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

FDA Table 10

table

FDA

safety

adverse events

Code

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

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

# Pre-processing --------------------------------------------
adae <- adae |>
  filter(
    # safety population
    SAFFL == "Y",
    # serious adverse events
    AESER == "Y"
  )

Code

tbl <- adae |>
  tbl_hierarchical(
    variables = c(AESOC, AEDECOD),
    by = TRT01A,
    id = USUBJID,
    denominator = adsl,
    overall_row = TRUE,
    label = "..ard_hierarchical_overall.." ~ "Any SAE"
  )

tbl

Code

ard <- gather_ard(tbl)
ard

$tbl_hierarchical

{cards} data frame: 36 x 15

   group1 group1_level group2 group2_level variable variable_level  context stat_name stat_label  stat stat_fmt fmt_fun warning error gts_column
1    <NA>                <NA>                TRT01A        Placebo tabulate         n          n    86       86       0                   stat_1
2    <NA>                <NA>                TRT01A        Placebo tabulate         N          N   306      306       0                   stat_1
3    <NA>                <NA>                TRT01A        Placebo tabulate         p          % 0.281     28.1    <fn>                   stat_1
4    <NA>                <NA>                TRT01A      Screen F… tabulate         n          n    52       52       0                   stat_2
5    <NA>                <NA>                TRT01A      Screen F… tabulate         N          N   306      306       0                   stat_2
6    <NA>                <NA>                TRT01A      Screen F… tabulate         p          %  0.17     17.0    <fn>                   stat_2
7    <NA>                <NA>                TRT01A      Xanomeli… tabulate         n          n    72       72       0                   stat_3
8    <NA>                <NA>                TRT01A      Xanomeli… tabulate         N          N   306      306       0                   stat_3
9    <NA>                <NA>                TRT01A      Xanomeli… tabulate         p          % 0.235     23.5    <fn>                   stat_3
10   <NA>                <NA>                TRT01A      Xanomeli… tabulate         n          n    96       96       0                   stat_4

ℹ 26 more rows

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