medsci-skills 5.6.0 → 5.8.0

package/README.md

@@ -4,7 +4,7 @@
 
 **51 skills that actually work.** Built by a physician-researcher, tested on real publications.
 
-*MedSci Skills is an end-to-end research tool for physician and medical-engineering researchers — design → scaffold → validate → publish — for the clinical manuscript and the medical-AI model behind it. Its moat is the compliance layer — 41 reporting guidelines and risk-of-bias tools, reference/citation verification, and deterministic integrity gates before peer review — now extended by a model-engineering lane that scaffolds reproducible, leakage-safe training repos and audits model validation. Clinical AI model research engineering is in scope; a general AI-scientist platform is not. It competes on clinical submission reliability, not skill count.*
+*MedSci Skills is an end-to-end research tool for physician and medical-engineering researchers — design → scaffold → validate → publish — for the clinical manuscript and the medical-AI model behind it. Its moat is the compliance layer — 44 reporting guidelines and risk-of-bias tools, reference/citation verification, and deterministic integrity gates before peer review — now extended by a model-engineering lane that scaffolds reproducible, leakage-safe training repos and audits model validation. Clinical AI model research engineering is in scope; a general AI-scientist platform is not. It competes on clinical submission reliability, not skill count.*
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
 [![Release](https://img.shields.io/github/v/release/Aperivue/medsci-skills?style=flat-square&color=blue)](https://github.com/Aperivue/medsci-skills/releases/latest)
@@ -281,54 +281,54 @@ The E2E pipeline (`orchestrate --e2e`) produces everything up to `qc/`. The `sub
 
 ## What's New
 
-**v4.10** — reviewer-coverage expansion reverse-engineered from high-IF, CC-BY papers (learn-only under the `reverse_engineer/` license firewall), plus a clinician-friendly update path. Additive and backward-compatible; 45 skills / **41 guidelines** / 36 detectors / **15 domain-probe modules** (was 12):
+**v4.10** — reviewer-coverage expansion reverse-engineered from high-IF, CC-BY papers (learn-only under the `reverse_engineer/` license firewall), plus a clinician-friendly update path. Additive and backward-compatible; 45 skills / **44 guidelines** / 36 detectors / **15 domain-probe modules** (was 12):
 
 - **Three new reviewer domain-probe modules** (`/peer-review` + `/self-review`, vendored byte-identical): **Mendelian randomization** (MR1–MR8 — IV assumptions, pleiotropy-robust sensitivity suite, Steiger, sample overlap, NLMR, drug-target colocalization), **polygenic risk score** (PG1–PG8 — ancestry portability, base/target leakage, incremental value over the clinical model, screening-vs-discrimination, calibration), and **network meta-analysis** (NM1–NM8 — transitivity, incoherence, SUCRA over-interpretation, CINeMA/GRADE-NMA, component-NMA additivity). Plus observational **O17** (agnostic many-exposure-scan multiplicity: ExWAS/EWAS/MWAS).
 - **Two reporting-guideline checklists** (36 → 38): **STROBE-MR** and **PGS-RS / PRS-RS**, with study-type routing. Four new `/analyze-stats` analysis guides (multiplicity, MR, PRS, NMA) and a `/clean-data` implausible-value + cross-field validity reference.
 - **Clinician-friendly update reminders** — the classroom installers enable the in-app "update available" notice + one-click Desktop updater by default; the `npx`/manual paths print how to turn it on; the install guide recommends `npx medsci-skills install --enable-update-notify`.
 
-**v4.9** — analysis-integrity hardening promoted from real review cycles, plus journal-mechanics additions. Additive and backward-compatible; still 45 skills / 41 guidelines, analysis-integrity detectors **32 → 36**:
+**v4.9** — analysis-integrity hardening promoted from real review cycles, plus journal-mechanics additions. Additive and backward-compatible; still 45 skills / 44 guidelines, analysis-integrity detectors **32 → 36**:
 
 - **Four new gates** — a **duplicate-bibliography** check (`check_reference_duplication.py`) for the hybrid `[@key]` + hand-typed `## References` build that renders the list twice; a **cross-script binning / composite-indicator** consistency check (`check_binning_consistency.py`, `BINNING_DRIFT` / `DERIVED_DEF_DRIFT`) for a derived categorical or composite indicator defined inconsistently across analysis scripts; a **float citation-order** check (`check_citation_order.py`) for numbered Tables/Figures not first cited in ascending order per series; and an **audit-dump leak** gate (`/sync-submission`) that blocks a `/check-reporting` output mistakenly attached as a submission file.
 - **KJR technical-check conventions + percentage-decimal style**, reader-allocation-under-burden and generative-image-as-study-object reporting (`/design-ai-benchmarking`, `/check-reporting`), and a **Liver International** CSL with that journal's submission mechanics (`/manage-refs`).
 
-**v4.8** is the **review-harvest batch** — deterministic detector hardening promoted from real-manuscript review cycles. Additive and backward-compatible; still 45 skills / 41 guidelines, analysis-integrity detectors **30 → 32**:
+**v4.8** is the **review-harvest batch** — deterministic detector hardening promoted from real-manuscript review cycles. Additive and backward-compatible; still 45 skills / 44 guidelines, analysis-integrity detectors **30 → 32**:
 
 - **Two new gates** — `check_supplement_hygiene.py` lints the rendered supplement / tables / caption files (not just the manuscript) for §-labels, placeholders, build markers, response-letter framing, and unresolved body↔supplement cross-references; `check_null_calibration.py` flags a headline negative/equivalence claim made without a minimum-detectable-effect / power / equivalence statement.
 - **Four detector false-positive fixes** — gates no longer fire on a recommended colorblind-safe palette, author-footnote `§` daggers, a correctly-hedged disclaimer, or a tier-label digit; each with a regression fixture and three newly CI-wired test suites.
 - **Nine reviewer-side domain probes** (SR/MA, observational, diagnostic, AI-overclaiming, survival) plus a `/design-study` design-stage ceiling gate for perceptual/reader-AI studies and a reusable confidence-weighted-rating→AUC monotonicity template.
 
-**v4.7** is the **self-update foundation** — physician-researchers stay current without GitHub, git, or a terminal. Additive and backward-compatible; still 45 skills / 41 guidelines / 30 detectors:
+**v4.7** is the **self-update foundation** — physician-researchers stay current without GitHub, git, or a terminal. Additive and backward-compatible; still 45 skills / 44 guidelines / 30 detectors:
 
 - **Transactional, crash-recoverable installer.** Each install runs through a durable journal state machine recovered on the next run (roll back / forward-clean / fail-closed), with per-target SHA-256 inventories — your modified or third-party skills are backed up and never clobbered or auto-deleted.
 - **One-click self-updater** (`~/.medsci-skills/updater/`, `install.py --check-update`). Verifies the download against the github.com API digest and **never `extractall()`s** (per-entry rejection of traversal / symlink / duplicate / zip-bomb + an allowlist & per-file hash). The release pipeline injects a verified `provenance.json`, attests build provenance, runs on a protected `release` environment, and verifies each ZIP round-trips through the updater's own safe-extract before publishing.
 - **Opt-in update notice (off by default):** `install.py --enable-update-notify` shows a one-line "update available" message at Claude Code session start — no telemetry, reads nothing about your session, installs nothing. `--disable-update-notify` / `MEDSCI_NO_UPDATE_CHECK=1` turn it off. *(Honest scope: the digest/attestation detect transport tampering, not a compromised publisher account — see `SECURITY.md`.)*
 
-**v4.6** is a maintainability, governance, and review-depth release — still 45 skills / 41 guidelines; analysis-integrity detectors **28 → 30**, domain probes 11 → 12:
+**v4.6** is a maintainability, governance, and review-depth release — still 45 skills / 44 guidelines; analysis-integrity detectors **28 → 30**, domain probes 11 → 12:
 
 - **Fairness / equity / subgroup-performance probe (EQ0–EQ6)** for AI/prediction/diagnostic studies that claim cross-population performance, plus two new detectors: an **AI-disclosure + data/code-availability** check (`/sync-submission`) and a **structured-summary-box conformance** check (`/academic-aio`).
 - **Governance + answer-engine layer:** `ROADMAP.md`, `MAINTAINERS.md`, `SECURITY.md`, a maintainer workflow + release checklist, an AEO/GEO `docs/faq.md`, a "Start here: 3 workflows" + "Validation status" section in this README, and a new `maturity` field (official / experimental / community) on every skill.
 - **Token diet (pilot):** `write-paper` Phase 7 integrity audits moved to a load-on-demand reference (~2,559 tokens saved per invocation). Positioning now leads with the compliance moat rather than skill count.
 
-**v4.5** deepens the review + submission surface with no new skill or reporting-guideline count (still 45 skills / 41 guidelines); analysis-integrity detectors **27 → 28**:
+**v4.5** deepens the review + submission surface with no new skill or reporting-guideline count (still 45 skills / 44 guidelines); analysis-integrity detectors **27 → 28**:
 
 - **`/clean-data` + `/analyze-stats` — reverse-coded-item / negative-alpha detector.** A multi-item Likert scale with a negatively-worded item must be recoded `(min+max) − x` before the scale total or Cronbach's alpha is computed; left un-recoded, the item correlates negatively with the rest of the scale and alpha collapses (often negative). A negative alpha is a coding bug, not a "multidimensional construct." New stdlib-only `check_reverse_coding.py` returns `REVERSE_CODING_LIKELY` / `REVERSE_CODING_SUSPECT` / `OK` from per-item item-rest correlations + raw alpha; the Likert summary template gains a `--reverse-items` recode flag.
 - **`/peer-review` + `/self-review` — SR/MA + DTA + prediction-model probe batch.** `sr_ma.md` **P12** risk-of-bias table row-sum ↔ traffic-light figure-matrix reconciliation and **P13** included-study ↔ reference-list completeness; `diagnostic_accuracy.md` **D7** index-test-as-enrollment-criterion circularity; `clinical_prediction_model.md` **CP5** intended-use horizon leakage and **CP6** development/CV vs held-out/external validation-nomenclature conflation. Vendored byte-identical into `/self-review`.
 - **`/sync-submission` — embedded absolute-path leak scan.** A `word/*.xml` attribute (e.g. a pandoc-embedded image's `<pic:cNvPr descr="…">`) carrying an absolute home-dir path (`/Users/…`, `/home/…`) is a username leak invisible to a rendered-text scan; now flagged as `docx_embedded_abs_path` under `check_asset_anonymization.py`.
 
