From b1083727e2055c793952b832342f14f63213c3fb Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Tue, 19 Mar 2024 16:01:57 -0400
Subject: [PATCH 1/5] Rename function factories create_cut() and create_test()

---
 NAMESPACE                                     |   4 +-
 R/sim_gs_n.R                                  | 104 +++++++++---------
 _pkgdown.yml                                  |   4 +-
 man/{create_cutting.Rd => create_cut.Rd}      |   8 +-
 ...{create_cutting_test.Rd => create_test.Rd} |  10 +-
 man/multitest.Rd                              |  10 +-
 man/sim_gs_n.Rd                               |  68 ++++++------
 tests/testthat/helper-sim_gs_n.R              |   6 +-
 tests/testthat/test-unvalidated-multitest.R   |   6 +-
 tests/testthat/test-unvalidated-sim_gs_n.R    |  46 ++++----
 10 files changed, 135 insertions(+), 131 deletions(-)
 rename man/{create_cutting.Rd => create_cut.Rd} (90%)
 rename man/{create_cutting_test.Rd => create_test.Rd} (79%)

diff --git a/NAMESPACE b/NAMESPACE
index 4f6b6de3..56f69159 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,8 +1,8 @@
 # Generated by roxygen2: do not edit by hand
 
 export(counting_process)
-export(create_cutting)
-export(create_cutting_test)
+export(create_cut)
+export(create_test)
 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 8f0fddb1..ff225b92 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -22,18 +22,20 @@
 #' arguments will change as we add additional features.
 #'
 #' @inheritParams sim_fixed_n
-#' @param test A test function such as [wlr()], [maxcombo()], or [rmst()]. The
-#'   simulated data set is passed as the first positional argument to the test
-#'   function provided. Alternatively a list of functions created by
-#'   [create_cutting_test()]. The list form is experimental and currently
-#'   limited. It only accepts one test per cutting (in the future multiple tests
-#'   may be accepted), and all the tests must consistently return the same exact
-#'   results (again this may be more flexible in the future).
-#' @param cutting A list of cutting functions created by [create_cutting()],
+#' @param tests One or more test functions such as [wlr()], [maxcombo()], or
+#'   [rmst()]. If a single test function is provided, it will be applied at each
+#'   cut. Alternatively a list of functions created by [create_test()]. The list
+#'   form is experimental and currently limited. It only accepts one test per
+#'   cutting (in the future multiple tests may be accepted), and all the tests
+#'   must consistently return the same exact results (again this may be more
+#'   flexible in the future). Importantly, note that the simulated data set is
+#'   always passed as the first positional argument to each test function
+#'   provided.
+#' @param cuts A list of cutting functions created by [create_cut()],
 #'   see examples.
 #' @param seed Random seed.
-#' @param ... Arguments passed to the test function provided by the argument
-#'   `test`.
+#' @param ... Arguments passed to the test function(s) provided by the argument
+#'   `tests`.
 #'
 #' @return A data frame summarizing the simulation ID, analysis date,
 #'   z statistics or p-values.
@@ -79,7 +81,7 @@
 #' # - 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(
+#' ia1 <- create_cut(
 #'   planned_calendar_time = 20,
 #'   target_event_overall = 100,
 #'   max_extension_for_target_event = 24,
@@ -93,7 +95,7 @@
 #' # - 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(
+#' ia2 <- create_cut(
 #'   planned_calendar_time = 32,
 #'   target_event_overall = 200,
 #'   max_extension_for_target_event = 34,
@@ -104,7 +106,7 @@
 #' # 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(
+#' fa <- create_cut(
 #'   planned_calendar_time = 45,
 #'   target_event_overall = 350
 #' )
@@ -115,8 +117,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = wlr,
-#'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   tests = wlr,
+#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   weight = fh(rho = 0, gamma = 0)
 #' )
@@ -127,8 +129,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = wlr,
-#'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   tests = wlr,
+#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   weight = fh(rho = 0, gamma = 0.5)
 #' )
@@ -139,8 +141,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = wlr,
-#'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   tests = wlr,
+#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   weight = mb(delay = 3)
 #' )
@@ -151,8 +153,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = wlr,
-#'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   tests = wlr,
+#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   weight = early_zero(6)
 #' )
@@ -163,8 +165,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = rmst,
-#'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   tests = rmst,
+#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   tau = 20
 #' )
@@ -175,8 +177,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = milestone,
-#'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   tests = milestone,
+#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   ms_time = 10
 #' )
@@ -188,8 +190,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = maxcombo,
-#'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   tests = maxcombo,
+#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   rho = c(0, 0),
 #'   gamma = c(0, 0.5)
@@ -203,8 +205,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = maxcombo(test1 = wlr, test2 = milestone),
-#'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   tests = maxcombo(test1 = wlr, test2 = milestone),
+#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   test1_par = list(weight = fh(rho = 0, gamma = 0.5)),
 #'   test2_par = list(ms_time = 10)
@@ -219,8 +221,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   test = list(ia1 = wlr, ia2 = wlr, fa = maxcombo),
-#'   cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   tests = list(ia1 = wlr, ia2 = wlr, fa = maxcombo),
+#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   test_par = list(
 #'     ia1 = list(weight = fh(rho = 0, gamma = 0)),
@@ -246,8 +248,8 @@ sim_gs_n <- function(
       dropout_rate = rep(.001, 2)
     ),
     block = rep(c("experimental", "control"), 2),
-    test = wlr,
-    cutting = NULL,
+    tests = wlr,
+    cuts = NULL,
     seed = 2024,
     ...) {
   # Input checking
@@ -268,30 +270,30 @@ sim_gs_n <- function(
     )
 
