tlo.methods.cardio_metabolic_disorders module

The joint Cardio-Metabolic Disorders model determines onset, outcome and treatment of: * Diabetes * Hypertension * Chronic Kidney Disease * Chronic Ischemic Heart Disease * Stroke * Heart Attack

And: * Chronic Lower Back Pain

class CardioMetabolicDisorders(name=None, resourcefilepath=None, do_log_df: bool = False, do_condition_combos: bool = False)

CardioMetabolicDisorders module covers a subset of cardio-metabolic conditions and events. Conditions are binary and individuals experience a risk of acquiring or losing a condition based on annual probability and demographic/lifestyle risk factors.

Bases: tlo.core.Module

PARAMETERS:

Item	Type	Description
diabetes_onset	DICT	all the parameters that specify the linear models for onset of diabetes
hypertension_onset	DICT	all the parameters that specify the linear models for onset of hypertension
chronic_kidney_disease_onset	DICT	all the parameters that specify the linear models for onset of chronic_kidney_disease
chronic_lower_back_pain_onset	DICT	all the parameters that specify the linear models for onset of chronic_lower_back_pain
chronic_ischemic_hd_onset	DICT	all the parameters that specify the linear models for onset of chronic_ischemic_hd
diabetes_removal	DICT	all the parameters that specify the linear models for removal of diabetes
hypertension_removal	DICT	all the parameters that specify the linear models for removal of hypertension
chronic_kidney_disease_removal	DICT	all the parameters that specify the linear models for removal of chronic_kidney_disease
chronic_lower_back_pain_removal	DICT	all the parameters that specify the linear models for removal of chronic_lower_back_pain
chronic_ischemic_hd_removal	DICT	all the parameters that specify the linear models for removal of chronic_ischemic_hd
diabetes_hsi	DICT	all the parameters that specify diagnostic tests and treatments for diabetes
hypertension_hsi	DICT	all the parameters that specify diagnostic tests and treatments for hypertension
chronic_kidney_disease_hsi	DICT	all the parameters that specify diagnostic tests and treatments for chronic_kidney_disease
chronic_lower_back_pain_hsi	DICT	all the parameters that specify diagnostic tests and treatments for chronic_lower_back_pain
chronic_ischemic_hd_hsi	DICT	all the parameters that specify diagnostic tests and treatments for chronic_ischemic_hd
ever_stroke_onset	DICT	all the parameters that specify the linear models for onset of ever_stroke
ever_heart_attack_onset	DICT	all the parameters that specify the linear models for onset of ever_heart_attack
diabetes_death	DICT	all the parameters that specify the linear models for death from diabetes
hypertension_death	DICT	all the parameters that specify the linear models for death from hypertension
chronic_kidney_disease_death	DICT	all the parameters that specify the linear models for death from chronic_kidney_disease
chronic_lower_back_pain_death	DICT	all the parameters that specify the linear models for death from chronic_lower_back_pain
chronic_ischemic_hd_death	DICT	all the parameters that specify the linear models for death from chronic_ischemic_hd
ever_stroke_death	DICT	all the parameters that specify the linear models for death from ever_stroke
ever_heart_attack_death	DICT	all the parameters that specify the linear models for death from ever_heart_attack
ever_stroke_hsi	DICT	all the parameters that specify diagnostic tests and treatments for ever_stroke
ever_heart_attack_hsi	DICT	all the parameters that specify diagnostic tests and treatments for ever_heart_attack
diabetes_initial_prev	DICT	initial prevalence of condition
hypertension_initial_prev	DICT	initial prevalence of condition
chronic_kidney_disease_initial_prev	DICT	initial prevalence of condition
chronic_lower_back_pain_initial_prev	DICT	initial prevalence of condition
chronic_ischemic_hd_initial_prev	DICT	initial prevalence of condition
interval_between_polls	INT	months between the main polling event
pr_bmi_reduction	INT	probability of an individual having a reduction in BMI following weight loss treatment
prob_care_provided_given_seek_emergency_care	REAL	The probability that correct care is fully provided to persons that have sought emergency care for a Cardio-metabolic disorder.

