Closes #2308 #2328 Update ADPP and ADPC templates (#2333)

Update ADPP and ADPC templates #2308 #2328 Co-authored-by: Jeffrey Dickinson <dickinson.jeffrey@gene.com>
pharmaverse · Feb 13, 2024 · f71778f · f71778f
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diff --git a/NEWS.md b/NEWS.md
@@ -41,6 +41,8 @@ There is a possibility to get package dependency versions used for the workflows
 
 - The function `dplyr::transmute()` is superseded in favor of `dplyr::mutate(.keep = "none")`. Consequently, all the admiral functions that utilized the former have been updated accordingly. (#2274)
 
+- The templates for ADPP and ADPC are updated for missing variables (#2308) and to make `ATPT` and `ATPTN` consistent. (#2328)
+
 # admiral 1.0.1
 
 - Fix bug in `derive_vars_query()` where if AE terms were in mixed case no terms are flagged. (#2311)

diff --git a/inst/templates/ad_adpc.R b/inst/templates/ad_adpc.R
@@ -422,7 +422,7 @@ dtype <- adpc_aval %>%
     DOSEA = EXDOSE_next,
     BASETYPE = paste(AVISIT_next, "Baseline"),
     ATPT = "Pre-dose",
-    ATPTN = NFRLT,
+    ATPTN = -0.5,
     ABLFL = "Y",
     DTYPE = "COPY"
   ) %>%

diff --git a/inst/templates/ad_adpp.R b/inst/templates/ad_adpp.R
@@ -103,7 +103,8 @@ adpp_aval <- adpp_pp %>%
   ## Calculate AVAL and AVALC ----
   mutate(
     AVAL = PPSTRESN,
-    AVALC = PPSTRESC
+    AVALC = PPSTRESC,
+    AVALU = PPSTRESU,
   ) %>%
   # Remove variables
   select(-PPSTRESN, -PPSTRESC) %>%
@@ -121,14 +122,10 @@ adpp_aval <- adpp_pp %>%
 adpp_avisit <- adpp_aval %>%
   # Derive Timing
   mutate(
-    VISIT = "", # /!\ To remove
-    VISITNUM = NA, # /!\ To remove
-    AVISIT = case_when(
-      str_detect(VISIT, "SCREEN|UNSCHED|RETRIEVAL|AMBUL") ~ NA_character_,
-      !is.na(VISIT) ~ str_to_title(VISIT),
-      TRUE ~ NA_character_
-    ),
-    AVISITN = VISITNUM
+    AVISITN = ADY,
+    AVISIT = paste("Day", ADY),
+    VISITNUM = AVISITN,
+    VISIT = AVISIT
   ) %>%
   ## Assign TRTA, TRTP ----
   # See also the "Visit and Period Variables" vignette

diff --git a/vignettes/pk_adnca.Rmd b/vignettes/pk_adnca.Rmd
@@ -760,7 +760,7 @@ dtype <- adpc_aval %>%
     DOSEA = EXDOSE_next,
     BASETYPE = paste(AVISIT_next, "Baseline"),
     ATPT = "Pre-dose",
-    ATPTN = NFRLT,
+    ATPTN = -0.5,
     ABLFL = "Y",
     DTYPE = "COPY"
   ) %>%