From 5678911fd759141c62dd258eaa07a3cab4efbcd6 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 22 Feb 2024 13:44:42 -0500
Subject: [PATCH 01/13] Convert `example("sim_gs_n")` to tests from commit
 306de0d

---
 tests/testthat/test-unvalidated-sim_gs_n.R | 216 +++++++++++++++++++++
 1 file changed, 216 insertions(+)
 create mode 100644 tests/testthat/test-unvalidated-sim_gs_n.R

diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
new file mode 100644
index 00000000..06f1cf18
--- /dev/null
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -0,0 +1,216 @@
+# 2024-02-22: Converted `example("sim_gs_n")` to tests from commit 306de0d
+# https://github.com/Merck/simtrial/tree/306de0dbe380fdb1e906a59f34bf3871d3ee5312
+
+library(gsDesign2)
+# parameters for enrollment
+enroll_rampup_duration <- 4 # duration for enrollment ramp up
+enroll_duration <- 16       # total enrollment duration
+enroll_rate <- 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_col <- 9             # survival median of the control arm
+median_exp <- c(9, 14)      # survival median of the experimental arm
+dropout_rate <- 0.001
+fail_rate <- define_fail_rate(duration = c(delay_effect_duration, 100),
+                              fail_rate = log(2) /  median_col,
+                              hr = median_col / 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 (exp:col)
+# Define cuttings of 2 IAs and 1 FA
+# IA1
+# The 1st interim analysis will occur at the later of the following 3 conditions:
+# - At least 20 months have passed since the start of the study
+# - At least 100 events have occurred
+# - At least 20 months have elapsed after enrolling 200/400 subjects, with a
+#   minimum of 20 months follow-up
+# However, if events accumulation is slow, we will wait for a maximum of 24 months.
+ia1 <- get_analysis_date(data,
+                         planned_calendar_time = 20,
+                         target_event_overall = 100,
+                         max_extension_for_target_event = 24,
+                         min_n_overall = 200,
+                         min_followup = 20) |> quote()
+# IA2
+# The 2nd interim analysis will occur at the later of the following 3 conditions:
+# - At least 32 months have passed since the start of the study
+# - At least 250 events have occurred
+# - At least 10 months after IA1
+# However, if events accumulation is slow, we will wait for a maximum of 34 months.
+ia2 <- get_analysis_date(data,
+                         planned_calendar_time = 32,
+                         target_event_overall = 200,
+                         max_extension_for_target_event = 34,
+                         min_time_after_previous_analysis = 10) |> quote()
+# FA
+# The final analysis will occur at the later of the following 2 conditions:
+# - At least 45 months have passed since the start of the study
+# - At least 300 events have occurred
+fa <- get_analysis_date(data,
+                        planned_calendar_time = 45,
+                        target_event_overall = 350) |> quote()
+
+
+test_that("Test 1: regular logrank test", {
+  observed <- sim_gs_n(
+    n_sim = 3,
+    sample_size = 400,
+    enroll_rate = enroll_rate,
+    fail_rate = fail_rate,
+    test = wlr(data, weight = fh(rho = 0, gamma = 0)) |> quote(),
+    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    seed = 2024
+  )
+  expected <- data.frame(
+    rho = numeric(9),
+    gamma = numeric(9),
+    z = c(
+      -3.7486049782713247, -4.53034007934394, -4.316452743033609,
+      -3.4771440155825752, -3.8631501353780324, -3.2777779731288317,
+      -3.075862925191481, -3.619345457605645, -4.2225917786532925
+    ),
+    analysis = rep(1:3, 3),
+    cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699),
+    sim_id = rep(1:3, each = 3L)
+  )
+  expect_equal(observed, expected)
+})
+
+test_that("Test 2: weighted logrank test by FH(0, 0.5)", {
+  observed <- sim_gs_n(
+    n_sim = 3,
+    sample_size = 400,
+    enroll_rate = enroll_rate,
+    fail_rate = fail_rate,
+    test = wlr(data, weight = fh(rho = 0, gamma = 0.5)) |> quote(),
+    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    seed = 2024
+  )
+  expected <- data.frame(
+    rho = numeric(9),
+    gamma = rep(0.5, 9L),
+    z = c(
+      -4.149161171743935, -4.778107819550277, -4.2607297587160256,
+      -3.605092910242299, -3.945081123231263, -2.919179640988388,
+      -3.1432278107909206, -3.640458610667732, -4.243289152457
+    ),
+    analysis = rep(1:3, 3),
+    cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699),
+    sim_id = rep(1:3, each = 3L)
+  )
+  expect_equal(observed, expected)
+})
+
+test_that("Test 3: weighted logrank test by MB(6)", {
+  observed <- sim_gs_n(
+    n_sim = 3,
+    sample_size = 400,
+    enroll_rate = enroll_rate,
+    fail_rate = fail_rate,
+    test = wlr(data, weight = mb(delay = 3)) |> quote(),
+    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    seed = 2024
+  )
+  expected <- data.frame(
+    z = c(
+      -3.797133894694147, -4.581330588107247, -4.3496437937060906,
+      -3.5011312494121394, -3.886541892591609, -3.2792862684447983,
+      -3.114079263266195, -3.6587146250230145, -4.2632793831797855
+    ),
+    analysis = rep(1:3, 3),
+    cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699),
+    sim_id = rep(1:3, each = 3L)
+  )
+  expect_equal(observed, expected)
+})
+
+test_that("Test 4: weighted logrank test by early zero (6)", {
+  observed <- sim_gs_n(
+    n_sim = 3,
+    sample_size = 400,
+    enroll_rate = enroll_rate,
+    fail_rate = fail_rate,
+    test = wlr(data, weight = early_zero(6)) |> quote(),
+    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    seed = 2024
+  )
+  expected <- data.frame(
+    z = c(
+      -4.552617167258777, -5.188572984743822, -4.686073828268738,
+      -3.185533497487861, -3.5975030245947046, -2.786930008687834,
+      -2.3673440974318556, -3.0630537456426414, -3.7816194091003705
+    ),
+    analysis = rep(1:3, 3),
+    cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699),
+    sim_id = rep(1:3, each = 3L)
+  )
+  expect_equal(observed, expected)
+})
+
+test_that("Test 5: RMST", {
+  observed <- sim_gs_n(
+    n_sim = 3,
+    sample_size = 400,
+    enroll_rate = enroll_rate,
+    fail_rate = fail_rate,
+    test = rmst(data, tau = 20) |> quote(),
+    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    seed = 2024
+  )
+  expected <- data.frame(
+    rmst_arm1 = c(
+      12.466259284156251, 12.444204897288326, 12.425100778728808,
+      12.392111715564337, 12.496963791557544, 12.479119007501355, 12.62769367846186,
+      12.737915554271744, 12.740241766667666
+    ),
+    rmst_arm0 = c(
+      9.585107633112955, 9.591073977478539, 9.590592780789704, 9.824721964671674,
+      10.097271436421035, 10.110783864663125, 10.340195893022198,
+      10.289798076615766, 10.261299533752227
+    ),
+    rmst_diff = c(
+      2.8811516510432966, 2.8531309198097876, 2.834507997939104, 2.567389750892662,
+      2.3996923551365086, 2.36833514283823, 2.287497785439662, 2.4481174776559786,
+      2.478942232915438
+    ),
+    z = c(
+      3.7899815357169184, 3.991862864282945, 3.980100861311682, 3.474868814723485,
+      3.2950209410683957, 3.2541151987300845, 2.9805344295194454,
+      3.3009521580248022, 3.3504301652133
+    ),
+    analysis = rep(1:3, 3),
+    cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699),
+    sim_id = rep(1:3, each = 3L)
+  )
+  expect_equal(observed, expected)
+})
+
+
+test_that("Test 6: maxcombo (FH(0,0) + FH(0, 0.5))", {
+  observed <- sim_gs_n(
+    n_sim = 3,
+    sample_size = 400,
+    enroll_rate = enroll_rate,
+    fail_rate = fail_rate,
+    test = maxcombo(data,
+                    test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
+                    test2 = wlr(data, rho = 0, gamma = 0.5) |> quote()) |> quote(),
+    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    seed = 2024
+  )
+  expected <- data.frame(
+    p_value = c(
+      2.6155386454673746e-05, 1.4330486162172917e-06, 1.247801863046849e-05,
+      0.0002358380298724816, 6.130077643518028e-05, 0.0007667834024346343,
+      0.001216230102102256, 0.00020471863687732128, 1.7249355113824194e-05
+    ),
+    analysis = rep(1:3, 3),
+    cut_date = c(24, 32, 45, 24, 32, 46.219327415802894, 24, 32, 50.86585486314699),
+    sim_id = rep(1:3, each = 3L)
+  )
+  expect_equal(observed, expected)
+})

From da12f83d9c28c3476fa99a742d8301a1a2d4c1df Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 22 Feb 2024 13:58:47 -0500
Subject: [PATCH 02/13] Pass test function args via ... for sim_gs_n()

---
 DESCRIPTION                                |  2 +-
 R/sim_gs_n.R                               | 47 +++++++++++++---------
 man/sim_gs_n.Rd                            | 45 +++++++++++++--------
 tests/testthat/test-unvalidated-sim_gs_n.R | 34 +++++++++-------
 4 files changed, 77 insertions(+), 51 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5f26d104..0293b865 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.3.2.4
+Version: 0.3.2.5
 Authors@R: c(
     person("Keaven", "Anderson", email = "keaven_anderson@merck.com", role = c("aut")),
     person("Yilong", "Zhang", email = "elong0527@gmail.com", role =  c("aut")),
diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index b7463903..ab0c07de 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -18,9 +18,13 @@
 
