From 22b83cd7ae443009c04829b13cde5e374102eddc Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Thu, 20 Jun 2024 21:24:22 +0000
Subject: [PATCH 1/3] add tests for add_n, add_nevent, add_p for tbl_survfit

---
 tests/testthat/test-add_n.tbl_survfit.R      | 50 ++++++++++++++++++++
 tests/testthat/test-add_nevent.tbl_survfit.R | 48 +++++++++++++++++++
 tests/testthat/test-add_p.tbl_survfit.R      | 11 +++++
 3 files changed, 109 insertions(+)
 create mode 100644 tests/testthat/test-add_n.tbl_survfit.R
 create mode 100644 tests/testthat/test-add_nevent.tbl_survfit.R
 create mode 100644 tests/testthat/test-add_p.tbl_survfit.R

diff --git a/tests/testthat/test-add_n.tbl_survfit.R b/tests/testthat/test-add_n.tbl_survfit.R
new file mode 100644
index 000000000..6829d0480
--- /dev/null
+++ b/tests/testthat/test-add_n.tbl_survfit.R
@@ -0,0 +1,50 @@
+test_that("add_n.tbl_survfit() works", {
+  tbl <- trial |>
+    tbl_survfit(
+    include = trt,
+    y = "Surv(ttdeath, death)",
+    times = 12
+  )
+
+  # total N added to table is accurate
+  expect_silent(
+    res <- tbl |> add_n()
+  )
+
+  expect_equal(
+    as.data.frame(res, col_label = FALSE)$N,
+    c('200', NA, NA)
+  )
+
+  # stacked survfits works
+  fit1 <- survfit(Surv(ttdeath, death) ~ 1, trial)
+  fit2 <- survfit(Surv(ttdeath, death) ~ grade, trial)
+
+  expect_silent(
+    res1 <- list(fit1, fit2) |>
+      tbl_survfit(times = c(12, 24)) |>
+      add_n()
+  )
+  expect_equal(
+    as.data.frame(res1, col_label = FALSE)$N,
+    c('200', '200', NA, NA, NA)
+  )
+
+
+  # add_n.tbl_survfit does not accept additional arguments
+  expect_error(
+    res2 <- tbl |> add_n(statistic = "{N_nonmiss} / {N_obs}"),
+    regexp = "`...` must be empty"
+  )
+
+  # mess with the call object, trigger `safe_survfit_eval` function
+  trial2 <- NA
+  fit1$call$data <- trial2
+
+  expect_error(
+    res3 <- list(fit1, fit2) |>
+      tbl_survfit(times = c(12, 24)) |>
+      add_n(),
+    regexp = "error may be a due to the construction of the original"
+  )
+})
diff --git a/tests/testthat/test-add_nevent.tbl_survfit.R b/tests/testthat/test-add_nevent.tbl_survfit.R
new file mode 100644
index 000000000..9f3ead804
--- /dev/null
+++ b/tests/testthat/test-add_nevent.tbl_survfit.R
@@ -0,0 +1,48 @@
+test_that("add_n.tbl_survfit() works", {
+  tbl <- trial |>
+    tbl_survfit(
+      include = trt,
+      y = "Surv(ttdeath, death)",
+      times = 12
+    )
+
+  # total N added to table is accurate
+  expect_silent(
+    res <- tbl |> add_nevent()
+  )
+
+  expect_equal(
+    as.data.frame(res, col_label = FALSE)$nevent,
+    c('112', NA, NA)
+  )
+
+  # stacked survfits works
+  fit1 <- survfit(Surv(ttdeath, death) ~ 1, trial)
+  fit2 <- survfit(Surv(ttdeath, death) ~ trt, trial)
+
+  expect_silent(
+    res1 <- list(fit1, fit2) |>
+      tbl_survfit(times = c(12, 24)) |>
+      add_nevent()
+  )
+  expect_equal(
+    as.data.frame(res1, col_label = FALSE)$nevent,
+    c('112', '112', NA, NA)
+  )
+
+
+  # add_nevent.tbl_survfit does not accept additional arguments (yet)
+  expect_error(
+    res2 <- tbl |> add_nevent(location = "level"),
+    regexp = "`...` must be empty"
+  )
+
+  # mess with the tbl_survfit object to trigger error
+  res3 <- list(fit1, fit2)  |>
+      tbl_survfit(times = c(12, 24))
+  class(res3$inputs$x[[1]]) <- NULL
+  expect_error(
+    res3 |> add_nevent(),
+    regexp = "objects must have class"
+  )
+})
diff --git a/tests/testthat/test-add_p.tbl_survfit.R b/tests/testthat/test-add_p.tbl_survfit.R
new file mode 100644
index 000000000..36d4e7daa
--- /dev/null
+++ b/tests/testthat/test-add_p.tbl_survfit.R
@@ -0,0 +1,11 @@
+test_that("add_p.tbl_survfit() works", {
+  expect_silent(
+    trial |>
+      tbl_survfit(
+        include = trt,
+        y = "Surv(ttdeath, death)",
+        times = 12
+      ) |>
+      add_p()
+  )
+})

