vaccine

This module contains functionality for vaccine distribution.

add_scheduled_vaccine(campaign, start_day=1, demographic_coverage=1.0, target_num_individuals=None, node_ids=None, repetitions=1, timesteps_between_repetitions=365, ind_property_restrictions=None, target_age_min=0, target_age_max=MAX_AGE_YEARS, target_gender='All', target_residents_only=False, broadcast_event=None, intervention_name='SimpleVaccine', vaccine_type='AcquisitionBlocking', vaccine_take=1, vaccine_initial_effect=1, vaccine_box_duration=365, vaccine_decay_time_constant=100, efficacy_is_multiplicative=True)

Adds a scheduled SimpleVaccine event, with an optional BroadcastEvent, broadcast when vaccine is received.

Parameters:

Name	Type	Description	Default
campaign	EMODCampaign	campaign object to which the intervention will be added, and schema_path container	required
start_day	int	The day the intervention is given out.	1
demographic_coverage	float	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.	1.0
target_num_individuals	int	The exact number of people to select out of the targeted group. If this value is set, demographic_coverage parameter is ignored	None
node_ids	list	List of nodes to which to distribute the intervention. [] or None, indicates all nodes will get the intervention	None
repetitions	int	The number of times an intervention is given, used with timesteps_between_repetitions. -1 means the intervention repeats forever. Sets Number_Repetitions	1
timesteps_between_repetitions	int	The interval, in timesteps, between repetitions. Ignored if repetitions = 1. Sets Timesteps_Between_Repetitions	365
ind_property_restrictions	list	A list of dictionaries of IndividualProperties, which are needed for the individual to receive the intervention. Sets the Property_Restrictions_Within_Node	None
target_age_min	float	The lower end of ages targeted for an intervention, in years. Sets Target_Age_Min	0
target_age_max	float	The upper end of ages targeted for an intervention, in years. Sets Target_Age_Max	MAX_AGE_YEARS
target_gender	str	The gender targeted for an intervention: All, Male, or Female.	'All'
target_residents_only	bool	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)	False
broadcast_event	str	"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.	None
intervention_name	str	The optional name used to refer to this intervention as a means to differentiate it from others that use the same class	'SimpleVaccine'
vaccine_type	str	The type of vaccine to distribute in a vaccine intervention. Options are: "Generic", "TransmissionBlocking", "AcquisitionBlocking", "MortalityBlocking"	'AcquisitionBlocking'
vaccine_take	float	The rate at which delivered vaccines will successfully stimulate an immune response and achieve the desired efficacy.	1
vaccine_initial_effect	float	Initial efficacy of the vaccine, before decay.	1
vaccine_box_duration	int	Duration in days of initial efficacy of vaccine before it starts to decay.	365
vaccine_decay_time_constant	float	Time over which vaccine efficacy wanes and the vaccine_box_duration.	100
efficacy_is_multiplicative	bool	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.	True

Source code in emodpy_malaria/interventions/vaccine.py

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 = MAX_AGE_YEARS,
                          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 (emodpy.campaign.emod_campaign.EMODCampaign): 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.
    """

    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)

add_triggered_vaccine(campaign, start_day=1, trigger_condition_list=None, listening_duration=-1, delay_period_constant=0, demographic_coverage=1.0, node_ids=None, repetitions=1, timesteps_between_repetitions=365, ind_property_restrictions=None, target_age_min=0, target_age_max=MAX_AGE_YEARS, target_gender='All', target_residents_only=False, broadcast_event=None, intervention_name='SimpleVaccine', vaccine_type='AcquisitionBlocking', vaccine_take=1, vaccine_initial_effect=1, vaccine_box_duration=365, vaccine_decay_time_constant=100, efficacy_is_multiplicative=True)

Adds an event-triggered SimpleVaccine event, with an optional BroadcastEvent, broadcast when vaccine is received.

Parameters:

Name	Type	Description	Default
campaign	EMODCampaign	campaign object to which the intervention will be added, and schema_path container	required
start_day	int	The day the intervention is given out.	1
trigger_condition_list	list	A list of the events that will trigger intervention distribution.	None
listening_duration	int	The number of time steps that the distributed event will monitor for triggers. Default is -1, which is indefinitely.	-1
delay_period_constant	float	Optional. Delay, in days, before the intervention is given out after a trigger is received.	0
demographic_coverage	float	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.	1.0
node_ids	list	List of nodes to which to distribute the intervention. [] or None, indicates all nodes will get the intervention	None
repetitions	int	The number of times an intervention is given, used with timesteps_between_repetitions. -1 means the intervention repeats forever. Sets Number_Repetitions	1
timesteps_between_repetitions	int	The interval, in timesteps, between repetitions. Ignored if repetitions = 1. Sets Timesteps_Between_Repetitions	365
ind_property_restrictions	list	A list of dictionaries of IndividualProperties, which are needed for the individual to receive the intervention. Sets the Property_Restrictions_Within_Node	None
target_age_min	float	The lower end of ages targeted for an intervention, in years. Sets Target_Age_Min	0
target_age_max	float	The upper end of ages targeted for an intervention, in years. Sets Target_Age_Max	MAX_AGE_YEARS
target_gender	str	The gender targeted for an intervention: All, Male, or Female.	'All'
target_residents_only	bool	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)	False
broadcast_event	str	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.	None
intervention_name	str	The optional name used to refer to this intervention as a means to differentiate it from others that use the same class	'SimpleVaccine'
vaccine_type	str	The type of vaccine to distribute in a vaccine intervention. Options are: "Generic", "TransmissionBlocking", "AcquisitionBlocking", "MortalityBlocking"	'AcquisitionBlocking'
vaccine_take	float	The rate at which delivered vaccines will successfully stimulate an immune response and achieve the desired efficacy.	1
vaccine_initial_effect	float	Initial efficacy of the vaccine, before decay.	1
vaccine_box_duration	float	Duration in days of initial efficacy of vaccine before it starts to decay.	365
vaccine_decay_time_constant	float	Time over which vaccine efficacy wanes and the vaccine_box_duration.	100
efficacy_is_multiplicative	bool	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.	True

Source code in emodpy_malaria/interventions/vaccine.py

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 = MAX_AGE_YEARS,
                          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 (emodpy.campaign.emod_campaign.EMODCampaign): 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.
    """

    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)

new_intervention_as_file(campaign, start_day=0, filename='SimpleVaccine.json')

Write a campaign file to disk with a single bednet event, using defaults. Useful for testing and learning.

Parameters:

Name	Type	Description	Default
campaign	EMODCampaign	The obj:emod_api:emod_api.campaign object to which the intervention will be added.	required
start_day	int	The day of the simulation on which the bednets are distributed. We recommend aligning this with the start of the simulation.	0
filename	str	The campaign filename; can be omitted and default will be used and returned to user.	'SimpleVaccine.json'

Returns:

Type	Description
str	The campaign filename written to disk.

Source code in emodpy_malaria/interventions/vaccine.py

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 (emodpy.campaign.emod_campaign.EMODCampaign): 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:
        (str): The campaign filename written to disk.
    """
    add_scheduled_vaccine(campaign, start_day)
    campaign.save(filename)
    return filename