From 532aaf5785ab188f2018c9e041cb6ee3e4c69ec4 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Thu, 17 Oct 2024 23:20:46 +0800
Subject: [PATCH 01/37] Refactor code in the R/ folder

---
 R/dvloader.R | 150 +++++++++++++++++++++++++++++-------------
 R/utils.R    | 180 ++++++++++++++++++++++++++++++++-------------------
 2 files changed, 218 insertions(+), 112 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index a36a7b9..2d22547 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -1,61 +1,119 @@
-#' gets the NFS base path from an env var
-#' It assumes there is an env var
-#' called RXD_DATA which holds the path suffix.
-#' @return the NFS base path
+#' Get Base Directory Path
+#'
+#' This function retrieves the base directory path from a specified environment variable.
+#' It checks if the environment variable is set and if the directory exists.
+#'
+#' @param env_var [character(1)] The name of the environment variable containing the base directory path.
+#'
+#' @return [character(1)] The normalized path to the base directory.
+#'
+#' @examples
+#' # Create a temporary directory
+#' temp_dir <- tempdir()
+#' 
+#' # Set the BASE_DIR environment variable
+#' Sys.setenv(BASE_DIR = temp_dir)
+#' 
+#' # Get the base directory path
+#' get_base_dir("BASE_DIR")
+#'
 #' @export
-get_nfs_path <- function() {
-  base_path <- Sys.getenv("RXD_DATA")
-  # check that RXD_DATA is set
-  if (base_path == "") {
-    stop("Usage: get_nfs_path: RXD_DATA must be set")
+get_base_dir <- function(env_var) {
+  # Ensure env_var is a single character string
+  checkmate::assert_character(env_var, len = 1)
+
+  # Get the value of the environment variable
+  base_dir <- Sys.getenv(env_var)
+
+  # Stop if the environment variable is not set
+  if (base_dir == "") {
+    stop("Environment variable ", env_var, " is not set")
   }
-  return(base_path)
+
+  # Ensure the directory exists
+  checkmate::assert_directory_exists(base_dir)
+
+  # Return the normalized path
+  return(normalizePath(base_dir))
 }
 
-#' gets the NFS base path from an env var
-#' alias for get_nfs_path to maintain backwards compatibility
-#' @export
-get_cre_path <- get_nfs_path
-
-#' Loads data into memory based on study directory and one or more file_names.
-#' @param sub_dir A relative directory/folder that will be appended to a base path defined by `Sys.getenv("RXD_DATA")`.
-#' If the argument is left as NULL, the function will load data from the working directory `getwd()`.
-#' @param file_names Study file or file_names name(s) - can be a vector of strings.
-#' This is the only required argument.
-#' @param use_wd for "use working directory" - a flag used when importing local files
-#' not on NFS - default value is FALSE
-#' @param prefer_sas if set to TRUE, imports sas7bdat files first before looking for
-#' RDS files (the opposite of default behavior)
-#' @return a list of dataframes
+
+#' Get CRE Path
+#'
+#' This function retrieves the path to the CRE (Clinical Research Environment) directory.
+#' It uses the "RXD_DATA" environment variable as the base directory.
+#'
+#' @return [character(1)] The path to the CRE directory.
+#'
 #' @export
+get_cre_path <- function() {
+    get_base_dir(env_var = "RXD_DATA")
+}
+
+
+#' Load Data Files
+#'
+#' This function loads data files from a specified directory or the current working directory.
+#' It supports loading both RDS and SAS7BDAT files.
+#'
+#' @param sub_dir [character(1)] Optional character string specifying a subdirectory. Default is NULL.
+#' @param file_names [character(1+)] Character vector of file names to load (without extension).
+#' @param use_wd [logical(1)] Logical indicating whether to use the current working directory. Default is FALSE.
+#' @param prefer_sas [logical(1)] Logical indicating whether to prefer SAS7BDAT files over RDS. Default is FALSE.
+#' @param env_var [character(1)] The environment variable name for the base directory. Default is "RXD_DATA".
+#'
+#' @return A named list of data frames, where each name corresponds to a loaded file.
+#'
 #' @examples
 #' \dontrun{
-#' test_data_path <- "../inst/extdata/"
-#' data_list <- load_data(
-#'   sub_dir = test_data_path,
-#'   file_names = "dummyads2",
-#'   use_wd = TRUE
-#' )
+#' # Load RDS files from the directory specified by RXD_DATA environment variable
+#' data_list <- load_data(file_names = c("adsl", "adae"))
+#'
+#' # Load SAS files from a subdirectory in the current working directory
+#' data_list <- load_data(sub_dir = "adam", file_names = c("adsl", "adae"), use_wd = TRUE, prefer_sas = TRUE)
 #' }
-load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE) {
-  if (is.null(file_names)) {
-    stop("Usage: load_data: file_names: Must supply at least one file name")
-  }
-
-  study_path <- "" # will be built using args
+#' 
+#' # Set the BASE_DIR environment variable
+#' Sys.setenv(BASE_DIR = find.package("haven"))
+#' 
+#' # Get the base directory path
+#' base_dir <- get_base_dir("BASE_DIR")
+#' list.files(base_dir)
+#' list.files(file.path(base_dir, "examples"))
+#' 
+#' # Load data files
+#' data_list <- load_data(sub_dir = "examples", file_names = "iris.sas7bdat", env_var = "BASE_DIR")
+#' str(data_list)
+#' 
+#' @export
+load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE, env_var = "RXD_DATA") {
+  # Input validation
+  checkmate::assert_character(sub_dir, len = 1, null.ok = TRUE)
+  checkmate::assert_character(file_names, min.len = 1)
+  checkmate::assert_logical(use_wd, len = 1)
+  checkmate::assert_logical(prefer_sas, len = 1)
+  checkmate::assert_character(env_var, len = 1)
 
-  if (is.null(sub_dir)) {
-    study_path <- getwd()
+  # Determine the base directory
+  if (use_wd) {
+    base_dir <- getwd()
   } else {
-    if (use_wd) {
-      study_path <- file.path(getwd(), sub_dir)
-    } else {
-      study_path <- file.path(get_cre_path(), sub_dir)
-    }
+    base_dir <- get_base_dir(env_var = env_var)
   }
+  
+  # Construct the full directory path
+  dir_path <- if (is.null(sub_dir)) base_dir else file.path(base_dir, sub_dir)
+
+  # Determine the file extension based on preference
+  file_ext <- if (prefer_sas) "sas7bdat" else "rds"
+
+  # Get the full file paths
+  file_paths <- get_file_paths(dir_path = dir_path, file_names = file_names, prefer_sas = prefer_sas)
+
+  # Load the data files
+  data_list <- load_data_files(file_paths)
 
-  # create the output
-  data_list <- create_data_list(study_path, file_names, prefer_sas) # nolint
+  names(data_list) <- file_names
 
   return(data_list)
 }
diff --git a/R/utils.R b/R/utils.R
index a3791e1..fed9f31 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -1,81 +1,129 @@
-#' For each file name provided, reads in the first matching file and its meta data/attributes.
-#' Preference is given to RDS because its faster
-#' @param file_path the folder where the files are
-#' @param file_names CDISC names for the files
-#' @param prefer_sas if TRUE, imports .sas7bdat files first instead of .RDS files
-#' @return returns a list of dataframes with metadata as an attribute on each dataframe
-create_data_list <- function(file_path, file_names, prefer_sas) {
-  data_list <- lapply(file_names, function(x) {
-    extensions <- c("", ".rds", ".sas7bdat")
-    if (prefer_sas) {
-      extensions <- c("", ".sas7bdat", ".rds")
-    }
-
-    file_name_to_load <- NULL
-
-    candidates <- list.files(file_path)
-    uppercase_candidates <- Map(toupper, candidates)
-
-    for (ext in extensions) {
-      # Case insensitive file name match
-      uppercase_file_name <- toupper(paste0(x, ext))
-
-      match_count <- sum(uppercase_candidates == uppercase_file_name)
-      if (match_count > 1) {
-        stop(paste("create_data_list(): More than one case-insensitive file name match for", file_path, x))
+#' Get File Paths
+#'
+#' This function constructs file paths for given file names, handling both RDS and SAS7BDAT files.
+#' It can prioritize SAS files over RDS files based on the `prefer_sas` parameter.
+#'
+#' @param dir_path [character(1)] The directory path where the files are located.
+#' @param file_names [character(1+)] A vector of file names to process.
+#' @param prefer_sas [logical(1)] Whether to prefer SAS files over RDS files. Default is FALSE.
+#'
+#' @return [character] A vector of normalized file paths.
+#'
+#' @examples
+#' temp_dir <- tempdir()
+#' 
+#' file_names <- c("adsl", "adae")
+#' 
+#' file.create(file.path(temp_dir, paste0(file_names, ".rds")))
+#' file.create(file.path(temp_dir, paste0(file_names, ".sas7bdat")))
+#' 
+#' list.files(temp_dir)
+#' 
+#' get_file_paths(dir_path = temp_dir, file_names = file_names)
+#' get_file_paths(dir_path = temp_dir, file_names = file_names, prefer_sas = TRUE)
+#' 
+#' unlink(temp_dir, recursive = TRUE)
+#'
+#' @export
+get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
+  # Input validation
+  checkmate::assert_character(dir_path, len = 1)
+  checkmate::assert_character(file_names, min.len = 1)
+  checkmate::assert_logical(prefer_sas, len = 1)
+
+  file_paths <- lapply(file_names, function(file_name) {
+    file_path <- file.path(dir_path, file_name)
+    file_ext <- tools::file_ext(file_name)
+    
+    if (file_ext == "") {
+      # If no extension is provided, check for both RDS and SAS files
+      rds_file_name <- paste0(file_name, ".rds")
+      sas_file_name <- paste0(file_name, ".sas7bdat")
+      rds_file_path <- file.path(dir_path, rds_file_name)
+      sas_file_path <- file.path(dir_path, sas_file_name)
+      
+      if (isTRUE(prefer_sas)) {
+        # Prefer SAS file if it exists, otherwise use RDS
+        if (file.exists(sas_file_path)) {
+          return(sas_file_path)
+        } else if (file.exists(rds_file_path)) {
+          return(rds_file_path)
+        } else {
+          stop(dir_path, " does not contain: ", rds_file_name, " or ", sas_file_name)
+        }
+      } else if (isFALSE(prefer_sas)) {
+        # Prefer RDS file if it exists, otherwise use SAS
+        if (file.exists(rds_file_path)) {
+          return(rds_file_path)
+        } else if (file.exists(sas_file_path)) {
+          return(sas_file_path)
+        } else {
+          stop(dir_path, " does not contain: ", rds_file_name, " or ", sas_file_name)
+        }
       }
-
-      index <- match(uppercase_file_name, uppercase_candidates)
-      if (!is.na(index)) {
-        file_name_to_load <- candidates[[index]]
-        break
+    } else {
+      # If an extension is provided, use the exact file name
+      if (file.exists(file_path)) {
+        return(file_path)
+      } else {
+        stop(dir_path, " does not contain: ", file_name)
       }
     }
-
-    if (is.null(file_name_to_load)) {
-      stop(paste("create_data_list(): No RDS or SAS files found for", file_path, x))
-    }
-
-    output <- read_file(file_path, file_name_to_load)
-
-    return(output)
   })
 
-  names(data_list) <- file_names
-
-  return(data_list)
+  # Normalize all file paths
+  return(normalizePath(unlist(file_paths)))
 }
 
 
-#' Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path
-#' @param file_path a path to a file
-#' @param file_name name of a file
-#' @return a data object with an extra attribute of metadata
-read_file <- function(file_path, file_name) {
-  ext <- tools::file_ext(file_name)
 