PROPERTIES:

Item	Type	Description
nc_diabetes	BOOL	Whether or not someone has diabetes
nc_hypertension	BOOL	Whether or not someone has hypertension
nc_chronic_kidney_disease	BOOL	Whether or not someone has chronic_kidney_disease
nc_chronic_lower_back_pain	BOOL	Whether or not someone has chronic_lower_back_pain
nc_chronic_ischemic_hd	BOOL	Whether or not someone has chronic_ischemic_hd
nc_ever_stroke	BOOL	Whether or not someone has had a ever_stroke
nc_ever_heart_attack	BOOL	Whether or not someone has had a ever_heart_attack
nc_diabetes_ever_diagnosed	BOOL	Whether or not someone has ever been diagnosed with diabetes
nc_hypertension_ever_diagnosed	BOOL	Whether or not someone has ever been diagnosed with hypertension
nc_chronic_kidney_disease_ever_diagnosed	BOOL	Whether or not someone has ever been diagnosed with chronic_kidney_disease
nc_chronic_lower_back_pain_ever_diagnosed	BOOL	Whether or not someone has ever been diagnosed with chronic_lower_back_pain
nc_chronic_ischemic_hd_ever_diagnosed	BOOL	Whether or not someone has ever been diagnosed with chronic_ischemic_hd
nc_diabetes_date_diagnosis	DATE	When someone has been diagnosed with diabetes
nc_hypertension_date_diagnosis	DATE	When someone has been diagnosed with hypertension
nc_chronic_kidney_disease_date_diagnosis	DATE	When someone has been diagnosed with chronic_kidney_disease
nc_chronic_lower_back_pain_date_diagnosis	DATE	When someone has been diagnosed with chronic_lower_back_pain
nc_chronic_ischemic_hd_date_diagnosis	DATE	When someone has been diagnosed with chronic_ischemic_hd
nc_diabetes_date_last_test	DATE	When someone has last been tested for diabetes
nc_hypertension_date_last_test	DATE	When someone has last been tested for hypertension
nc_chronic_kidney_disease_date_last_test	DATE	When someone has last been tested for chronic_kidney_disease
nc_chronic_lower_back_pain_date_last_test	DATE	When someone has last been tested for chronic_lower_back_pain
nc_chronic_ischemic_hd_date_last_test	DATE	When someone has last been tested for chronic_ischemic_hd
nc_diabetes_on_medication	BOOL	Whether or not someone is on medication for diabetes
nc_hypertension_on_medication	BOOL	Whether or not someone is on medication for hypertension
nc_chronic_kidney_disease_on_medication	BOOL	Whether or not someone is on medication for chronic_kidney_disease
nc_chronic_lower_back_pain_on_medication	BOOL	Whether or not someone is on medication for chronic_lower_back_pain
nc_chronic_ischemic_hd_on_medication	BOOL	Whether or not someone is on medication for chronic_ischemic_hd
nc_diabetes_medication_prevents_death	BOOL	Whether or not medication (if provided) will prevent death from diabetes
nc_hypertension_medication_prevents_death	BOOL	Whether or not medication (if provided) will prevent death from hypertension
nc_chronic_kidney_disease_medication_prevents_death	BOOL	Whether or not medication (if provided) will prevent death from chronic_kidney_disease
nc_chronic_lower_back_pain_medication_prevents_death	BOOL	Whether or not medication (if provided) will prevent death from chronic_lower_back_pain
nc_chronic_ischemic_hd_medication_prevents_death	BOOL	Whether or not medication (if provided) will prevent death from chronic_ischemic_hd
nc_ever_stroke_date_last_event	DATE	Date of last ever_stroke
nc_ever_heart_attack_date_last_event	DATE	Date of last ever_heart_attack
nc_ever_stroke_ever_diagnosed	BOOL	Whether or not someone has ever been diagnosed with ever_stroke
nc_ever_heart_attack_ever_diagnosed	BOOL	Whether or not someone has ever been diagnosed with ever_heart_attack
nc_ever_stroke_date_diagnosis	DATE	When someone has last been diagnosed with ever_stroke
nc_ever_heart_attack_date_diagnosis	DATE	When someone has last been diagnosed with ever_heart_attack
nc_ever_stroke_on_medication	BOOL	Whether or not someone has ever been diagnosed with ever_stroke
nc_ever_heart_attack_on_medication	BOOL	Whether or not someone has ever been diagnosed with ever_heart_attack
nc_ever_stroke_medication_prevents_death	BOOL	Whether or not medication will prevent death from ever_stroke
nc_ever_heart_attack_medication_prevents_death	BOOL	Whether or not medication will prevent death from ever_heart_attack
nc_ever_stroke_scheduled_date_death	DATE	Scheduled date of death from ever_stroke
nc_ever_heart_attack_scheduled_date_death	DATE	Scheduled date of death from ever_heart_attack
nc_ever_weight_loss_treatment	BOOL	whether or not the person has ever had weight loss treatment
nc_weight_loss_worked	BOOL	whether or not weight loss treatment worked
nc_risk_score	INT	score to represent number of risk conditions the person has

