sir_rinit <- Csnippet("
  double pop[5];
  const double *s = &s1;
  
  double *S = &S1;
  double *E = &E1;
  double *I = &I1;
  double *R = &R1;
  double *V = &V1;
  double *inci = &inci1;
  ...
  for (i = 0; i < 5; i++) {
        S[i] = s[i]*pop[i];
        E[i] = I[i]*5;
        V[i] = 0;
        inci[i] = 0;
    }
 ...
   ")

dmeas <- Csnippet("
   const double *inci = &inci1;
   const double *S = &S1;
   const double *E = &E1;
   const double *I = &I1;
   const double *R = &R1;
   const double *V = &V1;
   
   double model_observed,model_population,rate ;
                  
   for (int i = 0; i < 5; i++) {
      model_observed += inci[i];
    }
   
   for (int i = 0; i < 5; i++) {
    model_population += S[i] + E[i] + I[i] +V[i] + R[i];
  }
     
   rate = model_observed*10000/model_population;
  
   lik = dpois(nearbyint(cases),rate,give_log);
  
")

rmeas <- Csnippet("
   const double *inci = &inci1;
   const double *S = &S1;
   const double *E = &E1;
   const double *I = &I1;
   const double *R = &R1;
   const  double *V = &V1;
   
   double model_observed,model_population,rate ;
                  
   for (int i = 0; i < 5; i++) {
      model_observed += inci[i];
    }
   
   for (int i = 0; i < 5; i++) {
    model_population += S[i] + E[i] + I[i] +V[i] + R[i];
  }
     
   cases = model_observed*10000/model_population;
  
")

mea_Model |>
  pfilter(Np=100) -> pfrick 

logLik(pfrick)
- Inf

Observed_data |> pomp(
  t0=1, time=seq(1,3121),
  dmeasure = dmeas,
  rmeasure = rmeas,
  covar= covariate_table(cov_data,times="time"),
  rinit=Csnippet(sir_rinit),
  rprocess=discrete_time(Csnippet(rproc)),
  params=c(b1=0.4,b2=0.2,b3=0.1,b4=0.25,b5=0.12,s1=0.9,s2=0.9,s3=0.5,s4=0.5,s5=0.5,
           start= 20000) ,
  format="data.frame",
  statenames=c(sprintf("S%d",1:5),sprintf("E%d",1:5),sprintf("I%d",1:5),
               sprintf("R%d",1:5),sprintf("V%d",1:5),sprintf("inci%d",1:5)),
  paramnames=c(sprintf("b%d",1:5),sprintf("s%d",1:5),"start")
) -> mea_Model

sum(dpois(round(data$cases),Observed_data$cases,log = TRUE))
-5844.778