Create high-performance clinical reporting tables (TLGs) from ADaM-like inputs. The package provides a consistent, programmatic API to generate common tables such as demographics, adverse event incidence, and laboratory summaries, using ‘data.table’ for fast aggregation over large populations. Functions support flexible target-variable selection, stratification by treatment, and customizable summary statistics, and return tidy, machine-readable results ready to render with downstream table/formatting packages in analysis pipelines.
Installation
install.packages("dtlg")Example
Creating an AET01 table:
library(dtlg)
head(adsl[, c("USUBJID", "ARM")])
#> USUBJID ARM
#> 1 AB12345-CHN-3-id-128 A: Drug X
#> 2 AB12345-CHN-15-id-262 C: Combination
#> 3 AB12345-RUS-3-id-378 C: Combination
#> 4 AB12345-CHN-11-id-220 B: Placebo
#> 5 AB12345-CHN-7-id-267 B: Placebo
#> 6 AB12345-CHN-15-id-201 C: Combination
head(aesi[, c("USUBJID", "ARM", "FATAL")])
#> USUBJID ARM FATAL
#> <char> <fctr> <lgcl>
#> 1: AB12345-BRA-1-id-134 A: Drug X FALSE
#> 2: AB12345-BRA-1-id-134 A: Drug X FALSE
#> 3: AB12345-BRA-1-id-134 A: Drug X FALSE
#> 4: AB12345-BRA-1-id-134 A: Drug X TRUE
#> 5: AB12345-BRA-1-id-141 C: Combination FALSE
#> 6: AB12345-BRA-1-id-141 C: Combination FALSE
AET01 <-
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")
)
AET01[, stats := strtrim(stats, 35)][]
#> stats A: Drug X B: Placebo C: Combination
#> <char> <char> <char> <char>
#> 1: Total number of patients with at le 100 (74.6%) 98 (73.1%) 103 (78.0%)
#> 2: Total number of AEs 502 480 604
#> 3: Total number of deaths 25 (18.7%) 23 (17.2%) 22 (16.7%)
#> 4: Total number of patients withdrawn 3 (2.2%) 6 (4.5%) 5 (3.8%)
#> 5: Total number of patients with at le
#> 6: AE with fatal outcome 5 (3.7%) 5 (3.7%) 6 (4.5%)
#> 7: Serious AE 85 (63.4%) 80 (59.7%) 87 (65.9%)
#> 8: Serious AE leading to withdrawal 6 (4.5%) 12 (9.0%) 9 (6.8%)
#> 9: Serious AE leading to dose modifi 36 (26.9%) 40 (29.9%) 47 (35.6%)
#> 10: Related Serious AE 64 (47.8%) 52 (38.8%) 64 (48.5%)
#> 11: AE leading to withdrawal from tre 20 (14.9%) 24 (17.9%) 26 (19.7%)
#> 12: AE leading to dose modification/i 63 (47.0%) 70 (52.2%) 77 (58.3%)
#> 13: Related AE 86 (64.2%) 85 (63.4%) 92 (69.7%)
#> 14: Related AE leading to withdrawal 10 (7.5%) 9 (6.7%) 12 (9.1%)
#> 15: Related AE leading to dose modifi 44 (32.8%) 44 (32.8%) 51 (38.6%)
#> 16: Severe AE (at greatest intensity) 77 (57.5%) 70 (52.2%) 79 (59.8%)