extract function into get_stan_defaults()

StatisticsHealthEconomics · Aug 12, 2024 · cc36f80 · cc36f80
1 parent 9e7d740
commit cc36f80
Showing 1 changed file with 38 additions and 38 deletions.
diff --git a/R/bmcm_stan.R b/R/bmcm_stan.R
@@ -132,42 +132,7 @@ bmcm_stan <- function(input_data,
 
   model_name <- paste0("bmcm_stan_", glue::glue_collapse(distns, sep = "_"))
 
-  # default sampler parameters
-  #TODO: cmdstanr and rstan are slightly different
-  #      harmonize automatically
-  rstan_dots <-
-    modifyList(
-      dots,
-      list(warmup = 100,
-           iter = 500,
-           thin = 1,
-           chains = 1,
-           control = list(adapt_delta = 0.99,
-                          max_treedepth = 100,
-                          stepsize = 0.05),
-           include = TRUE,
-           open_progress = TRUE)
-      # verbose = TRUE)
-    )
-
-  cmdstanr_dots <-
-    modifyList(
-      dots,
-      list(iter_warmup = 100,
-           iter_sampling = 500,
-           save_warmup = FALSE,
-           thin = 1,
-           chains = 1,
-           adapt_delta = 0.99,
-           max_treedepth = 100,
-           step_size = 0.05)
-    )
-
-  if (use_cmdstanr) {
-    dots <- cmdstanr_dots
-  } else {
-    dots <- rstan_dots
-  }
+  mcmc_params <- get_stan_defaults(use_cmdstanr, dots)
 
   ##############
   # fit model
@@ -198,8 +163,8 @@ bmcm_stan <- function(input_data,
   res <- list()
 
   res$output <- perform_sampling(use_cmdstanr, precompiled_model,
-                                 stan_inputs, dots)
-  res$dots <- dots
+                                 stan_inputs, mcmc_params)
+  res$mcmc_params <- mcmc_params
   res$call <- call
   res$distns <- distns
   res$inputs <- stan_inputs
@@ -263,3 +228,38 @@ perform_sampling <- function(use_cmdstanr, precompiled_model,
   output
 }
 
+# default sampler parameters
+#TODO: cmdstanr and rstan are slightly different
+#      harmonize automatically
+get_stan_defaults <- function(use_cmdstanr, dots) {
+  if (use_cmdstanr) {
+    return(
+      modifyList(
+        dots,
+        list(iter_warmup = 100,
+             iter_sampling = 500,
+             save_warmup = FALSE,
+             thin = 1,
+             chains = 1,
+             adapt_delta = 0.99,
+             max_treedepth = 100,
+             step_size = 0.05)
+      ))
+  } else {
+    return(
+      modifyList(
+        dots,
+        list(warmup = 100,
+             iter = 500,
+             thin = 1,
+             chains = 1,
+             control = list(
+               adapt_delta = 0.99,
+               max_treedepth = 100,
+               stepsize = 0.05),
+             include = TRUE,
+             open_progress = TRUE)
+        # verbose = TRUE)
+      ))
+  }
+}