Replace tags with labels

The `labels()` is reexported from `datatagr`. Reexport
is done because the labels function is valuable to the
end user of linelist as well.

R/has_tag.R

@@ -33,7 +33,7 @@ has_tag <- function(
 ) {
 
   dat <- tidyselect::peek_data(fn = "has_tag")
-  dat_tags <- tags(dat)
+  dat_tags <- labels(dat)
 
   cols_to_extract <- dat_tags[names(dat_tags) %in% tags]
 

R/labels.R

@@ -0,0 +1,3 @@
+#' @importFrom datatagr labels
+#' @export
+datatagr::labels

R/linelist-package.R

@@ -17,7 +17,7 @@
 #'
 #'   * [set_tags()]: to change or add tagged variables in a `linelist`
 #'
-#'   * [tags()]: to get the list of tags of a `linelist`
+#'   * [labels()]: to get the list of tags of a `linelist`
 #'
 #'   * [labels_df()]: to get a `data.frame` of all tagged variables
 #'
@@ -62,7 +62,7 @@
 #'   x
 #'
 #'   ## check tagged variables
-#'   tags(x)
+#'   labels(x)
 #'
 #'   ## robust renaming
 #'   names(x)[1] <- "identifier"
@@ -108,7 +108,7 @@
 #'       select(has_tag(c("gender", "age")))
 #'
 #'     x %>%
-#'       tags()
+#'       labels()
 #'
 #'     x %>%
 #'       select(starts_with("date"))

R/make_linelist.R

@@ -26,7 +26,7 @@
 #' * An overview of the [linelist] package
 #' * [tags_names()]: for a list of known tag names
 #' * [tags_types()]: for the associated accepted types/classes
-#' * [tags()]: for a list of tagged variables in a `linelist`
+#' * [labels()]: for a list of tagged variables in a `linelist`
 #' * [set_tags()]: for modifying tags
 #' * [labels_df()]: for selecting variables by tags
 #'
@@ -94,7 +94,7 @@
 #'   head(x)
 #'
 #'   ## check tags
-#'   tags(x)
+#'   labels(x)
 #'
 #'   ## Tags can also be passed as a list with the splice operator (!!!)
 #'   my_tags <- list(

R/names.R

@@ -31,15 +31,15 @@
 #'
 #'   ## see results: tags have been updated
 #'   head(x)
-#'   tags(x)
+#'   labels(x)
 #'
 #'  # This also works with using `dplyr::rename()` because it uses names<-()
 #'  # under hood
 #'  if (require(dplyr)) {
 #'    x <- x %>%
 #'      rename(case_id= case_label)
 #'    head(x)
-#'    tags(x)
+#'    labels(x)
 #'  }
 #' }
 `names<-.linelist` <- function(x, value) {
@@ -66,7 +66,7 @@
   }
 
   # Step 2
-  out_tags <- tags(x, TRUE)
+  out_tags <- labels(x, TRUE)
   for (i in seq_along(out_tags)) {
     if (!is.null(out_tags[[i]])) {
       idx <- match(out_tags[[i]], old_names)

R/print.linelist.R

@@ -42,7 +42,7 @@
 print.linelist <- function(x, ...) {
   cat("\n// linelist object\n")
   print(datatagr::drop_datatagr(x, remove_labels = TRUE))
-  tags_txt <- paste(names(tags(x)), unlist(tags(x)), sep = ":", collapse = ", ")
+  tags_txt <- paste(names(labels(x)), unlist(labels(x)), sep = ":", collapse = ", ")
   if (tags_txt == "") {
     tags_txt <- "[no tagged variable]"
   }

R/prune_tags.R

@@ -21,7 +21,7 @@ prune_tags <- function(x, lost_action = c("error", "warning", "none")) {
   lost_action <- match.arg(lost_action)
 
   # do stuff
-  old_tags <- tags(x, show_null = TRUE)
+  old_tags <- labels(x, show_null = TRUE)
 
   has_lost_column <- vapply(
     old_tags,

R/select_tags.R

@@ -20,7 +20,7 @@
 #' @export
 #'
 #' @seealso
-#' * [tags()] for existing tags in a `linelist`
+#' * [labels()] for existing tags in a `linelist`
 #' * [labels_df()] to get a `data.frame` of all tags
 #'
 #' @examples
@@ -39,7 +39,7 @@
 #'   head(x)
 #'
 #'   ## check tagged variables
-#'   tags(x)
+#'   labels(x)
 #'
 #'   # DEPRECATED!
 #'   select_tags(x, "gender", "age")

