Optimization develop roxugen

OlinkAnalyze/DESCRIPTION

@@ -59,16 +59,19 @@ Config/testthat/start-first: read_npx_l*, read_npx_w*
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.2
+Roxygen: list(markdown = TRUE)
 Depends: R (>= 4.1.0)
 Imports: 
     arrow (>= 14.0.0),
     cli (>= 3.6.1),
+    dbplyr,
     dplyr,
-    readxl,
+    duckdb,
     rlang,
     stringr,
     tidyr
 Suggests: 
+    readxl,
     testthat (>= 3.0.0),
     withr,
     writexl,

OlinkAnalyze/NAMESPACE

@@ -1,4 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+export(check_npx)
 export(read_NPX)
 export(read_npx)
+importFrom(dbplyr,memdb_frame)
+importFrom(duckdb,duckdb)

OlinkAnalyze/R/check_boolean.R

@@ -1,17 +1,18 @@
 #' Help function checking if a variable is a boolean vector.
 #'
-#' @author Klev Diamanti
+#' @author
+#'   Klev Diamanti
 #'
-#' @param bool Input to check.
-#' @param error Boolean to return error or a boolean (default).
+#' @param bool Boolean to check.
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return Boolean if the variable is a boolean vector or not, and an error if
-#' `error = TRUE`.
+#' "error = TRUE".
 #'
 #' @seealso
-#'   [check_is_character()]
-#'   [check_is_integer()]
-#'   [check_is_numeric()]
+#'   \code{\link{check_is_character}}
+#'   \code{\link{check_is_integer}}
+#'   \code{\link{check_is_numeric}}
 #'
 check_is_boolean <- function(bool,
                              error = FALSE) {
@@ -46,18 +47,19 @@ check_is_boolean <- function(bool,
 
 #' Help function checking if a variable is a boolean vector of length 1.
 #'
-#' @author Klev Diamanti
+#' @author
+#'   Klev Diamanti
 #'
-#' @param bool Input to check.
-#' @param error Boolean to return error or a boolean (default).
+#' @param bool Boolean vector to check.
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return Boolean if the variable is a boolean vector of length 1 or not, and
-#' an error if `error = TRUE`.
+#' an error if "error = TRUE".
 #'
 #' @seealso
-#'   [check_is_scalar_character()]
-#'   [check_is_scalar_integer()]
-#'   [check_is_scalar_numeric()]
+#'   \code{\link{check_is_scalar_character}}
+#'   \code{\link{check_is_scalar_integer}}
+#'   \code{\link{check_is_scalar_numeric}}
 #'
 check_is_scalar_boolean <- function(bool,
                                     error = FALSE) {

OlinkAnalyze/R/check_character.R

@@ -1,17 +1,18 @@
 #' Help function checking if a variable is a character vector.
 #'
-#' @author Klev Diamanti
+#' @author
+#'   Klev Diamanti
 #'
-#' @param string Input to check.
-#' @param error Boolean to return error or a boolean (default).
+#' @param string String to check.
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return Boolean if the variable is a character vector or not, and an error if
-#' `error = TRUE`.
+#' "error = TRUE".
 #'
 #' @seealso
-#'   [check_is_boolean()]
-#'   [check_is_integer()]
-#'   [check_is_numeric()]
+#'   \code{\link{check_is_boolean}}
+#'   \code{\link{check_is_integer}}
+#'   \code{\link{check_is_numeric}}
 #'
 check_is_character <- function(string,
                                error = FALSE) {
@@ -50,18 +51,19 @@ check_is_character <- function(string,
 
 #' Help function checking if a variable is a character vector of length 1.
 #'
-#' @author Klev Diamanti
+#' @author
+#'   Klev Diamanti
 #'
-#' @param string Input to check.
-#' @param error Boolean to return error or a boolean (default).
+#' @param string String vector to check.
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return Boolean if the variable is a character vector of length 1 or not, and
-#' an error if `error = TRUE`.
+#' an error if "error = TRUE".
 #'
 #' @seealso
-#'   [check_is_scalar_boolean()]
-#'   [check_is_scalar_integer()]
-#'   [check_is_scalar_numeric()]
+#'   \code{\link{check_is_scalar_boolean}}
+#'   \code{\link{check_is_scalar_integer}}
+#'   \code{\link{check_is_scalar_numeric}}
 #'
 check_is_scalar_character <- function(string,
                                       error = FALSE) {

OlinkAnalyze/R/check_columns.R

@@ -1,11 +1,13 @@
 #' Check that an input tibble or arrow object contains the required columns.
 #'
 #' @description
-#' `check_columns` checks if the input tibble or arrow object `data` contains
-#' all of the columns in \var{col_list}.
+#' Checks if the input tibble or arrow object \var{df} contains all of the
+#' columns in \var{col_list}.
 #'
+#' @details
 #' \var{col_list} might contain also vectors of characters as elements. In this
-#' case one of the characters in the vector is expected to be present.
+#' case one of the characters in the vector is expected to be present. See
+#' examples.
 #'
 #' @author
 #'   Klev Diamanti
@@ -138,7 +140,7 @@ check_columns <- function(df,
         one of the vectors of required columns: { missing_one }!",
         "i" = "Please make sure they are part of the input dataset."
       ),
-      call = NULL,
+      call = rlang::caller_env(),
       wrap = FALSE
       )
 