-**v4.4** adds reviewer/analysis depth with no new skill or reporting-guideline count (still 45 skills / 41 guidelines / 27 detectors):
+**v4.4** adds reviewer/analysis depth with no new skill or reporting-guideline count (still 45 skills / 44 guidelines / 27 detectors):
 
 - **`/author-strategy` — trajectory-archetype classification (optional).** Classifies a queried author's PubMed trajectory into abstract career archetypes (A1 infrastructure builder, A2 methodology rule-maker, A3 clinical→AI hybrid, A4 SR/MA volume engine, A5 large-consortium participation, A6 device/technique depth, + a computed composite) as an **explainable, multi-label, confidence-scored heuristic — not an objective verdict**. The rubric is a single canonical YAML (the narrative doc is generated from it); scores exclude `unavailable` signals (h-index/citation/venue-tier → `[VERIFY]`, never fabricated); a **disambiguation gate** binds an approved `corpus_manifest.json` to the CSV (csv + PMID-set hashes) so a surname alone never classifies, and target-author attribution never borrows a co-author's ORCID/affiliation.
 - **`/peer-review` + `/self-review` — Image-Synthesis / cross-modality probe (IS1–IS4)** for studies that synthesize one imaging modality from another and claim the output carries the target's information, plus a reviewer-side reference-integrity spot-check.
 - **`/verify-refs` — OpenAlex tertiary index** recovers conference-proceedings / non-DOI citations (NeurIPS/ICLR/ACL) that fall through PubMed and CrossRef, the free analogue of a portal's second index.
 
-**v4.3** hardens the **cross-sectional / observational cohort** review surface end-to-end, much of it reverse-engineered from real CC-BY cohort papers (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 41 guidelines); analysis-integrity detectors **25 → 27**:
+**v4.3** hardens the **cross-sectional / observational cohort** review surface end-to-end, much of it reverse-engineered from real CC-BY cohort papers (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 44 guidelines); analysis-integrity detectors **25 → 27**:
 
 - **Observational probes O1 → O14** (`/peer-review` + `/self-review`, vendored) — over-adjustment / analysis-unit clustering / outcome construct-validity (O7–O9), overlapping-subset gradient (O10), **complex-survey design & weighting** for NHANES/KNHANES (O11), **data-driven threshold / "inflection-point" mining** (O12), **cross-sectional mediation** temporal-order & sequential-ignorability (O13), and **interaction scale** — additive RERI/AP/S vs multiplicative (O14). Plus a new **clinical-prediction-model** probe module **CP1–CP4** and survival **S9** (panel-data / multistate variance).
 - **Two new detectors (25 → 27)** — `check_wordcount_cap.py` (the revision-inflation trap: body vs journal cap) and `check_paren_spans.py` (em-dash→paren conversions that wrap a whole sentence). Plus a `check_confounding_completeness.py` upgrade (DB-code↔prose alias map, SMD-from-mean±SD, exposure-defining-covariate exemption), a `check_cohort_arithmetic.py` `ANALYSIS_UNIT_UNDISCLOSED` check, a `check_scope_coherence.py` cross-sectional-yield lexicon, and a verify-refs corporate/collective-author render-abort fix.
 - **Analysis & submission tooling** — `/analyze-stats` gains **mediation** and **interaction & effect-modification** guides; `/sync-submission` gains `assemble_supplement.py` (S{N} index↔file integrity) and a `/revise` body-word-count exit gate; `/render-pdf-doc` gains a `scan_glyph_coverage.py` xelatex silent-glyph-drop scan.
 
-**v4.2** builds out the case-report capability end-to-end, grounded in real CC-BY case reports (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 41 guidelines); journal profiles **68 → 73**:
+**v4.2** builds out the case-report capability end-to-end, grounded in real CC-BY case reports (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 44 guidelines); journal profiles **68 → 73**:
 
 - **Case-report + case-series writing** — `/write-paper` gains a CARE narrative + 150-word-abstract case-report exemplar, a **case-series** paper type (methods-light mini-cohort, all-cases summary table, counts-not-rates), and **adverse-event/pharmacovigilance** (Naranjo/WHO-UMC causality) and **diagnostic-pitfall/mimic** subtypes.
 - **Radiology / imaging-led track** — a dedicated `exemplar_case_report_radiology.md` (per-modality technique→findings→impression, structured-reporting lexicons BI-RADS/LI-RADS/PI-RADS/TI-RADS/Lung-RADS/O-RADS, quantitative threshold honesty, an interventional-radiology procedure/complication subtype, DICOM de-identification) plus a `/make-figures` annotated multimodality imaging-panel exemplar.
@@ -452,7 +452,7 @@ ma-scout -> search-lit -> fulltext-retrieval -> design-study ──> write-proto
 | **search-lit** | PubMed + Semantic Scholar + bioRxiv search with anti-hallucination citation verification. Token-efficient error handling -- CrossRef failures are silently batched, not repeated. BibTeX output tags each entry with `verified`/`verified_by`/`verified_on` fields so downstream skills can trust the citation provenance. |
 | **verify-refs** | Pre-submission reference audit for `.md`, `.docx`, `.bib`, or `.tsv` inputs. Extracts references, verifies DOI/PMID via CrossRef/PubMed when available, and writes `qc/reference_audit.json` as the sole output — row-level status (OK / MISMATCH / UNVERIFIED / FABRICATED) lives inside the JSON `records[]` block. `/search-lit` produces candidate BibTeX; `/lit-sync` owns `manuscript/_src/refs.bib`. |
 | **fulltext-retrieval** | Batch open-access PDF downloader. Unpaywall → PMC → OpenAlex → CrossRef pipeline. OA-only -- no paywall bypass. Input: DOI list or TSV. Optional PDF→Markdown conversion via [pymupdf4llm](https://pymupdf.readthedocs.io/en/latest/pymupdf4llm/) for token-efficient LLM analysis of academic papers. |
-| **check-reporting** | Manuscript compliance audit against 41 reporting guidelines and risk of bias tools (STROBE, STROBE-MR, RECORD, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, CROSS, PRISMA, PRISMA-DTA, PRISMA-P, MOOSE, ARRIVE, CONSORT, CONSORT-AI, CARE, SPIRIT, SPIRIT-AI, CLAIM, DECIDE-AI, SQUIRE 2.0, CLEAR, GRRAS, MI-CLEAR-LLM, SWiM, AMSTAR 2, QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA). Machine-readable JSON summary with `compliance_pct` and `fixable_by_ai` flags for automated pipeline integration. |
+| **check-reporting** | Manuscript compliance audit against 44 reporting guidelines and risk of bias tools (STROBE, STROBE-MR, RECORD, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, CROSS, SRQR, COREQ, PRISMA, PRISMA-DTA, PRISMA-P, PRISMA-ScR, MOOSE, ARRIVE, CONSORT, CONSORT-AI, CARE, SPIRIT, SPIRIT-AI, CLAIM, DECIDE-AI, SQUIRE 2.0, CLEAR, GRRAS, MI-CLEAR-LLM, SWiM, AMSTAR 2, QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA). Machine-readable JSON summary with `compliance_pct` and `fixable_by_ai` flags for automated pipeline integration. |
 | **analyze-stats** | Statistical analysis code generation (Python/R) for diagnostic accuracy, DTA meta-analysis (bivariate/HSROC), inter-rater agreement, survival analysis, demographics tables, regression (logistic/linear), propensity score (matching/IPTW/overlap weighting), and repeated measures (RM ANOVA/GEE/mixed models). Calibration mandatory for prediction models. |
 | **meta-analysis** | Full systematic review and meta-analysis pipeline (8 phases). DTA (bivariate/HSROC) and intervention meta-analysis. Protocol to submission-ready manuscript with PRISMA-DTA compliance. |
 | **make-figures** | Publication-ready figures and visual abstracts: ROC curves, forest plots, PRISMA/CONSORT/STARD flow diagrams, Kaplan-Meier curves, Bland-Altman plots, confusion matrices, and journal-specific visual/graphical abstracts (python-pptx template-based). Communication-first design principles (Nat Hum Behav 2026 — key message, audience, cognitive load, figure-vs-table decision) and five flow-diagram production lessons (official-template fidelity, VML fallback PDF export, docx XML escape, sequential placeholder mapping, version freeze); critic rubric Section G adds 5 communication-first checks. `--study-type` auto-generates the full required figure set; structured `_figure_manifest.md` output for downstream pipeline consumption; D2 enforced as default for flow diagrams. |
@@ -621,8 +621,8 @@ Projects declare their source-of-truth layout in `SSOT.yaml`, and a `qc/migratio
 ### Meta-Analysis Failure Modes
 `/meta-analysis` ships empirical failure-mode references (data integrity, review orchestration, submission package drift, post-submission release ops) with four automation hooks: `scripts/prisma_5way_consistency.py` (DI-6 PRISMA number consistency), `scripts/extraction_consensus_log_init.py` (DI-1 dual-extraction scaffold), `scripts/tag_cleanup_gate.sh` (DI-8 placeholder tag gate), and `scripts/verify_package_integrity.py` (SPD SHA-256 manifest for submission bundles).
 
-### 41 Reporting Guidelines & RoB Tools Built-in
-`check-reporting` includes bundled checklists for 41 guidelines and risk-of-bias tools: STROBE, STROBE-MR, RECORD, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, CROSS, PRISMA 2020, PRISMA-DTA, PRISMA-P, MOOSE, ARRIVE, CONSORT, CONSORT-AI, CARE, SPIRIT, SPIRIT-AI, CLAIM, DECIDE-AI, SQUIRE 2.0, CLEAR, GRRAS, MI-CLEAR-LLM, SWiM, AMSTAR 2, QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA. Includes Results/Discussion section boundary checks and machine-readable JSON summary for pipeline integration.
+### 44 Reporting Guidelines & RoB Tools Built-in
+`check-reporting` includes bundled checklists for 44 guidelines and risk-of-bias tools: STROBE, STROBE-MR, RECORD, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, CROSS, SRQR, COREQ, PRISMA 2020, PRISMA-DTA, PRISMA-P, PRISMA-ScR, MOOSE, ARRIVE, CONSORT, CONSORT-AI, CARE, SPIRIT, SPIRIT-AI, CLAIM, DECIDE-AI, SQUIRE 2.0, CLEAR, GRRAS, MI-CLEAR-LLM, SWiM, AMSTAR 2, QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA. Includes Results/Discussion section boundary checks and machine-readable JSON summary for pipeline integration.
 
 ### Publication-Ready Output
 `analyze-stats` generates reproducible Python/R code for 13 analysis types -- including regression, propensity score, and repeated measures -- with mandatory calibration for prediction models. `make-figures` produces journal-specification figures (300 DPI, colorblind-safe palettes, proper dimensions), visual/graphical abstracts, and a tool selection guide (D2 for flow diagrams, matplotlib for data plots). `--study-type` auto-generates the complete figure set for each study design.

