Subjects With Common Adverse Events Occurring at ≥X% Frequency by Preferred Term, Safety Population, Pooled Analysis (or Trial X)

FDA Table 15

table

FDA

safety

adverse events

Code

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

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

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

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

Code

tbl <-
  tbl_hierarchical(
    data,
    variables = c(AEDECOD),
    by = TRT01A,
    id = USUBJID,
    denominator = adsl,
    label = AEDECOD ~ "**Preferred Term**"
  ) |>
  # filter for >=5% frequency
  filter_hierarchical(sum(n) / sum(N) >= 0.05)

tbl

Code

ard <- gather_ard(tbl)
ard

$tbl_hierarchical

{cards} data frame: 144 x 13

   group1 group1_level variable variable_level   context stat_name stat_label  stat stat_fmt fmt_fun warning error gts_column
1    <NA>                TRT01A        Placebo  tabulate         n          n    86       86       0                   stat_1
2    <NA>                TRT01A        Placebo  tabulate         N          N   254      254       0                   stat_1
3    <NA>                TRT01A        Placebo  tabulate         p          % 0.339     33.9    <fn>                   stat_1
4    <NA>                TRT01A      Xanomeli…  tabulate         n          n    72       72       0                   stat_2
5    <NA>                TRT01A      Xanomeli…  tabulate         N          N   254      254       0                   stat_2
6    <NA>                TRT01A      Xanomeli…  tabulate         p          % 0.283     28.3    <fn>                   stat_2
7    <NA>                TRT01A      Xanomeli…  tabulate         n          n    96       96       0                   stat_3
8    <NA>                TRT01A      Xanomeli…  tabulate         N          N   254      254       0                   stat_3
9    <NA>                TRT01A      Xanomeli…  tabulate         p          % 0.378     37.8    <fn>                   stat_3
10 TRT01A      Placebo  AEDECOD      APPLICAT… hierarch…         n          n     5        5    <fn>                   stat_1

ℹ 134 more rows

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