From 0bbdaa48d18d94dc464b99ac346d033a451459c3 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Wed, 13 Mar 2024 15:32:57 -0400
Subject: [PATCH 1/7] Add rmst.formula()

---
 DESCRIPTION                            |  2 +-
 NAMESPACE                              |  1 +
 R/rmst.R                               | 23 +++++++++++++
 tests/testthat/test-unvalidated-rmst.R | 47 ++++++++++++++++++++++++++
 4 files changed, 72 insertions(+), 1 deletion(-)
 create mode 100644 tests/testthat/test-unvalidated-rmst.R

diff --git a/DESCRIPTION b/DESCRIPTION
index ca21590c..02de5e3e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.3.2.10
+Version: 0.3.2.11
 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/NAMESPACE b/NAMESPACE
index 4f6b6de3..c818fb50 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -20,6 +20,7 @@ export(multitest)
 export(pvalue_maxcombo)
 export(randomize_by_fixed_block)
 export(rmst)
+export(rmst.formula)
 export(rpwexp)
 export(rpwexp_enroll)
 export(sim_fixed_n)
diff --git a/R/rmst.R b/R/rmst.R
index 8e4cfb86..7e37dd7a 100644
--- a/R/rmst.R
+++ b/R/rmst.R
@@ -299,3 +299,26 @@ rmst_single_arm <- function(
 
   return(ans)
 }
+
+#' @export
+rmst.formula <- function(formula, data, tau = 10, reference = "control",
+                         alpha = 0.05) {
+  stopifnot(is.data.frame(data))
+
+  variables <- colnames(stats::get_all_vars(formula = formula, data = data))
+  if (length(variables) != 3) {
+    stop("The formula interface requires exactly 3 variables specified")
+  }
+
+  ans <- rmst(
+    data = data,
+    tau = tau,
+    var_label_tte = variables[1],
+    var_label_event = variables[2],
+    var_label_group = variables[3],
+    reference = reference,
+    alpha = alpha
+  )
+
+  return(ans)
+}
diff --git a/tests/testthat/test-unvalidated-rmst.R b/tests/testthat/test-unvalidated-rmst.R
new file mode 100644
index 00000000..1a199d0f
--- /dev/null
+++ b/tests/testthat/test-unvalidated-rmst.R
@@ -0,0 +1,47 @@
+test_that("rmst() snapshot test", {
+  data(ex1_delayed_effect)
+  observed <- rmst(
+    data = ex1_delayed_effect,
+    var_label_tte = "month",
+    var_label_event = "evntd",
+    var_label_group = "trt",
+    tau = 10,
+    reference = "0"
+  )
+  expected <- data.frame(
+    rmst_arm1 = 6.495175253205431,
+    rmst_arm0 = 5.630125973237457,
+    rmst_diff = 0.8650492799679741,
+    z = 2.2178796367487963
+  )
+  expect_equal(observed, expected)
+})
+
+test_that("formula method matches default method", {
+  data(ex1_delayed_effect)
+
+  rmst_default <- rmst(
+    data = ex1_delayed_effect,
+    var_label_tte = "month",
+    var_label_event = "evntd",
+    var_label_group = "trt",
+    tau = 10,
+    reference = "0"
+  )
+
+  rmst_formula_1 <- rmst.formula(
+    month ~ evntd + trt,
+    data = ex1_delayed_effect,
+    tau = 10,
+    reference = "0"
+  )
+  expect_equal(rmst_formula_1, rmst_default)
+
+  rmst_formula_2 <- rmst.formula(
+    survival::Surv(month | evntd) ~ trt,
+    data = ex1_delayed_effect,
+    tau = 10,
+    reference = "0"
+  )
+  expect_equal(rmst_formula_2, rmst_default)
+})

From a5476ee627488fda0f1c40740232eb0893ccccd2 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Wed, 13 Mar 2024 17:00:13 -0400
Subject: [PATCH 2/7] Convert rmst() into an S3 generic

---
 DESCRIPTION                            |  2 +-
 NAMESPACE                              |  3 ++-
 R/rmst.R                               | 30 +++++++++++++++-----------
 R/sim_gs_n.R                           |  2 +-
 man/rmst.Rd                            | 12 ++---------
 tests/testthat/test-unvalidated-rmst.R |  8 +++----
 6 files changed, 28 insertions(+), 29 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 02de5e3e..f367bd43 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.3.2.11
+Version: 0.3.2.12
 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/NAMESPACE b/NAMESPACE
index c818fb50..b7e8b84f 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,5 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(rmst,default)
+S3method(rmst,formula)
 export(counting_process)
 export(create_cutting)
 export(create_cutting_test)
@@ -20,7 +22,6 @@ export(multitest)
 export(pvalue_maxcombo)
 export(randomize_by_fixed_block)
 export(rmst)
-export(rmst.formula)
 export(rpwexp)
 export(rpwexp_enroll)
 export(sim_fixed_n)
diff --git a/R/rmst.R b/R/rmst.R
index 7e37dd7a..5a2c9b5b 100644
--- a/R/rmst.R
+++ b/R/rmst.R
@@ -35,25 +35,31 @@
 #' @examples
 #' data(ex1_delayed_effect)
 #' rmst(
-#'   data = ex1_delayed_effect,
+#'   x = ex1_delayed_effect,
 #'   var_label_tte = "month",
 #'   var_label_event = "evntd",
 #'   var_label_group = "trt",
 #'   tau = 10,
 #'   reference = "0"
 #' )
-rmst <- function(
-    data,
+rmst <- function(x, ...) {
+  UseMethod("rmst")
+}
+
+#' @export
+rmst.default <- function(
+    x,
     tau = 10,
     var_label_tte = "tte",
     var_label_event = "event",
     var_label_group = "treatment",
     reference = "control",
-    alpha = 0.05) {
+    alpha = 0.05,
+    ...) {
   res <- rmst_two_arm(
-    time_var = data[[var_label_tte]],
-    event_var = data[[var_label_event]],
-    group_var = data[[var_label_group]],
+    time_var = x[[var_label_tte]],
+    event_var = x[[var_label_event]],
+    group_var = x[[var_label_group]],
     trunc_time = tau,
     reference = reference,
     alpha = alpha
@@ -301,17 +307,17 @@ rmst_single_arm <- function(
 }
 
