tlo.methods.diarrhoea module

Childhood Diarrhoea Module

Overview

Individuals are exposed to the risk of onset of diarrhoea. They can have diarrhoea caused by one pathogen at a time.

During an episode (prior to recovery- either natural or cured), the symptom of diarrhoea is present in addition to other possible symptoms. Diarrhoea may cause dehydration and this may progress to become ‘severe’ during an episode. The individual may recovery naturally or die.

Health care seeking is prompted by the onset of the symptom diarrhoea. The individual can be treated; if successful the

risk of death is removed and they are cured (symptom resolved) some days later.

Outstanding Issues * To include rotavirus vaccine * See todo

class Diarrhoea(name=None, resourcefilepath=None, do_checks=False)

Bases: tlo.core.Module

PARAMETERS:

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:

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’: <tlo.methods.causes.Cause object at 0x13610b310>, ‘Diarrhoea_shigella’: <tlo.methods.causes.Cause object at 0x136109590>, ‘Diarrhoea_adenovirus’: <tlo.methods.causes.Cause object at 0x136109710>, ‘Diarrhoea_cryptosporidium’: <tlo.methods.causes.Cause object at 0x136108a50>, ‘Diarrhoea_campylobacter’: <tlo.methods.causes.Cause object at 0x136108d90>, ‘Diarrhoea_ETEC’: <tlo.methods.causes.Cause object at 0x136109810>, ‘Diarrhoea_sapovirus’: <tlo.methods.causes.Cause object at 0x136108a10>, ‘Diarrhoea_norovirus’: <tlo.methods.causes.Cause object at 0x1361097d0>, ‘Diarrhoea_astrovirus’: <tlo.methods.causes.Cause object at 0x1361086d0>, ‘Diarrhoea_tEPEC’: <tlo.methods.causes.Cause object at 0x136109a90>}

CAUSES_OF_DISABILITY : {‘Diarrhoea’: <tlo.methods.causes.Cause object at 0x136109d50>}

INIT_DEPENDENCIES : {‘NewbornOutcomes’, ‘Wasting’, ‘HealthSystem’, ‘Lifestyle’, ‘Hiv’, ‘Demography’, ‘SymptomManager’}

METADATA : {<Metadata.USES_SYMPTOMMANAGER: 2>, <Metadata.USES_HEALTHBURDEN: 4>, <Metadata.USES_HEALTHSYSTEM: 3>, <Metadata.DISEASE_MODULE: 1>}

OPTIONAL_INIT_DEPENDENCIES : {‘HealthBurden’}

pathogens : [‘rotavirus’, ‘shigella’, ‘adenovirus’, ‘cryptosporidium’, ‘campylobacter’, ‘ETEC’, ‘sapovirus’, ‘norovirus’, ‘astrovirus’, ‘tEPEC’]

Functions (defined or overridden in class Diarrhoea):

__init__(name=None, resourcefilepath=None, do_checks=False)

Construct a new disease module ready to be included in a simulation.

Initialises an empty parameters dictionary and module-specific random number generator.

Parameters:

name – the name to use for this module. Defaults to the concrete subclass’ name.

read_parameters(data_folder)

Setup parameters values used by the module

initialise_population(population)

Sets that there is no one with diarrhoea at initiation.

initialise_simulation(sim)

Prepares for simulation: * Schedules the main polling event * Schedules the main logging event * Schedule the check properties event (if needed) * Establishes the linear models and other data structures using the parameters that have been read-in * Store the consumables that are required in each of the HSI * Register test for the determination of ‘danger signs’

on_birth(mother_id, child_id)

On birth, all children will have no diarrhoea

on_hsi_alert(person_id, treatment_id)

This is called whenever there is an HSI event commissioned by one of the other disease modules.

report_daly_values()

