| name | meta-analysis |
| description | Systematic review and meta-analysis pipeline for medical research. Covers protocol registration (PROSPERO), search strategy, screening, data extraction, risk of bias assessment (QUADAS-2/ROBINS-I), statistical synthesis (bivariate/HSROC for DTA, random-effects for intervention), and PRISMA-compliant reporting. Supports both DTA and intervention meta-analyses. |
| triggers | meta-analysis, systematic review, PROSPERO, forest plot, funnel plot, PRISMA, QUADAS, ROBINS, HSROC, bivariate model, pooled sensitivity, pooled specificity, search strategy, study selection, data extraction form |
| tools | Read, Write, Edit, Bash, Grep, Glob |
| model | inherit |
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 checklistQUADAS2.md -- 4 domains + signalling questionsROBINS_I.md -- 7 domains + pre-assessment + synthesis recommendationRoB2.md -- 5 domains + signalling questions + overall judgmentPROBAST.md -- 4 domains + AI extension + validation studiesNOS.md -- Cohort (8 items) + Case-control (8 items) + star interpretationJBI_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
| Type | RoB Tool | Statistical Model | Reporting Guideline |
|---|
| DTA (diagnostic test accuracy) | QUADAS-2 | 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.
Workflow Phases
Phase 1: Protocol Development
Goal: Produce a PROSPERO-ready protocol document.
-
Structure the research question:
- DTA: PIRD (Population, Index test, Reference standard, Diagnosis)
- Intervention: PICO (Population, Intervention, Comparator, Outcome)
-
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
-
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
-
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)
-
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
-
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.
-
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)
-
Combine with Boolean operators:
- Within blocks: OR
- Between blocks: AND
-
Execute search per database using /search-lit:
- PubMed: MeSH + free text
- Embase: Emtree + free text
- Additional databases as specified in protocol
-
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.
-
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)
- Define exclusion codes from protocol (e.g., E1=Not target population, E2=Not intervention, E3=Ineligible type, E4=Non-human, E5=Duplicate).
- For each record, screen title+abstract against eligibility criteria.
- Mark each record as INCLUDE / EXCLUDE / MAYBE with reason code.
- Output:
round1_{date}.tsv with color-coded decisions.
3b. Round 2 — Dual Independent Title/Abstract Screening
- A second independent reviewer (or AI as a documented second-pass tool with human verification) re-screens all R1 records.
- Compute Cohen's kappa at title/abstract stage; report in Methods.
- Tag each record's
round2_tag as INCLUDE / EXCLUDE / MAYBE based on R1+R2 agreement (MAYBE = disagreement OR either reviewer flagged uncertain).
- Output:
round2_{date}.tsv (adds round2_tag, round2_reason columns).
3c. Round 3 — Adjudication of Disagreements (first reviewer)
- Build R3 sheet: all MAYBE records first, followed by INCLUDE records (which receive a brief confirmation pass).
- The first reviewer independently adjudicates each row, recording
round3_decision (INCLUDE/EXCLUDE) and round3_reason (only when overturning R2).
- Optional AI-assisted pre-screening to compress R3 effort:
- Use
references/ai_pre_screening_template.py (customize per project).
- Pre-screen produces
ai_suggestion (INCLUDE/EXCLUDE/UNCERTAIN/CONFIRM-INCLUDE) + ai_reason columns.
- Sort priority: UNCERTAIN → EXCLUDE → INCLUDE → CONFIRM-INCLUDE.
- First reviewer must independently confirm or overturn every AI suggestion against the title, abstract, and (when needed) full text. AI suggestions are not final decisions.
- Methods boilerplate: "Round 3 adjudication was performed by the first reviewer with AI-assisted pre-screening ({model name and version}). The AI was prompted with the prespecified PECOS criteria and produced a suggestion plus brief justification for each record; the first reviewer independently confirmed or overturned every suggestion. AI suggestions were not used as final inclusion decisions."
- Output:
round3_{date}.tsv with finalized round3_decision.
3d. Round 4 — Full-text Screening
- For records with
round3_decision = INCLUDE, retrieve full-text PDFs (use /fulltext-retrieval).
- Apply full-text exclusion criteria (F1=No extractable outcome, F2=No comparative data, F3=Cannot separate target population data, F4=Inadequate sample/follow-up, F5=Full-text unavailable).
- Two independent reviewers; compute Cohen's kappa at full-text stage.
- Resolve disagreements by consensus or third reviewer.
- Flag comparative studies for priority extraction.
3e. PRISMA Flow
Track numbers at each stage for PRISMA flow diagram (R1 → R2 → R3 → R4 → final included).
