From ffc9d5abc6d0336673a1b9f019f388d860e15a37 Mon Sep 17 00:00:00 2001
From: *** Li Ma *** <li.ma2@merck.com>
Date: Tue, 28 Apr 2026 13:49:21 -0400
Subject: [PATCH] CheckIn - modification to issue_107 adding var in
 define_population and define_observation

---
 vignettes/forestly.Rmd | 32 ++++++++++++++++++++++----------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/vignettes/forestly.Rmd b/vignettes/forestly.Rmd
index 8172b0c..85d9382 100644
--- a/vignettes/forestly.Rmd
+++ b/vignettes/forestly.Rmd
@@ -94,12 +94,20 @@ We then define the related population (`population = "apat"`) and observation (`
 ```{r}
 meta <- meta |>
   define_population(
-    name = "apat", group = "TRTA", id = "USUBJID",
-    subset = SAFFL == "Y", label = "All Patient as Treated"
+    name = "apat", 
+    group = "TRTA", 
+    id = "USUBJID",
+    subset = SAFFL == "Y", 
+    label = "All Patient as Treated",
+    var = c("USUBJID", "SAFFL", "TRTA", "SITEID", "SEX", "RACE", "AGE")
   ) |>
   define_observation(
-    name = "apat", group = "TRTA",
-    subset = SAFFL == "Y", label = "All Patient as Treated"
+    name = "apat", 
+    group = "TRTA",
+    subset = SAFFL == "Y", 
+    label = "All Patient as Treated",
+    var = c("USUBJID", "SAFFL", "TRTA", "AEDECOD", "AEBODSYS", 
+            "AEREL", "AESER", "AEOUT", "AEACN", "AESDTH", "ASTDT", "AENDT")
   )
 ```
 
@@ -110,7 +118,8 @@ meta <- meta |>
     name = "any",
     subset = NULL,
     label = "Any AEs",
-    var = "AEDECOD", soc = "AEBODSYS"
+    var = "AEDECOD", 
+    soc = "AEBODSYS"
   )
 ```
 For drug related AEs (`"drug-related"`), its filter is `AEREL %in% c("PROBABLE", "POSSIBLE")`.
@@ -118,9 +127,10 @@ For drug related AEs (`"drug-related"`), its filter is `AEREL %in% c("PROBABLE",
 meta <- meta |>
   define_parameter(
     name = "drug-related",
-    subset = toupper(AREL) == "RELATED",
+    subset = toupper(AEREL) %in% c("PROBABLE", "POSSIBLE"),
     label = "Drug-related AEs",
-    var = "AEDECOD", soc = "AEBODSYS"
+    var = "AEDECOD", 
+    soc = "AEBODSYS"
   )
 ```
 Similarly, we define serious AE and drug related serious AEs.
@@ -130,13 +140,15 @@ meta <- meta |>
     name = "serious",
     subset = AESER == "Y",
     label = "Serious AEs",
-    var = "AEDECOD", soc = "AEBODSYS"
+    var = "AEDECOD", 
+    soc = "AEBODSYS"
   ) |>
   define_parameter(
     name = "drug-related-serious",
-    subset = AESER == "Y" & AEREL %in% c("PROBABLE", "POSSIBLE"),
+    subset = AESER == "Y" & toupper(AEREL) %in% c("PROBABLE", "POSSIBLE"),
     label = "Drug-related serious AEs",
-    var = "AEDECOD", soc = "AEBODSYS"
+    var = "AEDECOD", 
+    soc = "AEBODSYS"
   )
 ```