From 39225f09f5e738fd2eb5c4e719a1665a8220ab8b Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Mon, 8 Jan 2024 16:36:50 -0800
Subject: [PATCH 01/10] patch: get select working with grouping

---
 DESCRIPTION                  |  1 +
 NAMESPACE                    |  1 +
 tests/testthat/test-epi_df.R | 22 +++++++++++++++++++---
 3 files changed, 21 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index dc48eb86..339d5681 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -76,6 +76,7 @@ Collate:
     'data.R'
     'epi_df.R'
     'epiprocess.R'
+    'group_by_epi_df_methods.R'
     'methods-epi_archive.R'
     'grouped_epi_archive.R'
     'growth_rate.R'
diff --git a/NAMESPACE b/NAMESPACE
index 73db3483..c59004c8 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -23,6 +23,7 @@ S3method(groups,grouped_epi_archive)
 S3method(next_after,Date)
 S3method(next_after,integer)
 S3method(print,epi_df)
+S3method(select,epi_df)
 S3method(summary,epi_df)
 S3method(ungroup,epi_df)
 S3method(ungroup,grouped_epi_archive)
diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index 10b0015e..047438bb 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -36,6 +36,22 @@ test_that("as_epi_df errors when additional_metadata is not a list", {
       pol = rep(c("blue", "swing", "swing"), each = 2))
   
   expect_error(
-    as_epi_df(ex_input, additional_metadata = c(other_keys = "state", "pol")), 
-    "`additional_metadata` must be a list type.")
-})
\ No newline at end of file
+    as_epi_df(ex_input, additional_metadata = c(other_keys = "state", "pol")),
+    "`additional_metadata` must be a list type."
+  )
+})
+
+
+test_that("grouped epi_df maintains type for select", {
+  tib <- tibble::tibble(
+    x = 1:10, y = 1:10,
+    time_value = rep(seq(as.Date("2020-01-01"), by = 1, length.out = 5), times = 2),
+    geo_value = rep(c("ca", "hi"), each = 5)
+  )
+
+  epi_tib <- epiprocess::new_epi_df(tib)
+  epi_tib
+  grouped_epi <- epi_tib %>% group_by(geo_value)
+  selected_df <- grouped_epi %>% select(-y)
+  expect_true("epi_df" %in% class(selected_df))
+})

From 05aa645469588be96b5c6706722f6e5ab6f2a6f2 Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Tue, 9 Jan 2024 10:34:29 -0800
Subject: [PATCH 02/10] need the actual method

---
 R/group_by_epi_df_methods.R | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 R/group_by_epi_df_methods.R

diff --git a/R/group_by_epi_df_methods.R b/R/group_by_epi_df_methods.R
new file mode 100644
index 00000000..29e41762
--- /dev/null
+++ b/R/group_by_epi_df_methods.R
@@ -0,0 +1,10 @@
+#' @importFrom dplyr select
+#' @export
+select.epi_df <- function(.data, ...) {
+  selected <- NextMethod(.data)
+  return(dplyr_reconstruct(selected, .data))
+}
+
+# others to consider:
+# - arrange
+# -

From ac5f369839190ccdb604a0413a098651bf2352fa Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Tue, 9 Jan 2024 19:04:37 -0800
Subject: [PATCH 03/10] more thorough testing

---
 tests/testthat/test-epi_df.R | 85 ++++++++++++++++++++++++++++--------
 1 file changed, 68 insertions(+), 17 deletions(-)

diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index 047438bb..fbd31f7b 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -1,23 +1,27 @@
 test_that("new_epi_df works as intended", {
   # Empty tibble
-  wmsg = capture_warnings(a <- new_epi_df())
-  expect_match(wmsg[1],
-                 "Unknown or uninitialised column: `geo_value`.")
-  expect_match(wmsg[2],
-                 "Unknown or uninitialised column: `time_value`.")
+  wmsg <- capture_warnings(a <- new_epi_df())
+  expect_match(
+    wmsg[1],
+    "Unknown or uninitialised column: `geo_value`."
+  )
+  expect_match(
+    wmsg[2],
+    "Unknown or uninitialised column: `time_value`."
+  )
   expect_true(is_epi_df(a))
   expect_identical(attributes(a)$metadata$geo_type, "custom")
   expect_identical(attributes(a)$metadata$time_type, "custom")
   expect_true(lubridate::is.POSIXt(attributes(a)$metadata$as_of))
-  
+
   # Simple non-empty tibble with geo_value and time_value cols
   tib <- tibble::tibble(
     x = 1:10, y = 1:10,
     time_value = rep(seq(as.Date("2020-01-01"), by = 1, length.out = 5), times = 2),
     geo_value = rep(c("ca", "hi"), each = 5)
   )
-  
-  epi_tib = new_epi_df(tib)
+
+  epi_tib <- new_epi_df(tib)
   expect_true(is_epi_df(epi_tib))
   expect_length(epi_tib, 4L)
   expect_identical(attributes(epi_tib)$metadata$geo_type, "state")
@@ -32,26 +36,73 @@ test_that("as_epi_df errors when additional_metadata is not a list", {
     dplyr::slice_tail(n = 6) %>%
     tsibble::as_tsibble() %>%
     dplyr::mutate(
-      state = rep("MA",6),
-      pol = rep(c("blue", "swing", "swing"), each = 2))
-  
+      state = rep("MA", 6),
+      pol = rep(c("blue", "swing", "swing"), each = 2)
+    )
+
   expect_error(
     as_epi_df(ex_input, additional_metadata = c(other_keys = "state", "pol")),
     "`additional_metadata` must be a list type."
   )
 })
 
+# select fixes
 
+tib <- tibble::tibble(
+  x = 1:10, y = 1:10,
+  time_value = rep(seq(as.Date("2020-01-01"),
+    by = 1, length.out = 5
+  ), times = 2),
+  geo_value = rep(c("ca", "hi"), each = 5)
+)
+epi_tib <- epiprocess::new_epi_df(tib)
 test_that("grouped epi_df maintains type for select", {
+  grouped_epi <- epi_tib %>% group_by(geo_value)
+  selected_df <- grouped_epi %>% select(-y)
+  expect_true("epi_df" %in% class(selected_df))
+  # make sure that the attributes are right
+  epi_attr <- attributes(selected_df)
+  expect_identical(epi_attr$names, c("geo_value", "time_value", "x"))
+  expect_identical(epi_attr$row.names, seq(1, 10))
+  expect_identical(epi_attr$groups, attributes(grouped_epi)$groups)
+  expect_identical(epi_attr$metadata, attributes(epi_tib)$metadata)
+})
+
+test_that("grouped epi_df drops type when dropping keys", {
+  grouped_epi <- epi_tib %>% group_by(geo_value)
+  selected_df <- grouped_epi %>% select(geo_value)
+  expect_true(!("epi_df" %in% class(selected_df)))
+})
+
+test_that("grouped epi_df handles extra keys correctly", {
   tib <- tibble::tibble(
     x = 1:10, y = 1:10,
-    time_value = rep(seq(as.Date("2020-01-01"), by = 1, length.out = 5), times = 2),
-    geo_value = rep(c("ca", "hi"), each = 5)
+    time_value = rep(seq(as.Date("2020-01-01"),
+      by = 1, length.out = 5
+    ), times = 2),
+    geo_value = rep(c("ca", "hi"), each = 5),
+    extra_key = rep(seq(as.Date("2020-01-01"),
+      by = 1, length.out = 5
+    ), times = 2)
   )
-
-  epi_tib <- epiprocess::new_epi_df(tib)
-  epi_tib
+  epi_tib <- epiprocess::new_epi_df(tib,
+    additional_metadata = list(other_keys = "extra_key")
+  )
+  attributes(epi_tib)
   grouped_epi <- epi_tib %>% group_by(geo_value)
-  selected_df <- grouped_epi %>% select(-y)
+  selected_df <- grouped_epi %>% select(-extra_key)
+  selected_df
   expect_true("epi_df" %in% class(selected_df))
+  # make sure that the attributes are right
+  old_attr <- attributes(epi_tib)
+  epi_attr <- attributes(selected_df)
+  expect_identical(epi_attr$names, c("geo_value", "time_value", "x", "y"))
+  expect_identical(epi_attr$row.names, seq(1, 10))
+  expect_identical(epi_attr$groups, attributes(grouped_epi)$groups)
+  expect_identical(epi_attr$metadata, list(
+    geo_type = "state", time_type =
+      "day",
+    as_of = old_attr$metadata$as_of,
+    other_keys = character(0)
+  ))
 })

