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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.
##### Defining variable names to appear in the database
# Must be listed in the same order of variables they are returned by the model
vnames = ['Exposed','Infectious','Susceptible']
def Model(inits,simstep, totpop,theta=0, npass=0,bi={},bp={},values=()):
"""
This function implements the SIR model
- inits = (E,I,S)
- theta = infectious individuals from neighbor sites
"""
##### Get state variables' current values
if simstep == 1: #get initial values
E,I,S = (bi['e'], bi['i'], bi['s'])
else: # get last value
E,I,S = inits
##### Defining N, the total population
N = totpop
##### Getting values for the model parameters
beta,alpha,e,r,delta,B,w,p = (bp['beta'],bp['alpha'],bp['e'],bp['r'],bp['delta'],bp['b'],bp['w'],bp['p'])
##### Defining a Vacination event (optional)
if bp['vaccineNow']:
S -= bp['vaccov']*S
##### Modeling the number of new cases (incidence function)
Lpos = beta*S*((I+theta)/(N+npass))**alpha #Number of new cases
##### Epidemiological model (SIR)
Ipos = (1-r)*I + Lpos
Spos = S + B - Lpos
Rpos = N-(Spos+Ipos)
# Number of infectious individuals commuting.
migInf = Ipos
return [0,Ipos,Spos], Lpos, migInf
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