 #' Simulate group sequantial designs with fixed sample size
 #' @inheritParams sim_fixed_n
-#' @param test a functional call of the test such as \code{wlr()} or \code{maxcombo()}
+#' @param test a test function such as \code{\link{wlr}},
+#'   \code{\link{maxcombo}}, or \code{\link{rmst}}. The simulated data set is
+#'   passed as the first positional argument to the test function provided.
 #' @param cutting a functional call of the cutting for IA(s) and FA, see examples
 #' @param seed random seed
+#' @param ... Arguments passed to the test function provided by the argument
+#'   \code{test}
 #'
 #' @return a data frame summaring the simulation ID, analysis date, z statistics or p-values
 #' @export
@@ -91,9 +95,10 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = wlr(data, weight = fh(rho = 0, gamma = 0)) |> quote(),
+#'   test = wlr,
 #'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-#'   seed = 2024)
+#'   seed = 2024,
+#'   weight = fh(rho = 0, gamma = 0))
 #'
 #' # Test 2: weighted logrank test by FH(0, 0.5)
 #' sim_gs_n(
@@ -101,9 +106,10 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = wlr(data, weight = fh(rho = 0, gamma = 0.5)) |> quote(),
+#'   test = wlr,
 #'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-#'   seed = 2024)
+#'   seed = 2024,
+#'   weight = fh(rho = 0, gamma = 0.5))
 #'
 #'
 #' # Test 3: weighted logrank test by MB(6)
@@ -112,9 +118,10 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = wlr(data, weight = mb(delay = 3)) |> quote(),
+#'   test = wlr,
 #'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-#'   seed = 2024)
+#'   seed = 2024,
+#'   weight = mb(delay = 3))
 #'
 #' # Test 4: weighted logrank test by early zero (6)
 #' sim_gs_n(
@@ -122,9 +129,10 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = wlr(data, weight = early_zero(6)) |> quote(),
+#'   test = wlr,
 #'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-#'   seed = 2024)
+#'   seed = 2024,
+#'   weight = early_zero(6))
 #'
 #' # Test 5: RMST
 #' sim_gs_n(
@@ -132,9 +140,10 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = rmst(data, tau = 20) |> quote(),
+#'   test = rmst,
 #'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-#'   seed = 2024)
+#'   seed = 2024,
+#'   tau = 20)
 #'
 #' # Test 6: maxcombo (FH(0,0) + FH(0, 0.5))
 #' sim_gs_n(
@@ -142,11 +151,11 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = maxcombo(data,
-#'                   test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-#'                   test2 = wlr(data, rho = 0, gamma = 0.5) |> quote()) |> quote(),
+#'   test = maxcombo,
 #'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-#'   seed = 2024)
+#'   seed = 2024,
+#'   test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
+#'   test2 = wlr(data, rho = 0, gamma = 0.5) |> quote())
 sim_gs_n <- function(
     # number of simulations
   n_sim = 1000,
@@ -168,11 +177,13 @@ sim_gs_n <- function(
   block = rep(c("experimental", "control"), 2),
   # default is to to logrank testing
   # but alternative tests (such as rmst, maxcombo) can be specified
-  test = wlr(weight = fh(rho = 0, gamma = 0)) |> quote(),
+  test = wlr,
   # cutting for IA(s) and FA
   cutting = NULL,
   # random seed
-  seed = 2024
+  seed = 2024,
+  # arguments passed to `test`
+  ...
 ){
   # input checking
   # TODO
@@ -208,7 +219,7 @@ sim_gs_n <- function(
       simu_data_cut <- simu_data |> cut_data_by_date(cut_date[i_analysis])
 
       # test
-      ans_1sim_new <- eval(test, envir = rlang::env(data = simu_data_cut))
+      ans_1sim_new <- test(simu_data_cut, ...)
       ans_1sim_new$analysis <- i_analysis
       ans_1sim_new$cut_date <- cut_date[i_analysis]
       ans_1sim_new$sim_id <- sim_id
diff --git a/man/sim_gs_n.Rd b/man/sim_gs_n.Rd
index 728a7079..0191f0f1 100644
--- a/man/sim_gs_n.Rd
+++ b/man/sim_gs_n.Rd
@@ -12,9 +12,10 @@ sim_gs_n(
   fail_rate = data.frame(stratum = "All", duration = c(3, 100), fail_rate = log(2)/c(9,
     18), hr = c(0.9, 0.6), dropout_rate = rep(0.001, 2)),
   block = rep(c("experimental", "control"), 2),
-  test = quote(wlr(weight = fh(rho = 0, gamma = 0))),
+  test = wlr,
   cutting = NULL,
-  seed = 2024
+  seed = 2024,
+  ...
 )
 }
 \arguments{
@@ -35,11 +36,16 @@ for experimental vs. control, and dropout rates by stratum and time period.}
 \item{block}{As in \code{\link[=sim_pw_surv]{sim_pw_surv()}}. Vector of treatments to be included
 in each block.}
 
-\item{test}{a functional call of the test such as \code{wlr()} or \code{maxcombo()}}
+\item{test}{a test function such as \code{\link{wlr}},
+\code{\link{maxcombo}}, or \code{\link{rmst}}. The simulated data set is
+passed as the first positional argument to the test function provided.}
 
 \item{cutting}{a functional call of the cutting for IA(s) and FA, see examples}
 
 \item{seed}{random seed}
+
+\item{...}{Arguments passed to the test function provided by the argument
+\code{test}}
 }
 \value{
 a data frame summaring the simulation ID, analysis date, z statistics or p-values
@@ -113,9 +119,10 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = wlr(data, weight = fh(rho = 0, gamma = 0)) |> quote(),
+  test = wlr,
   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-  seed = 2024)
+  seed = 2024,
+  weight = fh(rho = 0, gamma = 0))
 
 # Test 2: weighted logrank test by FH(0, 0.5)
 sim_gs_n(
@@ -123,9 +130,10 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = wlr(data, weight = fh(rho = 0, gamma = 0.5)) |> quote(),
+  test = wlr,
   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-  seed = 2024)
+  seed = 2024,
+  weight = fh(rho = 0, gamma = 0.5))
 
 
 # Test 3: weighted logrank test by MB(6)
@@ -134,9 +142,10 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = wlr(data, weight = mb(delay = 3)) |> quote(),
+  test = wlr,
   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-  seed = 2024)
+  seed = 2024,
+  weight = mb(delay = 3))
 
 # Test 4: weighted logrank test by early zero (6)
 sim_gs_n(
@@ -144,9 +153,10 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = wlr(data, weight = early_zero(6)) |> quote(),
+  test = wlr,
   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-  seed = 2024)
+  seed = 2024,
+  weight = early_zero(6))
 
 # Test 5: RMST
 sim_gs_n(
@@ -154,9 +164,10 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = rmst(data, tau = 20) |> quote(),
+  test = rmst,
   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-  seed = 2024)
+  seed = 2024,
+  tau = 20)
 
 # Test 6: maxcombo (FH(0,0) + FH(0, 0.5))
 sim_gs_n(
@@ -164,9 +175,9 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = maxcombo(data,
-                  test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-                  test2 = wlr(data, rho = 0, gamma = 0.5) |> quote()) |> quote(),
+  test = maxcombo,
   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-  seed = 2024)
+  seed = 2024,
+  test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
+  test2 = wlr(data, rho = 0, gamma = 0.5) |> quote())
 }
diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
index 06f1cf18..83dc4e35 100644
--- a/tests/testthat/test-unvalidated-sim_gs_n.R
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -61,9 +61,10 @@ test_that("Test 1: regular logrank test", {
     sample_size = 400,
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
-    test = wlr(data, weight = fh(rho = 0, gamma = 0)) |> quote(),
+    test = wlr,
     cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-    seed = 2024
+    seed = 2024,
+    weight = fh(rho = 0, gamma = 0)
   )
   expected <- data.frame(
     rho = numeric(9),
@@ -86,9 +87,10 @@ test_that("Test 2: weighted logrank test by FH(0, 0.5)", {
     sample_size = 400,
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
-    test = wlr(data, weight = fh(rho = 0, gamma = 0.5)) |> quote(),
+    test = wlr,
     cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-    seed = 2024
+    seed = 2024,
+    weight = fh(rho = 0, gamma = 0.5)
   )
   expected <- data.frame(
     rho = numeric(9),
@@ -111,9 +113,10 @@ test_that("Test 3: weighted logrank test by MB(6)", {
     sample_size = 400,
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
-    test = wlr(data, weight = mb(delay = 3)) |> quote(),
+    test = wlr,
     cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-    seed = 2024
+    seed = 2024,
+    weight = mb(delay = 3)
   )
   expected <- data.frame(
     z = c(
@@ -134,9 +137,10 @@ test_that("Test 4: weighted logrank test by early zero (6)", {
     sample_size = 400,
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
-    test = wlr(data, weight = early_zero(6)) |> quote(),
+    test = wlr,
     cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-    seed = 2024
+    seed = 2024,
+    weight = early_zero(6)
   )
   expected <- data.frame(
     z = c(
@@ -157,9 +161,10 @@ test_that("Test 5: RMST", {
     sample_size = 400,
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
-    test = rmst(data, tau = 20) |> quote(),
+    test = rmst,
     cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-    seed = 2024
+    seed = 2024,
+    tau = 20
   )
   expected <- data.frame(
     rmst_arm1 = c(
@@ -189,18 +194,17 @@ test_that("Test 5: RMST", {
   expect_equal(observed, expected)
 })
 
