Generate Core Safety Tables (CSR Section 14.3.1) using tern/rtables
tern_AET01_table.Rdtern_AET01_table() produces a consolidated safety summary table using
rtables and tern. It mirrors the output and interface of
AET01_table(), generating standard adverse event summaries (e.g. death,
withdrawal, AESIs) for Clinical Study Reports (CSR) Section 14.3.1.
Usage
tern_AET01_table(
adsl,
adae,
patient_var,
treat_var,
aesi_vars,
aesi_heading = "Total number of patients with at least one",
indent = " "
)Arguments
- adsl
A subject-level dataset (typically ADaM ADSL).
- adae
A dataset of adverse events, preprocessed with AESI flags.
- patient_var
A string indicating the subject identifier variable (e.g.,
"USUBJID").- treat_var
A string indicating the treatment arm variable (e.g.,
"ARM").- aesi_vars
A character vector of binary AESI flags in
adae.- aesi_heading
Ignored (included for interface compatibility).
- indent
Ignored (included for interface compatibility).
Details
The function returns a single formatted rtables table summarising core
safety endpoints by treatment arm.
Examples
tern_AET01_table(
adsl = adsl,
adae = aesi,
patient_var = "USUBJID",
treat_var = "ARM",
aesi_vars = c("FATAL", "SER", "SERWD", "SERDSM", "RELSER",
"WD", "DSM", "REL", "RELWD", "RELDSM", "SEV")
)
#> A: Drug X B: Placebo C: Combination
#> (N=134) (N=134) (N=132)
#> ——————————————————————————————————————————————————————————————————————————————————————————————————————
#> Total number of patients with at least one AE 100 (74.6%) 98 (73.1%) 103 (78.0%)
#> Total number of AEs 502 480 604
#> Total number of deaths 25 (18.7%) 23 (17.2%) 22 (16.7%)
#> Total number of patients withdrawn from study due to an AE 3 (2.2%) 6 (4.5%) 5 (3.8%)
#> Total number of patients with at least one
#> AE with fatal outcome 5 (3.7%) 5 (3.7%) 6 (4.5%)
#> Serious AE 85 (63.4%) 80 (59.7%) 87 (65.9%)
#> Serious AE leading to withdrawal from treatment 6 (4.5%) 12 (9.0%) 9 (6.8%)
#> Serious AE leading to dose modification/interruption 36 (26.9%) 40 (29.9%) 47 (35.6%)
#> Related Serious AE 64 (47.8%) 52 (38.8%) 64 (48.5%)
#> AE leading to withdrawal from treatment 20 (14.9%) 24 (17.9%) 26 (19.7%)
#> AE leading to dose modification/interruption 63 (47.0%) 70 (52.2%) 77 (58.3%)
#> Related AE 86 (64.2%) 85 (63.4%) 92 (69.7%)
#> Related AE leading to withdrawal from treatment 10 (7.5%) 9 (6.7%) 12 (9.1%)
#> Related AE leading to dose modification/interruption 44 (32.8%) 44 (32.8%) 51 (38.6%)
#> Severe AE (at greatest intensity) 77 (57.5%) 70 (52.2%) 79 (59.8%)