Worked example: a small SDTM specification and its datasets

Builds the example specification shipped in inst/extdata (three SDTM domains - DM, AE and VS - with codelists, derivation methods, one comment, value level metadata on the two VS result variables and two MedDRA external codelists) together with the matching datasets, so every example, test and vignette in this package runs offline against real inputs.

define21_example()

Value

A list with elements spec (a define21_spec) and data (a named list with data frames DM, AE and VS).

Details

The specification and the data agree, so check_define() on them returns zero rows; change either side and the discrepancy shows up. The controlled terminology is not invented: the coded values of SEX, AGEU, AESEV, NY, VSTESTCD and the units codelist are real CDISC Submission Values, asserted against a shipped CDISC SDTM Terminology release in the test suite where that file is available.

Examples

ex <- define21_example()
ex$spec
#> 
#> ── Define-XML 2.1 specification ────────────────────────────────────────────────
#> ℹ Study: STUDY01 | standard: SDTMIG 3.4 (IG)
#> ℹ 3 dataset(s), 28 variable(s), 9 codelist(s), 2 method(s), 1 comment(s)
#> ℹ 6 value(s) across 2 value list(s), 3 where clause(s), 2 external codelist(s)
#> ✔ [DM] Demographics - 10 variable(s), One record per subject
#> ✔ [AE] Adverse Events - 10 variable(s), One record per adverse event per subject
#> ✔ [VS] Vital Signs - 8 variable(s), One record per vital sign measurement per subject
head(ex$data$DM, 3)
#>   STUDYID DOMAIN     USUBJID SUBJID AGE  AGEU SEX                      RACE
#> 1 STUDY01     DM STUDY01-001    001  64 YEARS   F                     WHITE
#> 2 STUDY01     DM STUDY01-002    002  58 YEARS   M                     ASIAN
#> 3 STUDY01     DM STUDY01-003    003  71 YEARS   F BLACK OR AFRICAN AMERICAN
#>          ARM    RFSTDTC
#> 1    Placebo 2024-01-15
#> 2 Drug 10 mg 2024-01-18
#> 3 Drug 10 mg 2024-01-22
ex$spec$value_levels[, c("variable", "value", "where_clause", "type")]
#> # A tibble: 6 × 4
#>   variable value where_clause type 
#>   <chr>    <chr> <chr>        <chr>
#> 1 VSSTRESN SYSBP VS_SYSBP     float
#> 2 VSSTRESN DIABP VS_DIABP     float
#> 3 VSSTRESN PULSE VS_PULSE     float
#> 4 VSSTRESU SYSBP VS_SYSBP     text 
#> 5 VSSTRESU DIABP VS_DIABP     text 
#> 6 VSSTRESU PULSE VS_PULSE     text