From eb24644c7ff421478611cd5ea8a737367efa0465 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 28 Oct 2024 13:29:34 +0000
Subject: [PATCH 01/13] feat: initial support for names(teal_data)

---
 DESCRIPTION                             |   2 +-
 NAMESPACE                               |   3 +-
 NEWS.md                                 |  10 +-
 R/deprecated.R                          |  35 +++++++
 R/join_keys.R                           |   1 -
 R/teal_data-class.R                     |  16 +---
 R/teal_data-datanames.R                 |  68 --------------
 R/teal_data-names.R                     |  53 +++++++++++
 man/datanames.Rd                        |  33 ++-----
 man/names.teal_data.Rd                  |  40 ++++++++
 man/new_teal_data.Rd                    |  10 +-
 man/teal_data-class.Rd                  |   4 -
 tests/testthat/test-datanames.R         | 116 +++++++++++++-----------
 tests/testthat/test-teal_data.R         |  16 +---
 vignettes/join-keys.Rmd                 |   4 -
 vignettes/teal-data-reproducibility.Rmd |   2 +-
 vignettes/teal-data.Rmd                 |  23 ++++-
 17 files changed, 234 insertions(+), 202 deletions(-)
 delete mode 100644 R/teal_data-datanames.R
 create mode 100644 R/teal_data-names.R
 create mode 100644 man/names.teal_data.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 25d9bb0c3..8fa36bb3c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -72,8 +72,8 @@ Collate:
     'join_keys.R'
     'teal.data.R'
     'teal_data-class.R'
-    'teal_data-datanames.R'
     'teal_data-get_code.R'
+    'teal_data-names.R'
     'teal_data-show.R'
     'teal_data.R'
     'testhat-helpers.R'
diff --git a/NAMESPACE b/NAMESPACE
index 71db8957b..5391bfda9 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -14,11 +14,12 @@ S3method(format,join_keys)
 S3method(join_keys,default)
 S3method(join_keys,join_keys)
 S3method(join_keys,teal_data)
+S3method(names,"teal_data<-")
+S3method(names,teal_data)
 S3method(parents,join_keys)
 S3method(parents,teal_data)
 S3method(print,join_keys)
 export("col_labels<-")
-export("datanames<-")
 export("get_join_keys<-")
 export("join_keys<-")
 export("parents<-")
diff --git a/NEWS.md b/NEWS.md
index c37b3a076..26db0f66e 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -3,16 +3,18 @@
 ### Breaking changes
 
 - soft deprecate `datanames` argument of `get_code()`. Use `names` instead.
+- Soft deprecate of `datanames()` and `datanames(x) <- value` functions. 
+Use `names()` and `names(x) <- value` instead.
 
 ### Enhancements
 
-- `datanames()`
-    - if `join_keys` are provided, the `datanames()` are now sorted in topological way (`Kahn` algorithm),
+- `names()` function is introduced replacing `datanames`.
+    - if `join_keys` are provided, the `names()` are now sorted in topological way (`Kahn` algorithm),
     which means the parent dataset always precedes the child dataset.
-    - are extended by the parent dataset name, if one of the child dataset exist in `datanames()` and
+    - are extended by the parent dataset name, if one of the child dataset exist in `names()` and
     the connection between child-parent is set through `join_keys` and `parent` exist in `teal_data` environment.
     - do not allow to set a dataset name that do not exist in `teal_data` environment.
-    - `teal_data` no longer set default `datanames()` based on `join_keys` names - it uses only data names.
+    - `teal_data` no longer set default `names()` based on `join_keys` names - it uses only data names.
 
 ### Miscellaneous
 
diff --git a/R/deprecated.R b/R/deprecated.R
index d4b3e9e93..b876fb2ac 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -343,3 +343,38 @@ get_join_keys <- function(...) {
 get_labels <- function(...) {
   .deprecate_function("get_labels()", "Use col_labels(data)")
 }
+
+#' Names of data sets in `teal_data` object
+#'
+#' @description
+#' `r lifecycle::badge("deprecated")`
+#'
+#' Use `names()` instead of `datanames()`.
+#'
+#' `datanames()` is deprecated. If object should be hidden, then use a `.` (dot)
+#' prefix for the object's name.
+#'
+#' @param x (`teal_data` or `qenv_error`) object to access or modify
+#' @param ... (`character`) new value for `@datanames`; all elements must be names of variables existing in `@env`
+#'
+#' @return The contents of `@datanames` or `teal_data` object with updated `@datanames`.
+#'
+#'
+#' @name datanames
+
+#' @rdname datanames
+#' @export
+datanames <- function(x, ...) {
+  lifecycle::deprecate_soft("0.6.1", "datanames()", details = "names()")
+  names(x)
+}
+
+#' @rdname datanames
+`datanames<-` <- function(x, value, ...) {
+  lifecycle::deprecate_soft(
+    "0.6.1",
+    "`datanames<-`()",
+    details = "Function has no effect. Use a `.` (dot) prefix to hide objects instead in `teal_data`. See the documentation for more details."
+  )
+  names(x)
+}
diff --git a/R/join_keys.R b/R/join_keys.R
index 1798a46af..47fb97836 100644
--- a/R/join_keys.R
+++ b/R/join_keys.R
@@ -142,7 +142,6 @@ join_keys.teal_data <- function(...) {
 #' join_keys(td)
 `join_keys<-.teal_data` <- function(x, value) {
   join_keys(x@join_keys) <- value
-  datanames(x) <- x@datanames # datanames fun manages some exceptions
   x
 }
 
diff --git a/R/teal_data-class.R b/R/teal_data-class.R
index 3015797b9..23fc7c8e6 100644
--- a/R/teal_data-class.R
+++ b/R/teal_data-class.R
@@ -26,9 +26,6 @@ setOldClass("join_keys")
 #' @slot messages (`character`) vector of messages raised when evaluating code.
 #' @slot join_keys (`join_keys`) object specifying joining keys for data sets in `@env`.
 #'  Access or modify with [join_keys()].
-#' @slot datanames (`character`) vector of names of data sets in `@env`.
-#'  Used internally to distinguish them from auxiliary variables.
-#'  Access or modify with [datanames()].
 #' @slot verified (`logical(1)`) flag signifying that code in `@code` has been proven to yield contents of `@env`.
 #'  Used internally. See [`verify()`] for more details.
 #'
@@ -37,10 +34,9 @@ setOldClass("join_keys")
 setClass(
   Class = "teal_data",
   contains = "qenv",
-  slots = c(join_keys = "join_keys", datanames = "character", verified = "logical"),
+  slots = c(join_keys = "join_keys", verified = "logical"),
   prototype = list(
     join_keys = join_keys(),
-    datanames = character(0),
     verified = logical(0)
   )
 )
@@ -53,18 +49,13 @@ setClass(
 #' @param code (`character` or `language`) code to reproduce the `data`.
 #'   Accepts and stores comments also.
 #' @param join_keys (`join_keys`) object
-#' @param datanames (`character`) names of datasets passed to `data`.
-#'   Needed when non-dataset objects are needed in the `env` slot.
 #' @rdname new_teal_data
 #' @keywords internal
 new_teal_data <- function(data,
                           code = character(0),
-                          join_keys = join_keys(),
-                          datanames = names(data)) {
+                          join_keys = join_keys()) {
   checkmate::assert_list(data)
   checkmate::assert_class(join_keys, "join_keys")
-  if (is.null(datanames)) datanames <- character(0) # todo: allow to specify
-  checkmate::assert_character(datanames)
   if (!any(is.language(code), is.character(code))) {
     stop("`code` must be a character or language object.")
   }
@@ -82,8 +73,6 @@ new_teal_data <- function(data,
   new_env <- rlang::env_clone(list2env(data), parent = parent.env(.GlobalEnv))
   lockEnvironment(new_env, bindings = TRUE)
 