This returns person-time live with disability values to the HealthBurden module. At the end of each episode, a record is made in a list, self.unreported_dalys, of the form (person_id, duration_in_days_of_episode * average_daly_weight). This record is used to create the pd.Series that is returned (index: person_id for all those alive, value: the average disability weight during the preceding month). The list is then cleared.

look_up_consumables()

Look up and store the consumables item codes used in each of the HSI.

do_treatment(person_id, hsi_event)

Method called by the HSI that enacts decisions about a treatment and its effect for diarrhoea caused by a pathogen. (It will do nothing if the diarrhoea is caused by another module.) Actions: * If the episode will cause death: if the treatment is successful, prevents this episode of diarrhoea from

causing a death and schedules Cure Event

• If the episode will not cause death: if treatment is succesful, schedules a CureEvent that will occur earlier

than the NaturalRecovery event.

• Records that treatment is provided.

NB. Provisions for cholera are not included See this report:

https://apps.who.int/iris/bitstream/handle/10665/104772/9789241506823_Chartbook_eng.pdf (page 3).

cancel_death_date(person_id)

Cancels a scheduled date of death due to diarrhoea for a person. This is called prior to the scheduling the CureEvent to prevent deaths happening in the time between a treatment being given and the cure event occurring.

end_episode(person_id, outcome)

Helper function that enacts the end of the episode of diarrhoea (either by natural recovery, death or cure) * Logs that the episode has ended * Stores the total time-lived-with-disability during the episode * Enacts the death (if the outcome==’death’); Otherwise, removes symptoms and resets properties

check_properties()

Check that the properties are ok: for use in testing only

do_at_generic_first_appt(patient_id: int, patient_details: PatientDetails, diagnosis_function: DiagnosisFunction, **kwargs) → IndividualPropertyUpdates

Actions to be take during a NON-emergency generic HSI.

Derived classes should overwrite this method so that they are compatible with the HealthSystem module, and can schedule HSI events when a patient presents symptoms indicative of the corresponding illness or condition.

When overwriting, arguments that are not required can be left out of the definition. If done so, the method MUST take a **kwargs input to avoid errors when looping over all disease modules and running their generic HSI methods.

HSI_Events should be scheduled by the Module implementing this method using the Module.healthsystem.schedule_hsi() method. However, they should not write updates back to the population DataFrame in this method - these values should be returned as a dictionary as described below:

The return value of this function should be a dictionary containing any changes that need to be made to the individual’s row in the population DataFrame. Key/value pairs should be the column name and the new value to assign to the patient. In the event no updates are required; return an object that evaluates to False when cast to a bool. Your options are: - Omit a return statement and value (preferred). - Return an empty dictionary. Use this case when patient details might need updating conditionally, on EG patient symptoms or consumable availability. In which case, an empty dictionary should be created and key-value pairs added to this dictionary as such conditionals are checked. If no conditionals are met, the empty dictionary will be returned. - Use a return statement with no values (use if the logic of your module-specific method necessitates the explicit return). - Return None (not recommended, use “return” on its own, as above).

Parameters:

• patient_id – Row index (ID) of the individual target of the HSI event in the population DataFrame.

• patient_details – Patient details as provided in the population DataFrame.

• symptoms – List of symptoms the patient is experiencing.

• diagnosis_function – A function that can run diagnosis tests based on the patient’s symptoms.

• consumables_checker – A function that can query the HealthSystem to check for available consumables.

• facility_level – The level of the facility that the patient presented at.

• treatment_id – The treatment id of the HSI event triggering the generic appointment.

• random_state – Random number generator to be used when making random choices during event creation.

class DiarrhoeaPollingEvent(module)

This is the main event that runs the acquisition of pathogens that cause Diarrhoea. It determines who is infected and schedules individual IncidentCase events to represent onset.

A known issue is that diarrhoea events are scheduled based on the risk of current age but occur a short time

later when the children will be slightly older. This means that when comparing the model output with data, the model slightly under-represents incidence among younger age-groups and over-represents incidence among older age-groups. This is a small effect when the frequency of the polling event is high.