 #' @export
-rmst.formula <- function(formula, data, tau = 10, reference = "control",
-                         alpha = 0.05) {
+rmst.formula <- function(x, data, tau = 10, reference = "control",
+                         alpha = 0.05, ...) {
   stopifnot(is.data.frame(data))
 
-  variables <- colnames(stats::get_all_vars(formula = formula, data = data))
+  variables <- colnames(stats::get_all_vars(formula = x, data = data))
   if (length(variables) != 3) {
     stop("The formula interface requires exactly 3 variables specified")
   }
 
-  ans <- rmst(
-    data = data,
+  ans <- rmst.default(
+    x = data,
     tau = tau,
     var_label_tte = variables[1],
     var_label_event = variables[2],
diff --git a/R/sim_gs_n.R b/R/sim_gs_n.R
index 34395994..8f0fddb1 100644
--- a/R/sim_gs_n.R
+++ b/R/sim_gs_n.R
@@ -285,7 +285,7 @@ sim_gs_n <- function(
 
     for (i_analysis in seq_len(n_analysis)) {
       # Get cut date
-      cut_date[i_analysis] <- cutting[[i_analysis]](data = simu_data)
+      cut_date[i_analysis] <- cutting[[i_analysis]](simu_data)
 
       # Cut the data
       simu_data_cut <- simu_data |> cut_data_by_date(cut_date[i_analysis])
diff --git a/man/rmst.Rd b/man/rmst.Rd
index b6822fdd..e6506cd5 100644
--- a/man/rmst.Rd
+++ b/man/rmst.Rd
@@ -4,15 +4,7 @@
 \alias{rmst}
 \title{RMST difference of 2 arms}
 \usage{
-rmst(
-  data,
-  tau = 10,
-  var_label_tte = "tte",
-  var_label_event = "event",
-  var_label_group = "treatment",
-  reference = "control",
-  alpha = 0.05
-)
+rmst(x, ...)
 }
 \arguments{
 \item{data}{A time-to-event dataset with a column \code{tte} indicating the
@@ -40,7 +32,7 @@ RMST difference of 2 arms
 \examples{
 data(ex1_delayed_effect)
 rmst(
-  data = ex1_delayed_effect,
+  x = ex1_delayed_effect,
   var_label_tte = "month",
   var_label_event = "evntd",
   var_label_group = "trt",
diff --git a/tests/testthat/test-unvalidated-rmst.R b/tests/testthat/test-unvalidated-rmst.R
index 1a199d0f..e3651b08 100644
--- a/tests/testthat/test-unvalidated-rmst.R
+++ b/tests/testthat/test-unvalidated-rmst.R
@@ -1,7 +1,7 @@
 test_that("rmst() snapshot test", {
   data(ex1_delayed_effect)
   observed <- rmst(
-    data = ex1_delayed_effect,
+    ex1_delayed_effect,
     var_label_tte = "month",
     var_label_event = "evntd",
     var_label_group = "trt",
@@ -21,7 +21,7 @@ test_that("formula method matches default method", {
   data(ex1_delayed_effect)
 
   rmst_default <- rmst(
-    data = ex1_delayed_effect,
+    ex1_delayed_effect,
     var_label_tte = "month",
     var_label_event = "evntd",
     var_label_group = "trt",
@@ -29,7 +29,7 @@ test_that("formula method matches default method", {
     reference = "0"
   )
 
-  rmst_formula_1 <- rmst.formula(
+  rmst_formula_1 <- rmst(
     month ~ evntd + trt,
     data = ex1_delayed_effect,
     tau = 10,
@@ -37,7 +37,7 @@ test_that("formula method matches default method", {
   )
   expect_equal(rmst_formula_1, rmst_default)
 
-  rmst_formula_2 <- rmst.formula(
+  rmst_formula_2 <- rmst(
     survival::Surv(month | evntd) ~ trt,
     data = ex1_delayed_effect,
     tau = 10,

From 09eccb50616615262d972989ac6ea8adc65b773c Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Wed, 13 Mar 2024 23:15:58 -0400
Subject: [PATCH 3/7] Document formula interface of rmst()

---
 R/rmst.R    | 33 ++++++++++++++++++++++++++++++++
 man/rmst.Rd | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++---
 2 files changed, 84 insertions(+), 3 deletions(-)

diff --git a/R/rmst.R b/R/rmst.R
index 5a2c9b5b..d601ed9a 100644
--- a/R/rmst.R
+++ b/R/rmst.R
@@ -18,6 +18,9 @@
 
