From 49b95f7c2f28be8109ad32a43c66a0c41f81a0b3 Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Mon, 24 Jun 2024 20:42:47 +0000
Subject: [PATCH 01/11] raise attention

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

diff --git a/R/add_stat.R b/R/add_stat.R
index 830d225b68..5fff22e5b9 100644
--- a/R/add_stat.R
+++ b/R/add_stat.R
@@ -147,7 +147,7 @@ add_stat <- function(x, fns, location = everything() ~ "label") {
   df_new_stat <-
     dplyr::tibble(variable = names(fns)) |>
     dplyr::mutate(
-      summary_type = map_chr(.data$variable, ~ x$inputs$type[[.x]]),
+      summary_type = map_chr(.data$variable, ~ x$inputs$type[[.x]]), # tbl_continuous objects generally don't have a "$inputs$type" object nested inside
       row_type = map_chr(.data$variable, ~ location[[.x]]),
       label = map2(
         .data$variable, .data$row_type,

From 7402616e9f23e6d50543f776bb0042f96b61ab5f Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Mon, 24 Jun 2024 21:08:50 +0000
Subject: [PATCH 02/11] need at least this to get old tests working

---
 R/tbl_continuous.R                            |  2 ++
 tests/testthat/test-add_stat.tbl_continuous.R | 28 +++++++++++++++++++
 2 files changed, 30 insertions(+)
 create mode 100644 tests/testthat/test-add_stat.tbl_continuous.R

diff --git a/R/tbl_continuous.R b/R/tbl_continuous.R
index 758f454ebb..4abf854aef 100644
--- a/R/tbl_continuous.R
+++ b/R/tbl_continuous.R
@@ -37,6 +37,7 @@ tbl_continuous <- function(data,
                            variable,
                            include = everything(),
                            digits = NULL,
+                           type = NULL,
                            by = NULL,
                            statistic = everything() ~ "{median} ({p25}, {p75})",
                            label = NULL) {
@@ -94,6 +95,7 @@ tbl_continuous <- function(data,
     digits = digits
   )
 
+  type <- assign_summary_type(data, variables = include, value = NULL)
 
   # save processed function inputs ---------------------------------------------
   tbl_continuous_inputs <- as.list(environment())
diff --git a/tests/testthat/test-add_stat.tbl_continuous.R b/tests/testthat/test-add_stat.tbl_continuous.R
new file mode 100644
index 0000000000..9f93e11501
--- /dev/null
+++ b/tests/testthat/test-add_stat.tbl_continuous.R
@@ -0,0 +1,28 @@
+test_that("add_stat for tbl_continuous() works", {
+  tt <-
+    trial %>%
+    tbl_continuous(
+      age,
+      include = grade,
+      by = trt
+    )
+
+  add_stat_test1 <- function(data, variable, by, ...) {
+    tibble::tibble(test_col = "Ugh")
+  }
+
+  add_stat_test2 <- function(data, variable, by, ...) {
+    tibble::tibble(test_col = rep_len("Ugh", 3))
+  }
+
+  expect_error(
+    tt %>%
+      add_stat(fns = everything() ~ add_stat_test1),
+    NA
+  )
+  expect_error(
+    tt %>%
+      add_stat(fns = everything() ~ add_stat_test2, location = everything() ~ "level"),
+    NA
+  )
+})

From 2c672f28f04cc5a2e553cc8b8db6d56b295b501e Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Mon, 24 Jun 2024 21:55:44 +0000
Subject: [PATCH 03/11] how to use include for formula formation?

---
 R/add_stat.R | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/R/add_stat.R b/R/add_stat.R
index 5fff22e5b9..bd2141eb58 100644
--- a/R/add_stat.R
+++ b/R/add_stat.R
@@ -147,7 +147,9 @@ add_stat <- function(x, fns, location = everything() ~ "label") {
   df_new_stat <-
     dplyr::tibble(variable = names(fns)) |>
     dplyr::mutate(
-      summary_type = map_chr(.data$variable, ~ x$inputs$type[[.x]]), # tbl_continuous objects generally don't have a "$inputs$type" object nested inside
+      summary_type = map_chr(.data$variable, ~ x$inputs$type[[.x]]),
+      # tbl_continuous objects generally didn't have a "$inputs$type" object nested inside
+      # added it back to tbl_continuous
       row_type = map_chr(.data$variable, ~ location[[.x]]),
       label = map2(
         .data$variable, .data$row_type,
@@ -231,6 +233,7 @@ eval_fn_safe <- function(variable, tbl, fn) {
         data = tbl$inputs$data,
         variable = variable,
         by = tbl$inputs$by,
+        include = tbl$inputs$include,
         tbl = tbl
       )
     )

