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Vaccination campaign

VaccinationCampaign

Defines a campaign to vaccinate a group of people in a given time span and with a given vaccine

Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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class VaccinationCampaign:
    """Defines a campaign to vaccinate a group of people in
    a given time span and with a given vaccine

    """

    def __init__(
        self,
        vaccine: Vaccine,
        days_to_next_dose: List[int],
        dose_numbers: List[int] = [0, 1],
        start_time: str = "2100-01-01",
        end_time: str = "2100-01-02",
        group_by: str = "age",
        group_type: str = "50-100",
        group_coverage: float = 1.0,
        last_dose_type: Optional[str] = None,
    ):
        """__init__.

        Parameters
        ----------
        vaccine : Vaccine
            vaccine to give out
        days_to_next_dose : List[int]
            days to wait from the moment a person is vaccinated to
            their next dose. Should have same length as dose_numbers
        dose_numbers : List[int]
            what doses to give out.
            Example: dose_numbers = [0,1] would give out first
            and second dose, whereas dose_numbers = [2] would
            only give a third dose
        start_time : str
            date at which to start vaccinating people
        end_time : str
            date at which to stop vaccinating people
        group_by : str
            defines what group to vaccinate.
            Examples: 'age', 'sex', 'residence', 'primary_activity'
        group_type : str
            from the group defined by group_by, what people to vaccinate.
            Examples:
            if group_by = 'age' -> group_type = '20-40' would vaccinate
            people aged between 20 and 40
            if group_by = 'residence' -> group_type = 'carehome' would vaccinate
            people living in care homes.
        group_coverage : float
            percentage of the eligible group to vaccinate. Must be between 0. and 1.
        last_dose_type : Optional[str]
            if not starting with a first dose (dose_numbers[0] = 0), whether to
            vaccinate only people whose previous vaccines where of a certain type.
        """
        self.start_time = read_date(start_time)
        self.end_time = read_date(end_time)
        self.vaccine = vaccine
        self.days_to_next_dose = days_to_next_dose
        self.group_attribute, self.group_value = self.process_group_description(
            group_by, group_type
        )
        self.total_days = (self.end_time - self.start_time).days
        self.group_coverage = group_coverage
        if last_dose_type is None:
            self.last_dose_type = []
        else:
            self.last_dose_type = last_dose_type
        self.dose_numbers = dose_numbers
        self.vaccinated_ids = set()
        self.starting_dose = self.dose_numbers[0]
        self.days_from_administered_to_finished = (
            sum(self.days_to_next_dose)
            + sum(
                [
                    self.vaccine.days_administered_to_effective[dose]
                    for dose in self.dose_numbers
                ]
            )
            + sum(
                [
                    self.vaccine.days_effective_to_waning[dose]
                    for dose in self.dose_numbers
                ]
            )
            + sum([self.vaccine.days_waning[dose] for dose in self.dose_numbers])
        )

    def is_active(self, date: datetime.datetime) -> bool:
        """Returns true if the policy is active, false otherwise

        Args:
            date (datetime.datetime): date to check

        """
        return self.start_time <= date < self.end_time

    def process_group_description(self, group_by: str, group_type: str) -> Tuple[str]:
        """process_group_description.

        Args:
            group_by (str): group_by
            group_type (str): group_type

        Returns:
            Tuple[str]: 

        """
        if group_by in ("residence", "primary_activity"):
            return f"{group_by}.group.spec", group_type
        else:
            return f"{group_by}", group_type

    def is_target_group(self, person: "Person") -> bool:
        """is_target_group.

        Args:
            person ("Person"): person

        Returns:
            bool: 

        """
        if self.group_attribute != "age":
            try:
                if (
                    operator.attrgetter(self.group_attribute)(person)
                    == self.group_value
                ):
                    return True
            except Exception:
                return False
        else:
            if (
                int(self.group_value.split("-")[0])
                <= getattr(person, self.group_attribute)
                < int(self.group_value.split("-")[1])
            ):
                return True
        return False

    def has_right_dosage(self, person: "Person") -> bool:
        """has_right_dosage.