Class attributes:

ADDITIONAL_DEPENDENCIES : {‘Depression’}

CAUSES_OF_DEATH : {‘diabetes’: <tlo.methods.causes.Cause object at 0x1361994d0>, ‘chronic_ischemic_hd’: <tlo.methods.causes.Cause object at 0x136199b50>, ‘ever_heart_attack’: <tlo.methods.causes.Cause object at 0x13619a950>, ‘ever_stroke’: <tlo.methods.causes.Cause object at 0x136198c10>, ‘chronic_kidney_disease’: <tlo.methods.causes.Cause object at 0x13619a390>}

CAUSES_OF_DISABILITY : {‘diabetes’: <tlo.methods.causes.Cause object at 0x13619b3d0>, ‘chronic_ischemic_hd’: <tlo.methods.causes.Cause object at 0x13619b610>, ‘heart_attack’: <tlo.methods.causes.Cause object at 0x13619ac10>, ‘stroke’: <tlo.methods.causes.Cause object at 0x13619bb50>, ‘chronic_kidney_disease’: <tlo.methods.causes.Cause object at 0x13619b6d0>, ‘lower_back_pain’: <tlo.methods.causes.Cause object at 0x13619a150>}

INIT_DEPENDENCIES : {‘SymptomManager’, ‘Demography’, ‘Lifestyle’, ‘HealthSystem’}

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

OPTIONAL_INIT_DEPENDENCIES : {‘HealthBurden’}

condition_date_diagnosis_list : {‘nc_diabetes_date_diagnosis’: DATE === When someone has been diagnosed with diabetes, ‘nc_hypertension_date_diagnosis’: DATE === When someone has been diagnosed with hypertension, ‘nc_chronic_kidney_disease_date_diagnosis’: DATE === When someone has been diagnosed with chronic_kidney_disease, ‘nc_chronic_lower_back_pain_date_diagnosis’: DATE === When someone has been diagnosed with chronic_lower_back_pain, ‘nc_chronic_ischemic_hd_date_diagnosis’: DATE === When someone has been diagnosed with chronic_ischemic_hd}

condition_date_of_last_test_list : {‘nc_diabetes_date_last_test’: DATE === When someone has last been tested for diabetes, ‘nc_hypertension_date_last_test’: DATE === When someone has last been tested for hypertension, ‘nc_chronic_kidney_disease_date_last_test’: DATE === When someone has last been tested for chronic_kidney_disease, ‘nc_chronic_lower_back_pain_date_last_test’: DATE === When someone has last been tested for chronic_lower_back_pain, ‘nc_chronic_ischemic_hd_date_last_test’: DATE === When someone has last been tested for chronic_ischemic_hd}

