tlo.methods.malaria module ========================== .. automodule:: tlo.methods.malaria .. autoclass:: Malaria Bases: :class:`tlo.core.Module` **PARAMETERS:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - interv - REAL - data frame of intervention coverage by year * - clin_inc - REAL - data frame of clinical incidence by age, district, intervention coverage * - inf_inc - REAL - data frame of infection incidence by age, district, intervention coverage * - sev_inc - REAL - data frame of severe case incidence by age, district, intervention coverage * - itn_district - REAL - data frame of ITN usage rates by district * - irs_district - REAL - data frame of IRS usage rates by district * - sev_symp_prob - REAL - probabilities of each symptom for severe malaria cases * - sensitivity_rdt - REAL - Sensitivity of rdt * - cfr - REAL - case-fatality rate for severe malaria * - dur_asym - REAL - duration (days) of asymptomatic malaria * - dur_clin - REAL - duration (days) of clinical symptoms of malaria * - dur_clin_para - REAL - duration (days) of parasitaemia for clinical malaria cases * - treatment_adjustment - REAL - probability of death from severe malaria if on treatment * - p_sev_anaemia_preg - REAL - probability of severe anaemia in pregnant women with clinical malaria * - itn_proj - REAL - coverage of ITN for projections 2020 onwards * - mortality_adjust - REAL - adjustment of case-fatality rate to match WHO/MAP * - data_end - REAL - final year of ICL malaria model outputs, after 2018 = projections * - irs_rates_boundary - REAL - threshold for indoor residual spraying coverage * - irs_rates_upper - REAL - indoor residual spraying high coverage * - irs_rates_lower - REAL - indoor residual spraying low coverage * - prob_malaria_case_tests - REAL - probability that a malaria case will have a scheduled rdt * - itn - REAL - projected future itn coverage * - rdt_testing_rates - REAL - per capita rdt testing rate of general population * - scaling_factor_for_rdt_availability - REAL - scaling factor applied to the reports of rdt usage to compensate fornon-availability of rdts at some facilities * - duration_iptp_protection_weeks - REAL - duration of protection against clinical malaria conferred by each dose of IPTp * - rr_clinical_malaria_hiv_under5 - REAL - relative risk of clinical malaria if HIV+ and aged under 5 years * - rr_clinical_malaria_hiv_over5 - REAL - relative risk of clinical malaria if HIV+ and aged over 5 years * - rr_clinical_malaria_hiv_pregnant - REAL - relative risk of clinical malaria if HIV+ and pregnant * - rr_clinical_malaria_cotrimoxazole - REAL - relative risk of clinical malaria if on cotrimoxazole * - rr_clinical_malaria_art - REAL - relative risk of clinical malaria if HIV+ and on ART and virally suppressed * - rr_clinical_malaria_iptp - REAL - relative risk of clinical malaria with each dose of IPTp * - rr_severe_malaria_hiv_under5 - REAL - relative risk of severe malaria if HIV+ and aged under 5 years * - rr_severe_malaria_hiv_over5 - REAL - relative risk of severe malaria if HIV+ and aged over 5 years * - rr_severe_malaria_hiv_pregnant - REAL - relative risk of clinical malaria if HIV+ and pregnant * - rr_severe_malaria_iptp - REAL - relative risk of severe malaria with each dose of IPTp * - prob_of_treatment_success - REAL - probability that treatment will clear malaria symptoms **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - ma_is_infected - BOOL - Current status of malaria * - ma_date_infected - DATE - Date of latest infection * - ma_date_symptoms - DATE - Date of symptom start for clinical infection * - ma_date_death - DATE - Date of death due to malaria * - ma_tx - CATEGORICAL - Type of anti-malarial treatment person is currently using. Possible values are: [none, uncomplicated, complicated, ] * - ma_date_tx - DATE - Date treatment started for most recent malaria episode * - ma_inf_type - CATEGORICAL - specific symptoms with malaria infection. Possible values are: [none, asym, clinical, severe, ] * - ma_age_edited - REAL - age values redefined to match with malaria data * - ma_clinical_counter - INT - annual counter for malaria clinical episodes * - ma_dx_counter - INT - annual counter for malaria diagnoses * - ma_tx_counter - INT - annual counter for malaria treatment episodes * - ma_clinical_preg_counter - INT - annual counter for malaria clinical episodes in pregnant women * - ma_iptp - BOOL - if woman has IPTp in current pregnancy **Class attributes:** ADDITIONAL_DEPENDENCIES : {'Tb', 'Hiv'} CAUSES_OF_DEATH : {'Malaria': } CAUSES_OF_DISABILITY : {'Malaria': } INIT_DEPENDENCIES : {'Contraception', 'Demography', 'SymptomManager', 'HealthSystem'} METADATA : {, , , } OPTIONAL_INIT_DEPENDENCIES : {'HealthBurden'} **Functions (defined or overridden in class Malaria):** .. automethod:: __init__ .. automethod:: read_parameters .. automethod:: pre_initialise_population .. automethod:: initialise_population .. automethod:: malaria_poll2 .. automethod:: general_population_rdt_scheduler .. automethod:: initialise_simulation .. automethod:: on_birth .. automethod:: report_daly_values .. automethod:: check_if_fever_is_caused_by_malaria .. automethod:: do_at_generic_first_appt .. automethod:: do_at_generic_first_appt_emergency .. autoclass:: MalariaPollingEventDistrict Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class MalariaPollingEventDistrict):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: MalariaIPTp Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class MalariaIPTp):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: MalariaEndIPTpProtection Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class MalariaEndIPTpProtection):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: MalariaDeathEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class MalariaDeathEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Malaria_rdt Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_Malaria_rdt):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Malaria_rdt_community Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_Malaria_rdt_community):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Malaria_Treatment Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_Malaria_Treatment):** .. automethod:: __init__ .. automethod:: apply .. automethod:: get_drugs .. automethod:: did_not_run .. autoclass:: HSI_Malaria_Treatment_Complicated Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_Malaria_Treatment_Complicated):** .. automethod:: __init__ .. automethod:: apply .. automethod:: did_not_run .. autoclass:: HSI_MalariaIPTp Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_MalariaIPTp):** .. automethod:: __init__ .. automethod:: apply .. automethod:: did_not_run .. autoclass:: MalariaUpdateEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class MalariaUpdateEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: MalariaParasiteClearanceEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class MalariaParasiteClearanceEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: MalariaLoggingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class MalariaLoggingEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: MalariaTxLoggingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class MalariaTxLoggingEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: MalariaPrevDistrictLoggingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class MalariaPrevDistrictLoggingEvent):** .. automethod:: __init__ .. automethod:: apply