     # Initialize the cut date of IA(s) and FA
-    n_analysis <- length(cutting)
+    n_analysis <- length(cuts)
     cut_date <- rep(-100, n_analysis)
     ans_1sim <- NULL
 
     # Organize tests for each cutting
-    if (is.function(test)) {
-      test_single <- test
-      test <- vector(mode = "list", length = n_analysis)
-      test[] <- list(test_single)
+    if (is.function(tests)) {
+      test_single <- tests
+      tests <- vector(mode = "list", length = n_analysis)
+      tests[] <- list(test_single)
     }
-    if (length(test) != length(cutting)) {
+    if (length(tests) != length(cuts)) {
       stop("If you want to run different tests at each cutting, the list of
            tests must be the same length as the list of cuttings")
     }
 
     for (i_analysis in seq_len(n_analysis)) {
       # Get cut date
-      cut_date[i_analysis] <- cutting[[i_analysis]](simu_data)
+      cut_date[i_analysis] <- cuts[[i_analysis]](simu_data)
 
       # Cut the data
       simu_data_cut <- simu_data |> cut_data_by_date(cut_date[i_analysis])
 
       # Test
-      ans_1sim_new <- test[[i_analysis]](simu_data_cut, ...)
+      ans_1sim_new <- tests[[i_analysis]](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
@@ -327,14 +329,14 @@ sim_gs_n <- function(
 #' # 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(
+#' cutting <- create_cut(
 #'   planned_calendar_time = 45,
 #'   target_event_overall = 350
 #' )
 #'
 #' # Cut the trial data
 #' cutting(trial_data)
-create_cutting <- function(...) {
+create_cut <- function(...) {
   function(data) {
     get_analysis_date(data, ...)
   }
@@ -352,7 +354,7 @@ create_cutting <- function(...) {
 #'
 #' @export
 #'
-#' @seealso [sim_gs_n()], [create_cutting()]
+#' @seealso [sim_gs_n()], [create_cut()]
 #'
 #' @examples
 #' # Simulate trial data
@@ -362,7 +364,7 @@ create_cutting <- function(...) {
 #' trial_data_cut <- cut_data_by_event(trial_data, 150)
 #'
 #' # Create a cutting test function that can be used by sim_gs_n()
-#' regular_logrank_test <- create_cutting_test(wlr, weight = fh(rho = 0, gamma = 0))
+#' regular_logrank_test <- create_test(wlr, weight = fh(rho = 0, gamma = 0))
 #'
 #' # Test the cutting
 #' regular_logrank_test(trial_data_cut)
@@ -372,7 +374,7 @@ create_cutting <- function(...) {
 #'   regular_logrank_test(trial_data_cut),
 #'   wlr(trial_data_cut, weight = fh(rho = 0, gamma = 0))
 #' ))
-create_cutting_test <- function(test, ...) {
+create_test <- function(test, ...) {
   stopifnot(is.function(test))
   function(data) {
     test(data, ...)
@@ -386,7 +388,7 @@ create_cutting_test <- function(test, ...) {
 #' features.
 #'
 #' @param data Trial data cut by [cut_data_by_event()] or [cut_data_by_date()]
-#' @param ... One or more test functions. Use [create_cutting_test()] to change
+#' @param ... One or more test functions. Use [create_test()] to change
 #'   the default arguments of each test function.
 #'
 #' @return A list of test results, one per test. If the test functions are named
@@ -394,16 +396,16 @@ create_cutting_test <- function(test, ...) {
 #'
 #' @export
 #'
-#' @seealso [create_cutting_test()]
+#' @seealso [create_test()]
 #'
 #' @examples
 #' trial_data <- sim_pw_surv(n = 200)
 #' trial_data_cut <- cut_data_by_event(trial_data, 150)
 #'
 #' # create cutting test functions
-#' wlr_partial <- create_cutting_test(wlr, weight = fh(rho = 0, gamma = 0))
-#' rmst_partial <- create_cutting_test(rmst, tau = 20)
-#' maxcombo_partial <- create_cutting_test(maxcombo, rho = c(0, 0), gamma = c(0, 0.5))
+#' wlr_partial <- create_test(wlr, weight = fh(rho = 0, gamma = 0))
+#' rmst_partial <- create_test(rmst, tau = 20)
+#' maxcombo_partial <- create_test(maxcombo, rho = c(0, 0), gamma = c(0, 0.5))
 #'
 #' multitest(
 #'   data = trial_data_cut,
diff --git a/_pkgdown.yml b/_pkgdown.yml
index bc86c907..4fb8c360 100644
--- a/_pkgdown.yml
+++ b/_pkgdown.yml
@@ -43,7 +43,7 @@ reference:
     - cut_data_by_event
     - get_cut_date_by_event
     - get_analysis_date
-    - create_cutting
+    - create_cut
 
