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.utils module
parse_log_file()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()LogsDictget_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_label()get_color_cause_of_death_label()squarify_neat()get_root_path()bin_hsi_event_details()compute_mean_across_runs()plot_stacked_bar_chart()plot_clustered_stacked()
- tlo.analysis.hsi_events module
- Module contents
- Submodules
- tlo.logging package
- tlo.methods package
- Submodules
- tlo.methods.alri module
- Overview
AlriAlriPollingEventAlriIncidentCaseAlriNaturalRecoveryEventAlriCureEventAlriDeathEventHSI_Alri_TreatmentAlriLoggingEventAlriCheckPropertiesEventAlriIndividualLoggingEventAlriPropertiesOfOtherModulesAlriIncidentCase_Lethal_DangerSigns_PneumoniaAlriIncidentCase_NonLethal_Fast_Breathing_Pneumonia
- tlo.methods.bed_days module
- tlo.methods.bladder_cancer module
- tlo.methods.breast_cancer module
- tlo.methods.cardio_metabolic_disorders module
CardioMetabolicDisordersCardioMetabolicDisorders_MainPollingEventCardioMetabolicDisordersEventCardioMetabolicDisordersDeathEventCardioMetabolicDisordersWeightLossEventCardioMetabolicDisorders_LoggingEventHSI_CardioMetabolicDisorders_CommunityTestingForHypertensionHSI_CardioMetabolicDisorders_InvestigationNotFollowingSymptomsHSI_CardioMetabolicDisorders_InvestigationFollowingSymptomsHSI_CardioMetabolicDisorders_StartWeightLossAndMedicationHSI_CardioMetabolicDisorders_Refill_MedicationHSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment
- tlo.methods.care_of_women_during_pregnancy module
CareOfWomenDuringPregnancyHSI_CareOfWomenDuringPregnancy_FirstAntenatalCareContactHSI_CareOfWomenDuringPregnancy_SecondAntenatalCareContactHSI_CareOfWomenDuringPregnancy_ThirdAntenatalCareContactHSI_CareOfWomenDuringPregnancy_FourthAntenatalCareContactHSI_CareOfWomenDuringPregnancy_FifthAntenatalCareContactHSI_CareOfWomenDuringPregnancy_SixthAntenatalCareContactHSI_CareOfWomenDuringPregnancy_SeventhAntenatalCareContactHSI_CareOfWomenDuringPregnancy_EighthAntenatalCareContactHSI_CareOfWomenDuringPregnancy_FocusedANCVisitHSI_CareOfWomenDuringPregnancy_PresentsForInductionOfLabourHSI_CareOfWomenDuringPregnancy_MaternalEmergencyAssessmentHSI_CareOfWomenDuringPregnancy_AntenatalWardInpatientCareHSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfAnaemiaHSI_CareOfWomenDuringPregnancy_AntenatalOutpatientManagementOfGestationalDiabetesHSI_CareOfWomenDuringPregnancy_PostAbortionCaseManagementHSI_CareOfWomenDuringPregnancy_TreatmentForEctopicPregnancyCareOfWomenDuringPregnancyLoggingEvent
- tlo.methods.causes module
- tlo.methods.chronicsyndrome module
- tlo.methods.consumables module
- tlo.methods.contraception module
- tlo.methods.demography module
- tlo.methods.depression module
- tlo.methods.diarrhoea module
- tlo.methods.dxmanager module
- tlo.methods.enhanced_lifestyle module
- tlo.methods.epi module
EpiBcgVaccineEventOpvEventDtpHepVaccineEventDtpHibHepVaccineEventRotavirusVaccineEventPneumococcalVaccineEventHibVaccineEventMeaslesVaccineEventMeaslesRubellaVaccineEventHpvScheduleEventHsiBaseVaccineHSI_BcgVaccineHSI_opvHSI_DtpHibHepVaccineHSI_RotaVaccineHSI_PneumoVaccineHSI_MeaslesRubellaVaccineHSI_HpvVaccineHSI_TdVaccineEpiLoggingEvent
- tlo.methods.epilepsy module
- tlo.methods.fullmodel module
- tlo.methods.healthburden module
- tlo.methods.healthseekingbehaviour module
- tlo.methods.healthsystem module
- tlo.methods.hiv module
HivHivRegularPollingEventHivInfectionEventHivInfectionDuringBreastFeedingEventHivAidsOnsetEventHivAidsDeathEventHivAidsTbDeathEventHiv_DecisionToContinueOnPrEPHiv_DecisionToContinueTreatmentHSI_Hiv_TestAndReferHSI_Hiv_CircHSI_Hiv_StartInfantProphylaxisHSI_Hiv_StartOrContinueOnPrepHSI_Hiv_StartOrContinueTreatmentHivLoggingEventHivCheckPropertiesEventDummyHivModule
- tlo.methods.hiv_tb_calibration module
- tlo.methods.hsi_generic_first_appts module
- tlo.methods.labour module
LabourLabourOnsetEventLabourAtHomeEventLabourDeathAndStillBirthEventBirthAndPostnatalOutcomesEventHSI_Labour_ReceivesSkilledBirthAttendanceDuringLabourHSI_Labour_ReceivesPostnatalCheckHSI_Labour_ReceivesComprehensiveEmergencyObstetricCareHSI_Labour_PostnatalWardInpatientCareLabourAndPostnatalCareAnalysisEventLabourLoggingEvent
