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

R/generate_simulated_data.R

@@ -64,6 +64,11 @@
 #' scaling factor.
 #' @param init_bool Boolean for making initial value of AUX site AR(1)
 #' process stationary( 1 or 0 ).
+#' @param init_stat Boolean. Should the initial value of the AR(1) be drawn
+#' from the process's stationary distribution (`TRUE`) or from the process's
+#' conditional error distribution (`FALSE`)? Note that the process only has
+#' a defined stationary distribution if `state_deviation_ar_coeff` < 1.
+#' Default `FALSE`.
 #'
 #' @return a list containing three dataframes. hosp_data is a dataframe
 #' containing the number of daily hospital admissions by day for a theoretical
@@ -104,7 +109,7 @@
 #'   sigma_eps = sqrt(0.02),
 #'   scaling_factor = 0.01,
 #'   aux_site_bool = TRUE,
-#'   init_bool = TRUE
+#'   init_stat = TRUE
 #' )
 #' hosp_data <- sim_data$hosp_data
 #' ww_data <- sim_data$ww_data
@@ -165,7 +170,7 @@ generate_simulated_data <- function(r_in_weeks = # nolint
                                     sigma_eps = sqrt(0.02),
                                     scaling_factor = 0.01,
                                     aux_site_bool = TRUE,
-                                    init_bool = TRUE) {
+                                    init_stat = TRUE) {
   # Some quick checks to make sure the inputs work as expected
   stopifnot(
     "weekly R(t) passed in isn't long enough" =
@@ -370,17 +375,17 @@ generate_simulated_data <- function(r_in_weeks = # nolint
   )
   # Auxiliary Site
   if (aux_site_bool) {
-    state_deviation_noise_vec <- state_deviation_noise_vec_aux_rng(
-      1,
-      1,
-      n_weeks
+    state_deviation_noise_vec <- rnorm(
+      n = n_time,
+      mean = 0,
+      sd = 0
     )
     log_r_site_aux <- construct_aux_rt(log_r_state_week,
       state_deviation_ar_coeff = phi_rt,
       scaling_factor,
       sigma_eps,
       state_deviation_noise_vec,
-      init_bool
+      init_stat
     )
     log_r_site <- rbind(
       log_r_site,

inst/stan/functions/aux_site_process_rng.stan

@@ -6,29 +6,28 @@
   * of spatial epsilon.
   * @param state_deviation_ar_coeff Coefficient for AR(1) temporal correlation on
   * state deviations for aux site.
-  * @param init_bool Boolean for making initial value stationary( 1 or 0 ).
+  * @param init_stat Boolean. Should the initial value of the AR(1) be drawn
+  * from the process's.
   * @return A vector for unadjusted Rt for aux site where columns are time points.
   */
 vector aux_site_process_rng(vector log_state_rt,
                               real scaling_factor,
                               real sigma_eps,
                               real state_deviation_ar_coeff,
-                              int init_bool) {
+                              int init_stat) {
 
 
   //Presets
   int n_time = size(log_state_rt);
 
   // creates vector of standard normal for contruct aux rt.
-  vector[n_time] z = state_deviation_noise_vec_aux_rng(1,
-                                                       1,
-                                                       n_time);
+  vector[n_time] z = standard_normal_rng();
   vector[n_time] log_aux_site_rt = construct_aux_rt(log_state_rt,
                                                     state_deviation_ar_coeff,
                                                     scaling_factor,
                                                     sigma_eps,
                                                     z,
-                                                    init_bool);
+                                                    init_stat);
 
   return log_aux_site_rt;
 }