add option cmdstanr_output_dir

closes #945

R/model.R

@@ -1123,7 +1123,7 @@ sample <- function(data = NULL,
                    refresh = NULL,
                    init = NULL,
                    save_latent_dynamics = FALSE,
-                   output_dir = NULL,
+                   output_dir = getOption("cmdstanr_output_dir"),
                    output_basename = NULL,
                    sig_figs = NULL,
                    chains = 4,
@@ -1334,7 +1334,7 @@ sample_mpi <- function(data = NULL,
                        refresh = NULL,
                        init = NULL,
                        save_latent_dynamics = FALSE,
-                       output_dir = NULL,
+                       output_dir = getOption("cmdstanr_output_dir"),
                        output_basename = NULL,
                        chains = 1,
                        chain_ids = seq_len(chains),
@@ -1484,7 +1484,7 @@ optimize <- function(data = NULL,
                      refresh = NULL,
                      init = NULL,
                      save_latent_dynamics = FALSE,
-                     output_dir = NULL,
+                     output_dir = getOption("cmdstanr_output_dir"),
                      output_basename = NULL,
                      sig_figs = NULL,
                      threads = NULL,
@@ -1622,7 +1622,7 @@ laplace <- function(data = NULL,
                     refresh = NULL,
                     init = NULL,
                     save_latent_dynamics = FALSE,
-                    output_dir = NULL,
+                    output_dir = getOption("cmdstanr_output_dir"),
                     output_basename = NULL,
                     sig_figs = NULL,
                     threads = NULL,
@@ -1769,7 +1769,7 @@ variational <- function(data = NULL,
                         refresh = NULL,
                         init = NULL,
                         save_latent_dynamics = FALSE,
-                        output_dir = NULL,
+                        output_dir = getOption("cmdstanr_output_dir"),
                         output_basename = NULL,
                         sig_figs = NULL,
                         threads = NULL,
@@ -1908,7 +1908,7 @@ pathfinder <- function(data = NULL,
                        refresh = NULL,
                        init = NULL,
                        save_latent_dynamics = FALSE,
-                       output_dir = NULL,
+                       output_dir = getOption("cmdstanr_output_dir"),
                        output_basename = NULL,
                        sig_figs = NULL,
                        opencl_ids = NULL,
@@ -2060,7 +2060,7 @@ CmdStanModel$set("public", name = "pathfinder", value = pathfinder)
 generate_quantities <- function(fitted_params,
                                 data = NULL,
                                 seed = NULL,
-                                output_dir = NULL,
+                                output_dir = getOption("cmdstanr_output_dir"),
                                 output_basename = NULL,
                                 sig_figs = NULL,
                                 parallel_chains = getOption("mc.cores", 1),
@@ -2125,7 +2125,7 @@ CmdStanModel$set("public", name = "generate_quantities", value = generate_quanti
 diagnose <- function(data = NULL,
                      seed = NULL,
                      init = NULL,
-                     output_dir = NULL,
+                     output_dir = getOption("cmdstanr_output_dir"),
                      output_basename = NULL,
                      epsilon = NULL,
                      error = NULL) {

R/options.R

@@ -21,6 +21,9 @@
 #' * `cmdstanr_no_ver_check`: Should the check for a more recent version of
 #' CmdStan be disabled? The default is `FALSE`.
 #'
+#' * `cmdstanr_output_dir`: The directory where CmdStan should write its output
+#' CSV files when fitting models. The default is a temporary directory.
+#'
 #' * `cmdstanr_verbose`: Should more information be printed
 #' when compiling or running models, including showing how CmdStan was called
 #' internally? The default is `FALSE`.
@@ -29,7 +32,7 @@
 #' only provided for a subset of parameters? The default is `TRUE`.
 #'
 #' * `cmdstanr_write_stan_file_dir`: The directory where [write_stan_file()]
-#' should write Stan files. The default is [tempdir()].
+#' should write Stan files. The default is a temporary directory.
 #'
 #' * `mc.cores`: The number of cores to use for various parallelization tasks
 #' (e.g. running MCMC chains, installing CmdStan). The default depends on the

man-roxygen/model-common-args.R

@@ -60,7 +60,8 @@
 #'   methods there will be a single file. For interactive use this can typically
 #'   be left at `NULL` (temporary directory) since CmdStanR makes the CmdStan
 #'   output (posterior draws and diagnostics) available in \R via methods of the
-#'   fitted model objects. The behavior of `output_dir` is as follows:
+#'   fitted model objects. This can be set for an entire \R session using
+#'   `options(cmdstanr_output_dir)`. The behavior of `output_dir` is as follows:
 #'   * If `NULL` (the default), then the CSV files are written to a temporary
 #'   directory and only saved permanently if the user calls one of the `$save_*`
 #'   methods of the fitted model object (e.g.,