"""
This module contains functionality for vaccine distribution.
"""
import math
from emod_api import schema_to_class as s2c
from emod_api.interventions import utils, common
from emodpy_malaria.interventions.common import add_campaign_event, add_triggered_campaign_delay_event
def _simple_vaccine(campaign,
intervention_name: str = "SimpleVaccine",
vaccine_type: str = "AcquisitionBlocking",
vaccine_take: float = 1,
vaccine_initial_effect: float = 1,
vaccine_box_duration: float = 365,
vaccine_decay_time_constant: float = 100,
efficacy_is_multiplicative: bool = True):
"""
Configures a SimpleVaccine intervention.
Args:
campaign: campaign object to which the intervention will be added, and schema_path container
intervention_name: The optional name used to refer to this intervention as a means to differentiate it
from others that use the same class
vaccine_type: The type of vaccine to distribute in a vaccine intervention. Options are: "Generic",
"TransmissionBlocking", "AcquisitionBlocking", "MortalityBlocking"
vaccine_take: The rate at which delivered vaccines will successfully stimulate an immune response and achieve
the desired efficacy.
vaccine_initial_effect: Initial efficacy of the vaccine, before decay.
vaccine_box_duration: Duration in days of initial efficacy of vaccine before it starts to decay.
vaccine_decay_time_constant: Time over which vaccine efficacy wanes and the vaccine_box_duration.
efficacy_is_multiplicative: The overall vaccine efficacy when individuals receive more than one vaccine.
When set to true (1), the vaccine efficacies are multiplied together; when set to false (0), the
efficacies are additive.
Returns:
Configured SimpleVaccine intervention
"""
vaccine_types = ["Generic", "TransmissionBlocking", "AcquisitionBlocking", "MortalityBlocking"]
if vaccine_type not in vaccine_types:
ValueError(f"Please specify a valid vaccine_type, vaccine_types are {vaccine_types}.")
schema_path = campaign.schema_path
intervention = s2c.get_class_with_defaults("SimpleVaccine", schema_path)
intervention.Intervention_Name = intervention_name
intervention.Vaccine_Type = vaccine_type
intervention.Vaccine_Take = vaccine_take
intervention.Efficacy_Is_Multiplicative = 1 if efficacy_is_multiplicative else 0
intervention.Waning_Config = utils.get_waning_from_params(schema_path=schema_path,
initial=vaccine_initial_effect,
box_duration=vaccine_box_duration,
decay_time_constant=vaccine_decay_time_constant)
return intervention
[docs]def add_scheduled_vaccine(campaign,
start_day: int = 1,
demographic_coverage: float = 1.0,
target_num_individuals: int = None,
node_ids: list = None,
repetitions: int = 1,
timesteps_between_repetitions: int = 365,
ind_property_restrictions: list = None,
target_age_min: float = 0,
target_age_max: float = 125,
target_gender: str = "All",
target_residents_only: bool = False,
broadcast_event: str = None,
intervention_name: str = "SimpleVaccine",
vaccine_type: str = "AcquisitionBlocking",
vaccine_take: float = 1,
vaccine_initial_effect: float = 1,
vaccine_box_duration: int = 365,
vaccine_decay_time_constant: float = 100,
efficacy_is_multiplicative: bool = True):
"""
Adds a scheduled SimpleVaccine event, with an optional BroadcastEvent, broadcast when vaccine is received.
Args:
campaign: campaign object to which the intervention will be added, and schema_path container
start_day: The day the intervention is given out.
demographic_coverage: This value is the probability that each individual in the target population will
receive the intervention. It does not guarantee that the exact fraction of the target population set by
Demographic_Coverage receives the intervention.
target_num_individuals: The exact number of people to select out of the targeted group. If this value is set,
demographic_coverage parameter is ignored
node_ids: List of nodes to which to distribute the intervention. [] or None, indicates all nodes
will get the intervention
repetitions: The number of times an intervention is given, used with timesteps_between_repetitions. -1 means
the intervention repeats forever. Sets **Number_Repetitions**
timesteps_between_repetitions: The interval, in timesteps, between repetitions. Ignored if repetitions = 1.
