tlo.methods.tb module ===================== .. automodule:: tlo.methods.tb .. autoclass:: Tb Bases: :class:`tlo.core.Module` **PARAMETERS:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - prop_mdr2010 - REAL - Proportion of active tb cases with multidrug resistance in 2010 * - who_incidence_estimates - REAL - WHO estimated active TB incidence per 100,000 population * - followup_times - DATA_FRAME - times(weeks) tb treatment monitoring required after tx start * - tb_high_risk_distr - LIST - list of ten high-risk districts * - ipt_coverage - DATA_FRAME - national estimates of coverage of IPT in PLHIV and paediatric contacts * - incidence_active_tb_2010 - REAL - incidence of active tb in 2010 in all ages * - rr_tb_child - REAL - relative risk of tb infection if under 16 years of age * - rr_bcg_inf - REAL - relative risk of tb infection with bcg vaccination * - monthly_prob_relapse_tx_complete - REAL - monthly probability of relapse once treatment complete * - monthly_prob_relapse_tx_incomplete - REAL - monthly probability of relapse if treatment incomplete * - monthly_prob_relapse_2yrs - REAL - monthly probability of relapse 2 years after treatment complete * - rr_relapse_hiv - REAL - relative risk of relapse for HIV-positive people * - scaling_factor_WHO - REAL - scaling factor applied to WHO estimates to account for the impact of interventions in place * - duration_active_disease_years - REAL - duration of active disease from onset to cure or death * - prop_smear_positive - REAL - proportion of new active cases that will be smear-positive * - prop_smear_positive_hiv - REAL - proportion of hiv+ active tb cases that will be smear-positive * - death_rate_smear_pos_untreated - REAL - probability of death in smear-positive tb cases with untreated tb * - death_rate_smear_neg_untreated - REAL - probability of death in smear-negative tb cases with untreated tb * - death_rate_child0_4_treated - REAL - probability of death in child aged 0-4 years with treated tb * - death_rate_child5_14_treated - REAL - probability of death in child aged 5-14 years with treated tb * - death_rate_adult_treated - REAL - probability of death in adult aged >=15 years with treated tb * - rr_tb_bcg - REAL - relative risk of progression to active disease for children with BCG vaccine * - rr_tb_hiv - REAL - relative risk of progression to active disease for PLHIV * - rr_tb_aids - REAL - relative risk of progression to active disease for PLHIV with AIDS * - rr_tb_art_adult - REAL - relative risk of progression to active disease for adults with HIV on ART * - rr_tb_art_child - REAL - relative risk of progression to active disease for adults with HIV on ART * - rr_tb_obese - REAL - relative risk of progression to active disease if obese * - rr_tb_diabetes1 - REAL - relative risk of progression to active disease with type 1 diabetes * - rr_tb_alcohol - REAL - relative risk of progression to active disease with heavy alcohol use * - rr_tb_smoking - REAL - relative risk of progression to active disease with smoking * - rr_ipt_adult - REAL - relative risk of active TB with IPT in adults * - rr_ipt_child - REAL - relative risk of active TB with IPT in children * - rr_ipt_adult_hiv - REAL - relative risk of active TB with IPT in adults with hiv * - rr_ipt_child_hiv - REAL - relative risk of active TB with IPT in children with hiv * - rr_ipt_art_adult - REAL - relative risk of active TB with IPT and ART in adults * - rr_ipt_art_child - REAL - relative risk of active TB with IPT and ART in children * - sens_xpert_smear_negative - REAL - sensitivity of Xpert test in smear negative TB cases * - sens_xpert_smear_positive - REAL - sensitivity of Xpert test in smear positive TB cases * - spec_xpert_smear_negative - REAL - specificity of Xpert test in smear negative TB cases * - spec_xpert_smear_positive - REAL - specificity of Xpert test in smear positive TB cases * - sens_sputum_smear_positive - REAL - sensitivity of sputum smear microscopy in sputum positive cases * - spec_sputum_smear_positive - REAL - specificity of sputum smear microscopy in sputum positive cases * - sens_clinical - REAL - sensitivity of clinical diagnosis in detecting active TB * - spec_clinical - REAL - specificity of clinical diagnosis in detecting TB * - sens_xray_smear_negative - REAL - sensitivity of x-ray diagnosis in smear negative TB cases * - sens_xray_smear_positive - REAL - sensitivity of x-ray diagnosis in smear positive TB cases * - spec_xray_smear_negative - REAL - specificity of x-ray diagnosis in smear negative TB cases * - spec_xray_smear_positive - REAL - specificity of x-ray diagnosis in smear positive TB cases * - prob_tx_success_ds - REAL - Probability of treatment success for new and relapse TB cases * - prob_tx_success_mdr - REAL - Probability of treatment success for MDR-TB cases * - prob_tx_success_0_4 - REAL - Probability of treatment success for children aged 0-4 years * - prob_tx_success_5_14 - REAL - Probability of treatment success for children aged 5-14 years * - prob_tx_success_shorter - REAL - Probability of treatment success for children aged <16 years on shorter regimen * - rate_testing_general_pop - REAL - rate of screening / testing per month in general population * - rate_testing_active_tb - DATA_FRAME - rate of screening / testing per month in population with active tb * - ds_treatment_length - REAL - length of treatment for drug-susceptible tb (first case) in months * - ds_retreatment_length - REAL - length of treatment for drug-susceptible tb (secondary case) in months * - mdr_treatment_length - REAL - length of treatment for mdr-tb in months * - child_shorter_treatment_length - REAL - length of treatment for shorter paediatric regimen in months * - prob_retained_ipt_6_months - REAL - probability of being retained on IPT every 6 months if still eligible * - age_eligibility_for_ipt - REAL - eligibility criteria (years of age) for IPT given to contacts of TB cases * - ipt_start_date - INT - year from which IPT is available for paediatric contacts of diagnosed active TB