Subjects With Serious Adverse Events by Organ System and OCMQ (Narrow), Safety Population, Pooled Analysis (or Trial X)
FDA Table 11
table
FDA
safety
adverse events
FDA IG Shell
Programming Notes
Background and Instructions
Table 11: Subjects With Serious Adverse Events provides a list of SAEs by organ system and OCMQs (narrow). Refer to Table 29 to view the specific preferred terms under each OCMQ.
Customization
Clinical reviewer may request a similar table of SAEs by organ system and OCMQs (broad) from CDS. Based on the assessment of the OCMQ results, clinical reviewer may request Table 41: Subjects With Select Narrow FDA Medical Queries found in Section 4.1 Optional Adverse Event Analyses to explore data on specific subjects.
Output
Code
# FDA TABLE 11 ---------------------------------------------------------------
# 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
# Pre-Processing - OCMQ information
set.seed(1)
adae <- adae |>
mutate(
OCMQ01SC = sample(c("NARROW", "BROAD"), size = nrow(adae), replace = TRUE),
OCMQ01NAM = sample(c("OCMQ1", "OCMQ2", "OCMQ3"), size = nrow(adae), replace = TRUE),
AE_serious = sample(c("Y", "N"), size = nrow(adae), replace = TRUE)
)
# Use safety population, Serious Adverse Event only and Narrow OCMQ
data <- adae |>
filter(SAFFL == "Y", AE_serious == "Y", OCMQ01SC == "NARROW")
sliced_data <- data |>
count(AEBODSYS, sort = TRUE) |>
slice_head(n = 3) |> # keep top 3 for display purposes
pull(AEBODSYS)
data <- data |>
filter(AEBODSYS %in% sliced_data)
# Stack ARD results of two analyses
ard <- ard_stack_hierarchical(
data,
variables = c(AEBODSYS, OCMQ01NAM),
by = TRT01A,
denominator = adsl,
id = USUBJID
)
tbl <- data |>
tbl_hierarchical(
variables = c(AEBODSYS, OCMQ01NAM),
by = TRT01A,
id = USUBJID,
include = OCMQ01NAM,
denominator = adsl,
overall_row = FALSE,
label = list(
AEBODSYS = "**Organ System**",
OCMQ01NAM = "**OCMQ (Narrow)**"
)
)
ard <- gtsummary::gather_ard(tbl)| ****Organ System**** ****OCMQ (Narrow)**** |
Placebo N = 861 |
Xanomeline High Dose N = 721 |
Xanomeline Low Dose N = 961 |
|---|---|---|---|
| CARDIAC DISORDERS | |||
| OCMQ1 | 2 (2.3%) | 1 (1.4%) | 5 (5.2%) |
| OCMQ2 | 4 (4.7%) | 2 (2.8%) | 1 (1.0%) |
| OCMQ3 | 4 (4.7%) | 2 (2.8%) | 2 (2.1%) |
| GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS | |||
| OCMQ1 | 1 (1.2%) | 8 (11%) | 9 (9.4%) |
| OCMQ2 | 3 (3.5%) | 9 (13%) | 13 (14%) |
| OCMQ3 | 7 (8.1%) | 8 (11%) | 8 (8.3%) |
| SKIN AND SUBCUTANEOUS TISSUE DISORDERS | |||
| OCMQ1 | 3 (3.5%) | 6 (8.3%) | 10 (10%) |
| OCMQ2 | 3 (3.5%) | 10 (14%) | 7 (7.3%) |
| OCMQ3 | 1 (1.2%) | 11 (15%) | 6 (6.3%) |
| 1 n (%) | |||
$tbl_hierarchical
# An ARD data frame: 93 × 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 86 86 0 <NULL> <NULL> stat_1
2 <NA> <NULL> <NA> <NULL> TRT01A Placebo tabulate N N 306 306 0 <NULL> <NULL> stat_1
3 <NA> <NULL> <NA> <NULL> TRT01A Placebo tabulate p % 0.281 28.1 <fn> <NULL> <NULL> stat_1
4 <NA> <NULL> <NA> <NULL> TRT01A Screen Failure tabulate n n 52 52 0 <NULL> <NULL> stat_2
5 <NA> <NULL> <NA> <NULL> TRT01A Screen Failure tabulate N N 306 306 0 <NULL> <NULL> stat_2
6 <NA> <NULL> <NA> <NULL> TRT01A Screen Failure tabulate p % 0.170 17.0 <fn> <NULL> <NULL> stat_2
7 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline High Dose tabulate n n 72 72 0 <NULL> <NULL> stat_3
8 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline High Dose tabulate N N 306 306 0 <NULL> <NULL> stat_3
9 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline High Dose tabulate p % 0.235 23.5 <fn> <NULL> <NULL> stat_3
