From e5d083838d3e8211156f8089d840ff4504344dad Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 13 Sep 2024 14:01:00 -0400
Subject: [PATCH 1/5] Add regression tests for summary.simtrial_gs_wlr()

---
 R/summary.R                               |  2 +-
 man/summary.Rd                            |  2 +-
 tests/testthat/test-unvalidated-summary.R | 91 +++++++++++++++++++++++
 3 files changed, 93 insertions(+), 2 deletions(-)
 create mode 100644 tests/testthat/test-unvalidated-summary.R

diff --git a/R/summary.R b/R/summary.R
index 4a67030d..97efe956 100644
--- a/R/summary.R
+++ b/R/summary.R
@@ -25,7 +25,7 @@
 #' @param ... Additional parameters (not used).
 #'
 #' @rdname summary
-#' @return A gt table
+#' @return A tibble
 #' @export
 #'
 #' @examples
diff --git a/man/summary.Rd b/man/summary.Rd
index e5c5d5ca..bc5d3648 100644
--- a/man/summary.Rd
+++ b/man/summary.Rd
@@ -17,7 +17,7 @@
 \item{...}{Additional parameters (not used).}
 }
 \value{
-A gt table
+A tibble
 }
 \description{
 Summary of group sequential simulations.
diff --git a/tests/testthat/test-unvalidated-summary.R b/tests/testthat/test-unvalidated-summary.R
new file mode 100644
index 00000000..4157de3c
--- /dev/null
+++ b/tests/testthat/test-unvalidated-summary.R
@@ -0,0 +1,91 @@
+test_that("summary.simtrial_gs_wlr() returns consistent results", {
+  # Test code adapted from example in ?summary.summary.simtrial_gs_wlr
+
+  # Parameters for enrollment
+  enroll_rampup_duration <- 4 # Duration for enrollment ramp up
+  enroll_duration <- 16 # Total enrollment duration
+  enroll_rate <- gsDesign2::define_enroll_rate(
+    duration = c(
+      enroll_rampup_duration, enroll_duration - enroll_rampup_duration),
+    rate = c(10, 30))
+
+  # Parameters for treatment effect
+  delay_effect_duration <- 3 # Delay treatment effect in months
+  median_ctrl <- 9 # Survival median of the control arm
+  median_exp <- c(9, 14) # Survival median of the experimental arm
+  dropout_rate <- 0.001
+  fail_rate <- gsDesign2::define_fail_rate(
+    duration = c(delay_effect_duration, 100),
+    fail_rate = log(2) / median_ctrl,
+    hr = median_ctrl / median_exp,
+    dropout_rate = dropout_rate)
+
+  # Other related parameters
+  alpha <- 0.025 # Type I error
+  beta <- 0.1 # Type II error
+  ratio <- 1 # Randomization ratio (experimental:control)
+
+  # Build a one-sided group sequential design
+  design <- gsDesign2::gs_design_ahr(
+    enroll_rate = enroll_rate, fail_rate = fail_rate,
+    ratio = ratio, alpha = alpha, beta = beta,
+    analysis_time = c(12, 24, 36),
+    upper = gsDesign2::gs_spending_bound,
+    upar = list(sf = gsDesign::sfLDOF, total_spend = alpha),
+    lower = gsDesign2::gs_b,
+    lpar = rep(-Inf, 3))
+
+  # Define cuttings of 2 IAs and 1 FA
+  ia1_cut <- create_cut(target_event_overall = ceiling(design$analysis$event[1]))
+  ia2_cut <- create_cut(target_event_overall = ceiling(design$analysis$event[2]))
+  fa_cut <- create_cut(target_event_overall = ceiling(design$analysis$event[3]))
+
+  # Run simulations
+  set.seed(1)
+  simulation <- sim_gs_n(
+    n_sim = 3,
+    sample_size = ceiling(design$analysis$n[3]),
+    enroll_rate = design$enroll_rate,
+    fail_rate = design$fail_rate,
+    test = wlr,
+    cut = list(ia1 = ia1_cut, ia2 = ia2_cut, fa = fa_cut),
+    weight = fh(rho = 0, gamma = 0.5))
+
+  # Summarize simulations
+  observed <- simulation |>
+    summary(bound = gsDesign::gsDesign(k = 3, test.type = 1, sfu = gsDesign::sfLDOF)$upper$bound)
+  expected <- tibble::tibble(
+    analysis = c(1, 2, 3),
+    sim_n = c(369.3333333333333, 505, 505),
+    sim_event = c(97, 305, 405),
+    sim_time = c(12.877359569828519, 24.990283397668506, 37.20491262038222),
+    sim_upper_prob = rep(NA_real_, 3L),
+  ) |>
+    structure(
+      class = c("simtrial_gs_wlr", "tbl_df", "tbl", "data.frame"),
+      compare_with_design = "no",
+      method = "FH(rho=0, gamma=0.5)"
+    )
+  expect_equal(observed, expected)
+
+  # Summarize simulation and compare with the planned design
+  observed <- simulation |> summary(design = design)
+  expected <- tibble::tibble(
+    analysis = c(1, 2, 3),
+    asy_upper_prob = c(0.00014865936645545522, 0.5723215057363614, 0.9000000002116888),
+    sim_upper_prob = rep(NA_real_, 3L),
+    sim_event = c(97, 305, 405),
+    sim_n = c(369.3333333333333, 505, 505),
+    sim_time = c(12.877359569828519, 24.990283397668506, 37.20491262038222),
+    asy_time = c(12, 24, 36),
+    asy_n = c(353.04671034431556, 504.3524433490222, 504.3524433490222),
+    asy_event = c(96.77457617908364, 304.00996193840484, 404.14196474655887),
+  ) |>
+    structure(
+      class = c("simtrial_gs_wlr", "tbl_df", "tbl", "data.frame"),
+      compare_with_design = "yes",
+      design_type = "one-sided",
+      method = "FH(rho=0, gamma=0.5)"
+    )
+  expect_equal(observed, expected)
+})

