# Pipeline Log — DEMO 3 (NHANES obesity<->diabetes), medsci-skills v3.7.0
Generated: 2026-06-07
Staging: <clean-room staging>/03_nhanes_obesity
MEDSCI_SKILLS_ROOT: ${MEDSCI_SKILLS_ROOT}
Environment: R 4.5.3 (survey 4.x + tableone, both pre-installed; NOT 4.8.0 as prompt suggested),
  Python 3.14.3 (pandas 2.3.3, read_sas), pandoc 3.9.0.2, d2 0.7.1, graphviz/dot 14.1.5

## Step 0 — Data download & preparation
- Downloaded 4 NHANES 2017-2018 XPT files via curl to data/ (valid SAS XPORT signatures).
  DEMO_J (9254 rows), BMX_J (8704), DIQ_J (8897), GHB_J (6401).
- 00_prepare_data.py: merged on SEQN, applied STROBE exclusion cascade, wrote data/nhanes_analytic.csv (n=5010).
- Exclusion: 9254 -> age>=20 (5569) -> measured BMI (5175) -> valid DM status (5010) -> positive MEC weight (5010 FINAL).

## Step 1 — /analyze-stats (survey-weighted)
- 01_survey_analysis.R: svydesign(id=SDMVPSU, strata=SDMVSTRA, weights=WTMEC2YR, nest=TRUE); design df=15.
- Outputs: tables/table1.csv, regression_or.csv, regression_or_hba1c_sensitivity.csv, key_scalars.csv, exclusion_cascade.csv; analysis/_analysis_outputs.md.
- Weighted diabetes prev 11.7% (10.6-12.8); obesity 42.3% (38.9-45.7).
- PRIMARY aOR obesity->diabetes = 3.03 (95% CI 2.29-4.02), p<0.001 (adj age, sex, race).
- Sensitivity (HbA1c>=6.5, n=4779): aOR 2.95 (2.18-3.98).
- Generated-code gate (check_generated_code.py --strict): 00_prepare_data.py PASS (0 findings); 01_survey_analysis.R PASS (0 findings).

## Step 2 — /make-figures (observational/STROBE)
- generate_flow_diagram.R --type strobe -> strobe_flow.{pdf,png,600.png}; DiagrammeRsvg -> strobe_flow.svg.
- 02_make_forest.py -> forest_or.{pdf,png} from regression_or.csv (obesity highlighted at OR 3.03).
- _figure_manifest.md written (2 figures). Generated-code gate on forest script: PASS (0 findings).

## Step 3 — /write-paper (IMRAD, association-only)
- manuscript/manuscript.md + title_page.md. refs.bib placeholder created; references left [UNVERIFIED] (methods demo).
- Body word count (Intro..Conclusion) = 1337; total manuscript ~1700 words.
- Step 7.1 classical-style QC (check_classical_style.py --strict): PASS (0 findings).
- AI-disclosure 4-token check: version (Claude Opus 4.8) + channel (API) + date (June 2026) + responsible party (the authors) ALL present; 0 placeholders.
- Placeholder/citation marker gate ([@NEW:]/[N]): clean.
- Scope: cross-sectional -> association-only; no prognostic/surveillance/causal claim in conclusions.

## Step 4 — /check-reporting (STROBE --json)
- Contract verified: check_checklist_exists.py --guideline STROBE -> OK.
- Genuine item-by-item assessment in qc/reporting_checklist.{json,md}.
- 34 items; 4 NOT_APPLICABLE (6b,12b,14c,16c); PRESENT 25, PARTIAL 4 (9,12c,14b,16a), MISSING 1 (10).
- compliance_pct = present/applicable = 25/30 = 83.3%.

## Step 5 — /self-review (--fix, deterministic detectors) + v3.7.0 detectors
- INITIAL: 1 genuine MAJOR (scope_coherence CROSS_SECTIONAL_PROGNOSTIC).
- Fix iter 1: reworded Abstract Conclusion + Discussion Limitations + Conclusion to drop
  prognostic/surveillance vocabulary; association-only meaning preserved.
- FINAL: scope_coherence CLEAN (exit 0). Verdict: ACCEPT-WITH-NOTES.
- Detector literal outputs -> qc/_detector_findings.md; JSON artifacts -> qc/*.json.
  - check_classical_style: CLEAN
  - check_cohort_arithmetic: CLEAN (cascade reconciles)
  - check_scope_coherence: CLEAN after fix (fired once initially -> fixed)
  - check_reference_adequacy: 2 Major EXPECTED ([UNVERIFIED] demo refs)
  - check_confounding_completeness: 2 Major FALSE POSITIVE (outcome-stratified T1 fed to exposure-stratified O1 check)
- Genuine unresolved MAJOR = 0; genuine deferred MINOR = 5 (STROBE 10 + 9/12c/14b/16a).

## Step 6 — DOCX build
- pandoc (title_page + manuscript) -> manuscript/manuscript_final.docx (17 KB).
- docx body XML carries all key numbers (3.03, 5,010, 42.3, 11.7) + disclosure.

## Step 7 — Dataset manifest
- version_dataset.py manifest over 6 derived CSVs (raw XPTs excluded for portability) -> manifest.lock.json (seed=42, per-column SHA-256).
- verify --strict: OK, 6/6 match (exit 0).

## Environment note
- Prompt specified R 4.8.0; actual usable R was 4.5.3 with survey + tableone pre-installed (fully functional). No substantive impact.