptomManager.have_what()
            • SymptomManager.causes_of()
            • SymptomManager.clear_symptoms()
            • SymptomManager.caused_by()
            • SymptomManager.get_persons_with_newly_onset_symptoms()
            • SymptomManager.reset_persons_with_newly_onset_symptoms()
          • SymptomManager_AutoOnsetEvent
            • SymptomManager_AutoOnsetEvent.__init__()
            • SymptomManager_AutoOnsetEvent.apply()
          • SymptomManager_AutoResolveEvent
            • SymptomManager_AutoResolveEvent.__init__()
            • SymptomManager_AutoResolveEvent.apply()
          • SymptomManager_SpuriousSymptomOnset
            • SymptomManager_SpuriousSymptomOnset.__init__()
            • SymptomManager_SpuriousSymptomOnset.get_generic_symptoms_dict()
            • SymptomManager_SpuriousSymptomOnset.apply()
          • SymptomManager_SpuriousSymptomResolve
            • SymptomManager_SpuriousSymptomResolve.__init__()
            • SymptomManager_SpuriousSymptomResolve.schedule_symptom_resolve()
            • SymptomManager_SpuriousSymptomResolve.apply()
        • tlo.methods.tb module
          • Tb
            • Tb.__init__()
            • Tb.read_parameters()
            • Tb.pre_initialise_population()
            • Tb._build_linear_models()
            • Tb.send_for_screening_general()
            • Tb.select_tb_test()
            • Tb.get_consumables_for_dx_and_tx()
            • Tb.initialise_population()
            • Tb.initialise_simulation()
            • Tb.update_parameters_for_program_scaleup()
            • Tb.on_birth()
            • Tb.report_daly_values()
            • Tb.calculate_untreated_proportion()
            • Tb.assign_active_tb()
            • Tb.consider_ipt_for_those_initiating_art()
            • Tb.relapse_event()
            • Tb.end_treatment()
            • Tb.check_config_of_properties()
          • TbActiveCasePoll
            • TbActiveCasePoll.__init__()
            • TbActiveCasePoll.apply()
          • TbRegularEvents
            • TbRegularEvents.__init__()
            • TbRegularEvents.apply()
          • TbScaleUpEvent
            • TbScaleUpEvent.__init__()
            • TbScaleUpEvent.apply()
          • TbActiveEvent
            • TbActiveEvent.__init__()
            • TbActiveEvent.apply()
          • TbSelfCureEvent
            • TbSelfCureEvent.__init__()
            • TbSelfCureEvent.apply()
          • HSI_Tb_ScreeningAndRefer
            • HSI_Tb_ScreeningAndRefer.__init__()
            • HSI_Tb_ScreeningAndRefer.apply()
          • HSI_Tb_ClinicalDiagnosis
            • HSI_Tb_ClinicalDiagnosis.__init__()
            • HSI_Tb_ClinicalDiagnosis.apply()
          • HSI_Tb_Xray_level1b
            • HSI_Tb_Xray_level1b.__init__()
            • HSI_Tb_Xray_level1b.apply()
          • HSI_Tb_Xray_level2
            • HSI_Tb_Xray_level2.__init__()
            • HSI_Tb_Xray_level2.apply()
          • HSI_Tb_StartTreatment
            • HSI_Tb_StartTreatment.__init__()
            • HSI_Tb_StartTreatment.apply()
            • HSI_Tb_StartTreatment.select_treatment()
          • HSI_Tb_FollowUp
            • HSI_Tb_FollowUp.__init__()
            • HSI_Tb_FollowUp.apply()
          • HSI_Tb_Start_or_Continue_Ipt
            • HSI_Tb_Start_or_Continue_Ipt.__init__()
            • HSI_Tb_Start_or_Continue_Ipt.apply()
          • HSI_Tb_EndOfLifeCare
            • HSI_Tb_EndOfLifeCare.__init__()
            • HSI_Tb_EndOfLifeCare.apply()
          • Tb_DecisionToContinueIPT
            • Tb_DecisionToContinueIPT.__init__()
            • Tb_DecisionToContinueIPT.apply()
          • TbDecideDeathEvent
            • TbDecideDeathEvent.__init__()
            • TbDecideDeathEvent.apply()
          • TbDeathEvent
            • TbDeathEvent.__init__()
            • TbDeathEvent.apply()
          • TbLoggingEvent
            • TbLoggingEvent.__init__()
            • TbLoggingEvent.apply()
          • TbCheckPropertiesEvent
            • TbCheckPropertiesEvent.__init__()
            • TbCheckPropertiesEvent.apply()
          • DummyTbModule
            • DummyTbModule.__init__()
            • DummyTbModule.read_parameters()
            • DummyTbModule.initialise_population()
            • DummyTbModule.initialise_simulation()
            • DummyTbModule.on_birth()
        • tlo.methods.wasting module
          • Wasting
            • Wasting.__init__()
            • Wasting.read_parameters()
            • Wasting.initialise_population()
            • Wasting.initialise_simulation()
            • Wasting.on_birth()
      • Module contents
        • Metadata
          • Metadata.DISEASE_MODULE
          • Metadata.USES_SYMPTOMMANAGER
          • Metadata.USES_HEALTHSYSTEM
          • Metadata.USES_HEALTHBURDEN
    • tlo.test package
      • Submodules
        • tlo.test.random_birth module
          • RandomBirth
            • RandomBirth.PARAMETERS
            • RandomBirth.PROPERTIES
            • RandomBirth.read_parameters()
            • RandomBirth.initialise_population()
            • RandomBirth.initialise_simulation()
            • RandomBirth.on_birth()
            • RandomBirth.parameters
          • RandomPregnancyEvent
            • RandomPregnancyEvent.apply()
          • DelayedBirthEvent
            • DelayedBirthEvent.apply()
        • tlo.test.random_death module
          • RandomDeath
            • RandomDeath.PARAMETERS
            • RandomDeath.PROPERTIES
            • RandomDeath.read_parameters()
            • RandomDeath.initialise_population()
            • RandomDeath.initialise_simulation()
            • RandomDeath.on_birth()
            • RandomDeath.parameters
          • RandomDeathEvent
            • RandomDeathEvent.apply()
      • Module contents
  • Submodules
    • tlo.cli module
      • print_basic_job_details()
      • load_config()
      • load_server_config()
      • get_batch_client()
      • load_scenario()
      • is_file_clean()
      • print_batch_exception()
      • create_file_share()
      • create_directory()
      • upload_local_file()
      • create_job()
      • add_tasks()
    • tlo.core module
      • Types
        • Types.DATE
        • Types.BOOL
        • Types.INT
        • Types.REAL
        • Types.CATEGORICAL
        • Types.LIST
        • Types.SERIES
        • Types.DATA_FRAME
        • Types.STRING
        • Types.DICT
        • Types.BITSET
      • Specifiable
        • Specifiable.PANDAS_TYPE_MAP
        • Specifiable.PYTHON_TYPE_MAP
        • Specifiable.python_type
        • Specifiable.pandas_type
      • Parameter
      • Property
        • Property.PANDAS_TYPE_DEFAULT_VALUE_MAP
        • Property.create_series()
      • Module
        • Module.INIT_DEPENDENCIES
        • Module.OPTIONAL_INIT_DEPENDENCIES
        • Module.ADDITIONAL_DEPENDENCIES
        • Module.ALTERNATIVE_TO
        • Module.METADATA
        • Module.CAUSES_OF_DEATH
        • Module.CAUSES_OF_DISABILITY
        • Module.PARAMETERS
        • Module.PROPERTIES
        • Module.parameters
        • Module.load_parameters_from_dataframe()
        • Module.read_parameters()
        • Module.initialise_population()
        • Module.initialise_simulation()
        • Module.pre_initialise_population()
        • Module.on_birth()
        • Module.on_simulation_end()
    • tlo.dependencies module
      • ModuleDependencyError
      • MultipleModuleInstanceError
      • get_init_dependencies()
      • get_all_dependencies()
      • get_missing_dependencies()
      • initialise_missing_dependencies()
      • get_all_required_dependencies()
      • topologically_sort_modules()
      • is_valid_tlo_module_subclass()
      • get_module_class_map()
      • get_dependencies_and_initialise()
      • check_dependencies_present()
    • tlo.docs module
      • get_package_name()
      • generate_module_dict()
      • get_classes_in_module()
      • get_fully_qualified_name()
      • write_rst_file()
      • get_class_output_string()
      • which_functions_to_print()
      • extract_bases()
      • get_base_string()
      • get_link()
      • create_table()
    • tlo.events module
      • Priority
        • Priority.START_OF_DAY
        • Priority.FIRST_HALF_OF_DAY
        • Priority.LAST_HALF_OF_DAY
        • Priority.END_OF_DAY
      • Event
        • Event.post_apply_hook()
        • Event.apply()
        • Event.run()
      • RegularEvent
        • RegularEvent.apply()
        • RegularEvent.post_apply_hook()
      • PopulationScopeEventMixin
        • PopulationScopeEventMixin.apply()
      • IndividualScopeEventMixin
        • IndividualScopeEventMixin.apply()
    • tlo.lm module
      • Predictor
        • Predictor.when()
        • Predictor.otherwise()
        • Predictor.apply()
      • LinearModelType
        • LinearModelType.ADDITIVE
        • LinearModelType.LOGISTIC
        • LinearModelType.MULTIPLICATIVE
        • LinearModelType.CUSTOM
      • LinearModel
        • LinearModel.lm_type
        • LinearModel.intercept
        • LinearModel.predictors
        • LinearModel.multiplicative()
        • LinearModel.custom()
        • LinearModel.predict()
    • tlo.population module
      • IndividualProperties
        • IndividualProperties.synchronize_updates_to_dataframe()
        • IndividualProperties.finalize()
      • Population
        • Population.initial_size
        • Population.props
        • Population.new_row
        • Population.new_rows
        • Population.next_person_id
        • Population.do_birth()
        • Population.make_test_property()
        • Population.individual_properties()
    • tlo.progressbar module
      • ProgressBar
        • ProgressBar.GLYPHS
        • ProgressBar.n_step
        • ProgressBar.description
        • ProgressBar.step
        • ProgressBar.prop_complete
        • ProgressBar.perc_complete
        • ProgressBar.elapsed_time
        • ProgressBar.iter_rate
        • ProgressBar.est_remaining_time
        • ProgressBar.n_block_filled
        • ProgressBar.n_block_empty
        • ProgressBar.prop_partial_block
        • ProgressBar.filled_blocks
        • ProgressBar.empty_blocks
        • ProgressBar.partial_block
        • ProgressBar.progress_bar
        • ProgressBar.bar_color
        • ProgressBar.stats
        • ProgressBar.prefix
        • ProgressBar.postfix
        • ProgressBar.reset()
        • ProgressBar.update()
        • ProgressBar.refresh()
        • ProgressBar.start()
        • ProgressBar.stop()
      • StreamDisplay
        • StreamDisplay.close()
        • StreamDisplay.update()
      • AnsiStreamDisplay
        • AnsiStreamDisplay.update()
      • BasicStreamDisplay
        • BasicStreamDisplay.update()
    • tlo.scenario module
      • BaseScenario
        • BaseScenario.parse_arguments()
        • BaseScenario.add_arguments()
        • BaseScenario.log_configuration()
        • BaseScenario.modules()
        • BaseScenario.draw_parameters()
        • BaseScenario.get_log_config()
        • BaseScenario.save_draws()
      • ScenarioLoader
        • ScenarioLoader.get_scenario()
      • DrawGenerator
        • DrawGenerator.setup_draws()
        • DrawGenerator.get_draw()
        • DrawGenerator.get_run_config()
        • DrawGenerator.save_config()
      • SampleRunner
        • SampleRunner.number_of_draws
        • SampleRunner.runs_per_draw
        • SampleRunner.get_draw()
        • SampleRunner.get_samples_for_draw()
        • SampleRunner.get_sample()
        • SampleRunner.run_sample_by_number()
        • SampleRunner.run()
        • SampleRunner.override_parameters()
        • SampleRunner.low_bias_32()
      • make_cartesian_parameter_grid()
    • tlo.simulation module
      • SimulationPreviouslyInitialisedError
      • SimulationNotInitialisedError
      • Simulation
        • Simulation.log_filepath
        • Simulation.register()
        • Simulation.make_initial_population()
        • Simulation.initialise()
        • Simulation.finalise()
        • Simulation.close_output_file()
        • Simulation.run_simulation_to()
        • Simulation.simulate()
        • Simulation.schedule_event()
        • Simulation.fire_single_event()
        • Simulation.do_birth()
