FDA Table 03

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

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Setup

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

adsl <- pharmaverseadam::adsl

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  "Inclusion/exclusion criteria not met", "Subject noncompliance", "Consent withdrawn", "Other"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

Build Table

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

Build ARD

ard <- gather_ard(tbl)

ard

$tbl_summary

{cards} data frame: 61 x 10

   variable variable_level  context stat_name stat_label  stat
1   SCRNFRS      Inclusio… tabulate         n          n    40
2   SCRNFRS      Inclusio… tabulate         N          N   306
3   SCRNFRS      Inclusio… tabulate         p          % 0.131
4   SCRNFRS          Other tabulate         n          n    35
5   SCRNFRS          Other tabulate         N          N   306
6   SCRNFRS          Other tabulate         p          % 0.114
7   SCRNFRS      Consent … tabulate         n          n    33
8   SCRNFRS      Consent … tabulate         N          N   306
9   SCRNFRS      Consent … tabulate         p          % 0.108
10  SCRNFRS      Subject … tabulate         n          n    27

ℹ 51 more rows

ℹ Use `print(n = ...)` to see more rows

ℹ 4 more variables: fmt_fun, warning, error, gts_column