Expose new stan args

R/args.R

@@ -43,7 +43,8 @@ CmdStanArgs <- R6::R6Class(
                           sig_figs = NULL,
                           opencl_ids = NULL,
                           model_variables = NULL,
-                          num_threads = NULL) {
+                          num_threads = NULL,
+                          save_cmdstan_config = NULL) {
 
       self$model_name <- model_name
       self$stan_code <- stan_code
@@ -60,6 +61,7 @@ CmdStanArgs <- R6::R6Class(
       self$save_latent_dynamics <- save_latent_dynamics
       self$using_tempdir <- is.null(output_dir)
       self$model_variables <- model_variables
+      self$save_cmdstan_config <- save_cmdstan_config
       if (os_is_wsl()) {
         # Want to ensure that any files under WSL are written to a tempdir within
         # WSL to avoid IO performance issues
@@ -87,6 +89,9 @@ CmdStanArgs <- R6::R6Class(
       self$opencl_ids <- opencl_ids
       self$num_threads = NULL
       self$method_args$validate(num_procs = length(self$proc_ids))
+      if (is.logical(self$save_cmdstan_config)) {
+        self$save_cmdstan_config <- as.integer(self$save_cmdstan_config)
+      }
       self$validate()
     },
     validate = function() {
@@ -111,7 +116,7 @@ CmdStanArgs <- R6::R6Class(
       } else if (type == "profile") {
         basename <- paste0(basename, "-profile")
       }
-      if (type ==  "output" && !is.null(self$output_basename)) {
+      if (type == "output" && !is.null(self$output_basename)) {
         basename <- self$output_basename
       }
       generate_file_names(
@@ -180,6 +185,9 @@ CmdStanArgs <- R6::R6Class(
       if (!is.null(profile_file)) {
         args$output <- c(args$output, paste0("profile_file=", wsl_safe_path(profile_file)))
       }
+      if (!is.null(self$save_cmdstan_config)) {
+        args$output <- c(args$output, paste0("save_cmdstan_config=", self$save_cmdstan_config))
+      }
       if (!is.null(self$opencl_ids)) {
         args$opencl <- c("opencl", paste0("platform=", self$opencl_ids[1]), paste0("device=", self$opencl_ids[2]))
       }
@@ -218,7 +226,8 @@ SampleArgs <- R6::R6Class(
                           term_buffer = NULL,
                           window = NULL,
                           fixed_param = FALSE,
-                          diagnostics = NULL) {
+                          diagnostics = NULL,
+                          save_metric = NULL) {
 
       self$iter_warmup <- iter_warmup
       self$iter_sampling <- iter_sampling
@@ -232,6 +241,7 @@ SampleArgs <- R6::R6Class(
       self$inv_metric <- inv_metric
       self$fixed_param <- fixed_param
       self$diagnostics <- diagnostics
+      self$save_metric <- save_metric
       if (identical(self$diagnostics, "")) {
         self$diagnostics <- NULL
       }
@@ -275,6 +285,9 @@ SampleArgs <- R6::R6Class(
       if (is.logical(self$save_warmup)) {
         self$save_warmup <- as.integer(self$save_warmup)
       }
+      if (is.logical(self$save_metric)) {
+        self$save_metric <- as.integer(self$save_metric)
+      }
       invisible(self)
     },
     validate = function(num_procs) {
@@ -314,7 +327,8 @@ SampleArgs <- R6::R6Class(
           .make_arg("adapt_engaged"),
           .make_arg("init_buffer"),
           .make_arg("term_buffer"),
-          .make_arg("window")
+          .make_arg("window"),
+          .make_arg("save_metric")
         )
       } else {
         new_args <- list(
@@ -335,7 +349,8 @@ SampleArgs <- R6::R6Class(
           .make_arg("adapt_engaged"),
           .make_arg("init_buffer"),
           .make_arg("term_buffer"),
-          .make_arg("window")
+          .make_arg("window"),
+          .make_arg("save_metric")
         )
       }
       new_args <- do.call(c, new_args)
@@ -682,6 +697,7 @@ validate_cmdstan_args <- function(self) {
   checkmate::assert_flag(self$save_latent_dynamics)
   checkmate::assert_integerish(self$refresh, lower = 0, null.ok = TRUE)
   checkmate::assert_integerish(self$sig_figs, lower = 1, upper = 18, null.ok = TRUE)
+  checkmate::assert_integerish(self$save_cmdstan_config, lower = 0, upper = 1, len = 1, null.ok = TRUE)
   if (!is.null(self$sig_figs) && cmdstan_version() < "2.25") {
     warning("The 'sig_figs' argument is only supported with cmdstan 2.25+ and will be ignored!", call. = FALSE)
   }
@@ -799,6 +815,15 @@ validate_sample_args <- function(self, num_procs) {
     checkmate::assert_subset(self$diagnostics, empty.ok = FALSE, choices = available_hmc_diagnostics())
   }
 