cases * - scenario - INT - integer value labelling the scenario to be run: default is 0 * - scenario_start_date - DATE - date from which different scenarios are run * - first_line_test - STRING - name of first test to be used for TB diagnosis * - second_line_test - STRING - name of second test to be used for TB diagnosis * - probability_access_to_xray - REAL - probability a person will have access to chest x-ray * - prob_tb_referral_in_generic_hsi - REAL - probability of referral to TB screening HSI if presenting with TB-related symptoms * - scaleup_parameters - DATA_FRAME - list of parameters and values changed in scenario analysis **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - tb_inf - CATEGORICAL - tb status. Possible values are: [uninfected, latent, active, ] * - tb_strain - CATEGORICAL - tb strain: drug-susceptible (ds) or multi-drug resistant (mdr). Possible values are: [none, ds, mdr, ] * - tb_date_latent - DATE - Date acquired tb infection (latent stage) * - tb_scheduled_date_active - DATE - Date active tb is scheduled to start * - tb_date_active - DATE - Date active tb started * - tb_smear - BOOL - smear positivity with active infection: False=negative, True=positive * - tb_date_tested - DATE - Date of last tb test * - tb_diagnosed - BOOL - person has current diagnosis of active tb * - tb_date_diagnosed - DATE - date most recent tb diagnosis * - tb_diagnosed_mdr - BOOL - person has current diagnosis of active mdr-tb * - tb_on_treatment - BOOL - on tb treatment regimen * - tb_date_treated - DATE - date most recent tb treatment started * - tb_treatment_regimen - CATEGORICAL - current tb treatment regimen. Possible values are: [none, tb_tx_adult, tb_tx_child, tb_tx_child_shorter, tb_retx_adult, tb_retx_child, tb_mdrtx, ] * - tb_ever_treated - BOOL - if ever treated for active tb * - tb_treatment_failure - BOOL - failed first line tb treatment * - tb_treated_mdr - BOOL - on tb treatment MDR regimen * - tb_date_treated_mdr - DATE - date tb MDR treatment started * - tb_on_ipt - BOOL - if currently on ipt * - tb_date_ipt - DATE - date ipt started **Class attributes:** CAUSES_OF_DEATH : {'TB': , 'AIDS_TB': } CAUSES_OF_DISABILITY : {'TB': } INIT_DEPENDENCIES : {'SymptomManager', 'Epi', 'Demography', 'Lifestyle', 'HealthSystem'} METADATA : {, , , } OPTIONAL_INIT_DEPENDENCIES : {'HealthBurden', 'Hiv'} SYMPTOMS : {'night_sweats', 'fatigue'} **Functions (defined or overridden in class Tb):** .. automethod:: __init__ .. automethod:: read_parameters .. automethod:: pre_initialise_population .. automethod:: send_for_screening_general .. automethod:: select_tb_test .. automethod:: get_consumables_for_dx_and_tx .. automethod:: initialise_population .. automethod:: initialise_simulation .. automethod:: on_birth .. automethod:: report_daly_values .. automethod:: calculate_untreated_proportion .. automethod:: assign_active_tb .. automethod:: consider_ipt_for_those_initiating_art .. automethod:: relapse_event .. automethod:: end_treatment .. automethod:: check_config_of_properties .. autoclass:: ScenarioSetupEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class ScenarioSetupEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: TbActiveCasePoll Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class TbActiveCasePoll):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: TbTreatmentAndRelapseEvents Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class TbTreatmentAndRelapseEvents):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: TbActiveEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class TbActiveEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: TbSelfCureEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class TbSelfCureEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Tb_ScreeningAndRefer Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Tb_ScreeningAndRefer):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Tb_ClinicalDiagnosis Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Tb_ClinicalDiagnosis):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Tb_Xray_level1b Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Tb_Xray_level1b):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Tb_Xray_level2 Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Tb_Xray_level2):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Tb_StartTreatment Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** EXPECTED_APPT_FOOTPRINT : **Functions (defined or overridden in class HSI_Tb_StartTreatment):** .. automethod:: __init__ .. automethod:: apply .. automethod:: post_apply_hook .. automethod:: select_treatment .. autoclass:: HSI_Tb_FollowUp Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Tb_FollowUp):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Tb_Start_or_Continue_Ipt Bases: :class:`tlo.methods.healthsystem.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class HSI_Tb_Start_or_Continue_Ipt):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: Tb_DecisionToContinueIPT Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class Tb_DecisionToContinueIPT):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: TbDeathEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class TbDeathEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: TbLoggingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class TbLoggingEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: TbCheckPropertiesEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class TbCheckPropertiesEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: DummyTbModule Bases: :class:`tlo.core.Module` **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - tb_inf - CATEGORICAL - tb status. Possible values are: [uninfected, latent, active, ] **Class attributes:** ALTERNATIVE_TO : {'Tb'} INIT_DEPENDENCIES : {'Demography'} **Functions (defined or overridden in class DummyTbModule):** .. automethod:: __init__ .. automethod:: read_parameters .. automethod:: initialise_population .. automethod:: initialise_simulation .. automethod:: on_birth