tlo.methods.diarrhoea module ============================ .. automodule:: tlo.methods.diarrhoea .. autoclass:: Diarrhoea Bases: :class:`tlo.core.Module` **PARAMETERS:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - base_inc_rate_diarrhoea_by_rotavirus - LIST - incidence rate (per person-year) of diarrhoea caused by rotavirus in age groups 0-11, 12-23, 24-59 months * - base_inc_rate_diarrhoea_by_shigella - LIST - incidence rate (per person-year) of diarrhoea caused by shigella spp in age groups 0-11, 12-23, 24-59 months * - base_inc_rate_diarrhoea_by_adenovirus - LIST - incidence rate (per person-year) of diarrhoea caused by adenovirus 40/41 in age groups 0-11, 12-23, 24-59 months * - base_inc_rate_diarrhoea_by_cryptosporidium - LIST - incidence rate (per person-year) of diarrhoea caused by cryptosporidium in age groups 0-11, 12-23, 24-59 months * - base_inc_rate_diarrhoea_by_campylobacter - LIST - incidence rate (per person-year) of diarrhoea caused by campylobacter spp in age groups 0-11, 12-23, 24-59 months * - base_inc_rate_diarrhoea_by_ETEC - LIST - incidence rate (per person-year) of diarrhoea caused by ETEC in age groups 0-11, 12-23, 24-59 months * - base_inc_rate_diarrhoea_by_sapovirus - LIST - incidence rate (per person-year) of diarrhoea caused by sapovirus in age groups 0-11, 12-23, 24-59 months * - base_inc_rate_diarrhoea_by_norovirus - LIST - incidence rate (per person-year) of diarrhoea caused by norovirus in age groups 0-11, 12-23, 24-59 months * - base_inc_rate_diarrhoea_by_astrovirus - LIST - incidence rate (per person-year) of diarrhoea caused by astrovirus in age groups 0-11, 12-23, 24-59 months * - base_inc_rate_diarrhoea_by_tEPEC - LIST - incidence rate (per person-year) of diarrhoea caused by tEPEC in age groups 0-11, 12-23, 24-59 months * - rr_diarrhoea_HHhandwashing - REAL - relative rate of diarrhoea with household handwashing with soap * - rr_diarrhoea_improved_sanitation - REAL - relative rate of diarrhoea for improved sanitation * - rr_diarrhoea_clean_water - REAL - relative rate of diarrhoea for access to clean drinking water * - rr_diarrhoea_exclusive_vs_partial_breastfeeding_<6mo - REAL - relative rate of diarrhoea for partial breastfeeding in <6 months old, compared to exclusive breastfeeding * - rr_diarrhoea_exclusive_vs_no_breastfeeding_<6mo - REAL - relative rate of diarrhoea for no breastfeeding in <6 months old, compared to exclusive breastfeeding * - rr_diarrhoea_any_vs_no_breastfeeding_6_11mo - REAL - relative rate of diarrhoea for no breastfeeding in 6 months old to 1 years old, compared to any breastfeeding at this age group * - rr_diarrhoea_untreated_HIV - REAL - relative rate of diarrhoea for HIV positive status * - rr_diarrhoea_SAM - REAL - relative rate of diarrhoea for severe malnutrition * - proportion_AWD_in_rotavirus - REAL - acute diarrhoea type caused in rotavirus-attributed diarrhoea * - proportion_AWD_in_shigella - REAL - acute diarrhoea type caused in shigella-attributed diarrhoea * - proportion_AWD_in_adenovirus - REAL - acute diarrhoea type caused in adenovirus-attributed diarrhoea * - proportion_AWD_in_cryptosporidium - REAL - acute diarrhoea type caused in cryptosporidium-attributed diarrhoea * - proportion_AWD_in_campylobacter - REAL - acute diarrhoea type caused in campylobacter-attributed diarrhoea * - proportion_AWD_in_ETEC - REAL - acute diarrhoea type caused in ETEC-attributed diarrhoea * - proportion_AWD_in_sapovirus - REAL - acute diarrhoea type caused in sapovirus-attributed diarrhoea * - proportion_AWD_in_norovirus - REAL - acute diarrhoea type caused in norovirus-attributed diarrhoea * - proportion_AWD_in_astrovirus - REAL - acute diarrhoea type caused in astrovirus-attributed diarrhoea * - proportion_AWD_in_tEPEC - REAL - acute diarrhoea type in tEPEC-attributed diarrhoea * - prob_dehydration_by_rotavirus - REAL - probability of any dehydration caused by rotavirus * - prob_dehydration_by_shigella - REAL - probability of any dehydration caused by shigella * - prob_dehydration_by_adenovirus - REAL - probability of any dehydration caused by adenovirus * - prob_dehydration_by_cryptosporidium - REAL - probability of any dehydration caused by cryptosporidium * - prob_dehydration_by_campylobacter - REAL - probability of any dehydration caused by campylobacter * - prob_dehydration_by_ETEC - REAL - probability of any dehydration caused by ETEC * - prob_dehydration_by_sapovirus - REAL - probability of any dehydration caused by