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# This is a custom model to used in place of Epigrass' built-in models. Custom
# models must always be on a file named CustomModel.py and contain at least
# a function named Model. Both the File name and the function Names are case-sensitive,
# so be careful. Please refer to the manual for intructions on how to write your
# own custom models.
def Model(self, vars, par, theta=0, npass=0):
"""
Calculates the model SIR, and return its values.
- inits = (E,I,S)
- par = (Beta, alpha, E,r,delta,B, w, p) see docs.
- theta = infectious individuals from neighbor sites
"""
#Defining variable names
self.parentSite.vnames = ('Exposed', 'Infeccious', 'Susceptible')
#Initializing
if self.parentSite.parentGraph.simstep == 1: #get initial values
E, I, S = (self.bi['e'], self.bi['i'], self.bi['s'])
else:
E, I, S = vars
N = self.parentSite.totpop
beta, alpha, e, r, delta, B, w, p = par
#Vacination event (optional)
if self.parentSite.vaccineNow:
S -= self.parentSite.vaccov * S
Lpos = beta * S * ((I + theta) / (N + npass)) ** alpha #Number of new cases
self.parentSite.totalcases += Lpos #update number of cases
# Model
Ipos = (1 - r) * I + Lpos
Spos = S + B - Lpos
Rpos = N - (Spos + Ipos)
# Updating stats
self.parentSite.incidence.append(Lpos)
# Raises site infected flag and adds parent site to the epidemic history list.
if not self.parentSite.infected:
if Lpos > 0:
#if not self.parentSite.infected:
self.parentSite.infected = self.parentSite.parentGraph.simstep
self.parentSite.parentGraph.epipath.append(
(self.parentSite.parentGraph.simstep, self.parentSite, self.parentSite.infector))
#Migrating infecctious
self.parentSite.migInf.append(Ipos)
return [0, Ipos, Spos]
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