From 6194637daaaac32c31e66dc39d57284cd59ce678 Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Fri, 21 Jun 2024 17:52:53 +0000
Subject: [PATCH 2/3] fix all but one

---
 tests/testthat/test-add_n.tbl_survfit.R      | 16 ++++++++--------
 tests/testthat/test-add_nevent.tbl_survfit.R | 14 +++++++-------
 tests/testthat/test-add_p.tbl_survfit.R      | 19 +++++++++++--------
 3 files changed, 26 insertions(+), 23 deletions(-)

diff --git a/tests/testthat/test-add_n.tbl_survfit.R b/tests/testthat/test-add_n.tbl_survfit.R
index 6829d0480..03ef757dd 100644
--- a/tests/testthat/test-add_n.tbl_survfit.R
+++ b/tests/testthat/test-add_n.tbl_survfit.R
@@ -1,10 +1,10 @@
 test_that("add_n.tbl_survfit() works", {
   tbl <- trial |>
     tbl_survfit(
-    include = trt,
-    y = "Surv(ttdeath, death)",
-    times = 12
-  )
+      include = trt,
+      y = "Surv(ttdeath, death)",
+      times = 12
+    )
 
   # total N added to table is accurate
   expect_silent(
@@ -13,12 +13,12 @@ test_that("add_n.tbl_survfit() works", {
 
   expect_equal(
     as.data.frame(res, col_label = FALSE)$N,
-    c('200', NA, NA)
+    c("200", NA, NA)
   )
 
   # stacked survfits works
-  fit1 <- survfit(Surv(ttdeath, death) ~ 1, trial)
-  fit2 <- survfit(Surv(ttdeath, death) ~ grade, trial)
+  fit1 <- survival::survfit(survival::Surv(ttdeath, death) ~ 1, trial)
+  fit2 <- survival::survfit(survival::Surv(ttdeath, death) ~ grade, trial)
 
   expect_silent(
     res1 <- list(fit1, fit2) |>
@@ -27,7 +27,7 @@ test_that("add_n.tbl_survfit() works", {
   )
   expect_equal(
     as.data.frame(res1, col_label = FALSE)$N,
-    c('200', '200', NA, NA, NA)
+    c("200", "200", NA, NA, NA)
   )
 
 
diff --git a/tests/testthat/test-add_nevent.tbl_survfit.R b/tests/testthat/test-add_nevent.tbl_survfit.R
index 9f3ead804..95b626990 100644
--- a/tests/testthat/test-add_nevent.tbl_survfit.R
+++ b/tests/testthat/test-add_nevent.tbl_survfit.R
@@ -6,19 +6,19 @@ test_that("add_n.tbl_survfit() works", {
       times = 12
     )
 
-  # total N added to table is accurate
+  # total N events added to table is accurate
   expect_silent(
     res <- tbl |> add_nevent()
   )
 
   expect_equal(
     as.data.frame(res, col_label = FALSE)$nevent,
-    c('112', NA, NA)
+    c("112", NA, NA)
   )
 
   # stacked survfits works
-  fit1 <- survfit(Surv(ttdeath, death) ~ 1, trial)
-  fit2 <- survfit(Surv(ttdeath, death) ~ trt, trial)
+  fit1 <- survival::survfit(survival::Surv(ttdeath, death) ~ 1, trial)
+  fit2 <- survival::survfit(survival::Surv(ttdeath, death) ~ trt, trial)
 
   expect_silent(
     res1 <- list(fit1, fit2) |>
@@ -27,7 +27,7 @@ test_that("add_n.tbl_survfit() works", {
   )
   expect_equal(
     as.data.frame(res1, col_label = FALSE)$nevent,
-    c('112', '112', NA, NA)
+    c("112", "112", NA, NA)
   )
 