From b9bac788b3c50555b885cc0d4c3b7fefe62b68e1 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 12 Jan 2024 18:37:16 -0800
Subject: [PATCH 04/10] Fix `names<-.epi_df`, introduce failing test for
 renaming in `select`

---
 R/epi_df.R                           |  5 ++++-
 R/group_by_epi_df_methods.R          |  2 +-
 R/methods-epi_df.R                   | 11 +++++++++--
 tests/testthat/test-methods-epi_df.R | 14 ++++++++++++++
 4 files changed, 28 insertions(+), 4 deletions(-)

diff --git a/R/epi_df.R b/R/epi_df.R
index 045c4aaf..53dca62b 100644
--- a/R/epi_df.R
+++ b/R/epi_df.R
@@ -122,6 +122,9 @@ new_epi_df = function(x = tibble::tibble(), geo_type, time_type, as_of,
   if (!is.list(additional_metadata)) {
     Abort("`additional_metadata` must be a list type.")
   }
+  if (is.null(additional_metadata[["other_keys"]])) {
+    additional_metadata[["other_keys"]] <- character(0L)
+  }
 
   # If geo type is missing, then try to guess it
   if (missing(geo_type)) {
@@ -334,4 +337,4 @@ as_epi_df.tbl_ts = function(x, geo_type, time_type, as_of,
 #' @export
 is_epi_df = function(x) {
   inherits(x, "epi_df")
-}
\ No newline at end of file
+}
diff --git a/R/group_by_epi_df_methods.R b/R/group_by_epi_df_methods.R
index 29e41762..8d02a887 100644
--- a/R/group_by_epi_df_methods.R
+++ b/R/group_by_epi_df_methods.R
@@ -2,7 +2,7 @@
 #' @export
 select.epi_df <- function(.data, ...) {
   selected <- NextMethod(.data)
-  return(dplyr_reconstruct(selected, .data))
+  return (dplyr_reconstruct(selected, .data))
 }
 
 # others to consider:
diff --git a/R/methods-epi_df.R b/R/methods-epi_df.R
index 6429b867..82acc107 100644
--- a/R/methods-epi_df.R
+++ b/R/methods-epi_df.R
@@ -180,9 +180,16 @@ dplyr_row_slice.epi_df = function(data, i, ...) {
 #' @export
 `names<-.epi_df` = function(x, value) {
   old_names = names(x)
-  old_other_keys = attributes(x)$metadata$other_keys
+  old_other_keys = attr(x, "metadata")[["other_keys"]]
   result = NextMethod()
-  attributes(x)$metadata$other_keys <- value[match(old_other_keys, old_names)]
+  new_other_keys_almost <- value[match(old_other_keys, old_names)]
+  attr(result, "metadata")[["other_keys"]] <-
+    # patch until we require `other_keys` to be `chr`; match NULL-ness of input `other_keys`:
+    # if (length(new_other_keys_almost) == 0L) NULL
+    # if (is.null(old_other_keys)) NULL
+    # else new_other_keys_almost
+    new_other_keys_almost
+  # decay to non-`epi_df` if needed:
   dplyr::dplyr_reconstruct(result, result)
 }
 
