Refactor ADPC

NEWS.md

@@ -1,6 +1,8 @@
 # random.cdisc.data 0.3.13.9062
 
 ### Enhancements
+* Refactor `adpc` and `adab` following the new CDISC standard.
+
 * Refactor `abab` parameters and visits to align with `adpc`.
 
 ### Breaking changes

R/package.R

@@ -29,5 +29,6 @@ utils::globalVariables(c(
   "VSSTRESC", "WEIGHT", "WORS01FL", "ada_bl", "any_pos_postbl", "any_pos_postbl_nab",
   "changeind", "comp_count", "first_date", "inc_postbl", "inc_postbl_nab", "ka", "ke",
   "last_ada", "n_pos", "nab_bl", "onset_ada", "pos_bl", "pos_bl_nab", "pos_last_postbl",
-  "publication_name", "row_check"
+  "publication_name", "row_check", "AFRLT", "ARRLT", "NFRLT", "NRRLT",
+  "eortc_qlq_c30", "expect", "gdsr_param_adqlqc"
 ))

R/radab.R

@@ -127,10 +127,10 @@ radab <- function(adsl,
           ARM,
           ACTARM,
           VISITDY,
-          ARELTM1,
-          NRELTM1,
-          ARELTM2,
-          NRELTM2,
+          AFRLT,
+          NFRLT,
+          ARRLT,
+          NRRLT,
           RELTMU
         ) %>%
         unique(),
@@ -139,7 +139,7 @@ radab <- function(adsl,
     rename(ISTPT = PCTPT)
 
   # mutate time from dose variables from adpc to convert into Days
-  adab_visit <- adab_visit %>% dplyr::mutate_at(c("ARELTM1", "NRELTM1", "ARELTM2", "NRELTM2"), ~ . / 24)
+  adab_visit <- adab_visit %>% dplyr::mutate_at(c("AFRLT", "NFRLT", "ARRLT", "NRRLT"), ~ . / 24)
 
 
 
@@ -230,12 +230,12 @@ radab <- function(adsl,
   adab <- adab %>%
     dplyr::mutate(
       RELTMU = "day",
-      ABLFL = ifelse(!is.na(NRELTM1) & NRELTM1 == 0, "Y", NA) # Baseline Record Flag
+      ABLFL = ifelse(!is.na(NFRLT) & NFRLT == 0, "Y", NA) # Baseline Record Flag
       ,
-      ADABLPFL = ifelse(PARAMCD == "RESULT1" & !is.na(NRELTM1) & NRELTM1 == 0, "Y", NA)
+      ADABLPFL = ifelse(PARAMCD == "RESULT1" & !is.na(NFRLT) & NFRLT == 0, "Y", NA)
       # Baseline ADA Eval. Param-Level Flag, only populate for ADA, not for NAB
       ,
-      ADPBLPFL = ifelse(PARAMCD == "RESULT1" & !is.na(NRELTM1) & NRELTM1 > 0 & !is.na(AVAL), "Y", NA)
+      ADPBLPFL = ifelse(PARAMCD == "RESULT1" & !is.na(NFRLT) & NFRLT > 0 & !is.na(AVAL), "Y", NA)
       # Post-Baseline ADA Eval. Param-Level Flag, only populate for ADA, not for NAB
     ) %>%
     dplyr::group_by(USUBJID) %>%
@@ -254,7 +254,7 @@ radab <- function(adsl,
       any_pos_postbl_nab = any(PARAM == "NAB interpreted per sample result" &
         is.na(ABLFL) & AVALC == "POSITIVE"),
       pos_last_postbl = any(PARAM == "ADA interpreted per sample result" &
-        NRELTM1 == max(NRELTM1) & AVALC == "POSITIVE"),
+        NFRLT == max(NFRLT) & AVALC == "POSITIVE"),
       ada_bl = AVAL[PARAM == "Antibody titer units" & !is.na(ABLFL)],
       nab_bl = AVAL[PARAM == "Neutralizing Antibody titer units" & !is.na(ABLFL)]
     )
@@ -267,13 +267,13 @@ radab <- function(adsl,
         is.na(ABLFL) & (AVAL - nab_bl) > 0.60),
       onset_ada = if (any(PARAM == "ADA interpreted per sample result" &
         AVALC == "POSITIVE")) {
-        min(NRELTM1[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"])
+        min(NFRLT[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"])
       } else {
         NA
       },
       last_ada = if (any(PARAM == "ADA interpreted per sample result" &
         AVALC == "POSITIVE")) {
-        max(NRELTM1[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"])
+        max(NFRLT[PARAM == "ADA interpreted per sample result" & AVALC == "POSITIVE"])
       } else {
         NA
       }
@@ -282,7 +282,7 @@ radab <- function(adsl,
     dplyr::left_join(pos_tots, by = "USUBJID") %>%
     dplyr::select(
       USUBJID,
-      NRELTM1,
+      NFRLT,
       pos_bl,
       pos_bl_nab,
       any_pos_postbl,
@@ -298,7 +298,7 @@ radab <- function(adsl,
 