sapovirus * - prob_dehydration_by_norovirus - REAL - probability of any dehydration caused by norovirus * - prob_dehydration_by_astrovirus - REAL - probability of any dehydration caused by astrovirus * - prob_dehydration_by_tEPEC - REAL - probability of any dehydration caused by tEPEC * - probability_of_severe_dehydration_if_some_dehydration - REAL - probability that someone with diarrhoea and some dehydration develops severe dehydration * - prob_prolonged_diarr_rotavirus - REAL - probability of prolonged episode in rotavirus-attributed diarrhoea * - prob_prolonged_diarr_shigella - REAL - probability of prolonged episode by shigella-attributed diarrhoea * - prob_prolonged_diarr_adenovirus - REAL - probability of prolonged episode by adenovirus-attributed diarrhoea * - prob_prolonged_diarr_cryptosporidium - REAL - probability of prolonged episode by cryptosporidium-attributed diarrhoea * - prob_prolonged_diarr_campylobacter - REAL - probability of prolonged episode by campylobacter-attributed diarrhoea * - prob_prolonged_diarr_ETEC - REAL - probability of prolonged episode by ETEC-attributed diarrhoea * - prob_prolonged_diarr_sapovirus - REAL - probability of prolonged episode by sapovirus-attributed diarrhoea * - prob_prolonged_diarr_norovirus - REAL - probability of prolonged episode by norovirus-attributed diarrhoea * - prob_prolonged_diarr_astrovirus - REAL - probability of prolonged episode by norovirus-attributed diarrhoea * - prob_prolonged_diarr_tEPEC - REAL - probability of prolonged episode by tEPEC-attributed diarrhoea * - prob_prolonged_to_persistent_diarr - REAL - probability of prolonged diarrhoea becoming persistent diarrhoea * - rr_bec_persistent_age>6mo - REAL - relative rate of acute diarrhoea becoming persistent diarrhoea for children over 6 months * - rr_bec_persistent_HIV - REAL - relative rate of acute diarrhoea becoming persistent diarrhoea for HIV positive * - rr_bec_persistent_SAM - REAL - relative rate of acute diarrhoea becoming persistent diarrhoea for severely acute malnutrition * - rr_bec_persistent_stunted - REAL - relative rate of acute diarrhoea becoming persistent diarrhoea for stunted children * - min_dur_acute - INT - The minimum duration (in days) for an episode that is classified as an acute episode * - min_dur_prolonged - INT - The minimum duration (in days) for an episode that is classified as a prolonged episode * - min_dur_persistent - INT - The minimum duration (in days) for an episode that is classified as a persistent episode * - max_dur_persistent - INT - The maximum duration (in days) for an episode that is classified as a persistent episode * - prob_fever_by_rotavirus - REAL - probability of fever caused by rotavirus * - prob_fever_by_shigella - REAL - probability of fever caused by shigella * - prob_fever_by_adenovirus - REAL - probability of fever caused by adenovirus * - prob_fever_by_cryptosporidium - REAL - probability of fever caused by cryptosporidium * - prob_fever_by_campylobacter - REAL - probability of fever caused by campylobacter * - prob_fever_by_ETEC - REAL - probability of fever caused by ETEC * - prob_fever_by_sapovirus - REAL - probability of fever caused by sapovirus * - prob_fever_by_norovirus - REAL - probability of fever caused by norovirus * - prob_fever_by_astrovirus - REAL - probability of fever caused by astrovirus * - prob_fever_by_tEPEC - REAL - probability of fever caused by tEPEC * - prob_vomiting_by_rotavirus - REAL - probability of vomiting caused by rotavirus * - prob_vomiting_by_shigella - REAL - probability of vomiting caused by shigella * - prob_vomiting_by_adenovirus - REAL - probability of vomiting caused by adenovirus * - prob_vomiting_by_cryptosporidium - REAL - probability of vomiting caused by cryptosporidium * - prob_vomiting_by_campylobacter - REAL - probability of vomiting caused by campylobacter * - prob_vomiting_by_ETEC - REAL - probability of vomiting caused by ETEC * - prob_vomiting_by_sapovirus - REAL - probability of vomiting caused by sapovirus * - prob_vomiting_by_norovirus - REAL - probability of vomiting caused by norovirus * - prob_vomiting_by_astrovirus - REAL - probability of vomiting caused by astrovirus * - prob_vomiting_by_tEPEC - REAL - probability of vomiting caused by tEPEC * - adjustment_factor_on_cfr - REAL - Factor by which fatality probabilities are multiplied (to be used in calibration) * - case_fatality_rate_AWD - REAL - case fatality rate for acute watery diarrhoea cases * - rr_diarr_death_bloody - REAL - relative risk of diarrhoea death (compared to `case_fatality_rate_AWD` if the diarrhoea is of type "bloody" (i.e. dyssentry). * - rr_diarr_death_age24to59mo - REAL - relative risk of diarrhoea death for ages 24 to 59 months * - rr_diarr_death_if_duration_longer_than_13_days - REAL - relative risk of diarrhoea death if the duration episode is 13 days or longer * - rr_diarr_death_severe_dehydration - REAL - relative risk of diarrhoea death for cases with severe dehyadration * - rr_diarr_death_untreated_HIV - REAL - relative risk of diarrhoea death for untreated HIV * - rr_diarr_death_SAM - REAL - relative risk of diarrhoea death for severe acute malnutrition * - rr_diarr_death_alri - REAL - relative risk of diarrhoea death if concurrent lower respiratory infection * - rr_diarr_death_cryptosporidium - REAL - relative risk of diarrhoea death if caused by cryptosporidium * - rr_diarr_death_shigella - REAL - relative risk of diarrhoea death if caused by shigella * - sensitivity_severe_dehydration_visual_inspection - REAL - sensitivity of IMCI severe dehydration algorithm for dehydration >9% loss of body weight * - specificity_severe_dehydration_visual_inspection - REAL - specificity of IMCI severe dehydration algorithm for dehydration >9% loss of body weight * - prob_hospitalization_on_danger_signs - REAL - probability of hospitalisation when danger signs are detected in an initial consultation * - prob_WHOPlanC_cures_dehydration_if_severe_dehydration - REAL - probability that severe dehydration is cured by Treatment Plan C * - prob_ORS_cures_dehydration_if_severe_dehydration - REAL - probability that severe dehydration is cured by ORS * - prob_ORS_cures_dehydration_if_non_severe_dehydration - REAL - probability that non-severe dehydration is cured by ORS * - prob_antibiotic_cures_dysentery - REAL - probability that blood-in-stool is removed by the use of antibiotics * - number_of_days_reduced_duration_with_zinc - INT - number of days reduced duration with zinc * - days_between_treatment_and_cure - INT - number of days between any treatment being given in an HSI and the cure occurring. * - rr_severe_dehydration_due_to_rotavirus_with_R1_under1yo - REAL - relative risk of severe dehydration with rotavirus vaccine, for under 1 years old. * - rr_severe_dehydration_due_to_rotavirus_with_R1_over1yo - REAL - relative risk of severe dehydration with rotavirus vaccine, for those aged 1 year and older. **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - gi_has_diarrhoea - BOOL - Whether or not the person currently has an episode of diarrhoea. * - gi_pathogen - CATEGORICAL - The attributable pathogen for the current episode of diarrhoea (np.nan if the person does not currently have diarrhoea).. Possible values are: [rotavirus, shigella, adenovirus, cryptosporidium, campylobacter, ETEC, sapovirus, norovirus, astrovirus, tEPEC, ] * - gi_type - CATEGORICAL - Type (watery or blood) of the current episode of diarrhoea (np.nan if the person does not currently have diarrhoea).. Possible values are: [watery, bloody, ] * - gi_dehydration - CATEGORICAL - Severity of dehydration for the current episode of diarrhoea (np.nan if the person does not currently have diarrhoea).. Possible values are: [none, some, severe, ] * - gi_duration_longer_than_13days - BOOL - Whether the duration of the current episode would last longer than 13 days if untreated. (False if does not have current episode) * - gi_number_of_episodes - INT - Number of episodes of diarrhoea caused by a pathogen * - gi_date_of_onset - DATE - Date of onset of current episode of diarrhoea (pd.NaT if does not have current episode of diarrhoea). * - gi_scheduled_date_recovery - DATE - Scheduled date of recovery from current episode of diarrhoea (pd.NaT if does not have current episode or current episode is scheduled to result in death). This is scheduled when the episode is onset and may be revised subsequently if the episode is cured by a treatment * - gi_scheduled_date_death - DATE - Scheduled date of death caused by current episode of diarrhoea (pd.NaT if does not have current episode or if current episode will not result in death). This is scheduled when the episode is onset and may be revised subsequently if the episode is cured by a treatment. * - gi_date_end_of_last_episode - DATE - The date on which the last episode of diarrhoea is fully resolved, including allowing for the possibility of HSI events (pd.NaT if has never had