foo.stan

data {
  int jj_n;
  int jj_idx[jj_n];
  int jj_groups[jj_n];
  ...
}
parameters {
  vector[3] beta;
  ...
}
model {
  beta ~ normal(0, 10);
  for (i in 1:jj_n) {
    y[jj_idx[i]] ~ normal(beta[jj_groups[i]] * x[jj_idx[i]], sigma);
  }
  ...
}

gistfile1.r

jj<-c(1,2,3,NA,NA,NA,1,2,3,NA,NA,NA,1,2,3)
jj_n <- sum(!is.na(jj))
jj_idx <- which(!is.na(jj))
jj_groups <- jj[!is.na(jj)]

gistfile2.txt

data {
  int n_groups; 
  int beta2_const_n;
  int beta2_const_idx[beta2_obs_n];
  int beta2_param_n;
  int beta2_param_idx[beta2_obs_n];
}
parameters {
  vector[n_groups] beta1;
  vector[beta2_n_obs] beta2_param;
  ...
}
transformed parameters {
  vector[N] p;
  vector[n_groups] beta2;
  
  for (i in 1:beta2_const_n) {
    beta2[beta2_const_idx[i]] <- 0.0;
  }
  for (i in 1:beta2_param_n) {
    beta2[beta2_param_idx[i]] <- beta2_param[i];
  }

  for (i in 1:N) {
    p[i] <- beta1[kk[n]] * x1[gg[n]]] + beta2[kk[n]] * x2[gg[n]];
  }
  ...
}
...