Subjects With Serious Adverse Events by System Organ Class and Preferred Term, Safety Population, Pooled Analysis (or Trial X)
FDA Table 10
table
FDA
safety
adverse events
FDA IG Shell
Programming Notes
Background and Instructions
Customization
Output
Code
# FDA TABLE 10 ---------------------------------------------------------------
# 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(gtsummary)
adsl <- pharmaverseadam::adsl
adae <- pharmaverseadam::adae
# Pre-processing --------------------------------------------
adae <- adae |>
filter(
# safety population
SAFFL == "Y",
# serious adverse events
AESER == "Y"
)
tbl <- adae |>
tbl_hierarchical(
variables = c(AESOC, AEDECOD),
by = TRT01A,
id = USUBJID,
denominator = adsl,
overall_row = TRUE,
label = "..ard_hierarchical_overall.." ~ "Any SAE"
)
ard <- gtsummary::gather_ard(tbl)$tbl_hierarchical
# An ARD data frame: 36 × 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 Xanomeline High Dose <NA> <NULL> ..ard_hierarchical_overall.. TRUE hierarchical n n 1 1 <fn> <NULL> <NULL> stat_1
14 TRT01A Xanomeline High Dose <NA> <NULL> ..ard_hierarchical_overall.. TRUE hierarchical N N 72 72 <fn> <NULL> <NULL> stat_1
15 TRT01A Xanomeline High Dose <NA> <NULL> ..ard_hierarchical_overall.. TRUE hierarchical p % 0.0139 1.4 <fn> <NULL> <NULL> stat_1
16 TRT01A Xanomeline Low Dose <NA> <NULL> ..ard_hierarchical_overall.. TRUE hierarchical n n 2 2 <fn> <NULL> <NULL> stat_2
17 TRT01A Xanomeline Low Dose <NA> <NULL> ..ard_hierarchical_overall.. TRUE hierarchical N N 96 96 <fn> <NULL> <NULL> stat_2
18 TRT01A Xanomeline Low Dose <NA> <NULL> ..ard_hierarchical_overall.. TRUE hierarchical p % 0.0208 2.1 <fn> <NULL> <NULL> stat_2
19 TRT01A Xanomeline High Dose <NA> <NULL> AESOC NERVOUS SYSTEM DISORDERS hierarchical n n 1 1 <fn> <NULL> <NULL> stat_1
20 TRT01A Xanomeline High Dose <NA> <NULL> AESOC NERVOUS SYSTEM DISORDERS hierarchical N N 72 72 <fn> <NULL> <NULL> stat_1
21 TRT01A Xanomeline High Dose <NA> <NULL> AESOC NERVOUS SYSTEM DISORDERS hierarchical p % 0.0139 1.4 <fn> <NULL> <NULL> stat_1
22 TRT01A Xanomeline Low Dose <NA> <NULL> AESOC NERVOUS SYSTEM DISORDERS hierarchical n n 2 2 <fn> <NULL> <NULL> stat_2
23 TRT01A Xanomeline Low Dose <NA> <NULL> AESOC NERVOUS SYSTEM DISORDERS hierarchical N N 96 96 <fn> <NULL> <NULL> stat_2
24 TRT01A Xanomeline Low Dose <NA> <NULL> AESOC NERVOUS SYSTEM DISORDERS hierarchical p % 0.0208 2.1 <fn> <NULL> <NULL> stat_2
25 TRT01A Xanomeline High Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD PARTIAL SEIZURES WITH SECONDARY GENERALISATION hierarchical n n 1 1 <fn> <NULL> <NULL> stat_1
26 TRT01A Xanomeline High Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD PARTIAL SEIZURES WITH SECONDARY GENERALISATION hierarchical N N 72 72 <fn> <NULL> <NULL> stat_1
27 TRT01A Xanomeline High Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD PARTIAL SEIZURES WITH SECONDARY GENERALISATION hierarchical p % 0.0139 1.4 <fn> <NULL> <NULL> stat_1
28 TRT01A Xanomeline Low Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD PARTIAL SEIZURES WITH SECONDARY GENERALISATION hierarchical n n 0 0 <fn> <NULL> <NULL> stat_2
29 TRT01A Xanomeline Low Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD PARTIAL SEIZURES WITH SECONDARY GENERALISATION hierarchical N N 96 96 <fn> <NULL> <NULL> stat_2
30 TRT01A Xanomeline Low Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD PARTIAL SEIZURES WITH SECONDARY GENERALISATION hierarchical p % 0 0 <fn> <NULL> <NULL> stat_2
31 TRT01A Xanomeline High Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD SYNCOPE hierarchical n n 0 0 <fn> <NULL> <NULL> stat_1
32 TRT01A Xanomeline High Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD SYNCOPE hierarchical N N 72 72 <fn> <NULL> <NULL> stat_1
33 TRT01A Xanomeline High Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD SYNCOPE hierarchical p % 0 0 <fn> <NULL> <NULL> stat_1
34 TRT01A Xanomeline Low Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD SYNCOPE hierarchical n n 2 2 <fn> <NULL> <NULL> stat_2
35 TRT01A Xanomeline Low Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD SYNCOPE hierarchical N N 96 96 <fn> <NULL> <NULL> stat_2
36 TRT01A Xanomeline Low Dose AESOC NERVOUS SYSTEM DISORDERS AEDECOD SYNCOPE hierarchical p % 0.0208 2.1 <fn> <NULL> <NULL> stat_2