Vaccine

name: str

Name of feature in the params file. Also used to name the attribute in Agent

stats: List[str]

Vaccine collects the following stats:

• vaccine - number of agents with active vaccine

get_acquisition_risk_multiplier(self, time, interaction_type)

Get a multiplier for how vaccine affects acquisition of HIV for the given interaction_type.

By default, returns 1.0

Parameters:

Name	Type	Description	Default
time	int	the current model time step	required
interaction_type	str	The type of interaction where the agent could acquire HIV (e.g. 'sex', 'injection' - from [params.classes.interaction_types])	required

Source code in titan/features/vaccine.py

def get_acquisition_risk_multiplier(self, time: int, interaction_type: str):
    """
    Get a multiplier for how vaccine affects acquisition of HIV for the given interaction_type.

    By default, returns 1.0

    args:
        time: the current model time step
        interaction_type: The type of interaction where the agent could acquire HIV (e.g. 'sex', 'injection' - from [params.classes.interaction_types])
    """
    # not protected the time step the agent is vaccinaetd
    if self.active and self.time is not None and self.time < time:
        vaccine_time_months = (
            (time - self.time)
            / self.agent.location.params.model.time.steps_per_year
        ) * 12

        if self.type == "HVTN702":
            return np.exp(
                -2.88 + 0.76 * (np.log((vaccine_time_months + 0.001) * 30))
            )
        elif self.type == "RV144":
            return np.exp(-2.40 + 0.76 * (np.log(vaccine_time_months)))
        else:
            return 1 - self.agent.location.params.vaccine.efficacy

    return 1.0

init_agent(self, pop, time)

Initialize the agent for this feature during population initialization (Population.create_agent). Called on only features that are enabled per the params.

If the agent is HIV-, randomly vaccinate per the params.

Parameters:

Name	Type	Description	Default
pop	population.Population	the population this agent is a part of	required
time	int	the current time step	required

Source code in titan/features/vaccine.py

def init_agent(self, pop: "population.Population", time: int):
    """
    Initialize the agent for this feature during population initialization (`Population.create_agent`).  Called on only features that are enabled per the params.

    If the agent is HIV-, randomly vaccinate per the params.

    args:
        pop: the population this agent is a part of
        time: the current time step
    """
    if (
        not self.agent.hiv.active  # type: ignore[attr-defined]
        and self.agent.location.params.vaccine.on_init
        and pop.pop_random.random()
        < self.agent.location.params.demographics[self.agent.race]
        .sex_type[self.agent.sex_type]
        .vaccine.init
    ):
        self.vaccinate(time)

set_stats(self, stats, time)

Update the stats dictionary passed for this agent. Called from output.get_stats for each enabled feature in the model.

The stats to be updated must be declared in the class attribute stats to make sure the dictionary has the expected keys/counter value initialized.

Parameters:

Name	Type	Description	Default
stats	Dict[str, int]	the dictionary to update with this agent's feature statistics	required
time	int	the time step of the model when the stats are set	required

Source code in titan/features/vaccine.py

def set_stats(self, stats: Dict[str, int], time: int):
    if self.active:
        stats["vaccine"] += 1

update_agent(self, model)

Update the agent for this feature for a time step. Called once per time step in TITAN.update_all_agents. Agent level updates are done after population level updates. Called on only features that are enabled per the params.

If PrEP feature is enable and the agent is not active PrEP and not HIV, either update or stochastically vaccinate the agent.

Parameters:

Name	Type	Description	Default
model	model.TITAN	the instance of TITAN currently being run	required

Source code in titan/features/vaccine.py

def update_agent(self, model: "model.TITAN"):
    """
    Update the agent for this feature for a time step.  Called once per time step in `TITAN.update_all_agents`. Agent level updates are done after population level updates.   Called on only features that are enabled per the params.

    If PrEP feature is enable and the agent is not active PrEP and not HIV, either update or stochastically vaccinate the agent.

    args:
        model: the instance of TITAN currently being run
    """
    if (
        not self.agent.prep.active  # type: ignore[attr-defined]
        and not self.agent.hiv.active  # type: ignore[attr-defined]
    ):
        vaccine_params = self.agent.location.params.vaccine
        agent_params = (
            self.agent.location.params.demographics[self.agent.race]
            .sex_type[self.agent.sex_type]
            .vaccine
        )

        if self.active:
            if (
                vaccine_params.booster
                and (model.time - self.time) == agent_params.booster.interval
                and model.run_random.random() < agent_params.booster.prob
            ):
                self.vaccinate(model.time)
        elif model.time == vaccine_params.start_time:
            if model.run_random.random() < agent_params.prob:
                self.vaccinate(model.time)

vaccinate(self, time)

Vaccinate an agent and update relevant fields.

Source code in titan/features/vaccine.py

def vaccinate(self, time):
    """
    Vaccinate an agent and update relevant fields.
    """
    self.active = True
    self.type = self.agent.location.params.vaccine.type
    self.time = time