tlo.methods.epi module

class Epi(name=None, resourcefilepath=None)

This is the expanded programme on immunisation module it sets up the vaccination schedule for all children from birth

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

PARAMETERS:

Item	Type	Description
baseline_coverage	DATA_FRAME	baseline vaccination coverage (all vaccines)
vaccine_schedule	SERIES	vaccination schedule applicable from 2018 onwards
prob_facility_level_for_vaccine	LIST	The probability of going to each facility-level (0 / 1a / 1b / 2) for child having vaccines given through childhood immunisation schedule. The probabilities must sum to 1.0

PROPERTIES:

Item	Type	Description
va_bcg	INT	number of doses of BCG vaccination
va_opv	INT	number of doses of OPV vaccine received
va_dtp	INT	number of doses of DTP vaccine received
va_hib	INT	number of doses of Hib vaccine received
va_hep	INT	number of doses of HepB vaccine received (infant series)
va_pneumo	INT	number of doses of pneumococcal vaccine received
va_rota	INT	number of doses of rotavirus vaccine received
va_measles	INT	number of doses of measles vaccine received
va_rubella	INT	number of doses of rubella vaccine received
va_hpv	INT	number of doses of hpv vaccine received
va_td	INT	number of doses of tetanus/diphtheria vaccine received by pregnant women
va_bcg_all_doses	BOOL	whether all doses have been received of the vaccine bcg
va_opv_all_doses	BOOL	whether all doses have been received of the OPV vaccine
va_dtp_all_doses	BOOL	whether all doses have been received of the DTP vaccine
va_hib_all_doses	BOOL	whether all doses have been received of the Hib vaccine
va_hep_all_doses	BOOL	whether all doses have been received of the HepB vaccine (infant series)
va_pneumo_all_doses	BOOL	whether all doses have been received of the pneumococcal vaccine
va_rota_all_doses	BOOL	whether all doses have been received of the rotavirus vaccine
va_measles_all_doses	BOOL	whether all doses have been received of the measles vaccine
va_rubella_all_doses	BOOL	whether all doses have been received of the rubella vaccine
va_hpv_all_doses	BOOL	whether all doses have been received of the HPV vaccine
va_td_all_doses	BOOL	whether all doses have been received of the tetanus/diphtheria vaccine

Class attributes:

INIT_DEPENDENCIES : {‘Demography’, ‘HealthSystem’}

METADATA : {<Metadata.USES_HEALTHSYSTEM: 3>}

__annotations__ : {}

Functions (defined or overridden in class Epi):

__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, 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.

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.

By default, all Property``s in ``self.PROPERTIES will have their columns in the population dataframe set to the default value.

Modules that wish to implement this behaviour do not need to implement this method, it will be inherited automatically. Modules that wish to perform additional steps during the initialise_population stage should reimplement this method and call

`python super().initialise_population(population=population) `

at the beginning of the method, then proceed with their additional steps. Modules that do not wish to inherit this default behaviour should re-implement initialise_population without the call to super() above.

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 in the simulation.

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_id, child_id)

Initialise our properties for a newborn individual

birth doses occur within 24 hours of delivery

2012 data is patchy, no record of Hep vaccine but it was used before 2012 assume hepB3 coverage in 2012 same as 2011 same with Hib

Measles - first dose, only one dose pre-2016 and no rubella Measles, rubella - first dose, 2018 onwards

Parameters:

• mother_id – the ID for the mother for this child

• child_id – the ID for the new child

report_daly_values()

epi module returns dalys=0 for all persons alive

increment_dose(person_id, vaccine)

get_item_codes()

Look-up the item-codes for each vaccine and update self.cons_item_codes

class HpvScheduleEvent(module)

HPV vaccine event - each year sample from 9 year old girls and schedule vaccine stagger vaccine administration across the year coverage estimates dependent on health system capacity average around 85% for 2018 WHO recommends 2 doses schedule doses 1 month apart