        • Simulation.find_events_for_person()
        • Simulation.save_to_pickle()
        • Simulation.load_from_pickle()
      • EventQueue
        • EventQueue.schedule()
        • EventQueue.pop_next_event_and_date()
        • EventQueue.date_of_next_event
    • tlo.util module
      • create_age_range_lookup()
      • transition_states()
      • sample_outcome()
      • BitsetHandler
        • BitsetHandler.df
        • BitsetHandler.element_repr()
        • BitsetHandler.to_strings()
        • BitsetHandler.set()
        • BitsetHandler.unset()
        • BitsetHandler.clear()
        • BitsetHandler.has()
        • BitsetHandler.has_all()
        • BitsetHandler.has_any()
        • BitsetHandler.get()
        • BitsetHandler.uncompress()
        • BitsetHandler.not_empty()
        • BitsetHandler.is_empty()
      • random_date()
      • str_to_pandas_date()
      • hash_dataframe()
      • get_person_id_to_inherit_from()
      • convert_excel_files_to_csv()
      • read_csv_files()
  • Module contents
• tlo.analysis package
  • Submodules
    • tlo.analysis.hsi_events module
      • is_valid_hsi_event_subclass()
      • get_hsi_event_classes_per_module()
      • get_details_of_defined_hsi_events()
      • sort_hsi_event_details()
      • format_hsi_event_details_as_csv()
      • format_hsi_event_details_as_table()
      • format_hsi_event_details_as_list()
      • merge_hsi_event_details()
      • get_all_defined_hsi_events_as_dataframe()
      • main()
    • tlo.analysis.life_expectancy module
      • calculate_probability_of_dying()
      • get_life_expectancy_estimates()
      • get_probability_of_premature_death()
    • tlo.analysis.utils module
      • parse_log_file()
      • merge_log_files()
      • write_log_to_excel()
      • make_calendar_period_lookup()
      • make_calendar_period_type()
      • make_age_grp_lookup()
      • make_age_grp_types()
      • to_age_group()
      • get_scenario_outputs()
      • get_scenario_info()
      • load_pickled_dataframes()
      • extract_params()
      • extract_results()
      • summarize()
      • get_grid()
      • format_gbd()
      • create_pickles_locally()
      • compare_number_of_deaths()
      • flatten_multi_index_series_into_dict_for_logging()
      • unflatten_flattened_multi_index_in_logging()
      • LogsDict
        • LogsDict.items()
        • LogsDict.keys()
        • LogsDict.values()
      • get_filtered_treatment_ids()
      • colors_in_matplotlib()
      • get_coarse_appt_type()
      • order_of_coarse_appt()
      • get_color_coarse_appt()
      • order_of_short_treatment_ids()
      • get_color_short_treatment_id()
      • order_of_cause_of_death_or_daly_label()
      • get_color_cause_of_death_or_daly_label()
      • squarify_neat()
      • get_root_path()
      • bin_hsi_event_details()
      • compute_mean_across_runs()
      • plot_stacked_bar_chart()
      • plot_clustered_stacked()
      • get_mappers_in_fullmodel()
      • get_parameters_for_status_quo()
      • get_parameters_for_standard_mode2_runs()
      • get_parameters_for_improved_healthsystem_and_healthcare_seeking()
      • mix_scenarios()
  • Module contents
• tlo.analysis.hsi_events module
  • is_valid_hsi_event_subclass()
  • get_hsi_event_classes_per_module()
  • get_details_of_defined_hsi_events()
  • sort_hsi_event_details()
  • format_hsi_event_details_as_csv()
  • format_hsi_event_details_as_table()
  • format_hsi_event_details_as_list()
  • merge_hsi_event_details()
  • get_all_defined_hsi_events_as_dataframe()
  • main()
• tlo.analysis.life_expectancy module
  • calculate_probability_of_dying()
  • get_life_expectancy_estimates()
  • get_probability_of_premature_death()
• tlo.analysis.utils module
  • parse_log_file()
  • merge_log_files()
  • write_log_to_excel()
  • make_calendar_period_lookup()
  • make_calendar_period_type()
  • make_age_grp_lookup()
  • make_age_grp_types()
  • to_age_group()
  • get_scenario_outputs()
  • get_scenario_info()
  • load_pickled_dataframes()
  • extract_params()
  • extract_results()
  • summarize()
  • get_grid()
  • format_gbd()
  • create_pickles_locally()
  • compare_number_of_deaths()
  • flatten_multi_index_series_into_dict_for_logging()
  • unflatten_flattened_multi_index_in_logging()
  • LogsDict
    • LogsDict.items()
    • LogsDict.keys()
    • LogsDict.values()
  • get_filtered_treatment_ids()
  • colors_in_matplotlib()
  • get_coarse_appt_type()
  • order_of_coarse_appt()
  • get_color_coarse_appt()
  • order_of_short_treatment_ids()
  • get_color_short_treatment_id()
  • order_of_cause_of_death_or_daly_label()
  • get_color_cause_of_death_or_daly_label()
  • squarify_neat()
  • get_root_path()
  • bin_hsi_event_details()
  • compute_mean_across_runs()
  • plot_stacked_bar_chart()
  • plot_clustered_stacked()
  • get_mappers_in_fullmodel()
  • get_parameters_for_status_quo()
  • get_parameters_for_standard_mode2_runs()
  • get_parameters_for_improved_healthsystem_and_healthcare_seeking()
  • mix_scenarios()
• tlo.cli module
  • print_basic_job_details()
  • load_config()
  • load_server_config()
  • get_batch_client()
  • load_scenario()
  • is_file_clean()
  • print_batch_exception()
  • create_file_share()
  • create_directory()
  • upload_local_file()
  • create_job()
  • add_tasks()
• tlo.core module
  • Types
    • Types.DATE
    • Types.BOOL
    • Types.INT
    • Types.REAL
    • Types.CATEGORICAL
    • Types.LIST
    • Types.SERIES
    • Types.DATA_FRAME
    • Types.STRING
    • Types.DICT
    • Types.BITSET
  • Specifiable
    • Specifiable.PANDAS_TYPE_MAP
    • Specifiable.PYTHON_TYPE_MAP
    • Specifiable.python_type
    • Specifiable.pandas_type
  • Parameter
  • Property
    • Property.PANDAS_TYPE_DEFAULT_VALUE_MAP
    • Property.create_series()
  • Module
    • Module.INIT_DEPENDENCIES
    • Module.OPTIONAL_INIT_DEPENDENCIES
    • Module.ADDITIONAL_DEPENDENCIES
    • Module.ALTERNATIVE_TO
    • Module.METADATA
    • Module.CAUSES_OF_DEATH
    • Module.CAUSES_OF_DISABILITY
    • Module.PARAMETERS
    • Module.PROPERTIES
    • Module.parameters
    • Module.load_parameters_from_dataframe()
    • Module.read_parameters()
    • Module.initialise_population()
    • Module.initialise_simulation()
    • Module.pre_initialise_population()
    • Module.on_birth()
    • Module.on_simulation_end()
• tlo.dependencies module
  • ModuleDependencyError
  • MultipleModuleInstanceError
  • get_init_dependencies()
  • get_all_dependencies()
  • get_missing_dependencies()
  • initialise_missing_dependencies()
  • get_all_required_dependencies()
  • topologically_sort_modules()
  • is_valid_tlo_module_subclass()
  • get_module_class_map()
  • get_dependencies_and_initialise()
  • check_dependencies_present()
• tlo.docs module
  • get_package_name()
  • generate_module_dict()
  • get_classes_in_module()
  • get_fully_qualified_name()
  • write_rst_file()
  • get_class_output_string()
  • which_functions_to_print()
  • extract_bases()
  • get_base_string()
  • get_link()
  • create_table()
• tlo.events module
  • Priority
    • Priority.START_OF_DAY
    • Priority.FIRST_HALF_OF_DAY
    • Priority.LAST_HALF_OF_DAY
    • Priority.END_OF_DAY
  • Event
    • Event.post_apply_hook()
    • Event.apply()
    • Event.run()
  • RegularEvent
    • RegularEvent.apply()
    • RegularEvent.post_apply_hook()
  • PopulationScopeEventMixin
    • PopulationScopeEventMixin.apply()
  • IndividualScopeEventMixin
    • IndividualScopeEventMixin.apply()
• tlo.lm module
  • Predictor
    • Predictor.when()
    • Predictor.otherwise()
    • Predictor.apply()
  • LinearModelType
    • LinearModelType.ADDITIVE
    • LinearModelType.LOGISTIC
    • LinearModelType.MULTIPLICATIVE
    • LinearModelType.CUSTOM
  • LinearModel
    • LinearModel.lm_type
    • LinearModel.intercept
    • LinearModel.predictors
    • LinearModel.multiplicative()
    • LinearModel.custom()
    • LinearModel.predict()
• tlo.logging package
  • Submodules
    • tlo.logging.core module
      • InconsistentLoggedColumnsWarning
      • initialise()
      • reset()
      • set_output_file()
      • disable()
      • getLogger()
      • Logger
        • Logger.HASH_LEN
        • Logger.level
        • Logger.handlers
        • Logger.addHandler()
        • Logger.isEnabledFor()
        • Logger.reset_attributes()
        • Logger.setLevel()
        • Logger.log()
        • Logger.critical()
        • Logger.debug()
        • Logger.info()
        • Logger.warning()
    • tlo.logging.encoding module
      • PandasEncoder
        • PandasEncoder.default()
    • tlo.logging.helpers module
      • set_logging_levels()
      • get_dataframe_row_as_dict_for_logging()
      • grouped_counts_with_all_combinations()
    • tlo.logging.reader module
      • LogData
        • LogData.parse_log_line()
        • LogData.get_log_dataframes()
        • LogData.parse_logged_dataframe()
  • Module contents
    • disable()
    • getLogger()
    • initialise()
    • reset()
    • set_output_file()
    • set_logging_levels()
• tlo.logging.core module
  • InconsistentLoggedColumnsWarning
  • initialise()
  • reset()
  • set_output_file()
  • disable()
  • getLogger()
  • Logger
    • Logger.HASH_LEN
    • Logger.level
    • Logger.handlers
    • Logger.addHandler()
    • Logger.isEnabledFor()
    • Logger.reset_attributes()
    • Logger.setLevel()
    • Logger.log()
    • Logger.critical()
    • Logger.debug()
    • Logger.info()
    • Logger.warning()
• tlo.logging.encoding module
  • PandasEncoder
    • PandasEncoder.default()
• tlo.logging.helpers module
  • set_logging_levels()
  • get_dataframe_row_as_dict_for_logging()
  • grouped_counts_with_all_combinations()
• tlo.logging.reader module
  • LogData
    • LogData.parse_log_line()
    • LogData.get_log_dataframes()
    • LogData.parse_logged_dataframe()
• tlo.methods package
  • Submodules
    • tlo.methods.alri module
      • Overview
      • Alri
        • Alri.__init__()
        • Alri.read_parameters()
        • Alri.check_params_read_in_ok()
        • Alri.define_symptoms()
        • Alri.pre_initialise_population()
        • Alri.initialise_population()
        • Alri.initialise_simulation()
        • Alri.on_birth()
        • Alri.report_daly_values()
        • Alri.over_ride_availability_of_certain_consumables()
        • Alri.look_up_consumables()
        • Alri.end_episode()
        • Alri.cancel_death_and_schedule_cure()
        • Alri.check_properties()
        • Alri.do_effects_of_treatment_and_return_outcome()
        • Alri.record_sought_care_for_alri()
        • Alri.get_imci_classification_based_on_symptoms()
        • Alri._ultimate_treatment_indicated_for_patient()
        • Alri.do_at_generic_first_appt()
        • Alri.do_at_generic_first_appt_emergency()
      • AlriPollingEvent
        • AlriPollingEvent.__init__()
        • AlriPollingEvent.get_probs_of_acquiring_pathogen()
        • AlriPollingEvent.get_persons_for_new_alri()
        • AlriPollingEvent.apply()
      • AlriIncidentCase
        • AlriIncidentCase.__init__()
        • AlriIncidentCase.determine_nature_of_the_case()
        • AlriIncidentCase.apply_characteristics_of_the_case()
        • AlriIncidentCase.apply()
      • AlriNaturalRecoveryEvent
        • AlriNaturalRecoveryEvent.__init__()
        • AlriNaturalRecoveryEvent.apply()
      • AlriCureEvent
        • AlriCureEvent.__init__()
        • AlriCureEvent.apply()
      • AlriDeathEvent
        • AlriDeathEvent.__init__()
        • AlriDeathEvent.apply()
      • HSI_Alri_Treatment
        • HSI_Alri_Treatment.__init__()
        • HSI_Alri_Treatment._as_out_patient()
        • HSI_Alri_Treatment._as_in_patient()
        • HSI_Alri_Treatment._refer_to_next_level_up()
        • HSI_Alri_Treatment._refer_to_become_inpatient()
        • HSI_Alri_Treatment._schedule_follow_up_following_treatment_failure()
        • HSI_Alri_Treatment._get_cons()
        • HSI_Alri_Treatment._get_cons_group()
        • HSI_Alri_Treatment._get_cons_with_backups()
        • HSI_Alri_Treatment._assess_and_treat()
        • HSI_Alri_Treatment._has_staph_aureus()
        • HSI_Alri_Treatment._get_imci_classification_based_on_symptoms()