 - title: "Compute p-values/test statistics"
   contents:
@@ -53,7 +53,7 @@ reference:
     - milestone
     - wlr
     - maxcombo
-    - create_cutting_test
+    - create_test
     - multitest
 
 - title: "Randomization algorithms"
diff --git a/man/create_cutting.Rd b/man/create_cut.Rd
similarity index 90%
rename from man/create_cutting.Rd
rename to man/create_cut.Rd
index de090b54..bcb7b6cb 100644
--- a/man/create_cutting.Rd
+++ b/man/create_cut.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/sim_gs_n.R
-\name{create_cutting}
-\alias{create_cutting}
+\name{create_cut}
+\alias{create_cut}
 \title{Create a cutting function}
 \usage{
-create_cutting(...)
+create_cut(...)
 }
 \arguments{
 \item{...}{Arguments passed to \code{\link[=get_analysis_date]{get_analysis_date()}}}
@@ -23,7 +23,7 @@ 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(
+cutting <- create_cut(
   planned_calendar_time = 45,
   target_event_overall = 350
 )
diff --git a/man/create_cutting_test.Rd b/man/create_test.Rd
similarity index 79%
rename from man/create_cutting_test.Rd
rename to man/create_test.Rd
index 62eb66bf..7f0a1c4d 100644
--- a/man/create_cutting_test.Rd
+++ b/man/create_test.Rd
@@ -1,10 +1,10 @@
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/sim_gs_n.R
-\name{create_cutting_test}
-\alias{create_cutting_test}
+\name{create_test}
+\alias{create_test}
 \title{Create a cutting test function}
 \usage{
-create_cutting_test(test, ...)
+create_test(test, ...)
 }
 \arguments{
 \item{test}{A test function such as \code{\link[=wlr]{wlr()}}, \code{\link[=maxcombo]{maxcombo()}}, or \code{\link[=rmst]{rmst()}}}
@@ -26,7 +26,7 @@ trial_data <- sim_pw_surv()
 trial_data_cut <- cut_data_by_event(trial_data, 150)
 
 # Create a cutting test function that can be used by sim_gs_n()
-regular_logrank_test <- create_cutting_test(wlr, weight = fh(rho = 0, gamma = 0))
+regular_logrank_test <- create_test(wlr, weight = fh(rho = 0, gamma = 0))
 
 # Test the cutting
 regular_logrank_test(trial_data_cut)
@@ -38,5 +38,5 @@ stopifnot(all.equal(
 ))
 }
 \seealso{
-\code{\link[=sim_gs_n]{sim_gs_n()}}, \code{\link[=create_cutting]{create_cutting()}}
+\code{\link[=sim_gs_n]{sim_gs_n()}}, \code{\link[=create_cut]{create_cut()}}
 }
diff --git a/man/multitest.Rd b/man/multitest.Rd
index 835a0d2b..31c8b06b 100644
--- a/man/multitest.Rd
+++ b/man/multitest.Rd
@@ -9,7 +9,7 @@ multitest(data, ...)
 \arguments{
 \item{data}{Trial data cut by \code{\link[=cut_data_by_event]{cut_data_by_event()}} or \code{\link[=cut_data_by_date]{cut_data_by_date()}}}
 
-\item{...}{One or more test functions. Use \code{\link[=create_cutting_test]{create_cutting_test()}} to change
+\item{...}{One or more test functions. Use \code{\link[=create_test]{create_test()}} to change
 the default arguments of each test function.}
 }
 \value{
@@ -26,9 +26,9 @@ trial_data <- sim_pw_surv(n = 200)
 trial_data_cut <- cut_data_by_event(trial_data, 150)
 
 # create cutting test functions
-wlr_partial <- create_cutting_test(wlr, weight = fh(rho = 0, gamma = 0))
-rmst_partial <- create_cutting_test(rmst, tau = 20)
-maxcombo_partial <- create_cutting_test(maxcombo, rho = c(0, 0), gamma = c(0, 0.5))
+wlr_partial <- create_test(wlr, weight = fh(rho = 0, gamma = 0))
+rmst_partial <- create_test(rmst, tau = 20)
+maxcombo_partial <- create_test(maxcombo, rho = c(0, 0), gamma = c(0, 0.5))
 
