Potential update to FDA 3 (#317)

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Emily de la Rua <emily.de_la_rua@contractors.roche.com>

Author: 3 people

quarto/catalog/fda-table_03/index.qmd

@@ -20,7 +20,7 @@ library(formatters)
 library(cards)
 library(gtsummary)
 
-adsl <- random.cdisc.data::cadsl
+adsl <- pharmaverseadam::adsl
 
 set.seed(1)
 adsl$RANDDT[sample(seq_len(nrow(adsl)), 100)] <- NA
@@ -35,76 +35,37 @@ data <- adsl |>
       levels = scrnfail_reas_lvls
     ),
     ENRLFL = with_label(!is.na(ENRLDT), "Subjects enrolled"),
-    RANDFL = with_label(!is.na(RANDDT), "Subjects randomized")
+    RANDFL = with_label(!is.na(RANDDT), "Subjects randomized"),
+    screen_fail = !ENRLFL # create a flag for screen failure
   )
 data$SCRNFRS[data$SCRNFL == "N" | !is.na(data$ENRLDT)] <- NA
 ```
 
-## Build ARD
-
-```{r ard, message=FALSE, warning=FALSE, results='hide'}
-ard <- data |>
-  ard_stack(
-    ard_dichotomous(
-      variables = SCRNFL,
-      value = list(SCRNFL = TRUE),
-      statistic = everything() ~ c("n")
-    ),
-    ard_categorical(
-      variables = SCRNFRS,
-      statistic = everything() ~ c("n", "p"),
-      denominator = data
-    ),
-    ard_dichotomous(
-      variables = c(ENRLFL, RANDFL),
-      value = list(ENRLFL = TRUE, RANDFL = TRUE),
-      statistic = everything() ~ c("n", "p"),
-      denominator = data
-    )
-  )
-
-ard
-```
-
-```{r, echo=FALSE}
-# Print ARD
-withr::local_options(width = 9999)
-print(ard, columns = "all", n = 40)
-```
-
 ## Build Table
 
 ```{r tbl, message=FALSE, warning=FALSE, results='hide'}
-tbl_scrn <- tbl_summary(
-  data = data,
-  by = TRT01A,
-  include = "SCRNFL",
-  missing = "no"
-)
-
-tbl_scrnfrs <- tbl_hierarchical(
-  data = data,
-  denominator = adsl,
-  id = USUBJID,
-  by = TRT01A,
-  variables = "SCRNFRS",
-  label = list(..ard_hierarchical_overall.. = "Screening failures"),
-  overall_row = TRUE
-) |>
-  modify_indent(columns = label, rows = row_type == "level", indent = 4L) |>
+tbl <- data |>
+  tbl_summary(
+    include = c(SCRNFL, screen_fail, SCRNFRS, ENRLFL, RANDFL),
+    # suppress number of missing observations
+    missing = "no",
+    # specify the denominator is always the no. obs. in `data`
+    percent = data,
+    # present SCRNFRS in descending order of frequency
+    sort = SCRNFRS ~ "frequency",
+    # update default screen failure label
+    label = list(screen_fail = "Screening failures")
+  ) |>
+  # remove the blank header row for SCRNFRS
+  remove_row_type(SCRNFRS, type = "header") |>
+  modify_header(
+    label = "**Disposition**",
+    stat_0 = "**Trial A**  \n N = {n}"
+  ) |>
+  # update indentation for screening failures subsection
+  modify_indent(columns = label, rows = variable == "screen_fail", indent = 4L) |>
   modify_indent(columns = label, rows = variable == "SCRNFRS", indent = 8L)
 
-tbl_enrl_rand <- tbl_summary(
-  data = data,
-  by = TRT01A,
-  include = c("ENRLFL", "RANDFL"),
-  missing = "no"
-)
-
-tbl <- list(tbl_scrn, tbl_scrnfrs, tbl_enrl_rand) |>
-  tbl_stack() |>
-  modify_header(label = "**Disposition**")
-
 tbl
 ```
 
@@ -115,4 +76,18 @@ gt::gtsave(as_gt(tbl), filename = "result.png")
 
 ```{r img, echo=FALSE, fig.align='center', out.width='60%'}
 ```
+
+## Build ARD
+
+```{r ard, message=FALSE, warning=FALSE, results='hide'}
+ard <- gather_ard(tbl)
+
+ard
+```
+
+```{r, echo=FALSE}
+# Print ARD
+withr::local_options(width = 9999)
+print(ard)
+```
 :::