R/set_tags.R

@@ -17,28 +17,28 @@
 #' if (require(outbreaks)) {
 #'   ## create a linelist
 #'   x <- make_linelist(measles_hagelloch_1861, date_onset = "date_of_rash")
-#'   tags(x)
+#'   labels(x)
 #'
 #'   ## add new tags and fix an existing one
 #'   x <- set_tags(x,
 #'     age = "age",
 #'     gender = "gender",
 #'     date_onset = "date_of_prodrome"
 #'   )
-#'   tags(x)
+#'   labels(x)
 #'
 #'   ## add non-default tags using allow_extra
 #'   x <- set_tags(x, severe = "complications", allow_extra = TRUE)
-#'   tags(x)
+#'   labels(x)
 #'
 #'   ## remove tags by setting them to NULL
-#'   old_tags <- tags(x)
+#'   old_tags <- labels(x)
 #'   x <- set_tags(x, age = NULL, gender = NULL)
-#'   tags(x)
+#'   labels(x)
 #'
 #'   ## setting tags providing a list (used to restore old tags here)
 #'   x <- set_tags(x, !!!old_tags)
-#'   tags(x)
+#'   labels(x)
 #' }
 #'
 set_tags <- function(x, ..., allow_extra = FALSE) {

R/square_bracket.R

@@ -94,7 +94,7 @@
   }
 
   # Case 2
-  old_tags <- tags(x, show_null = TRUE)
+  old_tags <- labels(x, show_null = TRUE)
   out <- restore_tags(out, old_tags, lost_action)
 
   out
@@ -107,7 +107,7 @@
 `[<-.linelist` <- function(x, i, j, value) {
   lost_action <- get_lost_tags_action()
   out <- NextMethod()
-  old_tags <- tags(x, show_null = TRUE)
+  old_tags <- labels(x, show_null = TRUE)
   out <- restore_tags(out, old_tags, lost_action)
   out
 }
@@ -119,7 +119,7 @@
 `[[<-.linelist` <- function(x, i, j, value) {
   lost_action <- get_lost_tags_action()
   out <- NextMethod()
-  old_tags <- tags(x, show_null = TRUE)
+  old_tags <- labels(x, show_null = TRUE)
   out <- restore_tags(out, old_tags, lost_action)
   out
 }
@@ -130,7 +130,7 @@
 `$<-.linelist` <- function(x, name, value) {
   lost_action <- get_lost_tags_action()
   out <- NextMethod()
-  old_tags <- tags(x, show_null = TRUE)
+  old_tags <- labels(x, show_null = TRUE)
   out <- restore_tags(out, old_tags, lost_action)
   out
 }

R/validate_tags.R

@@ -41,7 +41,7 @@
 #' }
 validate_tags <- function(x, allow_extra = FALSE) {
   checkmate::assert_class(x, "linelist")
-  x_tags <- tags(x, show_null = TRUE)
+  x_tags <- labels(x, show_null = TRUE)
 
   stopifnot(
     "`x` has no tags attribute" = !is.null(x_tags)
@@ -76,7 +76,7 @@ validate_tags <- function(x, allow_extra = FALSE) {
   }
 
   # check that tagged variables exist
-  x_tags_vec <- unlist(tags(x))
+  x_tags_vec <- unlist(labels(x))
   var_exists <- x_tags_vec %in% names(x)
   if (!all(var_exists)) {
     missing_var <- x_tags_vec[!var_exists]

tests/testthat/test-compat-dplyr.R

@@ -35,8 +35,8 @@ test_that("Compatibility with dplyr::filter()", {
   # nolint end: expect_named_linter
 
   expect_identical(
-    tags(dplyr::filter(x, dist > mean(dist))),
-    tags(x)
+    labels(dplyr::filter(x, dist > mean(dist))),
+    labels(x)
   )
 
 })
@@ -75,8 +75,8 @@ test_that("Compatibility with dplyr::mutate(.keep)", {
   x %>%
     dplyr::mutate(speed = as.integer(speed)) %>%
     expect_s3_class("linelist") %>%
-    tags() %>%
-    expect_identical(tags(x))
+    labels() %>%
+    expect_identical(labels(x))
 
 })
 
@@ -105,7 +105,7 @@ test_that("Compatibility with dplyr::relocate()", {
 test_that("Compatibility with dplyr::rename()", {
 
   expect_identical(
-    tags(dplyr::rename(x, toto = dist)),
+    labels(dplyr::rename(x, toto = dist)),
     list(date_onset = "toto", date_outcome = "speed")
   )
 