diff --git a/tests/testthat/test-methods-epi_df.R b/tests/testthat/test-methods-epi_df.R
index 9d03cf93..c9e38fff 100644
--- a/tests/testthat/test-methods-epi_df.R
+++ b/tests/testthat/test-methods-epi_df.R
@@ -124,3 +124,17 @@ test_that("Metadata and grouping are dropped by `as_tibble`", {
     !any(c("metadata", "groups") %in% names(attributes(grouped_converted)))
   )
 })
+
+test_that("Renaming columns gives appropriate colnames and metadata", {
+  edf <- tibble::tibble(geo_value = 1, time_value = 1, age = 1, value = 1) %>%
+    as_epi_df(additional_metadata = list(other_keys = "age"))
+  renamed_edf1 <- edf %>%
+    `[`(c("geo_value", "time_value", "age", "value")) %>%
+    `names<-`(c("geo_value", "time_value", "age_group", "value"))
+  expect_identical(names(renamed_edf1), c("geo_value", "time_value", "age_group", "value"))
+  expect_identical(attr(renamed_edf1, "metadata")$other_keys, c("age_group"))
+  renamed_edf2 <- edf %>%
+    as_epi_df(additional_metadata = list(other_keys = "age")) %>%
+    select(geo_value, time_value, age_group = age, value)
+  expect_identical(renamed_edf1, renamed_edf2)
+})

From 42eb793d02332bcf6773860869e3cc91b16dff6f Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 12 Jan 2024 18:43:40 -0800
Subject: [PATCH 05/10] Clean up some commented-out code

---
 R/methods-epi_df.R | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/R/methods-epi_df.R b/R/methods-epi_df.R
index 82acc107..5dea964c 100644
--- a/R/methods-epi_df.R
+++ b/R/methods-epi_df.R
@@ -182,13 +182,8 @@ dplyr_row_slice.epi_df = function(data, i, ...) {
   old_names = names(x)
   old_other_keys = attr(x, "metadata")[["other_keys"]]
   result = NextMethod()
-  new_other_keys_almost <- value[match(old_other_keys, old_names)]
-  attr(result, "metadata")[["other_keys"]] <-
-    # patch until we require `other_keys` to be `chr`; match NULL-ness of input `other_keys`:
-    # if (length(new_other_keys_almost) == 0L) NULL
-    # if (is.null(old_other_keys)) NULL
-    # else new_other_keys_almost
-    new_other_keys_almost
+  new_other_keys <- value[match(old_other_keys, old_names)]
+  attr(result, "metadata")[["other_keys"]] <- new_other_keys
   # decay to non-`epi_df` if needed:
   dplyr::dplyr_reconstruct(result, result)
 }

From 510e6d45b626b684265f13fa337402f284d31343 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 12 Jan 2024 19:14:29 -0800
Subject: [PATCH 06/10] Fix `names<-` metadata for grouped `epi_df`s

---
 R/methods-epi_df.R | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/R/methods-epi_df.R b/R/methods-epi_df.R
index 5dea964c..6e4666e7 100644
--- a/R/methods-epi_df.R
+++ b/R/methods-epi_df.R
@@ -179,11 +179,13 @@ dplyr_row_slice.epi_df = function(data, i, ...) {
 
 #' @export
 `names<-.epi_df` = function(x, value) {
-  old_names = names(x)
-  old_other_keys = attr(x, "metadata")[["other_keys"]]
-  result = NextMethod()
+  old_names <- names(x)
+  old_metadata <- attr(x, "metadata")
+  old_other_keys <- old_metadata[["other_keys"]]
   new_other_keys <- value[match(old_other_keys, old_names)]
-  attr(result, "metadata")[["other_keys"]] <- new_other_keys
+  new_metadata <- old_metadata
+  new_metadata[["other_keys"]] <- new_other_keys
+  result <- reclass(NextMethod(), new_metadata)
   # decay to non-`epi_df` if needed:
   dplyr::dplyr_reconstruct(result, result)
 }

From 9cc34370156f5f4d7862c25ecaef5bdf816740cd Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 12 Jan 2024 19:16:09 -0800
Subject: [PATCH 07/10] Fix grouped `epi_df` `select` when renaming

---
 R/group_by_epi_df_methods.R | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/group_by_epi_df_methods.R b/R/group_by_epi_df_methods.R
index 8d02a887..acdab378 100644
--- a/R/group_by_epi_df_methods.R
+++ b/R/group_by_epi_df_methods.R
@@ -2,7 +2,8 @@
 #' @export
 select.epi_df <- function(.data, ...) {
   selected <- NextMethod(.data)
-  return (dplyr_reconstruct(selected, .data))
+  might_decay <- reclass(selected, attr(selected, "metadata"))
+  return(dplyr_reconstruct(might_decay, might_decay))
 }
 
