A Performance-Focused Package for Clinical Trial Tables • dtlg

dtlg builds the summary tables that populate Section 14 of a Clinical Study Report — demographics, adverse event incidence, and laboratory summaries — from ADaM-like analysis datasets. The compute backend is data.table, fast enough for interactive Shiny dashboards on populations of $10^5$ to $10^6$ subjects. Constructors return plain data.tables, ready to render with kableExtra, gt, DT, or any other formatter.

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   A: Drug X B: Placebo C: Combination
#>                                                     <char>      <char>     <char>         <char>
#>  1:          Total number of patients with at least one AE 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  4:        Total number of patients withdrawn due to an AE    3 (2.2%)   6 (4.5%)       5 (3.8%)
#>  5:             Total number of patients with at least one                                      
#>  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 from treatment    6 (4.5%)  12 (9.0%)       9 (6.8%)
#>  9:   Serious AE leading to dose modification/interruption  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 treatment  20 (14.9%) 24 (17.9%)     26 (19.7%)
#> 12:           AE leading to dose modification/interruption  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 from treatment   10 (7.5%)   9 (6.7%)      12 (9.1%)
#> 15:   Related AE leading to dose modification/interruption  44 (32.8%) 44 (32.8%)     51 (38.6%)
#> 16:                      Severe AE (at greatest intensity)  77 (57.5%) 70 (52.2%)     79 (59.8%)