Update functions to use linelist style tagging

NAMESPACE

@@ -4,7 +4,6 @@ S3method("$<-",safeframe)
 S3method("[",safeframe)
 S3method("[<-",safeframe)
 S3method("[[<-",safeframe)
-S3method("names<-",safeframe)
 S3method(print,safeframe)
 export(get_lost_tags_action)
 export(has_tag)

R/drop_safeframe.R

@@ -18,7 +18,7 @@ drop_safeframe <- function(x, remove_tags = TRUE) {
   if (remove_tags) {
     # Set the label attribute to NULL for all variables in x
     for (var in names(x)) {
-      attr(x[[var]], "label") <- NULL
+      x <- remove_tag(x, var)
     }
   }
   x

R/has_tag.R

@@ -5,30 +5,26 @@
 #' @returns A numeric vector containing the position of the columns with the
 #'   requested tags
 #'
-#' @note Using this in a pipeline results in a 'safeframe' object, but does not
-#'   maintain the variable tags at this time. It is primarily useful to make
-#'   your pipelines human readable.
-#'
 #' @export
 #'
 #' @examples
 #' ## create safeframe
 #' x <- make_safeframe(cars,
-#'   speed = "Miles per hour",
-#'   dist = "Distance in miles"
+#'   mph = "speed",
+#'   distance = "dist"
 #' )
 #' head(x)
 #'
 #' if (require(dplyr) && require(magrittr)) {
 #'   x %>%
-#'     select(has_tag(c("Miles per hour", "Distance in miles"))) %>%
+#'     select(has_tag(c("mph", "distance"))) %>%
 #'     head()
 #' }
 has_tag <- function(tags) {
   dat <- tidyselect::peek_data(fn = "has_tag")
   dat_tags <- tags(dat)
 
-  cols_to_extract <- dat_tags[dat_tags %in% tags]
+  cols_to_extract <- dat_tags[names(dat_tags) %in% tags]
 
-  which(colnames(dat) %in% names(cols_to_extract))
+  which(colnames(dat) %in% cols_to_extract)
 }

R/make_safeframe.R

@@ -7,10 +7,8 @@
 #'
 #' @param x a `data.frame` or a `tibble`
 #'
-#' @param ... <[`dynamic-dots`][rlang::dyn-dots]> A named list with variable
-#' names in `x` as list names and the tags as list values. Values set to
-#' `NULL` remove the tag When specifying tags, please also see
-#' `default_values`.
+#' @param ... <[`dynamic-dots`][rlang::dyn-dots]> A series of tags provided as
+#'   `tag_name = "column_name"`
 #'
 #' @seealso
 #'
@@ -26,8 +24,8 @@
 #' @examples
 #'
 #' x <- make_safeframe(cars,
-#'   speed = "Miles per hour",
-#'   dist = "Distance in miles"
+#'   mph = "speed",
+#'   distance = "dist"
 #' )
 #'
 #' ## print result - just first few entries
@@ -38,8 +36,8 @@
 #'
 #' ## tags can also be passed as a list with the splice operator (!!!)
 #' my_tags <- list(
-#'   speed = "Miles per hour",
-#'   dist = "Distance in miles"
+#'   mph = "speed",
+#'   distance = "dist"
 #' )
 #' new_x <- make_safeframe(cars, !!!my_tags)
 #'
@@ -56,6 +54,6 @@ make_safeframe <- function(x,
   x <- tag_variables(x, tags)
 
   # shape output and return object
-  class(x) <- c("safeframe", class(x))
+  class(x) <- unique(c("safeframe", class(x)))
   x
 }

R/print.safeframe.R

@@ -13,8 +13,8 @@
 #' @examples
 #' ## create safeframe
 #' x <- make_safeframe(cars,
-#'   speed = "Miles per hour",
-#'   dist = "Distance in miles"
+#'   mph = "speed",
+#'   distance = "dist"
 #' )
 #'
 #' ## print object - using only the first few entries
@@ -25,8 +25,8 @@
 #'   cars %>%
 #'     tibble() %>%
 #'     make_safeframe(
-#'       speed = "Miles per hour",
-#'       dist = "Distance in miles"
+#'       mph = "speed",
+#'       distance = "dist"
 #'     )
 #' }
 print.safeframe <- function(x, ...) {

R/restore_tags.R

@@ -7,36 +7,34 @@
 #'
 #' @param x a `data.frame`
 #'
-#' @param tags a list of tags as returned by [tags()]; if default values
-#' are missing, they will be added to the new list of tags. Matches column
-#' names with `x` to restore tags. Throws an error if no matches are found.
+#' @param tags a list of tags as returned by [tags()].
 #'
 #' @param lost_action a `character` indicating the behaviour to adopt when
 #'   tagged variables have been lost: "error" (default) will issue an error;
 #'   "warning" will issue a warning; "none" will do nothing
 #'
 #' @noRd
 #'
-#' @return The function returns a `safeframe` object with updated tags.
+#' @return The function returns a `safeframe` object with restored tags.
 #'
 
-restore_tags <- function(x, newTags,
+restore_tags <- function(x, tags,
                          lost_action = c("error", "warning", "none")) {
   # assertions
   checkmate::assertClass(x, "data.frame")
-  checkmate::assertClass(newTags, "list")
+  checkmate::assertClass(tags, "list")
   lost_action <- match.arg(lost_action)
 