-  datanames <- .get_sorted_datanames(datanames = datanames, join_keys = join_keys, env = new_env)
-
   methods::new(
     "teal_data",
     env = new_env,
@@ -92,7 +81,6 @@ new_teal_data <- function(data,
     messages = rep("", length(code)),
     id = id,
     join_keys = join_keys,
-    datanames = datanames,
     verified = verified
   )
 }
diff --git a/R/teal_data-datanames.R b/R/teal_data-datanames.R
deleted file mode 100644
index d32727859..000000000
--- a/R/teal_data-datanames.R
+++ /dev/null
@@ -1,68 +0,0 @@
-#' Names of data sets in `teal_data` object
-#'
-#' Get or set the value of the `datanames` slot.
-#'
-#' The `@datanames` slot in a `teal_data` object specifies which of the variables stored in its environment
-#' (the `@env` slot) are data sets to be taken into consideration.
-#' The contents of `@datanames` can be specified upon creation and default to all variables in `@env`.
-#' Variables created later, which may well be data sets, are not automatically considered such.
-#' Use this function to update the slot.
-#'
-#' @param x (`teal_data`) object to access or modify
-#' @param value (`character`) new value for `@datanames`; all elements must be names of variables existing in `@env`
-#'
-#' @return The contents of `@datanames` or `teal_data` object with updated `@datanames`.
-#'
-#' @examples
-#' td <- teal_data(iris = iris)
-#' td <- within(td, mtcars <- mtcars)
-#' datanames(td)
-#'
-#' datanames(td) <- c("iris", "mtcars")
-#' datanames(td)
-#'
-#' @name datanames
-#' @aliases datanames,teal_data-method
-#' @aliases datanames<-,teal_data,character-method
-#' @aliases datanames,qenv.error-method
-#' @aliases datanames<-,qenv.error,character-method
-
-#' @rdname datanames
-#' @export
-setGeneric("datanames", function(x) standardGeneric("datanames"))
-setMethod("datanames", signature = "teal_data", definition = function(x) {
-  x@datanames
-})
-setMethod("datanames", signature = "qenv.error", definition = function(x) {
-  NULL
-})
-
-#' @rdname datanames
-#' @export
-setGeneric("datanames<-", function(x, value) standardGeneric("datanames<-"))
-setMethod("datanames<-", signature = c("teal_data", "character"), definition = function(x, value) {
-  checkmate::assert_subset(value, names(x@env))
-  x@datanames <- .get_sorted_datanames(datanames = value, join_keys = x@join_keys, env = x@env)
-  methods::validObject(x)
-  x
-})
-setMethod("datanames<-", signature = c("qenv.error", "character"), definition = function(x, value) {
-  methods::validObject(x)
-  x
-})
-
-
-#' @keywords internal
-.get_sorted_datanames <- function(datanames, join_keys, env) {
-  child_parent <- sapply(
-    datanames,
-    function(name) parent(join_keys, name),
-    USE.NAMES = TRUE,
-    simplify = FALSE
-  )
-
-  union(
-    intersect(unlist(topological_sort(child_parent)), ls(env)),
-    datanames
-  )
-}
diff --git a/R/teal_data-names.R b/R/teal_data-names.R
new file mode 100644
index 000000000..194d120f7
--- /dev/null
+++ b/R/teal_data-names.R
@@ -0,0 +1,53 @@
+#' Names of data sets in `teal_data` object
+#'
+#' Functions to get the names of a `teal_data` object.
+#' The names are extrapolated from the objects in the `qenv` environment and
+#' are not stored statically, unlike the normal behavior of `names()` function.
+#'
+#' Objects named with a `.` (dot) prefix will be ignored and not returned,
+#' unless `all.names` parameter is set to `TRUE`.
+#'
+#' @param x A (`teal_data`) object to access or modify.
+#' @param all.names (`logical(1)`) that specifies whether to include hidden
+#' objects.
+#' @param value Does nothing as the names assignment is not supported.
+#'
+#' @return A character vector of names.
+#'
+#' @examples
+#' td <- teal_data(iris = iris)
+#' td <- within(td, mtcars <- mtcars)
+#' names(td)
+#'
+#' td <- within(td, .CO2 <- CO2)
+#' names(td)
+#'
+#' @export
+names.teal_data <- function(x, all.names = FALSE) {
+  checkmate::assert_flag(all.names)
+  # Call method on qenv class
+  names_x <- utils::getS3method("names", class = "qenv")(x, all.names)
+  .get_sorted_names(names_x, join_keys(x), teal.code::get_env(x))
+}
+
+#' @rdname names.teal_data
+#' @export
+`names.teal_data<-` <- function(x, value) {
+  warning("`names(x) <- value` assignment does nothing for teal_data objects")
+  x
+}
+
+#' @keywords internal
+.get_sorted_names <- function(datanames, join_keys, env) {
+  child_parent <- sapply(
+    datanames,
+    function(name) parent(join_keys, name),
+    USE.NAMES = TRUE,
+    simplify = FALSE
+  )
+
+  union(
+    intersect(unlist(topological_sort(child_parent)), ls(env, all.names = TRUE)),
+    datanames
+  )
+}
diff --git a/man/datanames.Rd b/man/datanames.Rd
index 4908979a2..16307f003 100644
--- a/man/datanames.Rd
+++ b/man/datanames.Rd
@@ -1,42 +1,27 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/teal_data-datanames.R
+% Please edit documentation in R/deprecated.R
 \name{datanames}
 \alias{datanames}
-\alias{datanames,teal_data-method}
-\alias{datanames<-,teal_data,character-method}
-\alias{datanames,qenv.error-method}
-\alias{datanames<-,qenv.error,character-method}
 \alias{datanames<-}
 \title{Names of data sets in \code{teal_data} object}
 \usage{
-datanames(x)
+datanames(x, ...)
 
-datanames(x) <- value
+datanames(x, ...) <- value
 }
 \arguments{
-\item{x}{(\code{teal_data}) object to access or modify}
+\item{x}{(\code{teal_data} or \code{qenv_error}) object to access or modify}
 
-\item{value}{(\code{character}) new value for \verb{@datanames}; all elements must be names of variables existing in \verb{@env}}
+\item{...}{(\code{character}) new value for \verb{@datanames}; all elements must be names of variables existing in \verb{@env}}
 }
 \value{
 The contents of \verb{@datanames} or \code{teal_data} object with updated \verb{@datanames}.
 }
 \description{
-Get or set the value of the \code{datanames} slot.
-}
-\details{
-The \verb{@datanames} slot in a \code{teal_data} object specifies which of the variables stored in its environment
-(the \verb{@env} slot) are data sets to be taken into consideration.
-The contents of \verb{@datanames} can be specified upon creation and default to all variables in \verb{@env}.
-Variables created later, which may well be data sets, are not automatically considered such.
-Use this function to update the slot.
-}
-\examples{
-td <- teal_data(iris = iris)
-td <- within(td, mtcars <- mtcars)
-datanames(td)
+\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}
 
-datanames(td) <- c("iris", "mtcars")
-datanames(td)
+Use \code{names()} instead of \code{datanames()}.
 
+\code{datanames()} is deprecated. If object should be hidden, then use a \code{.} (dot)
+prefix for the object's name.
 }
diff --git a/man/names.teal_data.Rd b/man/names.teal_data.Rd
new file mode 100644
index 000000000..3daeee900
--- /dev/null
+++ b/man/names.teal_data.Rd
@@ -0,0 +1,40 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/teal_data-names.R
+\name{names.teal_data}
+\alias{names.teal_data}
+\alias{names.teal_data<-}
+\title{Names of data sets in \code{teal_data} object}
+\usage{
+\method{names}{teal_data}(x, all.names = FALSE)
+
+\method{names}{`teal_data<-`}(x, value)
+}
+\arguments{
+\item{x}{A (\code{teal_data}) object to access or modify.}
+
+\item{all.names}{(\code{logical(1)}) that specifies whether to include hidden
+objects.}
+
+\item{value}{Does nothing as the names assignment is not supported.}
+}
+\value{
+A character vector of names.
+}
+\description{
+Functions to get the names of a \code{teal_data} object.
+The names are extrapolated from the objects in the \code{qenv} environment and
+are not stored statically, unlike the normal behavior of \code{names()} function.
+}
+\details{
+Objects named with a \code{.} (dot) prefix will be ignored and not returned,
+unless \code{all.names} parameter is set to \code{TRUE}.
+}
+\examples{
+td <- teal_data(iris = iris)
+td <- within(td, mtcars <- mtcars)
+names(td)
+
+td <- within(td, .CO2 <- CO2)
+names(td)
+
+}
diff --git a/man/new_teal_data.Rd b/man/new_teal_data.Rd
index 4ddc43c95..2bdd63ee9 100644
--- a/man/new_teal_data.Rd
+++ b/man/new_teal_data.Rd
@@ -4,12 +4,7 @@
 \alias{new_teal_data}
 \title{Initialize \code{teal_data} object}
 \usage{
-new_teal_data(
-  data,
-  code = character(0),
-  join_keys = join_keys(),
-  datanames = names(data)
-)
+new_teal_data(data, code = character(0), join_keys = join_keys())
 }
 \arguments{
 \item{data}{(\verb{named list}) of data objects.}
@@ -18,9 +13,6 @@ new_teal_data(
 Accepts and stores comments also.}
 
 \item{join_keys}{(\code{join_keys}) object}
-
-\item{datanames}{(\code{character}) names of datasets passed to \code{data}.
-Needed when non-dataset objects are needed in the \code{env} slot.}
 }
 \description{
 Initialize \code{teal_data} object
diff --git a/man/teal_data-class.Rd b/man/teal_data-class.Rd
index ef1c1decb..d35268e77 100644
--- a/man/teal_data-class.Rd
+++ b/man/teal_data-class.Rd
@@ -36,10 +36,6 @@ Access with \code{\link[=get_warnings]{get_warnings()}}.}
 \item{\code{join_keys}}{(\code{join_keys}) object specifying joining keys for data sets in \verb{@env}.
 Access or modify with \code{\link[=join_keys]{join_keys()}}.}
 
-\item{\code{datanames}}{(\code{character}) vector of names of data sets in \verb{@env}.
-Used internally to distinguish them from auxiliary variables.
-Access or modify with \code{\link[=datanames]{datanames()}}.}
-
 \item{\code{verified}}{(\code{logical(1)}) flag signifying that code in \verb{@code} has been proven to yield contents of \verb{@env}.
 Used internally. See \code{\link[=verify]{verify()}} for more details.}
 }}
diff --git a/tests/testthat/test-datanames.R b/tests/testthat/test-datanames.R
index e0c99bb63..22e169fba 100644
--- a/tests/testthat/test-datanames.R
+++ b/tests/testthat/test-datanames.R
@@ -1,128 +1,136 @@
 # get ----
-testthat::test_that("datanames returns contents of @datanames slot", {
+testthat::test_that("names returns list of objects in teal_data", {
   td <- teal_data(i = iris, m = mtcars)
-  testthat::expect_identical(datanames(td), c("i", "m"))
+  testthat::expect_identical(names(td), c("i", "m"))
 })
 
-testthat::test_that("variables not in @datanames are omitted", {
+testthat::test_that("variables with dot prefix are omitted", {
   td <- teal_data(i = iris, m = mtcars)
-  td <- within(td, f <- faithful)
-  testthat::expect_identical(datanames(td), c("i", "m"))
+  td <- within(td, .f <- faithful)
+  testthat::expect_identical(names(td), c("i", "m"))
 })
 
-# set ----
-testthat::test_that("datanames can set value of @datanames", {
-  td <- teal_data(i = iris, m = mtcars)
-  testthat::expect_identical(datanames(td), c("i", "m"))
-  datanames(td) <- "i"
-  testthat::expect_identical(datanames(td), "i")
-})
+# set ---
+testthat::describe("names<- called on teal_data", {
+  testthat::it("throws warning", {
+    td <- teal_data(i = iris, m = mtcars)
+    testthat::expect_warning(names(td) <- c("a", "b", "c"), "assignment does nothing for qenv objects")
+  })
 