- tlo.methods.labour_lm module
- tlo.methods.malaria module
MalariaMalariaPollingEventDistrictMalariaScheduleTestingMalariaIPTpMalariaDeathEventHSI_Malaria_rdtHSI_Malaria_non_complicated_treatment_age0_5HSI_Malaria_non_complicated_treatment_age5_15HSI_Malaria_non_complicated_treatment_adultHSI_Malaria_complicated_treatment_childHSI_Malaria_complicated_treatment_adultHSI_MalariaIPTpMalariaCureEventMalariaParasiteClearanceEventMalariaLoggingEventMalariaTxLoggingEventMalariaPrevDistrictLoggingEventMalariaResetCounterEvent
- tlo.methods.measles module
- tlo.methods.mockitis module
- tlo.methods.newborn_outcomes module
- tlo.methods.newborn_outcomes_lm module
- tlo.methods.oesophagealcancer module
- tlo.methods.other_adult_cancers module
- tlo.methods.postnatal_supervisor module
- tlo.methods.postnatal_supervisor_lm module
- tlo.methods.pregnancy_helper_functions module
- tlo.methods.pregnancy_supervisor module
- tlo.methods.pregnancy_supervisor_lm module
- tlo.methods.prostate_cancer module
ProstateCancerProstateCancerMainPollingEventHSI_ProstateCancer_Investigation_Following_Urinary_SymptomsHSI_ProstateCancer_Investigation_Following_Pelvic_PainHSI_ProstateCancer_Investigation_Following_psa_positiveHSI_ProstateCancer_StartTreatmentHSI_ProstateCancer_PostTreatmentCheckHSI_ProstateCancer_PalliativeCareProstateCancerLoggingEvent
- tlo.methods.rti module
RTIRTIPollingEventRTI_Check_Death_No_MedRTI_Recovery_EventHSI_RTI_Imaging_EventHSI_RTI_Medical_InterventionHSI_RTI_Shock_TreatmentHSI_RTI_Fracture_CastHSI_RTI_Open_Fracture_TreatmentHSI_RTI_SutureHSI_RTI_Burn_ManagementHSI_RTI_Tetanus_VaccineHSI_RTI_Acute_Pain_ManagementHSI_RTI_Major_SurgeriesHSI_RTI_Minor_SurgeriesRTI_Medical_Intervention_Death_EventRTI_No_Lifesaving_Medical_Intervention_Death_EventRTI_Logging_Event
- tlo.methods.schisto module
- tlo.methods.simplified_births module
- tlo.methods.skeleton module
- tlo.methods.stunting module
- tlo.methods.symptommanager module
- tlo.methods.tb module
TbScenarioSetupEventTbActiveCasePollTbTreatmentAndRelapseEventsTbActiveEventTbSelfCureEventHSI_Tb_ScreeningAndReferHSI_Tb_Xray_level1bHSI_Tb_Xray_level2HSI_Tb_StartTreatmentHSI_Tb_FollowUpHSI_Tb_Start_or_Continue_IptTb_DecisionToContinueIPTTbDeathEventTbLoggingEventTbCheckPropertiesEventDummyTbModule
- tlo.methods.wasting module
- tlo.methods.alri module
- Module contents
- Submodules
- tlo.test package
Submodules¶
- tlo.cli module
- tlo.core module
TypesSpecifiableParameterPropertyModuleModule.INIT_DEPENDENCIESModule.OPTIONAL_INIT_DEPENDENCIESModule.ADDITIONAL_DEPENDENCIESModule.ALTERNATIVE_TOModule.METADATAModule.CAUSES_OF_DEATHModule.CAUSES_OF_DISABILITYModule.PARAMETERSModule.PROPERTIESModule.parametersModule.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
- tlo.docs module
- tlo.events module
- tlo.lm module
- tlo.lm_play module
- tlo.population module
- tlo.progressbar module
ProgressBarProgressBar.GLYPHSProgressBar.n_stepProgressBar.descriptionProgressBar.stepProgressBar.prop_completeProgressBar.perc_completeProgressBar.elapsed_timeProgressBar.iter_rateProgressBar.est_remaining_timeProgressBar.n_block_filledProgressBar.n_block_emptyProgressBar.prop_partial_blockProgressBar.filled_blocksProgressBar.empty_blocksProgressBar.partial_blockProgressBar.progress_barProgressBar.bar_colorProgressBar.statsProgressBar.prefixProgressBar.postfixProgressBar.reset()ProgressBar.update()ProgressBar.refresh()ProgressBar.start()ProgressBar.stop()
StreamDisplayAnsiStreamDisplayBasicStreamDisplay
- tlo.scenario module
- tlo.simulation module
- tlo.util module
create_age_range_lookup()transition_states()sample_outcome()BitsetHandlerBitsetHandler.dfBitsetHandler.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()hash_dataframe()get_person_id_to_inherit_from()
Module contents¶
The top-level TLO framework module.
We import our key classes so they’re available in the main namespace.
Pandas’ Timestamp is used as our main date type (even though it has nanosecond resolution…)