-
 test_that("Test 6: maxcombo (FH(0,0) + FH(0, 0.5))", {
   observed <- sim_gs_n(
     n_sim = 3,
     sample_size = 400,
     enroll_rate = enroll_rate,
     fail_rate = fail_rate,
-    test = maxcombo(data,
-                    test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-                    test2 = wlr(data, rho = 0, gamma = 0.5) |> quote()) |> quote(),
+    test = maxcombo,
     cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
-    seed = 2024
+    seed = 2024,
+    test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
+    test2 = wlr(data, rho = 0, gamma = 0.5) |> quote()
   )
   expected <- data.frame(
     p_value = c(

From 013ed5e2a0ef3881b5723b1a7fa848917a50bad5 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 22 Feb 2024 14:34:56 -0500
Subject: [PATCH 03/13] Use function factory create_cutting() to pass cutting
 functions

---
 DESCRIPTION                                |  3 +-
 NAMESPACE                                  |  1 +
 R/sim_gs_n.R                               | 77 +++++++++++++++-------
 man/create_cutting.Rd                      | 36 ++++++++++
 man/sim_gs_n.Rd                            | 40 ++++++-----
 tests/testthat/test-unvalidated-sim_gs_n.R | 32 ++++-----
 6 files changed, 132 insertions(+), 57 deletions(-)
 create mode 100644 man/create_cutting.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index 0293b865..903d2d6c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.3.2.5
+Version: 0.3.2.6
 Authors@R: c(
     person("Keaven", "Anderson", email = "keaven_anderson@merck.com", role = c("aut")),
     person("Yilong", "Zhang", email = "elong0527@gmail.com", role =  c("aut")),
@@ -44,7 +44,6 @@ Imports:
     future,
     methods,
     mvtnorm,
-    rlang,
     stats,
     survival,
     utils
diff --git a/NAMESPACE b/NAMESPACE
index 20a05c2a..c42f556d 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(counting_process)
+export(create_cutting)
 export(cut_data_by_date)
 export(cut_data_by_event)
 export(early_zero)
diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index ab0c07de..e948d6b1 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -16,17 +16,18 @@
 #  You should have received a copy of the GNU General Public License
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
-#' Simulate group sequantial designs with fixed sample size
+#' Simulate group sequential designs with fixed sample size
 #' @inheritParams sim_fixed_n
 #' @param test a test function such as \code{\link{wlr}},
 #'   \code{\link{maxcombo}}, or \code{\link{rmst}}. The simulated data set is
 #'   passed as the first positional argument to the test function provided.
-#' @param cutting a functional call of the cutting for IA(s) and FA, see examples
+#' @param cutting a list of cutting functions created by
+#'   \code{\link{create_cutting}}, see examples
 #' @param seed random seed
 #' @param ... Arguments passed to the test function provided by the argument
 #'   \code{test}
 #'
-#' @return a data frame summaring the simulation ID, analysis date, z statistics or p-values
+#' @return a data frame summarizing the simulation ID, analysis date, z statistics or p-values
 #' @export
 #'
 #' @examples
@@ -62,12 +63,13 @@
 #' # - At least 20 months have elapsed after enrolling 200/400 subjects, with a
 #' #   minimum of 20 months follow-up
 #' # However, if events accumulation is slow, we will wait for a maximum of 24 months.
-#' ia1 <- get_analysis_date(data,
-#'                          planned_calendar_time = 20,
-#'                          target_event_overall = 100,
-#'                          max_extension_for_target_event = 24,
-#'                          min_n_overall = 200,
-#'                          min_followup = 20) |> quote()
+#' ia1 <- create_cutting(
+#'   planned_calendar_time = 20,
+#'   target_event_overall = 100,
+#'   max_extension_for_target_event = 24,
+#'   min_n_overall = 200,
+#'   min_followup = 20
+#' )
 #'
 #' # IA2
 #' # The 2nd interim analysis will occur at the later of the following 3 conditions:
@@ -75,19 +77,21 @@
 #' # - At least 250 events have occurred
 #' # - At least 10 months after IA1
 #' # However, if events accumulation is slow, we will wait for a maximum of 34 months.
-#' ia2 <- get_analysis_date(data,
-#'                          planned_calendar_time = 32,
-#'                          target_event_overall = 200,
-#'                          max_extension_for_target_event = 34,
-#'                          min_time_after_previous_analysis = 10) |> quote()
+#' ia2 <- create_cutting(
+#'   planned_calendar_time = 32,
+#'   target_event_overall = 200,
+#'   max_extension_for_target_event = 34,
+#'   min_time_after_previous_analysis = 10
+#' )
 #'
 #' # FA
 #' # The final analysis will occur at the later of the following 2 conditions:
 #' # - At least 45 months have passed since the start of the study
 #' # - At least 300 events have occurred
-#' fa <- get_analysis_date(data,
-#'                        planned_calendar_time = 45,
-#'                        target_event_overall = 350) |> quote()
+#' fa <- create_cutting(
+#'   planned_calendar_time = 45,
+#'   target_event_overall = 350
+#' )
 #'
 #' # Test 1: regular logrank test
 #' sim_gs_n(
@@ -209,11 +213,7 @@ sim_gs_n <- function(
     for (i_analysis in 1:n_analysis) {
 
       # get cut date
-      if (i_analysis < n_analysis) {
-        cut_date[i_analysis] <- cutting[[paste0("ia", i_analysis)]] |> eval(envir = rlang::env(data = simu_data))
-      } else {
-        cut_date[i_analysis] <- cutting[["fa"]] |> eval(envir = rlang::env(data = simu_data))
-      }
+      cut_date[i_analysis] <- cutting[[i_analysis]](data = simu_data)
 
       # cut the data
       simu_data_cut <- simu_data |> cut_data_by_date(cut_date[i_analysis])
@@ -232,3 +232,36 @@ sim_gs_n <- function(
   }
   return(ans)
 }
+
+#' Create a cutting function
+#'
+#' Create a cutting function for use with \code{\link{sim_gs_n}}
+#'
+#' @param ... Arguments passed to \code{\link{get_analysis_date}}
+#'
+#' @return A function that accepts a data frame of simulated trial data and
+#'   returns a cut date
+#'
+#' @export
+#'
+#' @seealso \code{\link{get_analysis_date}}, \code{\link{sim_gs_n}}
+#'
+#' @examples
+#' # Simulate trial data
+#' trial_data <- sim_pw_surv()
+#'
+#' # Create a cutting function that applies the following 2 conditions:
+#' # - At least 45 months have passed since the start of the study
+#' # - At least 300 events have occurred
+#' cutting <- create_cutting(
+#'   planned_calendar_time = 45,
+#'   target_event_overall = 350
+#' )
+#'
+#' # Cut the trial data
+#' cutting(trial_data)
+create_cutting <- function(...) {
+  function(data) {
+    get_analysis_date(data, ...)
+  }
+}
diff --git a/man/create_cutting.Rd b/man/create_cutting.Rd
new file mode 100644
index 00000000..9e7b70eb
--- /dev/null
+++ b/man/create_cutting.Rd
@@ -0,0 +1,36 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/sim_gs_n.R
+\name{create_cutting}
+\alias{create_cutting}
+\title{Create a cutting function}
+\usage{
+create_cutting(...)
+}
+\arguments{
+\item{...}{Arguments passed to \code{\link{get_analysis_date}}}
+}
+\value{
+A function that accepts a data frame of simulated trial data and
+returns a cut date
+}
+\description{
+Create a cutting function for use with \code{\link{sim_gs_n}}
+}
+\examples{
+# Simulate trial data
+trial_data <- sim_pw_surv()
+
+# Create a cutting function that applies the following 2 conditions:
+# - At least 45 months have passed since the start of the study
+# - At least 300 events have occurred
+cutting <- create_cutting(
+  planned_calendar_time = 45,
+  target_event_overall = 350
+)
+
+# Cut the trial data
+cutting(trial_data)
+}
+\seealso{
+\code{\link{get_analysis_date}}, \code{\link{sim_gs_n}}
+}
diff --git a/man/sim_gs_n.Rd b/man/sim_gs_n.Rd
index 0191f0f1..95a798e5 100644
--- a/man/sim_gs_n.Rd
+++ b/man/sim_gs_n.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/sim_gs_n.R
 \name{sim_gs_n}
 \alias{sim_gs_n}
-\title{Simulate group sequantial designs with fixed sample size}
+\title{Simulate group sequential designs with fixed sample size}
 \usage{
 sim_gs_n(
   n_sim = 1000,
@@ -40,7 +40,8 @@ in each block.}
 \code{\link{maxcombo}}, or \code{\link{rmst}}. The simulated data set is
 passed as the first positional argument to the test function provided.}
 
-\item{cutting}{a functional call of the cutting for IA(s) and FA, see examples}
+\item{cutting}{a list of cutting functions created by
+\code{\link{create_cutting}}, see examples}
 