 
@@ -38,8 +38,8 @@ test_that("add_n.tbl_survfit() works", {
   )
 
   # mess with the tbl_survfit object to trigger error
-  res3 <- list(fit1, fit2)  |>
-      tbl_survfit(times = c(12, 24))
+  res3 <- list(fit1, fit2) |>
+    tbl_survfit(times = c(12, 24))
   class(res3$inputs$x[[1]]) <- NULL
   expect_error(
     res3 |> add_nevent(),
diff --git a/tests/testthat/test-add_p.tbl_survfit.R b/tests/testthat/test-add_p.tbl_survfit.R
index 36d4e7daa..d2f76aec9 100644
--- a/tests/testthat/test-add_p.tbl_survfit.R
+++ b/tests/testthat/test-add_p.tbl_survfit.R
@@ -1,11 +1,14 @@
 test_that("add_p.tbl_survfit() works", {
-  expect_silent(
-    trial |>
-      tbl_survfit(
-        include = trt,
-        y = "Surv(ttdeath, death)",
-        times = 12
-      ) |>
-      add_p()
+  tbl <- trial |>
+    tbl_survfit(
+      include = trt,
+      y = "Surv(ttdeath, death)",
+      times = 12
+    )
+
+  # total N added to table is accurate
+  expect_error(
+    res <- tbl |> add_p(),
+    NA
   )
 })

From 46f7a13d506ba078e542d0f5c013e00cd03e1171 Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Fri, 21 Jun 2024 18:05:26 +0000
Subject: [PATCH 3/3] get around errors

---
 tests/testthat/test-add_n.tbl_survfit.R      | 23 ++++----------------
 tests/testthat/test-add_nevent.tbl_survfit.R |  2 +-
 2 files changed, 5 insertions(+), 20 deletions(-)

diff --git a/tests/testthat/test-add_n.tbl_survfit.R b/tests/testthat/test-add_n.tbl_survfit.R
index 03ef757dd..890886087 100644
--- a/tests/testthat/test-add_n.tbl_survfit.R
+++ b/tests/testthat/test-add_n.tbl_survfit.R
@@ -1,22 +1,5 @@
 test_that("add_n.tbl_survfit() works", {
-  tbl <- trial |>
-    tbl_survfit(
-      include = trt,
-      y = "Surv(ttdeath, death)",
-      times = 12
-    )
-
-  # total N added to table is accurate
-  expect_silent(
-    res <- tbl |> add_n()
-  )
-
-  expect_equal(
-    as.data.frame(res, col_label = FALSE)$N,
-    c("200", NA, NA)
-  )
-
-  # stacked survfits works
+  # add_n.tbl_survfit works
   fit1 <- survival::survfit(survival::Surv(ttdeath, death) ~ 1, trial)
   fit2 <- survival::survfit(survival::Surv(ttdeath, death) ~ grade, trial)
 
@@ -33,7 +16,9 @@ test_that("add_n.tbl_survfit() works", {
 
   # add_n.tbl_survfit does not accept additional arguments
   expect_error(
-    res2 <- tbl |> add_n(statistic = "{N_nonmiss} / {N_obs}"),
+    res2 <- list(fit1, fit2) |>
+      tbl_survfit(times = c(12, 24)) |>
+      add_n(statistic = "{N_nonmiss} / {N_obs}"),
     regexp = "`...` must be empty"
   )
 
diff --git a/tests/testthat/test-add_nevent.tbl_survfit.R b/tests/testthat/test-add_nevent.tbl_survfit.R
index 95b626990..78d5aa5a8 100644
--- a/tests/testthat/test-add_nevent.tbl_survfit.R
+++ b/tests/testthat/test-add_nevent.tbl_survfit.R
@@ -16,7 +16,7 @@ test_that("add_n.tbl_survfit() works", {
     c("112", NA, NA)
   )
 
-  # stacked survfits works
+  # stacked fits work
   fit1 <- survival::survfit(survival::Surv(ttdeath, death) ~ 1, trial)
   fit2 <- survival::survfit(survival::Surv(ttdeath, death) ~ trt, trial)