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 HpvScheduleEvent):

__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

class HsiBaseVaccine(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=False)

This is a base class for all vaccination HSI_Events. Handles initialisation and requesting consumables needed for the vaccination. For custom behaviour, you can override __init__ in subclasses and implemented your own constructors (or inherit directly from HSI_Event) unless specified, default facility level is 1a unless specified, footprint returned in 1 EPI appt if vaccine occurs as part of a treatment package within another appointment, use suppress_footprint=True

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:

EXPECTED_APPT_FOOTPRINT : <property object at 0x117b4bf60>

__annotations__ : {}

Functions (defined or overridden in class HsiBaseVaccine):

__init__(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=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.

treatment_id()

subclasses should implement this method to return the TREATMENT_ID

apply(*args, **kwargs)

must be implemented by subclasses

class HSI_BcgVaccine(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=False)

gives bcg vaccine 24 hours after birth or as soon as possible afterwards

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.epi.HsiBaseVaccine, tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_BcgVaccine):

treatment_id()

subclasses should implement this method to return the TREATMENT_ID

apply(person_id, squeeze_factor)

must be implemented by subclasses

class HSI_opv(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=False)

gives poliovirus vaccine 24 hours after birth, plus weeks 6, 10, 14 or as soon as possible afterwards

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.epi.HsiBaseVaccine, tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_opv):

treatment_id()

subclasses should implement this method to return the TREATMENT_ID

apply(person_id, squeeze_factor)

must be implemented by subclasses

class HSI_DtpHibHepVaccine(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=False)

gives DTP-Hib_HepB vaccine

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.epi.HsiBaseVaccine, tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_DtpHibHepVaccine):

treatment_id()

subclasses should implement this method to return the TREATMENT_ID

apply(person_id, squeeze_factor)

must be implemented by subclasses

class HSI_RotaVaccine(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=False)

gives Rotavirus vaccine 6 and 10 weeks after birth

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.epi.HsiBaseVaccine, tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_RotaVaccine):

treatment_id()

subclasses should implement this method to return the TREATMENT_ID

apply(person_id, squeeze_factor)

must be implemented by subclasses

class HSI_PneumoVaccine(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=False)

gives Pneumococcal vaccine 6, 10 and 14 weeks after birth

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.epi.HsiBaseVaccine, tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_PneumoVaccine):

treatment_id()

subclasses should implement this method to return the TREATMENT_ID

apply(person_id, squeeze_factor)

must be implemented by subclasses

class HSI_MeaslesRubellaVaccine(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=False)

administers measles+rubella vaccine

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.epi.HsiBaseVaccine, tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_MeaslesRubellaVaccine):

treatment_id()

subclasses should implement this method to return the TREATMENT_ID

apply(person_id, squeeze_factor)

must be implemented by subclasses

class HSI_HpvVaccine(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=False)

gives HPV vaccine to 9 year old girls; recommended 2 doses (WHO)

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.epi.HsiBaseVaccine, tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_HpvVaccine):

treatment_id()

subclasses should implement this method to return the TREATMENT_ID

apply(person_id, squeeze_factor)

must be implemented by subclasses

class HSI_TdVaccine(module, person_id, facility_level_of_this_hsi='1a', suppress_footprint=False)

gives tetanus/diphtheria vaccine to pregnant women as part of routine antenatal care recommended 2+ doses (WHO)

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.epi.HsiBaseVaccine, tlo.methods.hsi_event.HSI_Event, tlo.events.IndividualScopeEventMixin

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class HSI_TdVaccine):

treatment_id()

subclasses should implement this method to return the TREATMENT_ID

apply(person_id, squeeze_factor)

must be implemented by subclasses

class EpiLoggingEvent(module)

output vaccine coverage every year

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

Class attributes:

__annotations__ : {}

Functions (defined or overridden in class EpiLoggingEvent):

__init__(module)

output vaccine coverage every year

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