june.infection.transmission_xnexp

class june.infection.transmission_xnexp.TransmissionXNExp(max_probability: float = 1.0, time_first_infectious: float = 2.6, norm_time: float = 1.0, n: float = 1.0, alpha: float = 5.0, max_symptoms: str = None, asymptomatic_infectious_factor: float = None, mild_infectious_factor: float = None)

Class that defines the time profile of the infectiousness to be of the form x^n exp(-x/alpha)

max_probability:

value of the infectiousness at its peak. Used to control the number of super spreaders

time_first_infectious:

time at which the person becomes infectious

norm_time:

controls the definition of x, x = (time_from_infection - time-first_infectious)/norm_time

n:

exponent of x in the x^n exp(-x/alpha) function

alpha:

denominator in exponential

max_symptoms:

maximum symptoms that the person will ever have, used to lower the infectiousness of asymptomatic and mild cases

asymptomatic_infectious_factor:

multiplier that lowers the infectiousness of asymptomatic cases

mild_infectious_factor:

multiplier that lowers the infectiousness of mild cases

__init__(max_probability: float = 1.0, time_first_infectious: float = 2.6, norm_time: float = 1.0, n: float = 1.0, alpha: float = 5.0, max_symptoms: str = None, asymptomatic_infectious_factor: float = None, mild_infectious_factor: float = None)

Class that defines the time profile of the infectiousness to be of the form x^n exp(-x/alpha)

max_probability:

value of the infectiousness at its peak. Used to control the number of super spreaders

time_first_infectious:

time at which the person becomes infectious

norm_time:

controls the definition of x, x = (time_from_infection - time-first_infectious)/norm_time

n:

exponent of x in the x^n exp(-x/alpha) function

alpha:

denominator in exponential

max_symptoms:

maximum symptoms that the person will ever have, used to lower the infectiousness of asymptomatic and mild cases

asymptomatic_infectious_factor:

multiplier that lowers the infectiousness of asymptomatic cases

mild_infectious_factor:

multiplier that lowers the infectiousness of mild cases

_modify_infectiousness_for_symptoms(max_symptoms: str, asymptomatic_infectious_factor, mild_infectious_factor)

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

max_symptoms:

maximum symptom severity the person will ever have

classmethod from_file(time_first_infectious: float, n: float, alpha: float, max_symptoms: Optional[june.infection.symptom_tag.SymptomTag] = None, config_path: str = PosixPath('/home/sadie/JUNE/configs/defaults/transmission/XNExp.yaml'))june.infection.transmission_xnexp.TransmissionXNExp

Generates transmission class from config file

time_first_infectious:

time at which the person becomes infectious

n:

exponent of x in the x^n exp(-x/alpha) function

alpha:

denominator in exponential

max_symptoms:

maximum symptoms that the person will ever have, used to lower the infectiousness of asymptomatic and mild cases

class instance

classmethod from_file_linked_symptoms(time_to_symptoms_onset: float, max_symptoms: Optional[june.infection.symptom_tag.SymptomTag] = None, config_path: str = PosixPath('/home/sadie/JUNE/configs/defaults/transmission/XNExp.yaml'))june.infection.transmission_xnexp.TransmissionXNExp

Generates transmission class from config file

time_first_infectious:

time at which the person becomes infectious

n:

exponent of x in the x^n exp(-x/alpha) function

alpha:

denominator in exponential

max_symptoms:

maximum symptoms that the person will ever have, used to lower the infectiousness of asymptomatic and mild cases

class 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 (in days).

alpha
n
norm
norm_time
probability
time_first_infectious
june.infection.transmission_xnexp.update_probability(time_from_infection: float, time_first_infectious: float, norm: float, norm_time: float, alpha: float, n: float) → float

Determines how the infectiousness profile is updated over time

time_from_infection:

time from infection

time_first_infectious:

time from infection at which the person becomes infectious

norm:

multiplier to the infectiousness profile

norm_time:

controls the definition of tau

alpha:

demominator in exponential for xnexp function

n:

exponent of x in xnexp

Value of infectiousness at time

june.infection.transmission_xnexp.xnexp(x: float, n: float, alpha: float) → float

Implementation of x^n exp(-x/alpha)

x:

x variable

n:

exponent of x

alpha:

denominator in exponential

evaluation fo xnexp function