Analysis Populations

Summary of Analysis Populations

Setup

See Prerequisites for installation instructions.

library(arframe)
library(pharmaverseadam)
library(dplyr, warn.conflicts = FALSE)
library(tidyr)

adsl <- pharmaverseadam::adsl |>
  blank_to_na() |>
  filter(TRT01A != "Screen Failure")

arm_levels <- c("Placebo", "Xanomeline Low Dose", "Xanomeline High Dose")

adsl_arms <- adsl |> filter(TRT01A %in% arm_levels)

arm_n <- adsl_arms |>
  count(TRT01A) |>
  pull(n, name = TRT01A)
arm_n <- arm_n[arm_levels]

N_total <- sum(arm_n)
n_vec <- c(arm_n, Total = N_total)

Data Preparation

n_pct <- function(n, denom) sprintf("%d (%.1f)", n, n / denom * 100)

# ── Define population flags ──
# Enrolled = all randomized (non-screen-failure) subjects
# Safety = SAFFL == "Y"
# ITT/Full Analysis Set = all randomized subjects (same as enrolled in this study)
pop_list <- list(
  "Enrolled"                = rep(TRUE, nrow(adsl_arms)),
  "Safety Population"       = adsl_arms$SAFFL == "Y",
  "ITT / Full Analysis Set" = rep(TRUE, nrow(adsl_arms))
)

# ── Build summary by arm ──
pop_rows <- lapply(names(pop_list), function(pop_name) {
  mask <- pop_list[[pop_name]]
  sub <- adsl_arms[mask, ]

  by_arm <- sub |>
    count(TRT01A) |>
    filter(TRT01A %in% arm_levels) |>
    mutate(value = mapply(n_pct, n, arm_n[TRT01A])) |>
    select(TRT01A, value) |>
    pivot_wider(names_from = TRT01A, values_from = value)

  total_n <- nrow(sub)
  total_val <- n_pct(total_n, N_total)

  bind_cols(
    tibble(population = pop_name),
    by_arm,
    tibble(Total = total_val)
  )
})

pop_wide <- bind_rows(pop_rows) |>
  mutate(across(all_of(c(arm_levels, "Total")), ~ replace_na(.x, "0 (0.0)")))

arframe Pipeline

The fr_table() pipeline:

pop_wide |>
  fr_table() |>
  fr_titles(
    "Table 14.1.3",
    "Summary of Analysis Populations",
    "Randomized Subjects"
  ) |>
  fr_cols(
    population = fr_col("Population", width = 2.5),
    !!!setNames(
      lapply(arm_levels, function(a) fr_col(a, align = "decimal")),
      arm_levels
    ),
    Total = fr_col("Total", align = "decimal"),
    .n = n_vec
  ) |>
  fr_header(bold = TRUE, align = "center") |>
  fr_footnotes(
    "n (%) where percentages are based on N randomized per treatment arm.",
    "Enrolled = all randomized subjects excluding screen failures.",
    "Safety Population = subjects who received at least one dose of study drug (SAFFL = 'Y').",
    "ITT / Full Analysis Set = all randomized subjects."
  )

Rendered Table

Table 14.1.3

Summary of Analysis Populations

Randomized Subjects

Population	Placebo (N=86)	Xanomeline High Dose (N=72)	Xanomeline Low Dose (N=96)	Total (N=254)
Enrolled	86 (100.0)	72 (100.0)	96 (100.0)	254 (100.0)
Safety Population	86 (100.0)	72 (100.0)	96 (100.0)	254 (100.0)
ITT / Full Analysis Set	86 (100.0)	72 (100.0)	96 (100.0)	254 (100.0)

n (%) where percentages are based on N randomized per treatment arm.

Enrolled = all randomized subjects excluding screen failures.

Safety Population = subjects who received at least one dose of study drug (SAFFL = 'Y').

ITT / Full Analysis Set = all randomized subjects.

/opt/quarto/share/rmd/rmd.R 01APR2026 09:52:34