10 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline Low Dose tabulate n n 96 96 0 <NULL> <NULL> stat_4
11 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline Low Dose tabulate N N 306 306 0 <NULL> <NULL> stat_4
12 <NA> <NULL> <NA> <NULL> TRT01A Xanomeline Low Dose tabulate p % 0.314 31.4 <fn> <NULL> <NULL> stat_4
13 TRT01A Placebo AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ1 hierarchical n n 2 2 <fn> <NULL> <NULL> stat_1
14 TRT01A Placebo AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ1 hierarchical N N 86 86 <fn> <NULL> <NULL> stat_1
15 TRT01A Placebo AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ1 hierarchical p % 0.0233 2.3 <fn> <NULL> <NULL> stat_1
16 TRT01A Xanomeline High Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ1 hierarchical n n 1 1 <fn> <NULL> <NULL> stat_2
17 TRT01A Xanomeline High Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ1 hierarchical N N 72 72 <fn> <NULL> <NULL> stat_2
18 TRT01A Xanomeline High Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ1 hierarchical p % 0.0139 1.4 <fn> <NULL> <NULL> stat_2
19 TRT01A Xanomeline Low Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ1 hierarchical n n 5 5 <fn> <NULL> <NULL> stat_3
20 TRT01A Xanomeline Low Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ1 hierarchical N N 96 96 <fn> <NULL> <NULL> stat_3
21 TRT01A Xanomeline Low Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ1 hierarchical p % 0.0521 5.2 <fn> <NULL> <NULL> stat_3
22 TRT01A Placebo AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ2 hierarchical n n 4 4 <fn> <NULL> <NULL> stat_1
23 TRT01A Placebo AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ2 hierarchical N N 86 86 <fn> <NULL> <NULL> stat_1
24 TRT01A Placebo AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ2 hierarchical p % 0.0465 4.7 <fn> <NULL> <NULL> stat_1
25 TRT01A Xanomeline High Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ2 hierarchical n n 2 2 <fn> <NULL> <NULL> stat_2
26 TRT01A Xanomeline High Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ2 hierarchical N N 72 72 <fn> <NULL> <NULL> stat_2
27 TRT01A Xanomeline High Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ2 hierarchical p % 0.0278 2.8 <fn> <NULL> <NULL> stat_2
28 TRT01A Xanomeline Low Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ2 hierarchical n n 1 1 <fn> <NULL> <NULL> stat_3
29 TRT01A Xanomeline Low Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ2 hierarchical N N 96 96 <fn> <NULL> <NULL> stat_3
30 TRT01A Xanomeline Low Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ2 hierarchical p % 0.0104 1.0 <fn> <NULL> <NULL> stat_3
31 TRT01A Placebo AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ3 hierarchical n n 4 4 <fn> <NULL> <NULL> stat_1
32 TRT01A Placebo AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ3 hierarchical N N 86 86 <fn> <NULL> <NULL> stat_1
33 TRT01A Placebo AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ3 hierarchical p % 0.0465 4.7 <fn> <NULL> <NULL> stat_1
34 TRT01A Xanomeline High Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ3 hierarchical n n 2 2 <fn> <NULL> <NULL> stat_2
35 TRT01A Xanomeline High Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ3 hierarchical N N 72 72 <fn> <NULL> <NULL> stat_2
36 TRT01A Xanomeline High Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ3 hierarchical p % 0.0278 2.8 <fn> <NULL> <NULL> stat_2
37 TRT01A Xanomeline Low Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ3 hierarchical n n 2 2 <fn> <NULL> <NULL> stat_3