+  checkmate::assert_integerish(self$save_metric,
+                               lower = 0, upper = 1,
+                               len = 1,
+                               null.ok = TRUE)
+
+  if (is.null(self$adapt_engaged) || (!self$adapt_engaged && !is.null(self$save_metric))) {
+    self$save_metric <- 0
+  }
+
   invisible(TRUE)
 }
 

R/fit.R

@@ -898,10 +898,13 @@ CmdStanFit$set("public", name = "cmdstan_diagnose", value = cmdstan_diagnose)
 #' Save output and data files
 #'
 #' @name fit-method-save_output_files
-#' @aliases fit-method-save_data_file fit-method-save_latent_dynamics_files fit-method-save_profile_files
-#'   fit-method-output_files fit-method-data_file fit-method-latent_dynamics_files fit-method-profile_files
-#'   save_output_files save_data_file save_latent_dynamics_files save_profile_files
-#'   output_files data_file latent_dynamics_files profile_files
+#' @aliases fit-method-save_data_file fit-method-save_latent_dynamics_files
+#'   fit-method-save_profile_files fit-method-output_files fit-method-data_file
+#'   fit-method-latent_dynamics_files fit-method-profile_files
+#'   fit-method-save_config_files fit-method-save_metric_files save_output_files
+#'   save_data_file save_latent_dynamics_files save_profile_files
+#'   save_config_files save_metric_files output_files data_file
+#'   latent_dynamics_files profile_files config_files metric_files
 #'
 #' @description All fitted model objects have methods for saving (moving to a
 #'   specified location) the files created by CmdStanR to hold CmdStan output
@@ -936,6 +939,14 @@ CmdStanFit$set("public", name = "cmdstan_diagnose", value = cmdstan_diagnose)
 #' `$save_output_files()` except `"-profile-"` is included in the new
 #' file name after `basename`.
 #'
+#' For `$save_metric_files()` everything is the same as for
+#' `$save_output_files()` except `"-metric-"` is included in the new
+#' file name after `basename`.
+#'
+#' For `$save_config_files()` everything is the same as for
+#' `$save_output_files()` except `"-config-"` is included in the new
+#' file name after `basename`.
+#'
 #' For `$save_data_file()` no `id` is included in the file name because even
 #' with multiple MCMC chains the data file is the same.
 #'
@@ -998,6 +1009,26 @@ save_data_file <- function(dir = ".",
 }
 CmdStanFit$set("public", name = "save_data_file", value = save_data_file)
 
+#' @rdname fit-method-save_output_files
+save_config_files <- function(dir = ".",
+                              basename = NULL,
+                              timestamp = TRUE,
+                              random = TRUE) {
+  self$runset$save_config_files(dir, basename, timestamp, random)
+}
+CmdStanFit$set("public", name = "save_config_files", value = save_config_files)
+
+#' @rdname fit-method-save_output_files
+save_metric_files <- function(dir = ".",
+                              basename = NULL,
+                              timestamp = TRUE,
+                              random = TRUE) {
+  self$runset$save_metric_files(dir, basename, timestamp, random)
+}
+CmdStanFit$set("public", name = "save_metric_files", value = save_metric_files)
+
+
+
 #' @rdname fit-method-save_output_files
 #' @param include_failed (logical) Should CmdStan runs that failed also be
 #'   included? The default is `FALSE.`
@@ -1024,6 +1055,17 @@ data_file <- function() {
 }
 CmdStanFit$set("public", name = "data_file", value = data_file)
 
+#' @rdname fit-method-save_output_files
+config_files <- function(include_failed = FALSE) {
+  self$runset$config_files(include_failed)
+}
+CmdStanFit$set("public", name = "config_files", value = config_files)
+
+#' @rdname fit-method-save_output_files
+metric_files <- function(include_failed = FALSE) {
+  self$runset$metric_files(include_failed)
+}
+CmdStanFit$set("public", name = "metric_files", value = metric_files)
 
 #' Report timing of CmdStan runs
 #'

R/model.R

@@ -1149,6 +1149,8 @@ sample <- function(data = NULL,
                    show_messages = TRUE,
                    show_exceptions = TRUE,
                    diagnostics = c("divergences", "treedepth", "ebfmi"),
+                   save_metric = if (cmdstan_version() > "2.34.0") { TRUE } else { NULL },
+                   save_cmdstan_config = if (cmdstan_version() > "2.34.0") { TRUE } else { NULL },
                    # deprecated
                    cores = NULL,
                    num_cores = NULL,
@@ -1240,7 +1242,8 @@ sample <- function(data = NULL,
     term_buffer = term_buffer,
     window = window,
     fixed_param = fixed_param,
-    diagnostics = diagnostics
+    diagnostics = diagnostics,
+    save_metric = save_metric
   )
   args <- CmdStanArgs$new(
     method_args = sample_args,
@@ -1260,7 +1263,8 @@ sample <- function(data = NULL,
     output_basename = output_basename,
     sig_figs = sig_figs,
     opencl_ids = assert_valid_opencl(opencl_ids, self$cpp_options()),
-    model_variables = model_variables
+    model_variables = model_variables,
+    save_cmdstan_config = save_cmdstan_config
   )
   runset <- CmdStanRun$new(args, procs)
   runset$run_cmdstan()
@@ -1357,6 +1361,7 @@ sample_mpi <- function(data = NULL,
                        show_messages = TRUE,
                        show_exceptions = TRUE,
                        diagnostics = c("divergences", "treedepth", "ebfmi"),
+                       save_cmdstan_config = if (cmdstan_version() > "2.34.0") { TRUE } else { NULL },
                        # deprecated
                        validate_csv = TRUE) {
 