-  if (!(toupper(ext) %in% c("RDS", "SAS7BDAT"))) {
-    stop("Usage error: read_file: file_name: file must either be RDS or SAS7BDAT.")
-  }
+#' Load Data Files
+#'
+#' This function reads data from multiple file paths and returns a list of data frames.
+#' It supports reading RDS and SAS7BDAT files.
+#'
+#' @param file_paths [character(1+)] A vector of file paths to read.
+#'
+#' @return [list] A named list of data frames, where each name is the basename of the corresponding file path.
+#'
+#' @examples
+#' path <- system.file("examples", "iris.sas7bdat", package = "haven")
+#' data_list <- load_data_files(file_paths = path)
+#' str(data_list)
+#' 
+#' @export
+load_data_files <- function(file_paths) {
+  # Validate input parameters
+  checkmate::assert_character(file_paths, min.len = 1)
+  checkmate::assert_file_exists(file_paths)
+
+  # Read each file and store in a list
+  data_list <- lapply(file_paths, function(file_path) {
+    # Get file extension
+    extension <- tools::file_ext(file_path)
+
+    # Read file based on its extension
+    if (tolower(extension) == "rds") {
+      data <- readRDS(file_path)
+    } else if (tolower(extension) == "sas7bdat") {
+      data <- haven::read_sas(file_path)
+    } else {
+      stop("Unsupported file extension: ", extension)
+    }
 
-  is_rds <- toupper(ext) == "RDS"
+    # Get file metadata
+    meta <- file.info(file_path, extra_cols = FALSE)
+    meta[["path"]] <- file_path
+    meta[["file_name"]] <- basename(file_path)
 
-  file <- file.path(file_path, file_name)
-  file_name <- tools::file_path_sans_ext(file_name)
+    # Add metadata as an attribute to the data
+    attr(data, "meta") <- as.list(meta)
 
-  # grab file info
-  meta <- file.info(file)[1L:6L]
-  meta[["path"]] <- row.names(meta)
-  meta[["file_name"]] <- file_name
-  meta <- data.frame(meta, stringsAsFactors = FALSE)
-  row.names(meta) <- NULL
+    return(data)
+  })
 
-  if (is_rds) {
-    out <- readRDS(file)
-  } else {
-    out <- haven::read_sas(file)
-  }
-  attr(out, "meta") <- meta
+  # Set names of the list elements to the basenames of the file paths
+  names(data_list) <- basename(file_paths)
 
-  return(out)
+  return(data_list)
 }

From ff5d20262174b036f00791a481ef3f1c08b491e4 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Fri, 18 Oct 2024 10:41:47 +0800
Subject: [PATCH 02/37] Update examples

---
 R/dvloader.R | 24 ++++++++----------------
 1 file changed, 8 insertions(+), 16 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index 2d22547..4a3e7b0 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -65,26 +65,18 @@ get_cre_path <- function() {
 #' @return A named list of data frames, where each name corresponds to a loaded file.
 #'
 #' @examples
-#' \dontrun{
-#' # Load RDS files from the directory specified by RXD_DATA environment variable
-#' data_list <- load_data(file_names = c("adsl", "adae"))
-#'
-#' # Load SAS files from a subdirectory in the current working directory
-#' data_list <- load_data(sub_dir = "adam", file_names = c("adsl", "adae"), use_wd = TRUE, prefer_sas = TRUE)
-#' }
+#' # Get the current value of the RXD_DATA environment variable
+#' base_dir <- Sys.getenv("RXD_DATA")
 #' 
-#' # Set the BASE_DIR environment variable
-#' Sys.setenv(BASE_DIR = find.package("haven"))
+#' # Set the RXD_DATA environment variable to the path of the haven package
+#' Sys.setenv(RXD_DATA = find.package("haven"))
 #' 
-#' # Get the base directory path
-#' base_dir <- get_base_dir("BASE_DIR")
-#' list.files(base_dir)
-#' list.files(file.path(base_dir, "examples"))
-#' 
-#' # Load data files
-#' data_list <- load_data(sub_dir = "examples", file_names = "iris.sas7bdat", env_var = "BASE_DIR")
+#' data_list <- load_data(sub_dir = "examples", file_names = c("iris.sas7bdat"))
 #' str(data_list)
 #' 
+#' # Reset the RXD_DATA environment variable to its original value
+#' Sys.setenv(RXD_DATA = base_dir)
+#' 
 #' @export
 load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE, env_var = "RXD_DATA") {
   # Input validation

From 432e835beb4e876e549410c600b10a955c2c45b5 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Fri, 18 Oct 2024 10:42:38 +0800
Subject: [PATCH 03/37]  Print the directory path and file names

---
 R/dvloader.R | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/R/dvloader.R b/R/dvloader.R
index 4a3e7b0..3e3d557 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -102,6 +102,10 @@ load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = F
   # Get the full file paths
   file_paths <- get_file_paths(dir_path = dir_path, file_names = file_names, prefer_sas = prefer_sas)
 
+  # Print the directory path and file names
+  cat("Loading data from", dir_path, "\n")
+  cat("Loading data file(s):", basename(file_paths), "\n")
+
   # Load the data files
   data_list <- load_data_files(file_paths)
 

From 9ec6f69872d8f46c6e109df8437fcdd74669b8d0 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Mon, 21 Oct 2024 16:12:22 +0800
Subject: [PATCH 04/37] Add an arugment to print file paths if requested

---
 R/dvloader.R | 11 +++++++----
 1 file changed, 7 insertions(+), 4 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index 3e3d557..b6cb43d 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -61,6 +61,7 @@ get_cre_path <- function() {
 #' @param use_wd [logical(1)] Logical indicating whether to use the current working directory. Default is FALSE.
 #' @param prefer_sas [logical(1)] Logical indicating whether to prefer SAS7BDAT files over RDS. Default is FALSE.
 #' @param env_var [character(1)] The environment variable name for the base directory. Default is "RXD_DATA".
+#' @param print_file_paths [logical(1)] Logical indicating whether to print the directory path and file names. Default is FALSE.
 #'
 #' @return A named list of data frames, where each name corresponds to a loaded file.
 #'
@@ -78,7 +79,7 @@ get_cre_path <- function() {
 #' Sys.setenv(RXD_DATA = base_dir)
 #' 
 #' @export
-load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE, env_var = "RXD_DATA") {
+load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE, env_var = "RXD_DATA", print_file_paths = FALSE) {
   # Input validation
   checkmate::assert_character(sub_dir, len = 1, null.ok = TRUE)
   checkmate::assert_character(file_names, min.len = 1)
@@ -102,9 +103,11 @@ load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = F
   # Get the full file paths
   file_paths <- get_file_paths(dir_path = dir_path, file_names = file_names, prefer_sas = prefer_sas)
 
-  # Print the directory path and file names
-  cat("Loading data from", dir_path, "\n")
-  cat("Loading data file(s):", basename(file_paths), "\n")
+  # Print the directory path and file names if requested
+  if (isTRUE(print_file_paths)) { 
+    cat("Loading data from", dir_path, "\n")
+    cat("Loading data file(s):", basename(file_paths), "\n")
+  }
 
   # Load the data files
   data_list <- load_data_files(file_paths)

From bda40b4bac503ac130c98d8c5701b94dc88ffe69 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Mon, 21 Oct 2024 16:14:58 +0800
Subject: [PATCH 05/37] Do not export get_base_dir()

---
 R/dvloader.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index b6cb43d..ae8d0fb 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -16,8 +16,7 @@
 #' 
 #' # Get the base directory path
 #' get_base_dir("BASE_DIR")
-#'
-#' @export
+#' 
 get_base_dir <- function(env_var) {
   # Ensure env_var is a single character string
   checkmate::assert_character(env_var, len = 1)

From b155b1aec2fac95fdd8422cc1d036810d75efb72 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Mon, 21 Oct 2024 16:42:13 +0800
Subject: [PATCH 06/37] Add get_nfs_path() function back

---
 R/dvloader.R | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index ae8d0fb..ee8bb82 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -36,12 +36,25 @@ get_base_dir <- function(env_var) {
   return(normalizePath(base_dir))
 }
 
+#' Get NFS Path
+#'
+#' This function retrieves the path to the NFS (Network File System) directory.
+#'
+#' @param env_var [character(1)] The environment variable name for the base directory. Default is "RXD_DATA".
+#' 
+#' @return [character(1)] The path to the NFS directory.
+#'
+#' @export
+get_nfs_path <- function(env_var = "RXD_DATA") {
+    get_base_dir(env_var = env_var)
+}
+
 
 #' Get CRE Path
 #'
 #' This function retrieves the path to the CRE (Clinical Research Environment) directory.
 #' It uses the "RXD_DATA" environment variable as the base directory.
-#'
+#' 
 #' @return [character(1)] The path to the CRE directory.
 #'
 #' @export

From f7601bf9c6454f570f753ced13641451eac0955f Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Mon, 21 Oct 2024 16:49:08 +0800
Subject: [PATCH 07/37] Keep the metadata format unchanged

---
 R/utils.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/utils.R b/R/utils.R
index fed9f31..93ac178 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -117,7 +117,8 @@ load_data_files <- function(file_paths) {
     meta[["file_name"]] <- basename(file_path)
 
     # Add metadata as an attribute to the data
-    attr(data, "meta") <- as.list(meta)
+    rownames(data) <- NULL
+    attr(data, "meta") <- meta
 
     return(data)
   })

From 65704612be3e7b30dce670fee17324e90cee46d1 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Tue, 22 Oct 2024 19:30:50 +0800
Subject: [PATCH 08/37] Update README

---
 README.md | 77 +++++++++++++++++++++++++++++++++++++++++++------------
 1 file changed, 61 insertions(+), 16 deletions(-)

diff --git a/README.md b/README.md
index 1199129..ab3eadc 100644
--- a/README.md
+++ b/README.md
@@ -1,30 +1,75 @@
-# Data Loading
-
-The {dv.loader} package provides a simple interface for loading data from a network file storage folder or 
-locally. It is designed to be used with `.RDS` and `.sas7bdat` file formats.
-The package provides a simple function, `load_data()`, which loads R and SAS data files into memory. 
-Loading data from SQL databases is not yet supported. The function returns a list named by the file names passed, 
-and containing data frames, along with metadata for that table. By default, the function will look for files in a
-sub-directory `sub_dir` of the base path defined by a environment variable "RXD_DATA". You can check if the base path
-is set by running `Sys.getenv("RXD_DATA")`. A single file or multiple files can be loaded at once. 
-To make the loading process faster for large datasets, it is suggested that '.sas7bdat' files are converted to 
-'.RDS' files. The function will prefer '.RDS' files over '.sas7bdat' files by default.
+# dv.loader
+
+The `dv.loader` package is designed to simplify the data loading process for creating modular Shiny applications within the DaVinci framework.
+
+Key features of `dv.loader` include:
+
+1. Capability to import multiple files from a data directory.
+
+2. Compatibility with both `.rds` and `.sas7bdat` file types.
+
+3. Smooth integration with other packages in the DaVinci ecosystem.
+
 
 ## Installation
 
+You can install the `dv.loader` package from GitHub using the `remotes` package:
+
 ```r
+# Install the remotes package if not already installed
 if (!require("remotes")) install.packages("remotes")
+
+# Install the dv.loader package from GitHub
 remotes::install_github("Boehringer-Ingelheim/dv.loader")
 ```
 
-## Basic usage
+## Examples
+
+The main function is `dv.loader::load_data()`, which loads data files from sub-directories of a network file system (NFS) or the working directory.
+
+### Example 1: Sub-directory of Network File System (NFS)
+
+To load data files from a NFS, you need to set the NFS path as an environment variable. By default, the environment variable name is `RXD_DATA`.
+
+You can run the following command to check the NFS path if it is already set.
 
 ```r
-# getting data from a network file storage folder
-dv.loader::load_data(sub_dir = "subdir1/subdir2", file_names = c("adsl", "adae"))
+# Check the NFS path
+dv.loader::get_nfs_path()
 ```
 
+If the NFS path is not set, you can set it by running the following command.
+
 ```r
-# getting data locally (e.g., if you have file `./data/adsl.RDS`)
-dv.loader::load_data(sub_dir = "data", file_names = c("adsl"), use_wd = TRUE)
+# Set the NFS path as an environment variable
+Sys.setenv(RXD_DATA = "path/to/network-file-system")
 ```
+
+The environment variable setup is not needed if you have already set the NFS path as an environment variable in your `.Renviron` or `.Rprofile` file. 
+
+If the NFS path has been properly set, you can load data files from the NFS and its sub-directories.
+
+```r
+# Load data files from the specified sub-directory of a network file system (NFS)
+dv.loader::load_data(
+    sub_dir = "sub-directory/of/network-file-system",
+    file_names = c("adsl.sas7bdat", "adae.sas7bdat")
+)
+```
+
+For the `file_names` argument, it is recommended to use the full file names including the file extension. 
+
+### Example 2: Sub-directory of the Working Directory
+
+To load data files from a local directory, there is no need to set an environment variable. You use `use_wd = TRUE` to indicate that the data files are loaded from a sub-directory of the working directory.
+
+```r
+# Load data files from the specified sub-directory of the working directory
+dv.loader::load_data(
+    sub_dir = "sub-directory/of/working-directory",
+    file_names = c("adsl.sas7bdat", "adae.sas7bdat"),
+    use_wd = TRUE
+)
+```
+
+Additional examples can be found in the package vignettes.