Use /make-figures to generate PRISMA flow diagram when numbers are finalized.
3f. Post-Consensus Count Reconciliation Gate (MANDATORY before Phase 5 write-up)
Before handing the screening artifacts to Phase 5 (statistical synthesis) or to /write-paper / /self-review, run an explicit ID-set reconciliation and record the canonical totals in a single source-of-truth file (typically 2_Screening/screening_consensus.md §Net Impact or equivalent):
Use the deterministic helper when TSV/CSV artifacts are available:
python "${CLAUDE_SKILL_DIR}/scripts/screening_reconcile.py" \
--screening 2_Screening/fulltext_screening.tsv \
--consensus 2_Screening/consensus_decisions.tsv \
--table1 6_Tables/table1_studies.csv \
--output 2_Screening/screening_consensus.json
Downstream stages should consume screening_consensus.json for counts and
ID sets. The Markdown consensus document remains the human explanation.
-
Enumerate ID sets from raw artifacts (not from prose summaries):
- A = screening TSV INCLUDE IDs
- B = consensus spreadsheet Exclude IDs
- C = consensus spreadsheet Include-qualitative IDs (FLAG-resolved additions)
- T = Table 1 / bivariate-eligible IDs (2×2-extractable studies)
-
Compute canonical totals via set algebra:
- k_qualitative = |A \ B| + |C|
- k_bivariate = |T|
- k_narrative-only = k_qualitative − k_bivariate
- k_FT-excluded = |full-text reviewed| − k_qualitative
-
List the narrative-only IDs explicitly. The highest-yield red flag is a numeric claim ("10 narrative-only studies") that does not match the enumerable ID set (A ∪ C) \ B \ T.
-
Prohibit "N → M" transitions without ID receipts. Any sentence of the form "k rose from 30 to 32 after FLAG consensus" must cite the specific added/removed IDs. A transition claim with no enumerable ID set is a P0 error and blocks the Phase 5 hand-off.
-
Record in a reconciliation table inside the screening-consensus document:
| Quantity | v_prev draft | v_current (ID-verified) | Derivation |
|---|
| k_full-text | ... | ... | ... |
| k_FT-excluded | ... | ... | |
| k_qualitative | ... | ... | |
| k_bivariate | ... | ... | |
| k_narrative-only | ... | ... (explicit IDs listed) | (A ∪ C) \ B \ T |
Precedent incident (a PRISMA-DTA meta-analysis revision): a late-revision manuscript shipped with k_qualitative = 32 / k_narrative-only = 10 / k_FT-excluded = 46. ID-set reconciliation (performed only after an adversarial audit at post-Stage 4 QC) revealed true counts 24/2/54. An early-draft prose total ("30 → 32 after FLAG consensus") had been carried forward without ever being reconciled against the screening TSV intersected with the consensus spreadsheet; four downstream artifacts echoed the same wrong total. This gate would have caught the drift at the Phase 5 hand-off.
3f.5 Pool composition lock (MANDATORY at adjudication freeze)
After Phase 3f reconciliation passes, freeze the pool composition into a
single source-of-truth YAML so every downstream artifact (extraction TSV,
manuscript prose counts, PRISMA flow caption, supplementary INDEX, cover
letter free-text) can be checked against it.
Why this lock exists
^^^^^^^^^^^^^^^^^^^^
Cross-project precedent (anonymized): an LLM reporting-quality SR carried
five documents that disagreed on INCLUDE (63 vs 64) and EXCLUDE
(108/109/111). Three EXCLUDE rows existed in the extraction sheet without
matching INCLUDE. The drift traced to a late round-3 adjudication whose
result was applied to some artifacts and not others — there was no single
canonical post-freeze count to reference.
How to lock
^^^^^^^^^^^
- Copy the template:
cp "${CLAUDE_SKILL_DIR}/templates/FINAL_POOL_LOCK.yaml.template" \
2_Data/FINAL_POOL_LOCK.yaml
- Fill in counts and UID lists from the reconciliation in Phase 3f.
- Compute the SHA-256 integrity hash from the sorted UID list.
- Commit the lock to git BEFORE starting Phase 4 extraction.
Downstream gates
^^^^^^^^^^^^^^^^
/meta-analysis Phase 4 entry: extraction TSV's UID set MUST equal
include_uids ∪ mixed_uids from the lock. See Phase 4 entry gate./sync-submission Phase 5
(scripts/cross_document_n_check.py --pool-lock): every numeric claim
in manuscript / abstract / supplementary that maps to a locked
category must match the locked value.- Manuscript prose: NEVER re-derive
k included from extraction TSV at
manuscript build time. Always reference final_pool_n from the lock.
