Merge pull request #823 from stan-dev/fix-example-errors

fix errors in doc for new methods

Author: jgabry

R/example.R

@@ -19,6 +19,7 @@
 #'   the individual methods for details.
 #' @param quiet (logical) If `TRUE` (the default) then fitting the model is
 #'   wrapped in [utils::capture.output()].
+#' @param force_recompile Passed to the [$compile()][model-method-compile] method.
 #'
 #' @return
 #' The fitted model object returned by the selected `method`.
@@ -51,7 +52,8 @@ cmdstanr_example <-
   function(example = c("logistic", "schools", "schools_ncp"),
            method = c("sample", "optimize", "variational", "diagnose"),
            ...,
-           quiet = TRUE) {
+           quiet = TRUE,
+           force_recompile = getOption("cmdstanr_force_recompile", default = FALSE)) {
 
     example <- match.arg(example)
     method <- match.arg(method)
@@ -63,7 +65,7 @@ cmdstanr_example <-
     if (!file.exists(tmp)) {
       file.copy(system.file(example_program, package = "cmdstanr"), tmp)
     }
-    mod <- cmdstan_model(tmp)
+    mod <- cmdstan_model(tmp, force_recompile = force_recompile)
     data_file <- system.file(example_data, package = "cmdstanr")
 
     if (quiet) {

R/fit.R

@@ -324,7 +324,7 @@ CmdStanFit$set("public", name = "init", value = init)
 #'
 #' @examples
 #' \dontrun{
-#' fit_mcmc <- cmdstanr_example("logistic", method = "sample")
+#' fit_mcmc <- cmdstanr_example("logistic", method = "sample", force_recompile = TRUE)
 #' fit_mcmc$init_model_methods()
 #' }
 #' @seealso [log_prob()], [grad_log_prob()], [constrain_variables()],
@@ -370,7 +370,7 @@ CmdStanFit$set("public", name = "init_model_methods", value = init_model_methods
 #'
 #' @examples
 #' \dontrun{
-#' fit_mcmc <- cmdstanr_example("logistic", method = "sample")
+#' fit_mcmc <- cmdstanr_example("logistic", method = "sample", force_recompile = TRUE)
 #' fit_mcmc$init_model_methods()
 #' fit_mcmc$log_prob(unconstrained_variables = c(0.5, 1.2, 1.1, 2.2))
 #' }
@@ -408,7 +408,7 @@ CmdStanFit$set("public", name = "log_prob", value = log_prob)
 #'
 #' @examples
 #' \dontrun{
-#' fit_mcmc <- cmdstanr_example("logistic", method = "sample")
+#' fit_mcmc <- cmdstanr_example("logistic", method = "sample", force_recompile = TRUE)
 #' fit_mcmc$init_model_methods()
 #' fit_mcmc$grad_log_prob(unconstrained_variables = c(0.5, 1.2, 1.1, 2.2))
 #' }
@@ -446,7 +446,7 @@ CmdStanFit$set("public", name = "grad_log_prob", value = grad_log_prob)
 #'
 #' @examples
 #' \dontrun{
-#' # fit_mcmc <- cmdstanr_example("logistic", method = "sample")
+#' fit_mcmc <- cmdstanr_example("logistic", method = "sample", force_recompile = TRUE)
 #' # fit_mcmc$init_model_methods(hessian = TRUE)
 #' # fit_mcmc$hessian(unconstrained_variables = c(0.5, 1.2, 1.1, 2.2))
 #' }
@@ -481,7 +481,7 @@ CmdStanFit$set("public", name = "hessian", value = hessian)
 #'
 #' @examples
 #' \dontrun{
-#' fit_mcmc <- cmdstanr_example("logistic", method = "sample")
+#' fit_mcmc <- cmdstanr_example("logistic", method = "sample", force_recompile = TRUE)
 #' fit_mcmc$init_model_methods()
 #' fit_mcmc$unconstrain_variables(list(alpha = 0.5, beta = c(0.7, 1.1, 0.2)))
 #' }
@@ -539,7 +539,7 @@ CmdStanFit$set("public", name = "unconstrain_variables", value = unconstrain_var
 #'
 #' @examples
 #' \dontrun{
-#' fit_mcmc <- cmdstanr_example("logistic", method = "sample")
+#' fit_mcmc <- cmdstanr_example("logistic", method = "sample", force_recompile = TRUE)
 #' fit_mcmc$init_model_methods()
 #'
 #' # Unconstrain all internal draws
@@ -618,7 +618,7 @@ CmdStanFit$set("public", name = "unconstrain_draws", value = unconstrain_draws)
 #'
 #' @examples
 #' \dontrun{
-#' fit_mcmc <- cmdstanr_example("logistic", method = "sample")
+#' fit_mcmc <- cmdstanr_example("logistic", method = "sample", force_recompile = TRUE)
 #' fit_mcmc$init_model_methods()
 #' fit_mcmc$variable_skeleton()
 #' }
@@ -656,7 +656,7 @@ CmdStanFit$set("public", name = "variable_skeleton", value = variable_skeleton)
 #'
 #' @examples
 #' \dontrun{
-#' fit_mcmc <- cmdstanr_example("logistic", method = "sample")
+#' fit_mcmc <- cmdstanr_example("logistic", method = "sample", force_recompile = TRUE)
 #' fit_mcmc$init_model_methods()
 #' fit_mcmc$constrain_variables(unconstrained_variables = c(0.5, 1.2, 1.1, 2.2))
 #' }

R/model.R

@@ -603,7 +603,7 @@ compile <- function(quiet = TRUE,
       wd = cmdstan_path(),
       echo = !quiet || is_verbose_mode(),
       echo_cmd = is_verbose_mode(),
-      spinner = quiet && interactive(),
+      spinner = quiet && interactive() && !identical(Sys.getenv("IN_PKGDOWN"), "true"),
       stderr_callback = function(x, p) {
         if (!startsWith(x, paste0(make_cmd(), ": *** No rule to make target"))) {
           message(x)