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

FDA Table 29

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Setup

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

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

set.seed(1)
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)
  ) |>
  # truncating table for demonstration
  filter(AESOC == "VASCULAR DISORDERS")
adae$OCMQ01SC[is.na(adae$OCMQ01SC)] <- "NARROW"

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

data <- adae |>
  filter(
    # safety population
    SAFFL == "Y",
    # serious AEs
    AESER == "Y",
    # treatment-emergent
    TRTEMFL == "Y",
    # narrow OCMQ scope
    OCMQ01SC == "NARROW"
  )

Build ARD

ard <- ard_stack_hierarchical(
  data,
  variables = c(AEBODSYS, OCMQ01NAM, AEDECOD),
  by = TRT01A,
  id = USUBJID,
  denominator = adsl,
  # variables to include AE rates for
  include = c(OCMQ01NAM, AEDECOD)
)

ard

{cards} data frame: 57 x 15

   group1 group1_level   group2 group2_level    group3 group3_level  variable variable_level   context stat_name stat_label  stat fmt_fun warning error
1    <NA>                  <NA>                   <NA>                 TRT01A        Placebo  tabulate         n          n    86       0              
2    <NA>                  <NA>                   <NA>                 TRT01A        Placebo  tabulate         N          N   254       0              
3    <NA>                  <NA>                   <NA>                 TRT01A        Placebo  tabulate         p          % 0.339    <fn>              
4    <NA>                  <NA>                   <NA>                 TRT01A      Xanomeli…  tabulate         n          n    72       0              
5    <NA>                  <NA>                   <NA>                 TRT01A      Xanomeli…  tabulate         N          N   254       0              
6    <NA>                  <NA>                   <NA>                 TRT01A      Xanomeli…  tabulate         p          % 0.283    <fn>              
7    <NA>                  <NA>                   <NA>                 TRT01A      Xanomeli…  tabulate         n          n    96       0              
8    <NA>                  <NA>                   <NA>                 TRT01A      Xanomeli…  tabulate         N          N   254       0              
9    <NA>                  <NA>                   <NA>                 TRT01A      Xanomeli…  tabulate         p          % 0.378    <fn>              
10 TRT01A      Placebo AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ1 hierarch…         n          n     1       0              
11 TRT01A      Placebo AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ1 hierarch…         N          N    86       0              
12 TRT01A      Placebo AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ1 hierarch…         p          % 0.012    <fn>              
13 TRT01A    Xanomeli… AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ1 hierarch…         n          n     1       0              
14 TRT01A    Xanomeli… AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ1 hierarch…         N          N    96       0              
15 TRT01A    Xanomeli… AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ1 hierarch…         p          %  0.01    <fn>              
16 TRT01A      Placebo AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ1   AEDECOD      HYPOTENS… hierarch…         n          n     1       0              
17 TRT01A      Placebo AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ1   AEDECOD      HYPOTENS… hierarch…         N          N    86       0              
18 TRT01A      Placebo AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ1   AEDECOD      HYPOTENS… hierarch…         p          % 0.012    <fn>              
19 TRT01A    Xanomeli… AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ1   AEDECOD      HYPOTENS… hierarch…         n          n     1       0              
20 TRT01A    Xanomeli… AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ1   AEDECOD      HYPOTENS… hierarch…         N          N    96       0              
21 TRT01A    Xanomeli… AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ1   AEDECOD      HYPOTENS… hierarch…         p          %  0.01    <fn>              
22 TRT01A      Placebo AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ2 hierarch…         n          n     1       0              
23 TRT01A      Placebo AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ2 hierarch…         N          N    86       0              
24 TRT01A      Placebo AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ2 hierarch…         p          % 0.012    <fn>              
25 TRT01A    Xanomeli… AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ2 hierarch…         n          n     1       0              
26 TRT01A    Xanomeli… AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ2 hierarch…         N          N    96       0              
27 TRT01A    Xanomeli… AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ2 hierarch…         p          %  0.01    <fn>              
28 TRT01A      Placebo AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HOT FLUSH hierarch…         n          n     0       0              
29 TRT01A      Placebo AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HOT FLUSH hierarch…         N          N    86       0              
30 TRT01A      Placebo AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HOT FLUSH hierarch…         p          %     0    <fn>              
31 TRT01A    Xanomeli… AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HOT FLUSH hierarch…         n          n     1       0              
32 TRT01A    Xanomeli… AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HOT FLUSH hierarch…         N          N    96       0              
33 TRT01A    Xanomeli… AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HOT FLUSH hierarch…         p          %  0.01    <fn>              
34 TRT01A      Placebo AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HYPOTENS… hierarch…         n          n     1       0              
35 TRT01A      Placebo AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HYPOTENS… hierarch…         N          N    86       0              
36 TRT01A      Placebo AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HYPOTENS… hierarch…         p          % 0.012    <fn>              
37 TRT01A    Xanomeli… AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HYPOTENS… hierarch…         n          n     0       0              
38 TRT01A    Xanomeli… AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HYPOTENS… hierarch…         N          N    96       0              
39 TRT01A    Xanomeli… AEBODSYS    VASCULAR… OCMQ01NAM        OCMQ2   AEDECOD      HYPOTENS… hierarch…         p          %     0    <fn>              
40 TRT01A      Placebo AEBODSYS    VASCULAR…      <NA>              OCMQ01NAM          OCMQ3 hierarch…         n          n     2       0              

ℹ 17 more rows

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

Build Table

# create table using ARD-first approach (ARD -> table)
tbl <-
  tbl_ard_hierarchical(
    ard,
    variables = c(AEBODSYS, OCMQ01NAM, AEDECOD),
    by = TRT01A,
    # variables to display AE rates for
    include = c(OCMQ01NAM, AEDECOD)
  ) |>
  # add custom variable label
  modify_header(label = "**Organ System**")

tbl