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DST01 Table 2 (Supplementary) Patient Disposition Table 2.

dst01_2.Rd

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,
  arm_var = "ARM",
  status_var = "EOSSTT",
  disc_reason_var = "DCSREAS",
  lbl_overall = "All Patients",
  deco = std_deco("DST01"),
  ...
)

dst01_2_lyt(
  arm_var,
  status_var,
  disc_reason_var,
  completed_lbl,
  ongoing_lbl,
  discontinued_lbl,
  lbl_overall,
  deco = std_deco("DST01")
)

dst01_2_pre(adam_db, status_var = "EOSSTT", disc_reason_var = "DCSREAS", ...)

dst01_2_post(tlg, prune_0 = TRUE, deco = std_deco("DST01"), ...)

dst01_2

Format

An object of class chevron_t of length 1.

Arguments

adam_db

(dm) object containing the ADaM datasets

arm_var

(character) variable used for column splitting

status_var

(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.

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

deco

(character) decoration with title, subtitles and main_footer content

...

not used.

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.

tlg

(TableTree, Listing or ggplot) object typically produced by a main function.

prune_0

(logical) remove 0 count rows

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

  • dst01_2_post(): Postprocessing

Note

  • adam_db object must contain an adsl table with the columns specified by status_var and disc_reason_var.

Examples

library(dm)
library(magrittr)

db <- syn_data %>%
  dst01_2_pre()