Bases: tlo.events.RegularEvent, tlo.events.Event, tlo.events.PopulationScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class DiarrhoeaPollingEvent):

__init__(module)

Create a new regular event.

Parameters:

• module – the module that created this event

• frequency (pandas.tseries.offsets.DateOffset) – the interval from one occurrence to the next (must be supplied as a keyword argument)

compute_fraction_of_year_between_polling_event()

Compute fraction of a year that elapses between polling event. This is used to adjust the risk of infection

apply(population)

Apply this event to the given target.

This is a no-op; subclasses should override this method.

Parameters:

target – the target of the event

class DiarrhoeaIncidentCase(module, person_id, pathogen)

This Event is for the onset of the infection that causes diarrhoea.

• Refreshes all the properties so that they pertain to this current episode of diarrhoea

• Imposes the symptoms

• Schedules relevant natural history event {(DiarrhoeaSevereDehydrationEvent) and (either DiarrhoeaNaturalRecoveryEvent or DiarrhoeaDeathEvent)}

• Updates a counter for incident cases

Bases: tlo.events.Event, tlo.events.IndividualScopeEventMixin

Functions (defined or overridden in class DiarrhoeaIncidentCase):

__init__(module, person_id, pathogen)

Create a new event.

Note that just creating an event does not schedule it to happen; that must be done by calling Simulation.schedule_event.

Parameters:

• module – the module that created this event. All subclasses of Event take this as the first argument in their constructor, but may also take further keyword arguments.

• priority – a keyword-argument to set the priority (see Priority enum)

apply(person_id)

Apply this event to the given target.

Must be implemented by subclasses.

Parameters:

target – the target of the event

class DiarrhoeaNaturalRecoveryEvent(module, person_id)

This is the Natural Recovery event. It is part of the natural history and represents the end of an episode of Diarrhoea. It does the following:

• resolves all symptoms caused by diarrhoea

Bases: tlo.events.Event, tlo.events.IndividualScopeEventMixin

Functions (defined or overridden in class DiarrhoeaNaturalRecoveryEvent):

__init__(module, person_id)

Create a new event.

Note that just creating an event does not schedule it to happen; that must be done by calling Simulation.schedule_event.

Parameters:

• module – the module that created this event. All subclasses of Event take this as the first argument in their constructor, but may also take further keyword arguments.

• priority – a keyword-argument to set the priority (see Priority enum)

apply(person_id)

Apply this event to the given target.

Must be implemented by subclasses.

Parameters:

target – the target of the event

class DiarrhoeaDeathEvent(module, person_id)

This Event is for the death of someone that is caused by the infection with a pathogen that causes diarrhoea. The person dies if the ‘diarrhoea_death_date’ that was set at onset of the episode is equal to the current date. (It will have been reset to pd.NaT if there has been a treatment in the intervening time).

Bases: tlo.events.Event, tlo.events.IndividualScopeEventMixin

Functions (defined or overridden in class DiarrhoeaDeathEvent):

__init__(module, person_id)

Create a new event.

Note that just creating an event does not schedule it to happen; that must be done by calling Simulation.schedule_event.

Parameters:

• module – the module that created this event. All subclasses of Event take this as the first argument in their constructor, but may also take further keyword arguments.

• priority – a keyword-argument to set the priority (see Priority enum)

apply(person_id)

Apply this event to the given target.

Must be implemented by subclasses.

Parameters:

target – the target of the event

class DiarrhoeaCureEvent(module, person_id)

This is the cure event. It is scheduled by an HSI treatment event. It enacts the actual “cure” of the person that is caused (after some delay) by the treatment administered. It does the following:

• Sets the date of recovery to today’s date

• Resolves all symptoms caused by diarrhoea

NB. This is the event that would be called if another module has caused the symptom of diarrhoea and care is sought.

Bases: tlo.events.Event, tlo.events.IndividualScopeEventMixin

Functions (defined or overridden in class DiarrhoeaCureEvent):

__init__(module, person_id)

Create a new event.

