vaccinations

vaccinations.py

module

Vaccination module, initialize and store all vaccination objects.

Attibutes

vaccinations (list): List of vacination objects

__init__(self, vacc_params, comm) special

Initializes vaccination module.

Parameters:

Name	Type	Description	Default
vacc_params	list	List of parsed vaccinations parameters.	required
comm	comorbuss.community	Community object	required

Source code in

def __init__(self, vacc_params, comm):
    """Initializes vaccination module.

    Args:
        vacc_params (list): List of parsed vaccinations parameters.
        comm (comorbuss.community): Community object
    """
    super(module, self).__init__(vacc_params, comm, name=__name__)

    self.pop.add_attribute("particles_coefficients", {}, store=False)

    # Initialize vaccinations
    self.vaccinations = []
    for i, vacc_param in enumerate(vacc_params):
        self.init_vacc(vacc_param, i + 1)

    for vaccination in self.vaccinations:
        setattr(self, vaccination.name, vaccination)

    # Check if module has valid vaccination configuration.
    self.loaded = False
    self.check_loaded()
    self.list = self.vaccinations

init_vacc(self, vacc_param, i)

Initialize vaccination policies.

Parameters:

Name	Type	Description	Default
vacc_param	dict	Parameters for the module.	required
i	community	Vaccination id.	required

Returns:

Type	Description
List	List of the vaccination objects.

Source code in

def init_vacc(self, vacc_param, i):
    """Initialize vaccination policies.

    Args:
        vacc_param (dict): Parameters for the module.
        i (community): Vaccination id.

    Returns:
        List: List of the vaccination objects.
    """
    vacc_param["effectiveness"], eff_ok = effectiveness_parse(
        vacc_param["effectiveness"], vacc_param["name"], self.comm
    )
    vacc_param["filter"], fok = filter_parse(
        vacc_param["filter"],
        self.comm,
        allowed_filters=["tracing", "service", "module", "workers"],
    )
    vacc_param["id"] = i
    if eff_ok and fok:
        vacc = vaccination(vacc_param, self.comm, self)
        self.vaccinations.append(vacc)
        return vacc, eff_ok and fok
    else:
        self.comm.event_log(
            "Can't activate {} vaccination protocol, there is an invalid filter or effectiveness.".format(
                vacc_param["name"]
            ),
            S.MSG_WRNG,
        )

log_results(self)

Aggregate vaccinations related results at the end of the simulation.

Source code in

def log_results(self):
    """Aggregate vaccinations related results at the end of the simulation."""
    nvac = np.sum(self.pop.time_vaccinated >= 0)
    self.event_log("Total number vaccinated: {:}".format(nvac), S.MSG_RSLT)
    calculate_efficacy = nvac < self.pop.Nparticles
    if calculate_efficacy:
        self.comm.add_to_store("efficacy", "comm.vaccinations.efficacy", False)
        self.efficacy = []
    else:
        self.event_log(
            "Can't calculate efficacy of vaccinations, there is no unvaccinated particles.",
            S.MSG_RSLT,
        )
    for vacc in self.vaccinations:
        nvac = np.sum(self.pop.immunity_state == vacc.id)
        self.event_log('"{}" vaccination: {:}'.format(vacc.name, nvac), S.MSG_RSLT)
        if calculate_efficacy:
            efficacy, limits = vacc.calculate_efficacy()
            self.efficacy.append((efficacy, limits))
            self.event_log(
                '"{}" efficacy: {:.1f}%'.format(vacc.name, 100 * efficacy),
                S.MSG_RSLT,
            )

run(self, at_start=False)

Runs the vaccination campaigns set on self.vaccinations.

Source code in

def run(self, at_start=False):
    """Runs the vaccination campaigns set on self.vaccinations."""
    for vacc in self.vaccinations:
        vacc(at_start=at_start)

    self.update_disease_coeficients()

update_disease_coeficients(self)

Update coefficients for each affected disease attribute.

Source code in

def update_disease_coeficients(self):
    """Update coefficients for each affected disease attribute."""
    for attr in self.pop.particles_coefficients:
        self.pop.disease.set_coefficient(
            attr,
            self.pop.particles_coefficients[attr][self.clk.today, :],
            "vaccinations",
        )

triage

Parses vaccinations parameters.

Parameters:

Name	Type	Description	Default
vaccinations	list	List of vaccinations parameters.	required
sim_parameters	dict	Parsed simulation parameters.	required
clk	clock	Clock object.	required
event_log	function	Event_log function.	required

Returns:

Type	Description
list	List of parsed vaccinations parameters.

Source code in

def triage(vaccinations, sim_parameters, clk, event_log):
    """Parses vaccinations parameters.

    Args:
        vaccinations (list):  List of vaccinations parameters.
        sim_parameters (dict): Parsed simulation parameters.
        clk (clock): Clock object.
        event_log (function): Event_log function.

    Returns:
        list: List of parsed vaccinations parameters.
    """
    from ...triage import parse_from_defaults, merge_list_of_dicts

    vaccinations = merge_list_of_dicts(vaccinations, "vaccinations", event_log)

    for vacc in vaccinations:
        parse_from_defaults(vacc, "vaccination", DEFAULTS, DEFAULTS_TYPES, event_log)

        vacc["doses_per_day"] = int(
            np.max([vacc["doses_per_day"] / sim_parameters["norm_N"], 1])
        )

    return vaccinations

ADULTS

Apply the default number of doses on adults citizens (age groups 5 to 21, 20+ years old).

CHILDRENS

Apply the default number of doses on child citizens (age groups 0 to 4, 0-19 years old).

DIAG_NO

Apply the default number of doses on citizens that where not diagnosed.

HOSPITALS_WORKERS

Apply the default number of doses on hospitals workers.

MAKETS_WORKERS

Apply the default number of doses on markets workers.

SENIORS

Apply the default number of doses on senior citizens (age groups 12 to 21, 60+ years old).

VACC_NYET

Marker for particles not vaccinated