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

FDA Table 13

table

FDA

safety

adverse events

Code

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

set.seed(1)
adsl <- pharmaverseadam::adsl
adae <- pharmaverseadam::adae

adae <- adae |>
  rename(OCMQ01SC = AEHLTCD) |>
  mutate(
    AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
    OCMQ01NAM = sample(c("OCMQ1", "OCMQ2", "OCMQ3"), size = nrow(adae), replace = TRUE)
  )

adae$OCMQ01SC[is.na(adae$OCMQ01SC)] <- "NARROW"

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

data <- adae |>
  filter(
    # safety population
    SAFFL == "Y",
    # narrow OCMQ
    OCMQ01SC == "NARROW"
  )

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

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

Code

ard <- ard_stack_hierarchical(
  data,
  variables = c(AEBODSYS, OCMQ01NAM),
  by = TRT01A,
  denominator = adsl,
  id = USUBJID
)

ard

{cards} data frame: 117 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   254       0              
3    <NA>                  <NA>                 TRT01A        Placebo  tabulate         p          % 0.339    <fn>              
4    <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         n          n    72       0              
5    <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         N          N   254       0              
6    <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         p          % 0.283    <fn>              
7    <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         n          n    96       0              
8    <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         N          N   254       0              
9    <NA>                  <NA>                 TRT01A      Xanomeli…  tabulate         p          % 0.378    <fn>              
10 TRT01A      Placebo     <NA>               AEBODSYS      GENERAL … hierarch…         n          n    21       0              
11 TRT01A      Placebo     <NA>               AEBODSYS      GENERAL … hierarch…         N          N    86       0              
12 TRT01A      Placebo     <NA>               AEBODSYS      GENERAL … hierarch…         p          % 0.244    <fn>              
13 TRT01A    Xanomeli…     <NA>               AEBODSYS      GENERAL … hierarch…         n          n    36       0              
14 TRT01A    Xanomeli…     <NA>               AEBODSYS      GENERAL … hierarch…         N          N    72       0              
15 TRT01A    Xanomeli…     <NA>               AEBODSYS      GENERAL … hierarch…         p          %   0.5    <fn>              
16 TRT01A    Xanomeli…     <NA>               AEBODSYS      GENERAL … hierarch…         n          n    51       0              
17 TRT01A    Xanomeli…     <NA>               AEBODSYS      GENERAL … hierarch…         N          N    96       0              
18 TRT01A    Xanomeli…     <NA>               AEBODSYS      GENERAL … hierarch…         p          % 0.531    <fn>              
19 TRT01A      Placebo AEBODSYS    GENERAL … OCMQ01NAM          OCMQ1 hierarch…         n          n     8       0              
20 TRT01A      Placebo AEBODSYS    GENERAL … OCMQ01NAM          OCMQ1 hierarch…         N          N    86       0              
21 TRT01A      Placebo AEBODSYS    GENERAL … OCMQ01NAM          OCMQ1 hierarch…         p          % 0.093    <fn>              
22 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ1 hierarch…         n          n    23       0              
23 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ1 hierarch…         N          N    72       0              
24 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ1 hierarch…         p          % 0.319    <fn>              
25 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ1 hierarch…         n          n    25       0              
26 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ1 hierarch…         N          N    96       0              
27 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ1 hierarch…         p          %  0.26    <fn>              
28 TRT01A      Placebo AEBODSYS    GENERAL … OCMQ01NAM          OCMQ2 hierarch…         n          n    11       0              
29 TRT01A      Placebo AEBODSYS    GENERAL … OCMQ01NAM          OCMQ2 hierarch…         N          N    86       0              
30 TRT01A      Placebo AEBODSYS    GENERAL … OCMQ01NAM          OCMQ2 hierarch…         p          % 0.128    <fn>              
31 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ2 hierarch…         n          n    22       0              
32 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ2 hierarch…         N          N    72       0              
33 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ2 hierarch…         p          % 0.306    <fn>              
34 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ2 hierarch…         n          n    26       0              
35 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ2 hierarch…         N          N    96       0              
36 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ2 hierarch…         p          % 0.271    <fn>              
37 TRT01A      Placebo AEBODSYS    GENERAL … OCMQ01NAM          OCMQ3 hierarch…         n          n    14       0              
38 TRT01A      Placebo AEBODSYS    GENERAL … OCMQ01NAM          OCMQ3 hierarch…         N          N    86       0              
39 TRT01A      Placebo AEBODSYS    GENERAL … OCMQ01NAM          OCMQ3 hierarch…         p          % 0.163    <fn>              
40 TRT01A    Xanomeli… AEBODSYS    GENERAL … OCMQ01NAM          OCMQ3 hierarch…         n          n    26       0

ℹ 77 more rows

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

Code

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

tbl