Add handling for variable order, fix chains return in draws

Author: andrjohns

R/fit.R

@@ -518,7 +518,7 @@ unconstrain_variables <- function(variables) {
          " not provided!", call. = FALSE)
   }
 
-  variables_vector <- unlist(variables, recursive = TRUE, use.names = FALSE)
+  variables_vector <- unlist(variables[model_par_names], recursive = TRUE)
   private$model_methods_env_$unconstrain_variables(private$model_methods_env_$model_ptr_, variables_vector)
 }
 CmdStanFit$set("public", name = "unconstrain_variables", value = unconstrain_variables)
@@ -598,7 +598,7 @@ unconstrain_draws <- function(files = NULL, draws = NULL,
   unconstrained <- private$model_methods_env_$unconstrain_draws(private$model_methods_env_$model_ptr_, draws)
   uncon_names <- private$model_methods_env_$unconstrained_param_names(private$model_methods_env_$model_ptr_, FALSE, FALSE)
   names(unconstrained) <- repair_variable_names(uncon_names)
-  maybe_convert_draws_format(unconstrained, format)
+  maybe_convert_draws_format(unconstrained, format, .nchains = posterior::nchains(draws))
 }
 CmdStanFit$set("public", name = "unconstrain_draws", value = unconstrain_draws)
 

R/model.R

@@ -465,10 +465,10 @@ compile <- function(quiet = TRUE,
                     stanc_options = list(),
                     force_recompile = getOption("cmdstanr_force_recompile", default = FALSE),
                     compile_model_methods = FALSE,
-                    compile_hessian_method = FALSE,
                     compile_standalone = FALSE,
                     dry_run = FALSE,
                     #deprecated
+                    compile_hessian_method = FALSE,
                     threads = FALSE) {
 
   if (length(self$stan_file()) == 0) {
@@ -505,6 +505,11 @@ compile <- function(quiet = TRUE,
     cpp_options[["stan_threads"]] <- TRUE
   }
 
+  # temporary deprecation warnings
+  if (isTRUE(compile_hessian_method)) {
+    warning("'compile_hessian_method' is deprecated. The hessian method is compiled with all models.")
+  }
+
   if (length(self$exe_file()) == 0) {
     if (is.null(dir)) {
       exe_base <- self$stan_file()

R/utils.R

@@ -409,19 +409,19 @@ valid_draws_formats <- function() {
     "draws_rvars", "rvars")
 }
 
-maybe_convert_draws_format <- function(draws, format) {
+maybe_convert_draws_format <- function(draws, format, ...) {
   if (is.null(draws)) {
     return(draws)
   }
   format <- sub("^draws_", "", format)
   switch(
     format,
-    "array" = posterior::as_draws_array(draws),
-    "df" = posterior::as_draws_df(draws),
-    "data.frame" = posterior::as_draws_df(draws),
-    "list" = posterior::as_draws_list(draws),
-    "matrix" = posterior::as_draws_matrix(draws),
-    "rvars" = posterior::as_draws_rvars(draws),
+    "array" = posterior::as_draws_array(draws, ...),
+    "df" = posterior::as_draws_df(draws, ...),
+    "data.frame" = posterior::as_draws_df(draws, ...),
+    "list" = posterior::as_draws_list(draws, ...),
+    "matrix" = posterior::as_draws_matrix(draws, ...),
+    "rvars" = posterior::as_draws_rvars(draws, ...),
     stop("Invalid draws format.", call. = FALSE)
   )
 }