From bac05213e0b479ceac75d295d5baa2c517894992 Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Tue, 25 Jun 2024 15:53:08 +0000
Subject: [PATCH 04/11] should work

---
 R/tbl_continuous.R                            |  3 +-
 man/tbl_strata.Rd                             |  2 +-
 tests/testthat/test-add_stat.tbl_continuous.R | 48 +++++++++++++++----
 3 files changed, 40 insertions(+), 13 deletions(-)

diff --git a/R/tbl_continuous.R b/R/tbl_continuous.R
index 4abf854aef..e1029bc8c2 100644
--- a/R/tbl_continuous.R
+++ b/R/tbl_continuous.R
@@ -37,7 +37,6 @@ tbl_continuous <- function(data,
                            variable,
                            include = everything(),
                            digits = NULL,
-                           type = NULL,
                            by = NULL,
                            statistic = everything() ~ "{median} ({p25}, {p75})",
                            label = NULL) {
@@ -95,7 +94,7 @@ tbl_continuous <- function(data,
     digits = digits
   )
 
-  type <- assign_summary_type(data, variables = include, value = NULL)
+  type <- rlang::rep_named(include, list("categorical"))
 
   # save processed function inputs ---------------------------------------------
   tbl_continuous_inputs <- as.list(environment())
diff --git a/man/tbl_strata.Rd b/man/tbl_strata.Rd
index 9a7ea24e70..807b38950d 100644
--- a/man/tbl_strata.Rd
+++ b/man/tbl_strata.Rd
@@ -67,7 +67,7 @@ curly brackets will be evaluated according to \code{glue::glue()} syntax.
 
 The evaluated value of \code{.header} is also available within \code{tbl_strata2(.tbl_fun)}}
 
-\item{.stack_group_header}{DEPRECATED.}
+\item{.stack_group_header}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}}
 
 \item{.quiet}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}}
 }
diff --git a/tests/testthat/test-add_stat.tbl_continuous.R b/tests/testthat/test-add_stat.tbl_continuous.R
index 9f93e11501..98ae70d5ae 100644
--- a/tests/testthat/test-add_stat.tbl_continuous.R
+++ b/tests/testthat/test-add_stat.tbl_continuous.R
@@ -8,21 +8,49 @@ test_that("add_stat for tbl_continuous() works", {
     )
 
   add_stat_test1 <- function(data, variable, by, ...) {
-    tibble::tibble(test_col = "Ugh")
+    tibble::tibble(addtl = "Data from elsewhere")
   }
 
+  expect_equal(
+    tt %>%
+      add_stat(fns = everything() ~ add_stat_test1) %>%
+      as_tibble() %>%
+      dplyr::pull(addtl),
+    c("Data from elsewhere", NA, NA, NA)
+  )
+})
+
+
+test_that("add_stat for tbl_continuous() works", {
+  tt <-
+    trial %>%
+    tbl_continuous(
+      age,
+      include = grade,
+      by = trt
+    )
+
+  p_vals <- lapply(
+    dplyr::group_split(trial, grade),
+    function(x) t.test(x$age ~ x$trt)$p.value
+  ) %>%
+    unlist %>%
+    round(3) %>%
+    as.character
+
   add_stat_test2 <- function(data, variable, by, ...) {
-    tibble::tibble(test_col = rep_len("Ugh", 3))
+    lapply(
+      dplyr::group_split(trial, grade),
+      function(x) t.test(x$age ~ x$trt)$p.value
+    ) %>%
+      unlist
   }
 
-  expect_error(
-    tt %>%
-      add_stat(fns = everything() ~ add_stat_test1),
-    NA
-  )
-  expect_error(
+  expect_equal(
     tt %>%
-      add_stat(fns = everything() ~ add_stat_test2, location = everything() ~ "level"),
-    NA
+      add_stat(fns = everything() ~ add_stat_test2, location = everything() ~ "level") %>%
+      as_tibble() %>%
+      dplyr::pull(add_stat_1),
+    c(NA, p_vals)
   )
 })

From 02400095f6da4ce6abb882956bac871a520ddcd3 Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Tue, 25 Jun 2024 16:05:54 +0000
Subject: [PATCH 05/11] as a fun exercise