-testthat::test_that("only names of existing variables are accepted", {
-  td <- teal_data(i = iris, m = mtcars)
-  testthat::expect_no_error(datanames(td) <- "i")
-  testthat::expect_error(datanames(td) <- "f", "Assertion .* failed: Must be a subset")
+  testthat::it("does not change it", {
+    td <- teal_data(i = iris, m = mtcars)
+    tdc <- td <- teal_data(i = iris, m = mtcars)
+    suppressWarnings(names(td) <- c("a", "b", "c"))
+    testthat::expect_identical(qe, qec)
+  })
 })
 
 # qenv.error support ----
-testthat::test_that("datanames supports qenv.error class", {
+testthat::test_that("names supports qenv.error class", {
   qe <- within(teal_data(), stop())
-  testthat::expect_no_error(datanames(qe))
-  testthat::expect_no_error(datanames(qe) <- "name")
+  testthat::expect_no_error(names(qe))
 })
 
-testthat::test_that("datanames called on qenv.error returns NULL", {
+testthat::test_that("names called on qenv.error returns NULL", {
   qe <- within(teal_data(), stop())
-  testthat::expect_null(datanames(qe))
+  testthat::expect_null(names(qe))
 })
 
-testthat::test_that("datanames<- called on qenv.error does not change qenv.error", {
-  qe <- within(teal_data(), stop())
-  qec <- qe
-  testthat::expect_identical(qe, qec)
+testthat::describe("names<- called on qenv.error", {
+  testthat::it("throws warning", {
+    qe <- within(teal_data(), stop())
+    testthat::expect_warning(names(qe) <- c("a", "b", "c"), "assignment does nothing for qenv.error objects")
+  })
+  testthat::test_that("does not change qenv.error", {
+    qe <- within(teal_data(), stop())
+    qec <- within(teal_data(), stop())
+    suppressWarnings(names(qe) <- c("a", "b", "c"))
+    testthat::expect_identical(qe, qec)
+  })
 })
 
 # topological_order ----
 
-testthat::test_that("datanames are set in topological order in constructor if join_keys are specified", {
+testthat::test_that("names are set in topological order in constructor if join_keys are specified", {
   data <-
     teal_data(b = data.frame(), a = data.frame(), join_keys = join_keys(join_key("a", "b", "id")))
   testthat::expect_identical(
-    datanames(data),
+    names(data),
     c("a", "b")
   )
 })
 
-testthat::test_that("datanames return parent if in constructor it was provided in join_keys and exists in env", {
-  data <-
-    teal_data(b = data.frame(), a = data.frame(), join_keys = join_keys(join_key("a", "b", "id")))
-  datanames(data) <- "b"
-  testthat::expect_identical(
-    datanames(data),
-    c("a", "b")
+testthat::test_that("names return parent if in constructor it was provided in join_keys and exists in env", {
+  data <- teal_data(
+    b = data.frame(),
+    .a = data.frame(),
+    join_keys = join_keys(join_key(".a", "b", "id"))
   )
+  testthat::expect_setequal(names(data), c(".a", "b"))
 })
 
 testthat::test_that(
-  "datanames do not return parent if in constructor it was provided in join_keys but do not exists in env",
+  "names do not return parent if in constructor it was provided in join_keys but do not exists in env",
   {
-    data <-
-      teal_data(b = data.frame(), join_keys = join_keys(join_key("a", "b", "id")))
+    data <- teal_data(b = data.frame(), join_keys = join_keys(join_key("a", "b", "id")))
     testthat::expect_identical(
-      datanames(data),
+      names(data),
       "b"
     )
   }
 )
 
-testthat::test_that("datanames return topological order of datasets once join_keys are specified", {
+testthat::test_that("names return topological order of datasets once join_keys are specified", {
   data <- within(teal_data(), {
     ADTTE <- teal.data::rADTTE # nolint: object_name.
-    iris <- iris
+    ADTR <- teal.data::rADTR # nolint: object_name.
     ADSL <- teal.data::rADSL # nolint: object_name.
   })
-  datanames(data) <- c("ADTTE", "iris", "ADSL")
   join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
   testthat::expect_identical(
-    datanames(data),
-    c("ADSL", "ADTTE", "iris")
+    names(data),
+    c("ADTR", "ADSL", "ADTTE")
   )
 })
 
-testthat::test_that("datanames return topological order of datasets after datanames are called after join_keys", {
+testthat::test_that("names return topological order of datasets after new objects are added after join_keys", {
   data <- within(teal_data(), {
     ADTTE <- teal.data::rADTTE # nolint: object_name.
-    iris <- iris
     ADSL <- teal.data::rADSL # nolint: object_name.
   })
 
+  testthat::expect_identical(
+    names(data),
+    c("ADSL", "ADTTE")
+  )
+
   join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
-  datanames(data) <- c("ADTTE", "iris", "ADSL")
+  data <- within(data, ADTR <- teal.data::rADTR) # nolint: object_name.
 
   testthat::expect_identical(
-    datanames(data),
-    c("ADSL", "ADTTE", "iris")
+    names(data),
+    c("ADTR", "ADSL", "ADTTE")
   )
 })
 
 
-testthat::test_that("datanames return parent if join_keys were provided and parent exists in env", {
+testthat::test_that("names return parent if join_keys were provided and parent exists in env", {
   data <- within(teal_data(), {
     ADTTE <- teal.data::rADTTE # nolint: object_name.
     iris <- iris
-    ADSL <- teal.data::rADSL # nolint: object_name.
+    .ADSL <- teal.data::rADSL # nolint: object_name.
   })
 
   join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
-  datanames(data) <- c("ADTTE", "iris")
+  names(join_keys(data)) <- c(".ADSL", "ADTTE")
 
   testthat::expect_identical(
-    datanames(data),
+    names(data),
     c("ADSL", "ADTTE", "iris")
   )
 })
 
-testthat::test_that("datanames do not return parent if join_keys were provided and parent did not exists in env", {
+testthat::test_that("names do not return parent if join_keys were provided and parent did not exists in env", {
   data <- teal_data(
     ADTTE = teal.data::rADTTE, # nolint: object_name.
     iris = iris
@@ -131,7 +139,7 @@ testthat::test_that("datanames do not return parent if join_keys were provided a
   join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
 
   testthat::expect_identical(
-    datanames(data),
+    names(data),
     c("ADTTE", "iris")
   )
 })
diff --git a/tests/testthat/test-teal_data.R b/tests/testthat/test-teal_data.R
index 8391f72e2..e5d7ab895 100644
--- a/tests/testthat/test-teal_data.R
+++ b/tests/testthat/test-teal_data.R
@@ -21,34 +21,26 @@ testthat::test_that("teal_data allows to initialize empty teal_data with join_ke
   )
 })
 
-testthat::test_that("teal_data initializes teal_data object with @datanames taken from passed objects", {
-  testthat::expect_identical(
-    teal_data(iris = iris, mtcars = mtcars)@datanames,
-    c("iris", "mtcars")
-  )
-})
-
 testthat::test_that(
-  "teal_data initializes teal_data object without @datanames taken from join_keys if objects did not exist in env",
+  "teal_data initializes teal_data object without names taken from join_keys if objects did not exist in env",
   {
     testthat::expect_identical(
-      datanames(teal_data(join_keys = join_keys(join_key("parent", "child", "id")))),
+      names(teal_data(join_keys = join_keys(join_key("parent", "child", "id")))),
       character(0)
     )
   }
 )
 
 testthat::test_that(
-  "teal_data initializes teal_data object with @datanames taken only from passed objects and not join_keys",
+  "teal_data initializes teal_data object with names taken only from passed objects and not join_keys",
   {
     testthat::expect_identical(
-      datanames(teal_data(iris = iris, join_keys = join_keys(join_key("parent", "child", "id")))),
+      names(teal_data(iris = iris, join_keys = join_keys(join_key("parent", "child", "id")))),
       "iris"
     )
   }
 )
 
-
 testthat::test_that("teal_data returns teal_data when data passed as named list", {
   df1 <- data.frame(id = c("A", "B"), a = c(1L, 2L))
   testthat::expect_s4_class(teal_data(df1 = df1), "teal_data")
diff --git a/vignettes/join-keys.Rmd b/vignettes/join-keys.Rmd
index 9d06fed22..9ead04820 100644
--- a/vignettes/join-keys.Rmd
+++ b/vignettes/join-keys.Rmd
@@ -192,7 +192,6 @@ td_pk <- within(
   teal_data(),
   ds1 <- transform(iris, id = seq_len(nrow(iris)))
 )
-datanames(td_pk) <- "ds1"
 
 join_keys(td_pk) <- join_keys(join_key("ds1", keys = "id"))
 
@@ -209,7 +208,6 @@ td_pk <- within(
     ds3 <- data.frame(V = 5:14, N = 4)
   }
 )
-datanames(td_pk) <- c(datanames(td_pk), "ds2", "ds3")
 
 join_keys(td_pk)["ds2", "ds2"] <- c("V", "W")
 join_keys(td_pk)["ds3", "ds3"] <- c("V", "W")
@@ -239,7 +237,6 @@ td_fk <- within(
     ds3 <- data.frame(V = 5:14, N = 4)
   }
 )
-datanames(td_fk) <- c("ds1", "ds2", "ds3")
 
 join_keys(td_fk) <- join_keys(
   # Primary keys
@@ -275,7 +272,6 @@ td <- within(
     ds4 <- data.frame(V = 5:14, R = rnorm(10))
   }
 )
-datanames(td) <- c("ds1", "ds2", "ds3", "ds4")
 
 join_keys(td) <- join_keys(
   # Primary keys
diff --git a/vignettes/teal-data-reproducibility.Rmd b/vignettes/teal-data-reproducibility.Rmd
index f39d0a81b..b0b379cc9 100644
--- a/vignettes/teal-data-reproducibility.Rmd
+++ b/vignettes/teal-data-reproducibility.Rmd
@@ -105,7 +105,7 @@ Note that in when retrieving code for a specific dataset, the result is only the
 