 \item{seed}{random seed}
 
@@ -48,10 +49,10 @@ passed as the first positional argument to the test function provided.}
 \code{test}}
 }
 \value{
-a data frame summaring the simulation ID, analysis date, z statistics or p-values
+a data frame summarizing the simulation ID, analysis date, z statistics or p-values
 }
 \description{
-Simulate group sequantial designs with fixed sample size
+Simulate group sequential designs with fixed sample size
 }
 \examples{
 library(gsDesign2)
@@ -86,12 +87,13 @@ ratio <- 1                  # randomization ratio (exp:col)
 # - At least 20 months have elapsed after enrolling 200/400 subjects, with a
 #   minimum of 20 months follow-up
 # However, if events accumulation is slow, we will wait for a maximum of 24 months.
-ia1 <- get_analysis_date(data,
-                         planned_calendar_time = 20,
-                         target_event_overall = 100,
-                         max_extension_for_target_event = 24,
-                         min_n_overall = 200,
-                         min_followup = 20) |> quote()
+ia1 <- create_cutting(
+  planned_calendar_time = 20,
+  target_event_overall = 100,
+  max_extension_for_target_event = 24,
+  min_n_overall = 200,
+  min_followup = 20
+)
 
 # IA2
 # The 2nd interim analysis will occur at the later of the following 3 conditions:
@@ -99,19 +101,21 @@ ia1 <- get_analysis_date(data,
 # - At least 250 events have occurred
 # - At least 10 months after IA1
 # However, if events accumulation is slow, we will wait for a maximum of 34 months.
-ia2 <- get_analysis_date(data,
-                         planned_calendar_time = 32,
-                         target_event_overall = 200,
-                         max_extension_for_target_event = 34,
-                         min_time_after_previous_analysis = 10) |> quote()
+ia2 <- create_cutting(
+  planned_calendar_time = 32,
+  target_event_overall = 200,
+  max_extension_for_target_event = 34,
+  min_time_after_previous_analysis = 10
+)
 
 # FA
 # The final analysis will occur at the later of the following 2 conditions:
 # - At least 45 months have passed since the start of the study
 # - At least 300 events have occurred
-fa <- get_analysis_date(data,
-                       planned_calendar_time = 45,
-                       target_event_overall = 350) |> quote()
+fa <- create_cutting(
+  planned_calendar_time = 45,
+  target_event_overall = 350
+)
 
 # Test 1: regular logrank test
 sim_gs_n(
diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
index 83dc4e35..c3fa803e 100644
--- a/tests/testthat/test-unvalidated-sim_gs_n.R
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -29,31 +29,33 @@ ratio <- 1                  # randomization ratio (exp:col)
 # - At least 20 months have elapsed after enrolling 200/400 subjects, with a
 #   minimum of 20 months follow-up
 # However, if events accumulation is slow, we will wait for a maximum of 24 months.
-ia1 <- get_analysis_date(data,
-                         planned_calendar_time = 20,
-                         target_event_overall = 100,
-                         max_extension_for_target_event = 24,
-                         min_n_overall = 200,
-                         min_followup = 20) |> quote()
+ia1 <- create_cutting(
+  planned_calendar_time = 20,
+  target_event_overall = 100,
+  max_extension_for_target_event = 24,
+  min_n_overall = 200,
+  min_followup = 20
+)
 # IA2
 # The 2nd interim analysis will occur at the later of the following 3 conditions:
 # - At least 32 months have passed since the start of the study
 # - At least 250 events have occurred
 # - At least 10 months after IA1
 # However, if events accumulation is slow, we will wait for a maximum of 34 months.
-ia2 <- get_analysis_date(data,
-                         planned_calendar_time = 32,
-                         target_event_overall = 200,
-                         max_extension_for_target_event = 34,
-                         min_time_after_previous_analysis = 10) |> quote()
+ia2 <- create_cutting(
+  planned_calendar_time = 32,
+  target_event_overall = 200,
+  max_extension_for_target_event = 34,
+  min_time_after_previous_analysis = 10
+)
 # FA
 # The final analysis will occur at the later of the following 2 conditions:
 # - At least 45 months have passed since the start of the study
 # - At least 300 events have occurred
-fa <- get_analysis_date(data,
-                        planned_calendar_time = 45,
-                        target_event_overall = 350) |> quote()
-
+fa <- create_cutting(
+  planned_calendar_time = 45,
+  target_event_overall = 350
+)
 
 test_that("Test 1: regular logrank test", {
   observed <- sim_gs_n(

From e1b35d17915703e63a57d9947f4cd5d62231aaf6 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 22 Feb 2024 14:50:40 -0500
Subject: [PATCH 04/13] Update copyright year

---
 LICENSE                      | 4 ++--
 R/counting_process.R         | 2 +-
 R/cut_data_by_date.R         | 2 +-
 R/cut_data_by_event.R        | 2 +-
 R/early_zero_weight.R        | 2 +-
 R/ex1_delayed_effect.R       | 2 +-
 R/ex2_delayed_effect.R       | 2 +-
 R/ex3_cure_with_ph.R         | 2 +-
 R/ex4_belly.R                | 2 +-
 R/ex5_widening.R             | 2 +-
 R/ex6_crossing.R             | 2 +-
 R/fh_weight.R                | 2 +-
 R/fit_pwexp.R                | 2 +-
 R/get_analysis_date.R        | 2 +-
 R/get_cut_date_by_event.R    | 2 +-
 R/global.R                   | 2 +-
 R/input_checking.R           | 2 +-
 R/maxcombo.R                 | 2 +-
 R/mb_delayed_effect.R        | 2 +-
 R/mb_weight.R                | 2 +-
 R/pvalue_maxcombo.R          | 2 +-
 R/randomize_by_fixed_block.R | 2 +-
 R/rpwexp.R                   | 2 +-
 R/rpwexp_enroll.R            | 2 +-
 R/rpwexp_naive.R             | 2 +-
 R/sim_fixed_n.R              | 2 +-
 R/sim_gs_n.R                 | 2 +-
 R/sim_pw_surv.R              | 2 +-
 R/simtrial-package.R         | 2 +-
 R/to_sim_pw_surv.R           | 2 +-
 R/wlr.R                      | 2 +-
 R/wlr_weight.R               | 2 +-
 _pkgdown.yml                 | 2 +-
 33 files changed, 34 insertions(+), 34 deletions(-)

diff --git a/LICENSE b/LICENSE
index 603d1e58..2e3e301d 100644
--- a/LICENSE
+++ b/LICENSE
@@ -632,7 +632,7 @@ state the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
 
     simtrial: Clinical Trial Simulation
-    Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
+    Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
 
     This program is free software: you can redistribute it and/or modify
     it under the terms of the GNU General Public License as published by
@@ -652,7 +652,7 @@ Also add information on how to contact you by electronic and paper mail.
   If the program does terminal interaction, make it output a short
 notice like this when it starts in an interactive mode:
 
