stan model cleanup

Author: mitzimorris

knitr/car-iar-poisson/bym2.stan

@@ -34,14 +34,14 @@ model {
 
   // This is the prior for phi! (up to proportionality)
   target += -0.5 * dot_self(phi[node1] - phi[node2]);
+  // soft sum-to-zero constraint on phi
+  sum(phi) ~ normal(0, 0.001 * N); // equivalent to mean(phi) ~ normal(0,0.001)
 
   beta0 ~ normal(0.0, 1.0);
   betas ~ normal(0.0, 1.0);
   theta ~ normal(0.0, 1.0);
   sigma ~ normal(0, 1.0);
   rho ~ beta(0.5, 0.5);
-  // soft sum-to-zero constraint on phi)
-  sum(phi) ~ normal(0, 0.001 * N); // equivalent to mean(phi) ~ normal(0,0.001)
 }
 generated quantities {
   real logit_rho = log(rho / (1.0 - rho));

knitr/car-iar-poisson/simple_iar.stan

@@ -6,7 +6,6 @@ data {
 }
 parameters {
   vector[N] phi;
-  real sigma;
 }
 model {
   target += -0.5 * dot_self(phi[node1] - phi[node2]);