From 650d5eb73a061f8aa790b00d62274bf8614e0a7b Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 18 Jul 2024 15:09:51 -0400
Subject: [PATCH 1/2] Test and document forced evaluation of promises for
 parallel execution

---
 DESCRIPTION                                |  2 +-
 R/sim_gs_n.R                               |  4 +-
 man/sim_gs_n.Rd                            |  2 +-
 tests/testthat/test-unvalidated-sim_gs_n.R | 71 ++++++++++++++++++++++
 4 files changed, 76 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3d9a8e92..bf00d463 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -64,4 +64,4 @@ Suggests:
 LinkingTo:
     Rcpp
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index 593770ec..282687ed 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -222,6 +222,7 @@
 #'   test = list(ia1 = ia1_test, ia2 = ia2_test, fa = fa_test),
 #'   cut = list(ia1 = ia1_cut, ia2 = ia2_cut, fa = fa_cut)
 #' )
+#' }
 #'
 #' # Example 9: regular logrank test at all 3 analyses in parallel
 #' plan("multisession", workers = 2)
@@ -235,7 +236,6 @@
 #'   weight = fh(rho = 0, gamma = 0)
 #' )
 #' plan("sequential")
-#' }
 sim_gs_n <- function(
     n_sim = 1000,
     sample_size = 500,
@@ -360,7 +360,9 @@ sim_gs_n <- function(
 #' # Cut the trial data
 #' cutting(trial_data)
 create_cut <- function(...) {
+  # Force evaluation of input arguments (required for parallel computing)
   lapply(X = list(...), FUN = force)
+
   function(data) {
     get_analysis_date(data, ...)
   }
diff --git a/man/sim_gs_n.Rd b/man/sim_gs_n.Rd
index 80bf338b..c1fd71d9 100644
--- a/man/sim_gs_n.Rd
+++ b/man/sim_gs_n.Rd
@@ -242,6 +242,7 @@ sim_gs_n(
   test = list(ia1 = ia1_test, ia2 = ia2_test, fa = fa_test),
   cut = list(ia1 = ia1_cut, ia2 = ia2_cut, fa = fa_cut)
 )
+}
 
 # Example 9: regular logrank test at all 3 analyses in parallel
 plan("multisession", workers = 2)
@@ -255,6 +256,5 @@ sim_gs_n(
   weight = fh(rho = 0, gamma = 0)
 )
 plan("sequential")
-}
 \dontshow{\}) # examplesIf}
 }
diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
index b8b34735..5509a95e 100644
--- a/tests/testthat/test-unvalidated-sim_gs_n.R
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -486,3 +486,74 @@ test_that("convert_list_to_df_w_list_cols() is robust to diverse input", {
   )
   expect_equal(observed, expected)
 })
+
+test_that("create_cut() can accept variables as arguments", {
+  # https://github.com/Merck/simtrial/issues/260
+  ratio <- 1
+
+  enroll_rate <- gsDesign2::define_enroll_rate(duration = c(2, 2, 8),
+                                               rate = c(1, 2, 3))
+
+  fail_rate <- gsDesign2::define_fail_rate(duration = c(4, Inf),
+                                           fail_rate = log(2) / 12,
+                                           hr = c(1, .6),
+                                           dropout_rate = .001)
+
+  alpha <- 0.025
+  beta <- 0.1
+
+  upper <- gsDesign2::gs_spending_bound
+  upar <- list(sf = gsDesign::sfLDOF, total_spend = alpha)
+  test_upper <- rep(TRUE, 2)
+
+  lower <- gsDesign2::gs_spending_bound
+  lpar <- list(sf = gsDesign::sfLDOF, total_spend = beta)
+  test_lower <- c(TRUE, FALSE)
+  binding <- FALSE
+
+  info_frac = NULL
+  analysis_time = c(24, 36)
+
+  x <- gsDesign2::gs_design_ahr(enroll_rate = enroll_rate, fail_rate = fail_rate,
+                                alpha = alpha, beta = beta, ratio = ratio,
+                                info_frac = info_frac, analysis_time = analysis_time,
+                                upper = upper, upar = upar, test_upper = test_upper,
+                                lower = lower, lpar = lpar, test_lower = test_lower,
+                                binding = binding) |> gsDesign2::to_integer()
+
+  ia_cut <- simtrial::create_cut(planned_calendar_time = x$analysis$time[1])
+  fa_cut <- simtrial::create_cut(planned_calendar_time = x$analysis$time[2])
+
+  # Must run the parallel version first for 2 reasons:
+  #
+  # 1. In order to reproduce the bug that inspired this test, the cutting
+  # functions must not have been evaluated prior to running them in parallel
+  #
+  # 2. In order to avoid an R CMD check NOTE about detritus in the temp
+  # directory, need to run `future::plan("sequential")` to shut down parallel
+  # cluster
+  # https://future.futureverse.org/articles/future-7-for-package-developers.html#making-sure-to-stop-parallel-workers
+  future::plan("multisession", workers = 2)
+  set.seed(1)
+  results_parallel <- simtrial::sim_gs_n(
+    n_sim = 1e2,
+    sample_size = x$analysis$n[2],
+    enroll_rate = x$enroll_rate,
+    fail_rate = x$fail_rate,
+    test = simtrial::wlr,
+    cut = list(ia = ia_cut, fa = fa_cut),
+    weight = simtrial::fh(rho = 0, gamma = 0))
+
+  future::plan("sequential")
+  set.seed(1)
+  results_sequential <- simtrial::sim_gs_n(
+    n_sim = 1e2,
+    sample_size = x$analysis$n[2],
+    enroll_rate = x$enroll_rate,
+    fail_rate = x$fail_rate,
+    test = simtrial::wlr,
+    cut = list(ia = ia_cut, fa = fa_cut),
+    weight = simtrial::fh(rho = 0, gamma = 0))
+
+  expect_equal(results_parallel, results_sequential)
+})

From d536333e2e94f6b7bf056847846d42c3e1eaa8c1 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 8 Aug 2024 14:19:58 -0400
Subject: [PATCH 2/2] Install gsDesign2 from GitHub until next CRAN release

---
 DESCRIPTION | 1 +
 1 file changed, 1 insertion(+)

diff --git a/DESCRIPTION b/DESCRIPTION
index bf00d463..5beb416f 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -63,5 +63,6 @@ Suggests:
     tidyr
 LinkingTo:
     Rcpp
+Remotes: Merck/gsDesign2
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2