---
 tests/testthat/test-add_stat.tbl_continuous.R | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/tests/testthat/test-add_stat.tbl_continuous.R b/tests/testthat/test-add_stat.tbl_continuous.R
index 98ae70d5ae..cdfba1a42d 100644
--- a/tests/testthat/test-add_stat.tbl_continuous.R
+++ b/tests/testthat/test-add_stat.tbl_continuous.R
@@ -38,12 +38,13 @@ test_that("add_stat for tbl_continuous() works", {
     round(3) %>%
     as.character
 
-  add_stat_test2 <- function(data, variable, by, ...) {
-    lapply(
-      dplyr::group_split(trial, grade),
-      function(x) t.test(x$age ~ x$trt)$p.value
-    ) %>%
-      unlist
+  add_stat_test2 <- function(data, variable, by, tbl, ...) {
+    col_name <- tbl$inputs$include
+    col_sym <- sym(col_name)
+
+    strat <- dplyr::group_split(data, !!col_sym)
+
+    lapply(strat, function(x) t.test(x$age ~ x$trt)$p.value) %>% unlist
   }
 
   expect_equal(

From 9bdb68dd5905d88b6cc5e0e758cd9177369afe3d Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Tue, 25 Jun 2024 16:08:20 +0000
Subject: [PATCH 06/11] add comments

---
 tests/testthat/test-add_stat.tbl_continuous.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-add_stat.tbl_continuous.R b/tests/testthat/test-add_stat.tbl_continuous.R
index cdfba1a42d..8c2fcc6c0a 100644
--- a/tests/testthat/test-add_stat.tbl_continuous.R
+++ b/tests/testthat/test-add_stat.tbl_continuous.R
@@ -21,7 +21,7 @@ test_that("add_stat for tbl_continuous() works", {
 })
 
 
-test_that("add_stat for tbl_continuous() works", {
+test_that("add_stat for tbl_continuous() works using location", {
   tt <-
     trial %>%
     tbl_continuous(

From 7b37b2766b5b12fdf18ebd0797d47f8877d11ed5 Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Tue, 25 Jun 2024 17:05:30 +0000
Subject: [PATCH 07/11] nvm found the issue

---
 R/tbl_continuous.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/tbl_continuous.R b/R/tbl_continuous.R
index e1029bc8c2..f70e9a1010 100644
--- a/R/tbl_continuous.R
+++ b/R/tbl_continuous.R
@@ -94,8 +94,6 @@ tbl_continuous <- function(data,
     digits = digits
   )
 
-  type <- rlang::rep_named(include, list("categorical"))
-
   # save processed function inputs ---------------------------------------------
   tbl_continuous_inputs <- as.list(environment())
   call <- match.call()
@@ -190,6 +188,7 @@ tbl_continuous <- function(data,
   # add other information to the returned object
   x$cards <- list(tbl_continuous = cards)
   x$inputs <- tbl_continuous_inputs
+  x$inputs$type <- rlang::rep_named(include, list("categorical"))
   x$call_list <- list(tbl_continuous = call)
 
   x |>

From 4ca40c7bb413e42f40d37519b7eb0c7d4f5d6848 Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Tue, 25 Jun 2024 11:44:58 -0700
Subject: [PATCH 08/11] DS review updates

---
 R/add_stat.R                                  | 6 +++++-
 R/tbl_continuous.R                            | 1 -
 tests/testthat/test-add_stat.tbl_continuous.R | 8 ++++----
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/R/add_stat.R b/R/add_stat.R
index bd2141eb58..efb95f25cd 100644
--- a/R/add_stat.R
+++ b/R/add_stat.R
@@ -114,6 +114,11 @@ add_stat <- function(x, fns, location = everything() ~ "label") {
   check_not_missing(fns)
   check_class(x, c("tbl_summary", "tbl_svysummary", "tbl_continuous"))
 