-    simtrial  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
+    simtrial  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.
     This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
     This is free software, and you are welcome to redistribute it
     under certain conditions; type `show c' for details.
diff --git a/R/counting_process.R b/R/counting_process.R
index 288a8376..02751327 100644
--- a/R/counting_process.R
+++ b/R/counting_process.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/cut_data_by_date.R b/R/cut_data_by_date.R
index d8224c76..90bc9747 100644
--- a/R/cut_data_by_date.R
+++ b/R/cut_data_by_date.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/cut_data_by_event.R b/R/cut_data_by_event.R
index c17c6d15..3667d8f7 100644
--- a/R/cut_data_by_event.R
+++ b/R/cut_data_by_event.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/early_zero_weight.R b/R/early_zero_weight.R
index 42e769a9..3ee012c6 100644
--- a/R/early_zero_weight.R
+++ b/R/early_zero_weight.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex1_delayed_effect.R b/R/ex1_delayed_effect.R
index f8dd7acb..debb3177 100644
--- a/R/ex1_delayed_effect.R
+++ b/R/ex1_delayed_effect.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex2_delayed_effect.R b/R/ex2_delayed_effect.R
index 69bd3375..6546d0af 100644
--- a/R/ex2_delayed_effect.R
+++ b/R/ex2_delayed_effect.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex3_cure_with_ph.R b/R/ex3_cure_with_ph.R
index 9071b160..20975c4c 100644
--- a/R/ex3_cure_with_ph.R
+++ b/R/ex3_cure_with_ph.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex4_belly.R b/R/ex4_belly.R
index 835f10d6..60ce29a2 100644
--- a/R/ex4_belly.R
+++ b/R/ex4_belly.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex5_widening.R b/R/ex5_widening.R
index 7e19ec38..c4b489f9 100644
--- a/R/ex5_widening.R
+++ b/R/ex5_widening.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/ex6_crossing.R b/R/ex6_crossing.R
index 5ec12d78..1329db9c 100644
--- a/R/ex6_crossing.R
+++ b/R/ex6_crossing.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/fh_weight.R b/R/fh_weight.R
index 00dc7373..04d998b9 100644
--- a/R/fh_weight.R
+++ b/R/fh_weight.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/fit_pwexp.R b/R/fit_pwexp.R
index 13e0949c..cdd8d140 100644
--- a/R/fit_pwexp.R
+++ b/R/fit_pwexp.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/get_analysis_date.R b/R/get_analysis_date.R
index a703786c..7cbc987a 100644
--- a/R/get_analysis_date.R
+++ b/R/get_analysis_date.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/get_cut_date_by_event.R b/R/get_cut_date_by_event.R
index 1c6c311d..43e7e15d 100644
--- a/R/get_cut_date_by_event.R
+++ b/R/get_cut_date_by_event.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/global.R b/R/global.R
index 79176e64..71c2500d 100644
--- a/R/global.R
+++ b/R/global.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/input_checking.R b/R/input_checking.R
index af17165f..0aa90e69 100644
--- a/R/input_checking.R
+++ b/R/input_checking.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/maxcombo.R b/R/maxcombo.R
index ccad2fff..e6e9d971 100644
--- a/R/maxcombo.R
+++ b/R/maxcombo.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/mb_delayed_effect.R b/R/mb_delayed_effect.R
index 3a3cb042..56580361 100644
--- a/R/mb_delayed_effect.R
+++ b/R/mb_delayed_effect.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/mb_weight.R b/R/mb_weight.R
index ac78791b..7872774d 100644
--- a/R/mb_weight.R
+++ b/R/mb_weight.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/pvalue_maxcombo.R b/R/pvalue_maxcombo.R
index 71308428..273bd862 100644
--- a/R/pvalue_maxcombo.R
+++ b/R/pvalue_maxcombo.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/randomize_by_fixed_block.R b/R/randomize_by_fixed_block.R
index 5d0b0b67..995930ea 100644
--- a/R/randomize_by_fixed_block.R
+++ b/R/randomize_by_fixed_block.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/rpwexp.R b/R/rpwexp.R
index d05cc705..d2011b19 100644
--- a/R/rpwexp.R
+++ b/R/rpwexp.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/rpwexp_enroll.R b/R/rpwexp_enroll.R
index f3d1f6f4..c5e615c7 100644
--- a/R/rpwexp_enroll.R
+++ b/R/rpwexp_enroll.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/rpwexp_naive.R b/R/rpwexp_naive.R
index 64b83d3f..63a93140 100644
--- a/R/rpwexp_naive.R
+++ b/R/rpwexp_naive.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/sim_fixed_n.R b/R/sim_fixed_n.R
index d2e92acd..6348247f 100644
--- a/R/sim_fixed_n.R
+++ b/R/sim_fixed_n.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index e948d6b1..10bc59ca 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/sim_pw_surv.R b/R/sim_pw_surv.R
index 0c744b2a..f4189957 100644
--- a/R/sim_pw_surv.R
+++ b/R/sim_pw_surv.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/simtrial-package.R b/R/simtrial-package.R
index ec9503a0..6c225d57 100644
--- a/R/simtrial-package.R
+++ b/R/simtrial-package.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the pkglite program.
diff --git a/R/to_sim_pw_surv.R b/R/to_sim_pw_surv.R
index c589c008..537c4f1d 100644
--- a/R/to_sim_pw_surv.R
+++ b/R/to_sim_pw_surv.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/wlr.R b/R/wlr.R
index 3ef300e5..d9f8cd61 100644
--- a/R/wlr.R
+++ b/R/wlr.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/R/wlr_weight.R b/R/wlr_weight.R
index ff03e7ba..7428b487 100644
--- a/R/wlr_weight.R
+++ b/R/wlr_weight.R
@@ -1,4 +1,4 @@
-#  Copyright (c) 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
+#  Copyright (c) 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates.
 #  All rights reserved.
 #
 #  This file is part of the simtrial program.
diff --git a/_pkgdown.yml b/_pkgdown.yml
index ba44cdad..a3e6a003 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -20,7 +20,7 @@ footer:
     left: [developed_by, built_with, legal]
     right: [blank]
   components:
-    legal: "<br>Copyright &copy; 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved."
+    legal: "<br>Copyright &copy; 2024 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved."
     blank: "<span></span>"
 
 reference:

From e4dc1af7fee4eb98e7a9947511778b0a2c5b7bc1 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 22 Feb 2024 14:58:19 -0500
Subject: [PATCH 05/13] Apply Nan's code improvement suggestions

https://github.com/Merck/simtrial/pull/195#pullrequestreview-1876654204
---
 R/maxcombo.R   |  2 +-
 R/sim_gs_n.R   |  4 ++--
 R/wlr.R        |  6 +++---
 R/wlr_weight.R | 12 +++---------
 4 files changed, 9 insertions(+), 15 deletions(-)

diff --git a/R/maxcombo.R b/R/maxcombo.R
index e6e9d971..44000159 100644
--- a/R/maxcombo.R
+++ b/R/maxcombo.R
@@ -39,7 +39,7 @@ maxcombo <- function(data, test1, test2, ...){
   rho_vector <- NULL
   gamma_vector <- NULL
 
-  for (i in 1:n_test) {
+  for (i in seq_len(n_test)) {
     test_i <- get(paste0("test", i))
     rho_vector <- c(rho_vector, test_i$rho)
     gamma_vector <- c(gamma_vector, test_i$gamma)
diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index 10bc59ca..f6ca2b99 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -194,7 +194,7 @@ sim_gs_n <- function(
 
   # simulate for n_sim times
   ans <- NULL
-  for (sim_id in 1:n_sim) {
+  for (sim_id in seq_len(n_sim)) {
     set.seed(seed + sim_id)
     # generate data
     simu_data <- sim_pw_surv(
@@ -210,7 +210,7 @@ sim_gs_n <- function(
     cut_date <- rep(-100, n_analysis)
     ans_1sim <- NULL
 
-    for (i_analysis in 1:n_analysis) {
+    for (i_analysis in seq_len(n_analysis)) {
 
       # get cut date
       cut_date[i_analysis] <- cutting[[i_analysis]](data = simu_data)
diff --git a/R/wlr.R b/R/wlr.R
index d9f8cd61..84c9d1fa 100644
--- a/R/wlr.R
+++ b/R/wlr.R
@@ -38,12 +38,12 @@
 #'
 wlr <- function(data, weight){
 
-  if ("fh" %in% class(weight)) {
+  if (inherits(weight, "fh")) {
     ans <- data |>
       counting_process(arm = "experimental") |>
       fh_weight(rho_gamma = data.frame(rho = weight$rho, gamma = weight$gamma))
 
-  } else if ("mb" %in% class(weight)) {
+  } else if (inherits(weight, "mb")) {
     ans <- data |>
       counting_process(arm = "experimental") |>
       mb_weight(delay = weight$delay, w_max = weight$w_max) |>
@@ -52,7 +52,7 @@ wlr <- function(data, weight){
         v = sum(var_o_minus_e * mb_weight^2),
         z = s / sqrt(v)) |>
       dplyr::select(z)
-  } else if ("early_period" %in% class(weight)){
+  } else if (inherits(weight, "early_period")) {
     ans <- data |>
       counting_process(arm = "experimental") |>
       early_zero_weight(early_period = weight$early_period) |>
diff --git a/R/wlr_weight.R b/R/wlr_weight.R
index 7428b487..92ab253a 100644
--- a/R/wlr_weight.R
+++ b/R/wlr_weight.R
@@ -26,9 +26,7 @@
 #' @examples
 #' fh(rho = 0, gamma = 0.5)
 fh <- function(rho = 0, gamma = 0){
-  ans <- list(rho = rho, gamma = gamma)
-  class(ans) <- c(class(ans), "fh", "wlr")
-  return(ans)
+  structure(list(rho = rho, gamma = gamma), class = c("list", "fh", "wlr"))
 }
 
 #' Magirr and Burman weighting function
@@ -45,9 +43,7 @@ fh <- function(rho = 0, gamma = 0){
 #' @examples
 #' mb(delay = 6, w_max = 2)
 mb <- function(delay = 4, w_max = Inf){
-  ans <- list(delay = delay, w_max = w_max)
-  class(ans) <- c(class(ans), "mb", "wlr")
-  return(ans)
+  structure(list(delay = delay, w_max = w_max), class = c("list", "mb", "wlr"))
 }
 
 #' Zero early weighting function
@@ -64,7 +60,5 @@ mb <- function(delay = 4, w_max = Inf){
 #' @examples
 #' early_zero(6)
 early_zero <- function(early_period){
-  ans <- list(early_period = early_period)
-  class(ans) <- c(class(ans), "early_period", "wlr")
-  return(ans)
+  structure(list(early_period = early_period), class = c("list", "early_period", "wlr"))
 }

From 16b5b3280ced7cb33c0ab405f0ef7a9c3a3e0e23 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 22 Feb 2024 15:34:31 -0500
Subject: [PATCH 06/13] Convert wlr() from dplyr to data.table