 ## Tracking object dependencies
 
-Calling `get_code` with `datanames` specified initiates an analysis of the stored code, in which object dependencies are automatically discovered.
+Calling `get_code` with `names` specified initiates an analysis of the stored code, in which object dependencies are automatically discovered.
 If object `x` is created with an expression that uses object `y`, the lines that create object `y` must also be returned.
 This is quite effective when objects are created by simple assignments like `x <- foo(y)`.
 However, in rare cases discovering dependencies is impossible, _e.g._  when opening connections to databases or when objects are created by side effects (functions acting on their calling environment implicitly rather than returning a value that is then assigned).
diff --git a/vignettes/teal-data.Rmd b/vignettes/teal-data.Rmd
index 687b136d9..2288a7f5b 100644
--- a/vignettes/teal-data.Rmd
+++ b/vignettes/teal-data.Rmd
@@ -40,9 +40,8 @@ my_data[["data1"]]
 # get reproducible code
 get_code(my_data)
 
-# get or set datanames
-datanames(my_data) <- c("data1", "data2")
-datanames(my_data)
+# get datanames
+names(my_data)
 
 # print
 print(my_data)
@@ -55,7 +54,7 @@ A `teal_data` object keeps the following information:
 
 - `env` - an environment containing data.
 - `code` - a string containing code to reproduce `env` (details in [reproducibility](teal-data-reproducibility.html)).
-- `datanames` - a character vector listing objects of interest to `teal` modules (details in [this `teal` vignette](https://insightsengineering.github.io/teal/latest-tag/articles/including-data-in-teal-applications.html)).
+- `names` - a character vector listing objects of interest to `teal` modules (details in [this `teal` vignette](https://insightsengineering.github.io/teal/latest-tag/articles/including-data-in-teal-applications.html)).
 - `join_keys` - a `join_keys` object defining relationships between datasets (details in [Join Keys](join-keys.html)).
 
 ### Reproducibility
@@ -71,7 +70,6 @@ my_data <- within(my_data, data$id <- seq_len(nrow(data)))
 my_data # is verified
 ```
 
-
 ### Relational data models
 
 The `teal_data` class supports relational data.
@@ -94,3 +92,18 @@ join_keys(my_data) <- join_keys(
 
 join_keys(my_data)
 ```
+
+### Hidden objects
+
+An object is hidden in `teal_data` if its name starts with a dot (`.`).
+This can be used to pass auxiliary objects / function in the `teal_data` instance, without being visible in the `teal` summary and filter panel.
+
+```{r}
+my_data <- teal_data()
+my_data <- within(my_data, {
+  data <- data.frame(id = 1:10, x = 11:20)
+  .data2 <- data.frame(id = 1:20, data_id = c(1:10, 1:10), y = 21:30)
+})
+
+names(my_data)
+```

From b3fe731f55d93f3dcdcca02e475b66a71e01c409 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 28 Oct 2024 18:09:30 +0000
Subject: [PATCH 02/13] fix: remove extra parameters and deprecate
 names()<-.teal_data

---
 NAMESPACE              |  2 +-
 R/deprecated.R         | 15 +++++++++++++--
 R/teal_data-names.R    | 16 ++--------------
 man/datanames.Rd       |  4 ++--
 man/names.teal_data.Rd | 10 +---------
 5 files changed, 19 insertions(+), 28 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index 5391bfda9..565f57429 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -6,6 +6,7 @@ S3method("[[<-",join_keys)
 S3method("join_keys<-",join_keys)
 S3method("join_keys<-",teal_data)
 S3method("names<-",join_keys)
+S3method("names<-",teal_data)
 S3method("parents<-",join_keys)
 S3method("parents<-",teal_data)
 S3method(c,join_key_set)
@@ -14,7 +15,6 @@ S3method(format,join_keys)
 S3method(join_keys,default)
 S3method(join_keys,join_keys)
 S3method(join_keys,teal_data)
-S3method(names,"teal_data<-")
 S3method(names,teal_data)
 S3method(parents,join_keys)
 S3method(parents,teal_data)
diff --git a/R/deprecated.R b/R/deprecated.R
index b876fb2ac..5f35794f5 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -370,11 +370,22 @@ datanames <- function(x, ...) {
 }
 
 #' @rdname datanames
-`datanames<-` <- function(x, value, ...) {
+`datanames<-.teal_data` <- function(x, value, ...) {
   lifecycle::deprecate_soft(
     "0.6.1",
     "`datanames<-`()",
-    details = "Function has no effect. Use a `.` (dot) prefix to hide objects instead in `teal_data`. See the documentation for more details."
+    details = "invalid to use `datanames()<-` or `names()<-` on an object of class `teal_data`. See ?names.teal_data"
   )
   names(x)
 }
+
+#' @export
+#' @keywords internal
+`names<-.teal_data` <- function(x, value) {
+  lifecycle::deprecate_warn(
+    "0.6.1",
+    "`names.teal_data<-`()",
+    details = "invalid to use `datanames()<-` or `names()<-` on an object of class `teal_data`. See ?names.teal_data"
+  )
+  x
+}
diff --git a/R/teal_data-names.R b/R/teal_data-names.R
index 194d120f7..f8c97c041 100644
--- a/R/teal_data-names.R
+++ b/R/teal_data-names.R
@@ -8,9 +8,6 @@
 #' unless `all.names` parameter is set to `TRUE`.
 #'
 #' @param x A (`teal_data`) object to access or modify.
-#' @param all.names (`logical(1)`) that specifies whether to include hidden
-#' objects.
-#' @param value Does nothing as the names assignment is not supported.
 #'
 #' @return A character vector of names.
 #'
@@ -23,20 +20,11 @@
 #' names(td)
 #'
 #' @export
-names.teal_data <- function(x, all.names = FALSE) {
-  checkmate::assert_flag(all.names)
-  # Call method on qenv class
-  names_x <- utils::getS3method("names", class = "qenv")(x, all.names)
+names.teal_data <- function(x) {
+  names_x <- utils::getS3method("names", class = "qenv")(x)
   .get_sorted_names(names_x, join_keys(x), teal.code::get_env(x))
 }
 
-#' @rdname names.teal_data
-#' @export
-`names.teal_data<-` <- function(x, value) {
-  warning("`names(x) <- value` assignment does nothing for teal_data objects")
-  x
-}
-
 #' @keywords internal
 .get_sorted_names <- function(datanames, join_keys, env) {
   child_parent <- sapply(
diff --git a/man/datanames.Rd b/man/datanames.Rd
index 16307f003..16d34c579 100644
--- a/man/datanames.Rd
+++ b/man/datanames.Rd
@@ -2,12 +2,12 @@
 % Please edit documentation in R/deprecated.R
 \name{datanames}
 \alias{datanames}
-\alias{datanames<-}
+\alias{datanames<-.teal_data}
 \title{Names of data sets in \code{teal_data} object}
 \usage{
 datanames(x, ...)
 
-datanames(x, ...) <- value
+datanames.teal_data(x, ...) <- value
 }
 \arguments{
 \item{x}{(\code{teal_data} or \code{qenv_error}) object to access or modify}
diff --git a/man/names.teal_data.Rd b/man/names.teal_data.Rd
index 3daeee900..06fa3179a 100644
--- a/man/names.teal_data.Rd
+++ b/man/names.teal_data.Rd
@@ -2,20 +2,12 @@
 % Please edit documentation in R/teal_data-names.R
 \name{names.teal_data}
 \alias{names.teal_data}
-\alias{names.teal_data<-}
 \title{Names of data sets in \code{teal_data} object}
 \usage{
-\method{names}{teal_data}(x, all.names = FALSE)
-
-\method{names}{`teal_data<-`}(x, value)
+\method{names}{teal_data}(x)
 }
 \arguments{
 \item{x}{A (\code{teal_data}) object to access or modify.}
-
-\item{all.names}{(\code{logical(1)}) that specifies whether to include hidden
-objects.}
-
-\item{value}{Does nothing as the names assignment is not supported.}
 }
 \value{
 A character vector of names.

