medsci-skills 5.1.0 → 5.3.0

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 — 38 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 — 39 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 / **38 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 / **39 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 / 38 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 / 39 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 / 38 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 / 39 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 / 38 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 / 39 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 / 38 guidelines; analysis-integrity detectors **28 → 30**, domain probes 11 → 12:
+**v4.6** is a maintainability, governance, and review-depth release — still 45 skills / 39 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 / 38 guidelines); analysis-integrity detectors **27 → 28**:
+**v4.5** deepens the review + submission surface with no new skill or reporting-guideline count (still 45 skills / 39 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 / 38 guidelines / 27 detectors):
+**v4.4** adds reviewer/analysis depth with no new skill or reporting-guideline count (still 45 skills / 39 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 / 38 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 / 39 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 / 38 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 / 39 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 38 reporting guidelines and risk of bias tools (STROBE, STROBE-MR, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, 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 39 reporting guidelines and risk of bias tools (STROBE, STROBE-MR, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, 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. |
 | **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).
 
-### 38 Reporting Guidelines & RoB Tools Built-in
-`check-reporting` includes bundled checklists for 38 guidelines and risk-of-bias tools: STROBE, STROBE-MR, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, 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.
+### 39 Reporting Guidelines & RoB Tools Built-in
+`check-reporting` includes bundled checklists for 39 guidelines and risk-of-bias tools: STROBE, STROBE-MR, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, 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.
 
 ### 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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       "sha256": "ba44a3b38b4128fa713555c8b332f211e9087e6bc016d80af4c3074c3ca6ef8e"
     },
+    {
+      "path": "skills/model-evaluation/scripts/metric_reporting_challenge/fixture/det_good_wrapped.md",
+      "size": 285,
+      "sha256": "0c1f5ed5167969870602106e7a7c9a2ae53e3a3ddea5fa280c3beb6bf470c454"
+    },
+    {
+      "path": "skills/model-evaluation/scripts/metric_reporting_challenge/fixture/det_no_iou.md",
+      "size": 224,
+      "sha256": "08227fbe46829b8eecdfe15680e1bb32087f1e6c5a353b3df6055c67d8300fc0"
+    },
     {
       "path": "skills/model-evaluation/scripts/metric_reporting_challenge/fixture/seg_bad.md",
       "size": 119,
@@ -2663,8 +2693,8 @@
     },
     {
       "path": "skills/model-evaluation/scripts/metric_reporting_challenge/verify.sh",
-      "size": 1235,
-      "sha256": "f819d1333a7206db6383ccbd41c6eadae015004e61ae335e67a3334936c58cc8"
+      "size": 1663,
+      "sha256": "4aa6db49d3552f01a54ddb70484df5d214806d805b836b24beda81d9aca32bd6"
     },
     {
       "path": "skills/model-evaluation/skill.yml",
@@ -2718,8 +2748,13 @@
     },
     {
       "path": "skills/model-validation/SKILL.md",
-      "size": 9347,
-      "sha256": "ecd48672a03923bf1ace63528fd2dbcf138cd880103cc8c40345b3857d66ad1c"
+      "size": 9810,
+      "sha256": "1a75a5a1f21f5a8778d0b77db2e99574bf37edda2a291d8dde6aafea4a207ff0"
+    },
+    {
+      "path": "skills/model-validation/references/validation_design.md",
+      "size": 11427,
+      "sha256": "16d43b688ea63745174c7ca8fafd78a7342b26c34ad1e10e1fdbc117cceafb2e"
     },
     {
       "path": "skills/model-validation/scripts/check_split_leakage.py",
@@ -2769,7 +2804,7 @@
     {
       "path": "skills/orchestrate/SKILL.md",
       "size": 35203,
-      "sha256": "5adf3a50cee42451029b0d4ba32a2f74b2e81bd30e5220ebd0e36a9f538a40b7"
+      "sha256": "59b22bc48503a2b597bc4cb10dacf4e31e196c8f9e0e2e367752bb793425ab02"
     },
     {
       "path": "skills/orchestrate/references/dialogue_nodes.md",
@@ -2793,8 +2828,8 @@
     },
     {
       "path": "skills/peer-review/SKILL.md",
-      "size": 58493,
-      "sha256": "057c39cd131c49eeb1949560a0d510f176a012431a0c8d36dd803061f98e0629"
+      "size": 60277,
+      "sha256": "168a9aac2bb0c00707c85c75f4c56bfdc90b9e705ceb30d7e1e331dfbf9f51e6"
     },
     {
       "path": "skills/peer-review/references/aczel_2021_reviewer2_patterns.md",
@@ -2826,6 +2861,11 @@
       "size": 7665,
       "sha256": "83f2c5116317f96ba564f459f2b679489cc2ad8d2a3ec8078345ce1390680eb2"
     },
+    {
+      "path": "skills/peer-review/references/domain-probes/health_economic_evaluation.md",
+      "size": 8393,
+      "sha256": "b322a9a6ae2439c1dc97f6a750572eecb3ce1481c139516665a55c9d571dfe8e"
+    },
     {
       "path": "skills/peer-review/references/domain-probes/image_synthesis.md",
       "size": 6295,
@@ -3333,8 +3373,8 @@
     },
     {
       "path": "skills/self-review/SKILL.md",
-      "size": 94657,
-      "sha256": "14c982c492d6305c238737366f0996415133fe02ff9aaad7e2c2207d78d260a2"
+      "size": 94894,
+      "sha256": "4145ec34a171e5783205bd2f11b62709302e1f86d6761b4cd9d545da492cbc75"
     },
     {
       "path": "skills/self-review/references/domain-probes/ai_overclaiming.md",
@@ -3361,6 +3401,11 @@
       "size": 7665,
       "sha256": "83f2c5116317f96ba564f459f2b679489cc2ad8d2a3ec8078345ce1390680eb2"
     },
+    {
+      "path": "skills/self-review/references/domain-probes/health_economic_evaluation.md",
+      "size": 8393,
+      "sha256": "b322a9a6ae2439c1dc97f6a750572eecb3ce1481c139516665a55c9d571dfe8e"
+    },
     {
       "path": "skills/self-review/references/domain-probes/image_synthesis.md",
       "size": 6295,