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+      "path": "skills/peer-review/references/domain-probes/scoping_review.md",
+      "size": 7246,
+      "sha256": "c8d7ab314aaff513638715674d26be7dd32b3b4815cab48de8cef00cba6db2f8"
+    },
     {
       "path": "skills/peer-review/references/domain-probes/sr_ma.md",
       "size": 17239,
@@ -3393,8 +3418,8 @@
     },
     {
       "path": "skills/self-review/SKILL.md",
-      "size": 104683,
-      "sha256": "8cc62fbae95f1dd18c5c62f65931904d981daa8a565bad2f8418e3671ca56e7c"
+      "size": 105186,
+      "sha256": "202bf201cbe1b5dfc3703cddaaf2dfc025af5456d5446656132b1545243b0098"
     },
     {
       "path": "skills/self-review/references/domain-probes/ai_overclaiming.md",
@@ -3466,6 +3491,11 @@
       "size": 9718,
       "sha256": "2e383fec4cf2034c62f9e1a419a0ff61e27bc5b3c132f7115b2335bd72472452"
     },
+    {
+      "path": "skills/self-review/references/domain-probes/qualitative_research.md",
+      "size": 7014,
+      "sha256": "fd82024939bbfc7f30f284a85a06712b69a269b89a2c8e3752484fb6fb23ebea"
+    },
     {
       "path": "skills/self-review/references/domain-probes/radiomics.md",
       "size": 5344,
@@ -3481,6 +3511,11 @@
       "size": 7574,
       "sha256": "04174053da808ee99f72f21d41225d76e856e94aff5088dffd8040ec40a4aa4e"
     },
+    {
+      "path": "skills/self-review/references/domain-probes/scoping_review.md",
+      "size": 7246,
+      "sha256": "c8d7ab314aaff513638715674d26be7dd32b3b4815cab48de8cef00cba6db2f8"
+    },
     {
       "path": "skills/self-review/references/domain-probes/sr_ma.md",
       "size": 17239,

package/metadata/distribution_manifest.json

@@ -1,6 +1,6 @@
 {
   "schema_version": 1,
-  "version": "5.6.0",
+  "version": "5.8.0",
   "owned_skills": [
     "academic-aio",
     "add-journal",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "medsci-skills",
-  "version": "5.6.0",
+  "version": "5.8.0",
   "description": "MedSci Skills — a medical/scientific research skill suite for AI coding agents (Claude Code, Codex, Cursor, Copilot). The npm package is a terminal-friendly installer shortcut; the canonical distribution remains the GitHub repository and the Claude Code plugin marketplace.",
   "license": "SEE LICENSE IN LICENSE",
   "homepage": "https://github.com/Aperivue/medsci-skills#readme",

package/skills/check-reporting/SKILL.md

@@ -1,7 +1,7 @@
 ---
 name: check-reporting
-description: Check manuscript compliance with medical research reporting guidelines. Supports 41 guidelines including STROBE, STROBE-MR, RECORD, CONSORT, CONSORT-AI, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, ARRIVE, PRISMA, PRISMA-DTA, PRISMA-P, CARE, SPIRIT, SPIRIT-AI, CLAIM, DECIDE-AI, MI-CLEAR-LLM, SQUIRE 2.0, CLEAR, MOOSE, GRRAS, SWiM, AMSTAR 2, CHEERS 2022, CROSS (survey studies), and risk of bias tools (QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA). Generates item-by-item assessment with PRESENT/MISSING/PARTIAL status.
-triggers: checklist, reporting guideline, STROBE, STROBE-MR, Mendelian randomization, CONSORT, CONSORT-AI, STARD, STARD-AI, TRIPOD, TRIPOD-LLM, PGS-RS, PRS-RS, polygenic risk score, polygenic score, PRISMA, PRISMA-DTA, PRISMA-P, ARRIVE, CARE, CLAIM, DECIDE-AI, MI-CLEAR-LLM, SPIRIT, SPIRIT-AI, QUADAS, QUADAS-C, RoB, ROBINS, ROBINS-E, ROBIS, ROB-ME, PROBAST, NOS, COSMIN, AMSTAR, SWiM, CHEERS, economic evaluation, cost-effectiveness, cost-utility, QALY, ICER, RECORD, RECORD-PE, routinely-collected data, registry, claims, electronic health records, EHR, real-world data, CROSS, CHERRIES, survey, questionnaire, KAP, e-survey, response rate, risk of bias, compliance check, LLM accuracy, large language model, clinical deployment
+description: Check manuscript compliance with medical research reporting guidelines. Supports 44 guidelines including STROBE, STROBE-MR, RECORD, CONSORT, CONSORT-AI, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, ARRIVE, PRISMA, PRISMA-DTA, PRISMA-P, PRISMA-ScR (scoping reviews), CARE, SPIRIT, SPIRIT-AI, CLAIM, DECIDE-AI, MI-CLEAR-LLM, SQUIRE 2.0, CLEAR, MOOSE, GRRAS, SWiM, AMSTAR 2, CHEERS 2022, CROSS (survey studies), SRQR and COREQ (qualitative research), and risk of bias tools (QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA). Generates item-by-item assessment with PRESENT/MISSING/PARTIAL status.
+triggers: checklist, reporting guideline, STROBE, STROBE-MR, Mendelian randomization, CONSORT, CONSORT-AI, STARD, STARD-AI, TRIPOD, TRIPOD-LLM, PGS-RS, PRS-RS, polygenic risk score, polygenic score, PRISMA, PRISMA-DTA, PRISMA-P, PRISMA-ScR, scoping review, scoping, evidence map, ARRIVE, CARE, CLAIM, DECIDE-AI, MI-CLEAR-LLM, SPIRIT, SPIRIT-AI, QUADAS, QUADAS-C, RoB, ROBINS, ROBINS-E, ROBIS, ROB-ME, PROBAST, NOS, COSMIN, AMSTAR, SWiM, CHEERS, economic evaluation, cost-effectiveness, cost-utility, QALY, ICER, RECORD, RECORD-PE, routinely-collected data, registry, claims, electronic health records, EHR, real-world data, CROSS, CHERRIES, survey, questionnaire, KAP, e-survey, response rate, SRQR, COREQ, qualitative research, interviews, focus groups, thematic analysis, grounded theory, reflexivity, risk of bias, compliance check, LLM accuracy, large language model, clinical deployment
 tools: Read, Write, Edit, Bash, Grep, Glob
 model: inherit
 ---
@@ -32,6 +32,9 @@ compliance report suitable for journal submission.
   - `CHEERS_2022.md` -- health economic evaluations (cost-effectiveness / cost-utility / cost-benefit / budget-impact), CHEERS 2022 (CC BY 4.0, Husereau et al. BMJ 2022)
   - `RECORD.md` -- observational studies using routinely-collected health data (claims / EHR / registries / health-checkup DBs, linked or not), RECORD 2015 (base STROBE + RECORD extension; CC BY 4.0, Benchimol et al. PLoS Med 2015; RECORD-PE for drug studies)
   - `CROSS.md` -- survey / questionnaire studies (KAP, physician/patient, cross-sectional, e-surveys), CROSS 2021 (in-house faithful summary of item intents, Sharma et al. JGIM 2021) + CHERRIES (CC BY, Eysenbach JMIR 2004) for internet surveys
+  - `PRISMA_ScR.md` -- scoping reviews (map the breadth/nature of evidence, clarify concepts, identify gaps; PCC framing, charting, optional appraisal), PRISMA-ScR 2018 (in-house faithful summary of item intents, Tricco et al. Ann Intern Med 2018; DOI 10.7326/M18-0850)
+  - `SRQR.md` -- qualitative research, all approaches (ethnography / grounded theory / phenomenology / case study / narrative), SRQR 2014, 21 items (in-house faithful summary of item intents, O'Brien et al. Acad Med 2014; DOI 10.1097/ACM.0000000000000388)
+  - `COREQ.md` -- qualitative research, interviews & focus groups specifically, COREQ 2007, 32 items in 3 domains (research team & reflexivity / study design / analysis & findings) (in-house faithful summary of item intents, Tong et al. Int J Qual Health Care 2007; DOI 10.1093/intqhc/mzm042)
   - `PRISMA_2020.md` -- systematic reviews (CC BY)
   - `ARRIVE_2.md` -- animal studies (CC0)
   - `PRISMA_DTA.md` -- DTA systematic reviews (CC BY, McInnes et al. JAMA 2018)
@@ -94,6 +97,8 @@ user specification.
 | Health economic evaluation (cost-effectiveness / cost-utility / cost-benefit / budget-impact) | CHEERS 2022 | -- |
 | Observational study using routinely-collected data (claims / EHR / registry / health-checkup DB) | RECORD (base STROBE + RECORD extension; RECORD-PE for drug studies) | -- |
 | Survey / questionnaire study (KAP, physician/patient, cross-sectional, e-survey) | CROSS (+ CHERRIES for internet surveys) | -- |
+| Scoping review (maps breadth/nature of evidence, clarifies concepts, identifies gaps — not a focused effectiveness/accuracy question) | PRISMA-ScR (base PRISMA + scoping-review extension) | -- |
+| Qualitative study (interviews, focus groups, ethnography, grounded theory, phenomenology, document analysis) | SRQR (all qualitative approaches); COREQ (interviews/focus groups specifically) | -- |
 | Randomized controlled trial | CONSORT 2025 | CONSORT-AI |
 | Diagnostic accuracy study | STARD 2015 | STARD-AI |
 | Prediction model (development/validation) | TRIPOD | TRIPOD+AI |