---
 DESCRIPTION |  2 +-
 R/wlr.R     | 34 +++++++++++++++++++++++-----------
 man/wlr.Rd  |  3 ++-
 3 files changed, 26 insertions(+), 13 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 903d2d6c..a9294091 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -35,7 +35,7 @@ BugReports: https://github.com/Merck/simtrial/issues
 Encoding: UTF-8
 LazyData: true
 VignetteBuilder: knitr
-Depends: R (>= 4.1.0)
+Depends: R (>= 4.3.0)
 Imports:
     Rcpp,
     data.table (>= 1.12.4),
diff --git a/R/wlr.R b/R/wlr.R
index 84c9d1fa..f8fd9057 100644
--- a/R/wlr.R
+++ b/R/wlr.R
@@ -19,9 +19,13 @@
 #' Weighted logrank test
 #'
 #' @param data cutted dataset generated by sim_pw_surv
-#' @param weight weighting functions, such as \code{fh_weight}, \code{mb_weight}, and \code{early_zero_weight}.
+#' @param weight weighting functions, such as \code{\link{fh_weight}},
+#'   \code{\link{mb_weight}}, and \code{\link{early_zero_weight}}.
 #'
 #' @return test results
+#'
+#' @importFrom data.table setDF setDT
+#'
 #' @export
 #' @examples
 #' sim_pw_surv(n = 200) |>
@@ -47,20 +51,28 @@ wlr <- function(data, weight){
     ans <- data |>
       counting_process(arm = "experimental") |>
       mb_weight(delay = weight$delay, w_max = weight$w_max) |>
-      dplyr::summarize(
-        s = sum(o_minus_e * mb_weight),
-        v = sum(var_o_minus_e * mb_weight^2),
-        z = s / sqrt(v)) |>
-      dplyr::select(z)
+      setDT() |>
+      _[,
+        .(
+          s = sum(o_minus_e * mb_weight),
+          v = sum(var_o_minus_e * mb_weight^2)
+        )
+      ] |>
+      _[, .(z = s / sqrt(v))] |>
+      setDF()
   } else if (inherits(weight, "early_period")) {
     ans <- data |>
       counting_process(arm = "experimental") |>
       early_zero_weight(early_period = weight$early_period) |>
-      dplyr::summarize(
-        s = sum(o_minus_e * weight),
-        v = sum(var_o_minus_e * weight^2),
-        z = s / sqrt(v)) |>
-      dplyr::select(z)
+      setDT() |>
+      _[,
+        .(
+          s = sum(o_minus_e * weight),
+          v = sum(var_o_minus_e * weight^2)
+        )
+      ] |>
+      _[, .(z = s / sqrt(v))] |>
+      setDF()
   }
   return(ans)
 }
diff --git a/man/wlr.Rd b/man/wlr.Rd
index a718f676..8a017f8a 100644
--- a/man/wlr.Rd
+++ b/man/wlr.Rd
@@ -9,7 +9,8 @@ wlr(data, weight)
 \arguments{
 \item{data}{cutted dataset generated by sim_pw_surv}
 
-\item{weight}{weighting functions, such as \code{fh_weight}, \code{mb_weight}, and \code{early_zero_weight}.}
+\item{weight}{weighting functions, such as \code{\link{fh_weight}},
+\code{\link{mb_weight}}, and \code{\link{early_zero_weight}}.}
 }
 \value{
 test results

From ba1118e1807ee5e99cbfad8d2998cb992bb1f2b9 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 22 Feb 2024 15:49:57 -0500
Subject: [PATCH 07/13] Don't use native pipe with data.table (requires R >=
 4.3.0)

---
 DESCRIPTION |  2 +-
 R/wlr.R     | 38 ++++++++++++++++++--------------------
 2 files changed, 19 insertions(+), 21 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a9294091..903d2d6c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -35,7 +35,7 @@ BugReports: https://github.com/Merck/simtrial/issues
 Encoding: UTF-8
 LazyData: true
 VignetteBuilder: knitr
-Depends: R (>= 4.3.0)
+Depends: R (>= 4.1.0)
 Imports:
     Rcpp,
     data.table (>= 1.12.4),
diff --git a/R/wlr.R b/R/wlr.R
index f8fd9057..fdd65265 100644
--- a/R/wlr.R
+++ b/R/wlr.R
@@ -50,29 +50,27 @@ wlr <- function(data, weight){
   } else if (inherits(weight, "mb")) {
     ans <- data |>
       counting_process(arm = "experimental") |>
-      mb_weight(delay = weight$delay, w_max = weight$w_max) |>
-      setDT() |>
-      _[,
-        .(
-          s = sum(o_minus_e * mb_weight),
-          v = sum(var_o_minus_e * mb_weight^2)
-        )
-      ] |>
-      _[, .(z = s / sqrt(v))] |>
-      setDF()
+      mb_weight(delay = weight$delay, w_max = weight$w_max)
+    setDT(ans)
+    ans <- ans[,
+               .(
+                 s = sum(o_minus_e * mb_weight),
+                 v = sum(var_o_minus_e * mb_weight^2)
+               )
+    ][, .(z = s / sqrt(v))]
+    setDF(ans)
   } else if (inherits(weight, "early_period")) {
     ans <- data |>
       counting_process(arm = "experimental") |>
-      early_zero_weight(early_period = weight$early_period) |>
-      setDT() |>
-      _[,
-        .(
-          s = sum(o_minus_e * weight),
-          v = sum(var_o_minus_e * weight^2)
-        )
-      ] |>
-      _[, .(z = s / sqrt(v))] |>
-      setDF()
+      early_zero_weight(early_period = weight$early_period)
+    setDT(ans)
+    ans <- ans[,
+               .(
+                 s = sum(o_minus_e * weight),
+                 v = sum(var_o_minus_e * weight^2)
+               )
+    ][, .(z = s / sqrt(v))]
+    setDF(ans)
   }
   return(ans)
 }

From f8a68789d7624db60516c6a082bd8ac291bae606 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 22 Feb 2024 16:10:57 -0500
Subject: [PATCH 08/13] Add create_cutting() to pkgdown site

---
 _pkgdown.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/_pkgdown.yml b/_pkgdown.yml
index a3e6a003..ac94271d 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -43,6 +43,7 @@ reference:
     - cut_data_by_event
     - get_cut_date_by_event
     - get_analysis_date
+    - create_cutting
 
 - title: "Compute p-values/test statistics"
   contents:

From 2ec28361ef55c8ef6a48234847145b2ca9d65581 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 23 Feb 2024 10:52:47 -0500
Subject: [PATCH 09/13] Add test for maxcombo()

---
 tests/testthat/test-unvalidated-maxcombo.R | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 tests/testthat/test-unvalidated-maxcombo.R

diff --git a/tests/testthat/test-unvalidated-maxcombo.R b/tests/testthat/test-unvalidated-maxcombo.R
new file mode 100644
index 00000000..b984b9f2
--- /dev/null
+++ b/tests/testthat/test-unvalidated-maxcombo.R
@@ -0,0 +1,12 @@
+# 2024-02-23: Converted `example("maxcombo")` to tests from commit 914c604
+# https://github.com/Merck/simtrial/pull/201/commits/914c6049cf9afb526f2286fdacfabf883050e175
+
+test_that("maxcombo returns consistent results", {
+  set.seed(1)
+  observed <- sim_pw_surv(n = 200) |>
+   cut_data_by_event(150) |>
+   maxcombo(test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
+            test2 = wlr(data, rho = 0, gamma = 0.5) |> quote())
+  expected <- data.frame(p_value = 1.5739680815363144e-06)
+  expect_equal(observed, expected)
+})

From ae86fe7fb0f4613330caf68c2af53c9c63c3f7b4 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 23 Feb 2024 11:05:56 -0500
Subject: [PATCH 10/13] Change the maxcombo() interface to accept vectors

---
 DESCRIPTION                                |  2 +-
 R/maxcombo.R                               | 36 ++++++++++------------
 R/sim_gs_n.R                               |  4 +--
 man/maxcombo.Rd                            | 16 +++++-----
 man/sim_gs_n.Rd                            |  4 +--
 tests/testthat/test-unvalidated-maxcombo.R | 13 ++++++--
 tests/testthat/test-unvalidated-sim_gs_n.R |  4 +--
 7 files changed, 43 insertions(+), 36 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 903d2d6c..c90ea708 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.3.2.6
+Version: 0.3.2.7
 Authors@R: c(
     person("Keaven", "Anderson", email = "keaven_anderson@merck.com", role = c("aut")),
     person("Yilong", "Zhang", email = "elong0527@gmail.com", role =  c("aut")),
diff --git a/R/maxcombo.R b/R/maxcombo.R
index 44000159..c36721bc 100644
--- a/R/maxcombo.R
+++ b/R/maxcombo.R
@@ -19,37 +19,33 @@
 #' Maxcombo test
 #'
 #' @param data a tte dataset
-#' @param test1 maxcombo test1
-#' @param test2 maxcombo test2
-#' @param ... additional tests
+#' @param rho Numeric vector passed to \code{\link{fh_weight}}. Must be greater
+#'   than or equal to zero. Must be the same length as \code{gamma}.
+#' @param gamma Numeric vector passed to \code{\link{fh_weight}}. Must be
+#'   greater than or equal to zero. Must be the same length as \code{rho}.
 #'
 #' @return pvalues
 #' @export
 #'
+#' @seealso \code{\link{fh_weight}}
+#'
 #' @examples
 #' sim_pw_surv(n = 200) |>
 #'   cut_data_by_event(150) |>
-#'   maxcombo(test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-#'            test2 = wlr(data, rho = 0, gamma = 0.5) |> quote())
-maxcombo <- function(data, test1, test2, ...){
-  all_args <- match.call(expand.dots = FALSE)
-  args <- all_args[-1]  # Exclude the first element (function name)
-
-  n_test <- length(args) - 1
-  rho_vector <- NULL
-  gamma_vector <- NULL
-
-  for (i in seq_len(n_test)) {
-    test_i <- get(paste0("test", i))
-    rho_vector <- c(rho_vector, test_i$rho)
-    gamma_vector <- c(gamma_vector, test_i$gamma)
-  }
+#'   maxcombo(rho = c(0, 0), gamma = c(0, 0.5))
+maxcombo <- function(data, rho, gamma){
+  stopifnot(
+    is.numeric(rho), is.numeric(gamma),
+    rho >= 0, gamma >= 0,
+    length(rho) == length(gamma)
+  )
 
   ans <- data |>
     counting_process(arm = "experimental") |>
     fh_weight(
-      rho_gamma = data.frame(rho = rho_vector, gamma = gamma_vector),
-      return_corr = TRUE)
+      rho_gamma = data.frame(rho = rho, gamma = gamma),
+      return_corr = TRUE
+    )
 
   ans <-  data.frame(p_value = pvalue_maxcombo(ans))
 
diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index f6ca2b99..6e3c09f2 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -158,8 +158,8 @@
 #'   test = maxcombo,
 #'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
-#'   test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-#'   test2 = wlr(data, rho = 0, gamma = 0.5) |> quote())
+#'   rho = c(0, 0),
+#'   gamma = c(0, 0.5))
 sim_gs_n <- function(
     # number of simulations
   n_sim = 1000,
diff --git a/man/maxcombo.Rd b/man/maxcombo.Rd
index 35e32c75..28eca247 100644
--- a/man/maxcombo.Rd
+++ b/man/maxcombo.Rd
@@ -4,16 +4,16 @@
 \alias{maxcombo}
 \title{Maxcombo test}
 \usage{
-maxcombo(data, test1, test2, ...)
+maxcombo(data, rho, gamma)
 }
 \arguments{
 \item{data}{a tte dataset}
 