 #' RMST difference of 2 arms
 #'
+#' @param x Either a time-to-event dataset (see argument `data`) or a formula
+#'   that indicates the TTE, event, and group variables (in that exact order;
+#'   see Details below).
 #' @param data A time-to-event dataset with a column `tte` indicating the
 #'   survival time and a column of `event` indicating whether it is
 #'   event or censor.
@@ -27,6 +30,18 @@
 #' @param var_label_group Column name of the grouping variable.
 #' @param reference A group label indicating the reference group.
 #' @param alpha Type I error.
+#' @param ... Currently unused (required for S3 generic function)
+#'
+#' @details
+#' The formula interface is provided as a convenience to easily specify the TTE,
+#' event, and grouping variables. Note however that only the order of the three
+#' variables is actually used by the underlying function. Any functions applied
+#' in the formula are ignored, and thus should only be used for documenting your
+#' intent. For example, you can use the syntax from the survival package
+#' `Surv(tte | event) ~ group` to highlight the relation between the TTE and
+#' event variables, but the function `Surv()` is never actually executed.
+#' Importantly, you shouldn't apply any transformation functions such as `log()`
+#' since these will also be ignored.
 #'
 #' @return The z statistics.
 #'
@@ -42,10 +57,27 @@
 #'   tau = 10,
 #'   reference = "0"
 #' )
+#'
+#' # Formula interface
+#' rmst(
+#'   month ~ evntd + trt,
+#'   data = ex1_delayed_effect,
+#'   tau = 10,
+#'   reference = "0"
+#' )
+#'
+#' library("survival")
+#' rmst(
+#'   Surv(month | evntd) ~ trt,
+#'   data = ex1_delayed_effect,
+#'   tau = 10,
+#'   reference = "0"
+#' )
 rmst <- function(x, ...) {
   UseMethod("rmst")
 }
 
+#' @rdname rmst
 #' @export
 rmst.default <- function(
     x,
@@ -306,6 +338,7 @@ rmst_single_arm <- function(
   return(ans)
 }
 
+#' @rdname rmst
 #' @export
 rmst.formula <- function(x, data, tau = 10, reference = "control",
                          alpha = 0.05, ...) {
diff --git a/man/rmst.Rd b/man/rmst.Rd
index e6506cd5..c89da8aa 100644
--- a/man/rmst.Rd
+++ b/man/rmst.Rd
@@ -2,14 +2,31 @@
 % Please edit documentation in R/rmst.R
 \name{rmst}
 \alias{rmst}
+\alias{rmst.default}
+\alias{rmst.formula}
 \title{RMST difference of 2 arms}
 \usage{
 rmst(x, ...)
+
+\method{rmst}{default}(
+  x,
+  tau = 10,
+  var_label_tte = "tte",
+  var_label_event = "event",
+  var_label_group = "treatment",
+  reference = "control",
+  alpha = 0.05,
+  ...
+)
+
+\method{rmst}{formula}(x, data, tau = 10, reference = "control", alpha = 0.05, ...)
 }
 \arguments{
-\item{data}{A time-to-event dataset with a column \code{tte} indicating the
-survival time and a column of \code{event} indicating whether it is
-event or censor.}
+\item{x}{Either a time-to-event dataset (see argument \code{data}) or a formula
+that indicates the TTE, event, and group variables (in that exact order;
+see Details below).}
+
+\item{...}{Currently unused (required for S3 generic function)}
 
 \item{tau}{RMST analysis time.}
 
@@ -22,6 +39,10 @@ event or censor.}
 \item{reference}{A group label indicating the reference group.}
 
 \item{alpha}{Type I error.}
+
+\item{data}{A time-to-event dataset with a column \code{tte} indicating the
+survival time and a column of \code{event} indicating whether it is
+event or censor.}
 }
 \value{
 The z statistics.
@@ -29,6 +50,17 @@ The z statistics.
 \description{
 RMST difference of 2 arms
 }
+\details{
+The formula interface is provided as a convenience to easily specify the TTE,
+event, and grouping variables. Note however that only the order of the three
+variables is actually used by the underlying function. Any functions applied
+in the formula are ignored, and thus should only be used for documenting your
+intent. For example, you can use the syntax from the survival package
+\code{Surv(tte | event) ~ group} to highlight the relation between the TTE and
+event variables, but the function \code{Surv()} is never actually executed.
+Importantly, you shouldn't apply any transformation functions such as \code{log()}
+since these will also be ignored.
+}
 \examples{
 data(ex1_delayed_effect)
 rmst(
@@ -39,4 +71,20 @@ rmst(
   tau = 10,
   reference = "0"
 )
+
+# Formula interface
+rmst(
+  month ~ evntd + trt,
+  data = ex1_delayed_effect,
+  tau = 10,
+  reference = "0"
+)
+
+library("survival")
+rmst(
+  Surv(month | evntd) ~ trt,
+  data = ex1_delayed_effect,
+  tau = 10,
+  reference = "0"
+)
 }

From 9ed6d32660deb16a2516329545c1b922facbc9f7 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Wed, 13 Mar 2024 23:21:41 -0400
Subject: [PATCH 4/7] styler:::style_active_pkg()