package/skills/check-reporting/references/checklists/COREQ.md

@@ -0,0 +1,86 @@
+# COREQ Checklist (qualitative — interviews & focus groups)
+
+**Consolidated criteria for reporting qualitative research**
+Version: COREQ 2007 — 32 items in 3 domains. **Specific to in-depth interviews and focus groups** (the dominant qualitative data-collection methods in health research). For other qualitative approaches, use the broader **SRQR** (`SRQR.md`).
+Source: Tong A, Sainsbury P, Craig J. *Int J Qual Health Care* 2007;19(6):349–357 (the COREQ statement; DOI 10.1093/intqhc/mzm042). EQUATOR Network.
+
+Apply when the manuscript reports an **interview or focus-group** qualitative study. For the design/conduct review of the same study, pair with the QL1–QL8 domain probes in `peer-review` / `self-review` `references/domain-probes/qualitative_research.md`; for a non-interview qualitative approach (ethnography, document analysis, etc.), use `SRQR.md`.
+
+> Licensing note: COREQ is published in the *International Journal for Quality in Health Care* (© Oxford University Press), with **no Creative Commons licence**. The items below are an **in-house, faithful summary of the criteria (facts/intents, paraphrased — not the verbatim COREQ wording)** for item-by-item assessment; consult the published article (DOI 10.1093/intqhc/mzm042) for exact item text.
+
+## Criteria (grouped by domain)
+
+### Domain 1 — Research team and reflexivity
+**Personal characteristics**
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 1 | Interviewer / facilitator | Which author(s) conducted the interviews or focus groups. |
+| 2 | Credentials | The interviewer's/facilitator's credentials (e.g. PhD, MD, RN). |
+| 3 | Occupation | Their occupation/role at the time of the study. |
+| 4 | Gender | The researcher's gender (where relevant to the dynamic). |
+| 5 | Experience & training | The interviewer's experience and training in qualitative methods. |
+
+**Relationship with participants**
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 6 | Relationship established | Whether a relationship existed between researcher and participants **before** the study. |
+| 7 | Participant knowledge of the interviewer | What participants knew about the researcher (e.g. personal goals, reasons for the research). |
+| 8 | Interviewer characteristics | Reported researcher characteristics — assumptions, interests, reasons for doing the research. |
+
+### Domain 2 — Study design
+**Theoretical framework**
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 9 | Methodological orientation & theory | The methodological orientation/theory underpinning the study (e.g. grounded theory, content analysis, phenomenology). |
+
+**Participant selection**
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 10 | Sampling | How participants were selected (purposive, convenience, consecutive, snowball). |
+| 11 | Method of approach | How participants were approached (face-to-face, telephone, mail, email). |
+| 12 | Sample size | The number of participants. |
+| 13 | Non-participation | How many declined or dropped out, and why (where known). |
+
+**Setting**
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 14 | Setting of data collection | Where the data were collected (home, clinic, workplace). |
+| 15 | Presence of non-participants | Whether anyone besides participants and researchers was present. |
+| 16 | Description of sample | The sample's key characteristics (e.g. demographics, dates). |
+
+**Data collection**
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 17 | Interview guide | Whether questions/prompts/guides were provided, and whether they were pilot-tested. |
+| 18 | Repeat interviews | Whether any interviews were repeated, and how many. |
+| 19 | Audio/visual recording | Whether the data were audio- or video-recorded. |
+| 20 | Field notes | Whether field notes were made during/after the interview or focus group. |
+| 21 | Duration | The duration of the interviews or focus groups. |
+| 22 | Data saturation | Whether **data saturation** was discussed/reached. |
+| 23 | Transcripts returned | Whether participants received the transcripts to review, comment on, or correct. |
+
+### Domain 3 — Analysis and findings
+**Data analysis**
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 24 | Number of data coders | How many coders coded the data. |
+| 25 | Description of the coding tree | Whether a description of the coding tree/framework is provided. |
+| 26 | Derivation of themes | Whether themes were identified in advance or derived from the data. |
+| 27 | Software | Any software used to manage/analyse the data. |
+| 28 | Participant checking | Whether participants provided feedback on the findings (**member checking**). |
+
+**Reporting**
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 29 | Quotations presented | Whether participant **quotations** illustrate the themes/findings, and whether each is identified (e.g. participant number). |
+| 30 | Data & findings consistent | Whether the reported findings cohere with the underlying data shown. |
+| 31 | Clarity of major themes | Whether the major themes are presented clearly in the results. |
+| 32 | Clarity of minor themes | Whether deviant/diverse cases and minor themes are addressed, not only the dominant ones. |
+
+---
+
+## Notes for Assessors
+
+- The **highest-yield** checks (where interview/focus-group studies most often fail review): **Domain 1 reflexivity** (items 1–8 — who interviewed, their relationship to participants, and their assumptions; the single most-omitted COREQ domain), **item 9** (a named methodological orientation — not "themes emerged" with no method), **items 10/22** (a stated sampling approach and a **saturation** discussion), **items 24–28** (the coding/analysis process — how many coders, the coding framework, software, member checking), and **item 29** (themes substantiated by **identified participant quotations**).
+- **Do not apply quantitative criteria**: a small purposive sample is appropriate, "generalizability" is **transferability**, and there are no power/effect-size/p-value requirements. A "sample too small / not generalizable" comment is mis-calibrated for an interview study.
+- COREQ is interview/focus-group-specific; for ethnography, document analysis, or other qualitative approaches use `SRQR.md`. This is an **in-house faithful summary of the COREQ criteria (paraphrased intents, not verbatim)**; map the manuscript's content to the items rather than to exact wording, and verify against the published checklist (Tong et al. *Int J Qual Health Care* 2007; DOI 10.1093/intqhc/mzm042). Verified 2026-06-30.

package/skills/check-reporting/references/checklists/PRISMA_ScR.md

@@ -0,0 +1,70 @@
+# PRISMA-ScR Checklist (scoping reviews)
+
+**Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews**
+Version: PRISMA-ScR 2018 — 20 essential items + 2 optional (items 12 and 16, critical appraisal). Organised by the IMRAD-plus-Funding sections of the source.
+Source: Tricco AC, Lillie E, Zarin W, O'Brien KK, Colquhoun H, Levac D, et al. *Ann Intern Med* 2018;169(7):467–473 (the PRISMA-ScR statement; DOI 10.7326/M18-0850). EQUATOR Network. Scoping-review conduct guidance: JBI (Peters et al.); Arksey & O'Malley; Levac et al.
+
+Apply when the manuscript is a **scoping review** — a review that *maps* the breadth of evidence on a topic, characterises concepts/definitions, and identifies gaps, rather than answering a focused effectiveness/accuracy question (that is a systematic review → use PRISMA 2020 / PRISMA-DTA). For the design/conduct review of the same study, pair with the SC1–SC8 domain probes in `peer-review` / `self-review` `references/domain-probes/scoping_review.md`; for the flow diagram use `make-figures` (PRISMA-style); for an SR/MA instead, use `PRISMA_2020.md` / `PRISMA_DTA.md`.
+
+> Licensing note: the PRISMA-ScR statement is published in *Annals of Internal Medicine* (© American College of Physicians); the official EQUATOR checklist carries only the citation, with **no Creative Commons licence** (one secondary source lists CC BY-NC-SA 3.0 — also not permissively reusable). The items below are an **in-house, faithful summary of the reporting items (facts/intents, paraphrased — not the verbatim PRISMA-ScR wording)** for item-by-item assessment; consult the published article (DOI 10.7326/M18-0850) for exact item text. Items 12 and 16 (critical appraisal) are **optional** — a scoping review is not required to appraise risk of bias.
+
+## Reporting items (grouped by section)
+
+### Title
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 1 | Title | The report is identified as a **scoping review** in the title. |
+
+### Abstract
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 2 | Structured summary | A structured abstract that, as relevant, states the background and objectives, the eligibility criteria and the evidence sources searched, the **charting** approach, and the headline results and conclusions tied to the review questions. |
+
+### Introduction
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 3 | Rationale | The rationale situated against existing knowledge, and **why the question suits a scoping (mapping) approach** rather than a systematic review. |
+| 4 | Objectives | Explicit questions/objectives stated with their key elements — **Population, Concept, Context (PCC)** or equivalent — used to frame the review. |
+
+### Methods
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 5 | Protocol and registration | Whether an a-priori **protocol** exists, where it can be accessed, and any registration details. (Note: PROSPERO does **not** register scoping reviews; OSF/Figshare or a published protocol is used.) |
+| 6 | Eligibility criteria | Characteristics used as eligibility criteria (years, language, publication status, source types) **with a rationale**. |
+| 7 | Information sources | All information sources searched (databases with coverage dates, grey-literature sources, author contact) and the date the most recent search was run. |
+| 8 | Search | A reproducible search strategy for **one or more databases** (search terms and any limits), detailed enough to be repeated by another team. |
+| 9 | Selection of sources of evidence | The process for selecting **sources of evidence** (screening and eligibility) into the review. |
+| 10 | Data charting process | The **data-charting** methods (calibrated/team-tested form; whether charting was independent/duplicate; iterative refinement) and any process for obtaining/confirming data from investigators. "Charting," not "extraction." |
+| 11 | Data items | The data items charted — every variable sought — plus any assumptions or simplifications made. |
+| 12 | Critical appraisal of individual sources of evidence (**optional**) | *If done*, the rationale for critical appraisal, the methods used, and how the information was used. Scoping reviews are **not required** to appraise; "critical appraisal" is used instead of "risk of bias." |
+| 13 | Synthesis of results | The methods for **handling and summarising (charting/mapping)** the charted data. |
+
+### Results
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 14 | Selection of sources of evidence | Numbers screened, assessed for eligibility, and included, with reasons for exclusion at each stage — ideally a **flow diagram**. |
+| 15 | Characteristics of sources of evidence | Per-source characteristics for which data were charted, with citations. |
+| 16 | Critical appraisal within sources of evidence (**optional**) | *If done* (see item 12), the critical-appraisal data per source. Optional. |
+| 17 | Results of individual sources of evidence | For each included source, the relevant charted data that relate to the review questions/objectives. |
+| 18 | Synthesis of results | The charting results **summarised/mapped** in relation to the review questions/objectives — a **map/characterisation, not a pooled effect estimate**. |
+
+### Discussion
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 19 | Summary of evidence | The main results summarised (overview of concepts, themes, evidence types), linked to the questions/objectives and their relevance to key groups. |
+| 20 | Limitations | Limitations of the **scoping-review process**. |
+| 21 | Conclusions | A general interpretation against the questions/objectives, with potential implications and/or next steps (e.g. whether a systematic review is warranted). |
+
+### Funding
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 22 | Funding | Sources of funding for the included sources of evidence **and** for the scoping review, and the funders' role. |
+
+---
+
+## Notes for Assessors
+
+- The **highest-yield** checks (where scoping reviews most often go wrong): **item 4** (objectives framed as PCC mapping, not a focused PICO effectiveness question — a study that asks "is X effective/accurate?" should be a systematic review, not a scoping review), **item 18** (results presented as a **map** — counts, categories, themes, evidence gaps — **not** a pooled OR/RR/AUC or a definitive effectiveness/accuracy conclusion), and **items 12/16** (critical appraisal is **optional** — do not penalise a scoping review for omitting risk-of-bias, and do not let it claim GRADE-style certainty it did not derive).
+- A "scoping review" that reports pooled effect estimates / a meta-analysis, or concludes that an intervention is effective / a test is accurate, has overstepped its design — its synthesis (item 18) and conclusions (item 21) should be downgraded to descriptive mapping, or the study reframed as a systematic review.
+- Terminology matters: **charting** (not extraction), **sources of evidence** (not only studies), **critical appraisal** (not risk of bias). A scoping review claiming PROSPERO registration is in error (PROSPERO excludes scoping reviews).
+- This is an **in-house faithful summary of the PRISMA-ScR items (paraphrased intents, not verbatim)**; map the manuscript's content to the items rather than to exact wording, and verify against the published statement (Tricco et al. *Ann Intern Med* 2018; DOI 10.7326/M18-0850). Verified 2026-06-30.