        • HSI_Alri_Treatment._get_imci_classification_by_SpO2_measure()
        • HSI_Alri_Treatment._get_classification_given_by_health_worker()
        • HSI_Alri_Treatment._get_disease_classification_for_treatment_decision()
        • HSI_Alri_Treatment._do_action_given_classification()
        • HSI_Alri_Treatment._provide_bronchodilator_if_wheeze()
        • HSI_Alri_Treatment.do_on_follow_up_following_treatment_failure()
        • HSI_Alri_Treatment.apply()
        • HSI_Alri_Treatment.never_ran()
      • AlriLoggingEvent
        • AlriLoggingEvent.__init__()
        • AlriLoggingEvent.new_case()
        • AlriLoggingEvent.new_recovered_case()
        • AlriLoggingEvent.new_cured_case()
        • AlriLoggingEvent.new_death()
        • AlriLoggingEvent.new_seeking_care()
        • AlriLoggingEvent.new_treated()
        • AlriLoggingEvent.new_pulmonary_complication_case()
        • AlriLoggingEvent.new_systemic_complication_case()
        • AlriLoggingEvent.new_hypoxaemic_case()
        • AlriLoggingEvent.apply()
      • AlriCheckPropertiesEvent
        • AlriCheckPropertiesEvent.__init__()
        • AlriCheckPropertiesEvent.apply()
      • AlriIndividualLoggingEvent
        • AlriIndividualLoggingEvent.__init__()
        • AlriIndividualLoggingEvent.apply()
      • AlriPropertiesOfOtherModules
        • AlriPropertiesOfOtherModules.read_parameters()
        • AlriPropertiesOfOtherModules.initialise_population()
        • AlriPropertiesOfOtherModules.initialise_simulation()
        • AlriPropertiesOfOtherModules.on_birth()
      • AlriIncidentCase_Lethal_DangerSigns_Pneumonia
        • AlriIncidentCase_Lethal_DangerSigns_Pneumonia.__init__()
        • AlriIncidentCase_Lethal_DangerSigns_Pneumonia.apply()
      • AlriIncidentCase_NonLethal_Fast_Breathing_Pneumonia
        • AlriIncidentCase_NonLethal_Fast_Breathing_Pneumonia.__init__()
        • AlriIncidentCase_NonLethal_Fast_Breathing_Pneumonia.apply()
    • tlo.methods.bed_days module
    • tlo.methods.bladder_cancer module
      • BladderCancer
        • BladderCancer.__init__()
        • BladderCancer.read_parameters()
        • BladderCancer.initialise_population()
        • BladderCancer.initialise_simulation()
        • BladderCancer.on_birth()
        • BladderCancer.on_hsi_alert()
        • BladderCancer.report_daly_values()
        • BladderCancer.do_at_generic_first_appt()
      • BladderCancerMainPollingEvent
        • BladderCancerMainPollingEvent.__init__()
        • BladderCancerMainPollingEvent.apply()
      • HSI_BladderCancer_Investigation_Following_Blood_Urine
        • HSI_BladderCancer_Investigation_Following_Blood_Urine.__init__()
        • HSI_BladderCancer_Investigation_Following_Blood_Urine.apply()
      • HSI_BladderCancer_Investigation_Following_pelvic_pain
        • HSI_BladderCancer_Investigation_Following_pelvic_pain.__init__()
        • HSI_BladderCancer_Investigation_Following_pelvic_pain.apply()
      • HSI_BladderCancer_StartTreatment
        • HSI_BladderCancer_StartTreatment.__init__()
        • HSI_BladderCancer_StartTreatment.apply()
      • HSI_BladderCancer_PostTreatmentCheck
        • HSI_BladderCancer_PostTreatmentCheck.__init__()
        • HSI_BladderCancer_PostTreatmentCheck.apply()
      • HSI_BladderCancer_PalliativeCare
        • HSI_BladderCancer_PalliativeCare.__init__()
        • HSI_BladderCancer_PalliativeCare.apply()
      • BladderCancerLoggingEvent
        • BladderCancerLoggingEvent.__init__()
        • BladderCancerLoggingEvent.apply()
    • tlo.methods.breast_cancer module
      • BreastCancer
        • BreastCancer.__init__()
        • BreastCancer.read_parameters()
        • BreastCancer.initialise_population()
        • BreastCancer.initialise_simulation()
        • BreastCancer.on_birth()
        • BreastCancer.on_hsi_alert()
        • BreastCancer.report_daly_values()
        • BreastCancer.do_at_generic_first_appt()
      • BreastCancerMainPollingEvent
        • BreastCancerMainPollingEvent.__init__()
        • BreastCancerMainPollingEvent.apply()
      • HSI_BreastCancer_Investigation_Following_breast_lump_discernible
        • HSI_BreastCancer_Investigation_Following_breast_lump_discernible.__init__()
        • HSI_BreastCancer_Investigation_Following_breast_lump_discernible.apply()
      • HSI_BreastCancer_StartTreatment
        • HSI_BreastCancer_StartTreatment.__init__()
        • HSI_BreastCancer_StartTreatment.apply()
      • HSI_BreastCancer_PostTreatmentCheck
        • HSI_BreastCancer_PostTreatmentCheck.__init__()
        • HSI_BreastCancer_PostTreatmentCheck.apply()
      • HSI_BreastCancer_PalliativeCare
        • HSI_BreastCancer_PalliativeCare.__init__()
        • HSI_BreastCancer_PalliativeCare.apply()
      • BreastCancerLoggingEvent
        • BreastCancerLoggingEvent.__init__()
        • BreastCancerLoggingEvent.apply()
    • tlo.methods.cancer_consumables module
    • tlo.methods.cardio_metabolic_disorders module
      • CardioMetabolicDisorders
        • CardioMetabolicDisorders.__init__()
        • CardioMetabolicDisorders.read_parameters()
        • CardioMetabolicDisorders.initialise_population()
        • CardioMetabolicDisorders.initialise_simulation()
        • CardioMetabolicDisorders.build_linear_model()
        • CardioMetabolicDisorders.build_linear_model_symptoms()
        • CardioMetabolicDisorders.on_birth()
        • CardioMetabolicDisorders.update_risk_score()
        • CardioMetabolicDisorders.report_daly_values()
        • CardioMetabolicDisorders.on_hsi_alert()
        • CardioMetabolicDisorders.do_at_generic_first_appt()
        • CardioMetabolicDisorders.do_at_generic_first_appt_emergency()
      • CardioMetabolicDisorders_MainPollingEvent
        • CardioMetabolicDisorders_MainPollingEvent.__init__()
        • CardioMetabolicDisorders_MainPollingEvent.apply()
      • CardioMetabolicDisordersEvent
        • CardioMetabolicDisordersEvent.__init__()
        • CardioMetabolicDisordersEvent.apply()
      • CardioMetabolicDisordersDeathEvent
        • CardioMetabolicDisordersDeathEvent.__init__()
        • CardioMetabolicDisordersDeathEvent.apply()
        • CardioMetabolicDisordersDeathEvent.check_if_event_and_do_death()
      • CardioMetabolicDisordersWeightLossEvent
        • CardioMetabolicDisordersWeightLossEvent.__init__()
        • CardioMetabolicDisordersWeightLossEvent.apply()
      • CardioMetabolicDisorders_LoggingEvent
        • CardioMetabolicDisorders_LoggingEvent.__init__()
        • CardioMetabolicDisorders_LoggingEvent.apply()
      • HSI_CardioMetabolicDisorders_CommunityTestingForHypertension
        • HSI_CardioMetabolicDisorders_CommunityTestingForHypertension.__init__()
        • HSI_CardioMetabolicDisorders_CommunityTestingForHypertension.apply()
      • HSI_CardioMetabolicDisorders_Investigations
        • HSI_CardioMetabolicDisorders_Investigations.__init__()
        • HSI_CardioMetabolicDisorders_Investigations.do_for_each_condition()
        • HSI_CardioMetabolicDisorders_Investigations.apply()
      • HSI_CardioMetabolicDisorders_StartWeightLossAndMedication
        • HSI_CardioMetabolicDisorders_StartWeightLossAndMedication.__init__()
        • HSI_CardioMetabolicDisorders_StartWeightLossAndMedication.apply()
      • HSI_CardioMetabolicDisorders_Refill_Medication
        • HSI_CardioMetabolicDisorders_Refill_Medication.__init__()
        • HSI_CardioMetabolicDisorders_Refill_Medication.apply()
        • HSI_CardioMetabolicDisorders_Refill_Medication.did_not_run()
      • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment
        • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment.__init__()
        • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment.do_for_each_event_to_be_investigated()
        • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment.apply()
        • HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment.did_not_run()
    • tlo.methods.care_of_women_during_pregnancy module
      • CareOfWomenDuringPregnancy
        • CareOfWomenDuringPregnancy.__init__()
        • CareOfWomenDuringPregnancy.read_parameters()
        • CareOfWomenDuringPregnancy.initialise_population()
        • CareOfWomenDuringPregnancy.get_and_store_pregnancy_item_codes()
        • CareOfWomenDuringPregnancy.initialise_simulation()
        • CareOfWomenDuringPregnancy.care_of_women_in_pregnancy_property_reset()
        • CareOfWomenDuringPregnancy.on_birth()
        • CareOfWomenDuringPregnancy.further_on_birth_care_of_women_in_pregnancy()
        • CareOfWomenDuringPregnancy.on_hsi_alert()
        • CareOfWomenDuringPregnancy.get_approx_days_of_pregnancy()
        • CareOfWomenDuringPregnancy.determine_gestational_age_for_next_contact()
        • CareOfWomenDuringPregnancy.antenatal_care_scheduler()
        • CareOfWomenDuringPregnancy.schedule_admission()
        • CareOfWomenDuringPregnancy.call_if_maternal_emergency_assessment_cant_run()
        • CareOfWomenDuringPregnancy.check_intervention_should_run_and_update_mni()
        • CareOfWomenDuringPregnancy.screening_interventions_delivered_at_every_contact()
        • CareOfWomenDuringPregnancy.iron_and_folic_acid_supplementation()
        • CareOfWomenDuringPregnancy.balance_energy_and_protein_supplementation()
        • CareOfWomenDuringPregnancy.insecticide_treated_bed_net()
        • CareOfWomenDuringPregnancy.tb_screening()
        • CareOfWomenDuringPregnancy.tetanus_vaccination()
        • CareOfWomenDuringPregnancy.calcium_supplementation()
        • CareOfWomenDuringPregnancy.point_of_care_hb_testing()
        • CareOfWomenDuringPregnancy.albendazole_administration()
        • CareOfWomenDuringPregnancy.hep_b_testing()
        • CareOfWomenDuringPregnancy.syphilis_screening_and_treatment()
        • CareOfWomenDuringPregnancy.hiv_testing()
        • CareOfWomenDuringPregnancy.iptp_administration()
        • CareOfWomenDuringPregnancy.gdm_screening()
        • CareOfWomenDuringPregnancy.interventions_delivered_each_visit_from_anc2()
        • CareOfWomenDuringPregnancy.check_anc1_can_run()
        • CareOfWomenDuringPregnancy.check_subsequent_anc_can_run()
        • CareOfWomenDuringPregnancy.full_blood_count_testing()
        • CareOfWomenDuringPregnancy.antenatal_blood_transfusion()
        • CareOfWomenDuringPregnancy.initiate_maintenance_anti_hypertensive_treatment()
        • CareOfWomenDuringPregnancy.initiate_treatment_for_severe_hypertension()
        • CareOfWomenDuringPregnancy.treatment_for_severe_pre_eclampsia_or_eclampsia()
        • CareOfWomenDuringPregnancy.antibiotics_for_prom()
        • CareOfWomenDuringPregnancy.ectopic_pregnancy_treatment_doesnt_run()
        • CareOfWomenDuringPregnancy.calculate_beddays()
      • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact
        • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact.__init__()
        • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact.apply()
        • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContact.not_available()
      • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact
        • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact.__init__()
        • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact.apply()
        • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContact.not_available()
      • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact
        • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact.__init__()
        • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact.apply()
        • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContact.not_available()
      • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact
        • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact.__init__()
        • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact.apply()
        • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContact.not_available()
      • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact
        • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact.__init__()
        • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact.apply()
        • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContact.not_available()
      • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact
        • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact.__init__()
        • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact.apply()
        • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContact.not_available()
      • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact
        • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact.__init__()
        • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact.apply()
        • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContact.not_available()
      • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact
        • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact.__init__()
        • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact.apply()
        • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContact.not_available()
      • HSI_CareOfWomenDuringPregnancy_FocusedANCVisit
        • HSI_CareOfWomenDuringPregnancy_FocusedANCVisit.__init__()
        • HSI_CareOfWomenDuringPregnancy_FocusedANCVisit.apply()
      • HSI_CareOfWomenDuringPregnancy_PresentsForInductionOfLabour
        • HSI_CareOfWomenDuringPregnancy_PresentsForInductionOfLabour.__init__()
        • HSI_CareOfWomenDuringPregnancy_PresentsForInductionOfLabour.apply()
      • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare
        • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare.__init__()
        • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare.apply()
        • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCare.not_available()
      • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia
        • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia.__init__()
        • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia.apply()
        • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemia.not_available()
      • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes
        • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes.__init__()
        • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes.apply()
        • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetes.not_available()
      • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement
        • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement.__init__()
        • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement.apply()
        • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagement.not_available()
      • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy
        • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.__init__()
        • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.apply()
        • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.never_ran()
        • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.did_not_run()
        • HSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancy.not_available()
      • CareOfWomenDuringPregnancyLoggingEvent
        • CareOfWomenDuringPregnancyLoggingEvent.__init__()
        • CareOfWomenDuringPregnancyLoggingEvent.apply()
    • tlo.methods.causes module
    • tlo.methods.chronicsyndrome module
      • ChronicSyndrome
        • ChronicSyndrome.__init__()
        • ChronicSyndrome.read_parameters()
        • ChronicSyndrome.initialise_population()
        • ChronicSyndrome.initialise_simulation()
        • ChronicSyndrome.on_birth()
        • ChronicSyndrome.on_hsi_alert()
        • ChronicSyndrome.report_daly_values()
        • ChronicSyndrome.do_at_generic_first_appt_emergency()
      • ChronicSyndromeEvent
        • ChronicSyndromeEvent.__init__()
        • ChronicSyndromeEvent.apply()
      • ChronicSyndromeDeathEvent
        • ChronicSyndromeDeathEvent.__init__()
        • ChronicSyndromeDeathEvent.apply()
      • ChronicSyndrome_LaunchOutreachEvent
        • ChronicSyndrome_LaunchOutreachEvent.__init__()
        • ChronicSyndrome_LaunchOutreachEvent.apply()
      • HSI_ChronicSyndrome_SeeksEmergencyCareAndGetsTreatment
        • HSI_ChronicSyndrome_SeeksEmergencyCareAndGetsTreatment.__init__()
        • HSI_ChronicSyndrome_SeeksEmergencyCareAndGetsTreatment.apply()
        • HSI_ChronicSyndrome_SeeksEmergencyCareAndGetsTreatment.did_not_run()
      • HSI_ChronicSyndrome_Outreach_Individual
        • HSI_ChronicSyndrome_Outreach_Individual.__init__()
        • HSI_ChronicSyndrome_Outreach_Individual.apply()
        • HSI_ChronicSyndrome_Outreach_Individual.did_not_run()
      • HSI_ChronicSyndrome_PopulationWideBehaviourChange
        • HSI_ChronicSyndrome_PopulationWideBehaviourChange.__init__()
        • HSI_ChronicSyndrome_PopulationWideBehaviourChange.apply()
      • ChronicSyndromeLoggingEvent
        • ChronicSyndromeLoggingEvent.__init__()
        • ChronicSyndromeLoggingEvent.apply()
    • tlo.methods.consumables module
    • tlo.methods.contraception module
      • Contraception
        • Contraception.__init__()
        • Contraception.read_parameters()
        • Contraception.pre_initialise_population()
        • Contraception.initialise_population()
        • Contraception.initialise_simulation()
        • Contraception.on_birth()
        • Contraception.end_pregnancy()
        • Contraception.process_params()
        • Contraception.update_params_for_interventions()
        • Contraception.select_contraceptive_following_birth()
        • Contraception.get_item_code_for_each_contraceptive()
        • Contraception.schedule_batch_of_contraceptive_changes()
        • Contraception.do_and_log_individual_contraception_change()
        • Contraception.schedule_births_for_first_9_months()
        • Contraception.on_simulation_end()
      • DirectBirth
        • DirectBirth.__init__()
        • DirectBirth.apply()
      • ContraceptionPoll
        • ContraceptionPoll.__init__()
        • ContraceptionPoll.apply()
        • ContraceptionPoll.update_contraceptive()
        • ContraceptionPoll.initiate()
        • ContraceptionPoll.discontinue_switch_or_continue()
        • ContraceptionPoll.update_pregnancy()
        • ContraceptionPoll.pregnancy_for_those_on_contraceptive()
        • ContraceptionPoll.pregnancy_for_those_not_on_contraceptive()
        • ContraceptionPoll.set_new_pregnancy()
      • ContraceptionLoggingEvent
        • ContraceptionLoggingEvent.__init__()
        • ContraceptionLoggingEvent.apply()
      • HSI_Contraception_FamilyPlanningAppt
        • HSI_Contraception_FamilyPlanningAppt.__init__()
        • HSI_Contraception_FamilyPlanningAppt.apply()
        • HSI_Contraception_FamilyPlanningAppt.post_apply_hook()
        • HSI_Contraception_FamilyPlanningAppt.reschedule()
        • HSI_Contraception_FamilyPlanningAppt.never_ran()
      • StartInterventions
        • StartInterventions.__init__()
        • StartInterventions.apply()
      • SimplifiedPregnancyAndLabour
        • SimplifiedPregnancyAndLabour.__init__()
        • SimplifiedPregnancyAndLabour.read_parameters()
        • SimplifiedPregnancyAndLabour.initialise_population()
        • SimplifiedPregnancyAndLabour.initialise_simulation()
        • SimplifiedPregnancyAndLabour.on_birth()
        • SimplifiedPregnancyAndLabour.set_date_of_labour()
      • EndOfPregnancyEvent
        • EndOfPregnancyEvent.__init__()
        • EndOfPregnancyEvent.apply()
    • tlo.methods.copd module
      • Copd
        • Copd.__init__()
        • Copd.read_parameters()
        • Copd.pre_initialise_population()
        • Copd.initialise_population()
        • Copd.initialise_simulation()
        • Copd.on_birth()
        • Copd.report_daly_values()
        • Copd.define_symptoms()
        • Copd.lookup_item_codes()
        • Copd.do_logging()
        • Copd._common_first_appt()
        • Copd.do_at_generic_first_appt()
        • Copd.do_at_generic_first_appt_emergency()
      • CopdPollEvent
        • CopdPollEvent.__init__()
        • CopdPollEvent.apply()
        • CopdPollEvent.gen_random_date_in_next_three_months()
        • CopdPollEvent.increment_category()
        • CopdPollEvent.progress_to_next_lung_function()
      • CopdExacerbationEvent
        • CopdExacerbationEvent.__init__()
        • CopdExacerbationEvent.apply()
      • CopdDeath
        • CopdDeath.__init__()
        • CopdDeath.apply()
      • HSI_Copd_TreatmentOnSevereExacerbation
        • HSI_Copd_TreatmentOnSevereExacerbation.__init__()
        • HSI_Copd_TreatmentOnSevereExacerbation.apply()
    • tlo.methods.demography module
      • Demography
        • Demography.__init__()
        • Demography.read_parameters()
        • Demography.pre_initialise_population()
        • Demography.initialise_population()
        • Demography.initialise_simulation()
        • Demography.on_birth()
        • Demography._edit_init_pop_to_prevent_persons_greater_than_max_age()
        • Demography._edit_init_pop_so_that_equal_number_in_each_district()
        • Demography.process_causes_of_death()
        • Demography.do_death()
        • Demography.create_mappers_from_causes_of_death_to_label()
        • Demography.calc_py_lived_in_last_year()
        • Demography.compute_initial_model_to_data_popsize_ratio()
      • AgeUpdateEvent
        • AgeUpdateEvent.__init__()
        • AgeUpdateEvent.apply()
      • OtherDeathPoll
        • OtherDeathPoll.__init__()
        • OtherDeathPoll.get_mort_risk_per_poll()
        • OtherDeathPoll.get_all_cause_mort_risk_per_poll()
        • OtherDeathPoll.get_proportion_of_deaths_to_represent_as_other_deaths()
        • OtherDeathPoll.apply()
      • InstantaneousDeath
        • InstantaneousDeath.__init__()
        • InstantaneousDeath.apply()
      • DemographyLoggingEvent
        • DemographyLoggingEvent.__init__()
        • DemographyLoggingEvent.apply()
    • tlo.methods.depression module
      • Depression
        • Depression.__init__()
        • Depression.read_parameters()
        • Depression.apply_linear_model()
        • Depression.initialise_population()
        • Depression.initialise_simulation()
        • Depression.on_birth()
        • Depression.on_hsi_alert()
        • Depression.report_daly_values()
        • Depression._check_for_suspected_depression()
        • Depression.do_on_presentation_to_care()
        • Depression.do_when_suspected_depression()
        • Depression.do_at_generic_first_appt()
        • Depression.do_at_generic_first_appt_emergency()
      • DepressionPollingEvent
        • DepressionPollingEvent.__init__()
        • DepressionPollingEvent.apply()
      • DepressionSelfHarmEvent
        • DepressionSelfHarmEvent.__init__()
        • DepressionSelfHarmEvent.apply()
      • DepressionSuicideEvent
        • DepressionSuicideEvent.__init__()
        • DepressionSuicideEvent.apply()
      • DepressionLoggingEvent
        • DepressionLoggingEvent.__init__()
        • DepressionLoggingEvent.apply()
      • HSI_Depression_TalkingTherapy
        • HSI_Depression_TalkingTherapy.__init__()
        • HSI_Depression_TalkingTherapy.apply()
      • HSI_Depression_Start_Antidepressant
        • HSI_Depression_Start_Antidepressant.__init__()
        • HSI_Depression_Start_Antidepressant.apply()
      • HSI_Depression_Refill_Antidepressant
        • HSI_Depression_Refill_Antidepressant.__init__()
        • HSI_Depression_Refill_Antidepressant.apply()
        • HSI_Depression_Refill_Antidepressant.did_not_run()
    • tlo.methods.diarrhoea module
      • Overview
      • Diarrhoea
        • Diarrhoea.__init__()
        • Diarrhoea.read_parameters()
        • Diarrhoea.initialise_population()
        • Diarrhoea.initialise_simulation()
        • Diarrhoea.on_birth()
        • Diarrhoea.on_hsi_alert()
        • Diarrhoea.report_daly_values()
        • Diarrhoea.look_up_consumables()
        • Diarrhoea.do_treatment()
        • Diarrhoea.cancel_death_date()
        • Diarrhoea.end_episode()
        • Diarrhoea.check_properties()
        • Diarrhoea.do_at_generic_first_appt()
      • DiarrhoeaPollingEvent
        • DiarrhoeaPollingEvent.__init__()
        • DiarrhoeaPollingEvent.compute_fraction_of_year_between_polling_event()
        • DiarrhoeaPollingEvent.apply()
      • DiarrhoeaIncidentCase