---
 R/maxcombo.R                               |  4 ++--
 R/wlr.R                                    | 26 +++++++++++-----------
 R/wlr_weight.R                             |  6 ++---
 tests/testthat/helper-pmvnorm.R            |  2 +-
 tests/testthat/helper-sim_gs_n.R           | 22 +++++++++---------
 tests/testthat/helper-simfix.R             |  2 +-
 tests/testthat/test-unvalidated-sim_gs_n.R | 16 ++++++-------
 7 files changed, 40 insertions(+), 38 deletions(-)

diff --git a/R/maxcombo.R b/R/maxcombo.R
index 18e3eb08..a8b93bc1 100644
--- a/R/maxcombo.R
+++ b/R/maxcombo.R
@@ -36,7 +36,7 @@
 #' sim_pw_surv(n = 200) |>
 #'   cut_data_by_event(150) |>
 #'   maxcombo(rho = c(0, 0), gamma = c(0, 0.5))
-maxcombo <- function(data, rho, gamma){
+maxcombo <- function(data, rho, gamma) {
   stopifnot(
     is.numeric(rho), is.numeric(gamma),
     rho >= 0, gamma >= 0,
@@ -50,7 +50,7 @@ maxcombo <- function(data, rho, gamma){
       return_corr = TRUE
     )
 
-  ans <-  data.frame(p_value = pvalue_maxcombo(ans))
+  ans <- data.frame(p_value = pvalue_maxcombo(ans))
 
   return(ans)
 }
diff --git a/R/wlr.R b/R/wlr.R
index 672c8262..d855588c 100644
--- a/R/wlr.R
+++ b/R/wlr.R
@@ -40,23 +40,22 @@
 #'   cut_data_by_event(150) |>
 #'   wlr(weight = early_zero(early_period = 4))
 #'
-wlr <- function(data, weight){
-
+wlr <- function(data, 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 (inherits(weight, "mb")) {
     ans <- data |>
       counting_process(arm = "experimental") |>
       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)
-               )
+    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")) {
@@ -64,11 +63,12 @@ wlr <- function(data, weight){
       counting_process(arm = "experimental") |>
       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)
-               )
+    ans <- ans[
+      ,
+      .(
+        s = sum(o_minus_e * weight),
+        v = sum(var_o_minus_e * weight^2)
+      )
     ][, .(z = s / sqrt(v))]
     setDF(ans)
   }
diff --git a/R/wlr_weight.R b/R/wlr_weight.R
index b4ae8d63..cfb0a542 100644
--- a/R/wlr_weight.R
+++ b/R/wlr_weight.R
@@ -25,7 +25,7 @@
 #' @return A list of parameters of the Fleming-Harrington weighting function
 #' @examples
 #' fh(rho = 0, gamma = 0.5)
-fh <- function(rho = 0, gamma = 0){
+fh <- function(rho = 0, gamma = 0) {
   structure(list(rho = rho, gamma = gamma), class = c("list", "fh", "wlr"))
 }
 
@@ -42,7 +42,7 @@ fh <- function(rho = 0, gamma = 0){
 #'
 #' @examples
 #' mb(delay = 6, w_max = 2)
-mb <- function(delay = 4, w_max = Inf){
+mb <- function(delay = 4, w_max = Inf) {
   structure(list(delay = delay, w_max = w_max), class = c("list", "mb", "wlr"))
 }
 
@@ -59,6 +59,6 @@ mb <- function(delay = 4, w_max = Inf){
 #'
 #' @examples
 #' early_zero(6)
-early_zero <- function(early_period){
+early_zero <- function(early_period) {
   structure(list(early_period = early_period), class = c("list", "early_period", "wlr"))
 }
diff --git a/tests/testthat/helper-pmvnorm.R b/tests/testthat/helper-pmvnorm.R
index 2b00eb63..f5cc23b9 100644
--- a/tests/testthat/helper-pmvnorm.R
+++ b/tests/testthat/helper-pmvnorm.R
@@ -137,7 +137,7 @@ ptvnorm <- function(h, r, ro) {
   hp2 <- (h2 * rr133 - h1 * f3 - h3 * f2) / fac / sqrt(rr133)
   TV <- w * exp((rr12 * h12 - h122) / rr122) / sqrt(rr122) * pnorm(hp1) *
     r12 + w * exp((rr13 * h13 - h132) / rr133) / sqrt(rr133) * pnorm(hp2) *
-    r13
+      r13
   TV <- sum(TV)
   rho <- matrix(c(1, r23, r23, 1), 2, 2)
   p2 <- mvtnorm::pmvnorm(-Inf, c(h2, h3), c(0, 0), rho)
diff --git a/tests/testthat/helper-sim_gs_n.R b/tests/testthat/helper-sim_gs_n.R
index 94e49a7b..49828a54 100644
--- a/tests/testthat/helper-sim_gs_n.R
+++ b/tests/testthat/helper-sim_gs_n.R
@@ -3,10 +3,12 @@
 test_enroll_rate <- function() {
   # parameters for enrollment
   enroll_rampup_duration <- 4 # duration for enrollment ramp up
-  enroll_duration <- 16       # total enrollment duration
+  enroll_duration <- 16 # total enrollment duration
   enroll_rate <- gsDesign2::define_enroll_rate(
-    duration = c(enroll_rampup_duration,
-                 enroll_duration - enroll_rampup_duration),
+    duration = c(
+      enroll_rampup_duration,
+      enroll_duration - enroll_rampup_duration
+    ),
     rate = c(10, 30)
   )
   return(enroll_rate)
@@ -14,13 +16,13 @@ test_enroll_rate <- function() {
 