From 488d6792b9cbdb5904e99c6dfc0ef8b5aad5cccf Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Tue, 22 Oct 2024 19:47:44 +0800
Subject: [PATCH 09/37] Update package vignettes

---
 vignettes/.gitignore                   |  2 +
 vignettes/integration-guide.Rmd        | 65 ++++++++++++++++++++++++++
 vignettes/loading-data-into-memory.Rmd | 45 ------------------
 3 files changed, 67 insertions(+), 45 deletions(-)
 create mode 100644 vignettes/.gitignore
 create mode 100644 vignettes/integration-guide.Rmd
 delete mode 100644 vignettes/loading-data-into-memory.Rmd

diff --git a/vignettes/.gitignore b/vignettes/.gitignore
new file mode 100644
index 0000000..097b241
--- /dev/null
+++ b/vignettes/.gitignore
@@ -0,0 +1,2 @@
+*.html
+*.R
diff --git a/vignettes/integration-guide.Rmd b/vignettes/integration-guide.Rmd
new file mode 100644
index 0000000..802f252
--- /dev/null
+++ b/vignettes/integration-guide.Rmd
@@ -0,0 +1,65 @@
+---
+title: "Integration Guide"
+output: rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Integration Guide}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>"
+)
+```
+
+This vignette showcases the integration of the {dv.loader} package with other packages from the DaVinci framework. It guides you through the process of combining {dv.loader} with {dv.manager} and {dv.listings} to create a modular Shiny application.
+
+```{r, eval=FALSE}
+# Install the {remotes} package if you haven't already
+if (!require("remotes")) install.packages("remotes")
+
+# Define the packages to install
+pkgs <- c("dv.loader", "dv.manager", "dv.listings")
+
+# Install the packages from GitHub
+remotes::install_github(repo = paste0("Boehringer-Ingelheim/", pkgs))
+```
+
+## Step 1: Load data files
+
+```{r, eval=FALSE}
+# Set the NFS path as an environment variable
+Sys.setenv(RXD_DATA = "path/to/network-file-system")
+
+# Load data files from the specified sub-directory of a network file system (NFS)
+data_list <- dv.loader::load_data(
+    sub_dir = "sub-directory/of/network-file-system",
+    file_names = c("adsl.sas7bdat", "adae.sas7bdat")
+)
+```
+
+## Step 2: Create a module list
+
+```{r, eval=FALSE}
+# Include a module containing two data listings
+module_list <- list(
+  "Data Listings" = dv.listings::mod_listings(
+    module_id = "data_listings",
+    dataset_names = c("adsl.sas7bdat", "adae.sas7bdat")
+  )
+)
+```
+
+## Step 3: Run the DaVinci application
+
+```{r, eval=FALSE}
+# Run the DaVinci application with data and module lists defined earlier
+dv.manager::run_app(
+  data = list("Datasets" = data_list),
+  module_list = module_list,
+  filter_data = "adsl.sas7bdat",
+  title = "DaVinci Application"
+)
+```
diff --git a/vignettes/loading-data-into-memory.Rmd b/vignettes/loading-data-into-memory.Rmd
deleted file mode 100644
index 577da15..0000000
--- a/vignettes/loading-data-into-memory.Rmd
+++ /dev/null
@@ -1,45 +0,0 @@
----
-title: "Loading Data into Memory"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{Loading Data into Memory}
-  %\VignetteEngine{knitr::rmarkdown}
-  %\VignetteEncoding{UTF-8}
----
-
-```{r, include = FALSE}
-knitr::opts_chunk$set(
-  collapse = TRUE,
-  comment = "#>"
-)
-```
-
-```{r setup}
-library(dv.loader)
-```
-
-Note: `use_wd = TRUE` can be used to source from local folder. Just set your working directory before using with `setwd()`, or use an explicit path in `sub_dir`.
-
-## Usage: `load_data()`
-
-```{r}
-test_data_path <- "../tests/testthat/inst/extdata"
-data_list <- load_data(
-  sub_dir = test_data_path,
-  file_names = "dummyads2",
-  use_wd = TRUE
-)
-
-
-class(data_list)
-
-class(data_list[["dummyads2"]])
-
-head(data_list[["dummyads2"]])
-```
-
-Get the dataframe's metadata through its attributes:
-
-```{r}
-attr(data_list[["dummyads2"]], "meta")
-```

From 1f256bcb4a5839b28fca458f643150030044fdf3 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Tue, 22 Oct 2024 22:53:56 +0800
Subject: [PATCH 10/37] Add sample data for docs and tests

---
 inst/extdata/data.R                           |  41 ++++++++++++++++++
 inst/extdata/pharmaverseadam/adae_sample.rds  | Bin 0 -> 5592 bytes
 .../pharmaverseadam/adae_sample.sas7bdat      | Bin 0 -> 69632 bytes
 inst/extdata/pharmaverseadam/adsl_sample.rds  | Bin 0 -> 2201 bytes
 .../pharmaverseadam/adsl_sample.sas7bdat      | Bin 0 -> 28672 bytes
 5 files changed, 41 insertions(+)
 create mode 100644 inst/extdata/data.R
 create mode 100644 inst/extdata/pharmaverseadam/adae_sample.rds
 create mode 100644 inst/extdata/pharmaverseadam/adae_sample.sas7bdat
 create mode 100644 inst/extdata/pharmaverseadam/adsl_sample.rds
 create mode 100644 inst/extdata/pharmaverseadam/adsl_sample.sas7bdat

diff --git a/inst/extdata/data.R b/inst/extdata/data.R
new file mode 100644
index 0000000..29c1d03
--- /dev/null
+++ b/inst/extdata/data.R
@@ -0,0 +1,41 @@
+# Create directory for pharmaverseadam data if it doesn't exist
+data_dir <- file.path("inst", "extdata", "pharmaverseadam")
+if (!dir.exists(data_dir)) {
+  dir.create(data_dir, recursive = TRUE)
+}
+
+# Sample 10 subjects from adsl data
+set.seed(123) # For reproducibility
+adsl_sample <- pharmaverseadam::adsl |> 
+  dplyr::sample_n(size = 10)
+
+# Filter adae data for the 10 subjects in adsl_sample
+adae_sample <- pharmaverseadam::adae |> 
+  dplyr::filter(USUBJID %in% adsl_sample$USUBJID)
+
+# Save adsl_sample to rds file
+saveRDS(
+  object = adsl_sample,
+  file = file.path(data_dir, "adsl_sample.rds")
+)
+
+# Save adae_sample to rds file
+saveRDS(
+  object = adae_sample,
+  file = file.path(data_dir, "adae_sample.rds")
+)
+
+# Write adsl_sample to sas7bdat file
+haven::write_sas(
+  data = adsl_sample,
+  path = file.path(data_dir, "adsl_sample.sas7bdat")
+)
+
+# Write adae_sample to sas7bdat file
+haven::write_sas(
+  data = adae_sample,
+  path = file.path(data_dir, "adae_sample.sas7bdat")
+)
+
+# Add a message to confirm data creation
+message("Sample data files have been created in ", data_dir)
diff --git a/inst/extdata/pharmaverseadam/adae_sample.rds b/inst/extdata/pharmaverseadam/adae_sample.rds
new file mode 100644
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From 088feb57a1d57c91e77ebf57886b4734a087c974 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 10:23:27 +0800
Subject: [PATCH 11/37] Update Rd files

---
 man/create_data_list.Rd | 23 ------------------
 man/get_base_dir.Rd     | 30 ++++++++++++++++++++++++
 man/get_cre_path.Rd     | 10 ++++----
 man/get_file_paths.Rd   | 38 ++++++++++++++++++++++++++++++
 man/get_nfs_path.Rd     | 15 ++++++------
 man/load_data.Rd        | 52 +++++++++++++++++++++++++----------------
 man/load_data_files.Rd  | 24 +++++++++++++++++++
 man/read_file.Rd        | 19 ---------------
 8 files changed, 137 insertions(+), 74 deletions(-)
 delete mode 100644 man/create_data_list.Rd
 create mode 100644 man/get_base_dir.Rd
 create mode 100644 man/get_file_paths.Rd
 create mode 100644 man/load_data_files.Rd
 delete mode 100644 man/read_file.Rd

