Fix styler issues.

R/load_data.R

@@ -22,13 +22,13 @@
 #' @importFrom lifecycle deprecate_warn
 load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = FALSE) {
   lifecycle::deprecate_warn("3.0.0", "load_data()", "read_data()")
-  
+
   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
-  
+
   if (is.null(sub_dir)) {
     study_path <- getwd()
   } else {
@@ -38,10 +38,10 @@ load_data <- function(sub_dir = NULL, file_names, use_wd = FALSE, prefer_sas = F
       study_path <- file.path(get_cre_path(), sub_dir)
     }
   }
-  
+
   # create the output
   data_list <- create_data_list(study_path, file_names, prefer_sas) # nolint
-  
+
   return(data_list)
 }
 
@@ -75,39 +75,39 @@ create_data_list <- function(file_path, file_names, prefer_sas) {
     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))
       }
-      
+
       index <- match(uppercase_file_name, uppercase_candidates)
       if (!is.na(index)) {
         file_name_to_load <- candidates[[index]]
         break
       }
     }
-    
+
     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)
 }
 
@@ -118,29 +118,29 @@ create_data_list <- function(file_path, file_names, prefer_sas) {
 #' @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.")
   }
-  
+
   is_rds <- toupper(ext) == "RDS"
-  
+
   file <- file.path(file_path, file_name)
   file_name <- tools::file_path_sans_ext(file_name)
-  
+
   # 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
-  
+
   if (is_rds) {
     out <- readRDS(file)
   } else {
     out <- haven::read_sas(file)
   }
   attr(out, "meta") <- meta
-  
+
   return(out)
 }

R/load_rds.R

@@ -9,37 +9,37 @@
 #' temp_dir <- tempdir()
 #' adsl_rds_file <- file.path(temp_dir, "adsl.rds")
 #' adae_rds_file <- file.path(temp_dir, "adae.rds")
-#' 
+#'
 #' # Write example data to RDS files
 #' saveRDS(pharmaverseadam::adsl, adsl_rds_file)
 #' saveRDS(pharmaverseadam::adae, adae_rds_file)
-#' 
+#'
 #' # Load RDS files
 #' rds_data_list <- load_rds(c(adsl_rds_file, adae_rds_file))
-#' 
+#'
 #' # Clean up
 #' unlink(c(adsl_rds_file, adae_rds_file))
 #' @export
 load_rds <- function(files) {
   # Check if files is a character vector
   checkmate::assert_character(files)
-  
+
   # Read each file and add metadata
   data_list <- lapply(files, function(file) {
     # Check if file exists
     checkmate::assert_file_exists(file)
     # Check if file is an RDS file
     check_file_ext(file, extension = "rds")
-    
+
     # Read RDS file
     data <- readRDS(file)
-    
+
     # Get file info and add to data as an attribute
     attr(data, "meta") <- file_info(file)
-    
+
     return(data)
   })
-  
+
   # Set names of data_list to the file names
   names(data_list) <- basename(files)
 

R/load_sas.R

@@ -9,37 +9,37 @@
 #' temp_dir <- tempdir()
 #' adsl_sas_file <- file.path(temp_dir, "adsl.sas7bdat")
 #' adae_sas_file <- file.path(temp_dir, "adae.sas7bdat")
-#' 
+#'
 #' # Write example data to SAS files
 #' haven::write_sas(pharmaverseadam::adsl, adsl_sas_file)
 #' haven::write_sas(pharmaverseadam::adae, adae_sas_file)
-#' 
+#'
 #' # Load SAS files
 #' sas_data_list <- load_sas(c(adsl_sas_file, adae_sas_file))
-#' 
+#'
 #' # Clean up
 #' unlink(c(adsl_sas_file, adae_sas_file))
 #' @export
 load_sas <- function(files) {
   # Check if files is a character vector
   checkmate::assert_character(files)
-  
+
   # Read each file and add metadata
   data_list <- lapply(files, function(file) {
     # Check if file exists
     checkmate::assert_file_exists(file)
     # Check if file is a SAS file
     check_file_ext(file, extension = "sas7bdat")
-        
+
     # Read SAS file
     data <- haven::read_sas(file)
-    
+
     # Get file info and add to data as an attribute
     attr(data, "meta") <- file_info(file)
-    
+
     return(data)
   })
-  
+
   # Set names of data_list to the file names
   names(data_list) <- basename(files)
   return(data_list)

R/load_xpt.R

@@ -9,16 +9,16 @@
 #' temp_dir <- tempdir()
 #' adsl_xpt_file <- file.path(temp_dir, "adsl.xpt")
 #' adae_xpt_file <- file.path(temp_dir, "adae.xpt")
-#' 
+#'
 #' # Write example data to XPT files
 #' haven::write_xpt(pharmaverseadam::adsl, adsl_xpt_file)
 #' haven::write_xpt(pharmaverseadam::adae, adae_xpt_file)
-#' 
+#'
 #' # Load XPT files
 #' xpt_data_list <- load_xpt(c(adsl_xpt_file, adae_xpt_file))
-#' 
+#'
 #' # Clean up
-#' unlink(c(adsl_xpt_file, adae_xpt_file))  
+#' unlink(c(adsl_xpt_file, adae_xpt_file))
 #' @export
 load_xpt <- function(files) {
   # Check if files is a character vector
@@ -30,16 +30,16 @@ load_xpt <- function(files) {
     checkmate::assert_file_exists(file)
     # Check if file is an XPT file
     check_file_ext(file, extension = "xpt")
-    
+
     # Read XPT file
     data <- haven::read_xpt(file)
-    
+
     # Get file info and add to data as an attribute
     attr(data, "meta") <- file_info(file)
-    
+
     return(data)
   })
-  
+
   # Set names of data_list to the file names
   names(data_list) <- basename(files)
 

