DST01 Table 2 (Supplementary) Patient Disposition Table 2.

The DST01_2 Disposition Table provides an overview of patients study completion. For patients who discontinued the study, the reason provided is categorized as "Safety" or "Non-Safety" issue.

Usage

dst01_2_main(
  adam_db,
  armvar = .study$planarm,
  status_var = .study$status_var,
  disc_reason_var = .study$disc_reason_var,
  lbl_overall = .study$lbl_overall,
  prune_0 = TRUE,
  deco = std_deco("DST01"),
  .study = list(planarm = "ARM", lbl_overall = "All Patients", disc_reason_var =
    "DCSREAS", status_var = "EOSSTT")
)

dst01_2_lyt(
  armvar = .study$planarm,
  status = .study$status,
  disc_reason_var = .study$disc_reason_var,
  completed_lbl = "COMPLETED",
  ongoing_lbl = "ONGOING",
  discontinued_lbl = "DISCONTINUED",
  lbl_overall = .study$lbl_overall,
  deco = std_deco("DST01"),
  .study = list(planarm = "ARM", lbl_overall = "All Patients", status = "EOSSTT",
    disc_reason_var = "DCSREAS")
)

dst01_2_pre(
  adam_db,
  status = .study$status,
  disc_reason_var = .study$disc_reason_var,
  .study = list(status = "EOSSTT", disc_reason_var = "DCSREAS"),
  ...
)

dst01_2

Format

An object of class chevron_tlg of length 1.

Arguments

adam_db: (dm) object containing the ADaM datasets
armvar: (character) variable used for column splitting
status_var: (character) variable used to define patient status. Default is EOSSTT, however can also be a variable name with the pattern EOPxxSTT where xx must be substituted by 2 digits referring to the analysis period.
disc_reason_var: (string) variable used to define reason for patient withdrawal. Default is DCSREAS, however can also be a variable with the pattern DCPxxRS where xx must be substituted by 2 digits referring to the analysis period.
lbl_overall: (character) label used for overall column, if set to NULL the overall column is omitted
prune_0: (logical) remove 0 count rows
deco: (character) decoration with title, subtitles and main_footer content
.study: (list) with default values for the arguments of the function
status: (string) variable used to define patient status. Default is EOSSTT, however can also be a variable name with the pattern EOPxxSTT where xx must be substituted by 2 digits referring to the analysis period.
completed_lbl: (string) associated with completed study and found in the columns given by status. By Default COMPLETED.
ongoing_lbl: (string) associated with ongoing treatment and found in the columns given by status_treatment. By Default `ONGOING.
discontinued_lbl: (string) associated with discontinued study and found in the columns given by status. By Default DISCONTINUED.
...: not used.

Details

Non-standard disposition table summarizing the reasons for patient withdrawal.
Withdrawal reasons are grouped into Safety and Non-Safety issues.
Safety issues include Death and Adverse events.
Numbers represent absolute numbers of patients and fraction of N.
Remove zero-count rows.
Split columns by arm.
Include a total column by default.
Sort withdrawal reasons by alphabetic order.

Since the two parts of the tables are pruned differently, the layout function returns a list of layouts, which allows the tables to be constructed and pruned separately before binding.

Functions

dst01_2_main(): Main TLG function
dst01_2_lyt(): Layout
dst01_2_pre(): Preprocessing

Examples

library(dm)
library(magrittr)

db <- syn_test_data() %>%
  dst01_2_pre()