package/metadata/distribution_manifest.json

@@ -1,6 +1,6 @@
 {
   "schema_version": 1,
-  "version": "5.1.0",
+  "version": "5.3.0",
   "owned_skills": [
     "academic-aio",
     "add-journal",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "medsci-skills",
-  "version": "5.1.0",
+  "version": "5.3.0",
   "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/analyze-stats/SKILL.md

@@ -456,6 +456,15 @@ tbl %>% as_flex_table() %>% flextable::save_as_docx(path = "table.docx")
 - Present a **network plot** (node ∝ sample size, edge ∝ #trials); report global **τ²**; **ranking (SUCRA/P-score) is not a superiority test** — report it with the league table, intervals, and certainty
 - Certainty **per estimate** via **CINeMA / GRADE-NMA** (downgrade indirect-only); component NMA assumes **additivity** (state/check it). Report against **PRISMA-NMA**; risk of bias via **RoB-NMA**. Review-side probes: NM1–NM8 in `network_meta_analysis.md`
 
+### Health Economic Evaluation
+
+- **Guide**: Load `analysis_guides/health_economic_evaluation.md` before generating code
+- For cost-effectiveness (CEA), cost-utility (CUA, QALY), cost-benefit (CBA), cost-minimisation, or budget-impact analyses; trial-based or decision-model-based (decision tree, **Markov/state-transition**, discrete-event simulation)
+- Compute **incremental cost ΔC, incremental effect ΔE, and the ICER = ΔC/ΔE**; with ≥3 options remove **dominated / extended-dominated** strategies before sequential ICERs; prefer **net benefit (INMB = λΔE − ΔC)** for regression/probabilistic summaries
+- State and justify the **perspective, time horizon (lifetime for chronic disease), discount rate (both costs and outcomes), currency + price year**; QALYs from a named preference-based instrument + value set
+- **Uncertainty is the analytic core**: one-way / **tornado** for drivers, **probabilistic sensitivity analysis (PSA)** with justified parameter distributions (beta for probabilities/utilities, gamma/log-normal for costs) → **cost-effectiveness plane + CEAC**; scenario analyses for structural choices
+- R `heemod` / `dampack` / `hesim` / `BCEA` (state-transition + PSA + CEAC + EVPI), `flexsurv` for survival extrapolation. Report against **CHEERS 2022**; make the "cost-effective" conclusion conditional on a stated willingness-to-pay threshold. Review-side probes: HE1–HE8 in `health_economic_evaluation.md`
+
 ### Survey/Likert
 
