FDA Table 08

Deaths, Safety Population, Pooled Analysis (or Trial X)

Table Preview

Setup

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

adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae

# Pre-processing --------------------------------------------
adsl <- adsl |>
  filter(SAFFL == "Y") # safety population

data <- adae |>
  filter(
    # safety population
    SAFFL == "Y",
    # deaths
    DTHFL == "Y"
  )

Build Table

tbl_dthcaus <- data |>
  tbl_hierarchical(
    variables = DTHCAUS,
    id = USUBJID,
    by = TRT01A,
    denominator = adsl,
    overall_row = TRUE,
    label = list("..ard_hierarchical_overall.." = "Death details", DTHCAUS = "**Deaths**")
  ) |>
  sort_hierarchical() |>
  modify_indent(columns = label, rows = variable == "DTHCAUS", indent = 4L)

tbl_aesdth <- data |>
  filter(AESDTH == "Y") |>
  tbl_hierarchical(
    variables = AEDECOD,
    id = USUBJID,
    by = TRT01A,
    denominator = adsl,
    overall_row = TRUE,
    label = list("..ard_hierarchical_overall.." = "Adverse events with an outcome of death", AEDECOD = "**Deaths**")
  ) |>
  sort_hierarchical() |>
  modify_indent(columns = label, rows = variable == "AEDECOD", indent = 4L)

tbl <- tbl_stack(list(tbl_dthcaus, tbl_aesdth))

tbl

Build ARD

ard <- gather_ard(tbl)
ard

[[1]]
[[1]]$tbl_hierarchical

{cards} data frame: 81 x 13

   group1 group1_level                     variable variable_level stat_name stat_label  stat stat_fmt
1    <NA>                                    TRT01A      A: Drug X         n          n   134      134
2    <NA>                                    TRT01A      A: Drug X         N          N   400      400
3    <NA>                                    TRT01A      A: Drug X         p          % 0.335     33.5
4    <NA>                                    TRT01A      B: Place…         n          n   134      134
5    <NA>                                    TRT01A      B: Place…         N          N   400      400
6    <NA>                                    TRT01A      B: Place…         p          % 0.335     33.5
7    <NA>                                    TRT01A      C: Combi…         n          n   132      132
8    <NA>                                    TRT01A      C: Combi…         N          N   400      400
9    <NA>                                    TRT01A      C: Combi…         p          %  0.33     33.0
10 TRT01A    A: Drug X ..ard_hierarchical_overall..           TRUE         n          n    24       24

ℹ 71 more rows

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

ℹ 5 more variables: context, fmt_fun, warning, error, gts_column

[[2]]
[[2]]$tbl_hierarchical

{cards} data frame: 36 x 13

   group1 group1_level                     variable variable_level stat_name stat_label  stat stat_fmt
1    <NA>                                    TRT01A      A: Drug X         n          n   134      134
2    <NA>                                    TRT01A      A: Drug X         N          N   400      400
3    <NA>                                    TRT01A      A: Drug X         p          % 0.335     33.5
4    <NA>                                    TRT01A      B: Place…         n          n   134      134
5    <NA>                                    TRT01A      B: Place…         N          N   400      400
6    <NA>                                    TRT01A      B: Place…         p          % 0.335     33.5
7    <NA>                                    TRT01A      C: Combi…         n          n   132      132
8    <NA>                                    TRT01A      C: Combi…         N          N   400      400
9    <NA>                                    TRT01A      C: Combi…         p          %  0.33     33.0
10 TRT01A    A: Drug X ..ard_hierarchical_overall..           TRUE         n          n    18       18

ℹ 26 more rows

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

ℹ 5 more variables: context, fmt_fun, warning, error, gts_column