diff --git a/man/create_data_list.Rd b/man/create_data_list.Rd
deleted file mode 100644
index 2368307..0000000
--- a/man/create_data_list.Rd
+++ /dev/null
@@ -1,23 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{create_data_list}
-\alias{create_data_list}
-\title{For each file name provided, reads in the first matching file and its meta data/attributes.
-Preference is given to RDS because its faster}
-\usage{
-create_data_list(file_path, file_names, prefer_sas)
-}
-\arguments{
-\item{file_path}{the folder where the files are}
-
-\item{file_names}{CDISC names for the files}
-
-\item{prefer_sas}{if TRUE, imports .sas7bdat files first instead of .RDS files}
-}
-\value{
-returns a list of dataframes with metadata as an attribute on each dataframe
-}
-\description{
-For each file name provided, reads in the first matching file and its meta data/attributes.
-Preference is given to RDS because its faster
-}
diff --git a/man/get_base_dir.Rd b/man/get_base_dir.Rd
new file mode 100644
index 0000000..891d825
--- /dev/null
+++ b/man/get_base_dir.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/dvloader.R
+\name{get_base_dir}
+\alias{get_base_dir}
+\title{Get Base Directory Path}
+\usage{
+get_base_dir(env_var)
+}
+\arguments{
+\item{env_var}{[character(1)] The name of the environment variable containing the base directory path.}
+}
+\value{
+[character(1)] The normalized path to the base directory.
+}
+\description{
+This function retrieves the base directory path from a specified environment variable.
+It checks if the environment variable is set and if the directory exists.
+}
+\examples{
+# Create a temporary directory
+temp_dir <- tempdir()
+
+# Set the BASE_DIR environment variable
+Sys.setenv(BASE_DIR = temp_dir)
+
+# Get the base directory path
+dv.loader:::get_base_dir("BASE_DIR")
+
+}
+\keyword{internal}
diff --git a/man/get_cre_path.Rd b/man/get_cre_path.Rd
index 86b2b78..03686b2 100644
--- a/man/get_cre_path.Rd
+++ b/man/get_cre_path.Rd
@@ -2,12 +2,14 @@
 % Please edit documentation in R/dvloader.R
 \name{get_cre_path}
 \alias{get_cre_path}
-\title{gets the NFS base path from an env var
-alias for get_nfs_path to maintain backwards compatibility}
+\title{Get CRE Path}
 \usage{
 get_cre_path()
 }
+\value{
+[character(1)] The path to the CRE directory.
+}
 \description{
-gets the NFS base path from an env var
-alias for get_nfs_path to maintain backwards compatibility
+This function retrieves the path to the CRE (Clinical Research Environment) directory.
+It uses the "RXD_DATA" environment variable as the base directory.
 }
diff --git a/man/get_file_paths.Rd b/man/get_file_paths.Rd
new file mode 100644
index 0000000..dc19143
--- /dev/null
+++ b/man/get_file_paths.Rd
@@ -0,0 +1,38 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{get_file_paths}
+\alias{get_file_paths}
+\title{Get File Paths}
+\usage{
+get_file_paths(dir_path, file_names, prefer_sas = FALSE)
+}
+\arguments{
+\item{dir_path}{[character(1)] The directory path where the files are located.}
+
+\item{file_names}{[character(1+)] A vector of file names to process.}
+
+\item{prefer_sas}{[logical(1)] Whether to prefer SAS files over RDS files. Default is FALSE.}
+}
+\value{
+[character] A vector of normalized file paths.
+}
+\description{
+This function constructs file paths for given file names, handling both RDS and SAS7BDAT files.
+It can prioritize SAS files over RDS files based on the `prefer_sas` parameter.
+}
+\examples{
+temp_dir <- tempdir()
+
+file_names <- c("adsl", "adae")
+
+file.create(file.path(temp_dir, paste0(file_names, ".rds")))
+file.create(file.path(temp_dir, paste0(file_names, ".sas7bdat")))
+
+list.files(temp_dir)
+
+get_file_paths(dir_path = temp_dir, file_names = file_names)
+get_file_paths(dir_path = temp_dir, file_names = file_names, prefer_sas = TRUE)
+
+unlink(temp_dir, recursive = TRUE)
+
+}
diff --git a/man/get_nfs_path.Rd b/man/get_nfs_path.Rd
index 5cbad09..3c4ba73 100644
--- a/man/get_nfs_path.Rd
+++ b/man/get_nfs_path.Rd
@@ -2,17 +2,16 @@
 % Please edit documentation in R/dvloader.R
 \name{get_nfs_path}
 \alias{get_nfs_path}
-\title{gets the NFS base path from an env var
-It assumes there is an env var
-called RXD_DATA which holds the path suffix.}
+\title{Get NFS Path}
 \usage{
-get_nfs_path()
+get_nfs_path(env_var = "RXD_DATA")
+}
+\arguments{
+\item{env_var}{[character(1)] The environment variable name for the base directory. Default is "RXD_DATA".}
 }
 \value{
-the NFS base path
+[character(1)] The path to the NFS directory.
 }
 \description{
-gets the NFS base path from an env var
-It assumes there is an env var
-called RXD_DATA which holds the path suffix.
+This function retrieves the path to the NFS (Network File System) directory.
 }
diff --git a/man/load_data.Rd b/man/load_data.Rd
index 5367158..50f7187 100644
--- a/man/load_data.Rd
+++ b/man/load_data.Rd
@@ -2,36 +2,48 @@
 % Please edit documentation in R/dvloader.R
 \name{load_data}
 \alias{load_data}
-\title{Loads data into memory based on study directory and one or more file_names.}
+\title{Load Data Files}
 \usage{
-load_data(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE)
+load_data(
+  sub_dir = NULL,
+  file_names,
+  use_wd = FALSE,
+  prefer_sas = FALSE,
+  env_var = "RXD_DATA",
+  print_file_paths = FALSE
+)
 }
 \arguments{
-\item{sub_dir}{A relative directory/folder that will be appended to a base path defined by `Sys.getenv("RXD_DATA")`. 
-If the argument is left as NULL, the function will load data from the working directory `getwd()`.}
+\item{sub_dir}{[character(1)] Optional character string specifying a subdirectory. Default is NULL.}
+
+\item{file_names}{[character(1+)] Character vector of file names to load (without extension).}
+
+\item{use_wd}{[logical(1)] Logical indicating whether to use the current working directory. Default is FALSE.}
 
-\item{file_names}{Study file or file_names name(s) - can be a vector of strings.
-This is the only required argument.}
+\item{prefer_sas}{[logical(1)] Logical indicating whether to prefer SAS7BDAT files over RDS. Default is FALSE.}
 
-\item{use_wd}{for "use working directory" - a flag used when importing local files
-not on NFS - default value is FALSE}
+\item{env_var}{[character(1)] The environment variable name for the base directory. Default is "RXD_DATA".}
 
-\item{prefer_sas}{if set to TRUE, imports sas7bdat files first before looking for
-RDS files (the opposite of default behavior)}
+\item{print_file_paths}{[logical(1)] Logical indicating whether to print the directory path and file names. Default is FALSE.}
 }
 \value{
-a list of dataframes
+A named list of data frames, where each name corresponds to a loaded file.
 }
 \description{
-Loads data into memory based on study directory and one or more file_names.
+This function loads data files from a specified directory or the current working directory.
+It supports loading both RDS and SAS7BDAT files.
 }
 \examples{
-\dontrun{
-test_data_path <- "../inst/extdata/"
-data_list <- load_data(
-  sub_dir = test_data_path,
-  file_names = "dummyads2",
-  use_wd = TRUE
-)
-}
+# Get the current value of the RXD_DATA environment variable
+base_dir <- Sys.getenv("RXD_DATA")
+
+# Set the RXD_DATA environment variable to the path of the haven package
+Sys.setenv(RXD_DATA = find.package("haven"))
+
+data_list <- load_data(sub_dir = "examples", file_names = c("iris.sas7bdat"))
+str(data_list)
+
+# Reset the RXD_DATA environment variable to its original value
+Sys.setenv(RXD_DATA = base_dir)
+
 }
diff --git a/man/load_data_files.Rd b/man/load_data_files.Rd
new file mode 100644
index 0000000..ccaac13
--- /dev/null
+++ b/man/load_data_files.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/utils.R
+\name{load_data_files}
+\alias{load_data_files}
+\title{Load Data Files}
+\usage{
+load_data_files(file_paths)
+}
+\arguments{
+\item{file_paths}{[character(1+)] A vector of file paths to read.}
+}
+\value{
+[list] A named list of data frames, where each name is the basename of the corresponding file path.
+}
+\description{
+This function reads data from multiple file paths and returns a list of data frames.
+It supports reading RDS and SAS7BDAT files.
+}
+\examples{
+path <- system.file("examples", "iris.sas7bdat", package = "haven")
+data_list <- load_data_files(file_paths = path)
+str(data_list)
+
+}
diff --git a/man/read_file.Rd b/man/read_file.Rd
deleted file mode 100644
index e46767b..0000000
--- a/man/read_file.Rd
+++ /dev/null
@@ -1,19 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/utils.R
-\name{read_file}
-\alias{read_file}
-\title{Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path}
-\usage{
-read_file(file_path, file_name)
-}
-\arguments{
-\item{file_path}{a path to a file}
-
-\item{file_name}{name of a file}
-}
-\value{
-a data object with an extra attribute of metadata
-}
-\description{
-Reads RDS/SAS file and metadatas from first 6 items from file.info() its file path
-}

From 30619aba5051fdbd973ea81d63a89919a2378a8e Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 13:50:20 +0800
Subject: [PATCH 12/37] Update tests

---
 tests/testthat.R       |  5 ++++-
 tests/testthat/tests.R | 15 +++++++++++++++
 2 files changed, 19 insertions(+), 1 deletion(-)

diff --git a/tests/testthat.R b/tests/testthat.R
index 8d34285..784ab0f 100644
--- a/tests/testthat.R
+++ b/tests/testthat.R
@@ -1,3 +1,6 @@
 pkg_name <- "dv.loader"
+
+library(testthat)
 library(pkg_name, character.only = TRUE)
-testthat::test_check(pkg_name)
+
+test_check(pkg_name)
diff --git a/tests/testthat/tests.R b/tests/testthat/tests.R
index d5e5747..b5e0527 100644
--- a/tests/testthat/tests.R
+++ b/tests/testthat/tests.R
@@ -205,3 +205,18 @@ test_that(
     expect_equal(grepl(".RDS$", actual), TRUE)
   }
 )
+
+test_that(
+  "prefer_sas is not used if file extension is included in file_names" %>%
+    vdoc[["add_spec"]](specs$prefer_sas),
+  {
+    data_list <- load_data(
+      sub_dir = local_test_path,
+      file_names = c("dummyads1.RDS", "dummyads2.sas7bdat"),
+      use_wd = TRUE,
+      prefer_sas = FALSE
+    )
+    expect_equal(tools::file_ext(attr(data_list[[1]], "meta")$path), "RDS")
+    expect_equal(tools::file_ext(attr(data_list[[2]], "meta")$path), "sas7bdat")
+  }
+)

From 8298ec2c1beb7927434516b948d129418def066f Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 13:59:31 +0800
Subject: [PATCH 13/37] Update test setup file

---
 tests/testthat/setup.R | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 1dab7a6..47bcc78 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -1,9 +1,7 @@
 # validation (S)
 vdoc <- local({
-  #                      ##########
   # package_name is used # INSIDE # the sourced file below
-  #                      ##########
-  package_name <- read.dcf("../../DESCRIPTION")[, "Package"]
+  package_name <- "dv.loader" # read.dcf("../../DESCRIPTION")[, "Package"]
   utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
   source(utils_file_path, local = TRUE)[["value"]]
 })

From 9cb51ac4d4da716bdc2426e3556de34ef6597401 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 14:00:35 +0800
Subject: [PATCH 14/37] Update integration guide

---
 vignettes/integration-guide.Rmd | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/vignettes/integration-guide.Rmd b/vignettes/integration-guide.Rmd
index 802f252..f142d6c 100644
--- a/vignettes/integration-guide.Rmd
+++ b/vignettes/integration-guide.Rmd
@@ -31,12 +31,13 @@ remotes::install_github(repo = paste0("Boehringer-Ingelheim/", pkgs))
 
 ```{r, eval=FALSE}
 # Set the NFS path as an environment variable
-Sys.setenv(RXD_DATA = "path/to/network-file-system")
+Sys.setenv(RXD_DATA = find.package("dv.loader"))
 
 # Load data files from the specified sub-directory of a network file system (NFS)
 data_list <- dv.loader::load_data(
-    sub_dir = "sub-directory/of/network-file-system",
-    file_names = c("adsl.sas7bdat", "adae.sas7bdat")
+    sub_dir = "extdata/pharmaverseadam",
+    file_names = c("adsl_sample", "adae_sample"),
+    print_file_paths = TRUE
 )
 ```
 
