dst01_2.RdThe 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.
dst01_2(
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,
reason = .study$disc_reason_var,
.study = list(disc_reason_var = "DCSREAS")
)(dm) object containing the ADaM datasets
(character) variable used for column splitting
(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.
(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.
(character) label used for overall column, if set to NULL the overall column is omitted
(logical) remove 0 count rows
(character) decoration with title, subtitles and main_footer content
(list) with default values for the arguments of the function
(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.
(string) associated with completed study and found in the columns given by status. By
Default COMPLETED.
(string) associated with ongoing treatment and found in the columns given by status_treatment.
By Default `ONGOING.
(string) associated with discontinued study and found in the columns given by status. By
Default DISCONTINUED.
(character) the variable name for variable with the reason for discontinuation.
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.
dst01_2_lyt: dst01_2 Layout
dst01_2_pre: dst01_2 Preprocessing
library(dm)
db <- syn_test_data() %>%
dst01_2_pre()
dst01_2(db)
#> Patient Disposition: {Analysis Population}
#> Protocol: {{protocol}}
#>
#> ———————————————————————————————————————————————————————————————————————————————————————————
#> 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(db, lbl_overall = NULL)
#> Patient Disposition: {Analysis Population}
#> Protocol: {{protocol}}
#>
#> ————————————————————————————————————————————————————————————————————————————
#> 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:
#> EOP01STT (** analysis **)
#>
#>
#> $other
#> A Pre-data Table Layout
#>
#> Column-Split Structure:
#> ACTARM (lvls)
#> (all obs)
#>
#> Row-Split Structure:
#> EOP01STT (** analysis **)
#> EOP01STT (lvls) -> reasonGP (lvls) -> DCP01RS (** analysis **)
#>
#>
syn_test_data() %>%
dst01_2_pre()
#> ── Metadata ────────────────────────────────────────────────────────────────────
#> Tables: `adsl`, `adae`, `adaette`, `adcm`, `addv`, … (15 total)
#> Columns: 847
#> Primary keys: 2
#> Foreign keys: 1