        • DiarrhoeaIncidentCase.__init__()
        • DiarrhoeaIncidentCase.apply()
      • DiarrhoeaNaturalRecoveryEvent
        • DiarrhoeaNaturalRecoveryEvent.__init__()
        • DiarrhoeaNaturalRecoveryEvent.apply()
      • DiarrhoeaDeathEvent
        • DiarrhoeaDeathEvent.__init__()
        • DiarrhoeaDeathEvent.apply()
      • DiarrhoeaCureEvent
        • DiarrhoeaCureEvent.__init__()
        • DiarrhoeaCureEvent.apply()
      • HSI_Diarrhoea_Treatment_Outpatient
        • HSI_Diarrhoea_Treatment_Outpatient.__init__()
        • HSI_Diarrhoea_Treatment_Outpatient.apply()
      • HSI_Diarrhoea_Treatment_Inpatient
        • HSI_Diarrhoea_Treatment_Inpatient.__init__()
        • HSI_Diarrhoea_Treatment_Inpatient.apply()
      • DiarrhoeaPropertiesOfOtherModules
        • DiarrhoeaPropertiesOfOtherModules.__init__()
        • DiarrhoeaPropertiesOfOtherModules.read_parameters()
        • DiarrhoeaPropertiesOfOtherModules.initialise_population()
        • DiarrhoeaPropertiesOfOtherModules.initialise_simulation()
        • DiarrhoeaPropertiesOfOtherModules.on_birth()
      • DiarrhoeaCheckPropertiesEvent
        • DiarrhoeaCheckPropertiesEvent.__init__()
        • DiarrhoeaCheckPropertiesEvent.apply()
    • tlo.methods.dxmanager module
    • tlo.methods.enhanced_lifestyle module
      • Lifestyle
        • Lifestyle.__init__()
        • Lifestyle.read_parameters()
        • Lifestyle.pre_initialise_population()
        • Lifestyle.initialise_population()
        • Lifestyle.initialise_simulation()
        • Lifestyle.on_birth()
      • LifestyleEvent
        • LifestyleEvent.__init__()
        • LifestyleEvent.apply()
      • LifestylesLoggingEvent
        • LifestylesLoggingEvent.__init__()
        • LifestylesLoggingEvent.apply()
    • tlo.methods.epi module
      • Epi
        • Epi.__init__()
        • Epi.read_parameters()
        • Epi.initialise_population()
        • Epi.initialise_simulation()
        • Epi.on_birth()
        • Epi.report_daly_values()
        • Epi.increment_dose()
        • Epi.get_item_codes()
      • HpvScheduleEvent
        • HpvScheduleEvent.__init__()
        • HpvScheduleEvent.apply()
      • HsiBaseVaccine
        • HsiBaseVaccine.__init__()
        • HsiBaseVaccine.treatment_id()
        • HsiBaseVaccine.apply()
      • HSI_BcgVaccine
        • HSI_BcgVaccine.treatment_id()
        • HSI_BcgVaccine.apply()
      • HSI_opv
        • HSI_opv.treatment_id()
        • HSI_opv.apply()
      • HSI_DtpHibHepVaccine
        • HSI_DtpHibHepVaccine.treatment_id()
        • HSI_DtpHibHepVaccine.apply()
      • HSI_RotaVaccine
        • HSI_RotaVaccine.treatment_id()
        • HSI_RotaVaccine.apply()
      • HSI_PneumoVaccine
        • HSI_PneumoVaccine.treatment_id()
        • HSI_PneumoVaccine.apply()
      • HSI_MeaslesRubellaVaccine
        • HSI_MeaslesRubellaVaccine.treatment_id()
        • HSI_MeaslesRubellaVaccine.apply()
      • HSI_HpvVaccine
        • HSI_HpvVaccine.treatment_id()
        • HSI_HpvVaccine.apply()
      • HSI_TdVaccine
        • HSI_TdVaccine.treatment_id()
        • HSI_TdVaccine.apply()
      • EpiLoggingEvent
        • EpiLoggingEvent.__init__()
        • EpiLoggingEvent.apply()
    • tlo.methods.epilepsy module
      • Epilepsy
        • Epilepsy.__init__()
        • Epilepsy.read_parameters()
        • Epilepsy.initialise_population()
        • Epilepsy.initialise_simulation()
        • Epilepsy.on_birth()
        • Epilepsy.report_daly_values()
        • Epilepsy.transition_seizure_stat()
        • Epilepsy.stop_antiep()
        • Epilepsy.get_best_available_medicine()
        • Epilepsy.do_at_generic_first_appt_emergency()
      • EpilepsyEvent
        • EpilepsyEvent.__init__()
        • EpilepsyEvent.apply()
      • EpilepsyLoggingEvent
        • EpilepsyLoggingEvent.__init__()
        • EpilepsyLoggingEvent.apply()
      • HSI_Epilepsy_Start_Anti_Epileptic
        • HSI_Epilepsy_Start_Anti_Epileptic.__init__()
        • HSI_Epilepsy_Start_Anti_Epileptic.apply()
      • HSI_Epilepsy_Follow_Up
        • HSI_Epilepsy_Follow_Up.__init__()
        • HSI_Epilepsy_Follow_Up.apply()
    • tlo.methods.equipment module
    • tlo.methods.fullmodel module
    • tlo.methods.healthburden module
      • HealthBurden
        • HealthBurden.__init__()
        • HealthBurden.read_parameters()
        • HealthBurden.initialise_population()
        • HealthBurden.initialise_simulation()
        • HealthBurden.process_causes_of_disability()
        • HealthBurden.process_causes_of_dalys()
        • HealthBurden.on_birth()
        • HealthBurden.on_simulation_end()
        • HealthBurden.get_dalys()
        • HealthBurden.get_daly_weight()
        • HealthBurden.report_live_years_lost()
        • HealthBurden.decompose_yll_by_age_and_time()
        • HealthBurden.write_to_log()
        • HealthBurden.check_multi_index()
      • Get_Current_DALYS
        • Get_Current_DALYS.__init__()
        • Get_Current_DALYS.apply()
      • Healthburden_WriteToLog
        • Healthburden_WriteToLog.__init__()
        • Healthburden_WriteToLog.apply()
    • tlo.methods.healthseekingbehaviour module
      • HealthSeekingBehaviour
        • HealthSeekingBehaviour.__init__()
        • HealthSeekingBehaviour.read_parameters()
        • HealthSeekingBehaviour.initialise_population()
        • HealthSeekingBehaviour.initialise_simulation()
        • HealthSeekingBehaviour.on_birth()
        • HealthSeekingBehaviour.define_linear_models()
        • HealthSeekingBehaviour.do_at_generic_first_appt_emergency()
      • HealthSeekingBehaviourPoll
        • HealthSeekingBehaviourPoll.__init__()
        • HealthSeekingBehaviourPoll._has_any_symptoms()
        • HealthSeekingBehaviourPoll.apply()
    • tlo.methods.healthsystem module
      • HealthSystem
        • HealthSystem.__init__()
        • HealthSystem.read_parameters()
        • HealthSystem.pre_initialise_population()
        • HealthSystem.initialise_population()
        • HealthSystem.initialise_simulation()
        • HealthSystem.on_birth()
        • HealthSystem.on_simulation_end()
        • HealthSystem.setup_priority_policy()
        • HealthSystem.process_healthsystem_organisation_files()
        • HealthSystem.setup_daily_capabilities()
        • HealthSystem.format_daily_capabilities()
        • HealthSystem._rescale_capabilities_to_capture_effective_capability()
        • HealthSystem.update_consumables_availability_to_represent_merging_of_levels_1b_and_2()
        • HealthSystem.get_service_availability()
        • HealthSystem.get_cons_availability()
        • HealthSystem.get_beds_availability()
        • HealthSystem.get_equip_availability()
        • HealthSystem.schedule_to_call_never_ran_on_date()
        • HealthSystem.get_mode_appt_constraints()
        • HealthSystem.get_priority_policy_initial()
        • HealthSystem.load_priority_policy()
        • HealthSystem.schedule_hsi_event()
        • HealthSystem._add_hsi_event_queue_item_to_hsi_event_queue()
        • HealthSystem.enforce_priority_policy()
        • HealthSystem.check_hsi_event_is_valid()
        • HealthSystem.is_treatment_id_allowed()
        • HealthSystem.schedule_batch_of_individual_hsi_events()
        • HealthSystem.appt_footprint_is_valid()
        • HealthSystem.get_blank_appt_footprint()
        • HealthSystem.get_facility_info()
        • HealthSystem.get_appt_footprint_as_time_request()
        • HealthSystem.get_squeeze_factors()
        • HealthSystem.record_hsi_event()
        • HealthSystem.write_to_hsi_log()
        • HealthSystem.call_and_record_never_ran_hsi_event()
        • HealthSystem.write_to_never_ran_hsi_log()
        • HealthSystem.log_current_capabilities_and_usage()
        • HealthSystem.remove_beddays_footprint()
        • HealthSystem.find_events_for_person()
        • HealthSystem.reset_queue()
        • HealthSystem.get_item_codes_from_package_name()
        • HealthSystem.get_item_code_from_item_name()
        • HealthSystem.override_availability_of_consumables()
        • HealthSystem._write_hsi_event_counts_to_log_and_reset()
        • HealthSystem._write_never_ran_hsi_event_counts_to_log_and_reset()
        • HealthSystem.on_end_of_day()
        • HealthSystem.on_end_of_month()
        • HealthSystem.on_end_of_year()
        • HealthSystem.run_population_level_events()
        • HealthSystem.run_individual_level_events_in_mode_0_or_1()
      • HealthSystemScheduler
        • HealthSystemScheduler.__init__()
        • HealthSystemScheduler._is_last_day_of_the_year()
        • HealthSystemScheduler._is_last_day_of_the_month()
        • HealthSystemScheduler._get_events_due_today()
        • HealthSystemScheduler.process_events_mode_0_and_1()
        • HealthSystemScheduler.process_events_mode_2()
        • HealthSystemScheduler.apply()
      • HealthSystemChangeParameters
        • HealthSystemChangeParameters.__init__()
        • HealthSystemChangeParameters.apply()
      • DynamicRescalingHRCapabilities
        • DynamicRescalingHRCapabilities.__init__()
        • DynamicRescalingHRCapabilities._get_most_recent_year_specified_for_a_change_in_configuration()
        • DynamicRescalingHRCapabilities.apply()
      • ConstantRescalingHRCapabilities
        • ConstantRescalingHRCapabilities.__init__()
        • ConstantRescalingHRCapabilities.apply()
      • RescaleHRCapabilities_ByDistrict
        • RescaleHRCapabilities_ByDistrict.__init__()
        • RescaleHRCapabilities_ByDistrict.apply()
      • HealthSystemChangeMode
        • HealthSystemChangeMode.__init__()
        • HealthSystemChangeMode.apply()
    • tlo.methods.hiv module
      • Hiv
        • Hiv.__init__()
        • Hiv.read_parameters()
        • Hiv.pre_initialise_population()
        • Hiv._build_linear_models()
        • Hiv.initialise_population()
        • Hiv.initialise_baseline_prevalence()
        • Hiv.initialise_baseline_art()
        • Hiv.initialise_baseline_tested()
        • Hiv.initialise_simulation()
        • Hiv.update_parameters_for_program_scaleup()
        • Hiv.on_birth()
        • Hiv.report_daly_values()
        • Hiv.mtct_during_breastfeeding()
        • Hiv.do_new_infection()
        • Hiv.sample_time_from_infection_to_aids_given_parameters()
        • Hiv.get_time_from_infection_to_aids_distribution_parameters()
        • Hiv.get_time_from_aids_to_death()
        • Hiv.do_when_hiv_diagnosed()
        • Hiv.prob_art_start_after_test()
        • Hiv.prob_viral_suppression()
        • Hiv.stops_treatment()
        • Hiv.per_capita_testing_rate()
        • Hiv.decide_whether_hiv_test_for_mother()
        • Hiv.decide_whether_hiv_test_for_infant()
        • Hiv.check_config_of_properties()
        • Hiv.do_at_generic_first_appt()
      • HivRegularPollingEvent
        • HivRegularPollingEvent.__init__()
        • HivRegularPollingEvent.apply()
      • HivInfectionEvent
        • HivInfectionEvent.__init__()
        • HivInfectionEvent.apply()
      • HivInfectionDuringBreastFeedingEvent
        • HivInfectionDuringBreastFeedingEvent.__init__()
        • HivInfectionDuringBreastFeedingEvent.apply()
      • HivAidsOnsetEvent
        • HivAidsOnsetEvent.__init__()
        • HivAidsOnsetEvent.apply()
      • HivAidsDeathEvent
        • HivAidsDeathEvent.__init__()
        • HivAidsDeathEvent.apply()
      • HivAidsTbDeathEvent
        • HivAidsTbDeathEvent.__init__()
        • HivAidsTbDeathEvent.apply()
      • Hiv_DecisionToContinueOnPrEP
        • Hiv_DecisionToContinueOnPrEP.__init__()
        • Hiv_DecisionToContinueOnPrEP.apply()
      • Hiv_DecisionToContinueTreatment
        • Hiv_DecisionToContinueTreatment.__init__()
        • Hiv_DecisionToContinueTreatment.apply()
      • HivScaleUpEvent
        • HivScaleUpEvent.__init__()
        • HivScaleUpEvent.apply()
      • HSI_Hiv_TestAndRefer
        • HSI_Hiv_TestAndRefer.__init__()
        • HSI_Hiv_TestAndRefer.apply()
      • HSI_Hiv_Circ
        • HSI_Hiv_Circ.__init__()
        • HSI_Hiv_Circ.apply()
      • HSI_Hiv_StartInfantProphylaxis
        • HSI_Hiv_StartInfantProphylaxis.__init__()
        • HSI_Hiv_StartInfantProphylaxis.apply()
        • HSI_Hiv_StartInfantProphylaxis.never_ran()