If a late post-freeze decision changes the pool, treat it as a formal
PROSPERO amendment: file the amendment, re-freeze the lock as a new
file (FINAL_POOL_LOCK_v2.yaml), and propagate to every artifact.
Phase 4: Data Extraction
Goal: Create standardized extraction forms and extract 2x2 or effect size data.
4.0 Entry gate (MANDATORY): pool composition lock ↔ adjudication TSV
Before any extraction work begins, run the deterministic UID-set check
to confirm that the round-3 adjudication TSV and FINAL_POOL_LOCK.yaml
(produced in Phase 3f.5) agree on which UIDs are included.
python "${CLAUDE_SKILL_DIR}/scripts/check_pool_consistency.py" \
--lock 2_Data/FINAL_POOL_LOCK.yaml \
--adjudication-tsv 2_Screening/round3_adjudication.tsv \
--decision-col round3_decision \
--uid-col uid \
--include-labels "INCLUDE,INCLUDE_MIXED" \
--out qc/pool_consistency.json
Output qc/pool_consistency.json:
{
"submission_safe": false,
"match": false,
"lock_include_n": 42,
"tsv_include_n": 43,
"in_lock_not_tsv": ["UID_007"],
"in_tsv_not_lock": ["UID_055"]
}
The gate fails closed: any UID disagreement blocks extraction. To
resolve, either (a) re-freeze the lock with the corrected set of UIDs
and propagate to downstream artifacts, or (b) correct the adjudication
TSV if a row was mis-labeled. Do NOT proceed to Phase 4 with a
mismatch — the resulting extraction matrix will not align with the
locked pool, and the drift surfaces as a fabrication-grade red flag at
peer review.
Failure-mode cross-ref → references/data_integrity_checklist.md DI-1~DI-5 are mandatory during extraction (2x2 arm-swap, KM audit trail, methodology mismatch, PRISMA 5-way drift, single-source k).
Recommended extraction form: For SR-MA targeting high-impact radiology / medical AI journals, use ${CLAUDE_SKILL_DIR}/templates/extraction_form_v2.md. Dual-extractor + source-page-reference + verbatim-quote columns prevent the 2x2 cell-swap and cohort-overlap blind spots surfaced in recent SR-MA peer-review cycles. New required columns: cohort_source, source_page_ref, source_verbatim_quote, extraction_consensus_status, overlap_flag_reviewer1/2, sample_n_dta_pool vs sample_n_prognostic_pool.
4.0 AI-drafted starting document gate
Before opening the extraction form: if a senior mentor or collaborator has shared an AI-drafted starting document (Claude / ChatGPT / Gemini draft of the study list, 2x2 cells, or effect estimates) — even when the sender flags it as "참고용" — apply ~/.claude/rules/ai-drafted-document-policy.md:
- Save the file with a
_DO_NOT_USE_VERBATIM (or _AI_DRAFT_REFERENCE_ONLY) filename suffix.
- Treat every per-study N, denominator, event count, OR/CI, and author/year as hallucination-suspect until re-verified against the source PDF + own analysis script. AI-drafts collapse multiple denominator definitions (treatment-naïve / full-cohort / per-arm) into one and silently mis-route counts.
- Record any reconciled discrepancy in
extraction_consensus_log.md with a verbatim quote of the AI-draft value and the corrected value with PDF page coordinate.
- Trust hierarchy for this phase: SSOT (source PDF + own analysis stdout) > mentor's direct text (email / track-changes) > attached AI-draft. Do not promote an AI-draft from tier 3 to tier 2.
Precedent (an active meta-analysis project): Ishikawa 2017 "treatment support 5/70 vs no support 12/33" in Claude-drafted directive → source PDF was 35/68 (single arm). Verbatim absorption would have produced a denominator-hallucinated meta-analysis.
DTA Meta-Analysis:
Generate a data extraction form with:
- Study ID (first author, year)
- Study characteristics (country, design, setting, enrollment period)
- Population (n, age, sex, disease prevalence)
- Index test details (technique, threshold, manufacturer, reader experience)
- Reference standard details
- 2x2 table (TP, FP, FN, TN)
- Additional outcomes (AUC per study, if reported)
- Notes on partial verification, differential verification, uninterpretable results
Intervention Meta-Analysis:
Generate a data extraction form with:
- Study ID
- Study characteristics
- Population
- Intervention / comparator details
- Outcome data (means, SDs, event counts, sample sizes)
- Effect measures (OR, RR, HR, MD, SMD as appropriate)
Output: Excel/CSV template for data entry.
