FDA Table 04

Patient Disposition, Pooled Analyses

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Setup

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

adsl <- random.cdisc.data::cadsl

# Pre-processing --------------------------------------------

pop_vars <- c("SAFFL", "ITTFL")
lbl_pop_vars <- c("Safety population", "ITT/mITT population")

adsl <- adsl %>%
  mutate(across(everything(), ~ case_when(
    is.na(.) ~ "Missing",
    TRUE ~ as.character(.)
  ))) %>%
  mutate(
    across(all_of(pop_vars), ~ with_label(. == "Y", lbl_pop_vars[match(cur_column(), pop_vars)])),
    DISCSD = with_label(EOTSTT == "DISCONTINUED", "Discontinued study drug"),
    DISCSD_AE = with_label(EOTSTT == "DISCONTINUED" & DCSREAS == "ADVERSE EVENT", "Adverse event"),
    DISCSD_LOE = with_label(EOTSTT == "DISCONTINUED" & DCSREAS == "LACK OF EFFICACY", "Lack of efficacy"),
    DISCSD_PD = with_label(EOTSTT == "DISCONTINUED" & DCSREAS == "PROTOCOL DEVIATION", "Protocol deviation"),
    DISCSD_DT = with_label(EOTSTT == "DISCONTINUED" & DCSREAS == "DEATH", "Death"),
    DISCSD_WBS = with_label(EOTSTT == "DISCONTINUED" & DCSREAS == "WITHDRAWAL BY SUBJECT", "Withdrawal by subject"),
    DISCSD_OTH = with_label(EOTSTT == "DISCONTINUED" & DCSREAS == "OTHER", "Other"),
    DISCS = with_label(EOSSTT == "DISCONTINUED", "Discontinued study"),
    DISCS_DT = with_label(EOSSTT == "DISCONTINUED" & DCSREAS == "DEATH", "Death"),
    DISCS_LFU = with_label(EOSSTT == "DISCONTINUED" & DCSREAS == "LOST TO FOLLOW-UP", "Lost to follow-up"),
    DISCS_WBS = with_label(EOSSTT == "DISCONTINUED" & DCSREAS == "WITHDRAWAL BY SUBJECT", "Withdrawal by subject"),
    DISCS_PHD = with_label(EOSSTT == "DISCONTINUED" & DCSREAS == "PHYSICIAN DECISION", "Physician decision"),
    DISCS_PD = with_label(EOSSTT == "DISCONTINUED" & DCSREAS == "PROTOCOL VIOLATION", "Protocol deviation"),
    DISCS_OTH = with_label(EOSSTT == "DISCONTINUED" & DCSREAS == "OTHER", "Other")
  )

Build Table

tbl <- adsl %>%
  gtsummary::tbl_summary(
    by = "ARM",
    statistic = list(all_dichotomous() ~ "{n} ({p}%)"),
    include = all_of(c(
      pop_vars,
      "DISCSD", "DISCSD_AE", "DISCSD_LOE", "DISCSD_PD", "DISCSD_DT", "DISCSD_WBS", "DISCSD_OTH",
      "DISCS", "DISCS_DT", "DISCS_LFU", "DISCS_WBS", "DISCS_PHD", "DISCS_PD", "DISCS_OTH"
    )),
    digits = list(gtsummary::all_categorical() ~ c(0, 1))
  ) %>%
  add_overall(last = TRUE) %>%
  # Define which variables are children of parent variables
  modify_table_styling(
    columns = "label",
    rows = variable %in% c(
      "DISCSD_AE", "DISCSD_LOE", "DISCSD_PD", "DISCSD_DT",
      "DISCSD_WBS", "DISCSD_OTH"
    ),
    text_format = "indent"
  ) %>%
  modify_table_styling(
    columns = "label",
    rows = variable %in% c(
      "DISCS_DT", "DISCS_LFU", "DISCS_WBS", "DISCS_PHD",
      "DISCS_PD", "DISCS_OTH"
    ),
    text_format = "indent"
  ) %>%
  # Make all but main categories display as levels
  modify_table_body(
    ~ .x %>%
      mutate(row_type = case_when(
        variable %in% c(pop_vars, "DISCSD", "DISCS") ~ "label",
        TRUE ~ "level"
      ))
  )

Warning: The `text_format` argument of `modify_table_styling()` must be one of "bold" or
"italic" as of gtsummary 2.0.0.
ℹ Update function call to `modify_table_styling(x = ., columns = "label", rows
  = variable %in% c("DISCSD_AE", "DISCSD_LOE", "DISCSD_PD", "DISCSD_DT",
  "DISCSD_WBS", "DISCSD_OTH"), indent = 4L)`.

Warning: The `text_format` argument of `modify_table_styling()` must be one of "bold" or
"italic" as of gtsummary 2.0.0.
ℹ Update function call to `modify_table_styling(x = ., columns = "label", rows
  = variable %in% c("DISCS_DT", "DISCS_LFU", "DISCS_WBS", "DISCS_PHD",
  "DISCS_PD", "DISCS_OTH"), indent = 4L)`.

Build ARD

ard <- gather_ard(tbl)
ard

$tbl_summary

{cards} data frame: 428 x 12

   group1 group1_level  variable variable_level   context stat_name stat_label  stat fmt_fun warning error gts_column
1     ARM    A: Drug X     ITTFL           TRUE dichotom…         n          n   134    <fn>                   stat_1
2     ARM    A: Drug X     ITTFL           TRUE dichotom…         N          N   134       0                   stat_1
3     ARM    A: Drug X     ITTFL           TRUE dichotom…         p          %     1    <fn>                   stat_1
4     ARM    A: Drug X     SAFFL           TRUE dichotom…         n          n   134    <fn>                   stat_1
5     ARM    A: Drug X     SAFFL           TRUE dichotom…         N          N   134       0                   stat_1
6     ARM    A: Drug X     SAFFL           TRUE dichotom…         p          %     1    <fn>                   stat_1
7     ARM    A: Drug X    DISCSD           TRUE dichotom…         n          n    42    <fn>                   stat_1
8     ARM    A: Drug X    DISCSD           TRUE dichotom…         N          N   134       0                   stat_1
9     ARM    A: Drug X    DISCSD           TRUE dichotom…         p          % 0.313    <fn>                   stat_1
10    ARM    A: Drug X DISCSD_AE           TRUE dichotom…         n          n     3    <fn>                   stat_1

ℹ 418 more rows

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

$add_overall

{cards} data frame: 161 x 10

    variable variable_level   context stat_name stat_label stat fmt_fun warning error gts_column
1      ITTFL           TRUE dichotom…         n          n  400    <fn>                   stat_0
2      ITTFL           TRUE dichotom…         N          N  400    <fn>                   stat_0
3      ITTFL           TRUE dichotom…         p          %    1    <fn>                   stat_0
4      SAFFL           TRUE dichotom…         n          n  400    <fn>                   stat_0
5      SAFFL           TRUE dichotom…         N          N  400    <fn>                   stat_0
6      SAFFL           TRUE dichotom…         p          %    1    <fn>                   stat_0
7     DISCSD           TRUE dichotom…         n          n  120    <fn>                   stat_0
8     DISCSD           TRUE dichotom…         N          N  400    <fn>                   stat_0
9     DISCSD           TRUE dichotom…         p          %  0.3    <fn>                   stat_0
10 DISCSD_AE           TRUE dichotom…         n          n   14    <fn>                   stat_0

ℹ 151 more rows
ℹ Use `print(n = ...)` to see more rows