Subjects With Adverse Events by Organ System, OCMQ (Broad) and Preferred Term, Safety Population, Pooled Analysis (or Trial X)
FDA Table 43
table
FDA
safety
adverse events
Code
# Load libraries & data -------------------------------------
library(dplyr)
library(cards)
library(gtsummary)
adae <- pharmaverseadam::adae
adsl <- pharmaverseadam::adsl
set.seed(1)
adae <- adae |>
mutate(
AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
OCMQ01NAM = sample(c("OCMQ1", "OCMQ2", "OCMQ3"), size = nrow(adae), replace = TRUE),
OCMQ01SC = sample(c("BROAD", "NARROW"), size = nrow(adae), replace = TRUE)
)
# Pre-processing --------------------------------------------
adsl <- adsl |>
filter(SAFFL == "Y") # safety population
data <- adae |>
filter(
# safety population
SAFFL == "Y",
# treatment-emergent
TRTEMFL == "Y",
# broad OCMQ scope
OCMQ01SC == "BROAD",
# filtering here to reduce the size of the table
AESOC %in% c("EYE DISORDERS", "EAR AND LABYRINTH DISORDERS", "CONGENITAL, FAMILIAL AND GENETIC DISORDERS")
){cards} data frame: 144 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 CONGENIT… <NA> OCMQ01NAM OCMQ3 hierarch… n n 0 0
11 TRT01A Placebo AEBODSYS CONGENIT… <NA> OCMQ01NAM OCMQ3 hierarch… N N 86 0
12 TRT01A Placebo AEBODSYS CONGENIT… <NA> OCMQ01NAM OCMQ3 hierarch… p % 0 <fn>
13 TRT01A Xanomeli… AEBODSYS CONGENIT… <NA> OCMQ01NAM OCMQ3 hierarch… n n 1 0
14 TRT01A Xanomeli… AEBODSYS CONGENIT… <NA> OCMQ01NAM OCMQ3 hierarch… N N 72 0
15 TRT01A Xanomeli… AEBODSYS CONGENIT… <NA> OCMQ01NAM OCMQ3 hierarch… p % 0.014 <fn>
16 TRT01A Xanomeli… AEBODSYS CONGENIT… <NA> OCMQ01NAM OCMQ3 hierarch… n n 0 0
17 TRT01A Xanomeli… AEBODSYS CONGENIT… <NA> OCMQ01NAM OCMQ3 hierarch… N N 96 0
18 TRT01A Xanomeli… AEBODSYS CONGENIT… <NA> OCMQ01NAM OCMQ3 hierarch… p % 0 <fn>
19 TRT01A Placebo AEBODSYS CONGENIT… OCMQ01NAM OCMQ3 AEDECOD VENTRICU… hierarch… n n 0 0
20 TRT01A Placebo AEBODSYS CONGENIT… OCMQ01NAM OCMQ3 AEDECOD VENTRICU… hierarch… N N 86 0
21 TRT01A Placebo AEBODSYS CONGENIT… OCMQ01NAM OCMQ3 AEDECOD VENTRICU… hierarch… p % 0 <fn>
22 TRT01A Xanomeli… AEBODSYS CONGENIT… OCMQ01NAM OCMQ3 AEDECOD VENTRICU… hierarch… n n 1 0
23 TRT01A Xanomeli… AEBODSYS CONGENIT… OCMQ01NAM OCMQ3 AEDECOD VENTRICU… hierarch… N N 72 0
24 TRT01A Xanomeli… AEBODSYS CONGENIT… OCMQ01NAM OCMQ3 AEDECOD VENTRICU… hierarch… p % 0.014 <fn>
25 TRT01A Xanomeli… AEBODSYS CONGENIT… OCMQ01NAM OCMQ3 AEDECOD VENTRICU… hierarch… n n 0 0
26 TRT01A Xanomeli… AEBODSYS CONGENIT… OCMQ01NAM OCMQ3 AEDECOD VENTRICU… hierarch… N N 96 0
27 TRT01A Xanomeli… AEBODSYS CONGENIT… OCMQ01NAM OCMQ3 AEDECOD VENTRICU… hierarch… p % 0 <fn>
28 TRT01A Placebo AEBODSYS EAR AND … <NA> OCMQ01NAM OCMQ1 hierarch… n n 1 0
29 TRT01A Placebo AEBODSYS EAR AND … <NA> OCMQ01NAM OCMQ1 hierarch… N N 86 0
30 TRT01A Placebo AEBODSYS EAR AND … <NA> OCMQ01NAM OCMQ1 hierarch… p % 0.012 <fn>
31 TRT01A Xanomeli… AEBODSYS EAR AND … <NA> OCMQ01NAM OCMQ1 hierarch… n n 1 0
32 TRT01A Xanomeli… AEBODSYS EAR AND … <NA> OCMQ01NAM OCMQ1 hierarch… N N 72 0
33 TRT01A Xanomeli… AEBODSYS EAR AND … <NA> OCMQ01NAM OCMQ1 hierarch… p % 0.014 <fn>
34 TRT01A Xanomeli… AEBODSYS EAR AND … <NA> OCMQ01NAM OCMQ1 hierarch… n n 0 0
35 TRT01A Xanomeli… AEBODSYS EAR AND … <NA> OCMQ01NAM OCMQ1 hierarch… N N 96 0
36 TRT01A Xanomeli… AEBODSYS EAR AND … <NA> OCMQ01NAM OCMQ1 hierarch… p % 0 <fn>
37 TRT01A Placebo AEBODSYS EAR AND … OCMQ01NAM OCMQ1 AEDECOD EAR PAIN hierarch… n n 1 0
38 TRT01A Placebo AEBODSYS EAR AND … OCMQ01NAM OCMQ1 AEDECOD EAR PAIN hierarch… N N 86 0
39 TRT01A Placebo AEBODSYS EAR AND … OCMQ01NAM OCMQ1 AEDECOD EAR PAIN hierarch… p % 0.012 <fn>
40 TRT01A Xanomeli… AEBODSYS EAR AND … OCMQ01NAM OCMQ1 AEDECOD EAR PAIN hierarch… n n 0 0 ℹ 104 more rowsℹ Use `print(n = ...)` to see more rowsCode
# 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 labels
label = list(
AEBODSYS = "Organ System",
OCMQ01NAM = "OCMQ (Broad)",
AEDECOD = "Preferred Term"
)
)
tbl