4b. Special cases (KM reconstruction, composite exposure)
When studies report outcomes only as Kaplan-Meier curves (no raw event counts) or
when the intervention is a composite of multiple techniques, load
${CLAUDE_SKILL_DIR}/references/phase4_km_composite.md for the WebPlotDigitizer
→ IPDfromKM reconstruction procedure (cite Guyot et al. 2012,
doi:10.1186/1471-2288-12-9) and the 4-path composite-exposure disaggregation
decision tree. Pre-specify a sensitivity analysis excluding composite-exposure
studies and document extraction strategy in the form's Notes column.
Data Extraction Cross-Verification
When comparing extraction results between independent reviewers (minimum 2), check:
-
Inter-reviewer agreement: Calculate and report screening agreement: % agreement or Cohen's kappa at title/abstract and full-text stages. If kappa was not calculated, report the exact number of discrepant records and the resolution method.
-
Denominator consistency: Verify sample sizes match between reviewers.
Watch for per-patient vs per-lesion/per-tumor unit confusion.
CRITICAL: The denominator may differ across outcomes within the same study
(e.g., LTP assessed only among treatment-naive nodules, but complications assessed
among all treated tumors). For each outcome, back-calculate: event ÷ denominator
must equal the percentage reported in the paper's Tables. If it does not match,
investigate the analysis population definition in the Methods section.
If denominators differ, return to the original paper's Tables/Flow diagram.
-
Arithmetic verification: Back-calculate proportions from event/total counts and cross-check against original text (e.g., 78/91 = 85.7%).
-
Kaplan-Meier estimate distinction: KM curve estimates differ from raw event counts. Always record the data source (Table vs KM curve vs text) during extraction.
-
Discrepancy resolution: List all discrepancies → verify against original text → reach consensus → if consensus fails, use third reviewer. Log all consensus decisions in {project}/consensus_log.md.
-
Dataset lock: After resolving all discrepancies, lock the final dataset. Any subsequent changes require documented justification with date.
Phase 4c: Extraction QC & Cohort Overlap Detection
After dual-extractor consensus, run two QC scripts before locking the extraction table for statistical synthesis.
1. 2x2 Cell Integrity Check -- scripts/dta_extraction_qc.py:
Validates manuscript forest-plot cells (TP / FN / TN / FP) against source-paper-reported sens/spec within a tolerance (default 0.02). Catches sens/spec swap at extraction stage -- a common error pattern where a single-study k=1 subgroup outlier flips conclusions due to cell-assignment swap.
python3 "${CLAUDE_SKILL_DIR}/scripts/dta_extraction_qc.py" \
--input 2_Extraction/extraction.csv \
--tolerance 0.02 \
--out 2_Extraction/qc/dta_extraction_qc.tsv
Any FLAG_SWAP or FLAG_MISMATCH row requires third-reviewer adjudication before Phase 6 statistical synthesis.
2. Cohort Overlap Check -- scripts/cohort_overlap_check.py:
Clusters included studies by (a) shared public ICU/EHR database (MIMIC-IV, eICU, MIMIC-III, KNHIS, UK Biobank, Optum, MarketScan, TriNetX, IBM), (b) same institution + overlapping enrollment period, (c) shared first-author surname + ±2y year proximity. Flags HIGH / MEDIUM overlap confidence.
python3 "${CLAUDE_SKILL_DIR}/scripts/cohort_overlap_check.py" \
--input 2_Extraction/studies.csv \
--enrich \
--out 2_Extraction/qc/cohort_overlap.md
HIGH-confidence overlap pairs require Limitations acknowledgment + sensitivity analysis excluding one of the pair.
Cross-links: /peer-review Phase 2A P1 (cell integrity) + P2 (cohort overlap).
Phase 5: Risk of Bias Assessment
Goal: Guide structured RoB assessment with the appropriate tool.
Select tool based on meta-analysis type (see table above), then read the corresponding checklist:
| Tool | Checklist File |
|---|
| QUADAS-2 (DTA) | ${CLAUDE_SKILL_DIR}/references/checklists/QUADAS2.md |
| RoB 2 (RCT) | ${CLAUDE_SKILL_DIR}/references/checklists/RoB2.md |
| ROBINS-I (NRSI) | ${CLAUDE_SKILL_DIR}/references/checklists/ROBINS_I.md |
| PROBAST (Prediction) | ${CLAUDE_SKILL_DIR}/references/checklists/PROBAST.md |
| NOS (Observational) | ${CLAUDE_SKILL_DIR}/references/checklists/NOS.md |
| JBI (Case Series) | ${CLAUDE_SKILL_DIR}/references/checklists/JBI_Case_Series.md |
For AI/ML prediction models, also apply PROBAST+AI extensions.
Output: Summary table + traffic light plot (use /make-figures).
