aegis_sim.submodels.infection
Infection manager
Infection status: 0 .. susceptible 1 .. infected -1 .. dead
1"""Infection manager 2 3Infection status: 4 0 .. susceptible 5 1 .. infected 6 -1 .. dead 7""" 8 9import math 10import numpy as np 11from aegis_sim import variables 12 13 14class Infection: 15 """ 16 17 GUI 18 Infection is an optional source of mortality. 19 [[FATALITY_RATE]] specifies how deadly the infection is; thus if set to 0, no deaths from infection will occur. 20 The infection modeling is inspired by the SIR (susceptible-infectious-removed) model. 21 22 Individuals cannot gain immunity, thus can get reinfected many times. 23 The probability to die from an infection is constant as long as the individual is infected; there is no incubation period nor disease progression. 24 The same is true for recovering from the disease, which is equal to [[RECOVERY_RATE]]. 25 26 Both of these are independent of age and genetics. 27 28 The infectious agent can be transmitted from an individual to an individual but can also be contracted from the environment (and can therefore not be fully eradicated). 29 The probability to acquire the infection from the environment is equal to [[BACKGROUND_INFECTIVITY]], and from other infected individuals it grows with [[TRANSMISSIBILITY]] 30 but also (logistically) with the proportion of the infected population. 31 """ 32 33 def __init__(self, BACKGROUND_INFECTIVITY, TRANSMISSIBILITY, RECOVERY_RATE, FATALITY_RATE): 34 self.BACKGROUND_INFECTIVITY = BACKGROUND_INFECTIVITY 35 self.TRANSMISSIBILITY = TRANSMISSIBILITY 36 self.RECOVERY_RATE = RECOVERY_RATE 37 self.FATALITY_RATE = FATALITY_RATE 38 39 def get_infection_probability(self, infection_density): 40 return self.BACKGROUND_INFECTIVITY - 0.5 + 1 / (1 + math.exp(-self.TRANSMISSIBILITY * infection_density)) 41 42 def __call__(self, population): 43 """ 44 First try infecting susceptible. 45 """ 46 47 # TODO Do not change population here, only return new status 48 49 if len(population) == 0: 50 return 51 52 probs = variables.rng.random(len(population)) 53 54 # current status 55 infected = population.infection == 1 56 susceptible = population.infection == 0 57 58 # compute infection probability 59 infection_density = infected.sum() / len(population) 60 infection_probability = self.get_infection_probability(infection_density=infection_density) 61 62 # recoveries from old infections 63 population.infection[infected & (probs < self.RECOVERY_RATE)] = 0 64 65 # fatalities 66 # overrides recoveries 67 population.infection[infected & (probs < self.FATALITY_RATE)] = -1 68 69 # new infections 70 population.infection[susceptible & (probs < infection_probability)] = 1
class
Infection:
15class Infection: 16 """ 17 18 GUI 19 Infection is an optional source of mortality. 20 [[FATALITY_RATE]] specifies how deadly the infection is; thus if set to 0, no deaths from infection will occur. 21 The infection modeling is inspired by the SIR (susceptible-infectious-removed) model. 22 23 Individuals cannot gain immunity, thus can get reinfected many times. 24 The probability to die from an infection is constant as long as the individual is infected; there is no incubation period nor disease progression. 25 The same is true for recovering from the disease, which is equal to [[RECOVERY_RATE]]. 26 27 Both of these are independent of age and genetics. 28 29 The infectious agent can be transmitted from an individual to an individual but can also be contracted from the environment (and can therefore not be fully eradicated). 30 The probability to acquire the infection from the environment is equal to [[BACKGROUND_INFECTIVITY]], and from other infected individuals it grows with [[TRANSMISSIBILITY]] 31 but also (logistically) with the proportion of the infected population. 32 """ 33 34 def __init__(self, BACKGROUND_INFECTIVITY, TRANSMISSIBILITY, RECOVERY_RATE, FATALITY_RATE): 35 self.BACKGROUND_INFECTIVITY = BACKGROUND_INFECTIVITY 36 self.TRANSMISSIBILITY = TRANSMISSIBILITY 37 self.RECOVERY_RATE = RECOVERY_RATE 38 self.FATALITY_RATE = FATALITY_RATE 39 40 def get_infection_probability(self, infection_density): 41 return self.BACKGROUND_INFECTIVITY - 0.5 + 1 / (1 + math.exp(-self.TRANSMISSIBILITY * infection_density)) 42 43 def __call__(self, population): 44 """ 45 First try infecting susceptible. 46 """ 47 48 # TODO Do not change population here, only return new status 49 50 if len(population) == 0: 51 return 52 53 probs = variables.rng.random(len(population)) 54 55 # current status 56 infected = population.infection == 1 57 susceptible = population.infection == 0 58 59 # compute infection probability 60 infection_density = infected.sum() / len(population) 61 infection_probability = self.get_infection_probability(infection_density=infection_density) 62 63 # recoveries from old infections 64 population.infection[infected & (probs < self.RECOVERY_RATE)] = 0 65 66 # fatalities 67 # overrides recoveries 68 population.infection[infected & (probs < self.FATALITY_RATE)] = -1 69 70 # new infections 71 population.infection[susceptible & (probs < infection_probability)] = 1
GUI Infection is an optional source of mortality. [[FATALITY_RATE]] specifies how deadly the infection is; thus if set to 0, no deaths from infection will occur. The infection modeling is inspired by the SIR (susceptible-infectious-removed) model.
Individuals cannot gain immunity, thus can get reinfected many times. The probability to die from an infection is constant as long as the individual is infected; there is no incubation period nor disease progression. The same is true for recovering from the disease, which is equal to [[RECOVERY_RATE]].
Both of these are independent of age and genetics.
The infectious agent can be transmitted from an individual to an individual but can also be contracted from the environment (and can therefore not be fully eradicated). The probability to acquire the infection from the environment is equal to [[BACKGROUND_INFECTIVITY]], and from other infected individuals it grows with [[TRANSMISSIBILITY]] but also (logistically) with the proportion of the infected population.