@@ -47,7 +48,7 @@ data_list <- dv.loader::load_data(
 module_list <- list(
   "Data Listings" = dv.listings::mod_listings(
     module_id = "data_listings",
-    dataset_names = c("adsl.sas7bdat", "adae.sas7bdat")
+    dataset_names = c("adsl_sample", "adae_sample")
   )
 )
 ```
@@ -57,9 +58,9 @@ module_list <- list(
 ```{r, eval=FALSE}
 # Run the DaVinci application with data and module lists defined earlier
 dv.manager::run_app(
-  data = list("Datasets" = data_list),
+  data = list("Demo Data" = data_list),
   module_list = module_list,
-  filter_data = "adsl.sas7bdat",
+  filter_data = "adsl_sample",
   title = "DaVinci Application"
 )
 ```

From 01de80362398a9f717523100b8b16152fcba1473 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 14:01:23 +0800
Subject: [PATCH 15/37] Make get_base_dir internal function

---
 R/dvloader.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index ee8bb82..c07a534 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -15,8 +15,9 @@
 #' Sys.setenv(BASE_DIR = temp_dir)
 #' 
 #' # Get the base directory path
-#' get_base_dir("BASE_DIR")
+#' dv.loader:::get_base_dir("BASE_DIR")
 #' 
+#' @keywords internal
 get_base_dir <- function(env_var) {
   # Ensure env_var is a single character string
   checkmate::assert_character(env_var, len = 1)

From b111f9a5c38456acdcca990fe1ce2deff19bf14b Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 14:01:53 +0800
Subject: [PATCH 16/37] Export get_file_paths and load_data_files

---
 NAMESPACE | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 79ce8a0..be207da 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(get_cre_path)
+export(get_file_paths)
 export(get_nfs_path)
 export(load_data)
+export(load_data_files)

From a4801246b54c1fd1a58ee69ab2366c5de2f91ce7 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 14:02:11 +0800
Subject: [PATCH 17/37] Update DESCRIPTION file

---
 DESCRIPTION | 9 ++++++---
 1 file changed, 6 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a12e282..05bf0ab 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: dv.loader
 Type: Package
 Title: Data loading module 
-Version: 2.0.0
+Version: 2.1.0
 Authors@R: c(
         person( "Boehringer-Ingelheim Pharma GmbH & Co.KG", role = c("cph", "fnd")),
         person( given = "Ming", family = "Yang", role = c("aut", "cre"), email = "ming.yang.ext@boehringer-ingelheim.com"),
@@ -13,10 +13,13 @@ License: Apache License (>= 2)
 Encoding: UTF-8
 LazyData: true
 Depends: R (>= 3.5.0)
-Imports: haven
+Imports:
+    checkmate,
+    haven
 Suggests: 
-    testthat,
+    testthat (>= 3.0.0),
     knitr,
     rmarkdown
 RoxygenNote: 7.3.0
 VignetteBuilder: knitr
+Config/testthat/edition: 3

From 8722c94e24ca4f589a1ef706b3aca953a2251a52 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 14:20:45 +0800
Subject: [PATCH 18/37] Update changelog

---
 NEWS.md | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index a5c5124..e3df5dc 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,11 @@
+# dv.loader 2.1.0
+
+- Refactored code to improve readability and maintainability.
+
+- Fixed issue of partial matching when the `file_names` argument contains no file extensions.
+
+- Added arguments `env_var` and `print_file_paths` in `load_data()` function to provide more flexibility and control.
+
 # dv.loader 2.0.0
 
 - GitHub release with QC report

From 8bcefd3ffa78c10c7a969d652d10f0ab7d947478 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 14:43:10 +0800
Subject: [PATCH 19/37] Update roxygen examples

---
 R/utils.R             | 2 ++
 man/get_file_paths.Rd | 2 ++
 2 files changed, 4 insertions(+)

diff --git a/R/utils.R b/R/utils.R
index 93ac178..c7a0089 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -10,6 +10,7 @@
 #' @return [character] A vector of normalized file paths.
 #'
 #' @examples
+#' \dontrun{
 #' temp_dir <- tempdir()
 #' 
 #' file_names <- c("adsl", "adae")
@@ -23,6 +24,7 @@
 #' get_file_paths(dir_path = temp_dir, file_names = file_names, prefer_sas = TRUE)
 #' 
 #' unlink(temp_dir, recursive = TRUE)
+#' }
 #'
 #' @export
 get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
diff --git a/man/get_file_paths.Rd b/man/get_file_paths.Rd
index dc19143..57751eb 100644
--- a/man/get_file_paths.Rd
+++ b/man/get_file_paths.Rd
@@ -21,6 +21,7 @@ This function constructs file paths for given file names, handling both RDS and
 It can prioritize SAS files over RDS files based on the `prefer_sas` parameter.
 }
 \examples{
+\dontrun{
 temp_dir <- tempdir()
 
 file_names <- c("adsl", "adae")
@@ -34,5 +35,6 @@ get_file_paths(dir_path = temp_dir, file_names = file_names)
 get_file_paths(dir_path = temp_dir, file_names = file_names, prefer_sas = TRUE)
 
 unlink(temp_dir, recursive = TRUE)
+}
 
 }

From 5b719dd80cb812141672ba4b5ee379f496f9b12f Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 15:08:16 +0800
Subject: [PATCH 20/37] Fix lintr issues

---
 R/dvloader.R           | 12 ++++++++++--
 tests/testthat/setup.R |  2 +-
 2 files changed, 11 insertions(+), 3 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index c07a534..b983c00 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -74,7 +74,8 @@ get_cre_path <- function() {
 #' @param use_wd [logical(1)] Logical indicating whether to use the current working directory. Default is FALSE.
 #' @param prefer_sas [logical(1)] Logical indicating whether to prefer SAS7BDAT files over RDS. Default is FALSE.
 #' @param env_var [character(1)] The environment variable name for the base directory. Default is "RXD_DATA".
-#' @param print_file_paths [logical(1)] Logical indicating whether to print the directory path and file names. Default is FALSE.
+#' @param print_file_paths [logical(1)] Logical indicating whether to print the directory path and file names. 
+#' Default is FALSE.
 #'
 #' @return A named list of data frames, where each name corresponds to a loaded file.
 #'
@@ -92,7 +93,14 @@ get_cre_path <- function() {
 #' Sys.setenv(RXD_DATA = base_dir)
 #' 
 #' @export
-load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE, env_var = "RXD_DATA", print_file_paths = FALSE) {
+load_data <- function(
+    sub_dir = NULL, 
+    file_names, 
+    use_wd = FALSE, 
+    prefer_sas = FALSE, 
+    env_var = "RXD_DATA", 
+    print_file_paths = FALSE
+  ) {
   # Input validation
   checkmate::assert_character(sub_dir, len = 1, null.ok = TRUE)
   checkmate::assert_character(file_names, min.len = 1)
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 47bcc78..7e92070 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -1,7 +1,7 @@
 # validation (S)
 vdoc <- local({
   # package_name is used # INSIDE # the sourced file below
-  package_name <- "dv.loader" # read.dcf("../../DESCRIPTION")[, "Package"]
+  package_name <- "dv.loader" 
   utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
   source(utils_file_path, local = TRUE)[["value"]]
 })

From 62545e96e276152044cdd4ae60091aff978fb9c1 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 15:09:24 +0800
Subject: [PATCH 21/37] Fix styler issues

---
 R/dvloader.R                    | 41 ++++++++++++++++-----------------
 R/utils.R                       | 16 ++++++-------
 tests/testthat/setup.R          |  2 +-
 vignettes/integration-guide.Rmd |  6 ++---
 4 files changed, 32 insertions(+), 33 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index b983c00..139ea8c 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -10,13 +10,13 @@
 #' @examples
 #' # Create a temporary directory
 #' temp_dir <- tempdir()
-#' 
+#'
 #' # Set the BASE_DIR environment variable
 #' Sys.setenv(BASE_DIR = temp_dir)
-#' 
+#'
 #' # Get the base directory path
 #' dv.loader:::get_base_dir("BASE_DIR")
-#' 
+#'
 #' @keywords internal
 get_base_dir <- function(env_var) {
   # Ensure env_var is a single character string
@@ -42,12 +42,12 @@ get_base_dir <- function(env_var) {
 #' This function retrieves the path to the NFS (Network File System) directory.
 #'
 #' @param env_var [character(1)] The environment variable name for the base directory. Default is "RXD_DATA".
-#' 
+#'
 #' @return [character(1)] The path to the NFS directory.
 #'
 #' @export
 get_nfs_path <- function(env_var = "RXD_DATA") {
-    get_base_dir(env_var = env_var)
+  get_base_dir(env_var = env_var)
 }
 
 
@@ -55,12 +55,12 @@ get_nfs_path <- function(env_var = "RXD_DATA") {
 #'
 #' This function retrieves the path to the CRE (Clinical Research Environment) directory.
 #' It uses the "RXD_DATA" environment variable as the base directory.
-#' 
+#'
 #' @return [character(1)] The path to the CRE directory.
 #'
 #' @export
 get_cre_path <- function() {
-    get_base_dir(env_var = "RXD_DATA")
+  get_base_dir(env_var = "RXD_DATA")
 }
 
 
@@ -74,7 +74,7 @@ get_cre_path <- function() {
 #' @param use_wd [logical(1)] Logical indicating whether to use the current working directory. Default is FALSE.
 #' @param prefer_sas [logical(1)] Logical indicating whether to prefer SAS7BDAT files over RDS. Default is FALSE.
 #' @param env_var [character(1)] The environment variable name for the base directory. Default is "RXD_DATA".
-#' @param print_file_paths [logical(1)] Logical indicating whether to print the directory path and file names. 
+#' @param print_file_paths [logical(1)] Logical indicating whether to print the directory path and file names.
 #' Default is FALSE.
 #'
 #' @return A named list of data frames, where each name corresponds to a loaded file.
@@ -82,25 +82,24 @@ get_cre_path <- function() {
 #' @examples
 #' # Get the current value of the RXD_DATA environment variable
 #' base_dir <- Sys.getenv("RXD_DATA")
-#' 
+#'
 #' # Set the RXD_DATA environment variable to the path of the haven package
 #' Sys.setenv(RXD_DATA = find.package("haven"))
-#' 
+#'
 #' data_list <- load_data(sub_dir = "examples", file_names = c("iris.sas7bdat"))
 #' str(data_list)
-#' 
+#'
 #' # Reset the RXD_DATA environment variable to its original value
 #' Sys.setenv(RXD_DATA = base_dir)
-#' 
+#'
 #' @export
 load_data <- function(
-    sub_dir = NULL, 
-    file_names, 
-    use_wd = FALSE, 
-    prefer_sas = FALSE, 
-    env_var = "RXD_DATA", 
-    print_file_paths = FALSE
-  ) {
+    sub_dir = NULL,
+    file_names,
+    use_wd = FALSE,
+    prefer_sas = FALSE,
+    env_var = "RXD_DATA",
+    print_file_paths = FALSE) {
   # Input validation
   checkmate::assert_character(sub_dir, len = 1, null.ok = TRUE)
   checkmate::assert_character(file_names, min.len = 1)
@@ -114,7 +113,7 @@ load_data <- function(
   } else {
     base_dir <- get_base_dir(env_var = env_var)
   }
-  
+
   # Construct the full directory path
   dir_path <- if (is.null(sub_dir)) base_dir else file.path(base_dir, sub_dir)
 
@@ -125,7 +124,7 @@ load_data <- function(
   file_paths <- get_file_paths(dir_path = dir_path, file_names = file_names, prefer_sas = prefer_sas)
 
   # Print the directory path and file names if requested
-  if (isTRUE(print_file_paths)) { 
+  if (isTRUE(print_file_paths)) {
     cat("Loading data from", dir_path, "\n")
     cat("Loading data file(s):", basename(file_paths), "\n")
   }
diff --git a/R/utils.R b/R/utils.R
index c7a0089..b84d8c1 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -12,17 +12,17 @@
 #' @examples
 #' \dontrun{
 #' temp_dir <- tempdir()
-#' 
+#'
 #' file_names <- c("adsl", "adae")
-#' 
+#'
 #' file.create(file.path(temp_dir, paste0(file_names, ".rds")))
 #' file.create(file.path(temp_dir, paste0(file_names, ".sas7bdat")))
-#' 
+#'
 #' list.files(temp_dir)
-#' 
+#'
 #' get_file_paths(dir_path = temp_dir, file_names = file_names)
 #' get_file_paths(dir_path = temp_dir, file_names = file_names, prefer_sas = TRUE)
-#' 
+#'
 #' unlink(temp_dir, recursive = TRUE)
 #' }
 #'
@@ -36,14 +36,14 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
   file_paths <- lapply(file_names, function(file_name) {
     file_path <- file.path(dir_path, file_name)
     file_ext <- tools::file_ext(file_name)
-    
+
     if (file_ext == "") {
       # If no extension is provided, check for both RDS and SAS files
       rds_file_name <- paste0(file_name, ".rds")
       sas_file_name <- paste0(file_name, ".sas7bdat")
       rds_file_path <- file.path(dir_path, rds_file_name)
       sas_file_path <- file.path(dir_path, sas_file_name)
-      
+
       if (isTRUE(prefer_sas)) {
         # Prefer SAS file if it exists, otherwise use RDS
         if (file.exists(sas_file_path)) {
@@ -92,7 +92,7 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
 #' path <- system.file("examples", "iris.sas7bdat", package = "haven")
 #' data_list <- load_data_files(file_paths = path)
 #' str(data_list)
-#' 
+#'
 #' @export
 load_data_files <- function(file_paths) {
   # Validate input parameters
diff --git a/tests/testthat/setup.R b/tests/testthat/setup.R
index 7e92070..36b2e31 100644
--- a/tests/testthat/setup.R
+++ b/tests/testthat/setup.R
@@ -1,7 +1,7 @@
 # validation (S)
 vdoc <- local({
   # package_name is used # INSIDE # the sourced file below
-  package_name <- "dv.loader" 
+  package_name <- "dv.loader"
   utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
   source(utils_file_path, local = TRUE)[["value"]]
 })
diff --git a/vignettes/integration-guide.Rmd b/vignettes/integration-guide.Rmd
index f142d6c..5a38316 100644
--- a/vignettes/integration-guide.Rmd
+++ b/vignettes/integration-guide.Rmd
@@ -35,9 +35,9 @@ Sys.setenv(RXD_DATA = find.package("dv.loader"))
 
 # Load data files from the specified sub-directory of a network file system (NFS)
 data_list <- dv.loader::load_data(
-    sub_dir = "extdata/pharmaverseadam",
-    file_names = c("adsl_sample", "adae_sample"),
-    print_file_paths = TRUE
+  sub_dir = "extdata/pharmaverseadam",
+  file_names = c("adsl_sample", "adae_sample"),
+  print_file_paths = TRUE
 )
 ```
 

