FDA Table 3

Patient Screening and Enrollment, Trials A and B

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Setup

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

adsl <- random.cdisc.data::cadsl

set.seed(1)
adsl$RANDDT[sample(seq_len(nrow(adsl)), 100)] <- NA
scrnfail_reas_lvls <- c(
  "Inclusion/exclusion criteria not met", "Patient noncompliance", "Consent withdrawn", "Other"
)
data <- adsl |>
  mutate(
    ENRLDT = RANDDT,
    SCRNFL = with_label(TRUE, "Patients screened"),
    SCRNFRS = factor(sample(scrnfail_reas_lvls, size = nrow(adsl), replace = TRUE),
      levels = scrnfail_reas_lvls
    ),
    ENRLFL = with_label(!is.na(ENRLDT), "Patients enrolled"),
    RANDFL = with_label(!is.na(RANDDT), "Patients randomized")
  )
data$SCRNFRS[data$SCRNFL == "N" | !is.na(data$ENRLDT)] <- NA

Build ARD

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

{cards} data frame: 13 x 9

   variable variable_level   context stat_name stat_label  stat fmt_fun warning error
1    SCRNFL           TRUE dichotom…         n          n   400       0              
2   SCRNFRS      Inclusio… categori…         n          n    26       0              
3   SCRNFRS      Inclusio… categori…         p          % 0.065    <fn>              
4   SCRNFRS      Patient … categori…         n          n    20       0              
5   SCRNFRS      Patient … categori…         p          %  0.05    <fn>              
6   SCRNFRS      Consent … categori…         n          n    30       0              
7   SCRNFRS      Consent … categori…         p          % 0.075    <fn>              
8   SCRNFRS          Other categori…         n          n    24       0              
9   SCRNFRS          Other categori…         p          %  0.06    <fn>              
10   ENRLFL           TRUE dichotom…         n          n   300       0              
11   ENRLFL           TRUE dichotom…         p          %  0.75    <fn>              
12   RANDFL           TRUE dichotom…         n          n   300       0              
13   RANDFL           TRUE dichotom…         p          %  0.75    <fn>              

Build Table

tbl_scrn <- tbl_summary(
  data = data,
  include = "SCRNFL",
  statistic = SCRNFL ~ "{n}",
  missing = "no"
)

tbl_scrnfrs <- tbl_hierarchical(
  data = data,
  denominator = adsl,
  id = USUBJID,
  variables = "SCRNFRS",
  statistic = ~"{n} ({p}%)",
  label = list(..ard_hierarchical_overall.. = "Screening failures"),
  overall_row = TRUE
)

tbl_enrl_rand <- tbl_summary(
  data = data,
  include = c("ENRLFL", "RANDFL"),
  missing = "no"
)

tbl <- list(tbl_scrn, tbl_scrnfrs, tbl_enrl_rand) |>
  tbl_stack() |>
  modify_header(label = "**Disposition**", stat_0 = "**Trial A**") |>
  modify_column_indent("label", rows = !(variable %in% c("..ard_hierarchical_overall..", "SCRNFL", "ENRLFL", "RANDFL"))) |>
  remove_footnote_header(columns = everything())

tbl