Subject Screening and Enrollment, Screening Population, Trials A and B

FDA Table 03

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Setup

# Load libraries & data -------------------------------------
library(dplyr)
library(cards)
library(gtsummary)

adsl <- pharmaverseadam::adsl

set.seed(1)
scrnfail_reas_lvls <- c(
  "Inclusion/exclusion criteria not met", "Subject noncompliance", "Consent withdrawn", "Other"
)
data <- adsl |>
  mutate(
    ENRLDT = RANDDT,
    ENRLFL = !is.na(ENRLDT),
    RANDFL = !is.na(RANDDT),
    SCRNFL = TRUE,
    SCRNFRS = NA_character_
  ) |>
  mutate( # set screen failure reasons for relevant observations.
    SCRNFRS = factor(
      replace(
        SCRNFRS,
        TRT01A == "Screen Failure",
        sample(scrnfail_reas_lvls, size = sum(TRT01A == "Screen Failure"), replace = TRUE)
      ),
      levels = scrnfail_reas_lvls
    )
  )

Build Table

tbl_scrn <- tbl_summary(
  data = data,
  include = "SCRNFL",
  missing = "no",
  label = ~"Subjects screened"
)

tbl_scrnfrs <- tbl_hierarchical(
  data = data,
  denominator = adsl,
  id = USUBJID,
  variables = "SCRNFRS",
  label = list(..ard_hierarchical_overall.. = "Screening failures"),
  overall_row = TRUE
) |>
  modify_indent(columns = label, rows = row_type == "level", indent = 4L) |>
  modify_indent(columns = label, rows = variable == "SCRNFRS", indent = 8L)

tbl_enrl_rand <- tbl_summary(
  data = data,
  include = c("ENRLFL", "RANDFL"),
  missing = "no",
  label = list(ENRLFL = "Subjects enrolled", RANDFL = "Subjects randomized")
)

tbl <- list(tbl_scrn, tbl_scrnfrs, tbl_enrl_rand) |>
  tbl_stack() |>
  modify_header(label = "**Disposition**")

tbl

Build ARD

ard <- data |>
  ard_stack(
    ard_tabulate_value(
      variables = SCRNFL,
      value = list(SCRNFL = TRUE),
      statistic = everything() ~ c("n")
    ),
    ard_tabulate(
      variables = SCRNFRS,
      statistic = everything() ~ c("n", "p"),
      denominator = data
    ),
    ard_tabulate_value(
      variables = c(ENRLFL, RANDFL),
      value = list(ENRLFL = TRUE, RANDFL = TRUE),
      statistic = everything() ~ c("n", "p"),
      denominator = data
    )
  )

ard

{cards} data frame: 13 x 9

   variable variable_level   context stat_name stat_label  stat fmt_fun warning error
1    SCRNFL           TRUE tabulate…         n          n   306       0              
2   SCRNFRS      Inclusio…  tabulate         n          n    17       0              
3   SCRNFRS      Inclusio…  tabulate         p          % 0.056    <fn>              
4   SCRNFRS      Subject …  tabulate         n          n    17       0              
5   SCRNFRS      Subject …  tabulate         p          % 0.056    <fn>              
6   SCRNFRS      Consent …  tabulate         n          n    11       0              
7   SCRNFRS      Consent …  tabulate         p          % 0.036    <fn>              
8   SCRNFRS          Other  tabulate         n          n     7       0              
9   SCRNFRS          Other  tabulate         p          % 0.023    <fn>              
10   ENRLFL           TRUE tabulate…         n          n   254       0              
11   ENRLFL           TRUE tabulate…         p          %  0.83    <fn>              
12   RANDFL           TRUE tabulate…         n          n   254       0              
13   RANDFL           TRUE tabulate…         p          %  0.83    <fn>