FDA Table 10

Patients With Serious Adverse Events by System Organ Class and FDA Medical Query (Narrow), 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

# Pre-Processing - FMQ information
set.seed(1)
adae <- adae %>%
  mutate(
    FMQ01SC = sample(c("NARROW", "BROAD"), size = nrow(adae), replace = TRUE),
    FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
  )
# Use safety population, Serious Adverse Event only and Narrow FMQ
data <- adae %>%
  dplyr::filter(SAFFL == "Y", AESER == "Y", FMQ01SC == "NARROW")

Build ARD

# Stack ARD results of two analyses
ard <- ard_stack_hierarchical(
  data,
  variables = c(AEBODSYS, FMQ01NAM),
  by = TRT01A,
  denominator = adsl,
  id = USUBJID
)

ard

{cards} data frame: 153 x 13

   group1 group1_level   group2 group2_level variable variable_level   context stat_name stat_label  stat fmt_fun 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    34       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          % 0.254    <fn>              
13 TRT01A    B: Place…     <NA>              AEBODSYS         cl A.1 hierarch…         n          n    22       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          % 0.164    <fn>              
16 TRT01A    C: Combi…     <NA>              AEBODSYS         cl A.1 hierarch…         n          n    34       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          % 0.258    <fn>              
19 TRT01A    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         n          n    12       0              
20 TRT01A    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         N          N   134       0              
21 TRT01A    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         p          %  0.09    <fn>              
22 TRT01A    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         n          n     8       0              
23 TRT01A    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         N          N   134       0              
24 TRT01A    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         p          %  0.06    <fn>              
25 TRT01A    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         n          n    18       0              
26 TRT01A    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         N          N   132       0              
27 TRT01A    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ1 hierarch…         p          % 0.136    <fn>              
28 TRT01A    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         n          n    12       0              
29 TRT01A    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         N          N   134       0              
30 TRT01A    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         p          %  0.09    <fn>              
31 TRT01A    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         n          n    10       0              
32 TRT01A    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         N          N   134       0              
33 TRT01A    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.075    <fn>              
34 TRT01A    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         n          n     8       0              
35 TRT01A    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         N          N   132       0              
36 TRT01A    C: Combi… AEBODSYS       cl A.1 FMQ01NAM           FMQ2 hierarch…         p          % 0.061    <fn>              
37 TRT01A    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         n          n    13       0              
38 TRT01A    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         N          N   134       0              
39 TRT01A    A: Drug X AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         p          % 0.097    <fn>              
40 TRT01A    B: Place… AEBODSYS       cl A.1 FMQ01NAM           FMQ3 hierarch…         n          n    11       0              

ℹ 113 more rows

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

Build Table

tbl <- data %>%
  tbl_hierarchical(
    variables = c(AEBODSYS, FMQ01NAM),
    by = TRT01A,
    id = USUBJID,
    include = FMQ01NAM,
    denominator = adsl,
    overall_row = FALSE,
  ) %>%
  modify_header(label = "**Body System or Organ Class**  \n    **FMQ(Narrow)**") %>%
  remove_footnote_header(columns = everything())

tbl