 test_fail_rate <- function() {
   # parameters for treatment effect
-  delay_effect_duration <- 3  # delay treatment effect in months
-  median_ctrl <- 9            # survival median of the control arm
-  median_exp <- c(9, 14)      # survival median of the experimental arm
+  delay_effect_duration <- 3 # delay treatment effect in months
+  median_ctrl <- 9 # survival median of the control arm
+  median_exp <- c(9, 14) # survival median of the experimental arm
   dropout_rate <- 0.001
   fail_rate <- gsDesign2::define_fail_rate(
     duration = c(delay_effect_duration, 100),
-    fail_rate = log(2) /  median_ctrl,
+    fail_rate = log(2) / median_ctrl,
     hr = median_ctrl / median_exp,
     dropout_rate = dropout_rate
   )
@@ -29,9 +31,9 @@ test_fail_rate <- function() {
 
 test_cutting <- function() {
   # other related parameters
-  alpha <- 0.025              # type I error
-  beta <- 0.1                 # type II error
-  ratio <- 1                  # randomization ratio (exp:ctrl)
+  alpha <- 0.025 # type I error
+  beta <- 0.1 # type II error
+  ratio <- 1 # randomization ratio (exp:ctrl)
   # Define cuttings of 2 IAs and 1 FA
   # IA1
   # The 1st interim analysis will occur at the later of the following 3 conditions:
diff --git a/tests/testthat/helper-simfix.R b/tests/testthat/helper-simfix.R
index 1bbba3b9..5b9bf7f9 100644
--- a/tests/testthat/helper-simfix.R
+++ b/tests/testthat/helper-simfix.R
@@ -1,6 +1,6 @@
 # Helper functions used by test-double_programming_simfix.R
 
-test_simfix <- function () {
+test_simfix <- function() {
   # Study design using gsDesign
   alpha <- 0.025
   gamma <- c(5, 5, 47)
diff --git a/tests/testthat/test-unvalidated-sim_gs_n.R b/tests/testthat/test-unvalidated-sim_gs_n.R
index b6a3df23..80bc742a 100644
--- a/tests/testthat/test-unvalidated-sim_gs_n.R
+++ b/tests/testthat/test-unvalidated-sim_gs_n.R
@@ -154,14 +154,14 @@ test_that("Test 5: RMST", {
 
 test_that("Test 6: Milestone", {
   observed <- sim_gs_n(
-   n_sim = 3,
-   sample_size = 400,
-   enroll_rate = test_enroll_rate(),
-   fail_rate = test_fail_rate(),
-   test = milestone,
-   cutting = test_cutting(),
-   seed = 2024,
-   ms_time = 10
+    n_sim = 3,
+    sample_size = 400,
+    enroll_rate = test_enroll_rate(),
+    fail_rate = test_fail_rate(),
+    test = milestone,
+    cutting = test_cutting(),
+    seed = 2024,
+    ms_time = 10
   )
   expected <- data.frame(
     method = rep("milestone", 9L),

From 3ccb49388c6959c38c91c0debfe1f5770968b2d4 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Thu, 14 Mar 2024 11:28:00 -0400
Subject: [PATCH 5/7] Include `rmst()` formula example `~ Surv(month, evntd,
 trt)`

---
 R/rmst.R                               | 17 ++++++++++++++---
 man/rmst.Rd                            | 17 ++++++++++++++---
 tests/testthat/test-unvalidated-rmst.R |  8 ++++++++
 3 files changed, 36 insertions(+), 6 deletions(-)

diff --git a/R/rmst.R b/R/rmst.R
index d601ed9a..ce27abea 100644
--- a/R/rmst.R
+++ b/R/rmst.R
@@ -59,16 +59,27 @@
 #' )
 #'
 #' # Formula interface
+#' library("survival")
+#'
 #' rmst(
-#'   month ~ evntd + trt,
+#'   Surv(month | evntd) ~ trt,
 #'   data = ex1_delayed_effect,
 #'   tau = 10,
 #'   reference = "0"
 #' )
 #'
-#' library("survival")
+#' # alternative
 #' rmst(
-#'   Surv(month | evntd) ~ trt,
+#'   ~ Surv(month, evntd, trt),
+#'   data = ex1_delayed_effect,
+#'   tau = 10,
+#'   reference = "0"
+#' )
+#'
+#' # This example doesn't make statistical sense, but demonstrates that only the
+#' # order of the 3 variables actually matters
+#' rmst(
+#'   month ~ evntd + trt,
 #'   data = ex1_delayed_effect,
 #'   tau = 10,
 #'   reference = "0"
diff --git a/man/rmst.Rd b/man/rmst.Rd
index c89da8aa..c6a794ba 100644
--- a/man/rmst.Rd
+++ b/man/rmst.Rd
@@ -73,16 +73,27 @@ rmst(
 )
 
 # Formula interface
+library("survival")
+
 rmst(
-  month ~ evntd + trt,
+  Surv(month | evntd) ~ trt,
   data = ex1_delayed_effect,
   tau = 10,
   reference = "0"
 )
 