package/skills/check-reporting/references/checklists/SRQR.md

@@ -0,0 +1,64 @@
+# SRQR Checklist (qualitative research)
+
+**Standards for Reporting Qualitative Research**
+Version: SRQR 2014 — 21 items across Title/Abstract, Introduction, Methods, Results/Findings, Discussion, and Other. **Broad** — applies to all qualitative approaches (ethnography, grounded theory, phenomenology, case study, narrative research), not only interviews/focus groups.
+Source: O'Brien BC, Harris IB, Beckman TJ, Reed DA, Cook DA. *Acad Med* 2014;89(9):1245–1251 (the SRQR statement; DOI 10.1097/ACM.0000000000000388). EQUATOR Network.
+
+Apply when the manuscript is a **qualitative study** of any approach — interviews, focus groups, observation/ethnography, document analysis, grounded theory, phenomenology, narrative research. For **interview / focus-group** studies specifically, the more granular **COREQ** (`COREQ.md`) is the better-fit companion. For the design/conduct review of the same study, pair with the QL1–QL8 domain probes in `peer-review` / `self-review` `references/domain-probes/qualitative_research.md`.
+
+> Licensing note: SRQR is published in *Academic Medicine* (© AAMC), with **no Creative Commons licence**. The items below are an **in-house, faithful summary of the reporting items (facts/intents, paraphrased — not the verbatim SRQR wording)** for item-by-item assessment; consult the published article (DOI 10.1097/ACM.0000000000000388) for exact item text.
+
+## Reporting items (grouped by section)
+
+### Title and Abstract
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 1 | Title | A concise description of the study's nature/topic that **identifies it as qualitative** and (recommended) names the approach (e.g. ethnography, grounded theory) or data-collection method (e.g. interviews, focus groups). |
+| 2 | Abstract | A summary of the key elements in the journal's abstract format — typically background, purpose, methods, results, conclusions. |
+
+### Introduction
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 3 | Problem formulation | The problem/phenomenon studied and its significance, with a review of relevant theory and prior empirical work, and a problem statement. |
+| 4 | Purpose or research question | The study's purpose and its specific objectives or questions. |
+
+### Methods
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 5 | Qualitative approach & research paradigm | The chosen approach (ethnography / grounded theory / case study / phenomenology / narrative) and the guiding paradigm (e.g. postpositivist, constructivist/interpretivist), **with a rationale**. |
+| 6 | Researcher characteristics & **reflexivity** | The researchers' attributes, qualifications/experience, relationship with participants, and assumptions, and how these may have interacted with the questions, methods, findings, or transferability. |
+| 7 | Context | The setting/site and salient contextual factors, with a rationale. |
+| 8 | Sampling strategy | How and why participants/documents/events were selected, and the criterion for stopping sampling (e.g. **saturation**), with a rationale. |
+| 9 | Ethical issues (human subjects) | Ethics-board approval and participant consent (or an explanation for their absence), and confidentiality / data-security handling. |
+| 10 | Data collection methods | The data types and collection procedures — dates, iterative process, triangulation of sources/methods, and any procedure changes during the study — with a rationale. |
+| 11 | Data collection instruments & technologies | The instruments (e.g. interview guides, questionnaires) and devices (e.g. audio recorders), and whether/how they changed over the study. |
+| 12 | Units of study | The number and relevant characteristics of the participants/documents/events, and their level of participation. |
+| 13 | Data processing | How data were processed before/during analysis — transcription, data entry/management/security, integrity checks, coding, and de-identification of excerpts. |
+| 14 | Data analysis | The process by which inferences/themes were identified and developed, who analysed the data, and the referenced paradigm/approach, with a rationale. |
+| 15 | Techniques to enhance **trustworthiness** | The techniques used to enhance trustworthiness/credibility (e.g. member checking, audit trail, triangulation), with a rationale. |
+
+### Results / Findings
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 16 | Synthesis & interpretation | The main findings (interpretations, inferences, themes), and any theory/model development or integration with prior research. |
+| 17 | Links to empirical data | Evidence — participant **quotations**, field notes, text excerpts, images — that substantiates each analytic finding. |
+
+### Discussion
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 18 | Integration, implications, transferability, contribution | A short summary of findings; how they connect to / extend / challenge prior scholarship; the scope of application / **transferability**; and the study's unique contribution. |
+| 19 | Limitations | The trustworthiness and limitations of the findings. |
+
+### Other
+| # | Item | What to check is reported |
+|---|------|---------------------------|
+| 20 | Conflicts of interest | Potential sources of influence on the study and how they were managed. |
+| 21 | Funding | Sources of funding/support and the role of the funders in data collection, interpretation, and reporting. |
+
+---
+
+## Notes for Assessors
+
+- The **highest-yield** checks (where qualitative studies most often go wrong on review): **item 6** (researcher **reflexivity** — the researchers' position, assumptions, and relationship to participants is a core qualitative-rigor requirement, frequently omitted), **item 8** (a stated **sampling strategy and stopping criterion** — purposive logic and saturation, not a convenience sample with no rationale), **item 15** (explicit **trustworthiness** techniques — member checking / audit trail / triangulation), and **item 17** (analytic claims grounded in **quoted data**, not asserted).
+- **Do not apply quantitative criteria** to a qualitative study: a small purposive sample is not a flaw, "generalizability" is **transferability** (not statistical external validity), and there are no power calculations, effect sizes, or p-values to demand. Mis-calibrated "the sample is too small / not generalizable / no p-value" comments are inappropriate here.
+- This is an **in-house faithful summary of the SRQR items (paraphrased intents, not verbatim)**; map the manuscript's content to the items rather than to exact wording, and verify against the published statement (O'Brien et al. *Acad Med* 2014; DOI 10.1097/ACM.0000000000000388). For interview/focus-group designs, COREQ (`COREQ.md`) gives finer-grained items. Verified 2026-06-30.

package/skills/check-reporting/scripts/check_checklist_exists.py

@@ -49,6 +49,9 @@ ALIAS_TO_STEM = {
     "prisma": "PRISMA_2020",
     "prismadta": "PRISMA_DTA",
     "prismap": "PRISMA_P",
+    "prismascr": "PRISMA_ScR",
+    "scopingreview": "PRISMA_ScR",
+    "scoping": "PRISMA_ScR",
     "arrive": "ARRIVE_2",
     "care": "CARE",
     "spirit": "SPIRIT",
@@ -84,6 +87,9 @@ ALIAS_TO_STEM = {
     "cheers2022": "CHEERS_2022",
     "record": "RECORD",
     "cross": "CROSS",
+    "srqr": "SRQR",
+    "coreq": "COREQ",
+    "qualitative": "SRQR",
 }
 
 EXIT_OK = 0

package/skills/make-figures/references/reporting_guideline_figure_map.md

@@ -1,7 +1,7 @@
 # Reporting Guideline → Figure Requirements Map
 
 > **Bridge**: this file connects `/make-figures` to `/check-reporting`
-> (41 reporting guidelines). Each row tells you which figures the guideline
+> (44 reporting guidelines). Each row tells you which figures the guideline
 > **mandates** and how this skill currently supports them. Use during
 > Step 1 (Specify) once the study type is known.
 
@@ -25,6 +25,7 @@ Legend for **Status** column:
 | **PRISMA 2020** | Systematic review | Flow diagram (4-phase: identification → screening → eligibility → included) | ✅ | `templates/official/prisma2020/`; R `PRISMA2020` package |
 | **PRISMA-DTA** | DTA systematic review | Modified PRISMA flow + DTA-specific exclusion reasons | ⚠️ | Salameh et al., *BMJ* 2020 (PMID 32312813); use generic flow + extra columns |
 | **PRISMA-NMA** | Network MA | PRISMA flow + network plot | ❌ | Hutton et al., *Ann Intern Med* 2015; network plot via R `netmeta::netgraph()` |
+| **PRISMA-ScR** | Scoping review | PRISMA-ScR flow diagram (sources of evidence: identification → screening → eligibility → included; item 14) | ⚠️ | Tricco et al., *Ann Intern Med* 2018 (DOI 10.7326/M18-0850); use the generic PRISMA flow with "sources of evidence" wording |
 | **PRISMA-P** | Protocol of SR | (none mandated; PRISMA-S search strategy figure recommended) | ❌ | Rethlefsen et al., *Syst Rev* 2021 |
 | **CONSORT 2025** | RCT | Participant-flow diagram (enrollment → allocation → follow-up → analysis) | ✅ | `templates/official/consort2010/` (now CONSORT 2025); R generator |
 | **CONSORT-AI 2020** | AI intervention RCT | CONSORT flow extended with AI training/validation/deployment dataset boxes | ❌ | Liu et al., *Nat Med* 2020 (PMID 32908283), Fig. 1; D2 / Graphviz custom |
@@ -95,7 +96,7 @@ flags them:
 
 ## Cross-references
 
-- `/check-reporting` skill — supports all 41 guidelines, item-level audit
+- `/check-reporting` skill — supports all 44 guidelines, item-level audit
 - `flow_diagram_lessons.md` — production lessons that apply across all flows
 - `pipeline_concepts_medical_ai.md` — DICOM / annotation / federated /
   architecture diagram conventions

package/skills/orchestrate/SKILL.md

@@ -48,7 +48,7 @@ You do NOT do the work yourself. You classify, plan, and delegate.
 | **meta-analysis** | Systematic review | Full MA pipeline: protocol, search, screening, extraction, synthesis, PRISMA-DTA |
 | **write-paper** | Writing | IMRAD manuscript drafting (8-phase pipeline), any section writing |
 | **self-review** | Quality | Pre-submission self-check with domain probes (Survival / SR-MA / Radiomics / Narrative); optional `--panel` for a high-stakes final QC pass |
-| **check-reporting** | Compliance | Audit against 41 reporting guidelines and risk-of-bias tools |
+| **check-reporting** | Compliance | Audit against 44 reporting guidelines and risk-of-bias tools |
 | **revise** | Revision | Parse reviewer comments, generate point-by-point response, track changes |
 | **grant-builder** | Funding | Structure grant proposals: significance, innovation, approach, milestones |
 | **present-paper** | Presentation | Prepare academic talks: analyze paper, draft scripts, inject slide notes, Q&A prep |

package/skills/peer-review/SKILL.md

@@ -286,6 +286,18 @@ Apply this 8-probe checklist (SV1–SV8) **only when the manuscript is a self-re
 
 **Probe detail (SV1–SV8), with output templates and the leads-vs-findings discipline:** `${CLAUDE_SKILL_DIR}/references/domain-probes/survey_research.md`. Load it and apply each probe when the trigger fires. In this skill, map each probe finding to a Major / Minor comment; a convenience/self-selected sample generalised to a population with no representativeness assessment (SV1), a non-probability sample presented as representative (SV2), a response rate with no defined denominator or no non-response analysis behind a population estimate (SV3), or a novel unvalidated/un-piloted instrument carrying the headline (SV4) are design-level — surface them in the Confidential Comments to the Editor and place the strongest as the Major #1 candidate. Missing CHERRIES e-survey reporting (SV5), biased question design / unavailable instrument (SV6), unweighted estimates from a skewed sample or shifting denominators (SV7), and over-generalisation or missing ethics/consent (SV8) are validity/framing-level. For multi-item-scale reliability (incl. the reverse-coded-item α trap), pair with the analyze-stats Survey/Likert guidance.
 
