Subjects With Adverse Events by Male-Specific OCMQ (Broad) and Preferred Term, Male Safety Population, Pooled Analysis (or Trial X)
FDA Table 44
table
FDA
safety
adverse events
FDA IG Shell
Programming Notes
Background and Instructions
As discussed in Section 3.2.3.3 Subjects With Adverse Events by Sex-Specific OND Custom Medical Queries (Narrow) and Preferred Term, some OCMQs are relevant to only one sex. Table 44: Adverse Events by Male Specific FDA Medical Query is limited to male-specific broad OCMQs and the male population. Table 45: Adverse Events by Female Specific FDA Medical Query is limited to female-specific broad OCMQs and the female population.
Customization
Output
Code
# FDA TABLE 44 ---------------------------------------------------------------
# Self-contained template. Run top-to-bottom to build the objects below.
# Used by tests via run_template() and published in the catalog.
library(dplyr)
library(cards)
library(gtsummary)
adsl <- pharmaverseadam::adsl
adae <- pharmaverseadam::adae
set.seed(1)
adae <- adae |>
mutate(
OCMQ01SC = as.factor(sample(c("BROAD", "NARROW"), nrow(adae), replace = TRUE)),
OCMQ01NAM = if_else(
SEX == "M",
as.factor(sample(
c("Erectile Dysfunction", "Gynecomastia"),
n(),
replace = TRUE
)),
NA_character_
)
)
# Pre-processing --------------------------------------------
data <- adae |>
filter(
SAFFL == "Y",
SEX == "M",
OCMQ01SC == "BROAD",
# filtering here to reduce the size of the table
AEDECOD %in% c("COUGH", "COLD SWEAT", "SOMNOLENCE", "APPLICATION SITE ERYTHEMA")
) |>
select(OCMQ01SC, TRT01A, OCMQ01NAM, AEDECOD, USUBJID) |>
# setting an explicit level for NA values so empty strata combinations are shown.
mutate(across(everything(), ~ {
if (anyNA(.)) {
forcats::fct_na_value_to_level(as.factor(.), level = "<Missing>")
} else {
.
}
}))
# denominator values include only Male subjects in the arm with AEs
denom <- data |> distinct(USUBJID, TRT01A)
tbl <- data |>
tbl_hierarchical(
by = TRT01A,
variables = c(OCMQ01NAM, AEDECOD),
id = USUBJID,
denominator = denom,
# variables to calculate rates for
include = c(AEDECOD),
label = list(
OCMQ01NAM ~ "OCMQ (Broad)",
AEDECOD ~ "Preferred Term"
)
)
ard <- gtsummary::gather_ard(tbl)|
OCMQ (Broad) Preferred Term |
Placebo N = 31 |
Xanomeline High Dose N = 81 |
Xanomeline Low Dose N = 71 |
|---|---|---|---|
| Erectile Dysfunction | |||
| APPLICATION SITE ERYTHEMA | 0 (0%) | 3 (38%) | 3 (43%) |
| COUGH | 1 (33%) | 3 (38%) | 0 (0%) |
| SOMNOLENCE | 0 (0%) | 1 (13%) | 1 (14%) |
| Gynecomastia | |||
| APPLICATION SITE ERYTHEMA | 0 (0%) | 4 (50%) | 4 (57%) |
| COUGH | 1 (33%) | 1 (13%) | 0 (0%) |
| SOMNOLENCE | 1 (33%) | 0 (0%) | 1 (14%) |
| 1 n (%) | |||
$tbl_hierarchical
# An ARD data frame: 63 × 15
group1 group1_level group2 group2_level variable variable_level context stat_name stat_label stat stat_fmt fmt_fun warning error gts_column
<chr> <list> <chr> <list> <chr> <list> <chr> <chr> <chr> <list> <list> <list> <list> <list> <chr>
1 <NA> <NULL> <NA> <NULL> TRT01A Placebo tabulate n n 3 3 0 <NULL> <NULL> stat_1
2 <NA> <NULL> <NA> <NULL> TRT01A Placebo tabulate N N 18 18 0 <NULL> <NULL> stat_1
3 <NA> <NULL> <NA> <NULL> TRT01A Placebo tabulate p % 0.167 16.7 <fn> <NULL> <NULL> stat_1
4 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline High Dose tabulate n n 8 8 0 <NULL> <NULL> stat_2
5 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline High Dose tabulate N N 18 18 0 <NULL> <NULL> stat_2
