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[Review view] SDTM Phase 2: Example datasets + adnca_example fixes#1329

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[Review view] SDTM Phase 2: Example datasets + adnca_example fixes#1329
Gero1999 wants to merge 1 commit into
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sdtm-phase2-example-data

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⚠️ Review-only PR — do not merge

This is a review view into the SDTM changes from #1318. It isolates the example dataset changes for focused code review. The actual merge will happen via #1318.

Scope

New SDTM example datasets

  • pc_example — PC (concentrations) domain, one row per observation, derived from adnca_example
  • ex_example — EX (dosing) domain, one row per dose event
  • dm_example — DM (demographics) domain, one row per subject
  • Generated by data-raw/sdtm_example.R

adnca_example fixes

  • Fixed time-rounding issues that caused sub-second inconsistencies between SDTM-derived and original ADNCA timing variables
  • Renamed Tmax/Cmax parameters to t_max/c_max (lint compliance)
  • Rebuilt adnca_example.rda, adnca_example.csv, and test-multianalyte-ADNCA.csv

Metadata extension

  • Added 34 rows to metadata_nca_variables for SDTM, PC, EX, DM domains with mapping sections and defaults for the Shiny mapping UI

Files changed

Category Files
Data generation scripts data-raw/adnca_example.R, data-raw/sdtm_example.R
Package data data/pc_example.rda, data/ex_example.rda, data/adnca_example.rda, data/metadata_nca_variables.rda
CSV exports data/pc_example.csv, data/ex_example.csv, data/dm_example.csv, data-raw/adnca_example.csv
Metadata data-raw/metadata_nca_variables.csv
Test fixtures tests/testthat/data/test-pc-example.csv, test-ex-example.csv, test-dm-example.csv, test-multianalyte-ADNCA.csv
Tests tests/testthat/test-sdtm_example_data.R

What to review

  • SDTM column derivations in data-raw/sdtm_example.R (PCDTC, PCRFTDTC, PCELTM, EXSTDTC, EXENDTC, EXDUR, EXELTM)
  • adnca_example time-rounding changes — verify no existing tests break
  • Metadata CSV additions — correct mapping_section, sdtm_domain, Core values (DM uses Perm not Exp)
  • Test coverage for dataset consistency between SDTM and ADNCA formats

- Create pc_example, ex_example, dm_example datasets derived from
  adnca_example via data-raw/sdtm_example.R
- Fix time-rounding issues in adnca_example that caused inconsistencies
  between SDTM and ADNCA paths
- Extend metadata_nca_variables with SDTM, PC, EX, DM domain rows
  for the mapping UI
- Add SDTM example dataset validation tests
- Rename Tmax/Cmax to t_max/c_max in adnca_example.R (lint fix)

Co-authored-by: Ona <no-reply@ona.com>
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