june.infection.transmission.TransmissionGamma

class june.infection.transmission.TransmissionGamma(max_infectiousness: float = 1.0, shape: float = 2.0, rate: float = 3.0, shift: float = - 2.0, max_symptoms: Optional[str] = None, asymptomatic_infectious_factor: Optional[float] = None, mild_infectious_factor: Optional[float] = None)
Module to simulate the infectiousness profiles found in :
max_infectiousness:

value of the infectiousness at its peak

shape:

shape parameter of the gamma distribution (a for scipy stats)

rate:

rate parameter of the gamma distribution (1/rate = scale for scipy stats)

shift:

location parameter of the gamma distribution

max_symptoms:

maximum symptoms the individual will develop, used to reduce the infectiousness of asymptomatic and mild individuals if wanted

asymptomatic_infectious_factor:

factor to reduce the infectiousness of asymptomatic individuals

mild_infectious_factor:

factor to reduce the infectiousness of mild individuals

__init__(max_infectiousness: float = 1.0, shape: float = 2.0, rate: float = 3.0, shift: float = - 2.0, max_symptoms: Optional[str] = None, asymptomatic_infectious_factor: Optional[float] = None, mild_infectious_factor: Optional[float] = None)
max_infectiousness:

value of the infectiousness at its peak

shape:

shape parameter of the gamma distribution (a for scipy stats)

rate:

rate parameter of the gamma distribution (1/rate = scale for scipy stats)

shift:

location parameter of the gamma distribution

max_symptoms:

maximum symptoms the individual will develop, used to reduce the infectiousness of asymptomatic and mild individuals if wanted

asymptomatic_infectious_factor:

factor to reduce the infectiousness of asymptomatic individuals

mild_infectious_factor:

factor to reduce the infectiousness of mild individuals

_modify_infectiousness_for_symptoms(max_symptoms: str, asymptomatic_infectious_factor=None, mild_infectious_factor=None)

Lowers the infectiousness of asymptomatic and mild cases, by modifying the norm of the distribution

max_symptoms:

maximum symptom severity the person will ever have

asymptomatic_infectious_factor:

factor to reduce the infectiousness of asymptomatic individuals

mild_infectious_factor:

factor to reduce the infectiousness of mild individuals

classmethod from_file(max_symptoms: str = None, config_path: str = PosixPath('/home/sadie/JUNE/configs/defaults/transmission/nature.yaml'))june.infection.transmission.TransmissionGamma

Generate transmission class reading parameters from config file

max_symptoms:

maximum symptoms the individual will develop, used to reduce the infectiousness of asymptomatic and mild individuals if wanted

config_path:

path to config parameters

TransmissionGamma instance

classmethod from_file_linked_symptoms(time_to_symptoms_onset: float, max_symptoms: str = None, config_path: str = PosixPath('/home/sadie/JUNE/configs/defaults/transmission/nature.yaml'))june.infection.transmission.TransmissionGamma

Generate transmission class reading parameters from config file, linked to the time of symptoms onset

time_to_symptoms_onset:

time (from infection) at which the person becomes symptomatic

max_symptoms:

maximum symptoms the individual will develop, used to reduce the infectiousness of asymptomatic and mild individuals if wanted

config_path:

path to config parameters

TransmissionGamma instance

classmethod object_from_config()

Loads the default Transmission class from the general.ini config file and returns the class as object (not as an instance). This is used to set up the epidemiology model in world.py via configs if an input is not provided.

update_infection_probability(time_from_infection: float)

Performs a probability update given time from infection

time_from_infection:

time elapsed since person became infected

norm
probability
scale
shape
shift
property time_at_maximum_infectivity

Computes the time at which the individual is maximally infectious (in this case for a gamma distribution

t_max:

time at maximal infectiousness