6 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline High Dose tabulate p % 0.444 44.4 <fn> <NULL> <NULL> stat_2
7 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline Low Dose tabulate n n 7 7 0 <NULL> <NULL> stat_3
8 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline Low Dose tabulate N N 18 18 0 <NULL> <NULL> stat_3
9 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline Low Dose tabulate p % 0.389 38.9 <fn> <NULL> <NULL> stat_3
10 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD APPLICATION SITE ERYTHEMA hierarchical n n 0 0 <fn> <NULL> <NULL> stat_1
11 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD APPLICATION SITE ERYTHEMA hierarchical N N 3 3 <fn> <NULL> <NULL> stat_1
12 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD APPLICATION SITE ERYTHEMA hierarchical p % 0 0 <fn> <NULL> <NULL> stat_1
13 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD APPLICATION SITE ERYTHEMA hierarchical n n 3 3 <fn> <NULL> <NULL> stat_2
14 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD APPLICATION SITE ERYTHEMA hierarchical N N 8 8 <fn> <NULL> <NULL> stat_2
15 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD APPLICATION SITE ERYTHEMA hierarchical p % 0.375 38 <fn> <NULL> <NULL> stat_2
16 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD APPLICATION SITE ERYTHEMA hierarchical n n 3 3 <fn> <NULL> <NULL> stat_3
17 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD APPLICATION SITE ERYTHEMA hierarchical N N 7 7 <fn> <NULL> <NULL> stat_3
18 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD APPLICATION SITE ERYTHEMA hierarchical p % 0.429 43 <fn> <NULL> <NULL> stat_3
19 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD COUGH hierarchical n n 1 1 <fn> <NULL> <NULL> stat_1
20 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD COUGH hierarchical N N 3 3 <fn> <NULL> <NULL> stat_1
21 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD COUGH hierarchical p % 0.333 33 <fn> <NULL> <NULL> stat_1
22 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD COUGH hierarchical n n 3 3 <fn> <NULL> <NULL> stat_2
23 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD COUGH hierarchical N N 8 8 <fn> <NULL> <NULL> stat_2
24 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD COUGH hierarchical p % 0.375 38 <fn> <NULL> <NULL> stat_2
25 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD COUGH hierarchical n n 0 0 <fn> <NULL> <NULL> stat_3
26 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD COUGH hierarchical N N 7 7 <fn> <NULL> <NULL> stat_3
27 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD COUGH hierarchical p % 0 0 <fn> <NULL> <NULL> stat_3
28 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD SOMNOLENCE hierarchical n n 0 0 <fn> <NULL> <NULL> stat_1
29 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD SOMNOLENCE hierarchical N N 3 3 <fn> <NULL> <NULL> stat_1
30 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD SOMNOLENCE hierarchical p % 0 0 <fn> <NULL> <NULL> stat_1
31 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD SOMNOLENCE hierarchical n n 1 1 <fn> <NULL> <NULL> stat_2
32 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD SOMNOLENCE hierarchical N N 8 8 <fn> <NULL> <NULL> stat_2
33 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD SOMNOLENCE hierarchical p % 0.125 13 <fn> <NULL> <NULL> stat_2
34 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD SOMNOLENCE hierarchical n n 1 1 <fn> <NULL> <NULL> stat_3