 # others to consider:

From 113121fdf5ac4119bf387db63948496bbb2378c7 Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 12 Jan 2024 19:32:15 -0800
Subject: [PATCH 08/10] Add grouped epi_df names<- test, spruce up related
 tests

---
 tests/testthat/test-epi_df.R         | 11 +++++------
 tests/testthat/test-methods-epi_df.R | 17 +++++++++++++++++
 2 files changed, 22 insertions(+), 6 deletions(-)

diff --git a/tests/testthat/test-epi_df.R b/tests/testthat/test-epi_df.R
index fbd31f7b..decd6fd7 100644
--- a/tests/testthat/test-epi_df.R
+++ b/tests/testthat/test-epi_df.R
@@ -59,19 +59,20 @@ epi_tib <- epiprocess::new_epi_df(tib)
 test_that("grouped epi_df maintains type for select", {
   grouped_epi <- epi_tib %>% group_by(geo_value)
   selected_df <- grouped_epi %>% select(-y)
-  expect_true("epi_df" %in% class(selected_df))
+  expect_true(inherits(selected_df, "epi_df"))
   # make sure that the attributes are right
   epi_attr <- attributes(selected_df)
   expect_identical(epi_attr$names, c("geo_value", "time_value", "x"))
   expect_identical(epi_attr$row.names, seq(1, 10))
   expect_identical(epi_attr$groups, attributes(grouped_epi)$groups)
   expect_identical(epi_attr$metadata, attributes(epi_tib)$metadata)
+  expect_identical(selected_df, epi_tib %>% select(-y) %>% group_by(geo_value))
 })
 
 test_that("grouped epi_df drops type when dropping keys", {
   grouped_epi <- epi_tib %>% group_by(geo_value)
   selected_df <- grouped_epi %>% select(geo_value)
-  expect_true(!("epi_df" %in% class(selected_df)))
+  expect_true(!inherits(selected_df, "epi_df"))
 })
 
 test_that("grouped epi_df handles extra keys correctly", {
@@ -91,8 +92,7 @@ test_that("grouped epi_df handles extra keys correctly", {
   attributes(epi_tib)
   grouped_epi <- epi_tib %>% group_by(geo_value)
   selected_df <- grouped_epi %>% select(-extra_key)
-  selected_df
-  expect_true("epi_df" %in% class(selected_df))
+  expect_true(inherits(selected_df, "epi_df"))
   # make sure that the attributes are right
   old_attr <- attributes(epi_tib)
   epi_attr <- attributes(selected_df)
@@ -100,8 +100,7 @@ test_that("grouped epi_df handles extra keys correctly", {
   expect_identical(epi_attr$row.names, seq(1, 10))
   expect_identical(epi_attr$groups, attributes(grouped_epi)$groups)
   expect_identical(epi_attr$metadata, list(
-    geo_type = "state", time_type =
-      "day",
+    geo_type = "state", time_type = "day",
     as_of = old_attr$metadata$as_of,
     other_keys = character(0)
   ))
diff --git a/tests/testthat/test-methods-epi_df.R b/tests/testthat/test-methods-epi_df.R
index c9e38fff..6be7e89b 100644
--- a/tests/testthat/test-methods-epi_df.R
+++ b/tests/testthat/test-methods-epi_df.R
@@ -138,3 +138,20 @@ test_that("Renaming columns gives appropriate colnames and metadata", {
     select(geo_value, time_value, age_group = age, value)
   expect_identical(renamed_edf1, renamed_edf2)
 })
+
+test_that("Renaming columns while grouped gives appropriate colnames and metadata", {
+  gedf <- tibble::tibble(geo_value = 1, time_value = 1, age = 1, value = 1) %>%
+    as_epi_df(additional_metadata = list(other_keys = "age")) %>%
+    group_by(geo_value)
+  renamed_gedf1 <- gedf %>%
+    `[`(c("geo_value", "time_value", "age", "value")) %>%
+    `names<-`(c("geo_value", "time_value", "age_group", "value"))
+  expect_true(inherits(renamed_gedf1, "epi_df"))
+  expect_true(inherits(renamed_gedf1, "grouped_df"))
+  expect_identical(names(renamed_gedf1), c("geo_value", "time_value", "age_group", "value"))
+  expect_identical(attr(renamed_gedf1, "metadata")$other_keys, c("age_group"))
+  renamed_gedf2 <- gedf %>%
+    as_epi_df(additional_metadata = list(other_keys = "age")) %>%
+    select(geo_value, time_value, age_group = age, value)
+  expect_identical(renamed_gedf1, renamed_gedf2)
+})