dst01_2_main(db)
#> [[1]]
#>                   A: Drug X    B: Placebo   C: Combination   All Patients
#>                    (N=134)      (N=134)        (N=132)         (N=400)   
#> —————————————————————————————————————————————————————————————————————————
#> Completed Study   68 (50.7%)   66 (49.3%)     73 (55.3%)     207 (51.7%) 
#> 
#> [[2]]
#>                                     A: Drug X    B: Placebo   C: Combination   All Patients
#>                                      (N=134)      (N=134)        (N=132)         (N=400)   
#> ———————————————————————————————————————————————————————————————————————————————————————————
#> Ongoing                             24 (17.9%)   28 (20.9%)     21 (15.9%)      73 (18.2%) 
#> Discontinued Study                  42 (31.3%)   40 (29.9%)     38 (28.8%)     120 (30.0%) 
#>   Safety                            28 (20.9%)   29 (21.6%)     27 (20.5%)      84 (21.0%) 
#>     ADVERSE EVENT                    3 (2.2%)     6 (4.5%)       5 (3.8%)       14 (3.5%)  
#>     DEATH                           25 (18.7%)   23 (17.2%)     22 (16.7%)      70 (17.5%) 
#>     LACK OF EFFICACY                    0            0              0               0      
#>     PHYSICIAN DECISION                  0            0              0               0      
#>     PROTOCOL VIOLATION                  0            0              0               0      
#>     WITHDRAWAL BY PARENT/GUARDIAN       0            0              0               0      
#>     WITHDRAWAL BY SUBJECT               0            0              0               0      
#>   Non-Safety                        14 (10.4%)   11 (8.2%)      11 (8.3%)       36 (9.0%)  
#>     ADVERSE EVENT                       0            0              0               0      
#>     DEATH                               0            0              0               0      
#>     LACK OF EFFICACY                 2 (1.5%)     2 (1.5%)       3 (2.3%)        7 (1.8%)  
#>     PHYSICIAN DECISION               2 (1.5%)     3 (2.2%)       2 (1.5%)        7 (1.8%)  
#>     PROTOCOL VIOLATION               5 (3.7%)     3 (2.2%)       4 (3.0%)       12 (3.0%)  
#>     WITHDRAWAL BY PARENT/GUARDIAN    4 (3.0%)     2 (1.5%)       1 (0.8%)        7 (1.8%)  
#>     WITHDRAWAL BY SUBJECT            1 (0.7%)     1 (0.7%)       1 (0.8%)        3 (0.8%)  
#> 
dst01_2_main(db, lbl_overall = NULL)
#> [[1]]
#>                   A: Drug X    B: Placebo   C: Combination
#>                    (N=134)      (N=134)        (N=132)    
#> ——————————————————————————————————————————————————————————
#> Completed Study   68 (50.7%)   66 (49.3%)     73 (55.3%)  
#> 
#> [[2]]
#>                                     A: Drug X    B: Placebo   C: Combination
#>                                      (N=134)      (N=134)        (N=132)    
#> ————————————————————————————————————————————————————————————————————————————
#> Ongoing                             24 (17.9%)   28 (20.9%)     21 (15.9%)  
#> Discontinued Study                  42 (31.3%)   40 (29.9%)     38 (28.8%)  
#>   Safety                            28 (20.9%)   29 (21.6%)     27 (20.5%)  
#>     ADVERSE EVENT                    3 (2.2%)     6 (4.5%)       5 (3.8%)   
#>     DEATH                           25 (18.7%)   23 (17.2%)     22 (16.7%)  
#>     LACK OF EFFICACY                    0            0              0       
#>     PHYSICIAN DECISION                  0            0              0       
#>     PROTOCOL VIOLATION                  0            0              0       
#>     WITHDRAWAL BY PARENT/GUARDIAN       0            0              0       
#>     WITHDRAWAL BY SUBJECT               0            0              0       
#>   Non-Safety                        14 (10.4%)   11 (8.2%)      11 (8.3%)   
#>     ADVERSE EVENT                       0            0              0       
#>     DEATH                               0            0              0       
#>     LACK OF EFFICACY                 2 (1.5%)     2 (1.5%)       3 (2.3%)   
#>     PHYSICIAN DECISION               2 (1.5%)     3 (2.2%)       2 (1.5%)   
#>     PROTOCOL VIOLATION               5 (3.7%)     3 (2.2%)       4 (3.0%)   
#>     WITHDRAWAL BY PARENT/GUARDIAN    4 (3.0%)     2 (1.5%)       1 (0.8%)   
#>     WITHDRAWAL BY SUBJECT            1 (0.7%)     1 (0.7%)       1 (0.8%)   
#> 
dst01_2_pre(syn_data)
#> ── Metadata ────────────────────────────────────────────────────────────────────
#> Tables: `adsl`, `adab`, `adae`, `adaette`, `adcm`, … (19 total)
#> Columns: 1401
#> Primary keys: 1
#> Foreign keys: 18
run(dst01_2, syn_data)
#>                                       A: Drug X    B: Placebo   C: Combination   All Patients
#>                                        (N=134)      (N=134)        (N=132)         (N=400)   
#>   ———————————————————————————————————————————————————————————————————————————————————————————
#>   Completed Study                     68 (50.7%)   66 (49.3%)     73 (55.3%)     207 (51.7%) 
#>   Ongoing                             24 (17.9%)   28 (20.9%)     21 (15.9%)      73 (18.2%) 
#>   Discontinued Study                  42 (31.3%)   40 (29.9%)     38 (28.8%)     120 (30.0%) 
#>     Safety                            28 (20.9%)   29 (21.6%)     27 (20.5%)      84 (21.0%) 
#>       ADVERSE EVENT                    3 (2.2%)     6 (4.5%)       5 (3.8%)       14 (3.5%)  
#>       DEATH                           25 (18.7%)   23 (17.2%)     22 (16.7%)      70 (17.5%) 
#>     Non-Safety                        14 (10.4%)   11 (8.2%)      11 (8.3%)       36 (9.0%)  
#>       LACK OF EFFICACY                 2 (1.5%)     2 (1.5%)       3 (2.3%)        7 (1.8%)  
#>       PHYSICIAN DECISION               2 (1.5%)     3 (2.2%)       2 (1.5%)        7 (1.8%)  
#>       PROTOCOL VIOLATION               5 (3.7%)     3 (2.2%)       4 (3.0%)       12 (3.0%)  
#>       WITHDRAWAL BY PARENT/GUARDIAN    4 (3.0%)     2 (1.5%)       1 (0.8%)        7 (1.8%)  
#>       WITHDRAWAL BY SUBJECT            1 (0.7%)     1 (0.7%)       1 (0.8%)        3 (0.8%)