-library("survival")
+# alternative
 rmst(
-  Surv(month | evntd) ~ trt,
+  ~ Surv(month, evntd, trt),
+  data = ex1_delayed_effect,
+  tau = 10,
+  reference = "0"
+)
+
+# This example doesn't make statistical sense, but demonstrates that only the
+# order of the 3 variables actually matters
+rmst(
+  month ~ evntd + trt,
   data = ex1_delayed_effect,
   tau = 10,
   reference = "0"
diff --git a/tests/testthat/test-unvalidated-rmst.R b/tests/testthat/test-unvalidated-rmst.R
index e3651b08..e2f34eab 100644
--- a/tests/testthat/test-unvalidated-rmst.R
+++ b/tests/testthat/test-unvalidated-rmst.R
@@ -44,4 +44,12 @@ test_that("formula method matches default method", {
     reference = "0"
   )
   expect_equal(rmst_formula_2, rmst_default)
+
+  rmst_formula_3 <- rmst(
+    ~ survival::Surv(month, evntd, trt),
+    data = ex1_delayed_effect,
+    tau = 10,
+    reference = "0"
+  )
+  expect_equal(rmst_formula_3, rmst_default)
 })

From d38b2e9a5075bf91194803b7c690178aadefe936 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Mon, 18 Mar 2024 11:54:03 -0400
Subject: [PATCH 6/7] Use argument `formula` instead of S3 generic

Advantages:

* Less complex
* Able to use more informative arg names like `data` and `formula`
* Still easily pipe `data` as first arg even when using formula arg
---
 DESCRIPTION                            |  2 +-
 NAMESPACE                              |  2 -
 R/rmst.R                               | 75 ++++++++++----------------
 man/rmst.Rd                            | 42 +++++++--------
 tests/testthat/test-unvalidated-rmst.R | 36 ++++++++++---
 5 files changed, 77 insertions(+), 80 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f367bd43..41845a26 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: simtrial
 Type: Package
 Title: Clinical Trial Simulation
-Version: 0.3.2.12
+Version: 0.3.2.13
 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/NAMESPACE b/NAMESPACE
index b7e8b84f..4f6b6de3 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,7 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(rmst,default)
-S3method(rmst,formula)
 export(counting_process)
 export(create_cutting)
 export(create_cutting_test)
diff --git a/R/rmst.R b/R/rmst.R
index ce27abea..71413e46 100644
--- a/R/rmst.R
+++ b/R/rmst.R
@@ -18,9 +18,6 @@
 
 #' RMST difference of 2 arms
 #'
-#' @param x Either a time-to-event dataset (see argument `data`) or a formula
-#'   that indicates the TTE, event, and group variables (in that exact order;
-#'   see Details below).
 #' @param data A time-to-event dataset with a column `tte` indicating the
 #'   survival time and a column of `event` indicating whether it is
 #'   event or censor.
@@ -28,12 +25,16 @@
 #' @param var_label_tte Column name of the TTE variable.
 #' @param var_label_event Column name of the event variable.
 #' @param var_label_group Column name of the grouping variable.
+#' @param formula (default: `NULL`) A formula that indicates the TTE, event, and
+#'   group variables (in that exact order; see Details below). This is an
+#'   alternative to specifying the variables as strings. If a formula is
+#'   provided, the values passed to `var_label_tte`, `var_label_event`, and
+#'   `var_label_group` are ignored.
 #' @param reference A group label indicating the reference group.
 #' @param alpha Type I error.
-#' @param ... Currently unused (required for S3 generic function)
 #'
 #' @details
-#' The formula interface is provided as a convenience to easily specify the TTE,
+#' The argument `formula` is provided as a convenience to easily specify the TTE,
 #' event, and grouping variables. Note however that only the order of the three
 #' variables is actually used by the underlying function. Any functions applied
 #' in the formula are ignored, and thus should only be used for documenting your
@@ -50,7 +51,7 @@
 #' @examples
 #' data(ex1_delayed_effect)
 #' rmst(
-#'   x = ex1_delayed_effect,
+#'   data = ex1_delayed_effect,
 #'   var_label_tte = "month",
 #'   var_label_event = "evntd",
 #'   var_label_group = "trt",
@@ -62,16 +63,16 @@
 #' library("survival")
 #'
 #' rmst(
-#'   Surv(month | evntd) ~ trt,
 #'   data = ex1_delayed_effect,
+#'   formula = Surv(month | evntd) ~ trt,
 #'   tau = 10,
 #'   reference = "0"
 #' )
 #'
 #' # alternative
 #' rmst(
-#'   ~ Surv(month, evntd, trt),
 #'   data = ex1_delayed_effect,
+#'   formula = ~ Surv(month, evntd, trt),
 #'   tau = 10,
 #'   reference = "0"
 #' )
@@ -79,30 +80,36 @@
 #' # This example doesn't make statistical sense, but demonstrates that only the
 #' # order of the 3 variables actually matters
 #' rmst(
-#'   month ~ evntd + trt,
 #'   data = ex1_delayed_effect,
+#'   formula = month ~ evntd + trt,
 #'   tau = 10,
 #'   reference = "0"
 #' )
-rmst <- function(x, ...) {
-  UseMethod("rmst")
-}
-
-#' @rdname rmst
-#' @export
-rmst.default <- function(
-    x,
+rmst <- function(
+    data,
     tau = 10,
     var_label_tte = "tte",
     var_label_event = "event",
     var_label_group = "treatment",
+    formula = NULL,
     reference = "control",
-    alpha = 0.05,
-    ...) {
+    alpha = 0.05) {
+  stopifnot(is.data.frame(data))
+
+  if (!is.null(formula)) {
+    variables <- colnames(stats::get_all_vars(formula = formula, data = data))
+    if (length(variables) != 3) {
+      stop("The formula interface requires exactly 3 variables specified")
+    }
+    var_label_tte <- variables[1]
+    var_label_event <- variables[2]
+    var_label_group <- variables[3]
+  }
+
   res <- rmst_two_arm(
-    time_var = x[[var_label_tte]],
-    event_var = x[[var_label_event]],
-    group_var = x[[var_label_group]],
+    time_var = data[[var_label_tte]],
+    event_var = data[[var_label_event]],
+    group_var = data[[var_label_group]],
     trunc_time = tau,
     reference = reference,
     alpha = alpha
@@ -348,27 +355,3 @@ rmst_single_arm <- function(
 