condition_diagnosis_list : {‘nc_diabetes_ever_diagnosed’: BOOL === Whether or not someone has ever been diagnosed with diabetes, ‘nc_hypertension_ever_diagnosed’: BOOL === Whether or not someone has ever been diagnosed with hypertension, ‘nc_chronic_kidney_disease_ever_diagnosed’: BOOL === Whether or not someone has ever been diagnosed with chronic_kidney_disease, ‘nc_chronic_lower_back_pain_ever_diagnosed’: BOOL === Whether or not someone has ever been diagnosed with chronic_lower_back_pain, ‘nc_chronic_ischemic_hd_ever_diagnosed’: BOOL === Whether or not someone has ever been diagnosed with chronic_ischemic_hd}

condition_list : {‘nc_diabetes’: BOOL === Whether or not someone has diabetes, ‘nc_hypertension’: BOOL === Whether or not someone has hypertension, ‘nc_chronic_kidney_disease’: BOOL === Whether or not someone has chronic_kidney_disease, ‘nc_chronic_lower_back_pain’: BOOL === Whether or not someone has chronic_lower_back_pain, ‘nc_chronic_ischemic_hd’: BOOL === Whether or not someone has chronic_ischemic_hd}

condition_medication_death_list : {‘nc_diabetes_medication_prevents_death’: BOOL === Whether or not medication (if provided) will prevent death from diabetes, ‘nc_hypertension_medication_prevents_death’: BOOL === Whether or not medication (if provided) will prevent death from hypertension, ‘nc_chronic_kidney_disease_medication_prevents_death’: BOOL === Whether or not medication (if provided) will prevent death from chronic_kidney_disease, ‘nc_chronic_lower_back_pain_medication_prevents_death’: BOOL === Whether or not medication (if provided) will prevent death from chronic_lower_back_pain, ‘nc_chronic_ischemic_hd_medication_prevents_death’: BOOL === Whether or not medication (if provided) will prevent death from chronic_ischemic_hd}

condition_medication_list : {‘nc_diabetes_on_medication’: BOOL === Whether or not someone is on medication for diabetes, ‘nc_hypertension_on_medication’: BOOL === Whether or not someone is on medication for hypertension, ‘nc_chronic_kidney_disease_on_medication’: BOOL === Whether or not someone is on medication for chronic_kidney_disease, ‘nc_chronic_lower_back_pain_on_medication’: BOOL === Whether or not someone is on medication for chronic_lower_back_pain, ‘nc_chronic_ischemic_hd_on_medication’: BOOL === Whether or not someone is on medication for chronic_ischemic_hd}

conditions : [‘diabetes’, ‘hypertension’, ‘chronic_kidney_disease’, ‘chronic_lower_back_pain’, ‘chronic_ischemic_hd’]

death_conditions_param_dicts : {‘diabetes_death’: DICT === all the parameters that specify the linear models for death from diabetes, ‘hypertension_death’: DICT === all the parameters that specify the linear models for death from hypertension, ‘chronic_kidney_disease_death’: DICT === all the parameters that specify the linear models for death from chronic_kidney_disease, ‘chronic_lower_back_pain_death’: DICT === all the parameters that specify the linear models for death from chronic_lower_back_pain, ‘chronic_ischemic_hd_death’: DICT === all the parameters that specify the linear models for death from chronic_ischemic_hd}

death_events_param_dicts : {‘ever_stroke_death’: DICT === all the parameters that specify the linear models for death from ever_stroke, ‘ever_heart_attack_death’: DICT === all the parameters that specify the linear models for death from ever_heart_attack}

event_date_diagnosis_list : {‘nc_ever_stroke_date_diagnosis’: DATE === When someone has last been diagnosed with ever_stroke, ‘nc_ever_heart_attack_date_diagnosis’: DATE === When someone has last been diagnosed with ever_heart_attack}

event_date_last_list : {‘nc_ever_stroke_date_last_event’: DATE === Date of last ever_stroke, ‘nc_ever_heart_attack_date_last_event’: DATE === Date of last ever_heart_attack}

event_diagnosis_list : {‘nc_ever_stroke_ever_diagnosed’: BOOL === Whether or not someone has ever been diagnosed with ever_stroke, ‘nc_ever_heart_attack_ever_diagnosed’: BOOL === Whether or not someone has ever been diagnosed with ever_heart_attack}

