base learner documentation

- "under construction" flag removed
- _targets.R and pipeline_base_functions.R in inst/targets are synchronized

R/pipeline_base_functions.R

@@ -2205,8 +2205,7 @@ par_nest <-
 #' and tidymodels. With proper settings, users can utilize graphics
 #' processing units (GPU) to speed up the training process.
 #' @keywords Baselearner
-#' @note Spatiotemporal cross-validation strategy is not yet implemented.
-#'   tune package should be 1.2.0 or higher.
+#' @note tune package should be 1.2.0 or higher.
 #' @param dt_imputed The input data table to be used for fitting.
 #' @param folds pre-generated rset object. If NULL, it should be
 #'   numeric to be used in [rsample::vfold_cv].
@@ -2303,7 +2302,7 @@ fit_base_brulee <-
 #' With proper settings, users can utilize graphics
 #' processing units (GPU) to speed up the training process.
 #' @keywords Baselearner
-#' @note Spatiotemporal cross-validation strategy is not yet implemented.
+#' @note tune package should be 1.2.0 or higher.
 #' @param dt_imputed The input data table to be used for fitting.
 #' @param folds pre-generated rset object. If NULL, it should be
 #'   numeric to be used in [rsample::vfold_cv].
@@ -2390,7 +2389,7 @@ fit_base_xgb <-
 #' Elastic net model is fitted at the defined rate (`r_subsample`) of
 #' the input dataset by grid search.
 #' @keywords Baselearner
-#' @note Spatiotemporal cross-validation strategy is not yet implemented.
+#' @note tune package should be 1.2.0 or higher.
 #' @param dt_imputed The input data table to be used for fitting.
 #' @param folds pre-generated rset object. If NULL, it should be
 #'   numeric to be used in [rsample::vfold_cv].

_targets.R

@@ -15,14 +15,18 @@ tar_source("inst/targets/targets_arglist.R")
 # bypass option
 Sys.setenv("BTV_DOWNLOAD_PASS" = "TRUE")
 
+#
 # bind custom built GDAL
+# Users should export the right path to the GDAL library
+# by export LD_LIBRARY_PATH=.... command.
 .libPaths(
   c(
     "/ddn/gs1/biotools/R/lib64/R/custompkg",
     .libPaths()
   )
 )
 
+# arglist_common is generated by targets_arglist.R.
 plan(
   list(
     tweak(
@@ -51,6 +55,8 @@ if (Sys.getenv("BTV_DOWNLOAD_PASS") == "TRUE") {
 }
 
 # targets options
+# For GPU support, users should be aware of setting environment
+# variables and GPU versions of the packages.
 # TODO: check if the controller and resources setting are required
 tar_option_set(
   packages =
@@ -59,10 +65,11 @@ tar_option_set(
       #"crew", "crew.cluster", 
       "tigris", "dplyr",
       "future.batchtools", "qs", "collapse",
-      "tidymodels", "torch",
+      "tidymodels", "tune", "rsample", "torch", "brulee",
+      "glmnet", "xgboost",
       "future", "future.apply", "future.callr", "callr",
       #"sftime",
-      "stars", "rlang", "foreach", "parallelly"),
+      "stars", "rlang", "parallelly"),
   library = c("/ddn/gs1/biotools/R/lib64/R/custompkg", "/ddn/gs1/home/songi2/r-libs"),
   repository = "local",
   error = "stop",