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
  • QUADAS2.md -- 4 domains + signalling questions
  • 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

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.

Meta-Analysis Types

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

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. Define eligibility criteria:

   • Study design (cross-sectional DTA, cohort, RCT, etc.)
   • Population characteristics
   • Index test / intervention specifics
   • Comparator / reference standard
   • Outcome measures (Se/Sp for DTA; effect size for intervention)
   • Exclusion criteria with justification

3. Plan the search:

   • Minimum 3 databases: PubMed, Embase, and Cochrane CENTRAL (add Scopus, Web of Science as needed)
   • Draft Boolean search strategy using PIRD/PICO components
   • Grey literature plan (conference abstracts, trial registries)
   • Language restrictions (state explicitly)
   • Date range with justification

4. Plan RoB assessment:

   • Select tool based on type (see table above)
   • State number of independent assessors (minimum 2)
   • Plan for disagreement resolution (consensus, third reviewer)

5. Plan synthesis:

   • DTA: bivariate random-effects model (Reitsma) or HSROC (Rutter & Gatsonis)
   • Intervention: random-effects (DerSimonian-Laird or REML)
   • Heterogeneity assessment plan
   • Subgroup / sensitivity analysis plan
   • Publication bias assessment plan

6. Generate PROSPERO registration document:

   • Read ${CLAUDE_SKILL_DIR}/references/PROSPERO_template.md for field-by-field guidance
   • Generate all fields with word counts (stay within limits per field)
   • Structure: title, review question, PICO, searches, data collection, outcomes, synthesis, subgroups, stage, affiliation
   • For mixed designs (comparative + single-arm): explicitly address comparator for both arms
   • For RoB: map tool to study design (NOS for comparative, JBI for case series → select "Other" in form)
   • Output: Markdown + DOCX (via pandoc) for copy-paste into PROSPERO web form
   • Append Common Pitfalls Checklist (HTML entities, word limits, stage constraint)
   • Save to project 7_Submission/ or equivalent directory

Phase 2: Search Strategy

Goal: Develop and validate reproducible search strategies.

1. Build search blocks from PIRD/PICO:

   • Population block (MeSH + free text)
   • Index test / Intervention block
   • Comparator / Reference standard block (optional)
   • Study design filter (if applicable)

2. Combine with Boolean operators:

   • Within blocks: OR
   • Between blocks: AND

3. Execute search per database using /search-lit:

   • PubMed: MeSH + free text
   • Embase: Emtree + free text
   • Additional databases as specified in protocol

4. Report search per PRISMA-S (Rethlefsen et al. 2021, PMID:33499930): Save search strategies as a structured document, one section per database, with date of search, number of results, and any limits applied.

5. Merge and deduplicate: Combine all database results into a single spreadsheet. Deduplicate by DOI first, then PMID. Save raw counts for PRISMA flow.

Phase 3: Screening & Selection

Goal: Systematic title/abstract and full-text screening with two independent reviewers.

3a. Round 1 — Initial Title/Abstract Screening (single reviewer)

1. Define exclusion codes from protocol (e.g., E1=Not target population, E2=Not intervention, E3=Ineligible type, E4=Non-human, E5=Duplicate).
2. For each record, screen title+abstract against eligibility criteria.
3. Mark each record as INCLUDE / EXCLUDE / MAYBE with reason code.
4. Output: round1_{date}.tsv with color-coded decisions.

3b. Round 2 — Dual Independent Title/Abstract Screening

1. A second independent reviewer (or AI as a documented second-pass tool with human verification) re-screens all R1 records.
2. Compute Cohen's kappa at title/abstract stage; report in Methods.
3. Tag each record's round2_tag as INCLUDE / EXCLUDE / MAYBE based on R1+R2 agreement (MAYBE = disagreement OR either reviewer flagged uncertain).
4. Output: round2_{date}.tsv (adds round2_tag, round2_reason columns).

3c. Round 3 — Adjudication of Disagreements (first reviewer)

1. Build R3 sheet: all MAYBE records first, followed by INCLUDE records (which receive a brief