      • HSI_Hiv_StartOrContinueOnPrep
        • HSI_Hiv_StartOrContinueOnPrep.__init__()
        • HSI_Hiv_StartOrContinueOnPrep.apply()
        • HSI_Hiv_StartOrContinueOnPrep.never_ran()
      • HSI_Hiv_StartOrContinueTreatment
        • HSI_Hiv_StartOrContinueTreatment.__init__()
        • HSI_Hiv_StartOrContinueTreatment.apply()
        • HSI_Hiv_StartOrContinueTreatment.do_at_initiation()
        • HSI_Hiv_StartOrContinueTreatment.do_at_continuation()
        • HSI_Hiv_StartOrContinueTreatment.determine_vl_status()
        • HSI_Hiv_StartOrContinueTreatment.get_drugs()
        • HSI_Hiv_StartOrContinueTreatment.consider_tb()
        • HSI_Hiv_StartOrContinueTreatment.never_ran()
      • HSI_Hiv_EndOfLifeCare
        • HSI_Hiv_EndOfLifeCare.__init__()
        • HSI_Hiv_EndOfLifeCare.apply()
      • HivLoggingEvent
        • HivLoggingEvent.__init__()
        • HivLoggingEvent.apply()
      • HivCheckPropertiesEvent
        • HivCheckPropertiesEvent.__init__()
        • HivCheckPropertiesEvent.apply()
      • DummyHivModule
        • DummyHivModule.__init__()
        • DummyHivModule.read_parameters()
        • DummyHivModule.initialise_population()
        • DummyHivModule.initialise_simulation()
        • DummyHivModule.on_birth()
    • tlo.methods.hiv_tb_calibration module
      • Deviance
        • Deviance.__init__()
        • Deviance.read_parameters()
        • Deviance.initialise_population()
        • Deviance.initialise_simulation()
        • Deviance.on_birth()
        • Deviance.read_data_files()
        • Deviance.read_model_outputs()
        • Deviance.weighted_mean()
        • Deviance.record_death()
        • Deviance.on_simulation_end()
    • tlo.methods.hsi_event module
      • HSI_Event
        • HSI_Event.__init__()
        • HSI_Event._adjust_facility_level_to_merge_1b_and_2()
        • HSI_Event.apply()
        • HSI_Event.did_not_run()
        • HSI_Event.never_ran()
        • HSI_Event.post_apply_hook()
        • HSI_Event._run_after_hsi_event()
        • HSI_Event.run()
        • HSI_Event.get_consumables()
        • HSI_Event.make_beddays_footprint()
        • HSI_Event.is_all_beddays_allocated()
        • HSI_Event.make_appt_footprint()
        • HSI_Event.add_equipment()
        • HSI_Event.probability_all_equipment_available()
        • HSI_Event.initialise()
        • HSI_Event._check_if_appt_footprint_can_run()
        • HSI_Event._return_item_codes_in_dict()
        • HSI_Event.as_namedtuple()
      • HSIEventWrapper
        • HSIEventWrapper.__init__()
        • HSIEventWrapper.run()
    • tlo.methods.hsi_generic_first_appts module
      • _BaseHSIGenericFirstAppt
        • _BaseHSIGenericFirstAppt.__init__()
        • _BaseHSIGenericFirstAppt._diagnosis_function()
        • _BaseHSIGenericFirstAppt._do_at_generic_first_appt_for_module()
        • _BaseHSIGenericFirstAppt.apply()
      • HSI_GenericNonEmergencyFirstAppt
        • HSI_GenericNonEmergencyFirstAppt.__init__()
        • HSI_GenericNonEmergencyFirstAppt._do_at_generic_first_appt_for_module()
      • HSI_GenericEmergencyFirstAppt
        • HSI_GenericEmergencyFirstAppt.__init__()
        • HSI_GenericEmergencyFirstAppt._do_at_generic_first_appt_for_module()
      • HSI_EmergencyCare_SpuriousSymptom
        • HSI_EmergencyCare_SpuriousSymptom.__init__()
        • HSI_EmergencyCare_SpuriousSymptom.apply()
    • tlo.methods.labour module
      • Labour
        • Labour.__init__()
        • Labour.read_parameters()
        • Labour.initialise_population()
        • Labour.get_and_store_labour_item_codes()
        • Labour.initialise_simulation()
        • Labour.on_birth()
        • Labour.further_on_birth_labour()
        • Labour.on_hsi_alert()
        • Labour.report_daly_values()
        • Labour.set_date_of_labour()
        • Labour.predict()
        • Labour.reset_due_date()
        • Labour.check_labour_can_proceed()
        • Labour.set_intrapartum_complications()
        • Labour.set_postpartum_complications()
        • Labour.progression_of_hypertensive_disorders()
        • Labour.apply_risk_of_early_postpartum_death()
        • Labour.labour_characteristics_checker()
        • Labour.postpartum_characteristics_checker()
        • Labour.prophylactic_labour_interventions()
        • Labour.determine_delivery_mode_in_spe_or_ec()
        • Labour.assessment_and_treatment_of_severe_pre_eclampsia_mgso4()
        • Labour.assessment_and_treatment_of_hypertension()
        • Labour.assessment_and_treatment_of_eclampsia()
        • Labour.assessment_for_assisted_vaginal_delivery()
        • Labour.assessment_and_treatment_of_maternal_sepsis()
        • Labour.assessment_and_plan_for_antepartum_haemorrhage()
        • Labour.assessment_for_referral_uterine_rupture()
        • Labour.active_management_of_the_third_stage_of_labour()
        • Labour.assessment_and_treatment_of_pph_uterine_atony()
        • Labour.assessment_and_treatment_of_pph_retained_placenta()
        • Labour.surgical_management_of_pph()
        • Labour.blood_transfusion()
        • Labour.assessment_and_treatment_of_anaemia()
        • Labour.assessment_for_depression()
        • Labour.interventions_delivered_pre_discharge()
        • Labour.run_if_receives_skilled_birth_attendance_cant_run()
        • Labour.run_if_receives_postnatal_check_cant_run()
        • Labour.run_if_receives_comprehensive_emergency_obstetric_care_cant_run()
        • Labour.do_at_generic_first_appt_emergency()
      • LabourOnsetEvent
        • LabourOnsetEvent.__init__()
        • LabourOnsetEvent.apply()
      • LabourAtHomeEvent
        • LabourAtHomeEvent.__init__()
        • LabourAtHomeEvent.apply()
      • LabourDeathAndStillBirthEvent
        • LabourDeathAndStillBirthEvent.__init__()
        • LabourDeathAndStillBirthEvent.apply()
      • BirthAndPostnatalOutcomesEvent
        • BirthAndPostnatalOutcomesEvent.__init__()
        • BirthAndPostnatalOutcomesEvent.apply()
      • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour
        • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.__init__()
        • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.apply()
        • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.never_ran()
        • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.did_not_run()
        • HSI_Labour_ReceivesSkilledBirthAttendanceDuringLabour.not_available()
      • HSI_Labour_ReceivesPostnatalCheck
        • HSI_Labour_ReceivesPostnatalCheck.__init__()
        • HSI_Labour_ReceivesPostnatalCheck.apply()
        • HSI_Labour_ReceivesPostnatalCheck.never_ran()
        • HSI_Labour_ReceivesPostnatalCheck.did_not_run()
        • HSI_Labour_ReceivesPostnatalCheck.not_available()
        • HSI_Labour_ReceivesPostnatalCheck._get_facility_level_for_pnc()
      • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare
        • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.__init__()
        • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.apply()
        • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.never_ran()
        • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.did_not_run()
        • HSI_Labour_ReceivesComprehensiveEmergencyObstetricCare.not_available()
      • HSI_Labour_PostnatalWardInpatientCare
        • HSI_Labour_PostnatalWardInpatientCare.__init__()
        • HSI_Labour_PostnatalWardInpatientCare.apply()
        • HSI_Labour_PostnatalWardInpatientCare.did_not_run()
        • HSI_Labour_PostnatalWardInpatientCare.not_available()
      • LabourAndPostnatalCareAnalysisEvent
        • LabourAndPostnatalCareAnalysisEvent.__init__()
        • LabourAndPostnatalCareAnalysisEvent.apply()
      • LabourLoggingEvent
        • LabourLoggingEvent.__init__()
        • LabourLoggingEvent.apply()
    • tlo.methods.labour_lm module
    • tlo.methods.malaria module
      • Malaria
        • Malaria.__init__()
        • Malaria.read_parameters()
        • Malaria.pre_initialise_population()
        • Malaria._build_linear_models()
        • Malaria.initialise_population()
        • Malaria.malaria_poll2()
        • Malaria.general_population_rdt_scheduler()
        • Malaria.initialise_simulation()
        • Malaria.update_parameters_for_program_scaleup()
        • Malaria.on_birth()
        • Malaria.report_daly_values()
        • Malaria.check_if_fever_is_caused_by_malaria()
        • Malaria.do_at_generic_first_appt()
        • Malaria.do_at_generic_first_appt_emergency()
      • MalariaPollingEventDistrict
        • MalariaPollingEventDistrict.__init__()
        • MalariaPollingEventDistrict.apply()
      • MalariaScaleUpEvent
        • MalariaScaleUpEvent.__init__()
        • MalariaScaleUpEvent.apply()
      • MalariaIPTp
        • MalariaIPTp.__init__()
        • MalariaIPTp.apply()
      • MalariaEndIPTpProtection
        • MalariaEndIPTpProtection.__init__()
        • MalariaEndIPTpProtection.apply()
      • MalariaDeathEvent
        • MalariaDeathEvent.__init__()
        • MalariaDeathEvent.apply()
      • HSI_Malaria_rdt
        • HSI_Malaria_rdt.__init__()
        • HSI_Malaria_rdt.apply()
      • HSI_Malaria_rdt_community
        • HSI_Malaria_rdt_community.__init__()
        • HSI_Malaria_rdt_community.apply()
      • HSI_Malaria_Treatment
        • HSI_Malaria_Treatment.__init__()
        • HSI_Malaria_Treatment.apply()
        • HSI_Malaria_Treatment.get_drugs()
        • HSI_Malaria_Treatment.did_not_run()
      • HSI_Malaria_Treatment_Complicated
        • HSI_Malaria_Treatment_Complicated.__init__()
        • HSI_Malaria_Treatment_Complicated.apply()
        • HSI_Malaria_Treatment_Complicated.did_not_run()
      • HSI_MalariaIPTp
        • HSI_MalariaIPTp.__init__()
        • HSI_MalariaIPTp.apply()
        • HSI_MalariaIPTp.did_not_run()
      • MalariaUpdateEvent
        • MalariaUpdateEvent.__init__()
        • MalariaUpdateEvent.apply()
      • MalariaParasiteClearanceEvent
        • MalariaParasiteClearanceEvent.__init__()
        • MalariaParasiteClearanceEvent.apply()
      • MalariaLoggingEvent
        • MalariaLoggingEvent.__init__()
        • MalariaLoggingEvent.apply()
      • MalariaTxLoggingEvent
        • MalariaTxLoggingEvent.__init__()
        • MalariaTxLoggingEvent.apply()
      • MalariaPrevDistrictLoggingEvent
        • MalariaPrevDistrictLoggingEvent.__init__()
        • MalariaPrevDistrictLoggingEvent.apply()
    • tlo.methods.measles module
      • Measles
        • Measles.__init__()
        • Measles.read_parameters()
        • Measles.pre_initialise_population()
        • Measles.initialise_population()
        • Measles.initialise_simulation()
        • Measles.on_birth()
        • Measles.report_daly_values()
        • Measles.process_parameters()
        • Measles.do_at_generic_first_appt()
      • MeaslesEvent
        • MeaslesEvent.__init__()
        • MeaslesEvent.apply()
      • MeaslesOnsetEvent
        • MeaslesOnsetEvent.__init__()
        • MeaslesOnsetEvent.apply()
        • MeaslesOnsetEvent.assign_symptoms()
        • MeaslesOnsetEvent.get_prob_death()
      • MeaslesSymptomResolveEvent
        • MeaslesSymptomResolveEvent.__init__()
        • MeaslesSymptomResolveEvent.apply()
      • MeaslesDeathEvent
        • MeaslesDeathEvent.__init__()
        • MeaslesDeathEvent.apply()
      • HSI_Measles_Treatment
        • HSI_Measles_Treatment.__init__()
        • HSI_Measles_Treatment.apply()
        • HSI_Measles_Treatment.did_not_run()
      • MeaslesLoggingEvent
        • MeaslesLoggingEvent.__init__()
        • MeaslesLoggingEvent.apply()
      • MeaslesLoggingFortnightEvent
        • MeaslesLoggingFortnightEvent.__init__()
        • MeaslesLoggingFortnightEvent.apply()
      • MeaslesLoggingAnnualEvent
        • MeaslesLoggingAnnualEvent.__init__()
        • MeaslesLoggingAnnualEvent.apply()
    • tlo.methods.mockitis module
      • Mockitis
        • Mockitis.__init__()
        • Mockitis.read_parameters()
        • Mockitis.initialise_population()
        • Mockitis.initialise_simulation()
        • Mockitis.on_birth()
        • Mockitis.on_hsi_alert()
        • Mockitis.report_daly_values()
        • Mockitis.do_at_generic_first_appt_emergency()
