Subjects With Serious Adverse Events by Organ System and OCMQ (Narrow), Safety Population, Pooled Analysis (or Trial X)

FDA Table 11

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Setup

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

adsl <- pharmaverseadam::adsl
adae <- pharmaverseadam::adae

# Pre-Processing - OCMQ information
set.seed(1)
adae <- adae |>
  mutate(
    OCMQ01SC = sample(c("NARROW", "BROAD"), size = nrow(adae), replace = TRUE),
    OCMQ01NAM = sample(c("OCMQ1", "OCMQ2", "OCMQ3"), size = nrow(adae), replace = TRUE),
    AE_serious = sample(c("Y", "N"), size = nrow(adae), replace = TRUE)
  )
# Use safety population, Serious Adverse Event only and Narrow OCMQ
data <- adae |>
  filter(SAFFL == "Y", AE_serious == "Y", OCMQ01SC == "NARROW")

sliced_data <- data |>
  count(AEBODSYS, sort = TRUE) |>
  slice_head(n = 3) %>% # keep top 3 for display purposes
  pull(AEBODSYS)

data <- data |>
  filter(AEBODSYS %in% sliced_data)

Build ARD

# Stack ARD results of two analyses
ard <- ard_stack_hierarchical(
  data,
  variables = c(AEBODSYS, OCMQ01NAM),
  by = TRT01A,
  denominator = adsl,
  id = USUBJID
)

ard

{cards} data frame: 120 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        Placebo  tabulate         n          n    86       0              
2    <NA>                  <NA>                 TRT01A        Placebo  tabulate         N          N   306       0              
3    <NA>                  <NA>                 TRT01A        Placebo  tabulate         p          % 0.281    <fn>              
4    <NA>                  <NA>                 TRT01A      Screen F…  tabulate         n          n    52       0              
5    <NA>                  <NA>                 TRT01A      Screen F…  tabulate         N          N   306       0              
6    <NA>                  <NA>                 TRT01A      Screen F…  tabulate         p          %  0.17    <fn>              
7    <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         n          n    72       0              
8    <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         N          N   306       0              
9    <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         p          % 0.235    <fn>              
10   <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         n          n    96       0              
11   <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         N          N   306       0              
12   <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         p          % 0.314    <fn>              
13 TRT01A      Placebo     <NA>               AEBODSYS      CARDIAC … hierarch…         n          n     9       0              
14 TRT01A      Placebo     <NA>               AEBODSYS      CARDIAC … hierarch…         N          N    86       0              
15 TRT01A      Placebo     <NA>               AEBODSYS      CARDIAC … hierarch…         p          % 0.105    <fn>              
16 TRT01A    Xanomeli…     <NA>               AEBODSYS      CARDIAC … hierarch…         n          n     5       0              
17 TRT01A    Xanomeli…     <NA>               AEBODSYS      CARDIAC … hierarch…         N          N    72       0              
18 TRT01A    Xanomeli…     <NA>               AEBODSYS      CARDIAC … hierarch…         p          % 0.069    <fn>              
19 TRT01A    Xanomeli…     <NA>               AEBODSYS      CARDIAC … hierarch…         n          n     7       0              
20 TRT01A    Xanomeli…     <NA>               AEBODSYS      CARDIAC … hierarch…         N          N    96       0              
21 TRT01A    Xanomeli…     <NA>               AEBODSYS      CARDIAC … hierarch…         p          % 0.073    <fn>              
22 TRT01A      Placebo AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ1 hierarch…         n          n     2       0              
23 TRT01A      Placebo AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ1 hierarch…         N          N    86       0              
24 TRT01A      Placebo AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ1 hierarch…         p          % 0.023    <fn>              
25 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ1 hierarch…         n          n     1       0              
26 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ1 hierarch…         N          N    72       0              
27 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ1 hierarch…         p          % 0.014    <fn>              
28 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ1 hierarch…         n          n     5       0              
29 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ1 hierarch…         N          N    96       0              
30 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ1 hierarch…         p          % 0.052    <fn>              
31 TRT01A      Placebo AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ2 hierarch…         n          n     4       0              
32 TRT01A      Placebo AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ2 hierarch…         N          N    86       0              
33 TRT01A      Placebo AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ2 hierarch…         p          % 0.047    <fn>              
34 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ2 hierarch…         n          n     2       0              
35 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ2 hierarch…         N          N    72       0              
36 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ2 hierarch…         p          % 0.028    <fn>              
37 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ2 hierarch…         n          n     1       0              
38 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ2 hierarch…         N          N    96       0              
39 TRT01A    Xanomeli… AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ2 hierarch…         p          %  0.01    <fn>              
40 TRT01A      Placebo AEBODSYS    CARDIAC … OCMQ01NAM          OCMQ3 hierarch…         n          n     4       0              

ℹ 80 more rows

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

Build Table

tbl <- data |>
  tbl_hierarchical(
    variables = c(AEBODSYS, OCMQ01NAM),
    by = TRT01A,
    id = USUBJID,
    include = OCMQ01NAM,
    denominator = adsl,
    overall_row = FALSE,
    label = list(
      AEBODSYS = "**Organ System**",
      OCMQ01NAM = "**OCMQ (Narrow)**"
    )
  )

tbl