event_list : {‘nc_ever_stroke’: BOOL === Whether or not someone has had a ever_stroke, ‘nc_ever_heart_attack’: BOOL === Whether or not someone has had a ever_heart_attack}

event_medication_death_list : {‘nc_ever_stroke_medication_prevents_death’: BOOL === Whether or not medication will prevent death from ever_stroke, ‘nc_ever_heart_attack_medication_prevents_death’: BOOL === Whether or not medication will prevent death from ever_heart_attack}

event_medication_list : {‘nc_ever_stroke_on_medication’: BOOL === Whether or not someone has ever been diagnosed with ever_stroke, ‘nc_ever_heart_attack_on_medication’: BOOL === Whether or not someone has ever been diagnosed with ever_heart_attack}

event_scheduled_date_death_list : {‘nc_ever_stroke_scheduled_date_death’: DATE === Scheduled date of death from ever_stroke, ‘nc_ever_heart_attack_scheduled_date_death’: DATE === Scheduled date of death from ever_heart_attack}

events : [‘ever_stroke’, ‘ever_heart_attack’]

hsi_conditions_param_dicts : {‘diabetes_hsi’: DICT === all the parameters that specify diagnostic tests and treatments for diabetes, ‘hypertension_hsi’: DICT === all the parameters that specify diagnostic tests and treatments for hypertension, ‘chronic_kidney_disease_hsi’: DICT === all the parameters that specify diagnostic tests and treatments for chronic_kidney_disease, ‘chronic_lower_back_pain_hsi’: DICT === all the parameters that specify diagnostic tests and treatments for chronic_lower_back_pain, ‘chronic_ischemic_hd_hsi’: DICT === all the parameters that specify diagnostic tests and treatments for chronic_ischemic_hd}

hsi_events_param_dicts : {‘ever_stroke_hsi’: DICT === all the parameters that specify diagnostic tests and treatments for ever_stroke, ‘ever_heart_attack_hsi’: DICT === all the parameters that specify diagnostic tests and treatments for ever_heart_attack}

initial_prev_param_dicts : {‘diabetes_initial_prev’: DICT === initial prevalence of condition, ‘hypertension_initial_prev’: DICT === initial prevalence of condition, ‘chronic_kidney_disease_initial_prev’: DICT === initial prevalence of condition, ‘chronic_lower_back_pain_initial_prev’: DICT === initial prevalence of condition, ‘chronic_ischemic_hd_initial_prev’: DICT === initial prevalence of condition}

onset_conditions_param_dicts : {‘diabetes_onset’: DICT === all the parameters that specify the linear models for onset of diabetes, ‘hypertension_onset’: DICT === all the parameters that specify the linear models for onset of hypertension, ‘chronic_kidney_disease_onset’: DICT === all the parameters that specify the linear models for onset of chronic_kidney_disease, ‘chronic_lower_back_pain_onset’: DICT === all the parameters that specify the linear models for onset of chronic_lower_back_pain, ‘chronic_ischemic_hd_onset’: DICT === all the parameters that specify the linear models for onset of chronic_ischemic_hd}

onset_events_param_dicts : {‘ever_stroke_onset’: DICT === all the parameters that specify the linear models for onset of ever_stroke, ‘ever_heart_attack_onset’: DICT === all the parameters that specify the linear models for onset of ever_heart_attack}

other_params_dict : {‘interval_between_polls’: INT === months between the main polling event, ‘pr_bmi_reduction’: INT === probability of an individual having a reduction in BMI following weight loss treatment}

removal_conditions_param_dicts : {‘diabetes_removal’: DICT === all the parameters that specify the linear models for removal of diabetes, ‘hypertension_removal’: DICT === all the parameters that specify the linear models for removal of hypertension, ‘chronic_kidney_disease_removal’: DICT === all the parameters that specify the linear models for removal of chronic_kidney_disease, ‘chronic_lower_back_pain_removal’: DICT === all the parameters that specify the linear models for removal of chronic_lower_back_pain, ‘chronic_ischemic_hd_removal’: DICT === all the parameters that specify the linear models for removal of chronic_ischemic_hd}

Functions (defined or overridden in class CardioMetabolicDisorders):

__init__(name=None, resourcefilepath=None, do_log_df: bool = False, do_condition_combos: bool = 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)

Read parameter values from files for condition onset, removal, deaths, and initial prevalence.