+  # adding type if `tbl_continuous`...this is used later on
+  if (inherits(x, "tbl_continuous")) {
+    x$inputs$type <- rep_named(x$inputs$include, list("categorical"))
+  }
+
   # convert to named lists -----------------------------------------------------
   cards::process_formula_selectors(
     select_prep(x$table_body),
@@ -233,7 +238,6 @@ eval_fn_safe <- function(variable, tbl, fn) {
         data = tbl$inputs$data,
         variable = variable,
         by = tbl$inputs$by,
-        include = tbl$inputs$include,
         tbl = tbl
       )
     )
diff --git a/R/tbl_continuous.R b/R/tbl_continuous.R
index f70e9a1010..f850ff8896 100644
--- a/R/tbl_continuous.R
+++ b/R/tbl_continuous.R
@@ -188,7 +188,6 @@ tbl_continuous <- function(data,
   # add other information to the returned object
   x$cards <- list(tbl_continuous = cards)
   x$inputs <- tbl_continuous_inputs
-  x$inputs$type <- rlang::rep_named(include, list("categorical"))
   x$call_list <- list(tbl_continuous = call)
 
   x |>
diff --git a/tests/testthat/test-add_stat.tbl_continuous.R b/tests/testthat/test-add_stat.tbl_continuous.R
index 8c2fcc6c0a..d389a227e6 100644
--- a/tests/testthat/test-add_stat.tbl_continuous.R
+++ b/tests/testthat/test-add_stat.tbl_continuous.R
@@ -1,6 +1,6 @@
-test_that("add_stat for tbl_continuous() works", {
+test_that("add_stat() for 'tbl_continuous'", {
   tt <-
-    trial %>%
+    trial |>
     tbl_continuous(
       age,
       include = grade,
@@ -12,7 +12,7 @@ test_that("add_stat for tbl_continuous() works", {
   }
 
   expect_equal(
-    tt %>%
+    tt |>
       add_stat(fns = everything() ~ add_stat_test1) %>%
       as_tibble() %>%
       dplyr::pull(addtl),
@@ -21,7 +21,7 @@ test_that("add_stat for tbl_continuous() works", {
 })
 
 
-test_that("add_stat for tbl_continuous() works using location", {
+test_that("add_stat(location) for 'tbl_continuous'", {
   tt <-
     trial %>%
     tbl_continuous(

From 51c2151e383b0a64041d4855e1aa187b088d0cdb Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Tue, 25 Jun 2024 20:37:13 +0000
Subject: [PATCH 09/11] move the tests and take in feedback

---
 tests/testthat/test-add_stat.R                | 57 ++++++++++++++++++-
 tests/testthat/test-add_stat.tbl_continuous.R | 57 -------------------
 2 files changed, 56 insertions(+), 58 deletions(-)
 delete mode 100644 tests/testthat/test-add_stat.tbl_continuous.R

diff --git a/tests/testthat/test-add_stat.R b/tests/testthat/test-add_stat.R
index 4786dd7df2..338f3e5fdd 100644
--- a/tests/testthat/test-add_stat.R
+++ b/tests/testthat/test-add_stat.R
@@ -170,4 +170,59 @@ test_that("add_stat(x) messaging", {
 
 # TODO: Add `tbl_svysummary()` tests
 
-# TODO: Add `tbl_continuous()` tests
+# `tbl_continuous()` tests
+test_that("add_stat() for 'tbl_continuous'", {
+  tt <-
+    trial |>
+    tbl_continuous(
+      age,
+      include = grade,
+      by = trt
+    )
+
+  add_stat_test1 <- function(data, variable, by, ...) {
+    tibble::tibble(addtl = "Data from elsewhere")
+  }
+
+  expect_equal(
+    tt |>
+      add_stat(fns = everything() ~ add_stat_test1) |>
+      as_tibble() |>
+      dplyr::pull(addtl),
+    c("Data from elsewhere", NA, NA, NA)
+  )
+})
+
+
+test_that("add_stat(location) for 'tbl_continuous'", {
+  tt <-
+    trial |>
+    tbl_continuous(
+      age,
+      include = grade,
+      by = trt
+    )
+
+  p_vals <- lapply(
+    dplyr::group_split(trial, grade),
+    function(x) t.test(x$age ~ x$trt)$p.value
+  ) %>%
+    unlist() |>
+    round(3) %>%
+    as.character()
+
+  add_stat_test2 <- function(data, variable, by, tbl, ...) {
+    data |>
+      dplyr::group_split(!!sym(tbl$inputs$include)) |>
+      map_dbl(~ t.test(.x[[tbl$inputs$variable]] ~ .x[[by]])$p.value)
+  }
+
+  expect_equal(
+    tt |>
+      add_stat(fns = everything() ~ add_stat_test2, location = everything() ~ "level") |>
+      as_tibble() |>
+      dplyr::pull(add_stat_1),
+    c(NA, p_vals)
+  )
+})
+
diff --git a/tests/testthat/test-add_stat.tbl_continuous.R b/tests/testthat/test-add_stat.tbl_continuous.R
deleted file mode 100644
index d389a227e6..0000000000
--- a/tests/testthat/test-add_stat.tbl_continuous.R
+++ /dev/null
@@ -1,57 +0,0 @@
-test_that("add_stat() for 'tbl_continuous'", {
-  tt <-
-    trial |>
-    tbl_continuous(
-      age,
-      include = grade,
-      by = trt
-    )
-
-  add_stat_test1 <- function(data, variable, by, ...) {
-    tibble::tibble(addtl = "Data from elsewhere")
-  }
-
-  expect_equal(
-    tt |>
-      add_stat(fns = everything() ~ add_stat_test1) %>%
-      as_tibble() %>%
-      dplyr::pull(addtl),
-    c("Data from elsewhere", NA, NA, NA)
-  )
-})
-
-
-test_that("add_stat(location) for 'tbl_continuous'", {
-  tt <-
-    trial %>%
-    tbl_continuous(
-      age,
-      include = grade,
-      by = trt
-    )
-
-  p_vals <- lapply(
-    dplyr::group_split(trial, grade),
-    function(x) t.test(x$age ~ x$trt)$p.value
-  ) %>%
-    unlist %>%
-    round(3) %>%
-    as.character
-
-  add_stat_test2 <- function(data, variable, by, tbl, ...) {
-    col_name <- tbl$inputs$include
-    col_sym <- sym(col_name)
-
-    strat <- dplyr::group_split(data, !!col_sym)
-
-    lapply(strat, function(x) t.test(x$age ~ x$trt)$p.value) %>% unlist
-  }
-
-  expect_equal(
-    tt %>%
-      add_stat(fns = everything() ~ add_stat_test2, location = everything() ~ "level") %>%
-      as_tibble() %>%
-      dplyr::pull(add_stat_1),
-    c(NA, p_vals)
-  )
-})