+### Phase 2S: Scoping Review Extension
+
+Apply this 8-probe checklist (SC1–SC8) **only when the manuscript is a scoping review** — a review that *maps* the breadth/nature of evidence, clarifies concepts, or identifies gaps, rather than answering a focused effectiveness/accuracy question (that is a systematic review → PRISMA 2020 / PRISMA-DTA). These probes complement (do not replace) the generic Phase 2 checklist and the **PRISMA-ScR** reporting items (Tricco et al. *Ann Intern Med* 2018), and assume the JBI / Arksey & O'Malley / Levac conduct frameworks. They target whether the question genuinely suits a *mapping* review, whether the conduct uses scoping methods (PCC framing, charting, optional appraisal), and the commonest over-reach — a synthesis drifting from a map into pooled effect estimates and definitive effectiveness claims.
+
+**Probe detail (SC1–SC8), with output templates and the leads-vs-findings discipline:** `${CLAUDE_SKILL_DIR}/references/domain-probes/scoping_review.md`. Load it and apply each probe when the trigger fires. In this skill, map each probe finding to a Major / Minor comment; a focused effectiveness/accuracy question run as a scoping review to sidestep risk-of-bias and synthesis (SC1), or a scoping review reporting a pooled effect/accuracy estimate or definitive effectiveness conclusion (SC7) are design-level — surface them in the Confidential Comments to the Editor and place the strongest as the Major #1 candidate. Note the **asymmetric critical-appraisal calibration** (SC6): do **not** flag "no risk-of-bias assessment" as a deficiency for a scoping review, but do flag GRADE-style certainty claimed without appraisal. Wrong-registry (PROSPERO does not register scoping reviews) claims (SC2), narrow-search comprehensiveness claims (SC4), undocumented charting (SC5), and practice recommendations or mislabelling drawn from a map (SC8) are validity/framing-level.
+
+### Phase 2T: Qualitative Study Extension
+
+Apply this 8-probe checklist (QL1–QL8) **only when the manuscript is a qualitative study** — in-depth interviews, focus groups, observation/ethnography, document analysis, grounded theory, phenomenology, narrative research. These probes complement (do not replace) the generic Phase 2 checklist and the qualitative reporting standards — **COREQ** (interviews/focus groups; Tong et al. 2007) and **SRQR** (all qualitative approaches; O'Brien et al. 2014). They target what makes qualitative rigour distinct from quantitative validity: researcher **reflexivity**, a transparent **analysis** process, **trustworthiness** (credibility/dependability/confirmability/transferability) rather than statistical validity, and findings **grounded in quoted data**.
+
+**Probe detail (QL1–QL8), with output templates and the leads-vs-findings discipline:** `${CLAUDE_SKILL_DIR}/references/domain-probes/qualitative_research.md`. Load it and apply each probe when the trigger fires. In this skill, map each probe finding to a Major / Minor comment; a method–question mismatch (a quantitative question answered with a few interviews, QL1), absent **reflexivity** (QL2), an opaque "themes emerged" analysis with no coding process / audit trail (QL5), or interpretation not traceable to quoted data (QL7) are design-level — surface them in the Confidential Comments to the Editor and place the strongest as the Major #1 candidate. Note the **bidirectional calibration trap** (QL6): do **not** demand a power calculation, a "representative" sample, statistical generalizability, or treat inter-coder κ as the sole truth — these are quantitative yardsticks inappropriate to qualitative work (a small purposive sample is not a flaw; "generalizability" is **transferability**); but do flag authors who claim statistical generalizability or causal/prevalence/population over-reach (QL8) from qualitative data. Unjustified sampling / no saturation (QL3), thin data-collection reporting (QL4), and missing ethics/consent for identifiable quotes (QL8) are validity/framing-level. Map the study to **COREQ** (interviews/focus groups) or **SRQR** (broader).
+
 ### Phase 3: Draft Review
 
 Before writing comments, skim the relevant model in `references/exemplar_reviews/` for the

package/skills/peer-review/references/domain-probes/qualitative_research.md

@@ -0,0 +1,50 @@
+<!-- Domain probe module — shared, vendored BYTE-IDENTICAL by /peer-review and /self-review.
+     Severity words below (MAJOR / MINOR / major / minor) denote finding severity, NOT a journal
+     recommendation. Each consuming skill maps findings to its own output:
+       - peer-review: Major / Minor comments + Confidential Comments to the Editor; a
+         reflexivity / analysis-transparency / over-claim flaw is placed as Major #1.
+       - self-review: Anticipated Major / Minor Comments (Fatal / Fixable) mapped to category letters.
+     Do NOT edit one copy only — run `python3 scripts/check_domain_probe_sync.py --sync`. -->
+
+# Qualitative research probes (QL1–QL8)
+
+An 8-probe checklist for **qualitative studies** — in-depth interviews, focus groups, observation/ethnography, document analysis, grounded theory, phenomenology, narrative research. These probes complement (do not replace) the generic Phase 2 checklist and the qualitative reporting standards — **COREQ** (interviews/focus groups; Tong et al. 2007) and **SRQR** (all qualitative approaches; O'Brien et al. 2014). They target what makes qualitative rigour distinct from quantitative validity: researcher **reflexivity**, a transparent **analysis** process, **trustworthiness** (credibility/dependability/confirmability/transferability) rather than statistical validity, and findings **grounded in quoted data** — and they guard the most common mis-calibration on both sides: applying quantitative yardsticks (sample-size power, statistical generalizability, p-values) to qualitative work. QL2 (reflexivity), QL5 (analysis transparency), and QL6 (trustworthiness, not statistical validity) are the highest-yield; run them first.
+
+**QL1 — Approach/paradigm fit and research question**:
+- Is a **qualitative** approach justified for the question — exploring meaning, experience, process, or context, rather than measuring frequency/effect (which would be a quantitative design)?
+- Is a **named approach** (grounded theory, phenomenology, ethnography, case study, narrative) and guiding paradigm stated **with a rationale**, rather than an unspecified "qualitative study" / "thematic analysis" with no methodological orientation?
+- A question that is really quantitative (prevalence/effect) answered with a few interviews, or no named methodological orientation behind the analysis → MAJOR (method–question mismatch) / MINOR (unnamed approach).
+
+**QL2 — Reflexivity and researcher positioning**:
+- Are the **researcher's characteristics** reported — who collected the data, their credentials/role, experience/training, and **prior relationship to participants** — and is there reflexive consideration of how their assumptions/position may have shaped data collection and interpretation?
+- Reflexivity is a core qualitative-rigour requirement (COREQ Domain 1; SRQR item 6) and the **single most-omitted** element.
+- An interview/focus-group study with no reflexivity / no statement of who interviewed and their relationship to participants → MAJOR (or MINOR if partially addressed).
+
+**QL3 — Sampling logic and adequacy (purposive; information power / saturation)**:
+- Is the **sampling strategy** stated and justified — **purposive / theoretical / maximum-variation** logic appropriate to the question, not an unexplained convenience sample — and is there an argument for **when sampling stopped** (data **saturation** or information power)?
+- A **small sample is not a flaw** in qualitative work; the flaw is an *unjustified* sample with no purposive rationale and no saturation/information-power discussion.
+- Convenience sample presented with no rationale, or no account of sampling adequacy/saturation behind broad thematic claims → MINOR / MAJOR per centrality.
+
+**QL4 — Data-collection rigour**:
+- Are the **data-collection methods** described in enough detail to judge them — the **interview/topic guide** (and whether it was piloted/iterated), the **setting**, **recording and transcription**, **field notes**, and interview/focus-group **duration**?
+- Thinly reported data collection (no guide, unclear recording/transcription, no setting) that undercuts interpretability → MINOR.
+
+**QL5 — Analysis transparency and audit trail**:
+- Is the **analysis process** transparent — how many **coders**, the **coding framework/tree**, whether themes were **derived inductively or applied a priori**, any **software**, and an **audit trail**?
+- "Themes **emerged** from the data" with no described coding/analytic process is a black box.
+- An analysis with no described coding process / no audit trail behind the reported themes → MAJOR (analysis not reproducible/auditable).
+
+**QL6 — Trustworthiness, NOT statistical validity (the calibration trap)**:
+- Are **trustworthiness** techniques reported and matched to the four criteria — **credibility** (member checking, triangulation, prolonged engagement), **dependability** (audit trail), **confirmability** (reflexivity), **transferability** (thick description) — rather than quantitative "reliability/validity"?
+- The trap is bidirectional: (a) a **reviewer** must **not** demand a power calculation, a "representative" sample, statistical generalizability, or treat inter-coder κ as the sole truth — these are quantitative yardsticks inappropriate to qualitative work; (b) **authors** must **not** claim statistical generalizability or dress qualitative findings in quantitative certainty.
+- Missing trustworthiness strategies entirely, or quantitative-validity language misapplied (by either side) → MAJOR / MINOR per how load-bearing it is.
+
+**QL7 — Findings grounded in data (quotations, thick description, deviant cases)**:
+- Are the themes **substantiated by participant quotations / excerpts** (with participant identifiers), with enough **thick description** to let the reader judge the interpretation, and is there **consistency between the data and the findings**?
+- Are **negative / deviant cases** and minor themes considered, not just confirmatory exemplars?
+- Asserted themes with no quoted evidence, or interpretation not traceable to the data → MAJOR; cherry-picked confirmatory quotes with no deviant-case consideration → MINOR.
+
+**QL8 — Ethics, interpretive scope, and reporting standard**:
+- Are **ethics** reported (IRB approval/consent; confidentiality and de-identification of identifiable narrative quotes), and does interpretation **stay within what qualitative data support** — no **causal, effectiveness, prevalence, or population-level** claims, and no over-generalisation beyond the studied context (**transferability**, not generalizability)?
+- Is the study mapped to the appropriate reporting standard — **COREQ** (interviews/focus groups) or **SRQR** (broader qualitative)?
+- Causal/quantitative/population over-claiming from qualitative data, missing consent/de-identification for identifiable quotes, or no reporting-standard mapping → MAJOR (over-claim / ethics) / MINOR (reporting).

