tlo.methods.measles module
- class Measles(name=None, resourcefilepath=None)[source]
This module represents measles infections and disease.
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.
Bases:
tlo.core.Module
,tlo.methods.hsi_generic_first_appts.GenericFirstAppointmentsMixin
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
case_fatality_rate
DICT
Probability that case of measles will result in death if not treated
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 0x128e8cc50>}
CAUSES_OF_DISABILITY : {‘Measles’: <tlo.methods.causes.Cause object at 0x128e8dc50>}
INIT_DEPENDENCIES : {‘SymptomManager’, ‘Demography’, ‘HealthSystem’}
METADATA : {<Metadata.USES_HEALTHSYSTEM: 3>, <Metadata.USES_HEALTHBURDEN: 4>, <Metadata.DISEASE_MODULE: 1>, <Metadata.USES_SYMPTOMMANAGER: 2>}
OPTIONAL_INIT_DEPENDENCIES : {‘HealthBurden’}
__annotations__ : {}
Functions (defined or overridden in class Measles):
- __init__(name=None, resourcefilepath=None)[source]
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.
- pre_initialise_population()[source]
Carry out any work before any populations have been initialised
This optional method allows access to all other registered modules, before any of the modules have initialised a population. This is expected to be useful for when a module’s properties rely upon information from other modules.
- initialise_population(population)[source]
Set our property values for the initial population. set whole population to measles-free for 1st jan
- initialise_simulation(sim)[source]
Schedule measles event to start straight away. Each month it will assign new infections
- on_birth(mother_id, child_id)[source]
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
- process_parameters()[source]
Process the parameters (following being read-in) prior to the simulation starting. Make self.symptom_probs to be a dictionary keyed by age, with values of dictionaries keyed by symptoms and the probability of symptom onset.
- do_at_generic_first_appt(person_id: int, symptoms: List[str], schedule_hsi_event: HSIEventScheduler, **kwargs) None [source]
Actions to take during a non-emergency generic health system interaction (HSI).
Derived classes should overwrite this method so that they are compatible with the
HealthSystem
module, and can schedule HSI events when a individual 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
subclass implementing this method using theschedule_hsi_event
argument.Implementations of this method should not make any updates to the population dataframe directly - if the target individuals properties need to be updated this should be performed by updating the
individual_properties
argument.- Parameters:
person_id – Row index (ID) of the individual target of the HSI event in the population dataframe.
individual_properties – Properties of individual target as provided in the population dataframe. Updates to individual properties may be written to this object.
symptoms – List of symptoms the patient is experiencing.
schedule_hsi_event – A function that can schedule subsequent HSI events.
diagnosis_function – A function that can run diagnosis tests based on the patient’s symptoms.
consumables_checker – A function that can query the health system 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.
- class MeaslesEvent(module)[source]
MeaslesEvent runs every month and creates a number of new infections which are scattered across the month. * Seasonality is captured by the risk of infection changing according to the month. * Vaccination lowers an individual’s likelihood of getting the infection (one dose will be 85% protective and two
doses will be 99% protective).
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)
Bases:
tlo.events.RegularEvent
,tlo.events.Event
,tlo.events.PopulationScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class MeaslesEvent):
- class MeaslesOnsetEvent(module, person_id)[source]
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)
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class MeaslesOnsetEvent):
- __init__(module, person_id)[source]
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)
- class MeaslesSymptomResolveEvent(module, person_id)[source]
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)
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class MeaslesSymptomResolveEvent):
- __init__(module, person_id)[source]
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)
- class MeaslesDeathEvent(module, person_id)[source]
Performs the Death operation on an individual and logs it.
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)
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class MeaslesDeathEvent):
- __init__(module, person_id)[source]
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)
- class HSI_Measles_Treatment(module, person_id)[source]
Health System Interaction Event It is the event when a person with diagnosed measles receives treatment
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.
Bases:
tlo.methods.hsi_event.HSI_Event
,tlo.events.IndividualScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class HSI_Measles_Treatment):
- __init__(module, person_id)[source]
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.
- class MeaslesLoggingEvent(module)[source]
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)
Bases:
tlo.events.RegularEvent
,tlo.events.Event
,tlo.events.PopulationScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class MeaslesLoggingEvent):
- class MeaslesLoggingFortnightEvent(module)[source]
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)
Bases:
tlo.events.RegularEvent
,tlo.events.Event
,tlo.events.PopulationScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class MeaslesLoggingFortnightEvent):
- class MeaslesLoggingAnnualEvent(module)[source]
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)
Bases:
tlo.events.RegularEvent
,tlo.events.Event
,tlo.events.PopulationScopeEventMixin
Class attributes:
__annotations__ : {}
Functions (defined or overridden in class MeaslesLoggingAnnualEvent):