Phase 6: Statistical Synthesis
Goal: Execute meta-analysis and generate publication-ready outputs.
Failure-mode cross-ref → references/data_integrity_checklist.md DI-6/DI-7/DI-9 are the consistency gate (CSV ↔ script ↔ prose; single-source k; 3-way numeric reconciliation before Stage 4).
IMPORTANT: Always use R for meta-analysis (packages: meta, metafor, mada).
See ${CLAUDE_SKILL_DIR}/references/r_templates.md for full code templates.
| Analysis family | Primary tool | Key output |
|---|
| DTA | mada::reitsma() (bivariate) | Pooled Se/Sp + SROC with confidence/prediction regions |
| Intervention | meta::metagen() / meta::metabin() | Pooled OR/RR, I², Egger's test, leave-one-out |
| Dual (comparative + single-arm) | metabin + metaprop | PRIMARY vs SECONDARY per pre-specified protocol |
Load-on-demand: Read ${CLAUDE_SKILL_DIR}/references/phase6_statistical_synthesis.md
for the full R code templates, the dual-approach decision table (comparative vs
single-arm), practical cautions (method.tau, HK CI, zero-cell correction),
publication-bias test power, sensitivity-analysis menu, and error-handling rules.
Phase 6b: Post-Analysis Source Fidelity Audit (MANDATORY)
Goal: Catch numerical hallucinations that survived the forward pipeline (CSV → .R → manuscript).
Precedent failure pattern — treat this as a lived near-miss, not hypothetical:
In a revision-era comparative meta-analysis, a safety outcome was reported as "3/45 vs
0/56, p=0.085." The primary-source Table actually recorded "0/45 vs 1/56, p=0.37" —
direction reversed. The extraction CSV was correct; the R script's Fisher exact
matrix() was hand-typed after a column in the source Table was misread. Internal
consistency checks passed because every downstream artifact (Abstract, Discussion,
Table, forest caption) echoed the same wrong number. The reversal was caught only on
a second-pass audit with random extraction sampling against the primary paper.
Non-negotiable rules:
-
No hand-typed numerical matrices when a CSV exists.
- Use
read.csv(...) + subset / filter. Never copy a 2x2 table from a paper's Table into
matrix(c(...), ...) by eye.
- If hand entry is truly unavoidable (e.g., text-only extraction), the
matrix, c(), or
data.frame line MUST carry a comment citing the exact CSV row + column OR the exact
primary-source Table/Page coordinate. Example:
fisher.test(matrix(c(0, 45, 1, 55), nrow = 2, byrow = FALSE))
-
Comparative-arm subsets are a separate consensus-log row.
- When one study's arm-specific values (e.g., one arm of a multi-arm study) are used in a
comparative analysis while the full cohort of that study appears elsewhere,
extraction_consensus_log.md must carry an explicit row for the arm-specific values.
Pooled totals and arm-specific values MUST NOT share a row.
-
Random 3-claim back-check before closing Phase 6.
-
After the forest/funnel/subgroup outputs stabilize, randomly sample 3 numerical claims
from the Results section of the draft manuscript and trace each back to (a) the R output
log and (b) the original paper's Table/Figure.
-
Record the back-check as a small table in peer_review_<vN>_internal.md:
| Claim (manuscript line) | R output file:line | Primary source (paper, Table/Fig, page) | Match? |
|---|
-
A single mismatch is a P0 blocker — do not advance to Phase 7 until resolved.
-
Revision-introduced numbers must be tagged.
- Any new number added after v1 — including numbers produced by a new comparative / subgroup /
sensitivity script — MUST be wrapped inline as
[VERIFY-CSV] in the manuscript until the
Phase 2.5a audit in /self-review clears it.
-
Sensitivity analyses must be recomputed on the modified data, not copied.
- When you add a sensitivity / leave-one-out / erosion / alternative-model analysis, every
reported effect size (Cohen's dz/f, AUC, OR, HR, β, sens/spec, ICC) MUST be re-derived from
the modified dataset. If a sensitivity-table effect size is identical to the primary
analysis to two decimals across ≥4 values, the recomputation almost certainly did not run
and the primary values were transcribed — re-run the script on the modified data.
- The underlying means/SDs/counts will change even when the effect size looks similar; if the
effect sizes are byte-identical while the inputs differ, that is the tell. Probability of ≥4
independent values coinciding to 2 decimals by chance is ≈ (0.01)^4 — essentially zero.
- Precedent: a revision-era sensitivity analysis (1-voxel erosion) reported 8 effect-size values
(Cohen's dz + f across 4 VOIs) byte-identical to the primary tables while the means/SDs
differed — the erosion analysis had not actually been recomputed. Caught only by external QC.