From db59fcf97ec998bb3c8d25fa0a30568c31150677 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 13 Sep 2024 15:11:11 -0400
Subject: [PATCH 2/5] Return a data frame instead of a tibble

---
 R/summary.R                               |  3 ++-
 man/summary.Rd                            |  2 +-
 tests/testthat/test-unvalidated-summary.R | 12 ++++++------
 3 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/R/summary.R b/R/summary.R
index 97efe956..688b45e9 100644
--- a/R/summary.R
+++ b/R/summary.R
@@ -25,7 +25,7 @@
 #' @param ... Additional parameters (not used).
 #'
 #' @rdname summary
-#' @return A tibble
+#' @return A data frame
 #' @export
 #'
 #' @examples
@@ -213,6 +213,7 @@ summary.simtrial_gs_wlr <- function(object,
     attr(ans, "design_type") <- design_type
   }
 
+  ans <- as.data.frame(ans)
   class(ans) <- c("simtrial_gs_wlr", class(ans))
   attr(ans, "method") <- attributes(object)$method
 
diff --git a/man/summary.Rd b/man/summary.Rd
index bc5d3648..0c40142a 100644
--- a/man/summary.Rd
+++ b/man/summary.Rd
@@ -17,7 +17,7 @@
 \item{...}{Additional parameters (not used).}
 }
 \value{
-A tibble
+A data frame
 }
 \description{
 Summary of group sequential simulations.
diff --git a/tests/testthat/test-unvalidated-summary.R b/tests/testthat/test-unvalidated-summary.R
index 4157de3c..1a322dfe 100644
--- a/tests/testthat/test-unvalidated-summary.R
+++ b/tests/testthat/test-unvalidated-summary.R
@@ -54,15 +54,15 @@ test_that("summary.simtrial_gs_wlr() returns consistent results", {
   # Summarize simulations
   observed <- simulation |>
     summary(bound = gsDesign::gsDesign(k = 3, test.type = 1, sfu = gsDesign::sfLDOF)$upper$bound)
-  expected <- tibble::tibble(
+  expected <- data.frame(
     analysis = c(1, 2, 3),
     sim_n = c(369.3333333333333, 505, 505),
     sim_event = c(97, 305, 405),
     sim_time = c(12.877359569828519, 24.990283397668506, 37.20491262038222),
-    sim_upper_prob = rep(NA_real_, 3L),
+    sim_upper_prob = rep(NA_real_, 3L)
   ) |>
     structure(
-      class = c("simtrial_gs_wlr", "tbl_df", "tbl", "data.frame"),
+      class = c("simtrial_gs_wlr", "data.frame"),
       compare_with_design = "no",
       method = "FH(rho=0, gamma=0.5)"
     )
@@ -70,7 +70,7 @@ test_that("summary.simtrial_gs_wlr() returns consistent results", {
 