@@ -1420,7 +1425,8 @@ sample_mpi <- function(data = NULL,
     output_dir = output_dir,
     output_basename = output_basename,
     sig_figs = sig_figs,
-    model_variables = model_variables
+    model_variables = model_variables,
+    save_cmdstan_config = save_cmdstan_config
   )
   runset <- CmdStanRun$new(args, procs)
   runset$run_cmdstan_mpi(mpi_cmd, mpi_args)
@@ -1500,7 +1506,8 @@ optimize <- function(data = NULL,
                      tol_param = NULL,
                      history_size = NULL,
                      show_messages = TRUE,
-                     show_exceptions = TRUE) {
+                     show_exceptions = TRUE,
+                     save_cmdstan_config = if (cmdstan_version() > "2.34.0") { TRUE } else { NULL }) {
   procs <- CmdStanProcs$new(
     num_procs = 1,
     show_stderr_messages = show_exceptions,
@@ -1541,7 +1548,8 @@ optimize <- function(data = NULL,
     output_basename = output_basename,
     sig_figs = sig_figs,
     opencl_ids = assert_valid_opencl(opencl_ids, self$cpp_options()),
-    model_variables = model_variables
+    model_variables = model_variables,
+    save_cmdstan_config = save_cmdstan_config
   )
   runset <- CmdStanRun$new(args, procs)
   runset$run_cmdstan()
@@ -1632,7 +1640,8 @@ laplace <- function(data = NULL,
                     jacobian = TRUE, # different default than for optimize!
                     draws = NULL,
                     show_messages = TRUE,
-                    show_exceptions = TRUE) {
+                    show_exceptions = TRUE,
+                    save_cmdstan_config = if (cmdstan_version() > "2.34.0") { TRUE } else { NULL }) {
   if (cmdstan_version() < "2.32") {
     stop("This method is only available in cmdstan >= 2.32", call. = FALSE)
   }
@@ -1706,7 +1715,8 @@ laplace <- function(data = NULL,
     output_basename = output_basename,
     sig_figs = sig_figs,
     opencl_ids = assert_valid_opencl(opencl_ids, self$cpp_options()),
-    model_variables = model_variables
+    model_variables = model_variables,
+    save_cmdstan_config = save_cmdstan_config
   )
   runset <- CmdStanRun$new(args, procs)
   runset$run_cmdstan()
@@ -1786,7 +1796,8 @@ variational <- function(data = NULL,
                         output_samples = NULL,
                         draws = NULL,
                         show_messages = TRUE,
-                        show_exceptions = TRUE) {
+                        show_exceptions = TRUE,
+                        save_cmdstan_config = if (cmdstan_version() > "2.34.0") { TRUE } else { NULL }) {
   procs <- CmdStanProcs$new(
     num_procs = 1,
     show_stderr_messages = show_exceptions,
@@ -1827,7 +1838,8 @@ variational <- function(data = NULL,
     output_basename = output_basename,
     sig_figs = sig_figs,
     opencl_ids = assert_valid_opencl(opencl_ids, self$cpp_options()),
-    model_variables = model_variables
+    model_variables = model_variables,
+    save_cmdstan_config = save_cmdstan_config
   )
   runset <- CmdStanRun$new(args, procs)
   runset$run_cmdstan()
@@ -1929,7 +1941,8 @@ pathfinder <- function(data = NULL,
                        psis_resample = NULL,
                        calculate_lp = NULL,
                        show_messages = TRUE,
-                       show_exceptions = TRUE) {
+                       show_exceptions = TRUE,
+                       save_cmdstan_config = if (cmdstan_version() > "2.34.0") { TRUE } else { NULL }) {
   procs <- CmdStanProcs$new(
     num_procs = 1,
     show_stderr_messages = show_exceptions,
@@ -1976,7 +1989,8 @@ pathfinder <- function(data = NULL,
     sig_figs = sig_figs,
     opencl_ids = assert_valid_opencl(opencl_ids, self$cpp_options()),
     model_variables = model_variables,
-    num_threads = num_threads
+    num_threads = num_threads,
+    save_cmdstan_config = save_cmdstan_config
   )
   runset <- CmdStanRun$new(args, procs)
   runset$run_cmdstan()