tlo.methods.epi module¶
- class Epi(name=None, resourcefilepath=None)[source]¶
This is the expanded programme on immunisation module it sets up the vaccination schedule for all children from birth
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
district_vaccine_coverage
DATA_FRAME
coverage of each vaccine type by year and district
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 : {‘HealthSystem’, ‘Demography’}
METADATA : {<Metadata.USES_HEALTHSYSTEM: 3>}
Functions (defined or overridden in class Epi):
- __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.
- read_parameters(data_folder)[source]¶
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)[source]¶
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)[source]¶
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)[source]¶
Initialise our properties for a newborn individual
birth doses occur within 24 hours of delivery
from 2010-2018 data on vaccine coverage are used to determine probability of receiving vaccine vaccinations are scheduled to occur with a probability dependent on the year and district from 2019 onwards, probability will be determined by personnel and vaccine availability
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
for births up to end 2018 schedule the vaccine as individual event (not HSI) schedule the dates as the exact due date then from 2019 use the HSI events - only need the current vaccines in use that way
- Parameters
mother_id – the ID for the mother for this child
child_id – the ID for the new child
- class BcgVaccineEvent(module, *args, priority=Priority.FIRST_HALF_OF_DAY, **kwargs)[source]¶
give BCG vaccine at birth
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class BcgVaccineEvent):
- class OpvEvent(module, *args, priority=Priority.FIRST_HALF_OF_DAY, **kwargs)[source]¶
give oral poliovirus vaccine (OPV)
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class OpvEvent):
- class DtpHepVaccineEvent(module, *args, priority=Priority.FIRST_HALF_OF_DAY, **kwargs)[source]¶
give DTP_Hep vaccine
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class DtpHepVaccineEvent):
- class DtpHibHepVaccineEvent(module, *args, priority=Priority.FIRST_HALF_OF_DAY, **kwargs)[source]¶
give DTP_Hib_Hep vaccine
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class DtpHibHepVaccineEvent):
- class RotavirusVaccineEvent(module, *args, priority=Priority.FIRST_HALF_OF_DAY, **kwargs)[source]¶
give Rotavirus vaccine
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class RotavirusVaccineEvent):
- class PneumococcalVaccineEvent(module, *args, priority=Priority.FIRST_HALF_OF_DAY, **kwargs)[source]¶
give Pneumococcal vaccine (PCV)
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class PneumococcalVaccineEvent):
- class HibVaccineEvent(module, *args, priority=Priority.FIRST_HALF_OF_DAY, **kwargs)[source]¶
give Haemophilus influenza B vaccine
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HibVaccineEvent):
- class MeaslesVaccineEvent(module, *args, priority=Priority.FIRST_HALF_OF_DAY, **kwargs)[source]¶
give measles vaccine
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class MeaslesVaccineEvent):
- class MeaslesRubellaVaccineEvent(module, *args, priority=Priority.FIRST_HALF_OF_DAY, **kwargs)[source]¶
give measles/rubella vaccine
Bases:
tlo.events.Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class MeaslesRubellaVaccineEvent):
- class HpvScheduleEvent(module)[source]¶
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
Bases:
tlo.events.RegularEvent
,tlo.events.Event
,tlo.events.PopulationScopeEventMixin
Functions (defined or overridden in class HpvScheduleEvent):
- class HsiBaseVaccine(module, person_id)[source]¶
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)
Bases:
tlo.methods.healthsystem.HSI_Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HsiBaseVaccine):
- __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 HSI_BcgVaccine(module, person_id)[source]¶
gives bcg vaccine 24 hours after birth or as soon as possible afterwards
Bases:
tlo.methods.epi.HsiBaseVaccine
,tlo.methods.healthsystem.HSI_Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HSI_BcgVaccine):
- class HSI_opv(module, person_id)[source]¶
gives poliovirus vaccine 24 hours after birth, plus weeks 6, 10, 14 or as soon as possible afterwards
Bases:
tlo.methods.epi.HsiBaseVaccine
,tlo.methods.healthsystem.HSI_Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HSI_opv):
- class HSI_DtpHibHepVaccine(module, person_id)[source]¶
gives DTP-Hib_HepB vaccine
Bases:
tlo.methods.epi.HsiBaseVaccine
,tlo.methods.healthsystem.HSI_Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HSI_DtpHibHepVaccine):
- class HSI_RotaVaccine(module, person_id)[source]¶
gives Rotavirus vaccine 6 and 10 weeks after birth
Bases:
tlo.methods.epi.HsiBaseVaccine
,tlo.methods.healthsystem.HSI_Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HSI_RotaVaccine):
- class HSI_PneumoVaccine(module, person_id)[source]¶
gives Pneumococcal vaccine 6, 10 and 14 weeks after birth
Bases:
tlo.methods.epi.HsiBaseVaccine
,tlo.methods.healthsystem.HSI_Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HSI_PneumoVaccine):
- class HSI_MeaslesRubellaVaccine(module, person_id)[source]¶
administers measles+rubella vaccine
Bases:
tlo.methods.epi.HsiBaseVaccine
,tlo.methods.healthsystem.HSI_Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HSI_MeaslesRubellaVaccine):
- class HSI_HpvVaccine(module, person_id)[source]¶
gives HPV vaccine to 9 year old girls; recommended 2 doses (WHO)
Bases:
tlo.methods.epi.HsiBaseVaccine
,tlo.methods.healthsystem.HSI_Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HSI_HpvVaccine):
- class HSI_TdVaccine(module, person_id)[source]¶
gives tetanus/diphtheria vaccine to pregnant women as part of routine antenatal care recommended 2+ doses (WHO)
Bases:
tlo.methods.epi.HsiBaseVaccine
,tlo.methods.healthsystem.HSI_Event
,tlo.events.IndividualScopeEventMixin
Functions (defined or overridden in class HSI_TdVaccine):
- class EpiLoggingEvent(module)[source]¶
Bases:
tlo.events.RegularEvent
,tlo.events.Event
,tlo.events.PopulationScopeEventMixin
Functions (defined or overridden in class EpiLoggingEvent):