        Args:
            person ("Person"): person

        Returns:
            bool: 

        """
        if person.vaccinated is not None and self.starting_dose == 0:
            return False
        if self.starting_dose > 0:
            if person.vaccinated is None or person.vaccinated != self.starting_dose - 1:
                return False
            if self.last_dose_type and person.vaccine_type not in self.last_dose_type:
                return False
        return True

    def should_be_vaccinated(self, person: "Person") -> bool:
        """should_be_vaccinated.

        Args:
            person ("Person"): person

        Returns:
            bool: 

        """
        return self.has_right_dosage(person) and self.is_target_group(person)

    def vaccinate(
        self,
        person: "Person",
        date: datetime.datetime,
        record: Optional["Record"] = None,
    ):
        """vaccinate.

        Args:
            person ("Person"): person
            date (datetime.datetime): date
            record (Optional["Record"], optional): record (Default value = None)

        """

        vaccine_trajectory = self.vaccine.generate_trajectory(
            person=person,
            dose_numbers=self.dose_numbers,
            days_to_next_dose=self.days_to_next_dose,
            date=date,
        )
        #print("\nDOSAGE about to be updated via VACCINATE:")
        vaccine_trajectory.update_dosage(person=person, record=record, entered_via=0)
        person.vaccine_trajectory = vaccine_trajectory
        self.vaccinated_ids.add(person.id)

    def daily_vaccination_probability(self, days_passed: int) -> float:
        """daily_vaccination_probability.

        Args:
            days_passed (int): days_passed

        Returns:
            float: 

        """
        return self.group_coverage * (
            1 / (self.total_days - days_passed * self.group_coverage)
        )

__init__(vaccine, days_to_next_dose, dose_numbers=[0, 1], start_time='2100-01-01', end_time='2100-01-02', group_by='age', group_type='50-100', group_coverage=1.0, last_dose_type=None)

init.

Parameters

vaccine : Vaccine vaccine to give out days_to_next_dose : List[int] days to wait from the moment a person is vaccinated to their next dose. Should have same length as dose_numbers dose_numbers : List[int] what doses to give out. Example: dose_numbers = [0,1] would give out first and second dose, whereas dose_numbers = [2] would only give a third dose start_time : str date at which to start vaccinating people end_time : str date at which to stop vaccinating people group_by : str defines what group to vaccinate. Examples: 'age', 'sex', 'residence', 'primary_activity' group_type : str from the group defined by group_by, what people to vaccinate. Examples: if group_by = 'age' -> group_type = '20-40' would vaccinate people aged between 20 and 40 if group_by = 'residence' -> group_type = 'carehome' would vaccinate people living in care homes. group_coverage : float percentage of the eligible group to vaccinate. Must be between 0. and 1. last_dose_type : Optional[str] if not starting with a first dose (dose_numbers[0] = 0), whether to vaccinate only people whose previous vaccines where of a certain type.

Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def __init__(
    self,
    vaccine: Vaccine,
    days_to_next_dose: List[int],
    dose_numbers: List[int] = [0, 1],
    start_time: str = "2100-01-01",
    end_time: str = "2100-01-02",
    group_by: str = "age",
    group_type: str = "50-100",
    group_coverage: float = 1.0,
    last_dose_type: Optional[str] = None,
):
    """__init__.