From 3fc29f2d412a90b1b071937e31d2159dbb48b3bf Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Tue, 25 Jun 2024 20:44:20 +0000
Subject: [PATCH 10/11] remove unncessary comments and return tbl_continuous
 back to original shape

---
 R/add_stat.R       | 2 --
 R/tbl_continuous.R | 1 +
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/add_stat.R b/R/add_stat.R
index efb95f25cd..5d69d05a31 100644
--- a/R/add_stat.R
+++ b/R/add_stat.R
@@ -153,8 +153,6 @@ add_stat <- function(x, fns, location = everything() ~ "label") {
     dplyr::tibble(variable = names(fns)) |>
     dplyr::mutate(
       summary_type = map_chr(.data$variable, ~ x$inputs$type[[.x]]),
-      # tbl_continuous objects generally didn't have a "$inputs$type" object nested inside
-      # added it back to tbl_continuous
       row_type = map_chr(.data$variable, ~ location[[.x]]),
       label = map2(
         .data$variable, .data$row_type,
diff --git a/R/tbl_continuous.R b/R/tbl_continuous.R
index f850ff8896..758f454ebb 100644
--- a/R/tbl_continuous.R
+++ b/R/tbl_continuous.R
@@ -94,6 +94,7 @@ tbl_continuous <- function(data,
     digits = digits
   )
 
+
   # save processed function inputs ---------------------------------------------
   tbl_continuous_inputs <- as.list(environment())
   call <- match.call()

From 61d78119fb09badb33f0b67a0fed975c9d1d4b15 Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Tue, 25 Jun 2024 20:51:09 +0000
Subject: [PATCH 11/11] use native pipe only

---
 tests/testthat/test-add_stat.R | 10 ++++------
 1 file changed, 4 insertions(+), 6 deletions(-)

diff --git a/tests/testthat/test-add_stat.R b/tests/testthat/test-add_stat.R
index 338f3e5fdd..644ac3f70b 100644
--- a/tests/testthat/test-add_stat.R
+++ b/tests/testthat/test-add_stat.R
@@ -203,12 +203,10 @@ test_that("add_stat(location) for 'tbl_continuous'", {
       by = trt
     )
 
-  p_vals <- lapply(
-    dplyr::group_split(trial, grade),
-    function(x) t.test(x$age ~ x$trt)$p.value
-  ) %>%
-    unlist() |>
-    round(3) %>%
+  p_vals <- trial |>
+    dplyr::group_split(grade) |>
+    map_dbl(~ t.test(.x[["age"]] ~ .x[["trt"]])$p.value)|>
+    round(3) |>
     as.character()
 
   add_stat_test2 <- function(data, variable, by, tbl, ...) {