   # Match the remaining variables to the provided tags
-  common_vars <- intersect(names(x), names(newTags))
+  common_vars <- intersect(names(x), tags)
   if (length(common_vars) == 0 && length(names(x)) > 0) {
     stop("No matching tags provided.")
   }
 
-  lost_vars <- setdiff(names(newTags), names(x))
+  lost_vars <- setdiff(tags, names(x))
 
   if (lost_action != "none" && length(lost_vars) > 0) {
-    lost_tags <- lapply(lost_vars, function(tag) newTags[[tag]])
+    lost_tags <- names(lost_vars)
 
     lost_msg <- vars_tags(lost_vars, lost_tags)
     msg <- paste(
@@ -52,10 +50,12 @@ restore_tags <- function(x, newTags,
       stop(errorCondition(msg, class = "safeframe_error"))
     }
   }
+  # Get names that are in tags but not in lost_vars
+  remaining_names <- setdiff(names(tags), names(lost_vars))
+  # Subset tags with remaining names
+  tags <- tags[remaining_names]
 
-  for (name in common_vars) {
-    attr(x[[name]], "label") <- newTags[[name]]
-  }
+  x <- tag_variables(x, tags)
 
   # Ensure class consistency
   if (!inherits(x, "safeframe")) {

R/safeframe-package.R

@@ -1,4 +1,4 @@
-#' Base Tools for tagging and Validating Data
+#' Base Tools for Tagging and Validating Data
 #'
 #' The \pkg{safeframe} package provides tools to help tag and validate data.
 #' The 'safeframe' class adds column level attributes to a 'data.frame'.
@@ -33,7 +33,7 @@
 #'   pipelines).
 #'
 #'   * `names() <-` (and related functions, such as [dplyr::rename()]) will
-#'   rename tags as needed
+#'   rename variables and carry forward the existing tags
 #'
 #'   * `x[...] <-` and `x[[...]] <-` (see [sub_safeframe]): will adopt the
 #'    desired behaviour when tagged variables are lost
@@ -43,14 +43,15 @@
 #'
 #' @note The package does not aim to have complete integration with \pkg{dplyr}
 #' functions. For example, [dplyr::mutate()] and [dplyr::bind_rows()] will
-#' not preserve tags. We only provide compatibility for [dplyr::rename()].
+#' not preserve tags in all cases. We only provide compatibility for
+#' [dplyr::rename()].
 #'
 #' @examples
 #'
 #' # using base R style
 #' x <- make_safeframe(cars[1:50, ],
-#'   speed = "Miles per hour",
-#'   dist = "Distance in miles"
+#'   mph = "speed",
+#'   distance = "dist"
 #' )
 #' x
 #'
@@ -70,7 +71,7 @@
 #'
 #' ## to trigger errors when tags are dropped
 #' # lost_tags_action("error")
-#' # x[, 2:5]
+#' # x[, 1]
 #'
 #' ## reset default behaviour
 #' lost_tags_action()
@@ -84,17 +85,17 @@
 #'   x <- cars %>%
 #'     tibble() %>%
 #'     make_safeframe(
-#'       speed = "Miles per hour",
-#'       dist = "Distance in miles"
+#'       mph = "speed",
+#'       distance = "dist"
 #'     ) %>%
 #'     mutate(result = if_else(speed > 50, "fast", "slow")) %>%
-#'     set_tags(result = "Ticket yes/no")
+#'     set_tags(ticket = "result")
 #'
 #'   head(x)
 #'
 #'   ## extract tagged variables
 #'   x %>%
-#'     select(has_tag(c("Ticket yes/no")))
+#'     select(has_tag(c("ticket")))
 #'
 #'   ## Retrieve all tags
 #'   x %>%

R/set_tags.R

@@ -14,16 +14,16 @@
 #' @examples
 #'
 #' ## create a safeframe
-#' x <- make_safeframe(cars, speed = "Miles per hour")
+#' x <- make_safeframe(cars, mph = "speed")
 #' tags(x)
 #'
 #' ## add new tags and fix an existing one
-#' x <- set_tags(x, dist = "Distance")
+#' x <- set_tags(x, distance = "dist")
 #' tags(x)
 #'
 #' ## remove tags by setting them to NULL
 #' old_tags <- tags(x)
-#' x <- set_tags(x, speed = NULL, dist = NULL)
+#' x <- set_tags(x, mph = NULL, distance = NULL)
 #' tags(x)
 #'
 #' ## setting tags providing a list (used to restore old tags here)
@@ -32,6 +32,7 @@
 set_tags <- function(x, ...) {
   # assert inputs
   checkmate::assertClass(x, "safeframe")
+
   orig_class <- class(x)
 
   # For some reason, we cannot remove tags from safeframe objects by setting
@@ -42,11 +43,13 @@ set_tags <- function(x, ...) {
   # 3. readding the tags and the safeframe class
 
   new_tags <- rlang::list2(...)
-  existing_tags <- tags(x)
-
-  x <- drop_safeframe(x, remove_tags = TRUE)
+  old_tags <- tags(x)
+  x <- drop_safeframe(x)
 
-  x <- tag_variables(x, utils::modifyList(existing_tags, new_tags))
+  x <- tag_variables(
+    x,
+    utils::modifyList(old_tags, new_tags, keep.null = TRUE)
+  )
 
   class(x) <- orig_class