Closes #2484 Used restrict_derivation() with AVISITN > 0 to restrict …

…CHG and PCHG to post-baseline records (#2488)

* Used restrict_derivation() with AVISITN > 0 to restrict CHG and PCHG derivations to post-baseline observations. Note that NA visit changes are also not derived.

* feat: #2484 updated comments for CHG and PCHG

* feat: #2484 Manually added "Rothstein" to inst/WORDLIST

* feat: #2484 Updated CHG/PCHG comments and restrict_derivation call to notify that as per ADaM IG, the decision on how to populate pre-baseline and baseline values of CHG/PCHG is left to producer choice.

* feat: #2484 Changed 'sponsor' to 'producer'

* feat: #2484 Use restrict_derivation() with filter AVISITN > 0 to derive CHG and PCHG for post-baseline records only

* feat: #2484 Run style_file()

* feat: #2484 Add piping back to derive_var_obs_number() for adgdssf dataframe

inst/WORDLIST

@@ -317,6 +317,7 @@ repo
 reproducibility
 rlang
 roche
+Rothstein
 roxygen
 scalable
 signif

inst/templates/ad_adcm.R

@@ -89,7 +89,7 @@ adcm <- adcm %>%
   # Derive Follow-Up flag
   mutate(FUPFL = if_else(ASTDT > TRTEDT, "Y", NA_character_)) %>%
   # Derive ANL01FL
-  # This variable is sponsor specific and may be used to indicate particular
+  # This variable is producer specific and may be used to indicate particular
   # records to be used in subsequent derivations or analysis.
   mutate(ANL01FL = if_else(ONTRTFL == "Y", "Y", NA_character_)) %>%
   # Derive 1st Occurrence of Preferred Term Flag

inst/templates/ad_adeg.R

@@ -276,10 +276,18 @@ adeg <- adeg %>%
     source_var = ANRIND,
     new_var = BNRIND
   ) %>%
-  # Calculate CHG
-  derive_var_chg() %>%
-  # Calculate PCHG
-  derive_var_pchg()
+  # Calculate CHG for post-baseline records
+  # The decision on how to populate pre-baseline and baseline values of CHG is left to producer choice
+  restrict_derivation(
+    derivation = derive_var_chg,
+    filter = AVISITN > 0
+  ) %>%
+  # Calculate PCHG for post-baseline records
+  # The decision on how to populate pre-baseline and baseline values of PCHG is left to producer choice
+  restrict_derivation(
+    derivation = derive_var_pchg,
+    filter = AVISITN > 0
+  )
 
 ## ANL01FL: Flag last result within an AVISIT and ATPT for post-baseline records ----
 adeg <- adeg %>%

inst/templates/ad_adlb.R

@@ -224,11 +224,18 @@ adlb <- adlb %>%
     source_var = ANRIND,
     new_var = BNRIND
   ) %>%
-  # Calculate CHG
-  derive_var_chg() %>%
-  # Calculate PCHG
-  derive_var_pchg()
-
+  # Calculate CHG for post-baseline records
+  # The decision on how to populate pre-baseline and baseline values of CHG is left to producer choice
+  restrict_derivation(
+    derivation = derive_var_chg,
+    filter = AVISITN > 0
+  ) %>%
+  # Calculate PCHG for post-baseline records
+  # The decision on how to populate pre-baseline and baseline values of PCHG is left to producer choice
+  restrict_derivation(
+    derivation = derive_var_pchg,
+    filter = AVISITN > 0
+  )
 
 ## Calculate lab grading ----
 

inst/templates/ad_adpc.R

@@ -454,7 +454,13 @@ adpc_base <- adpc_dtype %>%
     filter = ABLFL == "Y"
   )
 
-adpc_chg <- derive_var_chg(adpc_base)
+# Calculate CHG for post-baseline records
+# The decision on how to populate pre-baseline and baseline values of CHG is left to producer choice
+adpc_chg <- restrict_derivation(
+  adpc_base,
+  derivation = derive_var_chg,
+  filter = AVISITN > 0
+)
 
 # ---- Add ASEQ ----
 

inst/templates/ad_advs.R

@@ -227,11 +227,18 @@ advs <- advs %>%
     source_var = ANRIND,
     new_var = BNRIND
   ) %>%
-  # Calculate CHG
-  derive_var_chg() %>%
-  # Calculate PCHG
-  derive_var_pchg()
-
+  # Calculate CHG for post-baseline records
+  # The decision on how to populate pre-baseline and baseline values of CHG is left to producer choice
+  restrict_derivation(
+    derivation = derive_var_chg,
+    filter = AVISITN > 0
+  ) %>%
+  # Calculate PCHG for post-baseline records
+  # The decision on how to populate pre-baseline and baseline values of PCHG is left to producer choice
+  restrict_derivation(
+    derivation = derive_var_pchg,
+    filter = AVISITN > 0
+  )
 
 ## ANL01FL: Flag last result within an AVISIT and ATPT for post-baseline records ----
 advs <- advs %>%

vignettes/pk_adnca.Rmd

@@ -836,7 +836,13 @@ adpc_base <- adpc_dtype %>%
     filter = ABLFL == "Y"
   )
 
-adpc_chg <- derive_var_chg(adpc_base)
+# Calculate CHG for post-baseline records
+# The decision on how to populate pre-baseline and baseline values of CHG is left to producer choice
+adpc_chg <- restrict_derivation(
+  adpc_base,
+  derivation = derive_var_chg,
+  filter = AVISITN > 0
+)
 
 # ---- Add ASEQ ----
 

vignettes/questionnaires.Rmd

@@ -218,8 +218,18 @@ adgdssf <- adgdssf %>%
     source_var = AVAL,
     new_var = BASE
   ) %>%
-  derive_var_chg() %>%
-  derive_var_pchg() %>%
+  # Calculate CHG for post-baseline records
+  # The decision on how to populate pre-baseline and baseline values of CHG is left to producer choice
+  restrict_derivation(
+    derivation = derive_var_chg,
+    filter = AVISITN > 0
+  ) %>%
+  # Calculate PCHG for post-baseline records
+  # The decision on how to populate pre-baseline and baseline values of PCHG is left to producer choice
+  restrict_derivation(
+    derivation = derive_var_pchg,
+    filter = AVISITN > 0
+  ) %>%
   # Derive sequence number
   derive_var_obs_number(
     by_vars = exprs(STUDYID, USUBJID),