38 TRT01A Xanomeline Low Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ3 hierarchical N N 96 96 <fn> <NULL> <NULL> stat_3
39 TRT01A Xanomeline Low Dose AEBODSYS CARDIAC DISORDERS OCMQ01NAM OCMQ3 hierarchical p % 0.0208 2.1 <fn> <NULL> <NULL> stat_3
40 TRT01A Placebo AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ1 hierarchical n n 1 1 <fn> <NULL> <NULL> stat_1
41 TRT01A Placebo AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ1 hierarchical N N 86 86 <fn> <NULL> <NULL> stat_1
42 TRT01A Placebo AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ1 hierarchical p % 0.0116 1.2 <fn> <NULL> <NULL> stat_1
43 TRT01A Xanomeline High Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ1 hierarchical n n 8 8 <fn> <NULL> <NULL> stat_2
44 TRT01A Xanomeline High Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ1 hierarchical N N 72 72 <fn> <NULL> <NULL> stat_2
45 TRT01A Xanomeline High Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ1 hierarchical p % 0.111 11 <fn> <NULL> <NULL> stat_2
46 TRT01A Xanomeline Low Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ1 hierarchical n n 9 9 <fn> <NULL> <NULL> stat_3
47 TRT01A Xanomeline Low Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ1 hierarchical N N 96 96 <fn> <NULL> <NULL> stat_3
48 TRT01A Xanomeline Low Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ1 hierarchical p % 0.0938 9.4 <fn> <NULL> <NULL> stat_3
49 TRT01A Placebo AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ2 hierarchical n n 3 3 <fn> <NULL> <NULL> stat_1
50 TRT01A Placebo AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ2 hierarchical N N 86 86 <fn> <NULL> <NULL> stat_1
51 TRT01A Placebo AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ2 hierarchical p % 0.0349 3.5 <fn> <NULL> <NULL> stat_1
52 TRT01A Xanomeline High Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ2 hierarchical n n 9 9 <fn> <NULL> <NULL> stat_2
53 TRT01A Xanomeline High Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ2 hierarchical N N 72 72 <fn> <NULL> <NULL> stat_2
54 TRT01A Xanomeline High Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ2 hierarchical p % 0.125 13 <fn> <NULL> <NULL> stat_2
55 TRT01A Xanomeline Low Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ2 hierarchical n n 13 13 <fn> <NULL> <NULL> stat_3
56 TRT01A Xanomeline Low Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ2 hierarchical N N 96 96 <fn> <NULL> <NULL> stat_3
57 TRT01A Xanomeline Low Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ2 hierarchical p % 0.135 14 <fn> <NULL> <NULL> stat_3
58 TRT01A Placebo AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ3 hierarchical n n 7 7 <fn> <NULL> <NULL> stat_1
59 TRT01A Placebo AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ3 hierarchical N N 86 86 <fn> <NULL> <NULL> stat_1
60 TRT01A Placebo AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ3 hierarchical p % 0.0814 8.1 <fn> <NULL> <NULL> stat_1
61 TRT01A Xanomeline High Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ3 hierarchical n n 8 8 <fn> <NULL> <NULL> stat_2
62 TRT01A Xanomeline High Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ3 hierarchical N N 72 72 <fn> <NULL> <NULL> stat_2
63 TRT01A Xanomeline High Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ3 hierarchical p % 0.111 11 <fn> <NULL> <NULL> stat_2
64 TRT01A Xanomeline Low Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ3 hierarchical n n 8 8 <fn> <NULL> <NULL> stat_3
65 TRT01A Xanomeline Low Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ3 hierarchical N N 96 96 <fn> <NULL> <NULL> stat_3
