From d935f1147dfe510f80193ce1fe1ba8ea05c25762 Mon Sep 17 00:00:00 2001
From: Youngrok Lee <youngrok.lee.dev@gmail.com>
Date: Sat, 11 Jul 2026 19:56:24 -0400
Subject: [PATCH 1/2] test definition of outcome and survival time for analysis
 model

---
 tests/testthat/test-apply_logics.R | 53 ++++++++++++++++++++++++++++++
 1 file changed, 53 insertions(+)
 create mode 100644 tests/testthat/test-apply_logics.R

diff --git a/tests/testthat/test-apply_logics.R b/tests/testthat/test-apply_logics.R
new file mode 100644
index 0000000..064f8a1
--- /dev/null
+++ b/tests/testthat/test-apply_logics.R
@@ -0,0 +1,53 @@
+test_that("definition of the outcome and survival time for each patient in each arm is correctly match to Maringe et al. (2020) for analysis model", {
+  data(patients13)
+
+  clones <- clone_arms(patients13, c("Control", "Surgery"))
+  policy <- create_policy_A(
+    arms = c("Control", "Surgery"),
+    treatment = "surgery",
+    time_to_treatment = "time_to_surgery",
+    grace_period = 182,
+    outcome = "death",
+    followup = "followup",
+    clone_outcome = "analysis_outcome",
+    clone_followup = "analysis_followup"
+  )
+  res <- apply_logics(clones, policy)
+
+  # check control arm results
+  expect_equal(
+    res$Control |>
+      dplyr::select(id, analysis_outcome, analysis_followup),
+    patients13 |>
+      dplyr::transmute(
+        id,
+        analysis_outcome = dplyr::case_when(
+          id %in% c("A", "B", "C", "D", "E") ~ 0,
+          id %in% c("F", "G", "H", "I", "J", "K", "L", "M") ~ death,
+        ),
+        analysis_followup = dplyr::case_when(
+          id %in% c("A", "B", "C", "D", "E") ~ time_to_surgery,
+          id %in% c("F", "G", "H", "I", "J", "K", "L", "M") ~ followup,
+        )
+      )
+  )
+
+  # check surgery arm results
+  expect_equal(
+    res$Surgery |>
+      dplyr::select(id, analysis_outcome, analysis_followup),
+    patients13 |>
+      dplyr::transmute(
+        id,
+        analysis_outcome = dplyr::case_when(
+          id %in% c("A", "B", "C", "D", "E") ~ death,
+          id %in% c("F", "G", "H", "I", "J", "L", "M") ~ 0,
+          id %in% c("K") ~ 1,
+        ),
+        analysis_followup = dplyr::case_when(
+          id %in% c("A", "B", "C", "D", "E") ~ followup,
+          id %in% c("F", "G", "H", "I", "J", "K", "L", "M") ~ pmin(182, followup),
+        )
+      )
+  )
+})

From 0742a29ad2516032feeee5be98721fd52b008a96 Mon Sep 17 00:00:00 2001
From: Youngrok Lee <youngrok.lee.dev@gmail.com>
Date: Sat, 11 Jul 2026 19:59:05 -0400
Subject: [PATCH 2/2] fix bug to correctly define outcome and survival time for
 analysis model in treatment arm

---
 R/apply_logics.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/apply_logics.R b/R/apply_logics.R
index 35c1cea..15d77b8 100644
--- a/R/apply_logics.R
+++ b/R/apply_logics.R
@@ -154,7 +154,7 @@ create_policy_A <- function(
           "{treatment} == 0 & {followup} <= {grace_period} ~ {outcome}"
         ),
         glue::glue(
-          "({treatment} == 0 & {followup} > {grace_period}) | ({treatment} == 0 & {time_to_treatment} > {grace_period}) ~ 0"
+          "({treatment} == 0 & {followup} > {grace_period}) | ({treatment} == 1 & {time_to_treatment} > {grace_period}) ~ 0"
         )
       ),
       followup = c(
@@ -165,7 +165,7 @@ create_policy_A <- function(
           "{treatment} == 0 & {followup} <= {grace_period} ~ {followup}"
         ),
         glue::glue(
-          "({treatment} == 0 & {followup} > {grace_period}) | ({treatment} == 0 & {time_to_treatment} > {grace_period}) ~ {grace_period}"
+          "({treatment} == 0 & {followup} > {grace_period}) | ({treatment} == 1 & {time_to_treatment} > {grace_period}) ~ {grace_period}"
         )
       )
     )