an episode). This is used to determine when a new episode can begin and stops successive episodes interfering with one another.This is notnull when the person has ever had an episode of diarrhoea. * - gi_treatment_date - DATE - The actual date on which treatment is first administered for the current episode (pd.NaT if does not have current episode or if no treatment has yet been provided in the current episode). **Class attributes:** ADDITIONAL_DEPENDENCIES : {'Stunting', 'Alri', 'Epi'} CAUSES_OF_DEATH : {'Diarrhoea_rotavirus': , 'Diarrhoea_shigella': , 'Diarrhoea_adenovirus': , 'Diarrhoea_cryptosporidium': , 'Diarrhoea_campylobacter': , 'Diarrhoea_ETEC': , 'Diarrhoea_sapovirus': , 'Diarrhoea_norovirus': , 'Diarrhoea_astrovirus': , 'Diarrhoea_tEPEC': } CAUSES_OF_DISABILITY : {'Diarrhoea': } INIT_DEPENDENCIES : {'NewbornOutcomes', 'Wasting', 'HealthSystem', 'Lifestyle', 'Hiv', 'Demography', 'SymptomManager'} METADATA : {, , , } OPTIONAL_INIT_DEPENDENCIES : {'HealthBurden'} pathogens : ['rotavirus', 'shigella', 'adenovirus', 'cryptosporidium', 'campylobacter', 'ETEC', 'sapovirus', 'norovirus', 'astrovirus', 'tEPEC'] **Functions (defined or overridden in class Diarrhoea):** .. automethod:: __init__ .. automethod:: read_parameters .. automethod:: initialise_population .. automethod:: initialise_simulation .. automethod:: on_birth .. automethod:: on_hsi_alert .. automethod:: report_daly_values .. automethod:: look_up_consumables .. automethod:: do_treatment .. automethod:: cancel_death_date .. automethod:: end_episode .. automethod:: check_properties .. automethod:: do_at_generic_first_appt .. autoclass:: DiarrhoeaPollingEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class DiarrhoeaPollingEvent):** .. automethod:: __init__ .. automethod:: compute_fraction_of_year_between_polling_event .. automethod:: apply .. autoclass:: DiarrhoeaIncidentCase Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class DiarrhoeaIncidentCase):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: DiarrhoeaNaturalRecoveryEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class DiarrhoeaNaturalRecoveryEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: DiarrhoeaDeathEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class DiarrhoeaDeathEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: DiarrhoeaCureEvent Bases: :class:`tlo.events.Event`, :class:`tlo.events.IndividualScopeEventMixin` **Functions (defined or overridden in class DiarrhoeaCureEvent):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Diarrhoea_Treatment_Outpatient Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_Diarrhoea_Treatment_Outpatient):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: HSI_Diarrhoea_Treatment_Inpatient Bases: :class:`tlo.methods.hsi_event.HSI_Event`, :class:`tlo.events.IndividualScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class HSI_Diarrhoea_Treatment_Inpatient):** .. automethod:: __init__ .. automethod:: apply .. autoclass:: DiarrhoeaPropertiesOfOtherModules Bases: :class:`tlo.core.Module` **PROPERTIES:** .. list-table:: :widths: 25 25 50 :header-rows: 1 * - Item - Type - Description * - hv_inf - BOOL - temporary property for HIV infection status * - hv_art - CATEGORICAL - temporary property for ART status. Possible values are: [not, on_VL_suppressed, on_not_VL_suppressed, ] * - ri_current_infection_status - BOOL - temporary property * - nb_breastfeeding_status - CATEGORICAL - temporary property. Possible values are: [none, non_exclusive, exclusive, ] * - un_clinical_acute_malnutrition - CATEGORICAL - temporary property. Possible values are: [MAM, SAM, well, ] * - un_HAZ_category - CATEGORICAL - temporary property. Possible values are: [HAZ<-3, -3<=HAZ<-2, HAZ>=-2, ] * - va_rota_all_doses - BOOL - temporary property **Class attributes:** ALTERNATIVE_TO : {'Stunting', 'Wasting', 'Epi', 'Hiv', 'Alri'} INIT_DEPENDENCIES : {'Demography'} **Functions (defined or overridden in class DiarrhoeaPropertiesOfOtherModules):** .. automethod:: __init__ .. automethod:: read_parameters .. automethod:: initialise_population .. automethod:: initialise_simulation .. automethod:: on_birth .. autoclass:: DiarrhoeaCheckPropertiesEvent Bases: :class:`tlo.events.RegularEvent`, :class:`tlo.events.Event`, :class:`tlo.events.PopulationScopeEventMixin` **Class attributes:** __annotations__ : {} **Functions (defined or overridden in class DiarrhoeaCheckPropertiesEvent):** .. automethod:: __init__ .. automethod:: apply