R/utils.R

@@ -9,7 +9,7 @@ check_file_ext <- function(file, extension) {
   # Check input types
   checkmate::assert_string(file)
   checkmate::assert_string(extension)
-  
+
   # Extract file extension (case-insensitive)
   file_ext <- tolower(tools::file_ext(file))
 
@@ -18,7 +18,7 @@ check_file_ext <- function(file, extension) {
 
   # Check that the file extension is one of the allowed choices
   checkmate::assert_choice(file_ext, choices = c("rds", "sas7bdat", "xpt"))
-  
+
   # Compare with the given extension (case-insensitive)
   return(file_ext == tolower(extension))
 }
@@ -39,7 +39,7 @@ file_info <- function(file) {
 
   # Get the path from the rownames
   path <- rownames(info)
-  
+
   # Check file and path are the same
   checkmate::assert_true(file == path)
 
@@ -49,7 +49,7 @@ file_info <- function(file) {
 
   # Convert to list to remove row names
   info <- as.list(info)
-    
+
   # Return the file information as a list
   return(info)
 }

tests/testthat/setup.R

@@ -47,15 +47,15 @@ Sys.setenv(RXD_DATA = temp_dir)
 # Load RDS data via load_data()
 lifecycle::expect_deprecated(
   iris_data_rds <- dv.loader::load_data(
-    sub_dir = ".", 
+    sub_dir = ".",
     file_names = "iris.rds"
   )
 )
 
 # Load SAS data via load_data()
 lifecycle::expect_deprecated(
   iris_data_sas <- dv.loader::load_data(
-    sub_dir = ".", 
+    sub_dir = ".",
     file_names = "iris.sas7bdat"
   )
 )

tests/testthat/test-data_integrity.R

@@ -1,17 +1,17 @@
 test_that(
   desc = vdoc[["add_spec"]](
-    desc = "Ensures that the data integrity is maintained across different file types and loading methods, 
+    desc = "Ensures that the data integrity is maintained across different file types and loading methods,
     comparing the loaded data against a known reference dataset.",
     spec = specs$data_integrity
-  ), 
-  code = { 
+  ),
+  code = {
     # load_data(): check that the RDS file is loaded correctly
     expect_equal(
       object = iris_data_rds[["iris.rds"]],
       expected = iris_data,
       ignore_attr = TRUE
     )
-    
+
     # load_data(): check that the SAS file is loaded correctly
     expect_equal(
       object = iris_data_sas[["iris.sas7bdat"]],
@@ -21,21 +21,21 @@ test_that(
 
     # load_rds(): check that the RDS file is loaded correctly
     expect_equal(
-      object = iris_rds[["iris.rds"]], 
+      object = iris_rds[["iris.rds"]],
       expected = iris_data,
       ignore_attr = TRUE
     )
-    
+
     # load_sas(): check that the SAS file is loaded correctly
     expect_equal(
-      object = iris_sas[["iris.sas7bdat"]], 
+      object = iris_sas[["iris.sas7bdat"]],
       expected = iris_data,
       ignore_attr = TRUE
     )
-    
+
     # load_xpt(): check that the XPT file is loaded correctly
     expect_equal(
-      object = iris_xpt[["iris.xpt"]], 
+      object = iris_xpt[["iris.xpt"]],
       expected = iris_data,
       ignore_attr = TRUE
     )

tests/testthat/test-default_dir.R

@@ -1,23 +1,23 @@
-test_that(  
+test_that(
   desc = vdoc[["add_spec"]](
-    desc = "Verifies that load_data() can correctly locate and load data files using 
+    desc = "Verifies that load_data() can correctly locate and load data files using
     relative paths from the current working directory.",
     spec = specs$default_dir
-  ), 
+  ),
   code = {
     # Save the current working directory
     old_wd <- getwd()
-    
+
     # Change the working directory to the temporary directory
     setwd(temp_dir)
-    
+
     lifecycle::expect_deprecated(
       # load_data(): load the RDS file with use_wd = TRUE
       data1 <- dv.loader::load_data(
         sub_dir = ".",
         file_names = "iris.rds",
         use_wd = TRUE
-      )    
+      )
     )
 
     lifecycle::expect_deprecated(
@@ -26,7 +26,7 @@ test_that(
         sub_dir = ".",
         file_names = "iris.sas7bdat",
         use_wd = TRUE
-      )      
+      )
     )
 
     # Expect that the RDS file is loaded