From 8406a837293dc943317e7fbc3ea19559b6ae52d2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 30 Oct 2024 18:57:04 +0000
Subject: [PATCH 03/13] feat: update to remove all @env mentions

---
 R/teal_data-class.R | 6 ++----
 R/teal_data-show.R  | 2 +-
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/R/teal_data-class.R b/R/teal_data-class.R
index 23fc7c8e6..d218ec281 100644
--- a/R/teal_data-class.R
+++ b/R/teal_data-class.R
@@ -51,9 +51,7 @@ setClass(
 #' @param join_keys (`join_keys`) object
 #' @rdname new_teal_data
 #' @keywords internal
-new_teal_data <- function(data,
-                          code = character(0),
-                          join_keys = join_keys()) {
+new_teal_data <- function(data, code = character(0), join_keys = join_keys()) {
   checkmate::assert_list(data)
   checkmate::assert_class(join_keys, "join_keys")
   if (!any(is.language(code), is.character(code))) {
@@ -75,7 +73,7 @@ new_teal_data <- function(data,
 
   methods::new(
     "teal_data",
-    env = new_env,
+    .xData = new_env,
     code = code,
     warnings = rep("", length(code)),
     messages = rep("", length(code)),
diff --git a/R/teal_data-show.R b/R/teal_data-show.R
index b47f29c10..fca8cf66e 100644
--- a/R/teal_data-show.R
+++ b/R/teal_data-show.R
@@ -16,5 +16,5 @@ setMethod("show", signature = "teal_data", function(object) {
   } else {
     cat("\u2716", "unverified teal_data object\n")
   }
-  rlang::env_print(object@env)
+  rlang::env_print(teal.code::get_env(object))
 })

From cd5a93884e86f667cdd458f15b9c09de49da10b3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 30 Oct 2024 19:46:41 +0000
Subject: [PATCH 04/13] fix: replace @env and corrects minor issues with qenv
 as environment

---
 NAMESPACE                                     |  1 +
 NEWS.md                                       |  7 +--
 R/deprecated.R                                | 12 +++--
 R/teal_data-class.R                           | 19 +++++---
 R/teal_data-get_code.R                        |  6 ++-
 R/teal_data-names.R                           |  4 +-
 R/verify.R                                    | 16 ++++---
 man/datanames.Rd                              | 13 ++++--
 man/get_code.Rd                               |  6 ++-
 man/teal_data-class.Rd                        | 19 +++++---
 man/verify.Rd                                 |  6 ++-
 tests/testthat/test-teal_data.R               |  8 ++--
 ...est-datanames.R => test-test_data-names.R} | 46 +++----------------
 tests/testthat/test-verify.R                  |  2 +-
 14 files changed, 80 insertions(+), 85 deletions(-)
 rename tests/testthat/{test-datanames.R => test-test_data-names.R} (71%)

diff --git a/NAMESPACE b/NAMESPACE
index 565f57429..49a6f08bb 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -20,6 +20,7 @@ S3method(parents,join_keys)
 S3method(parents,teal_data)
 S3method(print,join_keys)
 export("col_labels<-")
+export("datanames<-")
 export("get_join_keys<-")
 export("join_keys<-")
 export("parents<-")
diff --git a/NEWS.md b/NEWS.md
index 26db0f66e..bcf1da4d2 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,9 +2,10 @@
 
 ### Breaking changes
 
-- soft deprecate `datanames` argument of `get_code()`. Use `names` instead.
-- Soft deprecate of `datanames()` and `datanames(x) <- value` functions. 
-Use `names()` and `names(x) <- value` instead.
+- Soft deprecate `datanames` argument of `get_code()`. Use `names` instead.
+- Soft deprecate of `datanames()`. Use `names()` instead.
+- Deprecate of `datanames(x) <- value`. Does nothing, replace with renaming the objects inside the environment.
+
 
 ### Enhancements
 
diff --git a/R/deprecated.R b/R/deprecated.R
index 5f35794f5..97035fcd8 100644
--- a/R/deprecated.R
+++ b/R/deprecated.R
@@ -355,22 +355,23 @@ get_labels <- function(...) {
 #' prefix for the object's name.
 #'
 #' @param x (`teal_data` or `qenv_error`) object to access or modify
-#' @param ... (`character`) new value for `@datanames`; all elements must be names of variables existing in `@env`
+#' @param value (`character`) new value for `@datanames`; all elements must be names of variables existing in `@.xData`
 #'
 #' @return The contents of `@datanames` or `teal_data` object with updated `@datanames`.
-#'
+#' @aliases `datanames<-.teal_data`
 #'
 #' @name datanames
 
 #' @rdname datanames
 #' @export
-datanames <- function(x, ...) {
+datanames <- function(x) {
   lifecycle::deprecate_soft("0.6.1", "datanames()", details = "names()")
   names(x)
 }
 
 #' @rdname datanames
-`datanames<-.teal_data` <- function(x, value, ...) {
+#' @export
+`datanames<-` <- function(x, value) {
   lifecycle::deprecate_soft(
     "0.6.1",
     "`datanames<-`()",
@@ -379,12 +380,13 @@ datanames <- function(x, ...) {
   names(x)
 }
 
+#' @rdname datanames
 #' @export
 #' @keywords internal
 `names<-.teal_data` <- function(x, value) {
   lifecycle::deprecate_warn(
     "0.6.1",
-    "`names.teal_data<-`()",
+    "`names<-.teal_data`()",
     details = "invalid to use `datanames()<-` or `names()<-` on an object of class `teal_data`. See ?names.teal_data"
   )
   x
diff --git a/R/teal_data-class.R b/R/teal_data-class.R
index d218ec281..a5ddb439a 100644
--- a/R/teal_data-class.R
+++ b/R/teal_data-class.R
@@ -14,19 +14,24 @@ setOldClass("join_keys")
 #' @name teal_data-class
 #' @rdname teal_data-class
 #'
-#' @slot env (`environment`) environment containing data sets and possibly auxiliary variables.
-#'  Access variables with [get_var()] or [`[[`].
-#'  No setter provided. Evaluate code to add variables into `@env`.
-#' @slot code (`character`) vector representing code necessary to reproduce the contents of `@env`.
+#' @slot .xData (`environment`) environment containing data sets and possibly
+#'  auxiliary variables.
+#'  Access variables with [get()], [`$`], [get_var()] or [`[[`].
+#'  No setter provided. Evaluate code to add variables into `@.xData`.
+#' @slot code (`character`) vector representing code necessary to reproduce the
+#'  contents of `@.xData`.
 #'  Access with [get_code()].
 #'  No setter provided. Evaluate code to append code to the slot.
-#' @slot id (`integer`) random identifier assigned to each element of `@code`. Used internally.
+#' @slot id (`integer`) random identifier assigned to each element of `@code`.
+#'  Used internally.
 #' @slot warnings (`character`) vector of warnings raised when evaluating code.
 #'  Access with [get_warnings()].
 #' @slot messages (`character`) vector of messages raised when evaluating code.
-#' @slot join_keys (`join_keys`) object specifying joining keys for data sets in `@env`.
+#' @slot join_keys (`join_keys`) object specifying joining keys for data sets in
+#' `@.xData`.
 #'  Access or modify with [join_keys()].
-#' @slot verified (`logical(1)`) flag signifying that code in `@code` has been proven to yield contents of `@env`.
+#' @slot verified (`logical(1)`) flag signifying that code in `@code` has been
+#'  proven to yield contents of `@.xData`.
 #'  Used internally. See [`verify()`] for more details.
 #'
 #' @import teal.code
diff --git a/R/teal_data-get_code.R b/R/teal_data-get_code.R
index 1fd668193..d1292c7a5 100644
--- a/R/teal_data-get_code.R
+++ b/R/teal_data-get_code.R
@@ -2,8 +2,10 @@
 #'
 #' Retrieve code from `teal_data` object.
 #'
-#' Retrieve code stored in `@code`, which (in principle) can be used to recreate all objects found in `@env`.
-#' Use `names` to limit the code to one or more of the datasets enumerated in `@datanames`.
+#' Retrieve code stored in `@code`, which (in principle) can be used to recreate
+#' all objects found in `@.xData`.
+#' Use `names` to limit the code to one or more of the datasets enumerated in
+#' the environment.
 #'
 #' @section Extracting dataset-specific code:
 #' When `names` is specified, the code returned will be limited  to the lines needed to _create_
diff --git a/R/teal_data-names.R b/R/teal_data-names.R
index f8c97c041..2da0b187e 100644
--- a/R/teal_data-names.R
+++ b/R/teal_data-names.R
@@ -21,8 +21,8 @@
 #'
 #' @export
 names.teal_data <- function(x) {
-  names_x <- utils::getS3method("names", class = "qenv")(x)
-  .get_sorted_names(names_x, join_keys(x), teal.code::get_env(x))
+  names_x <- ls(x)
+  .get_sorted_names(names_x, join_keys(x), as.environment(x))
 }
 
 #' @keywords internal
diff --git a/R/verify.R b/R/verify.R
index 7caa648f2..df40e91bd 100644
--- a/R/verify.R
+++ b/R/verify.R
@@ -2,10 +2,12 @@
 #'
 #' Checks whether code in `teal_data` object reproduces the stored objects.
 #'
-#' If objects created by code in the `@code` slot of `x` are `all_equal` to the contents of the `@env` slot,
+#' If objects created by code in the `@code` slot of `x` are `all_equal` to the
+#' contents of the `@.xData` slot,
 #' the function updates the `@verified` slot to `TRUE` in the returned `teal_data` object.
 #' Once verified, the slot will always be set to `TRUE`.
-#' If the `@code` fails to recreate objects in `teal_data@env`, an error is raised.
+#' If the `@code` fails to recreate objects in `teal_data`'s environment, an
+#' error is raised.
 #'
 #' @return Input `teal_data` object or error.
 #'
@@ -65,7 +67,7 @@ setMethod("verify", signature = "teal_data", definition = function(x) {
     stop(conditionMessage(y), call. = FALSE)
   }
 
-  reproduced <- isTRUE(all.equal(x@env, y@env))
+  reproduced <- isTRUE(all.equal(teal.code::get_env(x), teal.code::get_env(y)))
   if (reproduced) {
     x@verified <- TRUE
     methods::validObject(x)
@@ -74,15 +76,15 @@ setMethod("verify", signature = "teal_data", definition = function(x) {
     error <- "Code verification failed."
 
     objects_diff <- vapply(
-      intersect(names(x@env), names(y@env)),
+      intersect(names(x), names(y)),
       function(element) {
-        isTRUE(all.equal(x@env[[element]], y@env[[element]]))
+        isTRUE(all.equal(x[[element]], y[[element]]))
       },
       logical(1)
     )
 
-    names_diff_other <- setdiff(names(y@env), names(x@env))
-    names_diff_inenv <- setdiff(names(x@env), names(y@env))
+    names_diff_other <- setdiff(names(y), names(x))
+    names_diff_inenv <- setdiff(names(x), names(y))
 
     if (length(objects_diff)) {
       error <- c(
diff --git a/man/datanames.Rd b/man/datanames.Rd
index 16d34c579..19cbb2a0e 100644
--- a/man/datanames.Rd
+++ b/man/datanames.Rd
@@ -2,17 +2,21 @@
 % Please edit documentation in R/deprecated.R
 \name{datanames}
 \alias{datanames}
-\alias{datanames<-.teal_data}
+\alias{`datanames<-.teal_data`}
+\alias{datanames<-}
+\alias{names<-.teal_data}
 \title{Names of data sets in \code{teal_data} object}
 \usage{
-datanames(x, ...)
+datanames(x)
 
