FDA Table 43
Subjects With Adverse Events by Organ System, OCMQ (Broad) and Preferred Term, Safety Population, Pooled Analysis (or Trial X)
table
FDA
safety
adverse events
Code
# Load libraries & data -------------------------------------
library(dplyr)
library(cards)
library(gtsummary)
adae <- random.cdisc.data::cadae
adsl <- random.cdisc.data::cadsl
set.seed(1)
adae <- adae |>
rename(OCMQ01SC = SMQ01SC) |>
mutate(
AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
OCMQ01NAM = sample(c("OCMQ1", "OCMQ2", "OCMQ3"), size = nrow(adae), replace = TRUE)
)
adae$OCMQ01SC[is.na(adae$OCMQ01SC)] <- "BROAD"
# 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"
){cards} data frame: 468 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 A: Drug X tabulate n n 134 0
2 <NA> <NA> <NA> TRT01A A: Drug X tabulate N N 400 0
3 <NA> <NA> <NA> TRT01A A: Drug X tabulate p % 0.335 <fn>
4 <NA> <NA> <NA> TRT01A B: Place… tabulate n n 134 0
5 <NA> <NA> <NA> TRT01A B: Place… tabulate N N 400 0
6 <NA> <NA> <NA> TRT01A B: Place… tabulate p % 0.335 <fn>
7 <NA> <NA> <NA> TRT01A C: Combi… tabulate n n 132 0
8 <NA> <NA> <NA> TRT01A C: Combi… tabulate N N 400 0
9 <NA> <NA> <NA> TRT01A C: Combi… tabulate p % 0.33 <fn>
10 TRT01A A: Drug X AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ1 hierarch… n n 32 0
11 TRT01A A: Drug X AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ1 hierarch… N N 134 0
12 TRT01A A: Drug X AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ1 hierarch… p % 0.239 <fn>
13 TRT01A B: Place… AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ1 hierarch… n n 29 0
14 TRT01A B: Place… AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ1 hierarch… N N 134 0
15 TRT01A B: Place… AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ1 hierarch… p % 0.216 <fn>
16 TRT01A C: Combi… AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ1 hierarch… n n 48 0
17 TRT01A C: Combi… AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ1 hierarch… N N 132 0
18 TRT01A C: Combi… AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ1 hierarch… p % 0.364 <fn>
19 TRT01A A: Drug X AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… n n 17 0
20 TRT01A A: Drug X AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… N N 134 0
21 TRT01A A: Drug X AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… p % 0.127 <fn>
22 TRT01A B: Place… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… n n 13 0
23 TRT01A B: Place… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… N N 134 0
24 TRT01A B: Place… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… p % 0.097 <fn>
25 TRT01A C: Combi… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… n n 29 0
26 TRT01A C: Combi… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… N N 132 0
27 TRT01A C: Combi… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… p % 0.22 <fn>
28 TRT01A A: Drug X AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… n n 20 0
29 TRT01A A: Drug X AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… N N 134 0
30 TRT01A A: Drug X AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… p % 0.149 <fn>
31 TRT01A B: Place… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… n n 20 0
32 TRT01A B: Place… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… N N 134 0
33 TRT01A B: Place… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… p % 0.149 <fn>
34 TRT01A C: Combi… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… n n 26 0
35 TRT01A C: Combi… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… N N 132 0
36 TRT01A C: Combi… AEBODSYS cl A.1 OCMQ01NAM OCMQ1 AEDECOD dcd A.1.… hierarch… p % 0.197 <fn>
37 TRT01A A: Drug X AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ2 hierarch… n n 35 0
38 TRT01A A: Drug X AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ2 hierarch… N N 134 0
39 TRT01A A: Drug X AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ2 hierarch… p % 0.261 <fn>
40 TRT01A B: Place… AEBODSYS cl A.1 <NA> OCMQ01NAM OCMQ2 hierarch… n n 40 0 ℹ 428 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