Add output_basename

R/args.R

@@ -30,6 +30,7 @@ CmdStanArgs <- R6::R6Class(
                           init = NULL,
                           refresh = NULL,
                           output_dir = NULL,
+                          output_basename = NULL,
                           validate_csv = TRUE,
                           sig_figs = NULL) {
 
@@ -51,6 +52,7 @@ CmdStanArgs <- R6::R6Class(
         self$output_dir <- output_dir %||% tempdir(check = TRUE)
       }
       self$output_dir <- repair_path(self$output_dir)
+      self$output_basename <- output_basename
       if (is.function(init)) {
         init <- process_init_function(init, length(self$proc_ids))
       } else if (is.list(init) && !is.data.frame(init)) {
@@ -83,12 +85,15 @@ CmdStanArgs <- R6::R6Class(
       } else if (type == "profile") {
         basename <- paste0(basename, "-profile")
       }
+      if (type ==  "output" && !is.null(self$output_basename)) {
+        basename <- self$output_basename
+      }
       generate_file_names( # defined in utils.R
         basename = basename,
         ext = ".csv",
         ids = self$proc_ids,
-        timestamp = TRUE,
-        random = TRUE
+        timestamp = is.null(self$output_basename),
+        random = is.null(self$output_basename)
       )
     },
     new_files = function(type = c("output", "diagnostic", "profile")) {

R/model.R

@@ -691,6 +691,7 @@ sample <- function(data = NULL,
                    init = NULL,
                    save_latent_dynamics = FALSE,
                    output_dir = NULL,
+                   output_basename = NULL,
                    sig_figs = NULL,
                    chains = 4,
                    parallel_chains = getOption("mc.cores", 1),
@@ -808,6 +809,7 @@ sample <- function(data = NULL,
     init = init,
     refresh = refresh,
     output_dir = output_dir,
+    output_basename = output_basename,
     sig_figs = sig_figs,
     validate_csv = validate_csv
   )
@@ -889,6 +891,7 @@ sample_mpi <- function(data = NULL,
                        init = NULL,
                        save_latent_dynamics = FALSE,
                        output_dir = NULL,
+                       output_basename = NULL,
                        chains = 1,
                        chain_ids = seq_len(chains),
                        iter_warmup = NULL,
@@ -944,6 +947,7 @@ sample_mpi <- function(data = NULL,
     init = init,
     refresh = refresh,
     output_dir = output_dir,
+    output_basename = output_basename,
     validate_csv = validate_csv,
     sig_figs = sig_figs
   )
@@ -1013,6 +1017,7 @@ optimize <- function(data = NULL,
                      init = NULL,
                      save_latent_dynamics = FALSE,
                      output_dir = NULL,
+                     output_basename = NULL,
                      sig_figs = NULL,
                      threads = NULL,
                      algorithm = NULL,
@@ -1061,6 +1066,7 @@ optimize <- function(data = NULL,
     init = init,
     refresh = refresh,
     output_dir = output_dir,
+    output_basename = output_basename,
     sig_figs = sig_figs
   )
 
@@ -1133,6 +1139,7 @@ variational <- function(data = NULL,
                         init = NULL,
                         save_latent_dynamics = FALSE,
                         output_dir = NULL,
+                        output_basename = NULL,
                         sig_figs = NULL,
                         threads = NULL,
                         algorithm = NULL,
@@ -1183,6 +1190,7 @@ variational <- function(data = NULL,
     init = init,
     refresh = refresh,
     output_dir = output_dir,
+    output_basename = output_basename,
     sig_figs = sig_figs
   )
 
@@ -1266,6 +1274,7 @@ generate_quantities <- function(fitted_params,
                                 data = NULL,
                                 seed = NULL,
                                 output_dir = NULL,
+                                output_basename = NULL,
                                 sig_figs = NULL,
                                 parallel_chains = getOption("mc.cores", 1),
                                 threads_per_chain = NULL) {
@@ -1299,6 +1308,7 @@ generate_quantities <- function(fitted_params,
     data_file = process_data(data),
     seed = seed,
     output_dir = output_dir,
+    output_basename = output_basename,
     sig_figs = sig_figs
   )
   cmdstan_procs <- CmdStanGQProcs$new(

man-roxygen/model-common-args.R

@@ -48,15 +48,20 @@
 #'   `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:
-#'  * 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 `$save_*`
-#'  methods of the fitted model object (e.g.,
-#'  [`$save_output_files()`][fit-method-save_output_files]). These temporary
-#'  files are removed when the fitted model object is
-#'  [garbage collected][base::gc] (manually or automatically).
-#'  * If a path, then the files are created in `output_dir` with names
-#'  corresponding to the defaults used by `$save_output_files()`.
+#'   * If `NULL` (the default), then the CSV files are written to a temporary
+#'   directory and only saved permanently if the user calls one of the `$save_*`
+#'   methods of the fitted model object (e.g.,
+#'   [`$save_output_files()`][fit-method-save_output_files]). These temporary
+#'   files are removed when the fitted model object is
+#'   [garbage collected][base::gc] (manually or automatically).
+#'   * If a path, then the files are created in `output_dir` with names
+#'   corresponding to the defaults used by `$save_output_files()`.
 #'
+#' @param output_basename (string) A string to use as a prefix for the
+#'   names of the output CSV files of CmdStan.
+#'   * If `NULL` (the default), the basename of the output CSV files
+#'   will be comprised from the model name, timestamp and 5 random characters.
+#' 
 #' @param sig_figs (positive integer) The number of significant figures used
 #'   when storing the output values. By default, CmdStan represent the output
 #'   values with 6 significant figures. The upper limit for `sig_figs` is 18.

tests/testthat/test-model-output_dir.R

@@ -1,4 +1,4 @@
-context("model-output_dir")
+context("model-output_dir-output-basename")
 
 if (not_on_cran()) {
   set_cmdstan_path()
@@ -29,6 +29,14 @@ test_that("all fitting methods work with output_dir", {
                         output_dir = method_dir)
     expect_equal(fit$runset$args$output_dir, absolute_path(method_dir))
     expect_equal(length(list.files(method_dir)), fit$num_procs())
+
+
+    # specifying output_dir
+    fit <- testing_fit("bernoulli", method = method, seed = 123,
+                       output_basename = "custom")
+    n_files <- length(fit$output_files())
+    files <- paste0("custom-", 1:n_files, ".csv")
+    expect_equal(basename(fit$output_files()), files)
   }
 
   # specifying output_dir and save_latent_dynamics