-\item{test1}{maxcombo test1}
+\item{rho}{Numeric vector passed to \code{\link{fh_weight}}. Must be greater
+than or equal to zero. Must be the same length as \code{gamma}.}
 
-\item{test2}{maxcombo test2}
-
-\item{...}{additional tests}
+\item{gamma}{Numeric vector passed to \code{\link{fh_weight}}. Must be
+greater than or equal to zero. Must be the same length as \code{rho}.}
 }
 \value{
 pvalues
@@ -24,6 +24,8 @@ Maxcombo test
 \examples{
 sim_pw_surv(n = 200) |>
   cut_data_by_event(150) |>
-  maxcombo(test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-           test2 = wlr(data, rho = 0, gamma = 0.5) |> quote())
+  maxcombo(rho = c(0, 0), gamma = c(0, 0.5))
+}
+\seealso{
+\code{\link{fh_weight}}
 }
diff --git a/man/sim_gs_n.Rd b/man/sim_gs_n.Rd
index 95a798e5..9aa3741f 100644
--- a/man/sim_gs_n.Rd
+++ b/man/sim_gs_n.Rd
@@ -182,6 +182,6 @@ sim_gs_n(
   test = maxcombo,
   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
-  test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-  test2 = wlr(data, rho = 0, gamma = 0.5) |> quote())
+  rho = c(0, 0),
+  gamma = c(0, 0.5))
 }
diff --git a/tests/testthat/test-unvalidated-maxcombo.R b/tests/testthat/test-unvalidated-maxcombo.R
index b984b9f2..a69f64b8 100644
--- a/tests/testthat/test-unvalidated-maxcombo.R
+++ b/tests/testthat/test-unvalidated-maxcombo.R
@@ -5,8 +5,17 @@ test_that("maxcombo returns consistent results", {
   set.seed(1)
   observed <- sim_pw_surv(n = 200) |>
    cut_data_by_event(150) |>
-   maxcombo(test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-            test2 = wlr(data, rho = 0, gamma = 0.5) |> quote())
+   maxcombo(rho = c(0, 0), gamma = c(0, 0.5))
   expected <- data.frame(p_value = 1.5739680815363144e-06)
   expect_equal(observed, expected)
 })
+
+test_that("maxcombo fails early with bad input", {
+  input <- observed <- sim_pw_surv(n = 200) |>
+    cut_data_by_event(150)
+  expect_error(maxcombo(input, rho = c(-1, 0), gamma = c(0, 0.5)))
+  expect_error(maxcombo(input, rho = c(0, 0), gamma = c(-1, 0.5)))
+  expect_error(maxcombo(input, rho = letters[1:2], gamma = c(0, 0.5)))
+  expect_error(maxcombo(input, rho = c(0, 0), gamma = letters[1:2]))
+  expect_error(maxcombo(input, rho = c(0), gamma = c(0, 0.5)))
+})
diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
index c3fa803e..eef6a7e0 100644
--- a/tests/testthat/test-unvalidated-sim_gs_n.R
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -205,8 +205,8 @@ test_that("Test 6: maxcombo (FH(0,0) + FH(0, 0.5))", {
     test = maxcombo,
     cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
     seed = 2024,
-    test1 = wlr(data, rho = 0, gamma = 0) |> quote(),
-    test2 = wlr(data, rho = 0, gamma = 0.5) |> quote()
+    rho = c(0, 0),
+    gamma = c(0, 0.5)
   )
   expected <- data.frame(
     p_value = c(

From d450b8a0005c5f253a7afb5532b1070aa9e4a725 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 23 Feb 2024 11:21:14 -0500
Subject: [PATCH 11/13] Qualify gsDesign2 namespace explicitly in sim_gs_n()
 tests

---
 tests/testthat/test-unvalidated-sim_gs_n.R | 19 +++++++++++--------
 1 file changed, 11 insertions(+), 8 deletions(-)

diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
index eef6a7e0..5e7acadb 100644
--- a/tests/testthat/test-unvalidated-sim_gs_n.R
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -1,22 +1,25 @@
 # 2024-02-22: Converted `example("sim_gs_n")` to tests from commit 306de0d
 # https://github.com/Merck/simtrial/tree/306de0dbe380fdb1e906a59f34bf3871d3ee5312
 
-library(gsDesign2)
 # parameters for enrollment
 enroll_rampup_duration <- 4 # duration for enrollment ramp up
 enroll_duration <- 16       # total enrollment duration
-enroll_rate <- define_enroll_rate(duration = c(enroll_rampup_duration,
-                                               enroll_duration - enroll_rampup_duration),
-                                  rate = c(10, 30))
+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_col <- 9             # survival median of the control arm
 median_exp <- c(9, 14)      # survival median of the experimental arm
 dropout_rate <- 0.001
-fail_rate <- define_fail_rate(duration = c(delay_effect_duration, 100),
-                              fail_rate = log(2) /  median_col,
-                              hr = median_col / median_exp,
-                              dropout_rate = dropout_rate)
+fail_rate <- gsDesign2::define_fail_rate(
+  duration = c(delay_effect_duration, 100),
+  fail_rate = log(2) /  median_col,
+  hr = median_col / median_exp,
+  dropout_rate = dropout_rate
+)
 # other related parameters
 alpha <- 0.025              # type I error
 beta <- 0.1                 # type II error

From c8629b3b696e3cde02faf22e354acecabbfef690 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 23 Feb 2024 11:30:25 -0500
Subject: [PATCH 12/13] Move sim_gs_n() test file scope code to helper
 functions

---
 tests/testthat/helper-sim_gs_n.R           | 72 ++++++++++++++++
 tests/testthat/test-unvalidated-sim_gs_n.R | 95 +++++-----------------
 2 files changed, 91 insertions(+), 76 deletions(-)
 create mode 100644 tests/testthat/helper-sim_gs_n.R

diff --git a/tests/testthat/helper-sim_gs_n.R b/tests/testthat/helper-sim_gs_n.R
new file mode 100644
index 00000000..fe6104da
--- /dev/null
+++ b/tests/testthat/helper-sim_gs_n.R
@@ -0,0 +1,72 @@
+# helper functions used by test-unvalidated-sim_gs_n.R
+
+test_enroll_rate <- function() {
+  # 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)
+  )
+  return(enroll_rate)
+}
+
+test_fail_rate <- function() {
+  # parameters for treatment effect
+  delay_effect_duration <- 3  # delay treatment effect in months
+  median_col <- 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_col,
+    hr = median_col / median_exp,
+    dropout_rate = dropout_rate
+  )
+  return(fail_rate)
+}
+
+test_cutting <- function() {
+  # other related parameters
+  alpha <- 0.025              # type I error
+  beta <- 0.1                 # type II error
+  ratio <- 1                  # randomization ratio (exp:col)
+  # Define cuttings of 2 IAs and 1 FA
+  # IA1
+  # The 1st interim analysis will occur at the later of the following 3 conditions:
+  # - At least 20 months have passed since the start of the study
+  # - At least 100 events have occurred
+  # - At least 20 months have elapsed after enrolling 200/400 subjects, with a
+  #   minimum of 20 months follow-up
+  # However, if events accumulation is slow, we will wait for a maximum of 24 months.
+  ia1 <- create_cutting(
+    planned_calendar_time = 20,
+    target_event_overall = 100,
+    max_extension_for_target_event = 24,
+    min_n_overall = 200,
+    min_followup = 20
+  )
+  # IA2
+  # The 2nd interim analysis will occur at the later of the following 3 conditions:
+  # - At least 32 months have passed since the start of the study
+  # - At least 250 events have occurred
+  # - At least 10 months after IA1
+  # However, if events accumulation is slow, we will wait for a maximum of 34 months.
+  ia2 <- create_cutting(
+    planned_calendar_time = 32,
+    target_event_overall = 200,
+    max_extension_for_target_event = 34,
+    min_time_after_previous_analysis = 10
+  )
+  # FA
+  # The final analysis will occur at the later of the following 2 conditions:
+  # - At least 45 months have passed since the start of the study
+  # - At least 300 events have occurred
+  fa <- create_cutting(
+    planned_calendar_time = 45,
+    target_event_overall = 350
+  )
+
+  return(list(ia1 = ia1, ia2 = ia2, fa = fa))
+}
diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
index 5e7acadb..c8f11916 100644
--- a/tests/testthat/test-unvalidated-sim_gs_n.R
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -1,73 +1,16 @@
 # 2024-02-22: Converted `example("sim_gs_n")` to tests from commit 306de0d
 # https://github.com/Merck/simtrial/tree/306de0dbe380fdb1e906a59f34bf3871d3ee5312
 
