implementation of aet05

insightsengineering · Jan 24, 2024 · 96156cc · 96156cc
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diff --git a/tests/testthat/_snaps/table_aet05.new.md b/tests/testthat/_snaps/table_aet05.new.md
@@ -0,0 +1,26 @@
+# AET05 variant 1 is produced correctly
+
+    Code
+      res
+    Output
+                                               Placebo        Xanomeline High Dose   Xanomeline Low Dose
+                                               (N=86)                (N=84)                (N=84)       
+      ——————————————————————————————————————————————————————————————————————————————————————————————————
+      Total patient-years at risk                8.4                  15.7                   1.4        
+      Number of adverse events observed          69                    79                    77         
+      AE rate per 100 patient-years            819.32                502.87                5624.85      
+      95% CI                              (626.00, 1012.64)     (391.98, 613.76)     (4368.49, 6881.21) 
+
+# AET05 variant 2 is produced correctly
+
+    Code
+      res
+    Output
+                                               Placebo        Xanomeline High Dose   Xanomeline Low Dose
+                                               (N=86)                (N=84)                (N=84)       
+      ——————————————————————————————————————————————————————————————————————————————————————————————————
+      Total patient-years at risk                8.4                  15.7                   1.4        
+      Number of adverse events observed          69                    79                    77         
+      AE rate per 100 patient-years            819.32                502.87                5624.85      
+      95% CI                              (637.48, 1036.90)     (398.13, 626.73)     (4439.04, 7030.10) 
+
diff --git a/tests/testthat/test-table_aet05.R b/tests/testthat/test-table_aet05.R
@@ -1,6 +1,16 @@
-# Test variants for AET05.
-adsl <- adsl_raw
-adaette <- adaette_raw
+adsl <- adsl_pharmaverse
+adae <- adae_pharmaverse
+adaette <- left_join(
+  select(adsl, USUBJID, ARM, TRTSDT),
+  select(filter(adae, AESEQ == 1), USUBJID, ASTDTM),
+  by = "USUBJID"
+) %>%
+  mutate(
+    PARAM = "Time to first occurrence of any adverse event",
+    AVAL = as.numeric(difftime(TRTSDT, ASTDTM, unit = "days"))/365.25,
+    AVALU = "YEARS",
+    CNSR = ifelse(is.na(AVAL), 1, 0)
+  )
 
 adsl <- df_explicit_na(adsl)
 adaette <- df_explicit_na(adaette)