tlo.methods.measles module

class Measles(name=None, resourcefilepath=None)

This module represents measles infections and disease.

Bases: tlo.core.Module

PARAMETERS:

Item	Type	Description
beta_baseline	REAL	Baseline measles transmission probability
beta_scale	REAL	Scale value for measles transmission probability sinusoidal function
phase_shift	REAL	Phase shift for measles transmission probability sinusoidal function
period	REAL	Period for measles transmission probability sinusoidal function
vaccine_efficacy_1	REAL	Efficacy of first measles vaccine dose against measles infection
vaccine_efficacy_2	REAL	Efficacy of second measles vaccine dose against measles infection
prob_severe	REAL	Probability of severe measles infection, requiring hospitalisation
risk_death_on_treatment	REAL	Risk of scheduled death occurring if on treatment for measles complications
symptom_prob	DATA_FRAME	Probability of each symptom with measles infection

PROPERTIES:

Item	Type	Description
me_has_measles	BOOL	Measles infection status
me_date_measles	DATE	Date of onset of measles
me_on_treatment	BOOL	Currently on treatment for measles complications

Class attributes:

CAUSES_OF_DEATH : {‘Measles’: <tlo.methods.causes.Cause object at 0x7feb91d2db20>}

CAUSES_OF_DISABILITY : {‘Measles’: <tlo.methods.causes.Cause object at 0x7feb91d2db80>}

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

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

OPTIONAL_INIT_DEPENDENCIES : {‘HealthBurden’}

SYMPTOMS : {‘otitis_media’, ‘encephalitis’, ‘rash’}

Functions (defined or overridden in class Measles):

__init__(name=None, resourcefilepath=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

initialise_population(population)

Set our property values for the initial population. set whole population to measles-free for 1st jan

initialise_simulation(sim)

Schedule measles event to start straight away. Each month it will assign new infections

on_birth(mother_id, child_id)

Initialise our properties for a newborn individual assume all newborns are uninfected

Parameters

• mother_id – the ID for the mother for this child

• child_id – the ID for the new child

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()

class MeaslesEvent(module)

MeaslesEvent runs every year and creates a number of new infections which are scattered across the year seasonality is captured using a cosine function vaccination lowers an individual’s likelihood of getting the disease assume one dose will be 85% protective and 2 doses will be 99% protective

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

Functions (defined or overridden in class MeaslesEvent):

__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 population.

Must be implemented by subclasses.

Parameters

population – the current population

class MeaslesOnsetEvent(module, person_id)

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

Functions (defined or overridden in class MeaslesOnsetEvent):

__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 person.

Must be implemented by subclasses.

Parameters

person_id – the person the event happens to

class MeaslesSymptomResolveEvent(module, person_id)

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

Functions (defined or overridden in class MeaslesSymptomResolveEvent):

__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)

this event is called by MeaslesOnsetEvent and HSI_Measles_Treatment

class MeaslesDeathEvent(module, person_id)

Performs the Death operation on an individual and logs it.

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

Functions (defined or overridden in class MeaslesDeathEvent):

__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 person.

Must be implemented by subclasses.

Parameters

person_id – the person the event happens to

class HSI_Measles_Treatment(module, person_id)

Health System Interaction Event It is the event when a person with diagnosed measles receives treatment

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

Functions (defined or overridden in class HSI_Measles_Treatment):

__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.

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 MeaslesLoggingEvent(module)

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

Functions (defined or overridden in class MeaslesLoggingEvent):

__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 population.

Must be implemented by subclasses.

Parameters

population – the current population

class MeaslesLoggingFortnightEvent(module)

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

Functions (defined or overridden in class MeaslesLoggingFortnightEvent):

__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 population.

Must be implemented by subclasses.

Parameters

population – the current population

class MeaslesLoggingAnnualEvent(module)

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

Functions (defined or overridden in class MeaslesLoggingAnnualEvent):

__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 population.

Must be implemented by subclasses.

Parameters

population – the current population