FDA Table 38
Patients With Adverse Events by System Organ Class, FDA Medical Query (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(FMQ01SC = SMQ01SC) %>%
mutate(
AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
)
adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "BROAD"
# Pre-processing --------------------------------------------
adsl <- adsl |>
filter(SAFFL == "Y") # safety population
data <- adae |>
filter(
# safety population
SAFFL == "Y",
# treatment-emergent
TRTEMFL == "Y",
# broad FMQ scope
FMQ01SC == "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_fn warning error
1 <NA> <NA> <NA> ARM A: Drug X categori… n n 134 0
2 <NA> <NA> <NA> ARM A: Drug X categori… N N 400 0
3 <NA> <NA> <NA> ARM A: Drug X categori… p % 0.335 <fn>
4 <NA> <NA> <NA> ARM B: Place… categori… n n 134 0
5 <NA> <NA> <NA> ARM B: Place… categori… N N 400 0
6 <NA> <NA> <NA> ARM B: Place… categori… p % 0.335 <fn>
7 <NA> <NA> <NA> ARM C: Combi… categori… n n 132 0
8 <NA> <NA> <NA> ARM C: Combi… categori… N N 400 0
9 <NA> <NA> <NA> ARM C: Combi… categori… p % 0.33 <fn>
10 ARM A: Drug X AEBODSYS cl A.1 <NA> FMQ01NAM FMQ1 hierarch… n n 32 0
11 ARM A: Drug X AEBODSYS cl A.1 <NA> FMQ01NAM FMQ1 hierarch… N N 134 0
12 ARM A: Drug X AEBODSYS cl A.1 <NA> FMQ01NAM FMQ1 hierarch… p % 0.239 <fn>
13 ARM B: Place… AEBODSYS cl A.1 <NA> FMQ01NAM FMQ1 hierarch… n n 29 0
14 ARM B: Place… AEBODSYS cl A.1 <NA> FMQ01NAM FMQ1 hierarch… N N 134 0
15 ARM B: Place… AEBODSYS cl A.1 <NA> FMQ01NAM FMQ1 hierarch… p % 0.216 <fn>
16 ARM C: Combi… AEBODSYS cl A.1 <NA> FMQ01NAM FMQ1 hierarch… n n 48 0
17 ARM C: Combi… AEBODSYS cl A.1 <NA> FMQ01NAM FMQ1 hierarch… N N 132 0
18 ARM C: Combi… AEBODSYS cl A.1 <NA> FMQ01NAM FMQ1 hierarch… p % 0.364 <fn>
19 ARM A: Drug X AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… n n 17 0
20 ARM A: Drug X AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… N N 134 0
21 ARM A: Drug X AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… p % 0.127 <fn>
22 ARM B: Place… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… n n 13 0
23 ARM B: Place… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… N N 134 0
24 ARM B: Place… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… p % 0.097 <fn>
25 ARM C: Combi… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… n n 29 0
26 ARM C: Combi… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… N N 132 0
27 ARM C: Combi… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… p % 0.22 <fn>
28 ARM A: Drug X AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… n n 20 0
29 ARM A: Drug X AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… N N 134 0
30 ARM A: Drug X AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… p % 0.149 <fn>
31 ARM B: Place… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… n n 20 0
32 ARM B: Place… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… N N 134 0
33 ARM B: Place… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… p % 0.149 <fn>
34 ARM C: Combi… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… n n 26 0
35 ARM C: Combi… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… N N 132 0
36 ARM C: Combi… AEBODSYS cl A.1 FMQ01NAM FMQ1 AEDECOD dcd A.1.… hierarch… p % 0.197 <fn>
37 ARM A: Drug X AEBODSYS cl A.1 <NA> FMQ01NAM FMQ2 hierarch… n n 35 0
38 ARM A: Drug X AEBODSYS cl A.1 <NA> FMQ01NAM FMQ2 hierarch… N N 134 0
39 ARM A: Drug X AEBODSYS cl A.1 <NA> FMQ01NAM FMQ2 hierarch… p % 0.261 <fn>
40 ARM B: Place… AEBODSYS cl A.1 <NA> FMQ01NAM FMQ2 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, FMQ01NAM, AEDECOD),
by = ARM,
# variables to display AE rates for
include = c(FMQ01NAM, AEDECOD),
# Add custom variable labels
label = list(
AEBODSYS = "Body System or Organ Class",
FMQ01NAM = "FMQ (Broad)",
AEDECOD = "Dictionary-Derived Term"
)
)
tbl