Sets **Timesteps_Between_Repetitions**
ind_property_restrictions: A list of dictionaries of IndividualProperties, which are needed for the individual
to receive the intervention. Sets the **Property_Restrictions_Within_Node**
target_age_min: The lower end of ages targeted for an intervention, in years. Sets **Target_Age_Min**
target_age_max: The upper end of ages targeted for an intervention, in years. Sets **Target_Age_Max**
target_gender: The gender targeted for an intervention: All, Male, or Female.
target_residents_only: When set to True, the intervention is only distributed to individuals that began
the simulation in the node (i.e. those that claim the node as their residence)
broadcast_event: "The name of the event to be broadcast. This event must be set in the
**Custom_Coordinator_Events** configuration parameter. When None or Empty, nothing is broadcast.
intervention_name: The optional name used to refer to this intervention as a means to differentiate it
from others that use the same class
vaccine_type: The type of vaccine to distribute in a vaccine intervention. Options are: "Generic",
"TransmissionBlocking", "AcquisitionBlocking", "MortalityBlocking"
vaccine_take: The rate at which delivered vaccines will successfully stimulate an immune response and achieve
the desired efficacy.
vaccine_initial_effect: Initial efficacy of the vaccine, before decay.
vaccine_box_duration: Duration in days of initial efficacy of vaccine before it starts to decay.
vaccine_decay_time_constant: Time over which vaccine efficacy wanes and the vaccine_box_duration.
efficacy_is_multiplicative: The overall vaccine efficacy when individuals receive more than one vaccine.
When set to true (1), the vaccine efficacies are multiplied together; when set to false (0), the
efficacies are additive.
Returns:
Nothing
"""
intervention = _simple_vaccine(campaign,
intervention_name=intervention_name,
vaccine_type=vaccine_type,
vaccine_take=vaccine_take,
vaccine_initial_effect=vaccine_initial_effect,
vaccine_box_duration=vaccine_box_duration,
vaccine_decay_time_constant=vaccine_decay_time_constant,
efficacy_is_multiplicative=efficacy_is_multiplicative)
if broadcast_event:
intervention = [intervention, common.BroadcastEvent(campaign, Event_Trigger=broadcast_event)]
add_campaign_event(campaign=campaign,
start_day=start_day,
demographic_coverage=demographic_coverage,
target_num_individuals=target_num_individuals,
node_ids=node_ids,
repetitions=repetitions,
timesteps_between_repetitions=timesteps_between_repetitions,
ind_property_restrictions=ind_property_restrictions,
target_age_min=target_age_min,
target_age_max=target_age_max,
target_gender=target_gender,
target_residents_only=target_residents_only,
individual_intervention=intervention)
[docs]def add_triggered_vaccine(campaign,
start_day: int = 1,
trigger_condition_list: list = None,
listening_duration: int = -1,
delay_period_constant: float = 0,
demographic_coverage: float = 1.0,
node_ids: list = None,
repetitions: int = 1,
timesteps_between_repetitions: int = 365,
ind_property_restrictions: list = None,
target_age_min: float = 0,
target_age_max: float = 125,
target_gender: str = "All",
target_residents_only: bool = False,
broadcast_event: str = None,
intervention_name: str = "SimpleVaccine",
vaccine_type: str = "AcquisitionBlocking",
vaccine_take: float = 1,
vaccine_initial_effect: float = 1,
vaccine_box_duration: float = 365,
vaccine_decay_time_constant: float = 100,
efficacy_is_multiplicative: bool = True):
"""
Adds an event-triggered SimpleVaccine event, with an optional BroadcastEvent, broadcast when vaccine is received.
Args:
campaign: campaign object to which the intervention will be added, and schema_path container
start_day: The day the intervention is given out.
trigger_condition_list: A list of the events that will trigger intervention distribution.
listening_duration: The number of time steps that the distributed event will monitor for triggers.