      • MockitisEvent
        • MockitisEvent.__init__()
        • MockitisEvent.apply()
      • MockitisDeathEvent
        • MockitisDeathEvent.__init__()
        • MockitisDeathEvent.apply()
      • HSI_Mockitis_PresentsForCareWithSevereSymptoms
        • HSI_Mockitis_PresentsForCareWithSevereSymptoms.__init__()
        • HSI_Mockitis_PresentsForCareWithSevereSymptoms.apply()
        • HSI_Mockitis_PresentsForCareWithSevereSymptoms.did_not_run()
      • HSI_Mockitis_StartTreatment
        • HSI_Mockitis_StartTreatment.__init__()
        • HSI_Mockitis_StartTreatment.apply()
        • HSI_Mockitis_StartTreatment.did_not_run()
      • HSI_Mockitis_TreatmentMonitoring
        • HSI_Mockitis_TreatmentMonitoring.__init__()
        • HSI_Mockitis_TreatmentMonitoring.apply()
        • HSI_Mockitis_TreatmentMonitoring.did_not_run()
      • MockitisLoggingEvent
        • MockitisLoggingEvent.__init__()
        • MockitisLoggingEvent.apply()
    • tlo.methods.newborn_outcomes module
      • NewbornOutcomes
        • NewbornOutcomes.__init__()
        • NewbornOutcomes.read_parameters()
        • NewbornOutcomes.initialise_population()
        • NewbornOutcomes.get_and_store_newborn_item_codes()
        • NewbornOutcomes.initialise_simulation()
        • NewbornOutcomes.eval()
        • NewbornOutcomes.apply_risk_of_congenital_anomaly()
        • NewbornOutcomes.apply_risk_of_neonatal_infection_and_sepsis()
        • NewbornOutcomes.apply_risk_of_encephalopathy()
        • NewbornOutcomes.apply_risk_of_preterm_respiratory_distress_syndrome()
        • NewbornOutcomes.apply_risk_of_not_breathing_at_birth()
        • NewbornOutcomes.scheduled_week_one_postnatal_event()
        • NewbornOutcomes.set_death_status()
        • NewbornOutcomes.set_disability_status()
        • NewbornOutcomes.essential_newborn_care()
        • NewbornOutcomes.breast_feeding()
        • NewbornOutcomes.kangaroo_mother_care()
        • NewbornOutcomes.hiv_screening_for_at_risk_newborns()
        • NewbornOutcomes.apply_effect_of_neonatal_resus()
        • NewbornOutcomes.assessment_and_treatment_newborn_sepsis()
        • NewbornOutcomes.link_twins()
        • NewbornOutcomes.schedule_pnc()
        • NewbornOutcomes.on_birth()
        • NewbornOutcomes.on_hsi_alert()
        • NewbornOutcomes.report_daly_values()
        • NewbornOutcomes.run_if_care_of_the_receives_postnatal_check_cant_run()
      • HSI_NewbornOutcomes_ReceivesPostnatalCheck
        • HSI_NewbornOutcomes_ReceivesPostnatalCheck.__init__()
        • HSI_NewbornOutcomes_ReceivesPostnatalCheck.apply()
        • HSI_NewbornOutcomes_ReceivesPostnatalCheck.never_ran()
        • HSI_NewbornOutcomes_ReceivesPostnatalCheck.did_not_run()
        • HSI_NewbornOutcomes_ReceivesPostnatalCheck.not_available()
        • HSI_NewbornOutcomes_ReceivesPostnatalCheck._get_facility_level_for_pnc()
      • HSI_NewbornOutcomes_NeonatalWardInpatientCare
        • HSI_NewbornOutcomes_NeonatalWardInpatientCare.__init__()
        • HSI_NewbornOutcomes_NeonatalWardInpatientCare.apply()
        • HSI_NewbornOutcomes_NeonatalWardInpatientCare.did_not_run()
        • HSI_NewbornOutcomes_NeonatalWardInpatientCare.not_available()
      • BreastfeedingStatusUpdateEventSixMonths
        • BreastfeedingStatusUpdateEventSixMonths.__init__()
        • BreastfeedingStatusUpdateEventSixMonths.apply()
      • BreastfeedingStatusUpdateEventTwoYears
        • BreastfeedingStatusUpdateEventTwoYears.__init__()
        • BreastfeedingStatusUpdateEventTwoYears.apply()
    • tlo.methods.newborn_outcomes_lm module
    • tlo.methods.oesophagealcancer module
      • OesophagealCancer
        • OesophagealCancer.__init__()
        • OesophagealCancer.read_parameters()
        • OesophagealCancer.initialise_population()
        • OesophagealCancer.initialise_simulation()
        • OesophagealCancer.on_birth()
        • OesophagealCancer.on_hsi_alert()
        • OesophagealCancer.report_daly_values()
        • OesophagealCancer.do_at_generic_first_appt()
      • OesCancerMainPollingEvent
        • OesCancerMainPollingEvent.__init__()
        • OesCancerMainPollingEvent.apply()
      • HSI_OesophagealCancer_Investigation_Following_Dysphagia
        • HSI_OesophagealCancer_Investigation_Following_Dysphagia.__init__()
        • HSI_OesophagealCancer_Investigation_Following_Dysphagia.apply()
      • HSI_OesophagealCancer_StartTreatment
        • HSI_OesophagealCancer_StartTreatment.__init__()
        • HSI_OesophagealCancer_StartTreatment.apply()
      • HSI_OesophagealCancer_PostTreatmentCheck
        • HSI_OesophagealCancer_PostTreatmentCheck.__init__()
        • HSI_OesophagealCancer_PostTreatmentCheck.apply()
      • HSI_OesophagealCancer_PalliativeCare
        • HSI_OesophagealCancer_PalliativeCare.__init__()
        • HSI_OesophagealCancer_PalliativeCare.apply()
      • OesCancerLoggingEvent
        • OesCancerLoggingEvent.__init__()
        • OesCancerLoggingEvent.apply()
    • tlo.methods.other_adult_cancers module
      • OtherAdultCancer
        • OtherAdultCancer.__init__()
        • OtherAdultCancer.read_parameters()
        • OtherAdultCancer.initialise_population()
        • OtherAdultCancer.initialise_simulation()
        • OtherAdultCancer.on_birth()
        • OtherAdultCancer.on_hsi_alert()
        • OtherAdultCancer.report_daly_values()
        • OtherAdultCancer.do_at_generic_first_appt()
      • OtherAdultCancerMainPollingEvent
        • OtherAdultCancerMainPollingEvent.__init__()
        • OtherAdultCancerMainPollingEvent.apply()
      • HSI_OtherAdultCancer_Investigation_Following_early_other_adult_ca_symptom
        • HSI_OtherAdultCancer_Investigation_Following_early_other_adult_ca_symptom.__init__()
        • HSI_OtherAdultCancer_Investigation_Following_early_other_adult_ca_symptom.apply()
      • HSI_OtherAdultCancer_StartTreatment
        • HSI_OtherAdultCancer_StartTreatment.__init__()
        • HSI_OtherAdultCancer_StartTreatment.apply()
        • HSI_OtherAdultCancer_StartTreatment.did_not_run()
      • HSI_OtherAdultCancer_PostTreatmentCheck
        • HSI_OtherAdultCancer_PostTreatmentCheck.__init__()
        • HSI_OtherAdultCancer_PostTreatmentCheck.apply()
        • HSI_OtherAdultCancer_PostTreatmentCheck.did_not_run()
      • HSI_OtherAdultCancer_PalliativeCare
        • HSI_OtherAdultCancer_PalliativeCare.__init__()
        • HSI_OtherAdultCancer_PalliativeCare.apply()
        • HSI_OtherAdultCancer_PalliativeCare.did_not_run()
      • OtherAdultCancerLoggingEvent
        • OtherAdultCancerLoggingEvent.__init__()
        • OtherAdultCancerLoggingEvent.apply()
    • tlo.methods.postnatal_supervisor module
      • PostnatalSupervisor
        • PostnatalSupervisor.__init__()
        • PostnatalSupervisor.read_parameters()
        • PostnatalSupervisor.initialise_population()
        • PostnatalSupervisor.initialise_simulation()
        • PostnatalSupervisor.on_birth()
        • PostnatalSupervisor.further_on_birth_postnatal_supervisor()
        • PostnatalSupervisor.on_hsi_alert()
        • PostnatalSupervisor.report_daly_values()
        • PostnatalSupervisor.apply_linear_model()
        • PostnatalSupervisor.set_postnatal_complications_mothers()
        • PostnatalSupervisor.apply_risk_of_neonatal_complications_in_week_one()
        • PostnatalSupervisor.set_postnatal_complications_neonates()
        • PostnatalSupervisor.apply_risk_of_maternal_or_neonatal_death_postnatal()
      • PostnatalSupervisorEvent
        • PostnatalSupervisorEvent.__init__()
        • PostnatalSupervisorEvent.apply()
      • PostnatalWeekOneMaternalEvent
        • PostnatalWeekOneMaternalEvent.__init__()
        • PostnatalWeekOneMaternalEvent.apply()
      • PostnatalWeekOneNeonatalEvent
        • PostnatalWeekOneNeonatalEvent.__init__()
        • PostnatalWeekOneNeonatalEvent.apply()
      • HSI_PostnatalSupervisor_TreatmentForObstetricFistula
        • HSI_PostnatalSupervisor_TreatmentForObstetricFistula.__init__()
        • HSI_PostnatalSupervisor_TreatmentForObstetricFistula.apply()
    • tlo.methods.postnatal_supervisor_lm module
    • tlo.methods.pregnancy_helper_functions module
    • tlo.methods.pregnancy_supervisor module
      • PregnancySupervisor
        • PregnancySupervisor.__init__()
        • PregnancySupervisor.read_parameters()
        • PregnancySupervisor.initialise_population()
        • PregnancySupervisor.initialise_simulation()
        • PregnancySupervisor.on_birth()
        • PregnancySupervisor.further_on_birth_pregnancy_supervisor()
        • PregnancySupervisor.on_hsi_alert()
        • PregnancySupervisor.report_daly_values()
        • PregnancySupervisor.pregnancy_supervisor_property_reset()
        • PregnancySupervisor.apply_linear_model()
        • PregnancySupervisor.schedule_anc_one()
        • PregnancySupervisor.apply_risk_of_spontaneous_abortion()
        • PregnancySupervisor.apply_risk_of_induced_abortion()
        • PregnancySupervisor.do_after_abortion()
        • PregnancySupervisor.apply_risk_of_abortion_complications()
        • PregnancySupervisor.apply_risk_of_anaemia()
        • PregnancySupervisor.apply_risk_of_gestational_diabetes()
        • PregnancySupervisor.apply_risk_of_hypertensive_disorders()
        • PregnancySupervisor.apply_risk_of_progression_of_hypertension()
        • PregnancySupervisor.apply_risk_of_death_from_hypertension()
        • PregnancySupervisor.apply_risk_of_placental_abruption()
        • PregnancySupervisor.apply_risk_of_antepartum_haemorrhage()
        • PregnancySupervisor.apply_risk_of_premature_rupture_of_membranes_and_chorioamnionitis()
        • PregnancySupervisor.apply_risk_of_preterm_labour()
        • PregnancySupervisor.update_variables_post_still_birth_for_data_frame()
        • PregnancySupervisor.update_variables_post_still_birth_for_individual()
        • PregnancySupervisor.apply_risk_of_still_birth()
        • PregnancySupervisor.induction_care_seeking_and_still_birth_risk()
        • PregnancySupervisor.care_seeking_pregnancy_loss_complications()
        • PregnancySupervisor.apply_risk_of_death_from_monthly_complications()
        • PregnancySupervisor.schedule_first_anc_contact_for_new_pregnancy()
        • PregnancySupervisor.do_at_generic_first_appt_emergency()
      • PregnancySupervisorEvent
        • PregnancySupervisorEvent.__init__()
        • PregnancySupervisorEvent.apply()
      • EctopicPregnancyEvent
        • EctopicPregnancyEvent.__init__()
        • EctopicPregnancyEvent.apply()
      • EctopicPregnancyRuptureEvent
        • EctopicPregnancyRuptureEvent.__init__()
        • EctopicPregnancyRuptureEvent.apply()
      • EarlyPregnancyLossDeathEvent
        • EarlyPregnancyLossDeathEvent.__init__()
        • EarlyPregnancyLossDeathEvent.apply()
      • GestationalDiabetesGlycaemicControlEvent
        • GestationalDiabetesGlycaemicControlEvent.__init__()
        • GestationalDiabetesGlycaemicControlEvent.apply()
      • SyphilisInPregnancyEvent
        • SyphilisInPregnancyEvent.__init__()
        • SyphilisInPregnancyEvent.apply()
      • ParameterUpdateEvent
        • ParameterUpdateEvent.__init__()
        • ParameterUpdateEvent.apply()
      • PregnancyAnalysisEvent
        • PregnancyAnalysisEvent.__init__()
        • PregnancyAnalysisEvent.apply()
      • PregnancyLoggingEvent
        • PregnancyLoggingEvent.__init__()
        • PregnancyLoggingEvent.apply()
    • tlo.methods.pregnancy_supervisor_lm module
    • tlo.methods.prostate_cancer module
      • ProstateCancer
        • ProstateCancer.__init__()
        • ProstateCancer.read_parameters()
        • ProstateCancer.initialise_population()
        • ProstateCancer.initialise_simulation()
        • ProstateCancer.on_birth()
        • ProstateCancer.on_hsi_alert()
        • ProstateCancer.report_daly_values()
        • ProstateCancer.do_at_generic_first_appt()
      • ProstateCancerMainPollingEvent
        • ProstateCancerMainPollingEvent.__init__()
        • ProstateCancerMainPollingEvent.apply()
      • HSI_ProstateCancer_Investigation_Following_Urinary_Symptoms
        • HSI_ProstateCancer_Investigation_Following_Urinary_Symptoms.__init__()
        • HSI_ProstateCancer_Investigation_Following_Urinary_Symptoms.apply()