From 2bbf397e7802579e944da524a2891065511832f3 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 18:15:25 +0800
Subject: [PATCH 22/37] Try to identify issue from tests

---
 R/utils.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/utils.R b/R/utils.R
index b84d8c1..331c9c1 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -39,7 +39,7 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
 
     if (file_ext == "") {
       # If no extension is provided, check for both RDS and SAS files
-      rds_file_name <- paste0(file_name, ".rds")
+      rds_file_name <- paste0(file_name, ".RDS")
       sas_file_name <- paste0(file_name, ".sas7bdat")
       rds_file_path <- file.path(dir_path, rds_file_name)
       sas_file_path <- file.path(dir_path, sas_file_name)

From a02950e21ecb10efb94d17dcfafaae17a83ff13a Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 19:57:31 +0800
Subject: [PATCH 23/37] Use pattern matching to find files when no file
 extension is provided

---
 R/utils.R | 46 +++++++++++++++++++++++++++++-----------------
 1 file changed, 29 insertions(+), 17 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 331c9c1..8b2ad1d 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -38,29 +38,41 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
     file_ext <- tools::file_ext(file_name)
 
     if (file_ext == "") {
-      # If no extension is provided, check for both RDS and SAS files
-      rds_file_name <- paste0(file_name, ".RDS")
-      sas_file_name <- paste0(file_name, ".sas7bdat")
-      rds_file_path <- file.path(dir_path, rds_file_name)
-      sas_file_path <- file.path(dir_path, sas_file_name)
+      # Get all files in the directory
+      candidates <- basename(list.files(dir_path))
 
+      # Find matching RDS files
+      rds_match <- grep(
+        pattern = paste0("^", file_name, "\\.rds$"), 
+        x = candidates,
+        ignore.case = TRUE,
+        value = TRUE
+      )
+
+      # Find matching SAS files
+      sas_match <- grep(
+        pattern = paste0("^", file_name, "\\.sas7bdat$"), 
+        x = candidates, 
+        ignore.case = TRUE,
+        value = TRUE
+      )
+
+      # Prefer SAS file if it exists, otherwise use RDS
       if (isTRUE(prefer_sas)) {
-        # Prefer SAS file if it exists, otherwise use RDS
-        if (file.exists(sas_file_path)) {
-          return(sas_file_path)
-        } else if (file.exists(rds_file_path)) {
-          return(rds_file_path)
+        if (length(sas_match) > 0) {
+          return(file.path(dir_path, sas_match[1]))
+        } else if (length(rds_match) > 0) {
+          return(file.path(dir_path, rds_match[1]))
         } else {
-          stop(dir_path, " does not contain: ", rds_file_name, " or ", sas_file_name)
+          stop(dir_path, " does not contain SAS or RDS file: ", file_name)
         }
       } else if (isFALSE(prefer_sas)) {
-        # Prefer RDS file if it exists, otherwise use SAS
-        if (file.exists(rds_file_path)) {
-          return(rds_file_path)
-        } else if (file.exists(sas_file_path)) {
-          return(sas_file_path)
+        if (length(rds_match) > 0) {
+          return(file.path(dir_path, rds_match[1]))
+        } else if (length(sas_match) > 0) {
+          return(file.path(dir_path, sas_match[1]))
         } else {
-          stop(dir_path, " does not contain: ", rds_file_name, " or ", sas_file_name)
+          stop(dir_path, " does not contain RDS or SAS file: ", file_name)
         }
       }
     } else {

From 51ba3ce9bef83c94c617985b6ea35077ba71d091 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 23 Oct 2024 20:04:25 +0800
Subject: [PATCH 24/37] Fix styler issues

---
 R/utils.R        | 6 +++---
 man/load_data.Rd | 3 ++-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/R/utils.R b/R/utils.R
index 8b2ad1d..17c4e12 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -43,7 +43,7 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
 
       # Find matching RDS files
       rds_match <- grep(
-        pattern = paste0("^", file_name, "\\.rds$"), 
+        pattern = paste0("^", file_name, "\\.rds$"),
         x = candidates,
         ignore.case = TRUE,
         value = TRUE
@@ -51,8 +51,8 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
 
       # Find matching SAS files
       sas_match <- grep(
-        pattern = paste0("^", file_name, "\\.sas7bdat$"), 
-        x = candidates, 
+        pattern = paste0("^", file_name, "\\.sas7bdat$"),
+        x = candidates,
         ignore.case = TRUE,
         value = TRUE
       )
diff --git a/man/load_data.Rd b/man/load_data.Rd
index 50f7187..9659710 100644
--- a/man/load_data.Rd
+++ b/man/load_data.Rd
@@ -24,7 +24,8 @@ load_data(
 
 \item{env_var}{[character(1)] The environment variable name for the base directory. Default is "RXD_DATA".}
 
-\item{print_file_paths}{[logical(1)] Logical indicating whether to print the directory path and file names. Default is FALSE.}
+\item{print_file_paths}{[logical(1)] Logical indicating whether to print the directory path and file names.
+Default is FALSE.}
 }
 \value{
 A named list of data frames, where each name corresponds to a loaded file.

From 6e4a18acbf8f1819c865e471891b1c145441f748 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Fri, 1 Nov 2024 15:41:01 +0800
Subject: [PATCH 25/37] Save demo data to a temp dir

---
 vignettes/integration-guide.Rmd | 25 ++++++++++++++++++++-----
 1 file changed, 20 insertions(+), 5 deletions(-)

diff --git a/vignettes/integration-guide.Rmd b/vignettes/integration-guide.Rmd
index 5a38316..99cc47f 100644
--- a/vignettes/integration-guide.Rmd
+++ b/vignettes/integration-guide.Rmd
@@ -27,16 +27,31 @@ pkgs <- c("dv.loader", "dv.manager", "dv.listings")
 remotes::install_github(repo = paste0("Boehringer-Ingelheim/", pkgs))
 ```
 
+For the purpose of this vignette, we will use the data from the {pharmaverseadam} package and save the `adsl` and `adae` datasets as .sas7bdat files in a temporary directory.
+
+```{r, eval=FALSE}
+# Create a temporary directory
+temp_dir <- tempdir()
+
+# Create a sub-directory for saving the pharmaverseadam data
+data_dir <- file.path(temp_dir, "pharmaverseadam")
+dir.create(data_dir)
+
+# Save the adsl and adae datasets to the temporary directory
+haven::write_sas(pharmaverseadam::adsl, file.path(data_dir, "adsl.sas7bdat"))
+haven::write_sas(pharmaverseadam::adae, file.path(data_dir, "adae.sas7bdat"))
+```
+
 ## Step 1: Load data files
 
 ```{r, eval=FALSE}
 # Set the NFS path as an environment variable
-Sys.setenv(RXD_DATA = find.package("dv.loader"))
+Sys.setenv(RXD_DATA = temp_dir)
 
