changes for R CMD check

R/0_imports.R

@@ -47,7 +47,7 @@ utils::globalVariables(
     "rowwise", ".best", "location", "msg", "..object", ".eval_time",
     ".pred_survival", ".pred_time", ".weight_censored", "nice_time",
     "time_metric", ".lower", ".upper", "i", "results", "term", ".alpha",
-    ".method", "old_term", ".lab_pre", ".model", ".num_models"
+    ".method", "old_term", ".lab_pre", ".model", ".num_models", "predict_stage"
   )
 )
 

R/loopy.R

@@ -335,7 +335,7 @@ rebind_grid <- function(...) {
 }
 
 get_output_columns <- function(x, syms = FALSE) {
-	pred_cols <- .get_prediction_column_names(x, syms = TRUE)
+	pred_cols <- parsnip::.get_prediction_column_names(x, syms = TRUE)
 	res <- c(list(outcome = rlang::syms(outcome_names(x))), pred_cols)
 	res
 }
@@ -379,6 +379,22 @@ update_reserve <- function(reserve, iter, predictions, grid_size) {
 
 opts <- list(event_level = "first", verbose = FALSE)
 
+#' Iterate over workflow settings
+#'
+#' @param sched A preprocessing schedule.
+#' @param grid A parameter grid.
+#' @param wflow A workflow object.
+#' @param tune_id A character vector of tuning parameter names.
+#' @param dat A list containing fit and prediction data.
+#' @param mtr A metric set.
+#' @param eval_time Optional. Evaluation time point(s).
+#'
+#' @returns
+#' A list containing two elements:
+#' * `metrics`: A tibble of computed metrics grouped by tuning parameters
+#' * `predictions`: A tibble of model predictions
+#'
+#' @export
 #' @export
 loopy <- function(sched, grid, wflow, tune_id, dat, mtr, eval_time = NULL) {
 	# ------------------------------------------------------------------------------

R/schedule.R

@@ -1,3 +1,12 @@
+#' Get tune schedule
+#'
+#' @param wflow A workflow object.
+#' @param param A dials parameters set.
+#' @param grid A tibble containing the parameter grid.
+#'
+#' @returns A schedule object, inheriting from either 'single_schedule',
+#' 'grid_schedule', or 'resample_schedule'.
+#'
 #' @export
 get_tune_schedule <- function(wflow, param, grid) {
 	if (!inherits(wflow, "workflow")) {
@@ -27,7 +36,7 @@ get_tune_schedule <- function(wflow, param, grid) {
 	# Merge the info in with the other parameters
 	param <- dplyr::left_join(param, model_param, by = "name") %>%
 		dplyr::mutate(
-			has_submodel = if_else(is.na(has_submodel), FALSE, has_submodel)
+			has_submodel = dplyr::if_else(is.na(has_submodel), FALSE, has_submodel)
 		)
 
 	# ------------------------------------------------------------------------------