    Parameters
    ----------
    vaccine : Vaccine
        vaccine to give out
    days_to_next_dose : List[int]
        days to wait from the moment a person is vaccinated to
        their next dose. Should have same length as dose_numbers
    dose_numbers : List[int]
        what doses to give out.
        Example: dose_numbers = [0,1] would give out first
        and second dose, whereas dose_numbers = [2] would
        only give a third dose
    start_time : str
        date at which to start vaccinating people
    end_time : str
        date at which to stop vaccinating people
    group_by : str
        defines what group to vaccinate.
        Examples: 'age', 'sex', 'residence', 'primary_activity'
    group_type : str
        from the group defined by group_by, what people to vaccinate.
        Examples:
        if group_by = 'age' -> group_type = '20-40' would vaccinate
        people aged between 20 and 40
        if group_by = 'residence' -> group_type = 'carehome' would vaccinate
        people living in care homes.
    group_coverage : float
        percentage of the eligible group to vaccinate. Must be between 0. and 1.
    last_dose_type : Optional[str]
        if not starting with a first dose (dose_numbers[0] = 0), whether to
        vaccinate only people whose previous vaccines where of a certain type.
    """
    self.start_time = read_date(start_time)
    self.end_time = read_date(end_time)
    self.vaccine = vaccine
    self.days_to_next_dose = days_to_next_dose
    self.group_attribute, self.group_value = self.process_group_description(
        group_by, group_type
    )
    self.total_days = (self.end_time - self.start_time).days
    self.group_coverage = group_coverage
    if last_dose_type is None:
        self.last_dose_type = []
    else:
        self.last_dose_type = last_dose_type
    self.dose_numbers = dose_numbers
    self.vaccinated_ids = set()
    self.starting_dose = self.dose_numbers[0]
    self.days_from_administered_to_finished = (
        sum(self.days_to_next_dose)
        + sum(
            [
                self.vaccine.days_administered_to_effective[dose]
                for dose in self.dose_numbers
            ]
        )
        + sum(
            [
                self.vaccine.days_effective_to_waning[dose]
                for dose in self.dose_numbers
            ]
        )
        + sum([self.vaccine.days_waning[dose] for dose in self.dose_numbers])
    )

daily_vaccination_probability(days_passed)

daily_vaccination_probability.

Parameters:

Name Type Description Default
days_passed int

days_passed

 required

Returns:

Name Type Description
float float
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def daily_vaccination_probability(self, days_passed: int) -> float:
    """daily_vaccination_probability.

    Args:
        days_passed (int): days_passed

    Returns:
        float: 

    """
    return self.group_coverage * (
        1 / (self.total_days - days_passed * self.group_coverage)
    )

has_right_dosage(person)

has_right_dosage.

Parameters:

Name Type Description Default
person Person

person

 required

Returns:

Name Type Description
bool bool
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def has_right_dosage(self, person: "Person") -> bool:
    """has_right_dosage.

    Args:
        person ("Person"): person

    Returns:
        bool: 

    """
    if person.vaccinated is not None and self.starting_dose == 0:
        return False
    if self.starting_dose > 0:
        if person.vaccinated is None or person.vaccinated != self.starting_dose - 1:
            return False
        if self.last_dose_type and person.vaccine_type not in self.last_dose_type:
            return False
    return True

is_active(date)

Returns true if the policy is active, false otherwise

Parameters:

Name Type Description Default
date datetime

date to check

 required
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def is_active(self, date: datetime.datetime) -> bool:
    """Returns true if the policy is active, false otherwise

    Args:
        date (datetime.datetime): date to check

    """
    return self.start_time <= date < self.end_time

is_target_group(person)

is_target_group.

Parameters:

Name Type Description Default
person Person

person

 required

Returns:

Name Type Description
bool bool
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def is_target_group(self, person: "Person") -> bool:
    """is_target_group.

    Args:
        person ("Person"): person

    Returns:
        bool: 

    """
    if self.group_attribute != "age":
        try:
            if (
                operator.attrgetter(self.group_attribute)(person)
                == self.group_value
            ):
                return True
        except Exception:
            return False
    else:
        if (
            int(self.group_value.split("-")[0])
            <= getattr(person, self.group_attribute)
            < int(self.group_value.split("-")[1])
        ):
            return True
    return False

process_group_description(group_by, group_type)

process_group_description.

Parameters:

Name Type Description Default
group_by str

group_by

 required
group_type str

group_type

 required

Returns:

Type Description
Tuple[str]

Tuple[str]:
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def process_group_description(self, group_by: str, group_type: str) -> Tuple[str]:
    """process_group_description.