   # Summarize simulation and compare with the planned design
   observed <- simulation |> summary(design = design)
-  expected <- tibble::tibble(
+  expected <- data.frame(
     analysis = c(1, 2, 3),
     asy_upper_prob = c(0.00014865936645545522, 0.5723215057363614, 0.9000000002116888),
     sim_upper_prob = rep(NA_real_, 3L),
@@ -79,10 +79,10 @@ test_that("summary.simtrial_gs_wlr() returns consistent results", {
     sim_time = c(12.877359569828519, 24.990283397668506, 37.20491262038222),
     asy_time = c(12, 24, 36),
     asy_n = c(353.04671034431556, 504.3524433490222, 504.3524433490222),
-    asy_event = c(96.77457617908364, 304.00996193840484, 404.14196474655887),
+    asy_event = c(96.77457617908364, 304.00996193840484, 404.14196474655887)
   ) |>
     structure(
-      class = c("simtrial_gs_wlr", "tbl_df", "tbl", "data.frame"),
+      class = c("simtrial_gs_wlr", "data.frame"),
       compare_with_design = "yes",
       design_type = "one-sided",
       method = "FH(rho=0, gamma=0.5)"

From 23bf58374ce892484ee6c7ca6e5008d306b2f6db Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 13 Sep 2024 15:16:13 -0400
Subject: [PATCH 3/5] Remove NOTE about wide line truncated in PDF manual

---
 R/summary.R    | 3 ++-
 man/summary.Rd | 3 ++-
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/summary.R b/R/summary.R
index 688b45e9..79abce9c 100644
--- a/R/summary.R
+++ b/R/summary.R
@@ -81,7 +81,8 @@
 #'   weight = fh(rho = 0, gamma = 0.5))
 #'
 #' # Summarize simulations
-#' simulation |> summary(bound = gsDesign::gsDesign(k = 3, test.type = 1, sfu = gsDesign::sfLDOF)$upper$bound)
+#' bound <- gsDesign::gsDesign(k = 3, test.type = 1, sfu = gsDesign::sfLDOF)$upper$bound
+#' simulation |> summary(bound = bound)
 #'
 #' # Summarize simulation and compare with the planned design
 #' simulation |> summary(design = design)
diff --git a/man/summary.Rd b/man/summary.Rd
index 0c40142a..8031f8ef 100644
--- a/man/summary.Rd
+++ b/man/summary.Rd
@@ -75,7 +75,8 @@ simulation <- sim_gs_n(
   weight = fh(rho = 0, gamma = 0.5))
 
 # Summarize simulations
-simulation |> summary(bound = gsDesign::gsDesign(k = 3, test.type = 1, sfu = gsDesign::sfLDOF)$upper$bound)
+bound <- gsDesign::gsDesign(k = 3, test.type = 1, sfu = gsDesign::sfLDOF)$upper$bound
+simulation |> summary(bound = bound)
 
 # Summarize simulation and compare with the planned design
 simulation |> summary(design = design)

From d520c7f6c028a3baa07bbb73f5b1419d8e399761 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 19 Sep 2024 16:12:28 -0400
Subject: [PATCH 4/5] Add regression test for summary.simtrial_gs_wlr() with
 two-sided design