 - Descriptive: median, IQR, frequency distribution per item

package/skills/analyze-stats/references/analysis_guides/health_economic_evaluation.md

@@ -0,0 +1,79 @@
+# Health Economic Evaluation Analysis Guide
+
+Comparing the **costs and consequences** of two or more interventions to inform a coverage,
+adoption, or treatment decision. The headline — an **incremental cost-effectiveness ratio (ICER)**
+— is arithmetically trivial; what fails review is **the structural choices behind it** (perspective,
+time horizon, discounting, the effectiveness source, the cost basis, the model, and the propagation
+of uncertainty). So the analysis is mostly the costing, the model, and the sensitivity suite, not the
+ratio. This is the analysis-side companion to review probes **HE1–HE8** in
+`health_economic_evaluation.md` and the **CHEERS 2022** reporting checklist.
+
+---
+
+## When to Use
+
+- A comparative decision question (adopt / reimburse / treat) where both **cost** and **health
+  outcome** differ between options: cost-effectiveness (CEA, natural units — life-years, events
+  avoided), **cost-utility** (CUA, QALYs — the default for reimbursement), cost-benefit (CBA,
+  monetised outcomes), cost-minimisation (only when outcomes are demonstrably equivalent), or
+  **budget-impact** (affordability, distinct from cost-effectiveness).
+- **Trial-based** (within-RCT patient-level costs and outcomes) or **decision-model-based** (decision
+  tree for short horizons; **Markov / state-transition** or **discrete-event simulation** when timing
+  and recurrence matter; lifetime horizons).
+- NOT for: a costing/burden-of-illness description with no comparator (not an economic *evaluation*);
+  asserting "cost-effective" from a point ICER with no uncertainty analysis; cost-minimisation when a
+  non-inferiority outcome claim has not actually been established.
+
+## Core quantities
+
+- **Incremental cost** ΔC and **incremental effect** ΔE between an intervention and its comparator;
+  the **ICER = ΔC / ΔE** (e.g. cost per QALY gained). With ≥3 options, rank by cost, remove
+  **dominated** (more costly, less effective) and **extended-dominated** strategies, then compute
+  ICERs sequentially along the efficient frontier.
+- **Net benefit** at a willingness-to-pay threshold λ: **INMB = λ·ΔE − ΔC** (monetary) or
+  **INHB = ΔE − ΔC/λ** (health). Net benefit is linear and avoids the ICER's quadrant ambiguity, so
+  it is preferred for regression and for probabilistic summaries.
+- **QALYs** = time × **utility** (preference-based, 0=dead, 1=full health) from a named instrument
+  (EQ-5D-3L/5L, SF-6D, HUI) and a stated **value set/tariff** for the relevant country.
+
+## The structural choices (state and justify each)
+
+- **Perspective** — healthcare-system/payer vs **societal**; determines which costs count (societal
+  adds productivity and informal-care costs). Apply it consistently.
+- **Time horizon** — long enough to capture all differential costs and effects; **lifetime** for
+  chronic disease or interventions with lasting effects. Extrapolation beyond trial data must be
+  modelled explicitly (e.g. parametric survival extrapolation) and tested.
+- **Discounting** — apply the jurisdiction's reference-case rate (commonly ~3% or 3.5%) to **both
+  costs and outcomes**; sensitivity at alternative rates.
+- **Costing** — report **resource quantities and unit costs separately**; state **currency, price
+  year**, and inflation/currency conversion. Match cost categories to the perspective.
+- **Model** — justify structure against natural history; state cycle length and half-cycle
+  correction (Markov); validate (internal/face/external/predictive); test **structural** uncertainty
+  via scenario analysis.
+
+## Uncertainty (the analytic core)
+
+- **Deterministic** — one-way and **tornado** diagrams to find the drivers; multi-way / scenario
+  analyses for methodological and structural choices (discount rate, time horizon, alternative
+  model structures).
+- **Probabilistic (PSA)** — assign each uncertain parameter a **distribution** (beta for
+  probabilities and utilities; gamma or log-normal for costs; Dirichlet for transition-probability
+  sets), propagate by **Monte Carlo**, and report the **cost-effectiveness plane** (the cloud of ΔC,
+  ΔE draws) and the **cost-effectiveness acceptability curve (CEAC)** — P(cost-effective) across a
+  range of λ. Report results as net benefit at the relevant threshold with its uncertainty, not a
+  bare point ICER.
+- **Value of information** (EVPI/EVPPI) is an optional extension quantifying the expected cost of
+  current decision uncertainty / the priority parameters for further research.
+
+## Reporting & tools
+
+- Report to **CHEERS 2022** (28 items): perspective, horizon, discount rate, currency/price year,
+  model rationale, study parameters with distributions, disaggregated costs/outcomes, the ICER,
+  and the uncertainty analysis (plane + CEAC). State the **willingness-to-pay threshold** and make
+  the "cost-effective" conclusion conditional on it and on the CEAC probability.
+- Tools: R — `heemod` / `dampack` / `hesim` (state-transition + PSA + CEAC), `BCEA` (Bayesian
+  cost-effectiveness, CEAC/EVPI), `survival`/`flexsurv` (survival extrapolation); also TreeAge, or
+  spreadsheet models with a documented PSA. Make the model or the health-economic analysis plan
+  available for scrutiny.
+- Companion review probes: **HE1–HE8** (`peer-review`/`self-review`
+  `references/domain-probes/health_economic_evaluation.md`).

