FDA Table 12

Patients With Adverse Events Leading to Treatment Discontinuation by System Organ Class and Preferred Term, Safety Population, Pooled Analyses

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Setup

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

adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae
adae$DCSREAS[is.na(adae$DCSREAS)] <- "ADVERSE EVENT"

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

data <- adae %>%
  filter(
    # safety population
    SAFFL == "Y",
    # discontinuation due to AE
    DCSREAS == "ADVERSE EVENT"
  )

Build ARD

ard <- ard_stack_hierarchical(
  data,
  variables = c(AEBODSYS, AEDECOD),
  by = TRT01A,
  denominator = adsl,
  id = USUBJID
)

ard

{cards} data frame: 162 x 13

   group1 group1_level   group2 group2_level variable variable_level   context stat_name stat_label  stat fmt_fn warning error
1    <NA>                  <NA>                TRT01A      A: Drug X categori…         n          n   134      0              
2    <NA>                  <NA>                TRT01A      A: Drug X categori…         N          N   400      0              
3    <NA>                  <NA>                TRT01A      A: Drug X categori…         p          % 0.335   <fn>              
4    <NA>                  <NA>                TRT01A      B: Place… categori…         n          n   134      0              
5    <NA>                  <NA>                TRT01A      B: Place… categori…         N          N   400      0              
6    <NA>                  <NA>                TRT01A      B: Place… categori…         p          % 0.335   <fn>              
7    <NA>                  <NA>                TRT01A      C: Combi… categori…         n          n   132      0              
8    <NA>                  <NA>                TRT01A      C: Combi… categori…         N          N   400      0              
9    <NA>                  <NA>                TRT01A      C: Combi… categori…         p          %  0.33   <fn>              
10 TRT01A    A: Drug X     <NA>              AEBODSYS         cl A.1 hierarch…         n          n    53      0              
11 TRT01A    A: Drug X     <NA>              AEBODSYS         cl A.1 hierarch…         N          N   134      0              
12 TRT01A    A: Drug X     <NA>              AEBODSYS         cl A.1 hierarch…         p          % 0.396   <fn>              
13 TRT01A    B: Place…     <NA>              AEBODSYS         cl A.1 hierarch…         n          n    55      0              
14 TRT01A    B: Place…     <NA>              AEBODSYS         cl A.1 hierarch…         N          N   134      0              
15 TRT01A    B: Place…     <NA>              AEBODSYS         cl A.1 hierarch…         p          %  0.41   <fn>              
16 TRT01A    C: Combi…     <NA>              AEBODSYS         cl A.1 hierarch…         n          n    69      0              
17 TRT01A    C: Combi…     <NA>              AEBODSYS         cl A.1 hierarch…         N          N   132      0              
18 TRT01A    C: Combi…     <NA>              AEBODSYS         cl A.1 hierarch…         p          % 0.523   <fn>              
19 TRT01A    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    37      0              
20 TRT01A    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
21 TRT01A    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.276   <fn>              
22 TRT01A    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    37      0              
23 TRT01A    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
24 TRT01A    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.276   <fn>              
25 TRT01A    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    50      0              
26 TRT01A    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   132      0              
27 TRT01A    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.379   <fn>              
28 TRT01A    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    33      0              
29 TRT01A    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
30 TRT01A    A: Drug X AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.246   <fn>              
31 TRT01A    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    31      0              
32 TRT01A    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
33 TRT01A    B: Place… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.231   <fn>              
34 TRT01A    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         n          n    40      0              
35 TRT01A    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         N          N   132      0              
36 TRT01A    C: Combi… AEBODSYS       cl A.1  AEDECOD      dcd A.1.… hierarch…         p          % 0.303   <fn>              
37 TRT01A    A: Drug X     <NA>              AEBODSYS         cl B.1 hierarch…         n          n    35      0              
38 TRT01A    A: Drug X     <NA>              AEBODSYS         cl B.1 hierarch…         N          N   134      0              
39 TRT01A    A: Drug X     <NA>              AEBODSYS         cl B.1 hierarch…         p          % 0.261   <fn>              
40 TRT01A    B: Place…     <NA>              AEBODSYS         cl B.1 hierarch…         n          n    41      0              

ℹ 122 more rows

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

Build Table

tbl <- tbl_hierarchical(
  data,
  variables = c(AEBODSYS, AEDECOD),
  by = TRT01A,
  id = USUBJID,
  denominator = adsl,
  overall_row = TRUE,
  label = list(..ard_hierarchical_overall.. = "Patients with at least one AE leading to discontinuation")
)

tbl