2024-08-08 update : prep testfile.

scratch/testfile.R

@@ -1,48 +1 @@
-# Expose the stan functions into the global environment
-model <- cmdstanr::cmdstan_model(
-  stan_file = file.path("inst", "stan", "wwinference.stan"),
-  compile = TRUE,
-  compile_standalone = TRUE,
-  force_recompile = TRUE
-)
-model$expose_functions(global = TRUE)
-model <- cmdstanr::cmdstan_model(
-  stan_file = file.path("inst", "stan", "functions", "spatial_functions.stan"),
-  compile = TRUE,
-  compile_standalone = TRUE,
-  force_recompile = TRUE
-)
-model$expose_functions(global = TRUE)
-
-n_time <- 150
-state_dev_ar_coeff <- 0.8
-log_state_rt <- rnorm(
-  n = n_time,
-  mean = 1.2,
-  sd = 0.05
-)
-state_dev_noise_vec <- state_deviation_noise_vec_aux_rng(
-  scaling_factor = 1.1,
-  sigma_eps = sqrt(0.2),
-  n_time = n_time
-)
-stan_log_aux_site_rt <- construct_aux_rt(
-  log_state_rt = log_state_rt,
-  state_deviation_ar_coeff = state_dev_ar_coeff,
-  state_deviation_noise_vec = state_dev_noise_vec
-)
-
-
-state_deviation_t_i <- 0
-log_aux_site_rt <- matrix(
-  data = 0,
-  ncol = n_time,
-  nrow = 1
-)
-for (t_i in 1:n_time) {
-  state_deviation_t_i <- state_dev_ar_coeff * state_deviation_t_i +
-    state_dev_noise_vec[t_i]
-  log_aux_site_rt[t_i] <- log_state_rt[t_i] + state_deviation_t_i
-}
-
-stan_log_aux_site_rt == log_aux_site_rt
+# prep for branch.