FDA Table 36

Patients With Adverse Events by System Organ Class and Preferred Term, Safety Population, Pooled Analysis (or Trial X)

table

FDA

safety

adverse events

Code

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

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

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

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

Code

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

ard

{cards} data frame: 135 x 13

   group1 group1_level group2 group2_level variable variable_level   context stat_name stat_label  stat fmt_fn warning error
1    <NA>                <NA>                   ARM      A: Drug X categori…         n          n   134      0              
2    <NA>                <NA>                   ARM      A: Drug X categori…         N          N   400      0              
3    <NA>                <NA>                   ARM      A: Drug X categori…         p          % 0.335   <fn>              
4    <NA>                <NA>                   ARM      B: Place… categori…         n          n   134      0              
5    <NA>                <NA>                   ARM      B: Place… categori…         N          N   400      0              
6    <NA>                <NA>                   ARM      B: Place… categori…         p          % 0.335   <fn>              
7    <NA>                <NA>                   ARM      C: Combi… categori…         n          n   132      0              
8    <NA>                <NA>                   ARM      C: Combi… categori…         N          N   400      0              
9    <NA>                <NA>                   ARM      C: Combi… categori…         p          %  0.33   <fn>              
10    ARM    A: Drug X   <NA>                 AESOC           cl A hierarch…         n          n    78      0              
11    ARM    A: Drug X   <NA>                 AESOC           cl A hierarch…         N          N   134      0              
12    ARM    A: Drug X   <NA>                 AESOC           cl A hierarch…         p          % 0.582   <fn>              
13    ARM    B: Place…   <NA>                 AESOC           cl A hierarch…         n          n    75      0              
14    ARM    B: Place…   <NA>                 AESOC           cl A hierarch…         N          N   134      0              
15    ARM    B: Place…   <NA>                 AESOC           cl A hierarch…         p          %  0.56   <fn>              
16    ARM    C: Combi…   <NA>                 AESOC           cl A hierarch…         n          n    89      0              
17    ARM    C: Combi…   <NA>                 AESOC           cl A hierarch…         N          N   132      0              
18    ARM    C: Combi…   <NA>                 AESOC           cl A hierarch…         p          % 0.674   <fn>              
19    ARM    A: Drug X  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         n          n    50      0              
20    ARM    A: Drug X  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
21    ARM    A: Drug X  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         p          % 0.373   <fn>              
22    ARM    B: Place…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         n          n    45      0              
23    ARM    B: Place…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
24    ARM    B: Place…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         p          % 0.336   <fn>              
25    ARM    C: Combi…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         n          n    63      0              
26    ARM    C: Combi…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         N          N   132      0              
27    ARM    C: Combi…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         p          % 0.477   <fn>              
28    ARM    A: Drug X  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         n          n    48      0              
29    ARM    A: Drug X  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
30    ARM    A: Drug X  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         p          % 0.358   <fn>              
31    ARM    B: Place…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         n          n    48      0              
32    ARM    B: Place…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         N          N   134      0              
33    ARM    B: Place…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         p          % 0.358   <fn>              
34    ARM    C: Combi…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         n          n    50      0              
35    ARM    C: Combi…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         N          N   132      0              
36    ARM    C: Combi…  AESOC         cl A  AEDECOD      dcd A.1.… hierarch…         p          % 0.379   <fn>              
37    ARM    A: Drug X   <NA>                 AESOC           cl B hierarch…         n          n    96      0              
38    ARM    A: Drug X   <NA>                 AESOC           cl B hierarch…         N          N   134      0              
39    ARM    A: Drug X   <NA>                 AESOC           cl B hierarch…         p          % 0.716   <fn>              
40    ARM    B: Place…   <NA>                 AESOC           cl B hierarch…         n          n    89      0

ℹ 95 more rows

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

Code

# create table using ARD-first approach (ARD -> table)
tbl <-
  tbl_ard_hierarchical(
    ard,
    variables = c(AESOC, AEDECOD),
    by = ARM,
    # add custom variable labels
    label = list(
      AESOC = "System Organ Class",
      AEDECOD = "Preferred Term"
    )
  )

tbl