    Args:
        group_by (str): group_by
        group_type (str): group_type

    Returns:
        Tuple[str]: 

    """
    if group_by in ("residence", "primary_activity"):
        return f"{group_by}.group.spec", group_type
    else:
        return f"{group_by}", group_type

should_be_vaccinated(person)

should_be_vaccinated.

Parameters:

Name Type Description Default
person Person

person

 required

Returns:

Name Type Description
bool bool
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def should_be_vaccinated(self, person: "Person") -> bool:
    """should_be_vaccinated.

    Args:
        person ("Person"): person

    Returns:
        bool: 

    """
    return self.has_right_dosage(person) and self.is_target_group(person)

vaccinate(person, date, record=None)

vaccinate.

Parameters:

Name Type Description Default
person Person

person

 required
date datetime

date

 required
record Optional[Record]

record (Default value = None)

 None
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def vaccinate(
    self,
    person: "Person",
    date: datetime.datetime,
    record: Optional["Record"] = None,
):
    """vaccinate.

    Args:
        person ("Person"): person
        date (datetime.datetime): date
        record (Optional["Record"], optional): record (Default value = None)

    """

    vaccine_trajectory = self.vaccine.generate_trajectory(
        person=person,
        dose_numbers=self.dose_numbers,
        days_to_next_dose=self.days_to_next_dose,
        date=date,
    )
    #print("\nDOSAGE about to be updated via VACCINATE:")
    vaccine_trajectory.update_dosage(person=person, record=record, entered_via=0)
    person.vaccine_trajectory = vaccine_trajectory
    self.vaccinated_ids.add(person.id)

VaccinationCampaigns

VaccinationCampaigns.

Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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class VaccinationCampaigns:
    """VaccinationCampaigns."""

    def __init__(self, vaccination_campaigns: List[VaccinationCampaign]):
        """__init__.

        Parameters
        ----------
        vaccination_campaigns : List[VaccinationCampaign]
            vaccination_campaigns
        """
        self.vaccination_campaigns = vaccination_campaigns

    @classmethod
    def from_disease_config(
        cls, disease_config: DiseaseConfig
    ):
        """from_config.

        Args:
            disease_config (DiseaseConfig): 

        """
        vaccines = Vaccines.from_config(disease_config=disease_config)

        config = disease_config.vaccination_manager.get_vaccination_campaigns()
        vaccination_campaigns = []
        for key, params_dict in config.items():
            vaccine_type = params_dict["vaccine_type"]

            params_dict["vaccine"] = vaccines.get_by_name(vaccine_type)

            campaign = VaccinationCampaign(
                **{k: v for k, v in params_dict.items() if k != "vaccine_type"}
            )
            vaccination_campaigns.append(campaign)

        return cls(vaccination_campaigns=vaccination_campaigns)

    def __iter__(
        self,
    ):
        """__iter__."""
        return iter(self.vaccination_campaigns)

    def get_active(self, date: datetime) -> List[VaccinationCampaign]:
        """get_active.

        Args:
            date (datetime): date

        Returns:
            List[VaccinationCampaign]: 

        """
        return [vc for vc in self.vaccination_campaigns if vc.is_active(date)]

    def apply(
        self, person: "Person", date: datetime, record: Optional["Record"] = None
    ):
        """apply.

        Args:
            person ("Person"): person
            date (datetime): date
            record (Optional["Record"], optional): record (Default value = None)

        """
        # Step 1: Get active vaccination campaigns
        active_campaigns = self.get_active(date=date)

        # Step 2: Check eligibility and calculate probabilities
        daily_probability, campaigns_to_chose_from = [], []
        counter = 0
        for vc in active_campaigns:
            counter += 1
            if vc.should_be_vaccinated(person=person):
                days_passed = (date - vc.start_time).days
                prob = vc.daily_vaccination_probability(days_passed=days_passed)
                daily_probability.append(prob)
                campaigns_to_chose_from.append(vc)

        # Proceed only if the person is eligible
        if daily_probability:

            daily_probability = np.array(daily_probability)
            norm = daily_probability.sum()