ResourceFile_cmd_condition_onset.xlsx = parameters for onset of conditions ResourceFile_cmd_condition_removal.xlsx = parameters for removal of conditions ResourceFile_cmd_condition_death.xlsx = parameters for death rate from conditions ResourceFile_cmd_condition_prevalence.xlsx = initial and target prevalence for conditions ResourceFile_cmd_condition_symptoms.xlsx = symptoms for conditions ResourceFile_cmd_condition_hsi.xlsx = HSI parameters for conditions ResourceFile_cmd_condition_testing.xlsx = community testing parameters for conditions (currently only hypertension) ResourceFile_cmd_events.xlsx = parameters for occurrence of events ResourceFile_cmd_events_death.xlsx = parameters for death rate from events ResourceFile_cmd_events_symptoms.xlsx = symptoms for events ResourceFile_cmd_events_hsi.xlsx = HSI parameters for events

initialise_population(population)

Set property values for the initial population.

initialise_simulation(sim)

Schedule: * Main Polling Event * Main Logging Event * Build the LinearModels for the onset/removal of each condition:

build_linear_model(condition, interval_between_polls, lm_type)

Build a linear model for the risk of onset, removal, or death from a condition, occurrence or death from an event, and community-based testing for hypertension. :param condition: the condition or event to build the linear model for :param interval_between_polls: the duration (in months) between the polls :param lm_type: whether or not the lm is for onset, removal, death, or event in order to select the correct parameter set below :return: a linear model

build_linear_model_symptoms(condition, interval_between_polls)

Build a linear model for the risk of symptoms from a condition. :param condition: the condition to build the linear model for :param interval_between_polls: the duration (in months) between the polls :return: a linear model

on_birth(mother_id, child_id)

Initialise our properties for a newborn individual. :param mother_id: the mother for this child :param child_id: the new child

update_risk_score()

Generates or updates the risk score for individuals at initialisation of population or at each polling event

report_daly_values()

Report disability weight (average values for the last month) to the HealthBurden module

on_hsi_alert(person_id, treatment_id)

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

do_at_generic_first_appt(patient_id: int, patient_details: PatientDetails, symptoms: List[str], **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.

do_at_generic_first_appt_emergency(patient_id: int, patient_details: PatientDetails = None, symptoms: List[str] = None, **kwargs) → IndividualPropertyUpdates

Actions to be take during an EMERGENCY generic HSI. Call signature and return values are identical to the do_at_generic_first_appt() method. 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.

class CardioMetabolicDisorders_MainPollingEvent(module, interval_between_polls)

The Main Polling Event. * Establishes onset of each condition * Establishes removal of each condition * Schedules events that arise, according the condition.

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class CardioMetabolicDisorders_MainPollingEvent):

__init__(module, interval_between_polls)

The Main Polling Event of the CardioMetabolicDisorders Module

Parameters:

module – the module that created this event

apply(population)

Apply this event to the population.

Parameters:

population – the current population

class CardioMetabolicDisordersEvent(module, person_id, event)

This is an Cardio Metabolic Disorders event (indicating an emergency occurrence of stroke or heart attack). It has been scheduled to occur by the CardioMetabolicDisorders_MainPollingEvent. :param event: the event occurring

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

Functions (defined or overridden in class CardioMetabolicDisordersEvent):

__init__(module, person_id, event)

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 CardioMetabolicDisordersDeathEvent(module, person_id, originating_cause)

Performs the Death operation on an individual and logs it. :param originating_cause: the originating cause of the death, which can be a condition or an event

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

Functions (defined or overridden in class CardioMetabolicDisordersDeathEvent):

__init__(module, person_id, originating_cause)

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

check_if_event_and_do_death(person_id)