      • HSI_ProstateCancer_Investigation_Following_Pelvic_Pain
        • HSI_ProstateCancer_Investigation_Following_Pelvic_Pain.__init__()
        • HSI_ProstateCancer_Investigation_Following_Pelvic_Pain.apply()
      • HSI_ProstateCancer_Investigation_Following_psa_positive
        • HSI_ProstateCancer_Investigation_Following_psa_positive.__init__()
        • HSI_ProstateCancer_Investigation_Following_psa_positive.apply()
      • HSI_ProstateCancer_StartTreatment
        • HSI_ProstateCancer_StartTreatment.__init__()
        • HSI_ProstateCancer_StartTreatment.apply()
      • HSI_ProstateCancer_PostTreatmentCheck
        • HSI_ProstateCancer_PostTreatmentCheck.__init__()
        • HSI_ProstateCancer_PostTreatmentCheck.apply()
      • HSI_ProstateCancer_PalliativeCare
        • HSI_ProstateCancer_PalliativeCare.__init__()
        • HSI_ProstateCancer_PalliativeCare.apply()
      • ProstateCancerLoggingEvent
        • ProstateCancerLoggingEvent.__init__()
        • ProstateCancerLoggingEvent.apply()
    • tlo.methods.rti module
      • RTI
        • RTI.__init__()
        • RTI.read_parameters()
        • RTI.rti_injury_diagnosis()
        • RTI.initialise_population()
        • RTI.initialise_simulation()
        • RTI.rti_do_when_diagnosed()
        • RTI.rti_do_for_major_surgeries()
        • RTI.rti_do_for_minor_surgeries()
        • RTI.rti_acute_pain_management()
        • RTI.rti_ask_for_suture_kit()
        • RTI.rti_ask_for_shock_treatment()
        • RTI.rti_ask_for_burn_treatment()
        • RTI.rti_ask_for_fracture_casts()
        • RTI.rti_ask_for_open_fracture_treatment()
        • RTI.rti_ask_for_tetanus()
        • RTI.schedule_hsi_event_for_tomorrow()
        • RTI.rti_find_injury_column()
        • RTI.rti_find_all_columns_of_treated_injuries()
        • RTI.rti_assign_daly_weights()
        • RTI.rti_alter_daly_post_treatment()
        • RTI.rti_swap_injury_daly_upon_treatment()
        • RTI.rti_determine_LOS()
        • RTI.rti_find_and_count_injuries()
        • RTI.rti_treated_injuries()
        • RTI.on_birth()
        • RTI.look_up_consumable_item_codes()
        • RTI.on_hsi_alert()
        • RTI.report_daly_values()
        • RTI.rti_assign_injuries()
        • RTI._common_first_appt_steps()
        • RTI.do_at_generic_first_appt()
        • RTI.do_at_generic_first_appt_emergency()
      • RTIPollingEvent
        • RTIPollingEvent.__init__()
        • RTIPollingEvent.apply()
      • RTI_Check_Death_No_Med
        • RTI_Check_Death_No_Med.__init__()
        • RTI_Check_Death_No_Med.apply()
      • RTI_Recovery_Event
        • RTI_Recovery_Event.__init__()
        • RTI_Recovery_Event.apply()
      • HSI_RTI_Imaging_Event
        • HSI_RTI_Imaging_Event.__init__()
        • HSI_RTI_Imaging_Event.apply()
        • HSI_RTI_Imaging_Event.did_not_run()
      • HSI_RTI_Medical_Intervention
        • HSI_RTI_Medical_Intervention.__init__()
        • HSI_RTI_Medical_Intervention.apply()
        • HSI_RTI_Medical_Intervention.did_not_run()
      • HSI_RTI_Shock_Treatment
        • HSI_RTI_Shock_Treatment.__init__()
        • HSI_RTI_Shock_Treatment.apply()
        • HSI_RTI_Shock_Treatment.did_not_run()
      • HSI_RTI_Fracture_Cast
        • HSI_RTI_Fracture_Cast.__init__()
        • HSI_RTI_Fracture_Cast.apply()
        • HSI_RTI_Fracture_Cast.did_not_run()
      • HSI_RTI_Open_Fracture_Treatment
        • HSI_RTI_Open_Fracture_Treatment.__init__()
        • HSI_RTI_Open_Fracture_Treatment.apply()
        • HSI_RTI_Open_Fracture_Treatment.did_not_run()
      • HSI_RTI_Suture
        • HSI_RTI_Suture.__init__()
        • HSI_RTI_Suture.apply()
        • HSI_RTI_Suture.did_not_run()
      • HSI_RTI_Burn_Management
        • HSI_RTI_Burn_Management.__init__()
        • HSI_RTI_Burn_Management.apply()
        • HSI_RTI_Burn_Management.did_not_run()
      • HSI_RTI_Tetanus_Vaccine
        • HSI_RTI_Tetanus_Vaccine.__init__()
        • HSI_RTI_Tetanus_Vaccine.apply()
        • HSI_RTI_Tetanus_Vaccine.did_not_run()
      • HSI_RTI_Acute_Pain_Management
        • HSI_RTI_Acute_Pain_Management.__init__()
        • HSI_RTI_Acute_Pain_Management.apply()
        • HSI_RTI_Acute_Pain_Management.did_not_run()
      • HSI_RTI_Major_Surgeries
        • HSI_RTI_Major_Surgeries.__init__()
        • HSI_RTI_Major_Surgeries.apply()
        • HSI_RTI_Major_Surgeries.did_not_run()
      • HSI_RTI_Minor_Surgeries
        • HSI_RTI_Minor_Surgeries.__init__()
        • HSI_RTI_Minor_Surgeries.apply()
        • HSI_RTI_Minor_Surgeries.did_not_run()
      • RTI_Medical_Intervention_Death_Event
        • RTI_Medical_Intervention_Death_Event.__init__()
        • RTI_Medical_Intervention_Death_Event.apply()
      • RTI_No_Lifesaving_Medical_Intervention_Death_Event
        • RTI_No_Lifesaving_Medical_Intervention_Death_Event.__init__()
        • RTI_No_Lifesaving_Medical_Intervention_Death_Event.apply()
      • RTI_Logging_Event
        • RTI_Logging_Event.__init__()
        • RTI_Logging_Event.apply()
    • tlo.methods.scenario_switcher module
      • ImprovedHealthSystemAndCareSeekingScenarioSwitcher
        • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.__init__()
        • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.read_parameters()
        • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.pre_initialise_population()
        • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.update_parameters()
        • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.initialise_population()
        • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.initialise_simulation()
        • ImprovedHealthSystemAndCareSeekingScenarioSwitcher.on_birth()
      • ScenarioSwitchEvent
        • ScenarioSwitchEvent.__init__()
        • ScenarioSwitchEvent.apply()
    • tlo.methods.schisto module
      • Schisto
        • Schisto.__init__()
        • Schisto.read_parameters()
        • Schisto.pre_initialise_population()
        • Schisto.initialise_population()
        • Schisto.initialise_simulation()
        • Schisto.on_birth()
        • Schisto.report_daly_values()
        • Schisto.do_effect_of_treatment()
        • Schisto._load_parameters_from_workbook()
        • Schisto._register_symptoms()
        • Schisto._get_disability_weight()
        • Schisto._get_item_code_for_praziquantel()
        • Schisto._schedule_mda_events()
        • Schisto.do_at_generic_first_appt()
      • SchistoInfectionWormBurdenEvent
        • SchistoInfectionWormBurdenEvent.__init__()
        • SchistoInfectionWormBurdenEvent.apply()
      • SchistoMatureWorms
        • SchistoMatureWorms.__init__()
        • SchistoMatureWorms.apply()
      • SchistoWormsNatDeath
        • SchistoWormsNatDeath.__init__()
        • SchistoWormsNatDeath.apply()
      • SchistoMDAEvent
        • SchistoMDAEvent.__init__()
        • SchistoMDAEvent.apply()
        • SchistoMDAEvent._select_recipients()
      • HSI_Schisto_TestingFollowingSymptoms
        • HSI_Schisto_TestingFollowingSymptoms.__init__()
        • HSI_Schisto_TestingFollowingSymptoms.apply()
      • HSI_Schisto_TreatmentFollowingDiagnosis
        • HSI_Schisto_TreatmentFollowingDiagnosis.__init__()
        • HSI_Schisto_TreatmentFollowingDiagnosis.apply()
      • HSI_Schisto_MDA
        • HSI_Schisto_MDA.__init__()
        • HSI_Schisto_MDA.apply()
      • SchistoLoggingEvent
        • SchistoLoggingEvent.__init__()
        • SchistoLoggingEvent.apply()
    • tlo.methods.simplified_births module
      • SimplifiedBirths
        • SimplifiedBirths.__init__()
        • SimplifiedBirths.read_parameters()
        • SimplifiedBirths.initialise_population()
        • SimplifiedBirths.initialise_simulation()
        • SimplifiedBirths.on_birth()
      • SimplifiedBirthsPoll
        • SimplifiedBirthsPoll.__init__()
        • SimplifiedBirthsPoll.apply()
        • SimplifiedBirthsPoll.set_new_pregnancies()
        • SimplifiedBirthsPoll.do_deliveries()
        • SimplifiedBirthsPoll.update_breastfed_status()
    • tlo.methods.skeleton module
      • Skeleton
        • Skeleton.__init__()
        • Skeleton.read_parameters()
        • Skeleton.initialise_population()
        • Skeleton.initialise_simulation()
        • Skeleton.on_birth()
        • Skeleton.report_daly_values()
        • Skeleton.on_hsi_alert()
      • Skeleton_Event
        • Skeleton_Event.__init__()
        • Skeleton_Event.apply()
      • Skeleton_LoggingEvent
        • Skeleton_LoggingEvent.__init__()
        • Skeleton_LoggingEvent.apply()
      • HSI_Skeleton_Example_Interaction
        • HSI_Skeleton_Example_Interaction.__init__()
        • HSI_Skeleton_Example_Interaction.apply()
        • HSI_Skeleton_Example_Interaction.did_not_run()
        • HSI_Skeleton_Example_Interaction.never_ran()
    • tlo.methods.stunting module
      • Overview
      • Stunting
        • Stunting.__init__()
        • Stunting.read_parameters()
        • Stunting.initialise_population()
        • Stunting.initialise_simulation()
        • Stunting.on_birth()
        • Stunting.look_up_consumable_item_codes()
        • Stunting.do_onset()
        • Stunting.do_progression()
        • Stunting.do_recovery()
        • Stunting.do_treatment()
        • Stunting.do_at_generic_first_appt()
      • StuntingPollingEvent
        • StuntingPollingEvent.__init__()
        • StuntingPollingEvent.apply()
        • StuntingPollingEvent.apply_model()
      • StuntingLoggingEvent
        • StuntingLoggingEvent.__init__()
        • StuntingLoggingEvent.apply()
      • HSI_Stunting_ComplementaryFeeding
        • HSI_Stunting_ComplementaryFeeding.__init__()
        • HSI_Stunting_ComplementaryFeeding.apply()
      • StuntingPropertiesOfOtherModules
        • StuntingPropertiesOfOtherModules.__init__()
        • StuntingPropertiesOfOtherModules.read_parameters()
        • StuntingPropertiesOfOtherModules.initialise_population()
        • StuntingPropertiesOfOtherModules.initialise_simulation()
        • StuntingPropertiesOfOtherModules.on_birth()
    • tlo.methods.symptommanager module
      • SymptomManager
        • SymptomManager.__init__()
        • SymptomManager.get_column_name_for_symptom()
        • SymptomManager.read_parameters()
        • SymptomManager.register_symptom()
        • SymptomManager.register_generic_symptoms()
        • SymptomManager.pre_initialise_population()
        • SymptomManager.initialise_population()
        • SymptomManager.initialise_simulation()
        • SymptomManager.on_birth()
        • SymptomManager.change_symptom()
        • SymptomManager.who_has()
        • SymptomManager.who_not_have()
        • SymptomManager.has_what()
        • SymptomManager.have_what()
        • SymptomManager.causes_of()
        • SymptomManager.clear_symptoms()
        • SymptomManager.caused_by()
        • SymptomManager.get_persons_with_newly_onset_symptoms()
        • SymptomManager.reset_persons_with_newly_onset_symptoms()
      • SymptomManager_AutoOnsetEvent
        • SymptomManager_AutoOnsetEvent.__init__()
        • SymptomManager_AutoOnsetEvent.apply()
      • SymptomManager_AutoResolveEvent
        • SymptomManager_AutoResolveEvent.__init__()
        • SymptomManager_AutoResolveEvent.apply()
      • SymptomManager_SpuriousSymptomOnset
        • SymptomManager_SpuriousSymptomOnset.__init__()
        • SymptomManager_SpuriousSymptomOnset.get_generic_symptoms_dict()
        • SymptomManager_SpuriousSymptomOnset.apply()
      • SymptomManager_SpuriousSymptomResolve
        • SymptomManager_SpuriousSymptomResolve.__init__()
        • SymptomManager_SpuriousSymptomResolve.schedule_symptom_resolve()
        • SymptomManager_SpuriousSymptomResolve.apply()
    • tlo.methods.tb module
      • Tb
        • Tb.__init__()
        • Tb.read_parameters()
        • Tb.pre_initialise_population()
        • Tb._build_linear_models()
        • Tb.send_for_screening_general()
        • Tb.select_tb_test()
        • Tb.get_consumables_for_dx_and_tx()
        • Tb.initialise_population()
        • Tb.initialise_simulation()
        • Tb.update_parameters_for_program_scaleup()
        • Tb.on_birth()
        • Tb.report_daly_values()