FDA Table 09

Patients With Serious Adverse Events by System Organ Class and Preferred Term, Safety Population, Pooled Analyses

table

FDA

safety

adverse events

Code

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

adsl <- random.cdisc.data::cadsl
adae <- random.cdisc.data::cadae

# Pre-processing --------------------------------------------

adae <- adae %>%
  dplyr::filter(
    # safety population
    SAFFL == "Y",
    # serious adverse events
    AESER == "Y"
  )

Code

tbl <- adae |>
  tbl_hierarchical(
    variables = c(AESOC, AEDECOD),
    by = ARM,
    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: 81 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>                                       ARM      A: Drug X categori…         n          n   134      134       0                   stat_1
2    <NA>                <NA>                                       ARM      A: Drug X categori…         N          N   400      400       0                   stat_1
3    <NA>                <NA>                                       ARM      A: Drug X categori…         p          % 0.335     33.5    <fn>                   stat_1
4    <NA>                <NA>                                       ARM      B: Place… categori…         n          n   134      134       0                   stat_2
5    <NA>                <NA>                                       ARM      B: Place… categori…         N          N   400      400       0                   stat_2
6    <NA>                <NA>                                       ARM      B: Place… categori…         p          % 0.335     33.5    <fn>                   stat_2
7    <NA>                <NA>                                       ARM      C: Combi… categori…         n          n   132      132       0                   stat_3
8    <NA>                <NA>                                       ARM      C: Combi… categori…         N          N   400      400       0                   stat_3
9    <NA>                <NA>                                       ARM      C: Combi… categori…         p          %  0.33     33.0    <fn>                   stat_3
10    ARM    A: Drug X   <NA>              ..ard_hierarchical_overall..           TRUE hierarch…         n          n   104      104    <fn>                   stat_1

ℹ 71 more rows

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