 multitest(
   data = trial_data_cut,
@@ -38,5 +38,5 @@ multitest(
 )
 }
 \seealso{
-\code{\link[=create_cutting_test]{create_cutting_test()}}
+\code{\link[=create_test]{create_test()}}
 }
diff --git a/man/sim_gs_n.Rd b/man/sim_gs_n.Rd
index 38538351..b5a57db4 100644
--- a/man/sim_gs_n.Rd
+++ b/man/sim_gs_n.Rd
@@ -12,8 +12,8 @@ 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 = wlr,
-  cutting = NULL,
+  tests = wlr,
+  cuts = NULL,
   seed = 2024,
   ...
 )
@@ -36,21 +36,23 @@ 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 test function such as \code{\link[=wlr]{wlr()}}, \code{\link[=maxcombo]{maxcombo()}}, or \code{\link[=rmst]{rmst()}}. The
-simulated data set is passed as the first positional argument to the test
-function provided. Alternatively a list of functions created by
-\code{\link[=create_cutting_test]{create_cutting_test()}}. The list form is experimental and currently
-limited. It only accepts one test per cutting (in the future multiple tests
-may be accepted), and all the tests must consistently return the same exact
-results (again this may be more flexible in the future).}
+\item{tests}{One or more test functions such as \code{\link[=wlr]{wlr()}}, \code{\link[=maxcombo]{maxcombo()}}, or
+\code{\link[=rmst]{rmst()}}. If a single test function is provided, it will be applied at each
+cut. Alternatively a list of functions created by \code{\link[=create_test]{create_test()}}. The list
+form is experimental and currently limited. It only accepts one test per
+cutting (in the future multiple tests may be accepted), and all the tests
+must consistently return the same exact results (again this may be more
+flexible in the future). Importantly, note that the simulated data set is
+always passed as the first positional argument to each test function
+provided.}
 
-\item{cutting}{A list of cutting functions created by \code{\link[=create_cutting]{create_cutting()}},
+\item{cuts}{A list of cutting functions created by \code{\link[=create_cut]{create_cut()}},
 see examples.}
 
 \item{seed}{Random seed.}
 
-\item{...}{Arguments passed to the test function provided by the argument
-\code{test}.}
+\item{...}{Arguments passed to the test function(s) provided by the argument
+\code{tests}.}
 }
 \value{
 A data frame summarizing the simulation ID, analysis date,
@@ -99,7 +101,7 @@ ratio <- 1 # Randomization ratio (experimental:control)
 # - 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(
+ia1 <- create_cut(
   planned_calendar_time = 20,
   target_event_overall = 100,
   max_extension_for_target_event = 24,
@@ -113,7 +115,7 @@ ia1 <- create_cutting(
 # - 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(
+ia2 <- create_cut(
   planned_calendar_time = 32,
   target_event_overall = 200,
   max_extension_for_target_event = 34,
@@ -124,7 +126,7 @@ ia2 <- create_cutting(
 # 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(
+fa <- create_cut(
   planned_calendar_time = 45,
   target_event_overall = 350
 )
@@ -135,8 +137,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = wlr,
-  cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  tests = wlr,
+  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   weight = fh(rho = 0, gamma = 0)
 )
@@ -147,8 +149,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = wlr,
-  cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  tests = wlr,
+  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   weight = fh(rho = 0, gamma = 0.5)
 )
@@ -159,8 +161,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = wlr,
-  cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  tests = wlr,
+  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   weight = mb(delay = 3)
 )
@@ -171,8 +173,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = wlr,
-  cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  tests = wlr,
+  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   weight = early_zero(6)
 )
@@ -183,8 +185,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = rmst,
-  cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  tests = rmst,
+  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   tau = 20
 )
@@ -195,8 +197,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = milestone,
-  cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  tests = milestone,
+  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   ms_time = 10
 )
@@ -208,8 +210,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = maxcombo,
-  cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  tests = maxcombo,
+  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   rho = c(0, 0),
   gamma = c(0, 0.5)
@@ -223,8 +225,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = maxcombo(test1 = wlr, test2 = milestone),
-  cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  tests = maxcombo(test1 = wlr, test2 = milestone),
+  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   test1_par = list(weight = fh(rho = 0, gamma = 0.5)),
   test2_par = list(ms_time = 10)
@@ -239,8 +241,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  test = list(ia1 = wlr, ia2 = wlr, fa = maxcombo),
-  cutting = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  tests = list(ia1 = wlr, ia2 = wlr, fa = maxcombo),
+  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   test_par = list(
     ia1 = list(weight = fh(rho = 0, gamma = 0)),
diff --git a/tests/testthat/helper-sim_gs_n.R b/tests/testthat/helper-sim_gs_n.R
index 49828a54..70f9a8b2 100644
--- a/tests/testthat/helper-sim_gs_n.R
+++ b/tests/testthat/helper-sim_gs_n.R
@@ -42,7 +42,7 @@ test_cutting <- function() {
   # - 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(
+  ia1 <- create_cut(
     planned_calendar_time = 20,
     target_event_overall = 100,
     max_extension_for_target_event = 24,
@@ -55,7 +55,7 @@ test_cutting <- function() {
   # - 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(
+  ia2 <- create_cut(
     planned_calendar_time = 32,
     target_event_overall = 200,
     max_extension_for_target_event = 34,
@@ -65,7 +65,7 @@ test_cutting <- function() {
   # 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(
+  fa <- create_cut(
     planned_calendar_time = 45,
     target_event_overall = 350
   )
diff --git a/tests/testthat/test-unvalidated-multitest.R b/tests/testthat/test-unvalidated-multitest.R
index d5bd7841..470aedd2 100644
--- a/tests/testthat/test-unvalidated-multitest.R
+++ b/tests/testthat/test-unvalidated-multitest.R
@@ -3,9 +3,9 @@ test_that("multitest() is equivalent to running tests individually", {
   trial_data_cut <- cut_data_by_event(trial_data, 150)
 