When this phase triggers: every time Phase 6 outputs change (first draft, revision, reviewer-
requested re-analysis). Not optional on "minor" re-runs — the precedent reversal above
occurred inside a "minor" revision-era re-analysis.
Phase 7: GRADE / Certainty of Evidence
Goal: Assess certainty of the body of evidence.
For DTA meta-analysis, apply GRADE-DTA framework:
- Risk of bias (from QUADAS-2)
- Indirectness (applicability concerns)
- Inconsistency (heterogeneity)
- Imprecision (wide CIs, small sample)
- Publication bias
For intervention meta-analysis, apply standard GRADE.
Output: Summary of Findings table.
Phase 8: Reporting & Manuscript
Goal: Generate PRISMA-compliant manuscript sections.
Failure-mode cross-ref → references/submission_package_drift.md — apply the _build.sh pattern + DO_NOT_EDIT_HERE gate when staging multi-journal submission folders.
- Check reporting compliance: Use
/check-reporting with PRISMA-DTA or PRISMA 2020
- Write manuscript: Use
/write-paper with meta-analysis type selected
- Figures: Use
/make-figures for:
- PRISMA flow diagram
- Forest plots (paired for DTA)
- SROC curve (DTA)
- Funnel plot
- RoB summary (traffic light plot)
- Tables:
- Characteristics of included studies
- 2x2 data per study (DTA)
- RoB assessment results
- Summary of findings / GRADE table
Phase 9: Co-author Circulation
Goal: Standardized pre-submission circulation of the manuscript to co-authors and
senior methodologist / reviewer, with a bounded review window and a controlled attachment
scope.
Trigger: Phase 8 is complete, and the draft has cleared Phase 6b source-fidelity
audit.
Summary: Reply to the prior-version email thread to preserve In-Reply-To continuity
(v1 → v2 → v3 tracked in one place). Attach the manuscript body with figures inline and,
for v≥2, a change summary — exclude graphical abstract, cover letter, COI forms, and
supplementary until the target journal is confirmed. TO = corresponding author + one
senior methodologist; CC = remaining co-authors. Set a 7-day deadline (5 business days +
weekend). Ask the corresponding author for target-journal preference, reviewer candidates,
and cover-letter framing.
Load-on-demand procedural detail (thread continuity, attachment scope rationale,
size-to-method table, journal-undetermined framing, response-tracking log):
${CLAUDE_SKILL_DIR}/references/phase9_circulation.md.
Failure-mode cross-ref → references/review_orchestration.md RO-1~RO-5 (dual-rating completeness, defensive-tone bias audit, response-matrix numeric tracking, 2nd-reviewer availability blocking).
Phase 10: Self-Audit Recovery (v{N} → v{N+1} sprint)
Goal: When an audit uncovers a structural data or protocol-application error,
withdraw the current version, rebuild, and re-circulate with a transparent audit trail.
Catching the error yourself before a journal reviewer does is the principal trust-building
move in this phase.
Trigger conditions (any one):
| # | Trigger | Source |
|---|
| T1 | Extraction CSV ↔ primary source disagreement for a cell feeding a pooled/subgroup estimate or reported proportion | Phase 6b audit |
| T2 | Included/excluded study violates the pre-specified criteria on re-read | Protocol review |
| T3 | Hand-typed numerical literal in the analysis script traces to a wrong value | Phase 6b audit |
| T4 | PROSPERO protocol ↔ delivered analysis disagreement on outcome, subgroup, or eligibility | Protocol ↔ analysis diff |
| T5 | Dual-reviewer consensus record ↔ locked dataset disagreement on inclusion | Consensus log diff |
Non-negotiable rule: if the trigger fires after Phase 9 circulation but before
journal submission, withdraw the current version within 24 hours. Reviewer discovery is
a strictly worse failure mode than self-withdrawal.
Sprint outline (12 steps): (10.1) audit log at qc/audit_vN_to_vNplus1.md →
(10.2) CSV re-verification with [VERIFY-CSV] tagging → (10.3) fresh script re-run
(fixed seed, logged) → (10.4) manuscript auto-sync (grep for v{N} residue) → (10.5)
supplementary regeneration (consensus log, RoB, GRADE/SoF, PRISMA flow) → (10.6) figure
regeneration via /make-figures → (10.7) change summary with delta table → (10.8)
PROSPERO amendment (application correction, not criteria change) → (10.9) re-circulation
in the Phase 9 thread with the "On re-review" framing → (10.10) anti-patterns to avoid
(hide-and-submit, "minor revision" reframe, cover-letter-only disclosure) → (10.11) post-
submission escalation path → (10.12) post-recovery loop (Phase 9 restart; tighten Phase
6b if a second sprint is needed).