   return(ans)
 }
-
-#' @rdname rmst
-#' @export
-rmst.formula <- function(x, data, tau = 10, reference = "control",
-                         alpha = 0.05, ...) {
-  stopifnot(is.data.frame(data))
-
-  variables <- colnames(stats::get_all_vars(formula = x, data = data))
-  if (length(variables) != 3) {
-    stop("The formula interface requires exactly 3 variables specified")
-  }
-
-  ans <- rmst.default(
-    x = data,
-    tau = tau,
-    var_label_tte = variables[1],
-    var_label_event = variables[2],
-    var_label_group = variables[3],
-    reference = reference,
-    alpha = alpha
-  )
-
-  return(ans)
-}
diff --git a/man/rmst.Rd b/man/rmst.Rd
index c6a794ba..d6099705 100644
--- a/man/rmst.Rd
+++ b/man/rmst.Rd
@@ -2,31 +2,23 @@
 % Please edit documentation in R/rmst.R
 \name{rmst}
 \alias{rmst}
-\alias{rmst.default}
-\alias{rmst.formula}
 \title{RMST difference of 2 arms}
 \usage{
-rmst(x, ...)
-
-\method{rmst}{default}(
-  x,
+rmst(
+  data,
   tau = 10,
   var_label_tte = "tte",
   var_label_event = "event",
   var_label_group = "treatment",
+  formula = NULL,
   reference = "control",
-  alpha = 0.05,
-  ...
+  alpha = 0.05
 )
-
-\method{rmst}{formula}(x, data, tau = 10, reference = "control", alpha = 0.05, ...)
 }
 \arguments{
-\item{x}{Either a time-to-event dataset (see argument \code{data}) or a formula
-that indicates the TTE, event, and group variables (in that exact order;
-see Details below).}
-
-\item{...}{Currently unused (required for S3 generic function)}
+\item{data}{A time-to-event dataset with a column \code{tte} indicating the
+survival time and a column of \code{event} indicating whether it is
+event or censor.}
 
 \item{tau}{RMST analysis time.}
 
@@ -36,13 +28,15 @@ see Details below).}
 
 \item{var_label_group}{Column name of the grouping variable.}
 
+\item{formula}{(default: \code{NULL}) A formula that indicates the TTE, event, and
+group variables (in that exact order; see Details below). This is an
+alternative to specifying the variables as strings. If a formula is
+provided, the values passed to \code{var_label_tte}, \code{var_label_event}, and
+\code{var_label_group} are ignored.}
+
 \item{reference}{A group label indicating the reference group.}
 
 \item{alpha}{Type I error.}
-
-\item{data}{A time-to-event dataset with a column \code{tte} indicating the
-survival time and a column of \code{event} indicating whether it is
-event or censor.}
 }
 \value{
 The z statistics.
@@ -51,7 +45,7 @@ The z statistics.
 RMST difference of 2 arms
 }
 \details{
-The formula interface is provided as a convenience to easily specify the TTE,
+The argument \code{formula} is provided as a convenience to easily specify the TTE,
 event, and grouping variables. Note however that only the order of the three
 variables is actually used by the underlying function. Any functions applied
 in the formula are ignored, and thus should only be used for documenting your
@@ -64,7 +58,7 @@ since these will also be ignored.
 \examples{
 data(ex1_delayed_effect)
 rmst(
-  x = ex1_delayed_effect,
+  data = ex1_delayed_effect,
   var_label_tte = "month",
   var_label_event = "evntd",
   var_label_group = "trt",
@@ -76,16 +70,16 @@ rmst(
 library("survival")
 
 rmst(
-  Surv(month | evntd) ~ trt,
   data = ex1_delayed_effect,
+  formula = Surv(month | evntd) ~ trt,
   tau = 10,
   reference = "0"
 )
 