35 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD SOMNOLENCE hierarchical N N 7 7 <fn> <NULL> <NULL> stat_3
36 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD SOMNOLENCE hierarchical p % 0.143 14 <fn> <NULL> <NULL> stat_3
37 TRT01A Placebo OCMQ01NAM Gynecomastia AEDECOD APPLICATION SITE ERYTHEMA hierarchical n n 0 0 <fn> <NULL> <NULL> stat_1
38 TRT01A Placebo OCMQ01NAM Gynecomastia AEDECOD APPLICATION SITE ERYTHEMA hierarchical N N 3 3 <fn> <NULL> <NULL> stat_1
39 TRT01A Placebo OCMQ01NAM Gynecomastia AEDECOD APPLICATION SITE ERYTHEMA hierarchical p % 0 0 <fn> <NULL> <NULL> stat_1
40 TRT01A Xanomeline High Dose OCMQ01NAM Gynecomastia AEDECOD APPLICATION SITE ERYTHEMA hierarchical n n 4 4 <fn> <NULL> <NULL> stat_2
41 TRT01A Xanomeline High Dose OCMQ01NAM Gynecomastia AEDECOD APPLICATION SITE ERYTHEMA hierarchical N N 8 8 <fn> <NULL> <NULL> stat_2
42 TRT01A Xanomeline High Dose OCMQ01NAM Gynecomastia AEDECOD APPLICATION SITE ERYTHEMA hierarchical p % 0.5 50 <fn> <NULL> <NULL> stat_2
43 TRT01A Xanomeline Low Dose OCMQ01NAM Gynecomastia AEDECOD APPLICATION SITE ERYTHEMA hierarchical n n 4 4 <fn> <NULL> <NULL> stat_3
44 TRT01A Xanomeline Low Dose OCMQ01NAM Gynecomastia AEDECOD APPLICATION SITE ERYTHEMA hierarchical N N 7 7 <fn> <NULL> <NULL> stat_3
45 TRT01A Xanomeline Low Dose OCMQ01NAM Gynecomastia AEDECOD APPLICATION SITE ERYTHEMA hierarchical p % 0.571 57 <fn> <NULL> <NULL> stat_3
46 TRT01A Placebo OCMQ01NAM Gynecomastia AEDECOD COUGH hierarchical n n 1 1 <fn> <NULL> <NULL> stat_1
47 TRT01A Placebo OCMQ01NAM Gynecomastia AEDECOD COUGH hierarchical N N 3 3 <fn> <NULL> <NULL> stat_1
48 TRT01A Placebo OCMQ01NAM Gynecomastia AEDECOD COUGH hierarchical p % 0.333 33 <fn> <NULL> <NULL> stat_1
49 TRT01A Xanomeline High Dose OCMQ01NAM Gynecomastia AEDECOD COUGH hierarchical n n 1 1 <fn> <NULL> <NULL> stat_2
50 TRT01A Xanomeline High Dose OCMQ01NAM Gynecomastia AEDECOD COUGH hierarchical N N 8 8 <fn> <NULL> <NULL> stat_2
51 TRT01A Xanomeline High Dose OCMQ01NAM Gynecomastia AEDECOD COUGH hierarchical p % 0.125 13 <fn> <NULL> <NULL> stat_2
52 TRT01A Xanomeline Low Dose OCMQ01NAM Gynecomastia AEDECOD COUGH hierarchical n n 0 0 <fn> <NULL> <NULL> stat_3
53 TRT01A Xanomeline Low Dose OCMQ01NAM Gynecomastia AEDECOD COUGH hierarchical N N 7 7 <fn> <NULL> <NULL> stat_3
54 TRT01A Xanomeline Low Dose OCMQ01NAM Gynecomastia AEDECOD COUGH hierarchical p % 0 0 <fn> <NULL> <NULL> stat_3
55 TRT01A Placebo OCMQ01NAM Gynecomastia AEDECOD SOMNOLENCE hierarchical n n 1 1 <fn> <NULL> <NULL> stat_1
56 TRT01A Placebo OCMQ01NAM Gynecomastia AEDECOD SOMNOLENCE hierarchical N N 3 3 <fn> <NULL> <NULL> stat_1
57 TRT01A Placebo OCMQ01NAM Gynecomastia AEDECOD SOMNOLENCE hierarchical p % 0.333 33 <fn> <NULL> <NULL> stat_1
58 TRT01A Xanomeline High Dose OCMQ01NAM Gynecomastia AEDECOD SOMNOLENCE hierarchical n n 0 0 <fn> <NULL> <NULL> stat_2
59 TRT01A Xanomeline High Dose OCMQ01NAM Gynecomastia AEDECOD SOMNOLENCE hierarchical N N 8 8 <fn> <NULL> <NULL> stat_2
60 TRT01A Xanomeline High Dose OCMQ01NAM Gynecomastia AEDECOD SOMNOLENCE hierarchical p % 0 0 <fn> <NULL> <NULL> stat_2
61 TRT01A Xanomeline Low Dose OCMQ01NAM Gynecomastia AEDECOD SOMNOLENCE hierarchical n n 1 1 <fn> <NULL> <NULL> stat_3
62 TRT01A Xanomeline Low Dose OCMQ01NAM Gynecomastia AEDECOD SOMNOLENCE hierarchical N N 7 7 <fn> <NULL> <NULL> stat_3
63 TRT01A Xanomeline Low Dose OCMQ01NAM Gynecomastia AEDECOD SOMNOLENCE hierarchical p % 0.143 14 <fn> <NULL> <NULL> stat_3