66 TRT01A Xanomeline Low Dose AEBODSYS GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS OCMQ01NAM OCMQ3 hierarchical p % 0.0833 8.3 <fn> <NULL> <NULL> stat_3
67 TRT01A Placebo AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ1 hierarchical n n 3 3 <fn> <NULL> <NULL> stat_1
68 TRT01A Placebo AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ1 hierarchical N N 86 86 <fn> <NULL> <NULL> stat_1
69 TRT01A Placebo AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ1 hierarchical p % 0.0349 3.5 <fn> <NULL> <NULL> stat_1
70 TRT01A Xanomeline High Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ1 hierarchical n n 6 6 <fn> <NULL> <NULL> stat_2
71 TRT01A Xanomeline High Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ1 hierarchical N N 72 72 <fn> <NULL> <NULL> stat_2
72 TRT01A Xanomeline High Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ1 hierarchical p % 0.0833 8.3 <fn> <NULL> <NULL> stat_2
73 TRT01A Xanomeline Low Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ1 hierarchical n n 10 10 <fn> <NULL> <NULL> stat_3
74 TRT01A Xanomeline Low Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ1 hierarchical N N 96 96 <fn> <NULL> <NULL> stat_3
75 TRT01A Xanomeline Low Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ1 hierarchical p % 0.104 10 <fn> <NULL> <NULL> stat_3
76 TRT01A Placebo AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ2 hierarchical n n 3 3 <fn> <NULL> <NULL> stat_1
77 TRT01A Placebo AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ2 hierarchical N N 86 86 <fn> <NULL> <NULL> stat_1
78 TRT01A Placebo AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ2 hierarchical p % 0.0349 3.5 <fn> <NULL> <NULL> stat_1
79 TRT01A Xanomeline High Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ2 hierarchical n n 10 10 <fn> <NULL> <NULL> stat_2
80 TRT01A Xanomeline High Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ2 hierarchical N N 72 72 <fn> <NULL> <NULL> stat_2
81 TRT01A Xanomeline High Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ2 hierarchical p % 0.139 14 <fn> <NULL> <NULL> stat_2
82 TRT01A Xanomeline Low Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ2 hierarchical n n 7 7 <fn> <NULL> <NULL> stat_3
83 TRT01A Xanomeline Low Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ2 hierarchical N N 96 96 <fn> <NULL> <NULL> stat_3
84 TRT01A Xanomeline Low Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ2 hierarchical p % 0.0729 7.3 <fn> <NULL> <NULL> stat_3
85 TRT01A Placebo AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ3 hierarchical n n 1 1 <fn> <NULL> <NULL> stat_1
86 TRT01A Placebo AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ3 hierarchical N N 86 86 <fn> <NULL> <NULL> stat_1
87 TRT01A Placebo AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ3 hierarchical p % 0.0116 1.2 <fn> <NULL> <NULL> stat_1
88 TRT01A Xanomeline High Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ3 hierarchical n n 11 11 <fn> <NULL> <NULL> stat_2
89 TRT01A Xanomeline High Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ3 hierarchical N N 72 72 <fn> <NULL> <NULL> stat_2
90 TRT01A Xanomeline High Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ3 hierarchical p % 0.153 15 <fn> <NULL> <NULL> stat_2
91 TRT01A Xanomeline Low Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ3 hierarchical n n 6 6 <fn> <NULL> <NULL> stat_3
92 TRT01A Xanomeline Low Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ3 hierarchical N N 96 96 <fn> <NULL> <NULL> stat_3
93 TRT01A Xanomeline Low Dose AEBODSYS SKIN AND SUBCUTANEOUS TISSUE DISORDERS OCMQ01NAM OCMQ3 hierarchical p % 0.0625 6.3 <fn> <NULL> <NULL> stat_3