---
 tests/testthat/test-unvalidated-summary.R | 94 ++++++++++++++++++++++-
 1 file changed, 93 insertions(+), 1 deletion(-)

diff --git a/tests/testthat/test-unvalidated-summary.R b/tests/testthat/test-unvalidated-summary.R
index 1a322dfe..700e36f3 100644
--- a/tests/testthat/test-unvalidated-summary.R
+++ b/tests/testthat/test-unvalidated-summary.R
@@ -1,4 +1,4 @@
-test_that("summary.simtrial_gs_wlr() returns consistent results", {
+test_that("summary.simtrial_gs_wlr() returns consistent results for one-sided design", {
   # Test code adapted from example in ?summary.summary.simtrial_gs_wlr
 
   # Parameters for enrollment
@@ -89,3 +89,95 @@ test_that("summary.simtrial_gs_wlr() returns consistent results", {
     )
   expect_equal(observed, expected)
 })
+
+test_that("summary.simtrial_gs_wlr() returns consistent results for two-sided design", {
+  # Parameters for enrollment
+  enroll_rampup_duration <- 4 # Duration for enrollment ramp up
+  enroll_duration <- 16 # Total enrollment duration
+  enroll_rate <- gsDesign2::define_enroll_rate(
+    duration = c(
+      enroll_rampup_duration, enroll_duration - enroll_rampup_duration),
+    rate = c(10, 30))
+
+  # Parameters for treatment effect
+  delay_effect_duration <- 3 # Delay treatment effect in months
+  median_ctrl <- 9 # Survival median of the control arm
+  median_exp <- c(9, 14) # Survival median of the experimental arm
+  dropout_rate <- 0.001
+  fail_rate <- gsDesign2::define_fail_rate(
+    duration = c(delay_effect_duration, 100),
+    fail_rate = log(2) / median_ctrl,
+    hr = median_ctrl / median_exp,
+    dropout_rate = dropout_rate)
+
+  # Other related parameters
+  alpha <- 0.025 # Type I error
+  beta <- 0.1 # Type II error
+  ratio <- 1 # Randomization ratio (experimental:control)
+
+  # Build a two-sided group sequential design
+  design <- gsDesign2::gs_design_ahr(
+    enroll_rate = enroll_rate, fail_rate = fail_rate,
+    ratio = ratio, alpha = alpha, beta = beta,
+    analysis_time = c(12, 24, 36),
+    upper = gsDesign2::gs_spending_bound,
+    upar = list(sf = gsDesign::sfLDOF, total_spend = alpha),
+    lower = gsDesign2::gs_spending_bound,
+    lpar = list(sf = gsDesign::sfLDOF, total_spend = beta))
+
+  # Define cuttings of 2 IAs and 1 FA
+  ia1_cut <- create_cut(target_event_overall = ceiling(design$analysis$event[1]))
+  ia2_cut <- create_cut(target_event_overall = ceiling(design$analysis$event[2]))
+  fa_cut <- create_cut(target_event_overall = ceiling(design$analysis$event[3]))
+
+  # Run simulations
+  set.seed(1)
+  simulation <- sim_gs_n(
+    n_sim = 3,
+    sample_size = ceiling(design$analysis$n[3]),
+    enroll_rate = design$enroll_rate,
+    fail_rate = design$fail_rate,
+    test = wlr,
+    cut = list(ia1 = ia1_cut, ia2 = ia2_cut, fa = fa_cut),
+    weight = fh(rho = 0, gamma = 0.5))
+
+  # Summarize simulations
+  observed <- simulation |>
+    summary(bound = gsDesign::gsDesign(k = 3, test.type = 1, sfu = gsDesign::sfLDOF)$upper$bound)
+  expected <- data.frame(
+    analysis = c(1, 2, 3),
+    sim_n = c(366.6666666666667, 535, 535),
+    sim_event = c(103, 323, 429),
+    sim_time = c(12.363838412468121, 24.374413483785986, 36.116791896100885),
+    sim_upper_prob = rep(NA_real_, 3L)
+  ) |>
+    structure(
+      compare_with_design = "no",
+      class = c("simtrial_gs_wlr", "data.frame"),
+      method = "FH(rho=0, gamma=0.5)"
+    )
+  expect_equal(observed, expected)
+
+  # Summarize simulation and compare with the planned design
+  observed <- simulation |> summary(design = design)
+  expected <- data.frame(
+    analysis = c(1, 2, 3),
+    asy_upper_prob = c(0.00016250401737420353, 0.6011019363189855, 0.9000000001924918),
+    asy_lower_prob = c(0.0007883883873094952, 0.05707064419933058, 0.10004018006137042),
+    sim_upper_prob = rep(NA_real_, 3L),
+    sim_lower_prob = c(NA, 1, NA),
+    sim_event = c(103, 323, 429),
+    sim_n = c(366.6666666666667, 535, 535),
+    sim_time = c(12.363838412468121, 24.374413483785986, 36.116791896100885),
+    asy_time = c(12, 24, 36),
+    asy_n = c(374.08958620608826, 534.4136945801262, 534.4136945801262),
+    asy_event = c(102.54269505243633, 322.13006815203613, 428.2303047466704)
+  ) |>
+    structure(
+      compare_with_design = "yes",
+      design_type = "two-sided",
+      class = c("simtrial_gs_wlr", "data.frame"),
+      method = "FH(rho=0, gamma=0.5)"
+    )
+  expect_equal(observed, expected)
+})

