june.infection.infection

class june.infection.infection.Infection(transmission: Transmission, symptoms: Symptoms, start_time: float = - 1)

The infection class combines the transmission (infectiousness profile) of the infected person, and their symptoms trajectory. We also keep track of how many people someone has infected, which is useful to compute R0. The infection probability is updated at every time step, according to an infectivity profile.

transmission:

instance of the class that controls the infectiousness profile

symptoms:

instance of the class that controls the symptoms’ evolution

start_time:

time at which the person is infected

__init__(transmission: Transmission, symptoms: Symptoms, start_time: float = - 1)
transmission:

instance of the class that controls the infectiousness profile

symptoms:

instance of the class that controls the symptoms’ evolution

start_time:

time at which the person is infected

length_of_infection(time)
update_health_status(time, delta_time)

Updates the infection probability and symptoms of the person’s infection given the simulation time. Returns the new status of the person.

time: float

total time since the beginning of the simulation (in days)

delta_time: float

duration of the time step.

status: str

new status of the person. one of ['recovered', 'dead', 'infected']

update_symptoms_and_transmission(time: float)

Updates the infection’s symptoms and transmission probability. Parameters ———- time:

time elapsed (in days) from time of infection

property dead
property infected_at_home
property infection_probability
property max_tag
number_of_infected
property should_be_in_hospital
start_time
symptoms
property tag
property time_of_infection
property time_of_symptoms_onset
transmission