   # add flags to ADAB dataset
   adab <- adab %>%
-    dplyr::left_join(adab_subj, by = c("USUBJID", "NRELTM1"))
+    dplyr::left_join(adab_subj, by = c("USUBJID", "NFRLT"))
 
   # derive subject-level variables
   adab[!(adab$PARAM %in% visit_lvl_params), ] <- adab %>%

R/radpc.R

@@ -124,5 +124,15 @@ radpc <- function(adsl,
     adpc <- mutate_na(ds = adpc, na_vars = na_vars, na_percentage = na_percentage)
   }
 
+  adpc <- adpc %>%
+    rename(
+      AVALCAT1 = AVALC,
+      NFRLT = NRELTM1,
+      AFRLT = ARELTM1,
+      NRRLT = NRELTM2,
+      ARRLT = ARELTM2
+    ) %>%
+    mutate(ANL02FL = "Y")
+
   adpc <- apply_metadata(adpc, "metadata/ADPC.yml")
 }

R/radqlqc.R

@@ -290,6 +290,7 @@ get_qs_data <- function(adsl,
                           QSORRES = c(1234, 0.2),
                           QSSTRESC = c(1234, 0.2)
                         )) {
+  load(system.file("sysdata.rda", package = "random.cdisc.data"))
   checkmate::assert_string(visit_format)
   checkmate::assert_integer(n_assessments, len = 1, any.missing = FALSE)
   checkmate::assert_integer(n_days, len = 1, any.missing = FALSE)
@@ -656,6 +657,7 @@ prep_adqlqc <- function(df) {
       TRUE ~ QSTESTCD
     )
   )
+  load(system.file("sysdata.rda", package = "random.cdisc.data"))
   adqlqc1 <- dplyr::left_join(
     adqlqc,
     gdsr_param_adqlqc,
@@ -679,7 +681,7 @@ calc_scales <- function(adqlqc1) {
   # parcat2 = scales or global health status
   # global health status/scales data
   # QSTESTCD: EOR0131 to EOR0145 (global health status and scales)
-
+  load(system.file("sysdata.rda", package = "random.cdisc.data"))
   eortc_qlq_c30_sub <- filter(
     eortc_qlq_c30,
     !(as.numeric(str_extract(QSTESTCD, "\\d+$")) >= 101 &

inst/metadata/ADAB.yml

@@ -42,15 +42,15 @@ variables:
  RELTMU:
     label: Relative Actual/Nominal Time Units
     type: factor
- NRELTM1:
-    label: Nominal Relative Time from First Dose
+ NFRLT:
+    label: Nom. Rel. Time from Analyte First Dose
     type: numeric
- ARELTM1:
-    label: Analysis Rel. Actual Time from First Dose
+ AFRLT:
+    label: Act. Rel. Time from Analyte First Dose
     type: numeric
- NRELTM2:
-    label: Nominal Relative Time from Most Recent Dose
+ NRRLT:
+    label: Nominal Rel. Time from Ref. Dose
     type: numeric
- ARELTM2:
-    label: Analysis Rel. Actual Time from Most Recent Dose
+ ARRLT:
+    label: Actual Rel. Time from Ref. Dose
     type: numeric

inst/metadata/ADPC.yml

@@ -3,17 +3,17 @@ domain:
   label: Pharmacokinetic Analysis Dataset
 
 variables:
- NRELTM1:
-    label: Nominal Relative Time from First Dose
+ NFRLT:
+    label: Nom. Rel. Time from Analyte First Dose
     type: numeric
- ARELTM1:
-    label: Analysis Rel. Actual Time from First Dose
+ AFRLT:
+    label: Act. Rel. Time from Analyte First Dose
     type: numeric
- NRELTM2:
-    label: Nominal Relative Time from Most Recent Dose
+ NRRLT:
+    label: Nominal Rel. Time from Ref. Dose
     type: numeric
- ARELTM2:
-    label: Analysis Rel. Actual Time from Most Recent Dose
+ ARRLT:
+    label: Actual Rel. Time from Ref. Dose
     type: numeric
  PCTPTNUM:
     label: Planned Time Point Number
@@ -30,8 +30,8 @@ variables:
  AVAL:
     label: Analysis Value
     type: numeric
- AVALC:
-    label: Analysis Value (C)
+ AVALCAT1:
+    label: Analysis Value Category 1
     type: character
  AVALU:
     label: Analysis Value Unit
@@ -51,3 +51,6 @@ variables:
  VISITDY:
     label: Visit (N)
     type: integer
+ ANL02FL:
+    label: Analysis Flag 02
+    type: character