-datanames.teal_data(x, ...) <- value
+datanames(x) <- value
+
+\method{names}{teal_data}(x) <- value
 }
 \arguments{
 \item{x}{(\code{teal_data} or \code{qenv_error}) object to access or modify}
 
-\item{...}{(\code{character}) new value for \verb{@datanames}; all elements must be names of variables existing in \verb{@env}}
+\item{value}{(\code{character}) new value for \verb{@datanames}; all elements must be names of variables existing in \verb{@.xData}}
 }
 \value{
 The contents of \verb{@datanames} or \code{teal_data} object with updated \verb{@datanames}.
@@ -25,3 +29,4 @@ Use \code{names()} instead of \code{datanames()}.
 \code{datanames()} is deprecated. If object should be hidden, then use a \code{.} (dot)
 prefix for the object's name.
 }
+\keyword{internal}
diff --git a/man/get_code.Rd b/man/get_code.Rd
index 8a21424e7..38bcaf41a 100644
--- a/man/get_code.Rd
+++ b/man/get_code.Rd
@@ -36,8 +36,10 @@ only code that \emph{creates} that dataset (not code that uses it) is returned.
 Retrieve code from \code{teal_data} object.
 }
 \details{
-Retrieve code stored in \verb{@code}, which (in principle) can be used to recreate all objects found in \verb{@env}.
-Use \code{names} to limit the code to one or more of the datasets enumerated in \verb{@datanames}.
+Retrieve code stored in \verb{@code}, which (in principle) can be used to recreate
+all objects found in \verb{@.xData}.
+Use \code{names} to limit the code to one or more of the datasets enumerated in
+the environment.
 }
 \section{Extracting dataset-specific code}{
 
diff --git a/man/teal_data-class.Rd b/man/teal_data-class.Rd
index d35268e77..707029e66 100644
--- a/man/teal_data-class.Rd
+++ b/man/teal_data-class.Rd
@@ -18,25 +18,30 @@ If errors are raised, a \code{qenv.error} object is returned.
 \section{Slots}{
 
 \describe{
-\item{\code{env}}{(\code{environment}) environment containing data sets and possibly auxiliary variables.
-Access variables with \code{\link[=get_var]{get_var()}} or [\code{[[}].
-No setter provided. Evaluate code to add variables into \verb{@env}.}
+\item{\code{.xData}}{(\code{environment}) environment containing data sets and possibly
+auxiliary variables.
+Access variables with \code{\link[=get]{get()}}, \code{\link{$}}, \code{\link[=get_var]{get_var()}} or [\code{[[}].
+No setter provided. Evaluate code to add variables into \verb{@.xData}.}
 
-\item{\code{code}}{(\code{character}) vector representing code necessary to reproduce the contents of \verb{@env}.
+\item{\code{code}}{(\code{character}) vector representing code necessary to reproduce the
+contents of \verb{@.xData}.
 Access with \code{\link[=get_code]{get_code()}}.
 No setter provided. Evaluate code to append code to the slot.}
 
-\item{\code{id}}{(\code{integer}) random identifier assigned to each element of \verb{@code}. Used internally.}
+\item{\code{id}}{(\code{integer}) random identifier assigned to each element of \verb{@code}.
+Used internally.}
 
 \item{\code{warnings}}{(\code{character}) vector of warnings raised when evaluating code.
 Access with \code{\link[=get_warnings]{get_warnings()}}.}
 
 \item{\code{messages}}{(\code{character}) vector of messages raised when evaluating code.}
 
-\item{\code{join_keys}}{(\code{join_keys}) object specifying joining keys for data sets in \verb{@env}.
+\item{\code{join_keys}}{(\code{join_keys}) object specifying joining keys for data sets in
+\verb{@.xData}.
 Access or modify with \code{\link[=join_keys]{join_keys()}}.}
 
-\item{\code{verified}}{(\code{logical(1)}) flag signifying that code in \verb{@code} has been proven to yield contents of \verb{@env}.
+\item{\code{verified}}{(\code{logical(1)}) flag signifying that code in \verb{@code} has been
+proven to yield contents of \verb{@.xData}.
 Used internally. See \code{\link[=verify]{verify()}} for more details.}
 }}
 
diff --git a/man/verify.Rd b/man/verify.Rd
index 630a08788..d3f7dcd77 100644
--- a/man/verify.Rd
+++ b/man/verify.Rd
@@ -18,10 +18,12 @@ Input \code{teal_data} object or error.
 Checks whether code in \code{teal_data} object reproduces the stored objects.
 }
 \details{
-If objects created by code in the \verb{@code} slot of \code{x} are \code{all_equal} to the contents of the \verb{@env} slot,
+If objects created by code in the \verb{@code} slot of \code{x} are \code{all_equal} to the
+contents of the \verb{@.xData} slot,
 the function updates the \verb{@verified} slot to \code{TRUE} in the returned \code{teal_data} object.
 Once verified, the slot will always be set to \code{TRUE}.
-If the \verb{@code} fails to recreate objects in \code{teal_data@env}, an error is raised.
+If the \verb{@code} fails to recreate objects in \code{teal_data}'s environment, an
+error is raised.
 }
 \examples{
 tdata1 <- teal_data()
diff --git a/tests/testthat/test-teal_data.R b/tests/testthat/test-teal_data.R
index e5d7ab895..a7d715d3e 100644
--- a/tests/testthat/test-teal_data.R
+++ b/tests/testthat/test-teal_data.R
@@ -85,9 +85,9 @@ testthat::test_that("teal_data code is concatenated into single string", {
   )
 })
 
-testthat::test_that("teal_data@env is locked. Not able to modify, add or remove bindings", {
+testthat::test_that("teal_data@.xData is locked. Not able to modify, add or remove bindings", {
   data <- teal_data(iris = iris)
-  testthat::expect_error(data@env$iris <- iris, "cannot change value of locked binding for 'iris'")
-  testthat::expect_error(data@env$iris2 <- iris, "cannot add bindings to a locked environment")
-  testthat::expect_error(rm("iris", envir = data@env), "cannot remove bindings from a locked environment")
+  testthat::expect_error(data@.xData$iris <- iris, "cannot change value of locked binding for 'iris'")
+  testthat::expect_error(data@.xData$iris2 <- iris, "cannot add bindings to a locked environment")
+  testthat::expect_error(rm("iris", envir = data@.xData), "cannot remove bindings from a locked environment")
 })
diff --git a/tests/testthat/test-datanames.R b/tests/testthat/test-test_data-names.R
similarity index 71%
rename from tests/testthat/test-datanames.R
rename to tests/testthat/test-test_data-names.R
index 22e169fba..5db8d9d14 100644
--- a/tests/testthat/test-datanames.R
+++ b/tests/testthat/test-test_data-names.R
@@ -11,18 +11,11 @@ testthat::test_that("variables with dot prefix are omitted", {
 })
 
 # set ---
-testthat::describe("names<- called on teal_data", {
-  testthat::it("throws warning", {
-    td <- teal_data(i = iris, m = mtcars)
-    testthat::expect_warning(names(td) <- c("a", "b", "c"), "assignment does nothing for qenv objects")
-  })
-
-  testthat::it("does not change it", {
-    td <- teal_data(i = iris, m = mtcars)
-    tdc <- td <- teal_data(i = iris, m = mtcars)
-    suppressWarnings(names(td) <- c("a", "b", "c"))
-    testthat::expect_identical(qe, qec)
-  })
+testthat::test_that("names<- called on teal_data does not change it", {
+  td <- teal_data(i = iris, m = mtcars)
+  tdc <- td <- teal_data(i = iris, m = mtcars)
+  suppressWarnings(names(td) <- c("a", "b", "c"))
+  testthat::expect_identical(td, tdc)
 })
 
 # qenv.error support ----
@@ -31,23 +24,6 @@ testthat::test_that("names supports qenv.error class", {
   testthat::expect_no_error(names(qe))
 })
 
-testthat::test_that("names called on qenv.error returns NULL", {
-  qe <- within(teal_data(), stop())
-  testthat::expect_null(names(qe))
-})
-
-testthat::describe("names<- called on qenv.error", {
-  testthat::it("throws warning", {
-    qe <- within(teal_data(), stop())
-    testthat::expect_warning(names(qe) <- c("a", "b", "c"), "assignment does nothing for qenv.error objects")
-  })
-  testthat::test_that("does not change qenv.error", {
-    qe <- within(teal_data(), stop())
-    qec <- within(teal_data(), stop())
-    suppressWarnings(names(qe) <- c("a", "b", "c"))
-    testthat::expect_identical(qe, qec)
-  })
-})
 
 # topological_order ----
 
@@ -124,10 +100,7 @@ testthat::test_that("names return parent if join_keys were provided and parent e
   join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
   names(join_keys(data)) <- c(".ADSL", "ADTTE")
 