@@ -124,8 +124,8 @@ test_that("Compatibility with dplyr::rename()", {
 test_that("Compatibility with dplyr::rename_with()", {
 
   expect_identical(
-    tags(dplyr::rename_with(x, toupper)),
-    lapply(tags(x), toupper)
+    labels(dplyr::rename_with(x, toupper)),
+    lapply(labels(x), toupper)
   )
 
   # Identity
@@ -145,15 +145,15 @@ test_that("Compatibility with dplyr::select()", {
   x %>%
     dplyr::select("dist") %>%
     expect_s3_class("linelist") %>%
-    tags() %>%
+    labels() %>%
     expect_identical(list(date_onset = "dist")) %>%
     expect_snapshot_warning()
 
   # Even when renames happen
   x %>%
     dplyr::select(dist, vitesse = speed) %>%
     expect_s3_class("linelist") %>%
-    tags() %>%
+    labels() %>%
     expect_identical(list(date_onset = "dist", date_outcome = "vitesse"))
 
 })
@@ -165,8 +165,8 @@ test_that("Compatibility with dplyr::bind_rows()", {
   rbound_x <- dplyr::bind_rows(x, x)
 
   expect_identical(
-    tags(x),
-    tags(rbound_x)
+    labels(x),
+    labels(rbound_x)
   )
 
   expect_s3_class(

tests/testthat/test-make_linelist.R

@@ -23,17 +23,17 @@ test_that("tests for make_linelist", {
   )
 
   # test functionalities
-  expect_identical(tags_defaults(), tags(make_linelist(cars), TRUE))
+  expect_identical(tags_defaults(), labels(make_linelist(cars), TRUE))
 
   x <- make_linelist(cars, date_onset = "dist", date_outcome = "speed")
-  expect_identical(tags(x)$date_onset, "dist")
-  expect_identical(tags(x)$date_outcome, "speed")
-  expect_null(tags(x)$outcome)
-  expect_null(tags(x)$date_reporting)
+  expect_identical(labels(x)$date_onset, "dist")
+  expect_identical(labels(x)$date_outcome, "speed")
+  expect_null(labels(x)$outcome)
+  expect_null(labels(x)$date_reporting)
 
   x <- make_linelist(cars, foo = "speed", bar = "dist", allow_extra = TRUE)
   expect_identical(
-    tags(x, TRUE),
+    labels(x, TRUE),
     c(tags_defaults(), foo = "speed", bar = "dist")
   )
 

tests/testthat/test-names.R

@@ -15,7 +15,7 @@ test_that("tests for the names<- operator", {
   # functionalities
   names(x) <- c("titi", "toto")
   expect_named(x, c("titi", "toto"))
-  expect_identical(tags(x), list(id = "titi", age = "toto"))
+  expect_identical(labels(x), list(id = "titi", age = "toto"))
   expect_s3_class(x, old_class)
   names(x) <- old_names
   expect_identical(x, old_x)

tests/testthat/test-prune_tags.R

@@ -16,7 +16,7 @@ test_that("tests for prune_tags", {
 
   # Check functionality
   y <- prune_tags(x, "none")
-  expect_identical(tags_defaults(), tags(y, TRUE))
+  expect_identical(tags_defaults(), labels(y, TRUE))
   expect_s3_class(y, "linelist")
 })
 

tests/testthat/test-restore_tags.R

@@ -10,10 +10,10 @@ test_that("tests for restore_tags", {
     " date_onset:dist, age:speed",
     sep = "\n"
   )
-  expect_error(restore_tags(z, tags(x), "error"), msg)
-  expect_warning(restore_tags(z, tags(x), "warning"), msg)
+  expect_error(restore_tags(z, labels(x), "error"), msg)
+  expect_warning(restore_tags(z, labels(x), "warning"), msg)
 
   # Check functionality
-  expect_identical(x, restore_tags(x, tags(x)))
-  expect_identical(x, restore_tags(y, tags(x)))
+  expect_identical(x, restore_tags(x, labels(x)))
+  expect_identical(x, restore_tags(y, labels(x)))
 })

tests/testthat/test-set_tags.R

@@ -15,8 +15,8 @@ test_that("tests for set_tags()", {
   # Check functionality
   expect_identical(x, set_tags(x))
   x <- set_tags(x, date_reporting = "speed")
-  expect_identical(tags(x)$date_reporting, "speed")
-  expect_identical(tags(x)$date_onset, "dist")
+  expect_identical(labels(x)$date_reporting, "speed")
+  expect_identical(labels(x)$date_onset, "dist")
 
   x <- set_tags(x, id = "speed", date_outcome = "dist")
   y <- set_tags(x, !!!list(id = "speed", date_outcome = "dist"))