From c4e7b666db252d4e282b591ae174a0059e55b018 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Tue, 24 Sep 2024 11:31:58 -0400
Subject: [PATCH 5/5] Fix sign of Z for summary.simtrial_gs_wlr()

https://github.com/Merck/simtrial/pull/282#issuecomment-2369432857
https://github.com/Merck/simtrial/pull/272
https://github.com/Merck/simtrial/issues/271
---
 DESCRIPTION                               | 2 +-
 R/summary.R                               | 2 +-
 tests/testthat/test-unvalidated-summary.R | 4 ++--
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5cd40db5..7171daaf 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.4.1.10
+Version: 0.4.1.11
 Authors@R: c(
     person("Keaven", "Anderson", email = "keaven_anderson@merck.com", role = c("aut")),
     person("Yujie", "Zhao", email = "yujie.zhao@merck.com", role =  c("ctb","cre")),
diff --git a/R/summary.R b/R/summary.R
index 79abce9c..ce685151 100644
--- a/R/summary.R
+++ b/R/summary.R
@@ -103,7 +103,7 @@ summary.simtrial_gs_wlr <- function(object,
 
     ans2 <- object |>
       dplyr::left_join(data.frame(analysis = 1:n_analysis, upper_bound = bound)) |>
-      dplyr::mutate(cross_upper = -z >= upper_bound) |>
+      dplyr::mutate(cross_upper = z >= upper_bound) |>
       dplyr::filter(cross_upper == TRUE) |>
       dplyr::group_by(sim_id) |>
       dplyr::filter(dplyr::row_number() == 1) |>
diff --git a/tests/testthat/test-unvalidated-summary.R b/tests/testthat/test-unvalidated-summary.R
index 700e36f3..d637e5a7 100644
--- a/tests/testthat/test-unvalidated-summary.R
+++ b/tests/testthat/test-unvalidated-summary.R
@@ -59,7 +59,7 @@ test_that("summary.simtrial_gs_wlr() returns consistent results for one-sided de
     sim_n = c(369.3333333333333, 505, 505),
     sim_event = c(97, 305, 405),
     sim_time = c(12.877359569828519, 24.990283397668506, 37.20491262038222),
-    sim_upper_prob = rep(NA_real_, 3L)
+    sim_upper_prob = c(NA, 1, NA)
   ) |>
     structure(
       class = c("simtrial_gs_wlr", "data.frame"),
@@ -149,7 +149,7 @@ test_that("summary.simtrial_gs_wlr() returns consistent results for two-sided de
     sim_n = c(366.6666666666667, 535, 535),
     sim_event = c(103, 323, 429),
     sim_time = c(12.363838412468121, 24.374413483785986, 36.116791896100885),
-    sim_upper_prob = rep(NA_real_, 3L)
+    sim_upper_prob = c(NA, 0.6666666666666666, 1)
   ) |>
     structure(
       compare_with_design = "no",