 # Load data files from the specified sub-directory of a network file system (NFS)
 data_list <- dv.loader::load_data(
-  sub_dir = "extdata/pharmaverseadam",
-  file_names = c("adsl_sample", "adae_sample"),
+  sub_dir = "pharmaverseadam",
+  file_names = c("adsl", "adae"),
   print_file_paths = TRUE
 )
 ```
@@ -48,7 +63,7 @@ data_list <- dv.loader::load_data(
 module_list <- list(
   "Data Listings" = dv.listings::mod_listings(
     module_id = "data_listings",
-    dataset_names = c("adsl_sample", "adae_sample")
+    dataset_names = c("adsl", "adae")
   )
 )
 ```
@@ -60,7 +75,7 @@ module_list <- list(
 dv.manager::run_app(
   data = list("Demo Data" = data_list),
   module_list = module_list,
-  filter_data = "adsl_sample",
+  filter_data = "adsl",
   title = "DaVinci Application"
 )
 ```

From 89413a77f7b4bdca1d2ceab35e7f3b6c9bc3bf08 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Fri, 1 Nov 2024 15:42:30 +0800
Subject: [PATCH 26/37] Remove pharmaverseadam data from package

---
 inst/extdata/data.R                           |  41 ------------------
 inst/extdata/pharmaverseadam/adae_sample.rds  | Bin 5592 -> 0 bytes
 .../pharmaverseadam/adae_sample.sas7bdat      | Bin 69632 -> 0 bytes
 inst/extdata/pharmaverseadam/adsl_sample.rds  | Bin 2201 -> 0 bytes
 .../pharmaverseadam/adsl_sample.sas7bdat      | Bin 28672 -> 0 bytes
 5 files changed, 41 deletions(-)
 delete mode 100644 inst/extdata/data.R
 delete mode 100644 inst/extdata/pharmaverseadam/adae_sample.rds
 delete mode 100644 inst/extdata/pharmaverseadam/adae_sample.sas7bdat
 delete mode 100644 inst/extdata/pharmaverseadam/adsl_sample.rds
 delete mode 100644 inst/extdata/pharmaverseadam/adsl_sample.sas7bdat

diff --git a/inst/extdata/data.R b/inst/extdata/data.R
deleted file mode 100644
index 29c1d03..0000000
--- a/inst/extdata/data.R
+++ /dev/null
@@ -1,41 +0,0 @@
-# Create directory for pharmaverseadam data if it doesn't exist
-data_dir <- file.path("inst", "extdata", "pharmaverseadam")
-if (!dir.exists(data_dir)) {
-  dir.create(data_dir, recursive = TRUE)
-}
-
-# Sample 10 subjects from adsl data
-set.seed(123) # For reproducibility
-adsl_sample <- pharmaverseadam::adsl |> 
-  dplyr::sample_n(size = 10)
-
-# Filter adae data for the 10 subjects in adsl_sample
-adae_sample <- pharmaverseadam::adae |> 
-  dplyr::filter(USUBJID %in% adsl_sample$USUBJID)
-
-# Save adsl_sample to rds file
-saveRDS(
-  object = adsl_sample,
-  file = file.path(data_dir, "adsl_sample.rds")
-)
-
-# Save adae_sample to rds file
-saveRDS(
-  object = adae_sample,
-  file = file.path(data_dir, "adae_sample.rds")
-)
-
-# Write adsl_sample to sas7bdat file
-haven::write_sas(
-  data = adsl_sample,
-  path = file.path(data_dir, "adsl_sample.sas7bdat")
-)
-
-# Write adae_sample to sas7bdat file
-haven::write_sas(
-  data = adae_sample,
-  path = file.path(data_dir, "adae_sample.sas7bdat")
-)
-
-# Add a message to confirm data creation
-message("Sample data files have been created in ", data_dir)
diff --git a/inst/extdata/pharmaverseadam/adae_sample.rds b/inst/extdata/pharmaverseadam/adae_sample.rds
deleted file mode 100644
index f806ce5f2455dcda329ba63dd5458b71127e9414..0000000000000000000000000000000000000000
GIT binary patch
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diff --git a/inst/extdata/pharmaverseadam/adsl_sample.sas7bdat b/inst/extdata/pharmaverseadam/adsl_sample.sas7bdat
deleted file mode 100644
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GIT binary patch
literal 0
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From 4665a231aeaad0c0c62f959e2d6f7530ec59620d Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 6 Nov 2024 16:19:19 +0800
Subject: [PATCH 27/37] Remove comments inside functions

---
 R/dvloader.R | 12 ------------
 R/utils.R    | 14 --------------
 2 files changed, 26 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index 139ea8c..91b7f34 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -19,21 +19,16 @@
 #'
 #' @keywords internal
 get_base_dir <- function(env_var) {
-  # Ensure env_var is a single character string
   checkmate::assert_character(env_var, len = 1)
 
-  # Get the value of the environment variable
   base_dir <- Sys.getenv(env_var)
 
-  # Stop if the environment variable is not set
   if (base_dir == "") {
     stop("Environment variable ", env_var, " is not set")
   }
 
-  # Ensure the directory exists
   checkmate::assert_directory_exists(base_dir)
 
-  # Return the normalized path
   return(normalizePath(base_dir))
 }
 
@@ -100,36 +95,29 @@ load_data <- function(
     prefer_sas = FALSE,
     env_var = "RXD_DATA",
     print_file_paths = FALSE) {
-  # Input validation
   checkmate::assert_character(sub_dir, len = 1, null.ok = TRUE)
   checkmate::assert_character(file_names, min.len = 1)
   checkmate::assert_logical(use_wd, len = 1)
   checkmate::assert_logical(prefer_sas, len = 1)
   checkmate::assert_character(env_var, len = 1)
 
-  # Determine the base directory
   if (use_wd) {
     base_dir <- getwd()
   } else {
     base_dir <- get_base_dir(env_var = env_var)
   }
 
-  # Construct the full directory path
   dir_path <- if (is.null(sub_dir)) base_dir else file.path(base_dir, sub_dir)
 
-  # Determine the file extension based on preference
   file_ext <- if (prefer_sas) "sas7bdat" else "rds"
 
-  # Get the full file paths
   file_paths <- get_file_paths(dir_path = dir_path, file_names = file_names, prefer_sas = prefer_sas)
 
-  # Print the directory path and file names if requested
   if (isTRUE(print_file_paths)) {
     cat("Loading data from", dir_path, "\n")
     cat("Loading data file(s):", basename(file_paths), "\n")
   }
 
-  # Load the data files
   data_list <- load_data_files(file_paths)
 
   names(data_list) <- file_names
diff --git a/R/utils.R b/R/utils.R
index 17c4e12..a856cb7 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -28,7 +28,6 @@
 #'
 #' @export
 get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
-  # Input validation
   checkmate::assert_character(dir_path, len = 1)
   checkmate::assert_character(file_names, min.len = 1)
   checkmate::assert_logical(prefer_sas, len = 1)
@@ -38,10 +37,8 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
     file_ext <- tools::file_ext(file_name)
 
     if (file_ext == "") {
-      # Get all files in the directory
       candidates <- basename(list.files(dir_path))
 
-      # Find matching RDS files
       rds_match <- grep(
         pattern = paste0("^", file_name, "\\.rds$"),
         x = candidates,
@@ -49,7 +46,6 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
         value = TRUE
       )
 
-      # Find matching SAS files
       sas_match <- grep(
         pattern = paste0("^", file_name, "\\.sas7bdat$"),
         x = candidates,
@@ -57,7 +53,6 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
         value = TRUE
       )
 
-      # Prefer SAS file if it exists, otherwise use RDS
       if (isTRUE(prefer_sas)) {
         if (length(sas_match) > 0) {
           return(file.path(dir_path, sas_match[1]))
@@ -76,7 +71,6 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
         }
       }
     } else {
-      # If an extension is provided, use the exact file name
       if (file.exists(file_path)) {
         return(file_path)
       } else {
@@ -85,7 +79,6 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
     }
   })
 
-  # Normalize all file paths
   return(normalizePath(unlist(file_paths)))
 }
 
@@ -107,16 +100,12 @@ get_file_paths <- function(dir_path, file_names, prefer_sas = FALSE) {
 #'
 #' @export
 load_data_files <- function(file_paths) {
-  # Validate input parameters
   checkmate::assert_character(file_paths, min.len = 1)
   checkmate::assert_file_exists(file_paths)
 
-  # Read each file and store in a list
   data_list <- lapply(file_paths, function(file_path) {
-    # Get file extension
     extension <- tools::file_ext(file_path)
 
-    # Read file based on its extension
     if (tolower(extension) == "rds") {
       data <- readRDS(file_path)
     } else if (tolower(extension) == "sas7bdat") {
@@ -125,19 +114,16 @@ load_data_files <- function(file_paths) {
       stop("Unsupported file extension: ", extension)
     }
 
-    # Get file metadata
     meta <- file.info(file_path, extra_cols = FALSE)
     meta[["path"]] <- file_path
     meta[["file_name"]] <- basename(file_path)
 
-    # Add metadata as an attribute to the data
     rownames(data) <- NULL
     attr(data, "meta") <- meta
 
     return(data)
   })
 
-  # Set names of the list elements to the basenames of the file paths
   names(data_list) <- basename(file_paths)
 
   return(data_list)

From 19ccc3d7fc389ab2e975a69225fb62d6d31a8ded Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 6 Nov 2024 16:53:38 +0800
Subject: [PATCH 28/37] Remvoe get_base_dir() and keep get_nfs_path()

---
 R/dvloader.R | 65 +++++++++++++---------------------------------------
 1 file changed, 16 insertions(+), 49 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index 91b7f34..a539b16 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -1,62 +1,32 @@
-#' Get Base Directory Path
+#' Get NFS Base Path from an Environment Variable
 #'
-#' This function retrieves the base directory path from a specified environment variable.
-#' It checks if the environment variable is set and if the directory exists.
+#' This function assumes that there is an environment variable called `RXD_DATA` 
+#' which is set to the base path of the NFS directory.
 #'
-#' @param env_var [character(1)] The name of the environment variable containing the base directory path.
+#' @return [character(1)] The normalized path to the NFS directory.
 #'
-#' @return [character(1)] The normalized path to the base directory.
-#'
-#' @examples
-#' # Create a temporary directory
-#' temp_dir <- tempdir()
-#'
-#' # Set the BASE_DIR environment variable
-#' Sys.setenv(BASE_DIR = temp_dir)
-#'
-#' # Get the base directory path
-#' dv.loader:::get_base_dir("BASE_DIR")
-#'
-#' @keywords internal
-get_base_dir <- function(env_var) {
-  checkmate::assert_character(env_var, len = 1)
-
-  base_dir <- Sys.getenv(env_var)
+#' @export
+get_nfs_path <- function() {
+  base_path <- Sys.getenv("RXD_DATA")
 
-  if (base_dir == "") {
-    stop("Environment variable ", env_var, " is not set")
+  if (base_path == "") {
+    stop("Environment variable RXD_DATA must be set")
   }
 
-  checkmate::assert_directory_exists(base_dir)
+  checkmate::assert_directory_exists(base_path)
 
-  return(normalizePath(base_dir))
-}
-
-#' Get NFS Path
-#'
-#' This function retrieves the path to the NFS (Network File System) directory.
-#'
-#' @param env_var [character(1)] The environment variable name for the base directory. Default is "RXD_DATA".
-#'
-#' @return [character(1)] The path to the NFS directory.
-#'
-#' @export
-get_nfs_path <- function(env_var = "RXD_DATA") {
-  get_base_dir(env_var = env_var)
+  return(normalizePath(base_path))
 }
 
 
-#' Get CRE Path
+#' Get CRE Base Path from an Environment Variable
 #'
-#' This function retrieves the path to the CRE (Clinical Research Environment) directory.
-#' It uses the "RXD_DATA" environment variable as the base directory.
+#' This function is an alias for `get_nfs_path()` to maintain backwards compatibility.  
 #'
-#' @return [character(1)] The path to the CRE directory.
+#' @return [character(1)] The normalized path to the CRE directory.
 #'
 #' @export
-get_cre_path <- function() {
-  get_base_dir(env_var = "RXD_DATA")
-}
+get_cre_path <- get_nfs_path
 
 
 #' Load Data Files
@@ -68,7 +38,6 @@ get_cre_path <- function() {
 #' @param file_names [character(1+)] Character vector of file names to load (without extension).
 #' @param use_wd [logical(1)] Logical indicating whether to use the current working directory. Default is FALSE.
 #' @param prefer_sas [logical(1)] Logical indicating whether to prefer SAS7BDAT files over RDS. Default is FALSE.
-#' @param env_var [character(1)] The environment variable name for the base directory. Default is "RXD_DATA".
 #' @param print_file_paths [logical(1)] Logical indicating whether to print the directory path and file names.
 #' Default is FALSE.
 #'
@@ -93,18 +62,16 @@ load_data <- function(
     file_names,
     use_wd = FALSE,
     prefer_sas = FALSE,
-    env_var = "RXD_DATA",
     print_file_paths = FALSE) {
   checkmate::assert_character(sub_dir, len = 1, null.ok = TRUE)
   checkmate::assert_character(file_names, min.len = 1)
   checkmate::assert_logical(use_wd, len = 1)
   checkmate::assert_logical(prefer_sas, len = 1)
-  checkmate::assert_character(env_var, len = 1)
 
   if (use_wd) {
     base_dir <- getwd()
   } else {
-    base_dir <- get_base_dir(env_var = env_var)
+    base_dir <- get_nfs_path()
   }
 
   dir_path <- if (is.null(sub_dir)) base_dir else file.path(base_dir, sub_dir)

From d164c100f7fe40ec005f787c7e6e2bed87358fce Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 6 Nov 2024 17:41:54 +0800
Subject: [PATCH 29/37] Update function docs

---
 R/dvloader.R | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index a539b16..de19181 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -1,9 +1,9 @@
-#' Get NFS Base Path from an Environment Variable
+#' Get Base Path from an Environment Variable
 #'
 #' This function assumes that there is an environment variable called `RXD_DATA` 
-#' which is set to the base path of the NFS directory.
+#' which is set to the base path of the data directory.
 #'
-#' @return [character(1)] The normalized path to the NFS directory.
+#' @return [character(1)] The normalized base path.
 #'
 #' @export
 get_nfs_path <- function() {
@@ -18,12 +18,11 @@ get_nfs_path <- function() {
   return(normalizePath(base_path))
 }
 
-
-#' Get CRE Base Path from an Environment Variable
+#' Get Base Path from an Environment Variable
 #'
 #' This function is an alias for `get_nfs_path()` to maintain backwards compatibility.  
 #'
-#' @return [character(1)] The normalized path to the CRE directory.
+#' @return [character(1)] The normalized base path.
 #'
 #' @export
 get_cre_path <- get_nfs_path

From 912957f270779303963d69e8658e8e3ca1b311a9 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 6 Nov 2024 17:43:08 +0800
Subject: [PATCH 30/37] Update examples in README

---
 README.md | 44 ++++++++++++--------------------------------
 1 file changed, 12 insertions(+), 32 deletions(-)

diff --git a/README.md b/README.md
index ab3eadc..c90a943 100644
--- a/README.md
+++ b/README.md
@@ -25,50 +25,30 @@ remotes::install_github("Boehringer-Ingelheim/dv.loader")
 
 ## Examples
 
-The main function is `dv.loader::load_data()`, which loads data files from sub-directories of a network file system (NFS) or the working directory.
+The `dv.loader` package provides two main functions for loading data:
 
-### Example 1: Sub-directory of Network File System (NFS)
+1. `load_data_files()`: A flexible function that loads multiple data files from any specified file paths, regardless of whether they are in the same directory or not.
 
-To load data files from a NFS, you need to set the NFS path as an environment variable. By default, the environment variable name is `RXD_DATA`.
+2. `load_data()`: A convenience wrapper around `load_data_files()` that simplifies loading multiple files from a single sub-directory of a base path.
 
-You can run the following command to check the NFS path if it is already set.
+### Example 1: `load_data_files()`
 
 ```r
-# Check the NFS path
-dv.loader::get_nfs_path()
-```
-
-If the NFS path is not set, you can set it by running the following command.
-
-```r
-# Set the NFS path as an environment variable
-Sys.setenv(RXD_DATA = "path/to/network-file-system")
-```
-
-The environment variable setup is not needed if you have already set the NFS path as an environment variable in your `.Renviron` or `.Rprofile` file. 
-
-If the NFS path has been properly set, you can load data files from the NFS and its sub-directories.
-
-```r
-# Load data files from the specified sub-directory of a network file system (NFS)
-dv.loader::load_data(
-    sub_dir = "sub-directory/of/network-file-system",
-    file_names = c("adsl.sas7bdat", "adae.sas7bdat")
+# Load data files from the specified file paths
+dv.loader::load_data_files(
+    file_paths = c("path/to/adsl.sas7bdat", "path/to/adae.sas7bdat")
 )
 ```
 
-For the `file_names` argument, it is recommended to use the full file names including the file extension. 
-
-### Example 2: Sub-directory of the Working Directory
+### Example 2: `load_data()`
 
-To load data files from a local directory, there is no need to set an environment variable. You use `use_wd = TRUE` to indicate that the data files are loaded from a sub-directory of the working directory.
+In order to use `load_data()`, you need to set the base path as an environment variable called `RXD_DATA`.
 