Load-on-demand procedural detail (exact audit-log fields, delta-table template,
amendment language template, re-circulation paragraph template, anti-pattern rationale):
${CLAUDE_SKILL_DIR}/references/phase10_recovery.md.
Failure-mode cross-ref → references/post_submission_release_ops.md Gate 4 covers reject/revise Zenodo versioning, tag-cleanup gate, and re-target workflow (avoid "new version" misuse on re-target).
Failure Modes (prior MA projects, anonymized)
Failure patterns observed across three prior MA projects (anonymized). Each topical reference extends the phase it cross-references above — consult alongside phase procedural docs, not in isolation.
| Domain | Phase span | Load-on-demand reference |
|---|
| Data integrity (2x2 arm-swap, KM audit, methodology mismatch, PRISMA 5-way drift, single-source k) | Phase 3 → 6 | references/data_integrity_checklist.md (DI-1~DI-9) |
| Review orchestration (2nd-reviewer blocking, dual-rating completeness, defensive-tone audit, response-matrix tracking) | Phase 9 circulation (extends phase9_circulation.md) | references/review_orchestration.md (RO-1~RO-5) |
Submission package drift (multi-journal folder hygiene, DO_NOT_EDIT_HERE gate, build artifact vs master) | Phase 8 → submission | references/submission_package_drift.md |
| Post-submission release ops (Zenodo DOI timing, tag-cleanup gate, reject-retarget versioning) | Submission → Phase 10 | references/post_submission_release_ops.md |
Automation hooks (invoke at the phase listed)
| When | Script | Gate |
|---|
| Phase 4 kickoff (before first extraction row) | python3 ${CLAUDE_SKILL_DIR}/../../scripts/extraction_consensus_log_init.py --output 2_Data/extraction_consensus_log.md | DI-1: creates standalone consensus log so comparative arm-specific rows are never folded into R-script comments. |
| Phase 3f reconciliation + every revision touching PRISMA numbers | python3 ${CLAUDE_SKILL_DIR}/../../scripts/prisma_5way_consistency.py --ssot prisma.yaml | DI-6: 5-surface drift check (abstract / main text / flow figure / supplement / CSV) against YAML SSOT. Non-zero exit blocks Phase 5 writeup. |
| Phase 8 pre-submission + every journal retarget | bash ${CLAUDE_SKILL_DIR}/../../scripts/tag_cleanup_gate.sh | DI-8: fails if VERIFY-CSV/TODO/FIXME/XXX survive in 7_Manuscript, supplement, SUBMISSION, etc. |
Phase 8 on first build per journal (--record), then before every re-submission (--verify) | python3 ${CLAUDE_SKILL_DIR}/../../scripts/verify_package_integrity.py --record --journal <name> then --verify --journal <name> | SPD: checksum-based drift detection between master manuscript and built SUBMISSION/{journal}/ folder. Journal-editable files (cover letter, response, MANIFEST, DO_NOT_EDIT_HERE.md) are auto-excluded. |
All four scripts are repo-shipped as of 2026-04 (FOLLOWUPS P10). Non-zero exit = gate failure; resolve before proceeding to the next phase.
Empirical Lessons (2026-05)
Synthesized from recent SR-MA peer-review cycles. Drives the Phase 4 extraction form schema, Phase 4c QC scripts, and submission-gate enhancements documented above.
-
Dual-extractor + source-page-reference + verbatim quote is mandatory for 2x2 cell integrity. Single-extractor without source-page citation invites sens/spec swap that is invisible to forest-plot-level review.
-
Cohort overlap detection must cluster by shared public database + institution + author. Independent-cohort assumption for MA pooling fails when multiple included studies use the same public ICU/EHR cohort with overlapping enrollment windows. Sensitivity analysis excluding overlap is the minimum acknowledgment.
-
Diagnostic subset N transparency in mixed DTA + prognostic MAs: report sample_n_dta_pool separately from sample_n_prognostic_pool with explicit prevalence. Aggregate N in Abstract misleads readers about diagnostic-subset power.
-
k=1 subgroups are not robust: any subgroup p-value driven by a single included study must be reframed as exploratory or removed from formal subgroup test. Post-hoc subgroups require PROSPERO amendment with visible record.
-
Supplementary 8-file package is the minimum bar for high-impact journals: PRISMA checklist, PROSPERO PDF, full search strategy, full-text exclusion list with reasons, per-study extraction table, per-study x per-domain RoB, subgroup forests, sensitivity / publication-bias analyses. See templates/supplementary_8file_checklist.md.