 # alternative
 rmst(
-  ~ Surv(month, evntd, trt),
   data = ex1_delayed_effect,
+  formula = ~ Surv(month, evntd, trt),
   tau = 10,
   reference = "0"
 )
@@ -93,8 +87,8 @@ rmst(
 # This example doesn't make statistical sense, but demonstrates that only the
 # order of the 3 variables actually matters
 rmst(
-  month ~ evntd + trt,
   data = ex1_delayed_effect,
+  formula = month ~ evntd + trt,
   tau = 10,
   reference = "0"
 )
diff --git a/tests/testthat/test-unvalidated-rmst.R b/tests/testthat/test-unvalidated-rmst.R
index e2f34eab..25c8426d 100644
--- a/tests/testthat/test-unvalidated-rmst.R
+++ b/tests/testthat/test-unvalidated-rmst.R
@@ -1,7 +1,7 @@
 test_that("rmst() snapshot test", {
-  data(ex1_delayed_effect)
+  data("ex1_delayed_effect")
   observed <- rmst(
-    ex1_delayed_effect,
+    data = ex1_delayed_effect,
     var_label_tte = "month",
     var_label_event = "evntd",
     var_label_group = "trt",
@@ -18,10 +18,10 @@ test_that("rmst() snapshot test", {
 })
 
 test_that("formula method matches default method", {
-  data(ex1_delayed_effect)
+  data("ex1_delayed_effect")
 
   rmst_default <- rmst(
-    ex1_delayed_effect,
+    data = ex1_delayed_effect,
     var_label_tte = "month",
     var_label_event = "evntd",
     var_label_group = "trt",
@@ -30,26 +30,48 @@ test_that("formula method matches default method", {
   )
 
   rmst_formula_1 <- rmst(
-    month ~ evntd + trt,
     data = ex1_delayed_effect,
+    formula = month ~ evntd + trt,
     tau = 10,
     reference = "0"
   )
   expect_equal(rmst_formula_1, rmst_default)
 
   rmst_formula_2 <- rmst(
-    survival::Surv(month | evntd) ~ trt,
     data = ex1_delayed_effect,
+    formula = survival::Surv(month | evntd) ~ trt,
     tau = 10,
     reference = "0"
   )
   expect_equal(rmst_formula_2, rmst_default)
 
   rmst_formula_3 <- rmst(
-    ~ survival::Surv(month, evntd, trt),
     data = ex1_delayed_effect,
+    formula = ~ survival::Surv(month, evntd, trt),
     tau = 10,
     reference = "0"
   )
   expect_equal(rmst_formula_3, rmst_default)
 })
+
+test_that("default and formula methods of rmst are pipeable", {
+  data("ex1_delayed_effect")
+
+  rmst_default <- ex1_delayed_effect |>
+    rmst(
+      var_label_tte = "month",
+      var_label_event = "evntd",
+      var_label_group = "trt",
+      tau = 10,
+      reference = "0"
+    )
+
+  rmst_formula_1 <- ex1_delayed_effect |>
+    rmst(
+      formula = month ~ evntd + trt,
+      tau = 10,
+      reference = "0"
+    )
+
+  expect_equal(rmst_formula_1, rmst_default)
+})

From 34f7789b27bcba42422092c0b186f6247b44b167 Mon Sep 17 00:00:00 2001
From: John Blischak <jdblischak@gmail.com>
Date: Mon, 18 Mar 2024 12:09:21 -0400
Subject: [PATCH 7/7] Test error handling of new rmst() argument `formula`

---
 R/rmst.R                               |  1 +
 tests/testthat/test-unvalidated-rmst.R | 38 ++++++++++++++++++++++++++
 2 files changed, 39 insertions(+)

diff --git a/R/rmst.R b/R/rmst.R
index 71413e46..5084c0c7 100644
--- a/R/rmst.R
+++ b/R/rmst.R
@@ -97,6 +97,7 @@ rmst <- function(
   stopifnot(is.data.frame(data))
 
   if (!is.null(formula)) {
+    stopifnot(inherits(formula, "formula"))
     variables <- colnames(stats::get_all_vars(formula = formula, data = data))
     if (length(variables) != 3) {
       stop("The formula interface requires exactly 3 variables specified")
diff --git a/tests/testthat/test-unvalidated-rmst.R b/tests/testthat/test-unvalidated-rmst.R
index 25c8426d..7aad6887 100644
--- a/tests/testthat/test-unvalidated-rmst.R
+++ b/tests/testthat/test-unvalidated-rmst.R
@@ -75,3 +75,41 @@ test_that("default and formula methods of rmst are pipeable", {
 
   expect_equal(rmst_formula_1, rmst_default)
 })
+
+test_that("formula argument throws error for bad input data", {
+  data("ex1_delayed_effect")
+
+  # formula with 2 variables
+  expect_error(
+    rmst_formula_1 <- rmst(
+      data = ex1_delayed_effect,
+      formula = month ~ evntd,
+      tau = 10,
+      reference = "0"
+    ),
+    "The formula interface requires exactly 3 variables specified"
+  )
+
+  # formula with 4 variables
+  expect_error(
+    rmst_formula_1 <- rmst(
+      data = ex1_delayed_effect,
+      formula = month ~ evntd + trt + id,
+      tau = 10,
+      reference = "0"
+    ),
+    "The formula interface requires exactly 3 variables specified"
+  )
+
+  # non-formula
+  expect_error(
+    rmst_formula_1 <- rmst(
+      data = ex1_delayed_effect,
+      formula = "month ~ evntd + trt + id",
+      tau = 10,
+      reference = "0"
+    ),
+    'inherits(formula, "formula") is not TRUE',
+    fixed = TRUE
+  )
+})