package/skills/check-reporting/SKILL.md

@@ -1,7 +1,7 @@
 ---
 name: check-reporting
-description: Check manuscript compliance with medical research reporting guidelines. Supports 38 guidelines including STROBE, STROBE-MR, 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, 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, risk of bias, compliance check, LLM accuracy, large language model, clinical deployment
+description: Check manuscript compliance with medical research reporting guidelines. Supports 39 guidelines including STROBE, STROBE-MR, 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, 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, risk of bias, compliance check, LLM accuracy, large language model, clinical deployment
 tools: Read, Write, Edit, Bash, Grep, Glob
 model: inherit
 ---
@@ -29,6 +29,7 @@ compliance report suitable for journal submission.
   - `TRIPOD_AI.md` -- prediction models with AI/ML (CC BY 4.0, Collins et al. BMJ 2024)
   - `TRIPOD_LLM.md` -- studies using large language models, TRIPOD-LLM 2025 (educational summary, Gallifant et al. Nat Med 2025)
   - `PGS_RS.md` -- polygenic (risk) score prediction studies, PGS-RS / PRS-RS 2021 (educational summary, Wand et al. Nature 2021)
+  - `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)
   - `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)
@@ -88,6 +89,7 @@ user specification.
 |------------|------------------|--------------|
 | Observational study | STROBE | -- |
 | Mendelian randomization study | STROBE-MR (base STROBE + MR extension) | -- |
+| Health economic evaluation (cost-effectiveness / cost-utility / cost-benefit / budget-impact) | CHEERS 2022 | -- |
 | 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/CHEERS_2022.md

