Correct SERREAS derivation in ael03 (#284)

Fixes #269 --------- Signed-off-by: Davide Garolini <[email protected]> Signed-off-by: Davide Garolini <[email protected]> Co-authored-by: Pawel Rucki <[email protected]> Co-authored-by: Emily de la Rua <[email protected]> Co-authored-by: Joe Zhu <[email protected]>
insightsengineering · Dec 2, 2024 · a69de29 · a69de29
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commit a69de29
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Showing 3 changed files with 15 additions and 11 deletions.
diff --git a/book/listings/adverse-events/ael03.qmd b/book/listings/adverse-events/ael03.qmd
@@ -12,6 +12,7 @@ library(dplyr)
 library(rlistings)
 
 adae <- random.cdisc.data::cadae
+adae$AESCONG[which(adae$AESER == "Y")[seq(3)]] <- "Y" # To mimic possibility of overlap
 
 out <- adae %>%
   filter(AESER == "Y") %>%
@@ -38,17 +39,20 @@ out <- adae %>%
       AEACN == "DRUG WITHDRAWN" ~ 5,
       AEACN == "NOT APPLICABLE" | AEACN == "NOT EVALUABLE" ~ 6,
       AEACN == "UNKNOWN" ~ 7
-    ),
-    SERREAS = case_when(
-      AESDTH == "Y" ~ "1",
-      AESLIFE == "Y" ~ "2",
-      AESHOSP == "Y" ~ "3",
-      AESDISAB == "Y" ~ "4",
-      AESCONG == "Y" ~ "5",
-      AESMIE == "Y" ~ "6",
-      TRUE ~ " "
     )
   ) %>%
+  rowwise() %>%
+  mutate(
+    SERREAS = paste(
+      which(
+        c(AESDTH, AESLIFE, AESHOSP, AESDISAB, AESCONG, AESMIE) == "Y"
+      ),
+      collapse = ", "
+    )
+  ) %>%
+  ungroup()
+
+out <- out %>%
   select(CPID, ASR, TRT01A, AEDECOD, Date_First, ASTDY, Duration, AESEV, Related, Outcome, Treated, Action, SERREAS)
 
 var_labels(out) <- c(

diff --git a/package/tests/testthat/_snaps/development/listings-adverse-events-ael03.md b/package/tests/testthat/_snaps/development/listings-adverse-events-ael03.md
@@ -18,7 +18,7 @@
       10 A: Drug X  BRA-1/id-93  34/F/ASIAN                     dcd D.1.1.1.1
          Date_First ASTDY Duration AESEV    Related Outcome Treated Action SERREAS
          <chr>      <int>    <dbl> <fct>    <chr>     <dbl> <chr>    <dbl> <chr>  
-       1 04NOV2020    321      149 MODERATE No            5 Yes          2 4      
+       1 04NOV2020    321      149 MODERATE No            5 Yes          2 4, 5   
        2 04NOV2020    393       43 MODERATE No            5 No           5 5      
        3 01JAN2020     64      630 SEVERE   Yes           1 No           6 1      
        4 01JAN2020    160      259 MODERATE No            2 Yes          2 4      

diff --git a/package/tests/testthat/_snaps/stable/listings-adverse-events-ael03.md b/package/tests/testthat/_snaps/stable/listings-adverse-events-ael03.md
@@ -18,7 +18,7 @@
       10 A: Drug X  BRA-1/id-93  34/F/ASIAN                     dcd D.1.1.1.1
          Date_First ASTDY Duration AESEV    Related Outcome Treated Action SERREAS
          <chr>      <int>    <dbl> <fct>    <chr>     <dbl> <chr>    <dbl> <chr>  
-       1 04NOV2020    321      149 MODERATE No            5 Yes          2 4      
+       1 04NOV2020    321      149 MODERATE No            5 Yes          2 4, 5   
        2 04NOV2020    393       43 MODERATE No            5 No           5 5      
        3 01JAN2020     64      630 SEVERE   Yes           1 No           6 1      
        4 01JAN2020    160      259 MODERATE No            2 Yes          2 4