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Glimpse a TTE dataset.

Source: R/adam_tte.R
glimpse_tte.Rd

Summarizes a TTE (Time-to-Event) dataset for synthetic simulation by extracting parameter combinations, preserving censoring column relationships, and extracting summaries of all other variables.

Usage

glimpse_tte(
  tte,
  syn_adsl,
  param_cols,
  censor_cols = character(),
  flag_cols = character(),
  ordered_col_sets = list(),
  seed = NULL
)

Arguments

tte

data.frame - input TTE dataset e.g. ADTTE.

syn_adsl

data.frame - synthetic ADSL to obtain subject-level data from. Should be created by simulate_adsl().

param_cols

character - parameter columns e.g. c("PARAM", "PARAMCD").

censor_cols

character - censoring columns e.g. c("CNSR", "EVNTDESC", "CNSDTDSC"). These columns are treated as an ordered set to preserve co-occurrence patterns. Only needed when multiple censor columns should be kept together. Default is an empty character vector (censor columns are treated as regular columns).

flag_cols

character - flag columns that will be sampled as Y/N in proportion to input e.g. c("ANL01FL"). Default is an empty character vector (no flag columns).

ordered_col_sets

list<character> - each element is a character vector naming columns whose combinations should be preserved e.g. list(c("REGION1", "REGION1N")). Default is an empty list.

seed

integer - random seed for reproducibility.

Value

summary_tte - summary object for TTE simulation.

Examples

# TTE simulation needs a synthetic ADSL to provide the subject spine.
syn_adsl <- data.frame(
  USUBJID = as.character(1:5),
  TRT01A = c("Placebo", "Placebo", "Drug A", "Drug A", "Drug A"),
  TRT01AN = c(1, 1, 2, 2, 2)
)
tte <- data.frame(
  USUBJID = as.character(rep(1:3, each = 2)),
  PARAM = rep(c("Overall Survival", "Progression Free Survival"), 3),
  PARAMCD = rep(c("OS", "PFS"), 3),
  CNSR = c(0, 1, 0, 1, 1, 0),
  EVNTDESC = c(
    "DEATH", "COMPLETED", "DEATH", "COMPLETED", "COMPLETED", "PROGRESSION"
  ),
  AVAL = c(365, 500, 180, 250, 600, 120)
)

tte_summary <- glimpse_tte(
  tte,
  syn_adsl,
  param_cols = c("PARAM", "PARAMCD"),
  censor_cols = c("CNSR", "EVNTDESC")
)
#> Glimpsing PARAM columns
#> Glimpsing ADSL columns from synthetic ADSL
#> Glimpsing censor column(s): CNSR, EVNTDESC
#> 1 ordered column combination(s) with count = 1 were masked and added to the most common combination.
#> Glimpsing column(s): AVAL
syn_tte <- simulate_tte(tte_summary, seed = 42)
#> Simulating PARAM and ADSL columns
#> Simulating column(s): censor
#> Simulating column(s): AVAL
head(syn_tte)
#>     USUBJID                     PARAM PARAMCD CNSR  EVNTDESC AVAL
#> 1         1          Overall Survival      OS    0     DEATH  559
#> 1.1       2          Overall Survival      OS    0     DEATH  570
#> 1.2       3          Overall Survival      OS    0     DEATH  257
#> 1.3       4          Overall Survival      OS    0     DEATH  519
#> 2         5          Overall Survival      OS    1 COMPLETED  428
#> 2.1       1 Progression Free Survival     PFS    1 COMPLETED  369