-# 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_col <- 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_col,
-  hr = median_col / 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 (exp:col)
-# Define cuttings of 2 IAs and 1 FA
-# IA1
-# The 1st interim analysis will occur at the later of the following 3 conditions:
-# - At least 20 months have passed since the start of the study
-# - At least 100 events have occurred
-# - At least 20 months have elapsed after enrolling 200/400 subjects, with a
-#   minimum of 20 months follow-up
-# However, if events accumulation is slow, we will wait for a maximum of 24 months.
-ia1 <- create_cutting(
-  planned_calendar_time = 20,
-  target_event_overall = 100,
-  max_extension_for_target_event = 24,
-  min_n_overall = 200,
-  min_followup = 20
-)
-# IA2
-# The 2nd interim analysis will occur at the later of the following 3 conditions:
-# - At least 32 months have passed since the start of the study
-# - At least 250 events have occurred
-# - At least 10 months after IA1
-# However, if events accumulation is slow, we will wait for a maximum of 34 months.
-ia2 <- create_cutting(
-  planned_calendar_time = 32,
-  target_event_overall = 200,
-  max_extension_for_target_event = 34,
-  min_time_after_previous_analysis = 10
-)
-# FA
-# The final analysis will occur at the later of the following 2 conditions:
-# - At least 45 months have passed since the start of the study
-# - At least 300 events have occurred
-fa <- create_cutting(
-  planned_calendar_time = 45,
-  target_event_overall = 350
-)
+# See helper-sim_gs_n.R for helper functions
 
 test_that("Test 1: regular logrank test", {
   observed <- sim_gs_n(
     n_sim = 3,
     sample_size = 400,
-    enroll_rate = enroll_rate,
-    fail_rate = fail_rate,
+    enroll_rate = test_enroll_rate(),
+    fail_rate = test_fail_rate(),
     test = wlr,
-    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    cutting = test_cutting(),
     seed = 2024,
     weight = fh(rho = 0, gamma = 0)
   )
@@ -90,10 +33,10 @@ test_that("Test 2: weighted logrank test by FH(0, 0.5)", {
   observed <- sim_gs_n(
     n_sim = 3,
     sample_size = 400,
-    enroll_rate = enroll_rate,
-    fail_rate = fail_rate,
+    enroll_rate = test_enroll_rate(),
+    fail_rate = test_fail_rate(),
     test = wlr,
-    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    cutting = test_cutting(),
     seed = 2024,
     weight = fh(rho = 0, gamma = 0.5)
   )
@@ -116,10 +59,10 @@ test_that("Test 3: weighted logrank test by MB(6)", {
   observed <- sim_gs_n(
     n_sim = 3,
     sample_size = 400,
-    enroll_rate = enroll_rate,
-    fail_rate = fail_rate,
+    enroll_rate = test_enroll_rate(),
+    fail_rate = test_fail_rate(),
     test = wlr,
-    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    cutting = test_cutting(),
     seed = 2024,
     weight = mb(delay = 3)
   )
@@ -140,10 +83,10 @@ test_that("Test 4: weighted logrank test by early zero (6)", {
   observed <- sim_gs_n(
     n_sim = 3,
     sample_size = 400,
-    enroll_rate = enroll_rate,
-    fail_rate = fail_rate,
+    enroll_rate = test_enroll_rate(),
+    fail_rate = test_fail_rate(),
     test = wlr,
-    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    cutting = test_cutting(),
     seed = 2024,
     weight = early_zero(6)
   )
@@ -164,10 +107,10 @@ test_that("Test 5: RMST", {
   observed <- sim_gs_n(
     n_sim = 3,
     sample_size = 400,
-    enroll_rate = enroll_rate,
-    fail_rate = fail_rate,
+    enroll_rate = test_enroll_rate(),
+    fail_rate = test_fail_rate(),
     test = rmst,
-    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    cutting = test_cutting(),
     seed = 2024,
     tau = 20
   )
@@ -203,10 +146,10 @@ test_that("Test 6: maxcombo (FH(0,0) + FH(0, 0.5))", {
   observed <- sim_gs_n(
     n_sim = 3,
     sample_size = 400,
-    enroll_rate = enroll_rate,
-    fail_rate = fail_rate,
+    enroll_rate = test_enroll_rate(),
+    fail_rate = test_fail_rate(),
     test = maxcombo,
-    cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+    cutting = test_cutting(),
     seed = 2024,
     rho = c(0, 0),
     gamma = c(0, 0.5)

From b302c3e9eea35b0dd2a579bfb16fafecb730ca50 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 23 Feb 2024 13:39:48 -0500
Subject: [PATCH 13/13] Document `sim_gs_n()` and `maxcombo()` as experimental

---
 R/maxcombo.R    | 3 +++
 R/sim_gs_n.R    | 4 ++++
 R/wlr_weight.R  | 4 ++--
 man/fh.Rd       | 4 ++--
 man/maxcombo.Rd | 3 ++-
 man/sim_gs_n.Rd | 3 ++-
 6 files changed, 15 insertions(+), 6 deletions(-)

diff --git a/R/maxcombo.R b/R/maxcombo.R
index c36721bc..b9a7f503 100644
--- a/R/maxcombo.R
+++ b/R/maxcombo.R
@@ -18,6 +18,9 @@
 
 #' Maxcombo test
 #'
+#' WARNING: This experimental function is a work-in-progress. The function
+#' arguments will change as we add additional features.
+#'
 #' @param data a tte dataset
 #' @param rho Numeric vector passed to \code{\link{fh_weight}}. Must be greater
 #'   than or equal to zero. Must be the same length as \code{gamma}.
diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index 6e3c09f2..043ab23c 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -17,6 +17,10 @@
 #  along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 #' Simulate group sequential designs with fixed sample size
+#'
+#' WARNING: This experimental function is a work-in-progress. The function
+#' arguments will change as we add additional features.
+#'
 #' @inheritParams sim_fixed_n
 #' @param test a test function such as \code{\link{wlr}},
 #'   \code{\link{maxcombo}}, or \code{\link{rmst}}. The simulated data set is
diff --git a/R/wlr_weight.R b/R/wlr_weight.R
index 92ab253a..f4106407 100644
--- a/R/wlr_weight.R
+++ b/R/wlr_weight.R
@@ -18,8 +18,8 @@
 
 #' Fleming-Harrington weighting function
 #'
-#' @param rho Non-negative number. \code{rho = 0, gamma = 0} is equavalent to regular logrank test.
-#' @param gamma Non-negative number. \code{rho = 0, gamma = 0} is equavalent to regular logrank test.
+#' @param rho Non-negative number. \code{rho = 0, gamma = 0} is equivalent to regular logrank test.
+#' @param gamma Non-negative number. \code{rho = 0, gamma = 0} is equivalent to regular logrank test.
 #'
 #' @export
 #' @return A list of parameters of the Fleming-Harrington weighting function
diff --git a/man/fh.Rd b/man/fh.Rd
index 4760a085..9f191609 100644
--- a/man/fh.Rd
+++ b/man/fh.Rd
@@ -7,9 +7,9 @@
 fh(rho = 0, gamma = 0)
 }
 \arguments{
-\item{rho}{Non-negative number. \code{rho = 0, gamma = 0} is equavalent to regular logrank test.}
+\item{rho}{Non-negative number. \code{rho = 0, gamma = 0} is equivalent to regular logrank test.}
 
-\item{gamma}{Non-negative number. \code{rho = 0, gamma = 0} is equavalent to regular logrank test.}
+\item{gamma}{Non-negative number. \code{rho = 0, gamma = 0} is equivalent to regular logrank test.}
 }
 \value{
 A list of parameters of the Fleming-Harrington weighting function
diff --git a/man/maxcombo.Rd b/man/maxcombo.Rd
index 28eca247..4159f060 100644
--- a/man/maxcombo.Rd
+++ b/man/maxcombo.Rd
@@ -19,7 +19,8 @@ greater than or equal to zero. Must be the same length as \code{rho}.}
 pvalues
 }
 \description{
-Maxcombo test
+WARNING: This experimental function is a work-in-progress. The function
+arguments will change as we add additional features.
 }
 \examples{
 sim_pw_surv(n = 200) |>
diff --git a/man/sim_gs_n.Rd b/man/sim_gs_n.Rd
index 9aa3741f..4df396b6 100644
--- a/man/sim_gs_n.Rd
+++ b/man/sim_gs_n.Rd
@@ -52,7 +52,8 @@ passed as the first positional argument to the test function provided.}
 a data frame summarizing the simulation ID, analysis date, z statistics or p-values
 }
 \description{
-Simulate group sequential designs with fixed sample size
+WARNING: This experimental function is a work-in-progress. The function
+arguments will change as we add additional features.
 }
 \examples{
 library(gsDesign2)