-
PROSPERO 13-char ID format (CRD42 + YYYY + 6-digit sequential); pre-2020 IDs may be 12 chars. Non-numeric tails or >13 chars are format anomalies. Request live registration URL in cover letter for protocol cross-check.
-
AI Disclosure presence for SR-MA submissions to RYAI / Radiology / RSNA / Lancet / JAMA / BMJ / Nature families. Absence triggers MINOR-to-MAJOR finding at peer review.
-
Sensitivity analyses are recomputed, not copied (Phase 6b rule 5). Leave-one-out / erosion / alternative-model effect sizes identical to the primary analysis to 2 decimals across ≥4 values means the recomputation did not run. Re-derive from the modified dataset; the inputs (means/SDs/counts) change even when the effect size is close.
-
Prognostic / survival-outcome MAs carry survival-specific concerns beyond the DTA pitfalls: censoring handling, competing risks (cause-specific vs Fine-Gray), cutoff-derivation optimism, comparator time-horizon alignment, C-index variant transparency (Harrell vs Uno vs IPCW), and calibration beyond discrimination. When pooling prognostic models, pre-specify these in the protocol and report them per study; for the reviewing counterpart see the survival/prognostic 7-probe in /peer-review.
DTA-Specific Pitfalls (Always Check)
| Pitfall | Problem | Solution |
|---|
| Separate pooling of Se/Sp | Ignores correlation | Use bivariate/HSROC model |
| Ignoring threshold effect | False heterogeneity | Check Spearman correlation, SROC plot |
| Standard funnel plot for DTA | Inappropriate | Use Deeks' funnel plot |
| I-squared only for heterogeneity | Doesn't capture threshold effect | Use prediction region on SROC |
| Missing GRADE | Common omission in DTA MA | Apply GRADE-DTA. If <4 studies, assess each domain narratively and state the limitation explicitly |
| Partial verification bias | Inflates sensitivity | Assess in QUADAS-2 Flow & Timing domain |
| Unevaluable results excluded | Biases accuracy estimates | Report intent-to-diagnose analysis |
Small Study Considerations
When the number of included studies is small (< 10):
- Bivariate/HSROC model may not converge -- consider univariate random-effects as fallback
- Publication bias tests are underpowered -- state this limitation
- Subgroup/meta-regression analysis not recommended
- Wide prediction regions expected -- emphasize uncertainty in conclusions
- Consider narrative synthesis as alternative/complement
Skill Interactions
| When | Call | Purpose |
|---|
| Need literature search | /search-lit | PubMed/Semantic Scholar search with verified citations |
| Need statistical code | /analyze-stats | Execute R/Python analysis scripts |
| Need figures | /make-figures | PRISMA flow, forest plots, SROC, funnel plots |
| Need reporting check | /check-reporting | PRISMA-DTA / PRISMA 2020 compliance (includes Step 4c registration / amendment timing) |
| Need manuscript writing | /write-paper | Full IMRAD manuscript generation |
| Need self-review | /self-review | Pre-submission quality check |
| Co-author circulation (Phase 9) | /gws + /handoff | Thread-reply send, deadline task registration |
| Self-audit recovery entrypoint (Phase 10) | /write-paper Step 7.4a | Recovery branch for polish pipelines that surface structural audit failures |
/sync-submission SR-MA gate | /sync-submission | Before submission, verify supplementary package matches all 8 files in templates/supplementary_8file_checklist.md (PRISMA, PROSPERO, search strategy, exclusion list, extraction table, per-study x per-domain RoB, subgroup forests, sensitivity / publication bias). AI Disclosure presence check (cross-link /peer-review Phase 2A P8). Cite-list duplicate check via /verify-refs Gate 5 (duplicate PMID/DOI). |
Error Handling
- If study type is ambiguous (DTA vs intervention), ask user to clarify before proceeding.
- If fewer than 4 studies for DTA, warn that bivariate model may not converge.
- If data extraction is incomplete (missing 2x2 cells), suggest contacting authors or sensitivity analysis with imputed values.
- If PROSPERO ID is missing, flag as a limitation but continue.
- Always remind user: this is a methodological support tool; final decisions rest with the research team and ideally include a biostatistician/methodologist.
Anti-Hallucination
- Never fabricate variable names, dataset column names, or variable codings. If a variable mapping is uncertain, output
[VERIFY: variable_name] and ask the user to confirm against the data dictionary.
- Never fabricate statistical results — no invented p-values, effect sizes, confidence intervals, or sample sizes. All numbers must come from executed code output.
- Never generate references from memory. Use
/search-lit for all citations.
- If a function, package, or API does not exist or you are unsure, say so explicitly rather than guessing.
