2024-08-07 update : adding matrix normalization func. and using AR1 in spatial func.

inst/stan/functions/construct_aux_rt.stan

@@ -15,19 +15,13 @@ vector construct_aux_rt(vector log_state_rt,
 
   // presets
   int n_time = dims(state_deviation_noise_vec)[1];
-  vector[n_time] log_aux_site_rt;
-  real state_deviation_t_i = 0;
-  // To explain state_deviation_t_i = 0 initialization,
-  // we need a state_deviation_t_i value for t_1 = 1, so we will
-  // initialize the process with index 1 of spatial
-  // deviation noise matrix w/out spatial_deviation ar coeff, so we set
-  // state_deviation_t_i to 0 initially.
-
-  for (t_i in 1:n_time) {
-    state_deviation_t_i = state_deviation_ar_coeff * state_deviation_t_i +
-        state_deviation_noise_vec[t_i];
-    log_aux_site_rt[t_i] = log_state_rt[t_i] + state_deviation_t_i;
-  }
+  vector[n_time] log_aux_site_rt = ar1(
+    log_state_rt,
+    state_deviation_ar_coeff,
+    1,
+    state_deviation_noise_vec,
+    0
+  );
 
   return log_aux_site_rt;
 }

inst/stan/functions/matrix_normalization.stan

@@ -0,0 +1,11 @@
+/**
+  * Normalizes a matrix using its determinant to the power of 1 / n.
+  * @param matrx A matrix, usually the correlation matrix need to normalize
+  * @return A matrix that has been normalized.
+  *
+  */
+matrix matrix_normalization(matrix matrx) {
+  int n = cols(matrx);
+  matrix[n,n] norm_matrx = matrx / pow(determinant(matrx), 1.0 / n);
+  return norm_matrx;
+}

inst/stan/functions/spatial_functions.stan

@@ -2,6 +2,7 @@
   * File to call all desired spatial functions for use with expose_functions()
   */
 functions{
+  #include ar1.stan
   #include exponential_decay_corr_func.stan
   #include independence_corr_func.stan
   #include construct_spatial_rt.stan
@@ -10,4 +11,5 @@ functions{
   #include construct_aux_rt.stan
   #include state_deviation_noise_vec_aux_rng.stan
   #include aux_site_process_rng.stan
+  #include matrix_normalization.stan
 }