   # create cutting test functions
-  wlr_partial <- create_cutting_test(wlr, weight = fh(rho = 0, gamma = 0))
-  rmst_partial <- create_cutting_test(rmst, tau = 20)
-  maxcombo_partial <- create_cutting_test(maxcombo, rho = c(0, 0), gamma = c(0, 0.5))
+  wlr_partial <- create_test(wlr, weight = fh(rho = 0, gamma = 0))
+  rmst_partial <- create_test(rmst, tau = 20)
+  maxcombo_partial <- create_test(maxcombo, rho = c(0, 0), gamma = c(0, 0.5))
 
   observed <- multitest(
     data = trial_data_cut,
diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
index 80bc742a..0f5e192e 100644
--- a/tests/testthat/test-unvalidated-sim_gs_n.R
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -9,8 +9,8 @@ test_that("Test 1: regular logrank test", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    test = wlr,
-    cutting = test_cutting(),
+    tests = wlr,
+    cuts = test_cutting(),
     seed = 2024,
     weight = fh(rho = 0, gamma = 0)
   )
@@ -37,8 +37,8 @@ test_that("Test 2: weighted logrank test by FH(0, 0.5)", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    test = wlr,
-    cutting = test_cutting(),
+    tests = wlr,
+    cuts = test_cutting(),
     seed = 2024,
     weight = fh(rho = 0, gamma = 0.5)
   )
@@ -65,8 +65,8 @@ test_that("Test 3: weighted logrank test by MB(3)", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    test = wlr,
-    cutting = test_cutting(),
+    tests = wlr,
+    cuts = test_cutting(),
     seed = 2024,
     weight = mb(delay = 3)
   )
@@ -91,8 +91,8 @@ test_that("Test 4: weighted logrank test by early zero (6)", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    test = wlr,
-    cutting = test_cutting(),
+    tests = wlr,
+    cuts = test_cutting(),
     seed = 2024,
     weight = early_zero(6)
   )
@@ -117,8 +117,8 @@ test_that("Test 5: RMST", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    test = rmst,
-    cutting = test_cutting(),
+    tests = rmst,
+    cuts = test_cutting(),
     seed = 2024,
     tau = 20
   )
@@ -158,8 +158,8 @@ test_that("Test 6: Milestone", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    test = milestone,
-    cutting = test_cutting(),
+    tests = milestone,
+    cuts = test_cutting(),
     seed = 2024,
     ms_time = 10
   )
@@ -211,8 +211,8 @@ test_that("Test 7: MaxCombo (WLR-FH(0,0) + WLR-FH(0, 0.5))", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    test = maxcombo,
-    cutting = test_cutting(),
+    tests = maxcombo,
+    cuts = test_cutting(),
     seed = 2024,
     rho = c(0, 0),
     gamma = c(0, 0.5)
@@ -233,17 +233,17 @@ test_that("Test 7: MaxCombo (WLR-FH(0,0) + WLR-FH(0, 0.5))", {
 })
 
 test_that("sim_gs_n() accepts different tests per cutting", {
-  wlr_cut1 <- create_cutting_test(wlr, weight = fh(rho = 0, gamma = 0))
-  wlr_cut2 <- create_cutting_test(wlr, weight = fh(rho = 0, gamma = 0.5))
-  wlr_cut3 <- create_cutting_test(wlr, weight = fh(rho = 0.5, gamma = 0))
+  wlr_cut1 <- create_test(wlr, weight = fh(rho = 0, gamma = 0))
+  wlr_cut2 <- create_test(wlr, weight = fh(rho = 0, gamma = 0.5))
+  wlr_cut3 <- create_test(wlr, weight = fh(rho = 0.5, gamma = 0))
 
   observed <- sim_gs_n(
     n_sim = 3,
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    test = list(wlr_cut1, wlr_cut2, wlr_cut3),
-    cutting = test_cutting(),
+    tests = list(wlr_cut1, wlr_cut2, wlr_cut3),
+    cuts = test_cutting(),
     seed = 2024
   )
   expected <- data.frame(
@@ -264,8 +264,8 @@ test_that("sim_gs_n() accepts different tests per cutting", {
 })
 
 test_that("sim_gs_n() requires a test for each cutting", {
-  wlr_cut1 <- create_cutting_test(wlr, weight = fh(rho = 0, gamma = 0))
-  wlr_cut2 <- create_cutting_test(wlr, weight = fh(rho = 0, gamma = 0.5))
+  wlr_cut1 <- create_test(wlr, weight = fh(rho = 0, gamma = 0))
+  wlr_cut2 <- create_test(wlr, weight = fh(rho = 0, gamma = 0.5))
 
   expect_error(
     sim_gs_n(
@@ -273,8 +273,8 @@ test_that("sim_gs_n() requires a test for each cutting", {
       sample_size = 400,
       enroll_rate = test_enroll_rate(),
       fail_rate = test_fail_rate(),
-      test = list(wlr_cut1, wlr_cut2),
-      cutting = test_cutting(),
+      tests = list(wlr_cut1, wlr_cut2),
+      cuts = test_cutting(),
       seed = 2024
     ),
     "If you want to run different tests at each cutting"