            # Step 3: Normalise probabilities and decide vaccination
            if random() < norm:
                daily_probability /= norm
                campaign = np.random.choice(campaigns_to_chose_from, p=daily_probability)
                #print(f"Person ID {person.id} is eligible for vaccination on {date}.")
                #print(f"Total Daily Vaccination Probability (Norm): {norm:.2f}")
                #print(
                #    f"Person ID {person.id} is vaccinated in Campaign '{counter}' on {date}."
                #)
                campaign.vaccinate(person=person, date=date, record=record)
            #else:
                #print(f"Person ID {person.id} did not get vaccinated (random chance).")

    def collect_all_dates_in_past(
        self, current_date: datetime.datetime
    ) -> Set[datetime.datetime]:
        """

        Args:
            current_date (datetime.datetime): 

        """
        dates = set()
        for cv in self.vaccination_campaigns:
            start_time = cv.start_time
            if start_time < current_date:
                days_to_finished = cv.days_from_administered_to_finished
                end_time = min(
                    current_date,
                    cv.end_time + datetime.timedelta(days=days_to_finished),
                )
                delta = end_time - start_time
                for i in range(delta.days + 1):
                    date = start_time + datetime.timedelta(days=i)
                    dates.add(date)
        return sorted(list(dates))

    def apply_past_campaigns(
        self, people, date: datetime.datetime, record: Optional["Record"] = None
    ):
        """

        Args:
            people: 
            date (datetime.datetime): 
            record (Optional["Record"], optional): (Default value = None)

        """
        dates_to_vaccinate = self.collect_all_dates_in_past(current_date=date)
        logger.info(f"Applying past vaccination campaigns...")

        total_people_updated = 0  # Counter to track people with updated vaccine trajectories
        tpv = 0
        for date_to_vax in dates_to_vaccinate:
            logger.info(f"Vaccinating at date {date_to_vax.date()}")
            for person in people:
                self.apply(person=person, date=date_to_vax, record=record)
                tpv +=1
                if person.vaccine_trajectory is not None:
                    person.vaccine_trajectory.update_vaccine_effect(
                        person=person, date=date_to_vax, record=record
                    )
                    total_people_updated += 1  # Increment the counter when updated

            if record is not None:
                record.time_step(timestamp=date_to_vax)
        logger.info(f"Total people updated with vaccine effects: {total_people_updated} out of {tpv}")
        logger.info(f"Finished applying past vaccinations campaigns.")

__init__(vaccination_campaigns)

init.

Parameters

vaccination_campaigns : List[VaccinationCampaign] vaccination_campaigns

Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def __init__(self, vaccination_campaigns: List[VaccinationCampaign]):
    """__init__.

    Parameters
    ----------
    vaccination_campaigns : List[VaccinationCampaign]
        vaccination_campaigns
    """
    self.vaccination_campaigns = vaccination_campaigns

__iter__()

iter.

Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def __iter__(
    self,
):
    """__iter__."""
    return iter(self.vaccination_campaigns)

apply(person, date, record=None)

apply.

Parameters:

Name Type Description Default
person Person

person

 required
date datetime

date

 required
record Optional[Record]

record (Default value = None)

 None
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def apply(
    self, person: "Person", date: datetime, record: Optional["Record"] = None
):
    """apply.

    Args:
        person ("Person"): person
        date (datetime): date
        record (Optional["Record"], optional): record (Default value = None)

    """
    # Step 1: Get active vaccination campaigns
    active_campaigns = self.get_active(date=date)

    # Step 2: Check eligibility and calculate probabilities
    daily_probability, campaigns_to_chose_from = [], []
    counter = 0
    for vc in active_campaigns:
        counter += 1
        if vc.should_be_vaccinated(person=person):
            days_passed = (date - vc.start_time).days
            prob = vc.daily_vaccination_probability(days_passed=days_passed)
            daily_probability.append(prob)
            campaigns_to_chose_from.append(vc)

    # Proceed only if the person is eligible
    if daily_probability:

        daily_probability = np.array(daily_probability)
        norm = daily_probability.sum()