dst01_2_main(db)
#>                                     A: Drug X    B: Placebo   C: Combination   All Patients
#>                                      (N=134)      (N=134)        (N=132)         (N=400)   
#> ———————————————————————————————————————————————————————————————————————————————————————————
#> Completed Study                     69 (51.5%)   69 (51.5%)     72 (54.5%)     210 (52.5%) 
#> Ongoing                             27 (20.1%)   22 (16.4%)     21 (15.9%)      70 (17.5%) 
#> Discontinued Study                  38 (28.4%)   43 (32.1%)     39 (29.5%)     120 (30.0%) 
#>   Safety                            28 (20.9%)   27 (20.1%)     21 (15.9%)      76 (19.0%) 
#>     ADVERSE EVENT                    6 (4.5%)     1 (0.7%)       2 (1.5%)        9 (2.2%)  
#>     DEATH                           22 (16.4%)   26 (19.4%)     19 (14.4%)      67 (16.8%) 
#>   Non-safety                        10 (7.5%)    16 (11.9%)     18 (13.6%)      44 (11.0%) 
#>     LACK OF EFFICACY                 2 (1.5%)     1 (0.7%)       2 (1.5%)        5 (1.2%)  
#>     PHYSICIAN DECISION                  0         1 (0.7%)       7 (5.3%)         8 (2%)   
#>     PROTOCOL VIOLATION                4 (3%)      7 (5.2%)       6 (4.5%)       17 (4.2%)  
#>     WITHDRAWAL BY PARENT/GUARDIAN    2 (1.5%)     5 (3.7%)       3 (2.3%)       10 (2.5%)  
#>     WITHDRAWAL BY SUBJECT            2 (1.5%)     2 (1.5%)          0             4 (1%)   
dst01_2_main(db, lbl_overall = NULL)
#>                                     A: Drug X    B: Placebo   C: Combination
#>                                      (N=134)      (N=134)        (N=132)    
#> ————————————————————————————————————————————————————————————————————————————
#> Completed Study                     69 (51.5%)   69 (51.5%)     72 (54.5%)  
#> Ongoing                             27 (20.1%)   22 (16.4%)     21 (15.9%)  
#> Discontinued Study                  38 (28.4%)   43 (32.1%)     39 (29.5%)  
#>   Safety                            28 (20.9%)   27 (20.1%)     21 (15.9%)  
#>     ADVERSE EVENT                    6 (4.5%)     1 (0.7%)       2 (1.5%)   
#>     DEATH                           22 (16.4%)   26 (19.4%)     19 (14.4%)  
#>   Non-safety                        10 (7.5%)    16 (11.9%)     18 (13.6%)  
#>     LACK OF EFFICACY                 2 (1.5%)     1 (0.7%)       2 (1.5%)   
#>     PHYSICIAN DECISION                  0         1 (0.7%)       7 (5.3%)   
#>     PROTOCOL VIOLATION                4 (3%)      7 (5.2%)       6 (4.5%)   
#>     WITHDRAWAL BY PARENT/GUARDIAN    2 (1.5%)     5 (3.7%)       3 (2.3%)   
#>     WITHDRAWAL BY SUBJECT            2 (1.5%)     2 (1.5%)          0       
dst01_2_lyt(
  armvar = "ACTARM",
  status = "EOP01STT",
  disc_reason_var = "DCP01RS"
)
#> $completed
#> A Pre-data Table Layout
#> 
#> Column-Split Structure:
#> ACTARM (lvls) 
#>  (all obs) 
#> 
#> Row-Split Structure:
#> DOMAIN (lvls) -> EOP01STT (** analysis **) 
#> 
#> 
#> $other
#> A Pre-data Table Layout
#> 
#> Column-Split Structure:
#> ACTARM (lvls) 
#>  (all obs) 
#> 
#> Row-Split Structure:
#> DOMAIN (lvls) -> EOP01STT (** analysis **) 
#> EOP01STT (lvls) -> reasonGP (lvls) -> DCP01RS (** analysis **) 
#> 
#> 
dst01_2_pre(syn_test_data())
#> ── Metadata ────────────────────────────────────────────────────────────────────
#> Tables: `adsl`, `adae`, `adaette`, `adcm`, `addv`, … (15 total)
#> Columns: 848
#> Primary keys: 2
#> Foreign keys: 1
run(dst01_2, syn_test_data())
#>                                     A: Drug X    B: Placebo   C: Combination   All Patients
#>                                      (N=134)      (N=134)        (N=132)         (N=400)   
#> ———————————————————————————————————————————————————————————————————————————————————————————
#> Completed Study                     69 (51.5%)   69 (51.5%)     72 (54.5%)     210 (52.5%) 
#> Ongoing                             27 (20.1%)   22 (16.4%)     21 (15.9%)      70 (17.5%) 
#> Discontinued Study                  38 (28.4%)   43 (32.1%)     39 (29.5%)     120 (30.0%) 
#>   Safety                            28 (20.9%)   27 (20.1%)     21 (15.9%)      76 (19.0%) 
#>     ADVERSE EVENT                    6 (4.5%)     1 (0.7%)       2 (1.5%)        9 (2.2%)  
#>     DEATH                           22 (16.4%)   26 (19.4%)     19 (14.4%)      67 (16.8%) 
#>   Non-safety                        10 (7.5%)    16 (11.9%)     18 (13.6%)      44 (11.0%) 
#>     LACK OF EFFICACY                 2 (1.5%)     1 (0.7%)       2 (1.5%)        5 (1.2%)  
#>     PHYSICIAN DECISION                  0         1 (0.7%)       7 (5.3%)         8 (2%)   
#>     PROTOCOL VIOLATION                4 (3%)      7 (5.2%)       6 (4.5%)       17 (4.2%)  
#>     WITHDRAWAL BY PARENT/GUARDIAN    2 (1.5%)     5 (3.7%)       3 (2.3%)       10 (2.5%)  
#>     WITHDRAWAL BY SUBJECT            2 (1.5%)     2 (1.5%)          0             4 (1%)