From ada0b241c6758242b61c2e4e3bc728d0a4b656ce Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 22 Mar 2024 11:16:03 -0400
Subject: [PATCH 2/5] Use the singular `cut` and `test` for consistency in arg
 names

---
 R/sim_gs_n.R                               | 56 +++++++++++-----------
 man/sim_gs_n.Rd                            | 50 +++++++++----------
 tests/testthat/test-unvalidated-sim_gs_n.R | 36 +++++++-------
 3 files changed, 71 insertions(+), 71 deletions(-)

diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index ff225b92..d9b31123 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -117,8 +117,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   tests = wlr,
-#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   test = wlr,
+#'   cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   weight = fh(rho = 0, gamma = 0)
 #' )
@@ -129,8 +129,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   tests = wlr,
-#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   test = wlr,
+#'   cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   weight = fh(rho = 0, gamma = 0.5)
 #' )
@@ -141,8 +141,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   tests = wlr,
-#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   test = wlr,
+#'   cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   weight = mb(delay = 3)
 #' )
@@ -153,8 +153,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   tests = wlr,
-#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   test = wlr,
+#'   cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   weight = early_zero(6)
 #' )
@@ -165,8 +165,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   tests = rmst,
-#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   test = rmst,
+#'   cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   tau = 20
 #' )
@@ -177,8 +177,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   tests = milestone,
-#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   test = milestone,
+#'   cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   ms_time = 10
 #' )
@@ -190,8 +190,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   tests = maxcombo,
-#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   test = maxcombo,
+#'   cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   rho = c(0, 0),
 #'   gamma = c(0, 0.5)
@@ -205,8 +205,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   tests = maxcombo(test1 = wlr, test2 = milestone),
-#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   test = maxcombo(test1 = wlr, test2 = milestone),
+#'   cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   test1_par = list(weight = fh(rho = 0, gamma = 0.5)),
 #'   test2_par = list(ms_time = 10)
@@ -221,8 +221,8 @@
 #'   sample_size = 400,
 #'   enroll_rate = enroll_rate,
 #'   fail_rate = fail_rate,
-#'   tests = list(ia1 = wlr, ia2 = wlr, fa = maxcombo),
-#'   cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+#'   test = list(ia1 = wlr, ia2 = wlr, fa = maxcombo),
+#'   cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
 #'   seed = 2024,
 #'   test_par = list(
 #'     ia1 = list(weight = fh(rho = 0, gamma = 0)),
@@ -248,8 +248,8 @@ sim_gs_n <- function(
       dropout_rate = rep(.001, 2)
     ),
     block = rep(c("experimental", "control"), 2),
-    tests = wlr,
-    cuts = NULL,
+    test = wlr,
+    cut = NULL,
     seed = 2024,
     ...) {
   # Input checking
@@ -270,30 +270,30 @@ sim_gs_n <- function(
     )
 
     # Initialize the cut date of IA(s) and FA
-    n_analysis <- length(cuts)
+    n_analysis <- length(cut)
     cut_date <- rep(-100, n_analysis)
     ans_1sim <- NULL
 
     # Organize tests for each cutting
-    if (is.function(tests)) {
-      test_single <- tests
-      tests <- vector(mode = "list", length = n_analysis)
-      tests[] <- list(test_single)
+    if (is.function(test)) {
+      test_single <- test
+      test <- vector(mode = "list", length = n_analysis)
+      test[] <- list(test_single)
     }
-    if (length(tests) != length(cuts)) {
+    if (length(test) != length(cut)) {
       stop("If you want to run different tests at each cutting, the list of
            tests must be the same length as the list of cuttings")
     }
 
     for (i_analysis in seq_len(n_analysis)) {
       # Get cut date
-      cut_date[i_analysis] <- cuts[[i_analysis]](simu_data)
+      cut_date[i_analysis] <- cut[[i_analysis]](simu_data)
 
       # Cut the data
       simu_data_cut <- simu_data |> cut_data_by_date(cut_date[i_analysis])
 
       # Test
-      ans_1sim_new <- tests[[i_analysis]](simu_data_cut, ...)
+      ans_1sim_new <- test[[i_analysis]](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 b5a57db4..a9f28787 100644
--- a/man/sim_gs_n.Rd
+++ b/man/sim_gs_n.Rd
@@ -12,8 +12,8 @@ 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),
-  tests = wlr,
-  cuts = NULL,
+  test = wlr,
+  cut = NULL,
   seed = 2024,
   ...
 )
@@ -36,6 +36,11 @@ 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{seed}{Random seed.}
+
+\item{...}{Arguments passed to the test function(s) provided by the argument
+\code{tests}.}
+
 \item{tests}{One or more test functions such as \code{\link[=wlr]{wlr()}}, \code{\link[=maxcombo]{maxcombo()}}, or
 \code{\link[=rmst]{rmst()}}. If a single test function is provided, it will be applied at each
 cut. Alternatively a list of functions created by \code{\link[=create_test]{create_test()}}. The list
@@ -48,11 +53,6 @@ provided.}
 