-  testthat::expect_identical(
-    names(data),
-    c("ADSL", "ADTTE", "iris")
-  )
+  testthat::expect_setequal(names(data), c(".ADSL", "ADTTE", "iris"))
 })
 
 testthat::test_that("names do not return parent if join_keys were provided and parent did not exists in env", {
@@ -135,11 +108,6 @@ testthat::test_that("names do not return parent if join_keys were provided and p
     ADTTE = teal.data::rADTTE, # nolint: object_name.
     iris = iris
   )
-
   join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADTTE")]
-
-  testthat::expect_identical(
-    names(data),
-    c("ADTTE", "iris")
-  )
+  testthat::expect_setequal(names(data), c("ADTTE", "iris"))
 })
diff --git a/tests/testthat/test-verify.R b/tests/testthat/test-verify.R
index a2b45a7bb..4e15fb696 100644
--- a/tests/testthat/test-verify.R
+++ b/tests/testthat/test-verify.R
@@ -17,7 +17,7 @@ testthat::test_that("verify returns the same object with changed @verified field
   testthat::expect_identical(tdata2@verified, FALSE)
   testthat::expect_identical(tdata2_ver@verified, TRUE)
   testthat::expect_identical(tdata2_ver@code, tdata2@code)
-  testthat::expect_identical(tdata2_ver@env, tdata2@env)
+  testthat::expect_identical(teal.code::get_env(tdata2_ver), teal.code::get_env(tdata2))
 })
 
 testthat::test_that("verify raises error if @code does not restore objects in @env", {

From 4f9246730cc7327f61b519a845a4ad2a9978e9e4 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Fri, 1 Nov 2024 14:57:15 +0000
Subject: [PATCH 05/13] fix: use names instead of ls

---
 R/teal_data-names.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/teal_data-names.R b/R/teal_data-names.R
index 2da0b187e..bae379f62 100644
--- a/R/teal_data-names.R
+++ b/R/teal_data-names.R
@@ -21,7 +21,7 @@
 #'
 #' @export
 names.teal_data <- function(x) {
-  names_x <- ls(x)
+  names_x <- names(as.environment(x))
   .get_sorted_names(names_x, join_keys(x), as.environment(x))
 }
 

From d35fcca1deb428d454f3df79cd32a9ac4f35889b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 4 Nov 2024 14:12:52 +0000
Subject: [PATCH 06/13] fix: names return sorted strings and adds github prefix
 to teal.code

---
 .pre-commit-config.yaml | 2 +-
 R/teal_data-names.R     | 4 +++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index ccfcc1c64..d67687526 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -20,7 +20,7 @@ repos:
           - methods
           - rlang
           - stats
-          - teal.code
+          - insightsengineering/teal.code
           - utils
           - yaml
       - id: spell-check
diff --git a/R/teal_data-names.R b/R/teal_data-names.R
index bae379f62..6504be8e2 100644
--- a/R/teal_data-names.R
+++ b/R/teal_data-names.R
@@ -21,7 +21,9 @@
 #'
 #' @export
 names.teal_data <- function(x) {
-  names_x <- names(as.environment(x))
+  # Sorting can be safely done as environments don't have any order
+  # nor support numeric-index subsetting
+  names_x <- sort(names(as.environment(x)))
   .get_sorted_names(names_x, join_keys(x), as.environment(x))
 }
 

From 711a7e9e643927eab46904d8f9324b9940d7a0e0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 4 Nov 2024 18:21:18 +0000
Subject: [PATCH 07/13] feat: exclude dot prefixed names from teal.data

---
 R/teal_data-names.R    | 23 +++++++++--------------
 man/names.teal_data.Rd | 10 +++++-----
 2 files changed, 14 insertions(+), 19 deletions(-)

diff --git a/R/teal_data-names.R b/R/teal_data-names.R
index 6504be8e2..8f234538c 100644
--- a/R/teal_data-names.R
+++ b/R/teal_data-names.R
@@ -1,11 +1,11 @@
 #' Names of data sets in `teal_data` object
 #'
 #' Functions to get the names of a `teal_data` object.
-#' The names are extrapolated from the objects in the `qenv` environment and
-#' are not stored statically, unlike the normal behavior of `names()` function.
+#' The names are obtained from the objects listed in the `qenv` environment.
 #'
-#' Objects named with a `.` (dot) prefix will be ignored and not returned,
-#' unless `all.names` parameter is set to `TRUE`.
+#' Objects named with a `.` (dot) prefix will be ignored and not returned.
+#' To get the names of all objects, use `ls(x, all.names = TRUE)`, however, it
+#' will not group the names by the join_keys topological structure.
 #'
 #' @param x A (`teal_data`) object to access or modify.
 #'
@@ -17,24 +17,19 @@
 #' names(td)
 #'
 #' td <- within(td, .CO2 <- CO2)
-#' names(td)
+#' names(td) # '.CO2' will not be returned
 #'
 #' @export
 names.teal_data <- function(x) {
-  # Sorting can be safely done as environments don't have any order
+  # Sorting from `ls` can be safely done as environments don't have any order
   # nor support numeric-index subsetting
-  names_x <- sort(names(as.environment(x)))
-  .get_sorted_names(names_x, join_keys(x), as.environment(x))
+  envir <- as.environment(x)
+  .get_sorted_names(ls(envir = envir), join_keys(x), envir)
 }
 
 #' @keywords internal
 .get_sorted_names <- function(datanames, join_keys, env) {
-  child_parent <- sapply(
-    datanames,
-    function(name) parent(join_keys, name),
-    USE.NAMES = TRUE,
-    simplify = FALSE
-  )
+  child_parent <- sapply(datanames, parent, x = join_keys, USE.NAMES = TRUE, simplify = FALSE)
 
   union(
     intersect(unlist(topological_sort(child_parent)), ls(env, all.names = TRUE)),
diff --git a/man/names.teal_data.Rd b/man/names.teal_data.Rd
index 06fa3179a..4f03fce70 100644
--- a/man/names.teal_data.Rd
+++ b/man/names.teal_data.Rd
@@ -14,12 +14,12 @@ A character vector of names.
 }
 \description{
 Functions to get the names of a \code{teal_data} object.
-The names are extrapolated from the objects in the \code{qenv} environment and
-are not stored statically, unlike the normal behavior of \code{names()} function.
+The names are obtained from the objects listed in the \code{qenv} environment.
 }
 \details{
-Objects named with a \code{.} (dot) prefix will be ignored and not returned,
-unless \code{all.names} parameter is set to \code{TRUE}.
+Objects named with a \code{.} (dot) prefix will be ignored and not returned.
+To get the names of all objects, use \code{ls(x, all.names = TRUE)}, however, it
+will not group the names by the join_keys topological structure.
 }
 \examples{
 td <- teal_data(iris = iris)
@@ -27,6 +27,6 @@ td <- within(td, mtcars <- mtcars)
 names(td)
 
 td <- within(td, .CO2 <- CO2)
-names(td)
+names(td) # '.CO2' will not be returned
 
 }

From cba8ac7f0d6fa196a75f9369f772f376bd2a409e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Mon, 4 Nov 2024 20:38:35 +0000
Subject: [PATCH 08/13] fix: pkgdown and adds custom length that only shows
 non-dot prefixed objects

---
 NAMESPACE           | 1 +
 R/teal_data-names.R | 3 +++
 _pkgdown.yml        | 1 +
 3 files changed, 5 insertions(+)

diff --git a/NAMESPACE b/NAMESPACE
index 49a6f08bb..a126ccc47 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -15,6 +15,7 @@ S3method(format,join_keys)
 S3method(join_keys,default)
 S3method(join_keys,join_keys)
 S3method(join_keys,teal_data)
+S3method(length,teal.data)
 S3method(names,teal_data)
 S3method(parents,join_keys)
 S3method(parents,teal_data)
diff --git a/R/teal_data-names.R b/R/teal_data-names.R
index 8f234538c..32e9d71de 100644
--- a/R/teal_data-names.R
+++ b/R/teal_data-names.R
@@ -27,6 +27,9 @@ names.teal_data <- function(x) {
   .get_sorted_names(ls(envir = envir), join_keys(x), envir)
 }
 
+#' @export
+length.teal.data <- function(x) length(ls(x))
+
 #' @keywords internal
 .get_sorted_names <- function(datanames, join_keys, env) {
   child_parent <- sapply(datanames, parent, x = join_keys, USE.NAMES = TRUE, simplify = FALSE)
diff --git a/_pkgdown.yml b/_pkgdown.yml
index 2ecf65392..cc6bbb0c3 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -41,6 +41,7 @@ reference:
       - join_key
       - join_keys
       - join_keys<-
+      - names.teal_data
       - names<-.join_keys
       - parents
       - parents<-

From 33de31f375f8c93048f95cbd087d12c56d06467c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Tue, 5 Nov 2024 17:39:14 +0000
Subject: [PATCH 09/13] chore: bumps versions

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 8fa36bb3c..45ffa7c97 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -29,7 +29,7 @@ URL: https://insightsengineering.github.io/teal.data/,
 BugReports: https://github.com/insightsengineering/teal.data/issues
 Depends:
     R (>= 4.0),
-    teal.code (>= 0.5.0.9011)
+    teal.code (>= 0.5.0.9012)
 Imports:
     checkmate (>= 2.1.0),
     lifecycle (>= 0.2.0),

From 64f16da15e529983632929b6fec62f7ae77881e9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 6 Nov 2024 16:19:55 +0100
Subject: [PATCH 10/13] Update .pre-commit-config.yaml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>
Signed-off-by: André Veríssimo <211358+averissimo@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d67687526..ccfcc1c64 100755
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -20,7 +20,7 @@ repos:
           - methods
           - rlang
           - stats
-          - insightsengineering/teal.code
+          - teal.code
           - utils
           - yaml
       - id: spell-check

From 583b145b7f2b7b7c8f7e035cdf581c8f611c08a3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 6 Nov 2024 18:43:29 +0000
Subject: [PATCH 11/13] feat: move code/id/warn/msg logic to teal.code and
 simplify

---
 R/teal_data-class.R    | 59 ++++++++++++++++--------------------------
 R/teal_data-get_code.R |  2 +-
 R/teal_data.R          |  5 ++--
 R/verify.R             |  2 +-
 man/get_code.Rd        |  2 +-
 man/new_teal_data.Rd   | 20 --------------
 man/verify.Rd          |  2 +-
 7 files changed, 29 insertions(+), 63 deletions(-)
 delete mode 100644 man/new_teal_data.Rd

diff --git a/R/teal_data-class.R b/R/teal_data-class.R
index a5ddb439a..80e97b7f6 100644
--- a/R/teal_data-class.R
+++ b/R/teal_data-class.R
@@ -46,44 +46,29 @@ setClass(
   )
 )
 
