joining functions in topics

Author: douwe

R/read.R

@@ -89,6 +89,7 @@ plate_to_df <- function(d) {
 }
 
 #' Read platedata formatted data from a spreadsheet
+#'
 #' @inherit read_keyvalue
 #' @return A data frame in long format
 #' @noRd
@@ -97,10 +98,14 @@ read_key_plate <- function(drfile, sheet, range, translate = FALSE, translations
   plate_to_df(plate)
 }
 
-#' Translate long variable names to short variable names
-#' @param v A vector of long variable names
+#' Translation between long and short variable names
+#'
+#' @description
+#' Translate between long and short variable names. If a translation is missing the original
+#' variable long or short variable name from `v` is returned.
+#' @param v A vector of variable names
 #' @param translations A named vector with long variable names as names and short variable names as values
-#' @return A vector of short variable names
+#' @return A vector of long or short variable names
 #' @export
 long_to_shortnames <- function(v, translations) {
   positions <- match(v, translations$long)
@@ -112,9 +117,8 @@ long_to_shortnames <- function(v, translations) {
   shortnames
 }
 
-#' Reverse translate short variable names to long variable names
-#' @inherit long_to_shortnames
 #' @return A vector of long variable names
+#' @rdname long_to_shortnames
 #' @export
 short_to_longnames <- function(v, translations) {
   positions <- match(v, translations$short)

R/utils.R

@@ -1,16 +1,3 @@
-# function to download information from a url, or if it is already in cache to
-# use the cache. Note that cacheEnv is initiated in the file aaa.R
-# download <- function(url) {
-#   if (exists(url, envir = .cacheEnv)) {
-#     return(get(url, envir = .cacheEnv))
-#   }
-#   file <- httr2::request(url) |>
-#     httr2::req_perform() |>
-#     httr2::resp_body_string()
-#   assign(url, file, envir = .cacheEnv)
-#   file
-# }
-
 #' Create a table from a list of key-value pairs
 #' @param kvlist A list of key-value pairs
 #' @param guide A data guide
@@ -34,25 +21,24 @@ kvlist_to_table <- function(kvlist, guide, reverse.translate = TRUE) {
   tbl
 }
 
-#' Convert a string with a star to a number
+#' @title Using stars to indicate rejected values
 #' @param x A character vector
-#' @return A numeric vector
 #' @description
-#' If a template uses the convention of putting a star in front of numbers that
-#' should be excluded then this function can be used to convert the variable to
-#' a number again.
-#'
+#' If a template uses the convention of putting a star in front of or behind
+#' numbers that should be rejected for further use then the function
+#' `star_to_number()` can be used to convert the variable to a number. The
+#' function `has_star()` checks whether a string has a star. It can be used to
+#' generate a logical vector indicating accepted/rejected values.
+#' @return Function `star_to_number()` returns a numeric vector, `has_star()`
+#' returns a logical vector.
 #' @export
 star_to_number <- function(x) {
   as.numeric(stringr::str_remove_all(x, "[*x?]"))
 }
 
 #' Check if a string has a star
-#' @param x A character vector
-#' @return A logical vector
-#' @description
-#' This function checks if a string has a star, x or a question mark.
 #' @export
+#' @rdname star_to_number
 #'
 has_star <- function(x) {
   stringr::str_detect(x, "[*x?]")

R/wells.R

@@ -47,8 +47,10 @@ check_wells <- function(wells, format, returnerror = TRUE) {
   wells
 }
 
-#' Calculate well number from row and column. Function used in `raw_map` function
-#' from package `platetools`.
+#' Calculate well number from row and column
+#'
+#' @description This function can be used in the `raw_map()` function from
+#' package `platetools`.
 #'
 #' @param row A character vector with the row names
 #' @param col A numeric vector with the column names