package/skills/peer-review/references/domain-probes/scoping_review.md

@@ -0,0 +1,51 @@
+<!-- Domain probe module — shared, vendored BYTE-IDENTICAL by /peer-review and /self-review.
+     Severity words below (MAJOR / MINOR / major / minor) denote finding severity, NOT a journal
+     recommendation. Each consuming skill maps findings to its own output:
+       - peer-review: Major / Minor comments + Confidential Comments to the Editor; a
+         scoping-fit / mapping-not-pooling / over-claim flaw is placed as Major #1.
+       - self-review: Anticipated Major / Minor Comments (Fatal / Fixable) mapped to category letters.
+     Do NOT edit one copy only — run `python3 scripts/check_domain_probe_sync.py --sync`. -->
+
+# Scoping review probes (SC1–SC8)
+
+An 8-probe checklist for **scoping reviews** — reviews that *map* the breadth of evidence on a topic, clarify concepts/definitions, and identify gaps. These probes complement (do not replace) the generic Phase 2 checklist and the **PRISMA-ScR** reporting items (Tricco et al. *Ann Intern Med* 2018), and assume the JBI / Arksey & O'Malley / Levac conduct frameworks. They target what is specific to a scoping design: whether the question genuinely suits a *mapping* (not an effectiveness/accuracy) review, whether the conduct uses scoping methods (PCC framing, charting, optional appraisal), and — the single most common over-reach — whether the synthesis stays a **map** rather than drifting into pooled effect estimates and definitive effectiveness claims. SC1 (scoping fit), SC6 (critical-appraisal calibration — the asymmetric trap), and SC7 (mapping not pooling) are the highest-yield; run them first.
+
+**SC1 — Scoping fit and objectives (mapping intent, PCC framing)**:
+- Is the review genuinely a **scoping** question — mapping the extent/range/nature of evidence, clarifying concepts, or identifying gaps — rather than a focused **effectiveness/accuracy** question that should be a systematic review (PRISMA 2020 / PRISMA-DTA)?
+- Are objectives framed with **Population, Concept, Context (PCC)** or an equivalent mapping structure, not a PICO effectiveness/comparison frame with a defined outcome estimate?
+- A focused "is X effective / is test Y accurate?" question run as a scoping review (to sidestep risk-of-bias and synthesis), or a scoping review whose objectives are really an SR's → MAJOR (reframe as a systematic review, or restate the objective as mapping).
+
+**SC2 — Protocol and registration (a-priori; OSF, not PROSPERO)**:
+- Is an **a-priori protocol** available (OSF / Figshare / a published protocol), with the question, eligibility, and charting plan pre-specified?
+- Note that **PROSPERO does not register scoping reviews** — a manuscript claiming PROSPERO registration for a scoping review is in error and should cite the correct registry/repository.
+- No protocol for a scoping review of any size, or a wrong-registry claim → MINOR (protocol absent → MAJOR if the charting plan appears post-hoc / outcome-driven).
+
+**SC3 — Eligibility by concept; sources of evidence (not only studies)**:
+- Are eligibility criteria specified by **PCC plus source characteristics** (years, language, publication status, source/evidence types) **with a rationale**?
+- Does the review admit the **heterogeneous "sources of evidence"** a scoping review is meant to map (quantitative and qualitative research, grey literature, policy/guidance, expert opinion) where relevant, rather than silently restricting to a narrow study type and presenting it as a comprehensive map?
+- Over-restrictive, study-only eligibility presented as a comprehensive map of the field, or eligibility with no rationale → MINOR.
+
+**SC4 — Search comprehensiveness and reproducibility**:
+- Is the **full search strategy for at least one database reproducible** (terms, limits), the date of the most recent search stated, and the information sources appropriate to a *mapping* aim — typically **multiple databases plus grey literature** rather than a single narrow source?
+- Given that scoping reviews aim for breadth, is the search broad enough to support a "map the field" claim?
+- A comprehensiveness/mapping claim resting on one narrow database with no grey-literature or no reproducible strategy → MAJOR / MINOR per the strength of the claim.
+
+**SC5 — Selection and data charting**:
+- Is the **two-stage selection** process (title/abstract then full-text) described, and the **data-charting** process specified — a calibrated/team-tested charting form, whether charting was **independent / in duplicate**, and any **iterative refinement** of the form (charting is iterative in scoping reviews)?
+- Is the correct terminology used (**charting**, not extraction; **sources of evidence**, not only studies)?
+- No charting process described, or single-reviewer charting with no calibration behind a large map → MINOR (or MAJOR if selection itself is undocumented).
+
+**SC6 — Critical appraisal is OPTIONAL (the asymmetric trap)**:
+- Critical appraisal / risk-of-bias is **not required** in a scoping review (PRISMA-ScR items 12/16 are optional). A reviewer must **not** flag "no risk-of-bias assessment" as a deficiency for a scoping review, and authors need not appraise.
+- Conversely, if appraisal **was** done, is the rationale, method, and use reported (items 12/16)? And does the review avoid claiming **certainty grading (GRADE) or quality-weighted conclusions** it never derived?
+- The trap is bidirectional: (a) demanding RoB of a scoping review is a mis-calibrated review comment; (b) a scoping review asserting GRADE-style certainty or "high-quality evidence shows…" without having appraised is over-claiming → MINOR/MAJOR per how load-bearing the certainty claim is.
+
+**SC7 — Synthesis is mapping, NOT pooling (no effect estimates)**:
+- Are results presented as a **map/characterisation** — counts, categories, concept/theme groupings, evidence-gap maps, charting tables — rather than a **meta-analytic pooled estimate** (pooled OR/RR/HR/AUC, summary sensitivity/specificity)?
+- A scoping review should **not** compute or headline a pooled effect/accuracy estimate; doing so is an estimand/scope mismatch (the design carries no risk-of-bias or synthesis machinery to support an effect claim).
+- A pooled effect/accuracy estimate, forest plot of effects, or quantitative effectiveness synthesis presented from a scoping review → MAJOR (move to a systematic review/meta-analysis, or relabel the figure as a descriptive frequency map).
+
+**SC8 — Interpretation, gaps, terminology, and reporting**:
+- Are conclusions matched to a **descriptive map** — what evidence exists, where the gaps are, whether a future systematic review/primary study is warranted — and free of **clinical-practice recommendations** or definitive effectiveness/accuracy claims a map cannot support (cf. the scope-coherence discipline)?
+- Is a **PRISMA-ScR flow diagram** present, the study correctly labelled a scoping review (not conflated with a systematic review), and the report mapped to **PRISMA-ScR**?
+- A practice recommendation or definitive effectiveness/accuracy conclusion drawn from a scoping map, mislabelling the study as a "systematic review," or missing PRISMA-ScR reporting → MAJOR (over-claim) / MINOR (reporting), per centrality.

package/skills/self-review/SKILL.md

@@ -359,6 +359,8 @@ These modules carry the same domain-specific critique probes used by `/peer-revi
 | Health economic evaluation (cost-effectiveness / cost-utility / cost-benefit / budget-impact; trial-based or decision-model-based — decision tree, Markov, DES) | `references/domain-probes/health_economic_evaluation.md` (HE1–HE8) |
 | Observational study using routinely-collected health data (administrative claims / EHR / disease or population registry / health-checkup DB, linked or not) | `references/domain-probes/record_routinely_collected_data.md` (RD1–RD8) |
 | Self-report survey / questionnaire study (KAP, physician/patient survey, cross-sectional questionnaire, web/e-survey) | `references/domain-probes/survey_research.md` (SV1–SV8) |
+| Scoping review (maps the breadth/nature of evidence, clarifies concepts, identifies gaps; PCC framing, charting, optional appraisal — not a focused effectiveness/accuracy question) | `references/domain-probes/scoping_review.md` (SC1–SC8) |
+| Qualitative study (interviews, focus groups, ethnography, grounded theory, phenomenology, document analysis; reflexivity, trustworthiness, thematic analysis — not quantitative validity) | `references/domain-probes/qualitative_research.md` (QL1–QL8) |
 
 When the manuscript matches a row, read `${CLAUDE_SKILL_DIR}/references/domain-probes/<module>.md` and apply each probe as an additional source of Anticipated Major / Minor Comments. The module severity words (MAJOR / MINOR) map to this skill's framing as follows: a conclusion-threatening or design-level finding becomes a **Fatal** Anticipated Major Comment, a reporting-level finding becomes a **Fixable** Anticipated Minor Comment, and each is tagged with the closest category letter (A–K). These probes **complement** categories A–K above; they do not replace them. (The modules are vendored byte-identical from `/peer-review`; do not edit one copy only — run `python3 scripts/check_domain_probe_sync.py --sync`.)
 

