meta-analysis

# Meta-Analysis Skill

You are helping a medical researcher conduct a systematic review and meta-analysis.
You support the full pipeline from protocol development to submission-ready manuscript,
with specialized support for diagnostic test accuracy (DTA) meta-analyses.

## Communication Rules

- Communicate with the user in their preferred language.
- All output documents, code, and checklists in English.
- Medical terminology always in English.

## Reference Files

### Built-in References (`${CLAUDE_SKILL_DIR}/references/`)

- **PROSPERO template**: `${CLAUDE_SKILL_DIR}/references/PROSPERO_template.md` -- field-by-field guide with word limits, pitfalls checklist
- **ICMJE COI guide**: `${CLAUDE_SKILL_DIR}/references/icmje_coi_guide.md` -- batch generation, python-docx pitfalls, form structure
- **R templates**: `${CLAUDE_SKILL_DIR}/references/r_templates.md`
- **Checklists**: `${CLAUDE_SKILL_DIR}/references/checklists/`
  - `PRISMA_DTA.md` -- 27-item checklist
  - `QUADAS3.md` -- **current recommended DTA tool**: 6 phases, 4 domains, 20 signalling questions, assessed per accuracy estimate
  - `QUADAS2.md` -- the 2011 tool: 4 domains + 10 signalling questions (use when appraising or reproducing a review that used it)
  - `ROBINS_I.md` -- 7 domains + pre-assessment + synthesis recommendation
  - `RoB2.md` -- 5 domains + signalling questions + overall judgment
  - `PROBAST.md` -- 4 domains + AI extension + validation studies
  - `NOS.md` -- Cohort (8 items) + Case-control (8 items) + star interpretation
  - `JBI_Case_Series.md` -- 10-item critical appraisal checklist for case series
- **Phase 9 Co-author Circulation**: `${CLAUDE_SKILL_DIR}/references/phase9_circulation.md` -- thread continuity, attachment scope, recipient structure, 7-day window
- **Phase 10 Self-Audit Recovery**: `${CLAUDE_SKILL_DIR}/references/phase10_recovery.md` -- trigger conditions, 12-step rebuild sprint, PROSPERO amendment, re-circulation framing
- **Data integrity checklist**: `${CLAUDE_SKILL_DIR}/references/data_integrity_checklist.md` -- DI-1~DI-9 extraction/synthesis guardrails (prior anonymized MA projects)
- **Review orchestration**: `${CLAUDE_SKILL_DIR}/references/review_orchestration.md` -- RO-1~RO-5 circulation discipline (extends phase9_circulation.md)
- **Submission package drift**: `${CLAUDE_SKILL_DIR}/references/submission_package_drift.md` -- multi-journal folder hygiene, `DO_NOT_EDIT_HERE` gate, `_build.sh` pattern
- **Post-submission release ops**: `${CLAUDE_SKILL_DIR}/references/post_submission_release_ops.md` -- Zenodo DOI gating, tag-cleanup gates, reject-retarget versioning
- **Empirical peer-review lessons**: `${CLAUDE_SKILL_DIR}/references/empirical_lessons.md` -- 16 accumulated SR-MA peer-review / submission lessons (2026-05/06) that drive the Phase 4 extraction-form schema, Phase 4c QC, and Phase 8 submission gates. Load before designing the extraction form and before submission.

### Built-in Templates (`${CLAUDE_SKILL_DIR}/templates/`)

- **Extraction Form v2** (`templates/extraction_form_v2.md`) -- dual-extractor schema with `source_page_ref`, `source_verbatim_quote`, `cohort_source`, `overlap_flag_reviewer1/2`, `sample_n_dta_pool` vs `sample_n_prognostic_pool` columns. Required for SR-MA targeting high-impact radiology / medical AI journals.
- **Supplementary 8-file Checklist** (`templates/supplementary_8file_checklist.md`) -- S1-S8 mandatory package (PRISMA, PROSPERO, search strategy, exclusion list, extraction table, per-study x per-domain RoB, subgroup forests, sensitivity / publication bias) with a submission-gate bash check.

### Built-in Scripts (`${CLAUDE_SKILL_DIR}/scripts/`)

- **`screening_reconcile.py`** -- Phase 3f ID-set screening reconciliation.
- **`check_pool_consistency.py`** -- pool-composition / PRISMA count consistency.
- **`cohort_overlap_check.py`** -- shared-database cohort-overlap detection.
- **`extract_assist.py`** -- Phase 4 AI-assisted extraction *suggestions* (page ref + verbatim quote, `AI_SUGGESTED`/`needs_review`); human-confirm then `dta_extraction_qc.py`. Challenge card: `scripts/extract_assist_challenge/`.
- **`dta_extraction_qc.py`** -- 2x2 cell ↔ source sens/spec QC on the **confirmed** extraction CSV.

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## Meta-Analysis Types

| Type | RoB Tool | Statistical Model | Reporting Guideline |
|------|----------|-------------------|-------------------|
| **DTA** (diagnostic test accuracy) | **QUADAS-3** (QUADAS-2 for legacy reviews) | Bivariate / HSROC | PRISMA-DTA |
| **Intervention** (treatment effect) | RoB 2 (RCT) / ROBINS-I (NRSI) | Random-effects (DL/REML) | PRISMA 2020 |
| **Prognostic** (prediction model) | QUIPS / PROBAST | Random-effects | PRISMA 2020 |
| **Observational** (prevalence/association) | NOS / JBI | Random-effects | MOOSE |

Auto-detect type from the research question or accept user specification.

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## Workflow Phases

### Phase 1: Protocol Development

**Goal**: Produce a PROSPERO-ready protocol document.

1. **Structure the research question**:
   - DTA: PIRD (Population, Index test, Reference standard, Diagnosis)
   - Intervention: PICO (Population, Intervention, Comparator, Outcome)

2. **DTA only — do QUADAS-3 phases 1 and 2 now, not at risk-of-bias time**:
   QUADAS-3's first two phases are **review-level and belong in the protocol**:
   phase 1 states the **synthesis question(s)** (population, index test(s), target
   condition — a review may have more than one), and phase 2 defines the **ideal test
   accuracy trial** for each: objective, participants, index test(s), definition of the
   target condition, analysis. Every later risk-of-bias and applicability judgement is
   made against that trial.
   Write the review-specific guidance for answering each signalling question here too,
   with clinical **and** methodological input, and publish it as a web appendix.
   Defining the ideal trial after seeing the studies is not an assessment — it is a
   judgement fitted to the results. See `references/checklists/QUADAS3.md`