Default is -1, which is indefinitely.
delay_period_constant: Optional. Delay, in days, before the intervention is given out after a trigger
is received.
demographic_coverage: This value is the probability that each individual in the target population will
receive the intervention. It does not guarantee that the exact fraction of the target population set by
Demographic_Coverage receives the intervention.
node_ids: List of nodes to which to distribute the intervention. [] or None, indicates all nodes
will get the intervention
repetitions: The number of times an intervention is given, used with timesteps_between_repetitions. -1 means
the intervention repeats forever. Sets **Number_Repetitions**
timesteps_between_repetitions: The interval, in timesteps, between repetitions. Ignored if repetitions = 1.
Sets **Timesteps_Between_Repetitions**
ind_property_restrictions: A list of dictionaries of IndividualProperties, which are needed for the individual
to receive the intervention. Sets the **Property_Restrictions_Within_Node**
target_age_min: The lower end of ages targeted for an intervention, in years. Sets **Target_Age_Min**
target_age_max: The upper end of ages targeted for an intervention, in years. Sets **Target_Age_Max**
target_gender: The gender targeted for an intervention: All, Male, or Female.
target_residents_only: When set to True, the intervention is only distributed to individuals that began
the simulation in the node (i.e. those that claim the node as their residence)
broadcast_event: The name of the event to be broadcast. This event must be set in the
**Custom_Coordinator_Events** configuration parameter. When None or "", nothing is broadcast.
intervention_name: The optional name used to refer to this intervention as a means to differentiate it
from others that use the same class
vaccine_type: The type of vaccine to distribute in a vaccine intervention. Options are: "Generic",
"TransmissionBlocking", "AcquisitionBlocking", "MortalityBlocking"
vaccine_take: The rate at which delivered vaccines will successfully stimulate an immune response and achieve
the desired efficacy.
vaccine_initial_effect: Initial efficacy of the vaccine, before decay.
vaccine_box_duration: Duration in days of initial efficacy of vaccine before it starts to decay.
vaccine_decay_time_constant: Time over which vaccine efficacy wanes and the vaccine_box_duration.
efficacy_is_multiplicative: The overall vaccine efficacy when individuals receive more than one vaccine.
When set to true (1), the vaccine efficacies are multiplied together; when set to false (0), the
efficacies are additive.
malaria_vaccine: Type of malaria vaccine, one of 'RTSS' (simple vaccine), 'PEV' (preerythrocytic vaccine),
'TBV' (sexual stage vaccine). Defaults is 'None'. Setting this parameter means you want pre-configured
malaria vaccine and any other vaccine configuration parameters will be ignored.
Returns:
Nothing
"""
intervention = _simple_vaccine(campaign,
intervention_name=intervention_name,
vaccine_type=vaccine_type,
vaccine_take=vaccine_take,
vaccine_initial_effect=vaccine_initial_effect,
vaccine_box_duration=vaccine_box_duration,
vaccine_decay_time_constant=vaccine_decay_time_constant,
efficacy_is_multiplicative=efficacy_is_multiplicative)
if broadcast_event:
intervention = [intervention, common.BroadcastEvent(campaign, Event_Trigger=broadcast_event)]
add_triggered_campaign_delay_event(campaign=campaign,
start_day=start_day,
trigger_condition_list=trigger_condition_list,
listening_duration=listening_duration,
delay_period_constant=delay_period_constant,
demographic_coverage=demographic_coverage,
node_ids=node_ids,
repetitions=repetitions,
timesteps_between_repetitions=timesteps_between_repetitions,
ind_property_restrictions=ind_property_restrictions,
target_age_min=target_age_min,
target_age_max=target_age_max,
target_gender=target_gender,
target_residents_only=target_residents_only,
individual_intervention=intervention)
[docs]def new_intervention_as_file(campaign, start_day: int = 0, filename: str = "SimpleVaccine.json"):
"""
Write a campaign file to disk with a single bednet event, using defaults. Useful for testing and learning.
Args:
campaign: The :py:obj:`emod_api:emod_api.campaign` object to which the intervention will be added.
start_day: The day of the simulation on which the bednets are distributed. We recommend
aligning this with the start of the simulation.
filename: The campaign filename; can be omitted and default will be used and returned to user.
Returns:
The campaign filename written to disk.
"""
add_scheduled_vaccine(campaign, start_day)
campaign.save(filename)
return filename