@@ -0,0 +1,81 @@
+# CHEERS 2022 Checklist
+
+**Consolidated Health Economic Evaluation Reporting Standards 2022**
+Version: CHEERS 2022 (28 items; replaces CHEERS 2013).
+Source: Husereau D, Drummond M, Augustovski F, et al. *BMJ* 2022;376:e067975 (the CHEERS 2022 statement), co-published simultaneously across BMJ, *Value in Health*, *PharmacoEconomics*, *Int J Technol Assess Health Care* and others. CC BY 4.0. https://www.equator-network.org/reporting-guidelines/cheers/ · ISPOR CHEERS Task Force.
+
+Apply when the manuscript is a **health economic evaluation** — a comparative analysis of costs and consequences of two or more courses of action: cost-effectiveness (CEA), cost-utility (CUA), cost-benefit (CBA), or cost-minimisation analysis, whether trial-based or decision-model-based (decision tree, Markov/state-transition, discrete-event simulation), including budget-impact and HTA submissions. For the design/validity review of the same study, pair with the HE1–HE8 domain probes in `peer-review` / `self-review` `references/domain-probes/health_economic_evaluation.md`; for the analysis, with `analyze-stats` `references/analysis_guides/health_economic_evaluation.md`.
+
+## Checklist Items (28 items)
+
+### Title
+
+| # | Item | Description |
+|---|------|-------------|
+| 1 | Title | Identify the study as an economic evaluation and specify the interventions being compared. |
+
+### Abstract
+
+| # | Item | Description |
+|---|------|-------------|
+| 2 | Abstract | Provide a structured summary that highlights context, key methods, results, and alternative analyses. |
+
+### Introduction
+
+| # | Item | Description |
+|---|------|-------------|
+| 3 | Background and objectives | Give the context for the study, the study question, and its practical relevance for decision making in policy or practice. |
+
+### Methods
+
+| # | Item | Description |
+|---|------|-------------|
+| 4 | Health economic analysis plan | Indicate whether a health economic analysis plan was developed and where available. |
+| 5 | Study population | Describe characteristics of the study population (such as age range, demographics, socioeconomic, or clinical characteristics). |
+| 6 | Setting and location | Provide relevant contextual information that may influence findings. |
+| 7 | Comparators | Describe the interventions or strategies being compared and why chosen. |
+| 8 | Perspective | State the perspective(s) adopted by the study and why chosen. |
+| 9 | Time horizon | State the time horizon for the study and why appropriate. |
+| 10 | Discount rate | Report the discount rate(s) and reason chosen. |
+| 11 | Selection of outcomes | Describe what outcomes were used as the measure(s) of benefit(s) and harm(s). |
+| 12 | Measurement of outcomes | Describe how outcomes used to capture benefit(s) and harm(s) were measured. |
+| 13 | Valuation of outcomes | Describe the population and methods used to measure and value outcomes. |
+| 14 | Measurement and valuation of resources and costs | Describe how costs were valued. |
+| 15 | Currency, price date, and conversion | Report the dates of the estimated resource quantities and unit costs, plus the currency and year of conversion. |
+| 16 | Rationale and description of model | If modelling is used, describe in detail and why used. Report whether the model is publicly available and where. |
+| 17 | Analytics and assumptions | Describe any methods for analysing or statistically transforming data, any extrapolation methods, and approaches for validating any model used. |
+| 18 | Characterising heterogeneity | Describe any methods used for estimating how the results of the study vary for subgroups. |
+| 19 | Characterising distributional effects | Describe how impacts are distributed across different individuals or whether adjustments were made to reflect priority populations. |
+| 20 | Characterising uncertainty | Describe methods to characterise any sources of uncertainty in the analysis. |
+| 21 | Approach to engagement with patients and others affected by the study | Describe any approaches to engage patients or service recipients, the general public, communities, or stakeholders (such as clinicians or payers) in the design of the study. |
+
+### Results
+
+| # | Item | Description |
+|---|------|-------------|
+| 22 | Study parameters | Report all analytic inputs (such as values, ranges, references) including uncertainty or distributional assumptions. |
+| 23 | Summary of main results | Report the mean values for the main categories of costs and outcomes of interest and summarise them in the most appropriate overall measure (e.g. the incremental cost-effectiveness ratio, ICER). |
+| 24 | Effect of uncertainty | Describe how uncertainty about analytic judgments, inputs, or projections affect findings. Report the effect of choice of discount rate and time horizon, if relevant. |
+| 25 | Effect of engagement with patients and others affected by the study | Report on any difference patient/service recipient, general public, community, or stakeholder involvement made to the approach or findings of the study. |
+
+### Discussion
+
+| # | Item | Description |
+|---|------|-------------|
+| 26 | Study findings, limitations, generalisability, and current knowledge | Report key findings, limitations, ethical or equity considerations, and how these could affect patients, policy, or practice. |
+
+### Other relevant information
+
+| # | Item | Description |
+|---|------|-------------|
+| 27 | Source of funding | Describe how the study was funded and the role of the funder in the identification, design, conduct, and reporting of the analysis. Describe other non-monetary sources of support. |
+| 28 | Conflicts of interest | Describe any potential for conflict of interest among study contributors in accordance with journal policy. In the absence of a journal policy, we recommend authors comply with International Committee of Medical Journal Editors (ICMJE) recommendations. |
+
+---
+
+## Notes for Assessors
+
+- **Highest-yield items** (where economic evaluations most often fail review): **8** (perspective stated and consistent with the costs counted — productivity/informal-care costs belong only to a societal perspective), **9** (time horizon long enough to capture all relevant differential costs and effects — a lifetime horizon for a chronic condition; a truncated horizon flatters whichever arm has early benefit), **10** (both costs *and* outcomes discounted at a stated, justified rate for any horizon beyond ~1 year), **15** (currency *and* price year stated, with the conversion method for multi-source costs), **16–17** (model type/structure justified and validated; structural assumptions and extrapolation declared), and **20 / 24** (uncertainty characterised by *probabilistic* sensitivity analysis — a cost-effectiveness acceptability curve / plane — not a single deterministic ICER). An evaluation that reports a point-estimate ICER with no probabilistic sensitivity analysis is non-compliant on items 20/24.
+- **CHEERS 2022 replaced CHEERS 2013**; cite the 2022 statement (do not cite the 2013 version as current). CHEERS 2022 added explicit items on the analysis plan (4), distributional/equity effects (19), and patient/stakeholder engagement (21/25); the engagement items are reported as "not done" rather than omitted when no engagement occurred.
+- ICER interpretation is not a CHEERS item per se but follows from items 23–24: incremental costs and effects must be reported (not just the ratio), dominance/extended dominance resolved, and the ICER interpreted against a *stated, justified* cost-effectiveness threshold (willingness-to-pay) rather than an arbitrary one. The HE1–HE8 design probes cover these judgments.
+- This checklist was authored as a faithful summary of the CHEERS 2022 statement (Husereau D, et al. *BMJ* 2022;376:e067975, **CC BY 4.0** — the item list and Explanation & Elaboration are reusable/adaptable with attribution) for item-by-item assessment; verify against the published statement and its Explanation & Elaboration for full item wording. Verified 2026-06-29.