OlinkAnalyze/R/check_df.R

@@ -4,11 +4,10 @@
 #'   Klev Diamanti
 #'
 #' @param df Data frame to check.
-#' @param error `TRUE` to return an error if \var{df} is not an arrow object;
-#' `FALSE` (default) to return a boolean.
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return A scalar boolean if the object is an arrow object or not, and an
-#' error if \var{error} = `TRUE`.
+#' error if "error = TRUE".
 #'
 #' @seealso
 #'   \code{\link{check_is_tibble}}
@@ -55,11 +54,10 @@ check_is_arrow_object <- function(df,
 #'   Klev Diamanti
 #'
 #' @param df Data frame to check.
-#' @param error `TRUE` to return an error if \var{df} is not a tibble; `FALSE`
-#' (default) to return a boolean.
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return A scalar boolean if the object is a tibble or not, and an error if
-#' \var{error} = `TRUE`.
+#' "error = TRUE".
 #'
 #' @seealso
 #'   \code{\link{check_is_arrow_object}}
@@ -106,11 +104,10 @@ check_is_tibble <- function(df,
 #'   Klev Diamanti
 #'
 #' @param df Data frame to check.
-#' @param error `TRUE` to return an error if \var{df} is not a tibble or an
-#' arrow object; `FALSE` (default) to return a boolean.
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return A scalar boolean if the object is a tibble or an arrow object or not,
-#' and an error if \var{error} = `TRUE`.
+#' and an error if "error = TRUE".
 #'
 #' @seealso
 #'   \code{\link{check_is_arrow_object}}

OlinkAnalyze/R/check_file_exists.R → OlinkAnalyze/R/check_file.R

@@ -1,14 +1,15 @@
 #' Help function checking if file exists.
 #'
-#' @author Klev Diamanti
-#'
-#' @param file Path to the file.
-#' @param error Boolean to return error or a boolean (default).
+#' @author
+#'   Klev Diamanti
 #'
 #' @description
-#' Only one file at a time!
+#' Check \strong{only one file at a time} if it exists.
+#'
+#' @param file Path to file.
+#' @param error Return error or a boolean (default = FALSE).
 #'
-#' @return Boolean if the file exists or not, and an error if `error = TRUE`.
+#' @return Boolean if the file exists or not, and an error if "error = TRUE".
 #'
 check_file_exists <- function(file,
                               error = FALSE) {
@@ -51,14 +52,20 @@ check_file_exists <- function(file,
 
 #' Help function checking if file extension is acceptable.
 #'
-#' @author Klev Diamanti
+#' @author
+#'   Klev Diamanti
 #'
-#' @param file Path to the file.
+#' @description
+#' Use variable \var{accepted_npx_file_ext} to check if extension of the input
+#' file is acceptable.
+#'
+#' @param file Path to file.
 #'
 #' @return The type of the file extension based on the global variable
-#' `accepted_npx_file_ext`
+#' \var{accepted_npx_file_ext}.
 #'
 check_file_extension <- function(file) {
+
   # check input ----
 
   check_is_scalar_character(string = file,
@@ -84,7 +91,7 @@ check_file_extension <- function(file) {
         "x" = "Unable to recognize the extension of the file {.file {file}}!",
         "i" = "Expected on of {.val {accepted_npx_file_ext}}!"
       ),
-      call = NULL,
+      call = rlang::caller_env(),
       wrap = FALSE
     )
 

OlinkAnalyze/R/check_integer.R

@@ -1,17 +1,18 @@
 #' Help function checking if a variable is an integer vector.
 #'
-#' @author Klev Diamanti
+#' @author
+#'   Klev Diamanti
 #'
-#' @param int Input to check.
-#' @param error Boolean to return error or a boolean (default).
+#' @param int Integer to check.
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return Boolean if the variable is an integer vector or not, and an error if
-#' `error = TRUE`.or.
+#' "error = TRUE".
 #'
 #' @seealso
-#'   [check_is_boolean()]
-#'   [check_is_character()]
-#'   [check_is_numeric()]
+#'   \code{\link{check_is_boolean}}
+#'   \code{\link{check_is_character}}
+#'   \code{\link{check_is_numeric}}
 #'
 check_is_integer <- function(int,
                              error = FALSE) {
@@ -50,18 +51,19 @@ check_is_integer <- function(int,
 
 #' Help function checking if a variable is an integer vector of length 1.
 #'
-#' @author Klev Diamanti
+#' @author
+#'   Klev Diamanti
 #'
-#' @param int Input to check.
-#' @param error Boolean to return error or a boolean (default).
+#' @param int Integer vector to check.
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return Boolean if the variable is an integer vector of length 1 or not, and
-#' an error if `error = TRUE`.
+#' an error if "error = TRUE".
 #'
 #' @seealso
-#'   [check_is_scalar_boolean()]
-#'   [check_is_scalar_character()]
-#'   [check_is_scalar_numeric()]
+#'   \code{\link{check_is_scalar_boolean}}
+#'   \code{\link{check_is_scalar_character}}
+#'   \code{\link{check_is_scalar_numeric}}
 #'
 check_is_scalar_integer <- function(int,
                                     error = FALSE) {

OlinkAnalyze/R/check_list.R

@@ -1,12 +1,13 @@
 #' Help function to check if the variable is a list.
 #'
-#' @author Klev Diamanti
+#' @author
+#'   Klev Diamanti
 #'
 #' @param lst List to check.
-#' @param error Boolean to return error or a boolean (default).
+#' @param error Return error or a boolean (default = FALSE).
 #'
 #' @return Boolean if the object is a list or not, and an error if
-#' `error = TRUE`.
+#' "error = TRUE".
 #'
 check_is_list <- function(lst,
                           error = FALSE) {