SEIR_epidemic_model_code

model{
##JAGS code for modelling Ebola using Lekone approach
# This is a joint model.

for(id in 1:14){
S[1,id]<-popsize[id]-round(E[1,id])-round(I[1,id])

#E[1,id]<-100

E[1,id]~dunif(0,1000) 
# likewise santermans


#I[1,id]<-30
I[1,id]~dunif(0,20)
for(t in 2:T){
   B[t-1,id]~dbin(P[t-1,id],S[t-1,id])
   P[t-1,id]<-1-exp(-beta[t-1,id]*round(I[t-1,id])/popsize[id])
   
   beta[t-1,id]<-betast[1,id]*(1-step(t-(T/12)))+betast[2,id]*step(t-(T/12))*(1-step(t-(2*T/12)))+ betast[3,id]*step(t-(2*T/12))*(1-step(t-(3*T/12)))+betast[4,id]*step(t-(3*T/12))*(1-step(t-(4*T/12)))+betast[5,id]*step(t-(4*T/12))*(1-step(t-(5*T/12)))+betast[6,id]*step(t-(5*T/12))*(1-step(t-(6*T/12)))+betast[7,id]*step(t-(6*T/12))*(1-step(t-(7*T/12)))+betast[8,id]*step(t-(7*T/12))*(1-step(t-(8*T/12)))+betast[9,id]*step(t-(8*T/12))*(1-step(t-(9*T/12)))+ betast[10,id]*step(t-(9*T/12))*(1-step(t-(10*T/12))) +betast[11,id]*step(t-(10*T/12))*(1-step(t-(11*T/12)))+ betast[12,id]*step(t-(11*T/12))
    
   C[t-1,id]~dbin(Pc, round(E[t-1,id]))
   D[t-1,id]~dbin(Pr, round(I[t-1,id]))
     
   S[t,id]<-S[t-1,id]-B[t-1,id]
   E[t,id]<-round(E[t-1,id])+B[t-1,id]-C[t-1,id]
   I[t,id]<-round(I[t-1,id])+C[t-1,id]-D[t-1,id]
   #R[id,t]<-R[id,t-1]+D[id,t]

   #Cpred[t-1, id]~dbin(Pc, E[t-1,id])
}
   for (j in 1:12){
        betast[j,id]~dnorm(mean.beta ,tau.beta)
		
	    RN[j,id]<-betast[j,id]/gamma
		#RN[j,id]<-betast[j,id]/gamma
		
}

}


incubation~dnorm(1.29,1/(0.006661227))
infectious~dnorm(1,1/(0.0006491755))
rho<-1/incubation
gamma<-1/infectious
Pc<-1-exp(-rho)
Pr<-1-exp(-gamma)
mean.beta~dnorm(1.4,1/(0.0014161))
tau.beta~dgamma(100,1)

sigma.beta<-1/tau.beta
}