From 0bf702f11cfd9ac13a65b7a1b62384937d38e33e Mon Sep 17 00:00:00 2001
From: "Logan C. Brooks" <lcbrooks+github@andrew.cmu.edu>
Date: Fri, 12 Jan 2024 19:41:32 -0800
Subject: [PATCH 09/10] Comment adding context for `group_by_epi_df_methods.R`

---
 R/group_by_epi_df_methods.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/R/group_by_epi_df_methods.R b/R/group_by_epi_df_methods.R
index acdab378..b531178f 100644
--- a/R/group_by_epi_df_methods.R
+++ b/R/group_by_epi_df_methods.R
@@ -1,3 +1,9 @@
+# These methods (and maybe some others in methods-epi_df.R) are here to augment
+# `?dplyr_extending` implementations to get the correct behavior on grouped
+# `epi_df`s. It would be nice if there were a way to replace these with a
+# generic core that automatically fixed all misbehaving methods; see
+# brainstorming within Issue #223.
+
 #' @importFrom dplyr select
 #' @export
 select.epi_df <- function(.data, ...) {

From ff3dfae096a10b26f494a2d6427cafdafe83b14f Mon Sep 17 00:00:00 2001
From: dsweber2 <david.weber2@pm.me>
Date: Tue, 16 Jan 2024 12:48:46 -0800
Subject: [PATCH 10/10] doc: minor annotations

---
 tests/testthat/test-methods-epi_df.R | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/tests/testthat/test-methods-epi_df.R b/tests/testthat/test-methods-epi_df.R
index 6be7e89b..aeb08ced 100644
--- a/tests/testthat/test-methods-epi_df.R
+++ b/tests/testthat/test-methods-epi_df.R
@@ -128,11 +128,13 @@ test_that("Metadata and grouping are dropped by `as_tibble`", {
 test_that("Renaming columns gives appropriate colnames and metadata", {
   edf <- tibble::tibble(geo_value = 1, time_value = 1, age = 1, value = 1) %>%
     as_epi_df(additional_metadata = list(other_keys = "age"))
+  # renaming using base R
   renamed_edf1 <- edf %>%
     `[`(c("geo_value", "time_value", "age", "value")) %>%
     `names<-`(c("geo_value", "time_value", "age_group", "value"))
   expect_identical(names(renamed_edf1), c("geo_value", "time_value", "age_group", "value"))
   expect_identical(attr(renamed_edf1, "metadata")$other_keys, c("age_group"))
+  # renaming using select
   renamed_edf2 <- edf %>%
     as_epi_df(additional_metadata = list(other_keys = "age")) %>%
     select(geo_value, time_value, age_group = age, value)
@@ -143,13 +145,17 @@ test_that("Renaming columns while grouped gives appropriate colnames and metadat
   gedf <- tibble::tibble(geo_value = 1, time_value = 1, age = 1, value = 1) %>%
     as_epi_df(additional_metadata = list(other_keys = "age")) %>%
     group_by(geo_value)
+  # renaming using base R
   renamed_gedf1 <- gedf %>%
     `[`(c("geo_value", "time_value", "age", "value")) %>%
     `names<-`(c("geo_value", "time_value", "age_group", "value"))
+  # tets type preservation
   expect_true(inherits(renamed_gedf1, "epi_df"))
   expect_true(inherits(renamed_gedf1, "grouped_df"))
+  # the names are right
   expect_identical(names(renamed_gedf1), c("geo_value", "time_value", "age_group", "value"))
   expect_identical(attr(renamed_gedf1, "metadata")$other_keys, c("age_group"))
+  # renaming using select
   renamed_gedf2 <- gedf %>%
     as_epi_df(additional_metadata = list(other_keys = "age")) %>%
     select(geo_value, time_value, age_group = age, value)