Note that just creating an event does not schedule it to happen; that must be done by calling Simulation.schedule_event.

Parameters:

• module – the module that created this event. All subclasses of Event take this as the first argument in their constructor, but may also take further keyword arguments.

• priority – a keyword-argument to set the priority (see Priority enum)

apply(person_id)

Apply this event to the given target.

Must be implemented by subclasses.

Parameters:

target – the target of the event

class HSI_Diarrhoea_Treatment_Outpatient(module, person_id)

This is a treatment for diarrhoea administered at outpatient. NB. This can be called when a child presents with Diarrhoea that is caused by another module/Symptom Manager.

Bases: tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_Diarrhoea_Treatment_Outpatient):

__init__(module, person_id)

Create a new event.

Note that just creating an event does not schedule it to happen; that must be done by calling Simulation.schedule_event.

Parameters:

module – the module that created this event. All subclasses of Event take this as the first argument in their constructor, but may also take further keyword arguments.

apply(person_id, squeeze_factor)

Run do_treatment for this person from an out-potient setting.

class HSI_Diarrhoea_Treatment_Inpatient(module, person_id)

This is a treatment for acute diarrhoea with severe dehydration administered at inpatient when danger_signs have been diagnosed.

Bases: tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_Diarrhoea_Treatment_Inpatient):

__init__(module, person_id)

Create a new event.

Note that just creating an event does not schedule it to happen; that must be done by calling Simulation.schedule_event.

Parameters:

module – the module that created this event. All subclasses of Event take this as the first argument in their constructor, but may also take further keyword arguments.

apply(person_id, squeeze_factor)

Run do_treatment for this person from an in-potient setting.

class DiarrhoeaPropertiesOfOtherModules(name=None)

For the purpose of the testing, this module generates the properties upon which the Alri module relies

Bases: tlo.core.Module

PROPERTIES:

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):

__init__(name=None)

Construct a new disease module ready to be included in a simulation.

Initialises an empty parameters dictionary and module-specific random number generator.

Parameters:

name – the name to use for this module. Defaults to the concrete subclass’ name.

read_parameters(data_folder)

Read parameter values from file, if required.

Must be implemented by subclasses.

Parameters:

data_folder – path of a folder supplied to the Simulation containing data files. Typically, modules would read a particular file within here.

initialise_population(population)

Set our property values for the initial population.

Must be implemented by subclasses.

This method is called by the simulation when creating the initial population, and is responsible for assigning initial values, for every individual, of those properties ‘owned’ by this module, i.e. those declared in its PROPERTIES dictionary.

TODO: We probably need to declare somehow which properties we ‘read’ here, so the simulation knows what order to initialise modules in!

Parameters:

population – the population of individuals

initialise_simulation(sim)

Get ready for simulation start.

Must be implemented by subclasses.

This method is called just before the main simulation loop begins, and after all modules have read their parameters and the initial population has been created. It is a good place to add initial events to the event queue.

on_birth(mother, child)

Initialise our properties for a newborn individual.

Must be implemented by subclasses.

This is called by the simulation whenever a new person is born.

Parameters:

• mother_id – the person id for the mother of this child (can be -1 if the mother is not identified).

• child_id – the person id of new child

class DiarrhoeaCheckPropertiesEvent(module)

This event runs daily and checks properties are in the right configuration. Only use whilst debugging!

Bases: tlo.events.RegularEvent, tlo.events.Event, tlo.events.PopulationScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class DiarrhoeaCheckPropertiesEvent):

__init__(module)

Create a new regular event.

Parameters:

• module – the module that created this event

• frequency (pandas.tseries.offsets.DateOffset) – the interval from one occurrence to the next (must be supplied as a keyword argument)

apply(population)

Apply this event to the given target.

This is a no-op; subclasses should override this method.

Parameters:

target – the target of the event