Helper function to perform do_death if person dies of a condition or event. If person dies of an event, this will only perform do_death if the scheduled date of death matches the current date (to allow for the possibility that treatment will intercede in an prevent death from the event).

class CardioMetabolicDisordersWeightLossEvent(module, person_id)

Gives an individual a probability of losing weight (via a reduction in li_bmi) and records the change in population.props

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

Functions (defined or overridden in class CardioMetabolicDisordersWeightLossEvent):

__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 CardioMetabolicDisorders_LoggingEvent(module)

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class CardioMetabolicDisorders_LoggingEvent):

__init__(module)

Produce a summary of the numbers of people with respect to the action of this module.

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 HSI_CardioMetabolicDisorders_CommunityTestingForHypertension(module, person_id)

This event is scheduled by HSI_GenericFirstApptAtFacilityLevel1 following presentation for care with any symptoms. This event results in a blood pressure measurement being taken that may result in diagnosis and the scheduling of treatment for a condition.

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_CardioMetabolicDisorders_CommunityTestingForHypertension):

__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)

Apply this event to the population.

Must be implemented by subclasses.

class HSI_CardioMetabolicDisorders_Investigations(module, person_id, conditions_to_investigate: List, has_any_cmd_symptom: bool = False)

This event is scheduled following presentation for care and a determination having been made about which conditions should be investigated for this person (either due to presentation with symptoms or a routine check). NB. If a treatment is needed, this does lead to multiple HSI to be scheduled for the person (relevant to each condition). :param conditions_to_investigate: list of the condition to investigate. :param has_any_cmd_symptom: bool to indicate whether the person has any symptoms that prompted the investigation

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_CardioMetabolicDisorders_Investigations):

__init__(module, person_id, conditions_to_investigate: List, has_any_cmd_symptom: bool = False)

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.

do_for_each_condition(_c) → bool

What to do for each condition that will be investigated. Returns bool signalling whether a follow-up HSI has been scheduled.

apply(person_id, squeeze_factor)

Apply this event to the population.

Must be implemented by subclasses.

class HSI_CardioMetabolicDisorders_StartWeightLossAndMedication(module, person_id, condition)

This is a Health System Interaction Event in which a person receives a recommendation of weight loss. This results in an individual having a probability of reducing their BMI by one category in the next 6-12 months. :param condition: the condition to start medication for

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_CardioMetabolicDisorders_StartWeightLossAndMedication):

__init__(module, person_id, condition)

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)

Apply this event to the population.

Must be implemented by subclasses.

class HSI_CardioMetabolicDisorders_Refill_Medication(module, person_id, condition)

This is a Health System Interaction Event in which a person seeks a refill prescription of medication. The next refill of medication is also scheduled. If the person is flagged as not being on medication, then the event does nothing and returns a blank footprint. If it does not run, then person ceases to be on medication and no further refill HSI are scheduled. :param condition: the condition to refill medication for

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_CardioMetabolicDisorders_Refill_Medication):

__init__(module, person_id, condition)

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)

Apply this event to the population.

Must be implemented by subclasses.

did_not_run()

Called when this event is due but it is not run. Return False to prevent the event being rescheduled, or True to allow the rescheduling. This is called each time that the event is tried to be run but it cannot be.

class HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment(module, person_id, events_to_investigate: List)

This is a Health System Interaction Event. It is the event when a person is investigated for certain condition following and emergency presentation. Treatment may be scheduled from this event, and this may take the form of multiple streams of HSI event if more than one condition is to be treated. :param events_to_investigate: list of the events for which emergency care is sought

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_CardioMetabolicDisorders_SeeksEmergencyCareAndGetsTreatment):

__init__(module, person_id, events_to_investigate: List)

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.

do_for_each_event_to_be_investigated(_ev)

Do what is required to be done for each event that is being investigated.

apply(person_id, squeeze_factor)

Apply this event to the population.

Must be implemented by subclasses.

did_not_run()

Called when this event is due but it is not run. Return False to prevent the event being rescheduled, or True to allow the rescheduling. This is called each time that the event is tried to be run but it cannot be.