        # Step 3: Normalise probabilities and decide vaccination
        if random() < norm:
            daily_probability /= norm
            campaign = np.random.choice(campaigns_to_chose_from, p=daily_probability)
            #print(f"Person ID {person.id} is eligible for vaccination on {date}.")
            #print(f"Total Daily Vaccination Probability (Norm): {norm:.2f}")
            #print(
            #    f"Person ID {person.id} is vaccinated in Campaign '{counter}' on {date}."
            #)
            campaign.vaccinate(person=person, date=date, record=record)

apply_past_campaigns(people, date, record=None)

Parameters:

Name Type Description Default
people
required
date datetime
required
record Optional[Record]

(Default value = None)

 None
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def apply_past_campaigns(
    self, people, date: datetime.datetime, record: Optional["Record"] = None
):
    """

    Args:
        people: 
        date (datetime.datetime): 
        record (Optional["Record"], optional): (Default value = None)

    """
    dates_to_vaccinate = self.collect_all_dates_in_past(current_date=date)
    logger.info(f"Applying past vaccination campaigns...")

    total_people_updated = 0  # Counter to track people with updated vaccine trajectories
    tpv = 0
    for date_to_vax in dates_to_vaccinate:
        logger.info(f"Vaccinating at date {date_to_vax.date()}")
        for person in people:
            self.apply(person=person, date=date_to_vax, record=record)
            tpv +=1
            if person.vaccine_trajectory is not None:
                person.vaccine_trajectory.update_vaccine_effect(
                    person=person, date=date_to_vax, record=record
                )
                total_people_updated += 1  # Increment the counter when updated

        if record is not None:
            record.time_step(timestamp=date_to_vax)
    logger.info(f"Total people updated with vaccine effects: {total_people_updated} out of {tpv}")
    logger.info(f"Finished applying past vaccinations campaigns.")

collect_all_dates_in_past(current_date)

Parameters:

Name Type Description Default
current_date datetime
required
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def collect_all_dates_in_past(
    self, current_date: datetime.datetime
) -> Set[datetime.datetime]:
    """

    Args:
        current_date (datetime.datetime): 

    """
    dates = set()
    for cv in self.vaccination_campaigns:
        start_time = cv.start_time
        if start_time < current_date:
            days_to_finished = cv.days_from_administered_to_finished
            end_time = min(
                current_date,
                cv.end_time + datetime.timedelta(days=days_to_finished),
            )
            delta = end_time - start_time
            for i in range(delta.days + 1):
                date = start_time + datetime.timedelta(days=i)
                dates.add(date)
    return sorted(list(dates))

from_disease_config(disease_config) classmethod

from_config.

Parameters:

Name Type Description Default
disease_config DiseaseConfig
required
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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@classmethod
def from_disease_config(
    cls, disease_config: DiseaseConfig
):
    """from_config.

    Args:
        disease_config (DiseaseConfig): 

    """
    vaccines = Vaccines.from_config(disease_config=disease_config)

    config = disease_config.vaccination_manager.get_vaccination_campaigns()
    vaccination_campaigns = []
    for key, params_dict in config.items():
        vaccine_type = params_dict["vaccine_type"]

        params_dict["vaccine"] = vaccines.get_by_name(vaccine_type)

        campaign = VaccinationCampaign(
            **{k: v for k, v in params_dict.items() if k != "vaccine_type"}
        )
        vaccination_campaigns.append(campaign)

    return cls(vaccination_campaigns=vaccination_campaigns)

get_active(date)

get_active.

Parameters:

Name Type Description Default
date datetime

date

 required

Returns:

Type Description
List[VaccinationCampaign]

List[VaccinationCampaign]:
Source code in june/epidemiology/vaccines/vaccination_campaign.py 
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def get_active(self, date: datetime) -> List[VaccinationCampaign]:
    """get_active.

    Args:
        date (datetime): date

    Returns:
        List[VaccinationCampaign]: 

    """
    return [vc for vc in self.vaccination_campaigns if vc.is_active(date)]