-#' Initialize `teal_data` object
+#' It initializes the `teal_data` class
 #'
-#' @name new_teal_data
-#'
-#' @param data (`named list`) of data objects.
-#' @param code (`character` or `language`) code to reproduce the `data`.
-#'   Accepts and stores comments also.
-#' @param join_keys (`join_keys`) object
-#' @rdname new_teal_data
-#' @keywords internal
-new_teal_data <- function(data, code = character(0), join_keys = join_keys()) {
-  checkmate::assert_list(data)
-  checkmate::assert_class(join_keys, "join_keys")
-  if (!any(is.language(code), is.character(code))) {
-    stop("`code` must be a character or language object.")
-  }
+#' Accepts .xData as a list and converts it to an environment before initializing
+#' parent constructor (`qenv`).
+#' @noRd
+setMethod(
+  "initialize",
+  "teal_data",
+  function(.Object, .xData = list(), join_keys = join_keys(), ...) { # nolint: object_name.
+    # Allow .xData to be a list and convert it to an environment
+    if (!missing(.xData) && inherits(.xData, "list")) {
+      .xData <- rlang::env_clone(list2env(.xData), parent = parent.env(.GlobalEnv))
+      lockEnvironment(.xData, bindings = TRUE)
+    }
+    checkmate::assert_environment(.xData)
 
-  if (is.language(code)) {
-    code <- paste(lang2calls(code), collapse = "\n")
-  }
-  if (length(code)) {
-    code <- paste(code, collapse = "\n")
-  }
-  verified <- (length(code) == 0L && length(data) == 0L)
+    .Object <- methods::callNextMethod(.Object, .xData, join_keys = join_keys, ...) # nolint: object_name.
 
-  id <- sample.int(.Machine$integer.max, size = length(code))
+    # teal data specific slots
+    checkmate::assert_class(join_keys, "join_keys")
+    .Object@verified <- (length(.Object@code) == 0L && length(.Object@.xData) == 0L)
+    .Object@join_keys <- join_keys
 
-  new_env <- rlang::env_clone(list2env(data), parent = parent.env(.GlobalEnv))
-  lockEnvironment(new_env, bindings = TRUE)
-
-  methods::new(
-    "teal_data",
-    .xData = new_env,
-    code = code,
-    warnings = rep("", length(code)),
-    messages = rep("", length(code)),
-    id = id,
-    join_keys = join_keys,
-    verified = verified
-  )
-}
+    .Object
+  }
+)
diff --git a/R/teal_data-get_code.R b/R/teal_data-get_code.R
index d1292c7a5..23002590d 100644
--- a/R/teal_data-get_code.R
+++ b/R/teal_data-get_code.R
@@ -3,7 +3,7 @@
 #' Retrieve code from `teal_data` object.
 #'
 #' Retrieve code stored in `@code`, which (in principle) can be used to recreate
-#' all objects found in `@.xData`.
+#' all objects found in the environment (`@.xData`).
 #' Use `names` to limit the code to one or more of the datasets enumerated in
 #' the environment.
 #'
diff --git a/R/teal_data.R b/R/teal_data.R
index ea32e624a..1721c94fe 100644
--- a/R/teal_data.R
+++ b/R/teal_data.R
@@ -60,8 +60,9 @@ teal_data <- function(...,
     if (length(data_objects) > 0 && !checkmate::test_names(names(data_objects), type = "named")) {
       stop("Dot (`...`) arguments on `teal_data()` must be named.")
     }
-    new_teal_data(
-      data = data_objects,
+    methods::new(
+      "teal_data",
+      .xData = data_objects,
       code = code,
       join_keys = join_keys
     )
diff --git a/R/verify.R b/R/verify.R
index df40e91bd..a3c1f24fe 100644
--- a/R/verify.R
+++ b/R/verify.R
@@ -3,7 +3,7 @@
 #' Checks whether code in `teal_data` object reproduces the stored objects.
 #'
 #' If objects created by code in the `@code` slot of `x` are `all_equal` to the
-#' contents of the `@.xData` slot,
+#' contents of the environment (`@.xData` slot),
 #' the function updates the `@verified` slot to `TRUE` in the returned `teal_data` object.
 #' Once verified, the slot will always be set to `TRUE`.
 #' If the `@code` fails to recreate objects in `teal_data`'s environment, an
diff --git a/man/get_code.Rd b/man/get_code.Rd
index 38bcaf41a..3d3b8cf25 100644
--- a/man/get_code.Rd
+++ b/man/get_code.Rd
@@ -37,7 +37,7 @@ Retrieve code from \code{teal_data} object.
 }
 \details{
 Retrieve code stored in \verb{@code}, which (in principle) can be used to recreate
-all objects found in \verb{@.xData}.
+all objects found in the environment (\verb{@.xData}).
 Use \code{names} to limit the code to one or more of the datasets enumerated in
 the environment.
 }
diff --git a/man/new_teal_data.Rd b/man/new_teal_data.Rd
deleted file mode 100644
index 2bdd63ee9..000000000
--- a/man/new_teal_data.Rd
+++ /dev/null
@@ -1,20 +0,0 @@
-% Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/teal_data-class.R
-\name{new_teal_data}
-\alias{new_teal_data}
-\title{Initialize \code{teal_data} object}
-\usage{
-new_teal_data(data, code = character(0), join_keys = join_keys())
-}
-\arguments{
-\item{data}{(\verb{named list}) of data objects.}
-
-\item{code}{(\code{character} or \code{language}) code to reproduce the \code{data}.
-Accepts and stores comments also.}
-
-\item{join_keys}{(\code{join_keys}) object}
-}
-\description{
-Initialize \code{teal_data} object
-}
-\keyword{internal}
diff --git a/man/verify.Rd b/man/verify.Rd
index d3f7dcd77..7b71ce489 100644
--- a/man/verify.Rd
+++ b/man/verify.Rd
@@ -19,7 +19,7 @@ Checks whether code in \code{teal_data} object reproduces the stored objects.
 }
 \details{
 If objects created by code in the \verb{@code} slot of \code{x} are \code{all_equal} to the
-contents of the \verb{@.xData} slot,
+contents of the environment (\verb{@.xData} slot),
 the function updates the \verb{@verified} slot to \code{TRUE} in the returned \code{teal_data} object.
 Once verified, the slot will always be set to \code{TRUE}.
 If the \verb{@code} fails to recreate objects in \code{teal_data}'s environment, an

From 1c2862527b4c0e056d7398e63b4ce2df744230da Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Wed, 6 Nov 2024 19:02:32 +0000
Subject: [PATCH 12/13] chore: fix lint error

---
 R/teal_data-class.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/teal_data-class.R b/R/teal_data-class.R
index 80e97b7f6..2bfb2ca8a 100644
--- a/R/teal_data-class.R
+++ b/R/teal_data-class.R
@@ -57,7 +57,7 @@ setMethod(
   function(.Object, .xData = list(), join_keys = join_keys(), ...) { # nolint: object_name.
     # Allow .xData to be a list and convert it to an environment
     if (!missing(.xData) && inherits(.xData, "list")) {
-      .xData <- rlang::env_clone(list2env(.xData), parent = parent.env(.GlobalEnv))
+      .xData <- rlang::env_clone(list2env(.xData), parent = parent.env(.GlobalEnv)) # nolint: object_name.
       lockEnvironment(.xData, bindings = TRUE)
     }
     checkmate::assert_environment(.xData)
@@ -66,8 +66,8 @@ setMethod(
 
     # teal data specific slots
     checkmate::assert_class(join_keys, "join_keys")
-    .Object@verified <- (length(.Object@code) == 0L && length(.Object@.xData) == 0L)
-    .Object@join_keys <- join_keys
+    .Object@verified <- (length(.Object@code) == 0L && length(.Object@.xData) == 0L) # nolint: object_name.
+    .Object@join_keys <- join_keys # nolint: object_name.
 
     .Object
   }

From 04fd26ef3da92e5258b0b2cd080fee879a275de3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andr=C3=A9=20Ver=C3=ADssimo?=
 <211358+averissimo@users.noreply.github.com>
Date: Thu, 7 Nov 2024 10:09:14 +0000
Subject: [PATCH 13/13] pr: apply suggestion by @gogonzo

---
 R/teal_data-class.R | 17 +++++++++--------
 1 file changed, 9 insertions(+), 8 deletions(-)

diff --git a/R/teal_data-class.R b/R/teal_data-class.R
index 2bfb2ca8a..aea827319 100644
--- a/R/teal_data-class.R
+++ b/R/teal_data-class.R
@@ -60,15 +60,16 @@ setMethod(
       .xData <- rlang::env_clone(list2env(.xData), parent = parent.env(.GlobalEnv)) # nolint: object_name.
       lockEnvironment(.xData, bindings = TRUE)
     }
+    args <- list(...)
     checkmate::assert_environment(.xData)
-
-    .Object <- methods::callNextMethod(.Object, .xData, join_keys = join_keys, ...) # nolint: object_name.
-
-    # teal data specific slots
     checkmate::assert_class(join_keys, "join_keys")
-    .Object@verified <- (length(.Object@code) == 0L && length(.Object@.xData) == 0L) # nolint: object_name.
-    .Object@join_keys <- join_keys # nolint: object_name.
-
-    .Object
+    checkmate::assert_list(args, names = "named")
+    methods::callNextMethod(
+      .Object,
+      .xData,
+      join_keys = join_keys,
+      verified = (length(args$code) == 0L && length(.xData) == 0L),
+      ...
+    )
   }
 )