 \item{cuts}{A list of cutting functions created by \code{\link[=create_cut]{create_cut()}},
 see examples.}
-
-\item{seed}{Random seed.}
-
-\item{...}{Arguments passed to the test function(s) provided by the argument
-\code{tests}.}
 }
 \value{
 A data frame summarizing the simulation ID, analysis date,
@@ -137,8 +137,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  tests = wlr,
-  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  test = wlr,
+  cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   weight = fh(rho = 0, gamma = 0)
 )
@@ -149,8 +149,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  tests = wlr,
-  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  test = wlr,
+  cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   weight = fh(rho = 0, gamma = 0.5)
 )
@@ -161,8 +161,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  tests = wlr,
-  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  test = wlr,
+  cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   weight = mb(delay = 3)
 )
@@ -173,8 +173,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  tests = wlr,
-  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  test = wlr,
+  cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   weight = early_zero(6)
 )
@@ -185,8 +185,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  tests = rmst,
-  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  test = rmst,
+  cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   tau = 20
 )
@@ -197,8 +197,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  tests = milestone,
-  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  test = milestone,
+  cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   ms_time = 10
 )
@@ -210,8 +210,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  tests = maxcombo,
-  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  test = maxcombo,
+  cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   rho = c(0, 0),
   gamma = c(0, 0.5)
@@ -225,8 +225,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  tests = maxcombo(test1 = wlr, test2 = milestone),
-  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  test = maxcombo(test1 = wlr, test2 = milestone),
+  cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   test1_par = list(weight = fh(rho = 0, gamma = 0.5)),
   test2_par = list(ms_time = 10)
@@ -241,8 +241,8 @@ sim_gs_n(
   sample_size = 400,
   enroll_rate = enroll_rate,
   fail_rate = fail_rate,
-  tests = list(ia1 = wlr, ia2 = wlr, fa = maxcombo),
-  cuts = list(ia1 = ia1, ia2 = ia2, fa = fa),
+  test = list(ia1 = wlr, ia2 = wlr, fa = maxcombo),
+  cut = list(ia1 = ia1, ia2 = ia2, fa = fa),
   seed = 2024,
   test_par = list(
     ia1 = list(weight = fh(rho = 0, gamma = 0)),
diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
index 0f5e192e..241e237a 100644
--- a/tests/testthat/test-unvalidated-sim_gs_n.R
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -9,8 +9,8 @@ test_that("Test 1: regular logrank test", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    tests = wlr,
-    cuts = test_cutting(),
+    test = wlr,
+    cut = test_cutting(),
     seed = 2024,
     weight = fh(rho = 0, gamma = 0)
   )
@@ -37,8 +37,8 @@ test_that("Test 2: weighted logrank test by FH(0, 0.5)", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    tests = wlr,
-    cuts = test_cutting(),
+    test = wlr,
+    cut = test_cutting(),
     seed = 2024,
     weight = fh(rho = 0, gamma = 0.5)
   )
@@ -65,8 +65,8 @@ test_that("Test 3: weighted logrank test by MB(3)", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    tests = wlr,
-    cuts = test_cutting(),
+    test = wlr,
+    cut = test_cutting(),
     seed = 2024,
     weight = mb(delay = 3)
   )
@@ -91,8 +91,8 @@ test_that("Test 4: weighted logrank test by early zero (6)", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    tests = wlr,
-    cuts = test_cutting(),
+    test = wlr,
+    cut = test_cutting(),
     seed = 2024,
     weight = early_zero(6)
   )
@@ -117,8 +117,8 @@ test_that("Test 5: RMST", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    tests = rmst,
-    cuts = test_cutting(),
+    test = rmst,
+    cut = test_cutting(),
     seed = 2024,
     tau = 20
   )
@@ -158,8 +158,8 @@ test_that("Test 6: Milestone", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    tests = milestone,
-    cuts = test_cutting(),
+    test = milestone,
+    cut = test_cutting(),
     seed = 2024,
     ms_time = 10
   )
@@ -211,8 +211,8 @@ test_that("Test 7: MaxCombo (WLR-FH(0,0) + WLR-FH(0, 0.5))", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    tests = maxcombo,
-    cuts = test_cutting(),
+    test = maxcombo,
+    cut = test_cutting(),
     seed = 2024,
     rho = c(0, 0),
     gamma = c(0, 0.5)
@@ -242,8 +242,8 @@ test_that("sim_gs_n() accepts different tests per cutting", {
     sample_size = 400,
     enroll_rate = test_enroll_rate(),
     fail_rate = test_fail_rate(),
-    tests = list(wlr_cut1, wlr_cut2, wlr_cut3),
-    cuts = test_cutting(),
+    test = list(wlr_cut1, wlr_cut2, wlr_cut3),
+    cut = test_cutting(),
     seed = 2024
   )
   expected <- data.frame(
@@ -273,8 +273,8 @@ test_that("sim_gs_n() requires a test for each cutting", {
       sample_size = 400,
       enroll_rate = test_enroll_rate(),
       fail_rate = test_fail_rate(),
-      tests = list(wlr_cut1, wlr_cut2),
-      cuts = test_cutting(),
+      test = list(wlr_cut1, wlr_cut2),
+      cut = test_cutting(),
       seed = 2024
     ),
     "If you want to run different tests at each cutting"

