update doc based on reviewer feedback

Author: jgabry

R/model.R

@@ -945,8 +945,15 @@ CmdStanModel$set("public", name = "check_syntax", value = check_syntax)
 #'   x ~ std_normal();
 #' }
 #' ")
+#'
+#' # set compile=FALSE then call format to fix old syntax
 #' mod <- cmdstan_model(file, compile = FALSE)
-#' mod$format(canonicalize = TRUE)
+#' mod$format(canonicalize = list("deprecations"))
+#'
+#' # overwrite the original file instead of just printing it
+#' mod$format(canonicalize = list("deprecations"), overwrite_file = TRUE)
+#' mod$compile()
+#'
 #'
 #' # Example of removing unnecessary whitespace
 #' file <- write_stan_file("