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

@@ -80,6 +80,8 @@ ALIAS_TO_STEM = {
     "strobemr": "STROBE_MR",
     "pgsrs": "PGS_RS",
     "prsrs": "PGS_RS",
+    "cheers": "CHEERS_2022",
+    "cheers2022": "CHEERS_2022",
 }
 
 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`
-> (38 reporting guidelines). Each row tells you which figures the guideline
+> (39 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.
 
@@ -95,7 +95,7 @@ flags them:
 
 ## Cross-references
 
-- `/check-reporting` skill — supports all 38 guidelines, item-level audit
+- `/check-reporting` skill — supports all 39 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/mllm-eval/SKILL.md

@@ -106,3 +106,11 @@ mllm-eval (this skill: harness design + completeness gate, model-agnostic)
   ├─ write-paper + check-reporting (TRIPOD-LLM / MI-CLEAR-LLM)
   └─ self-review / peer-review (ME0–ME8 reviewer probe)
 ```
+
+## Reference Files
+
+- `${CLAUDE_SKILL_DIR}/references/evaluation_axes.md` — the *why* behind the ME2–ME7 axes:
+  clinical-efficacy metrics beyond n-gram overlap (e.g. RadGraph-F1 / CheXbert-F1 vs BLEU/ROUGE),
+  faithfulness & hallucination, pretraining/benchmark contamination, prompt-sensitivity &
+  determinism, answer-matching, and the reader study — each mapped to its gate verdict. Load on
+  demand during Phases 2–4.