From ba959a39a3713152abcbbe197c54d7c1a4e7c19c Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 22 Mar 2024 11:27:55 -0400
Subject: [PATCH 3/5] Update argument names in documentation

---
 R/sim_gs_n.R    |  6 +++---
 man/sim_gs_n.Rd | 16 ++++++++--------
 2 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index d9b31123..6e2ab41b 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -22,7 +22,7 @@
 #' arguments will change as we add additional features.
 #'
 #' @inheritParams sim_fixed_n
-#' @param tests One or more test functions such as [wlr()], [maxcombo()], or
+#' @param test One or more test functions such as [wlr()], [maxcombo()], or
 #'   [rmst()]. If a single test function is provided, it will be applied at each
 #'   cut. Alternatively a list of functions created by [create_test()]. The list
 #'   form is experimental and currently limited. It only accepts one test per
@@ -31,8 +31,8 @@
 #'   flexible in the future). Importantly, note that the simulated data set is
 #'   always passed as the first positional argument to each test function
 #'   provided.
-#' @param cuts A list of cutting functions created by [create_cut()],
-#'   see examples.
+#' @param cut A list of cutting functions created by [create_cut()], see
+#'   examples.
 #' @param seed Random seed.
 #' @param ... Arguments passed to the test function(s) provided by the argument
 #'   `tests`.
diff --git a/man/sim_gs_n.Rd b/man/sim_gs_n.Rd
index a9f28787..4036b3c2 100644
--- a/man/sim_gs_n.Rd
+++ b/man/sim_gs_n.Rd
@@ -36,12 +36,7 @@ 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{seed}{Random seed.}
-
-\item{...}{Arguments passed to the test function(s) provided by the argument
-\code{tests}.}
-
-\item{tests}{One or more test functions such as \code{\link[=wlr]{wlr()}}, \code{\link[=maxcombo]{maxcombo()}}, or
+\item{test}{One or more test functions such as \code{\link[=wlr]{wlr()}}, \code{\link[=maxcombo]{maxcombo()}}, or
 \code{\link[=rmst]{rmst()}}. If a single test function is provided, it will be applied at each
 cut. Alternatively a list of functions created by \code{\link[=create_test]{create_test()}}. The list
 form is experimental and currently limited. It only accepts one test per
@@ -51,8 +46,13 @@ flexible in the future). Importantly, note that the simulated data set is
 always passed as the first positional argument to each test function
 provided.}
 
-\item{cuts}{A list of cutting functions created by \code{\link[=create_cut]{create_cut()}},
-see examples.}
+\item{cut}{A list of cutting functions created by \code{\link[=create_cut]{create_cut()}}, see
+examples.}
+
+\item{seed}{Random seed.}
+
+\item{...}{Arguments passed to the test function(s) provided by the argument
+\code{tests}.}
 }
 \value{
 A data frame summarizing the simulation ID, analysis date,

From 567c0416724dcd7b8b11eb2fc9cd118d7faeeedb Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Fri, 22 Mar 2024 11:39:03 -0400
Subject: [PATCH 4/5] Bump version

---
 DESCRIPTION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 41845a26..eef6c513 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.3.2.13
+Version: 0.3.2.14
 Authors@R: c(
     person("Keaven", "Anderson", email = "keaven_anderson@merck.com", role = c("aut")),
     person("Yilong", "Zhang", email = "elong0527@gmail.com", role =  c("aut")),

From d539ae69571753d76e878ec2424ae37424db8c55 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Mon, 25 Mar 2024 13:20:17 -0400
Subject: [PATCH 5/5] Fix documentation typo from argument renaming

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

diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index 6e2ab41b..863a7c5f 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -35,7 +35,7 @@
 #'   examples.
 #' @param seed Random seed.
 #' @param ... Arguments passed to the test function(s) provided by the argument
-#'   `tests`.
+#'   `test`.
 #'
 #' @return A data frame summarizing the simulation ID, analysis date,
 #'   z statistics or p-values.
diff --git a/man/sim_gs_n.Rd b/man/sim_gs_n.Rd
index 4036b3c2..06939310 100644
--- a/man/sim_gs_n.Rd
+++ b/man/sim_gs_n.Rd
@@ -52,7 +52,7 @@ examples.}
 \item{seed}{Random seed.}
 
 \item{...}{Arguments passed to the test function(s) provided by the argument
-\code{tests}.}
+\code{test}.}
 }
 \value{
 A data frame summarizing the simulation ID, analysis date,