 ```r
-# Load data files from the specified sub-directory of the working directory
+# Load data files from the specified sub-directory of a base path
 dv.loader::load_data(
-    sub_dir = "sub-directory/of/working-directory",
-    file_names = c("adsl.sas7bdat", "adae.sas7bdat"),
-    use_wd = TRUE
+    sub_dir = "sub-directory/of/base-path",
+    file_names = c("adsl.sas7bdat", "adae.sas7bdat")
 )
 ```
 

From 52d058bd1817e160e90858ece0849cfebd4bc0b2 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 6 Nov 2024 17:43:32 +0800
Subject: [PATCH 31/37] Update example in vignettes

---
 vignettes/integration-guide.Rmd | 15 +++++----------
 1 file changed, 5 insertions(+), 10 deletions(-)

diff --git a/vignettes/integration-guide.Rmd b/vignettes/integration-guide.Rmd
index 99cc47f..d7d36f5 100644
--- a/vignettes/integration-guide.Rmd
+++ b/vignettes/integration-guide.Rmd
@@ -45,14 +45,9 @@ haven::write_sas(pharmaverseadam::adae, file.path(data_dir, "adae.sas7bdat"))
 ## Step 1: Load data files
 
 ```{r, eval=FALSE}
-# Set the NFS path as an environment variable
-Sys.setenv(RXD_DATA = temp_dir)
-
-# Load data files from the specified sub-directory of a network file system (NFS)
-data_list <- dv.loader::load_data(
-  sub_dir = "pharmaverseadam",
-  file_names = c("adsl", "adae"),
-  print_file_paths = TRUE
+# Load data files from the specified file paths
+data_list <- dv.loader::load_data_files(
+  file_paths = file.path(data_dir, c("adsl.sas7bdat", "adae.sas7bdat"))
 )
 ```
 
@@ -63,7 +58,7 @@ data_list <- dv.loader::load_data(
 module_list <- list(
   "Data Listings" = dv.listings::mod_listings(
     module_id = "data_listings",
-    dataset_names = c("adsl", "adae")
+    dataset_names = c("adsl.sas7bdat", "adae.sas7bdat")
   )
 )
 ```
@@ -75,7 +70,7 @@ module_list <- list(
 dv.manager::run_app(
   data = list("Demo Data" = data_list),
   module_list = module_list,
-  filter_data = "adsl",
+  filter_data = "adsl.sas7bdat",
   title = "DaVinci Application"
 )
 ```

From c06a26a9b90826be9c98612d2f9d74c45a5d81f0 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 6 Nov 2024 17:44:44 +0800
Subject: [PATCH 32/37] Update R document files

---
 man/get_base_dir.Rd | 30 ------------------------------
 man/get_cre_path.Rd |  7 +++----
 man/get_nfs_path.Rd | 12 +++++-------
 man/load_data.Rd    |  3 ---
 4 files changed, 8 insertions(+), 44 deletions(-)
 delete mode 100644 man/get_base_dir.Rd

diff --git a/man/get_base_dir.Rd b/man/get_base_dir.Rd
deleted file mode 100644
index 891d825..0000000
--- a/man/get_base_dir.Rd
+++ /dev/null
@@ -1,30 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/dvloader.R
-\name{get_base_dir}
-\alias{get_base_dir}
-\title{Get Base Directory Path}
-\usage{
-get_base_dir(env_var)
-}
-\arguments{
-\item{env_var}{[character(1)] The name of the environment variable containing the base directory path.}
-}
-\value{
-[character(1)] The normalized path to the base directory.
-}
-\description{
-This function retrieves the base directory path from a specified environment variable.
-It checks if the environment variable is set and if the directory exists.
-}
-\examples{
-# Create a temporary directory
-temp_dir <- tempdir()
-
-# Set the BASE_DIR environment variable
-Sys.setenv(BASE_DIR = temp_dir)
-
-# Get the base directory path
-dv.loader:::get_base_dir("BASE_DIR")
-
-}
-\keyword{internal}
diff --git a/man/get_cre_path.Rd b/man/get_cre_path.Rd
index 03686b2..897a61c 100644
--- a/man/get_cre_path.Rd
+++ b/man/get_cre_path.Rd
@@ -2,14 +2,13 @@
 % Please edit documentation in R/dvloader.R
 \name{get_cre_path}
 \alias{get_cre_path}
-\title{Get CRE Path}
+\title{Get Base Path from an Environment Variable}
 \usage{
 get_cre_path()
 }
 \value{
-[character(1)] The path to the CRE directory.
+[character(1)] The normalized base path.
 }
 \description{
-This function retrieves the path to the CRE (Clinical Research Environment) directory.
-It uses the "RXD_DATA" environment variable as the base directory.
+This function is an alias for `get_nfs_path()` to maintain backwards compatibility.
 }
diff --git a/man/get_nfs_path.Rd b/man/get_nfs_path.Rd
index 3c4ba73..516256b 100644
--- a/man/get_nfs_path.Rd
+++ b/man/get_nfs_path.Rd
@@ -2,16 +2,14 @@
 % Please edit documentation in R/dvloader.R
 \name{get_nfs_path}
 \alias{get_nfs_path}
-\title{Get NFS Path}
+\title{Get Base Path from an Environment Variable}
 \usage{
-get_nfs_path(env_var = "RXD_DATA")
-}
-\arguments{
-\item{env_var}{[character(1)] The environment variable name for the base directory. Default is "RXD_DATA".}
+get_nfs_path()
 }
 \value{
-[character(1)] The path to the NFS directory.
+[character(1)] The normalized base path.
 }
 \description{
-This function retrieves the path to the NFS (Network File System) directory.
+This function assumes that there is an environment variable called `RXD_DATA` 
+which is set to the base path of the data directory.
 }
diff --git a/man/load_data.Rd b/man/load_data.Rd
index 9659710..2342a61 100644
--- a/man/load_data.Rd
+++ b/man/load_data.Rd
@@ -9,7 +9,6 @@ load_data(
   file_names,
   use_wd = FALSE,
   prefer_sas = FALSE,
-  env_var = "RXD_DATA",
   print_file_paths = FALSE
 )
 }
@@ -22,8 +21,6 @@ load_data(
 
 \item{prefer_sas}{[logical(1)] Logical indicating whether to prefer SAS7BDAT files over RDS. Default is FALSE.}
 
-\item{env_var}{[character(1)] The environment variable name for the base directory. Default is "RXD_DATA".}
-
 \item{print_file_paths}{[logical(1)] Logical indicating whether to print the directory path and file names.
 Default is FALSE.}
 }

From b8d3bc3a18953e67d975569c06d7c7164268cba3 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 6 Nov 2024 17:56:38 +0800
Subject: [PATCH 33/37] Fix styler issues

---
 R/dvloader.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index de19181..6ae0044 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -1,6 +1,6 @@
 #' Get Base Path from an Environment Variable
 #'
-#' This function assumes that there is an environment variable called `RXD_DATA` 
+#' This function assumes that there is an environment variable called `RXD_DATA`
 #' which is set to the base path of the data directory.
 #'
 #' @return [character(1)] The normalized base path.
@@ -20,7 +20,7 @@ get_nfs_path <- function() {
 
 #' Get Base Path from an Environment Variable
 #'
-#' This function is an alias for `get_nfs_path()` to maintain backwards compatibility.  
+#' This function is an alias for `get_nfs_path()` to maintain backwards compatibility.
 #'
 #' @return [character(1)] The normalized base path.
 #'

From abe10d67aca9bcabab78944b98c5a5f7c448614d Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 13 Nov 2024 14:09:02 +0800
Subject: [PATCH 34/37] Check argument print_file_paths

---
 R/dvloader.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/dvloader.R b/R/dvloader.R
index 6ae0044..82327c6 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -66,6 +66,7 @@ load_data <- function(
   checkmate::assert_character(file_names, min.len = 1)
   checkmate::assert_logical(use_wd, len = 1)
   checkmate::assert_logical(prefer_sas, len = 1)
+  checkmate::assert_logical(print_file_paths, len = 1)
 
   if (use_wd) {
     base_dir <- getwd()

From cf48a948f09bae10c5bd80bf5791a88dda816db0 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 13 Nov 2024 14:10:42 +0800
Subject: [PATCH 35/37] Remove unused code

---
 R/dvloader.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/R/dvloader.R b/R/dvloader.R
index 82327c6..c032317 100644
--- a/R/dvloader.R
+++ b/R/dvloader.R
@@ -76,8 +76,6 @@ load_data <- function(
 
   dir_path <- if (is.null(sub_dir)) base_dir else file.path(base_dir, sub_dir)
 
-  file_ext <- if (prefer_sas) "sas7bdat" else "rds"
-
   file_paths <- get_file_paths(dir_path = dir_path, file_names = file_names, prefer_sas = prefer_sas)
 
   if (isTRUE(print_file_paths)) {

From 6dc6e0ea18920904284ac1956130a3d29a9f10b7 Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 13 Nov 2024 14:25:46 +0800
Subject: [PATCH 36/37] Updated changelog

---
 NEWS.md | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/NEWS.md b/NEWS.md
index e3df5dc..fbc1679 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,10 +1,10 @@
 # dv.loader 2.1.0
 
-- Refactored code to improve readability and maintainability.
+- Introduced new `load_data_files()` function that provides flexible loading of data files from any file paths.
 
-- Fixed issue of partial matching when the `file_names` argument contains no file extensions.
+- Updated `load_data()` function to serve as a convenience wrapper around `load_data_files()` for loading files from a single directory.
 
-- Added arguments `env_var` and `print_file_paths` in `load_data()` function to provide more flexibility and control.
+- Added `print_file_paths` option to `load_data()` to display the full paths of loaded files, helping users identify potential file name matching issues.
 
 # dv.loader 2.0.0
 

From a14c5003b5438ad00169c6a6403a59920030f20d Mon Sep 17 00:00:00 2001
From: Ming Yang <hustyangming@gmail.com>
Date: Wed, 13 Nov 2024 14:37:19 +0800
Subject: [PATCH 37/37] Update Rd file

---
 man/get_nfs_path.Rd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/man/get_nfs_path.Rd b/man/get_nfs_path.Rd
index 516256b..4d331fe 100644
--- a/man/get_nfs_path.Rd
+++ b/man/get_nfs_path.Rd
@@ -10,6 +10,6 @@ get_nfs_path()
 [character(1)] The normalized base path.
 }
 \description{
-This function assumes that there is an environment variable called `RXD_DATA` 
+This function assumes that there is an environment variable called `RXD_DATA`
 which is set to the base path of the data directory.
 }