package/skills/self-review/references/domain-probes/qualitative_research.md

@@ -0,0 +1,50 @@
+<!-- Domain probe module — shared, vendored BYTE-IDENTICAL by /peer-review and /self-review.
+     Severity words below (MAJOR / MINOR / major / minor) denote finding severity, NOT a journal
+     recommendation. Each consuming skill maps findings to its own output:
+       - peer-review: Major / Minor comments + Confidential Comments to the Editor; a
+         reflexivity / analysis-transparency / over-claim flaw is placed as Major #1.
+       - self-review: Anticipated Major / Minor Comments (Fatal / Fixable) mapped to category letters.
+     Do NOT edit one copy only — run `python3 scripts/check_domain_probe_sync.py --sync`. -->
+
+# Qualitative research probes (QL1–QL8)
+
+An 8-probe checklist for **qualitative studies** — in-depth interviews, focus groups, observation/ethnography, document analysis, grounded theory, phenomenology, narrative research. These probes complement (do not replace) the generic Phase 2 checklist and the qualitative reporting standards — **COREQ** (interviews/focus groups; Tong et al. 2007) and **SRQR** (all qualitative approaches; O'Brien et al. 2014). They target what makes qualitative rigour distinct from quantitative validity: researcher **reflexivity**, a transparent **analysis** process, **trustworthiness** (credibility/dependability/confirmability/transferability) rather than statistical validity, and findings **grounded in quoted data** — and they guard the most common mis-calibration on both sides: applying quantitative yardsticks (sample-size power, statistical generalizability, p-values) to qualitative work. QL2 (reflexivity), QL5 (analysis transparency), and QL6 (trustworthiness, not statistical validity) are the highest-yield; run them first.
+
+**QL1 — Approach/paradigm fit and research question**:
+- Is a **qualitative** approach justified for the question — exploring meaning, experience, process, or context, rather than measuring frequency/effect (which would be a quantitative design)?
+- Is a **named approach** (grounded theory, phenomenology, ethnography, case study, narrative) and guiding paradigm stated **with a rationale**, rather than an unspecified "qualitative study" / "thematic analysis" with no methodological orientation?
+- A question that is really quantitative (prevalence/effect) answered with a few interviews, or no named methodological orientation behind the analysis → MAJOR (method–question mismatch) / MINOR (unnamed approach).
+
+**QL2 — Reflexivity and researcher positioning**:
+- Are the **researcher's characteristics** reported — who collected the data, their credentials/role, experience/training, and **prior relationship to participants** — and is there reflexive consideration of how their assumptions/position may have shaped data collection and interpretation?
+- Reflexivity is a core qualitative-rigour requirement (COREQ Domain 1; SRQR item 6) and the **single most-omitted** element.
+- An interview/focus-group study with no reflexivity / no statement of who interviewed and their relationship to participants → MAJOR (or MINOR if partially addressed).
+
+**QL3 — Sampling logic and adequacy (purposive; information power / saturation)**:
+- Is the **sampling strategy** stated and justified — **purposive / theoretical / maximum-variation** logic appropriate to the question, not an unexplained convenience sample — and is there an argument for **when sampling stopped** (data **saturation** or information power)?
+- A **small sample is not a flaw** in qualitative work; the flaw is an *unjustified* sample with no purposive rationale and no saturation/information-power discussion.
+- Convenience sample presented with no rationale, or no account of sampling adequacy/saturation behind broad thematic claims → MINOR / MAJOR per centrality.
+
+**QL4 — Data-collection rigour**:
+- Are the **data-collection methods** described in enough detail to judge them — the **interview/topic guide** (and whether it was piloted/iterated), the **setting**, **recording and transcription**, **field notes**, and interview/focus-group **duration**?
+- Thinly reported data collection (no guide, unclear recording/transcription, no setting) that undercuts interpretability → MINOR.
+
+**QL5 — Analysis transparency and audit trail**:
+- Is the **analysis process** transparent — how many **coders**, the **coding framework/tree**, whether themes were **derived inductively or applied a priori**, any **software**, and an **audit trail**?
+- "Themes **emerged** from the data" with no described coding/analytic process is a black box.
+- An analysis with no described coding process / no audit trail behind the reported themes → MAJOR (analysis not reproducible/auditable).
+
+**QL6 — Trustworthiness, NOT statistical validity (the calibration trap)**:
+- Are **trustworthiness** techniques reported and matched to the four criteria — **credibility** (member checking, triangulation, prolonged engagement), **dependability** (audit trail), **confirmability** (reflexivity), **transferability** (thick description) — rather than quantitative "reliability/validity"?
+- The trap is bidirectional: (a) a **reviewer** must **not** demand a power calculation, a "representative" sample, statistical generalizability, or treat inter-coder κ as the sole truth — these are quantitative yardsticks inappropriate to qualitative work; (b) **authors** must **not** claim statistical generalizability or dress qualitative findings in quantitative certainty.
+- Missing trustworthiness strategies entirely, or quantitative-validity language misapplied (by either side) → MAJOR / MINOR per how load-bearing it is.
+
+**QL7 — Findings grounded in data (quotations, thick description, deviant cases)**:
+- Are the themes **substantiated by participant quotations / excerpts** (with participant identifiers), with enough **thick description** to let the reader judge the interpretation, and is there **consistency between the data and the findings**?
+- Are **negative / deviant cases** and minor themes considered, not just confirmatory exemplars?
+- Asserted themes with no quoted evidence, or interpretation not traceable to the data → MAJOR; cherry-picked confirmatory quotes with no deviant-case consideration → MINOR.
+
+**QL8 — Ethics, interpretive scope, and reporting standard**:
+- Are **ethics** reported (IRB approval/consent; confidentiality and de-identification of identifiable narrative quotes), and does interpretation **stay within what qualitative data support** — no **causal, effectiveness, prevalence, or population-level** claims, and no over-generalisation beyond the studied context (**transferability**, not generalizability)?
+- Is the study mapped to the appropriate reporting standard — **COREQ** (interviews/focus groups) or **SRQR** (broader qualitative)?
+- Causal/quantitative/population over-claiming from qualitative data, missing consent/de-identification for identifiable quotes, or no reporting-standard mapping → MAJOR (over-claim / ethics) / MINOR (reporting).

package/skills/self-review/references/domain-probes/scoping_review.md

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+<!-- Domain probe module — shared, vendored BYTE-IDENTICAL by /peer-review and /self-review.
+     Severity words below (MAJOR / MINOR / major / minor) denote finding severity, NOT a journal
+     recommendation. Each consuming skill maps findings to its own output:
+       - peer-review: Major / Minor comments + Confidential Comments to the Editor; a
+         scoping-fit / mapping-not-pooling / over-claim flaw is placed as Major #1.
+       - self-review: Anticipated Major / Minor Comments (Fatal / Fixable) mapped to category letters.
+     Do NOT edit one copy only — run `python3 scripts/check_domain_probe_sync.py --sync`. -->
+
+# Scoping review probes (SC1–SC8)
+
+An 8-probe checklist for **scoping reviews** — reviews that *map* the breadth of evidence on a topic, clarify concepts/definitions, and identify gaps. These probes complement (do not replace) the generic Phase 2 checklist and the **PRISMA-ScR** reporting items (Tricco et al. *Ann Intern Med* 2018), and assume the JBI / Arksey & O'Malley / Levac conduct frameworks. They target what is specific to a scoping design: whether the question genuinely suits a *mapping* (not an effectiveness/accuracy) review, whether the conduct uses scoping methods (PCC framing, charting, optional appraisal), and — the single most common over-reach — whether the synthesis stays a **map** rather than drifting into pooled effect estimates and definitive effectiveness claims. SC1 (scoping fit), SC6 (critical-appraisal calibration — the asymmetric trap), and SC7 (mapping not pooling) are the highest-yield; run them first.
+
+**SC1 — Scoping fit and objectives (mapping intent, PCC framing)**:
+- Is the review genuinely a **scoping** question — mapping the extent/range/nature of evidence, clarifying concepts, or identifying gaps — rather than a focused **effectiveness/accuracy** question that should be a systematic review (PRISMA 2020 / PRISMA-DTA)?
+- Are objectives framed with **Population, Concept, Context (PCC)** or an equivalent mapping structure, not a PICO effectiveness/comparison frame with a defined outcome estimate?
+- A focused "is X effective / is test Y accurate?" question run as a scoping review (to sidestep risk-of-bias and synthesis), or a scoping review whose objectives are really an SR's → MAJOR (reframe as a systematic review, or restate the objective as mapping).
+
+**SC2 — Protocol and registration (a-priori; OSF, not PROSPERO)**:
+- Is an **a-priori protocol** available (OSF / Figshare / a published protocol), with the question, eligibility, and charting plan pre-specified?
+- Note that **PROSPERO does not register scoping reviews** — a manuscript claiming PROSPERO registration for a scoping review is in error and should cite the correct registry/repository.
+- No protocol for a scoping review of any size, or a wrong-registry claim → MINOR (protocol absent → MAJOR if the charting plan appears post-hoc / outcome-driven).
+
+**SC3 — Eligibility by concept; sources of evidence (not only studies)**:
+- Are eligibility criteria specified by **PCC plus source characteristics** (years, language, publication status, source/evidence types) **with a rationale**?
+- Does the review admit the **heterogeneous "sources of evidence"** a scoping review is meant to map (quantitative and qualitative research, grey literature, policy/guidance, expert opinion) where relevant, rather than silently restricting to a narrow study type and presenting it as a comprehensive map?
+- Over-restrictive, study-only eligibility presented as a comprehensive map of the field, or eligibility with no rationale → MINOR.
+
+**SC4 — Search comprehensiveness and reproducibility**:
+- Is the **full search strategy for at least one database reproducible** (terms, limits), the date of the most recent search stated, and the information sources appropriate to a *mapping* aim — typically **multiple databases plus grey literature** rather than a single narrow source?
+- Given that scoping reviews aim for breadth, is the search broad enough to support a "map the field" claim?
+- A comprehensiveness/mapping claim resting on one narrow database with no grey-literature or no reproducible strategy → MAJOR / MINOR per the strength of the claim.
+
+**SC5 — Selection and data charting**:
+- Is the **two-stage selection** process (title/abstract then full-text) described, and the **data-charting** process specified — a calibrated/team-tested charting form, whether charting was **independent / in duplicate**, and any **iterative refinement** of the form (charting is iterative in scoping reviews)?
+- Is the correct terminology used (**charting**, not extraction; **sources of evidence**, not only studies)?
+- No charting process described, or single-reviewer charting with no calibration behind a large map → MINOR (or MAJOR if selection itself is undocumented).
+
+**SC6 — Critical appraisal is OPTIONAL (the asymmetric trap)**:
+- Critical appraisal / risk-of-bias is **not required** in a scoping review (PRISMA-ScR items 12/16 are optional). A reviewer must **not** flag "no risk-of-bias assessment" as a deficiency for a scoping review, and authors need not appraise.
+- Conversely, if appraisal **was** done, is the rationale, method, and use reported (items 12/16)? And does the review avoid claiming **certainty grading (GRADE) or quality-weighted conclusions** it never derived?
+- The trap is bidirectional: (a) demanding RoB of a scoping review is a mis-calibrated review comment; (b) a scoping review asserting GRADE-style certainty or "high-quality evidence shows…" without having appraised is over-claiming → MINOR/MAJOR per how load-bearing the certainty claim is.
+
+**SC7 — Synthesis is mapping, NOT pooling (no effect estimates)**:
+- Are results presented as a **map/characterisation** — counts, categories, concept/theme groupings, evidence-gap maps, charting tables — rather than a **meta-analytic pooled estimate** (pooled OR/RR/HR/AUC, summary sensitivity/specificity)?
+- A scoping review should **not** compute or headline a pooled effect/accuracy estimate; doing so is an estimand/scope mismatch (the design carries no risk-of-bias or synthesis machinery to support an effect claim).
+- A pooled effect/accuracy estimate, forest plot of effects, or quantitative effectiveness synthesis presented from a scoping review → MAJOR (move to a systematic review/meta-analysis, or relabel the figure as a descriptive frequency map).
+
+**SC8 — Interpretation, gaps, terminology, and reporting**:
+- Are conclusions matched to a **descriptive map** — what evidence exists, where the gaps are, whether a future systematic review/primary study is warranted — and free of **clinical-practice recommendations** or definitive effectiveness/accuracy claims a map cannot support (cf. the scope-coherence discipline)?
+- Is a **PRISMA-ScR flow diagram** present, the study correctly labelled a scoping review (not conflated with a systematic review), and the report mapped to **PRISMA-ScR**?
+- A practice recommendation or definitive effectiveness/accuracy conclusion drawn from a scoping map, mislabelling the study as a "systematic review," or missing PRISMA-ScR reporting → MAJOR (over-claim) / MINOR (reporting), per centrality.