medsci-skills 5.18.0 → 5.20.0

package/README.md

@@ -4,7 +4,7 @@
 
 **55 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 — 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.*
+*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 — 46 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)
@@ -288,62 +288,66 @@ The E2E pipeline (`orchestrate --e2e`) produces everything up to `qc/`. The `sub
 
 ## What's New
 
-**v5.18** — reliability & workflow-integrity batch. A new deterministic **response-claim gate** for `/revise` and `/peer-review` (verifies a response letter's "we added / we now cite X" against the *revised manuscript body* — a claimed-but-absent edit is caught before it reaches a reviewer; **detectors 50 → 51**), a **reframe / headline-change survivor scan** (`--retired-term` / `--old-value`, finds stale framing or superseded values left in the body, supplement, and figure legends after a reframe), a pre-drafting **backbone full-text readiness gate** for `/write-paper` (the backbone article is *used*, not merely detected), a **skill-registry consistency validator** (`capabilities.yml` ⇄ `skill.yml`, CI-enforced), AI-tool **citation-framing** guidance for `/academic-aio`, and **Demo 4** (PneumoniaMNIST CNN, the model-engineering lane end to end). Additive and backward-compatible; **55 skills / 44 guidelines / 51 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.17.)
+**v5.20** — reviewer-arithmetic gates. Five deterministic `self-review` detectors promoted from a peer-review cycle, each recomputing what a manuscript already prints: `check_table_percentages` (an `n (%)` cell vs its column denominator), `check_nested_group_comparison` (a P value comparing an analysed subset against the parent cohort that **contains** it — nested, invalid), `check_reported_p_from_counts` (rebuilds each 2×2 row and recomputes Fisher / Pearson χ² ± Yates in **pure stdlib**, calibrating the family on rows that reproduce), `check_dta_denominators` (sensitivity/specificity denominators vs the reference-standard category counts, behind a matching grand total), and `check_paired_difference_estimator` (an odd-n integer-scale median cannot be non-integer; a zero-width CI; an unnamed estimator). Plus `/peer-review` request-type discipline (disclosure vs computation) and impossibility-claim verification. Additive and backward-compatible; **55 skills / 46 guidelines / 57 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.19.)
 
-**v5.17** — model-engineering produce-side depth, **completion**. Deployment safety + the final roadmap/candidate items: a new **`uncertainty-imaging`** skill + `check_uncertainty_reporting` gate (calibrated per-case uncertainty / OOD guard on a held-out set / abstention at a pre-specified target / calibration-under-shift — for a deployment-framed model), an **MLOps wiring reference** for `model-scaffold` (experiment tracking, config/data/environment versioning, CI-for-ML — pointing to W&B / MLflow / nnU-Net, reimplementing nothing), and an **`architecture-zoo` graph-neural-net family card** (GCN / GraphSAGE / GAT / GIN / BrainGNN for brain connectomes) that closes the last candidate gap. The six-item produce-side depth roadmap and its candidate list are now complete. Additive and backward-compatible; **55 skills / 44 guidelines / 50 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.16.)
+**v5.19** — reviewer-safety + reporting-checklist batch. A **PDF hidden-text / prompt-injection guard** for `/peer-review` — a PyMuPDF extractor plus a stdlib detector that catch a review-steering instruction hidden in a submitted PDF (white-on-white text, sub-visible fonts, off-page glyphs, invisible render mode, or a document-metadata field) before an LLM ingesting the text layer can be steered by it, and emit visible-only text to feed a model instead of the raw PDF; plus the **TARGET** (target-trial emulation; Cashin et al., *JAMA* 2025) and **REMARK** (prognostic tumour-marker; McShane et al.) reporting checklists. Additive and backward-compatible; **55 skills / 46 guidelines / 52 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.18.)
 
-**v5.16** — model-engineering produce-side depth, clinical fine-tuning focus (Items 3–4 of the [produce-side depth roadmap](docs/roadmap_model_engineering_depth.md)). A new **`radiomics-ml`** skill + `check_radiomics_ml` gate for the most common solo-doable clinical-ML workflow — radiomics / tabular features → any classical learner (LASSO / SVM / random forest / XGBoost / …) → a clinical outcome, no GPU — with a learner-agnostic nested-CV / calibration / stability gate; plus a **`model-scaffold` fine-tuning mode** (`--task finetune` + `--from-pretrained`) that adapts a pretrained backbone on collected clinical data with a frozen→unfrozen schedule, discriminative learning rates, and a pretrained-weight provenance record (`PRETRAINED.md` + a `PRETRAINED_PROVENANCE_MISSING` verdict on the existing `check_training_hygiene`, plus a MedSAM-adaptation + train-only diffusion-augmentation guide). Additive and backward-compatible; **54 skills / 44 guidelines / 49 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.15.)
+**v5.18** — reliability & workflow-integrity batch. A new deterministic **response-claim gate** for `/revise` and `/peer-review` (verifies a response letter's "we added / we now cite X" against the *revised manuscript body* — a claimed-but-absent edit is caught before it reaches a reviewer; **detectors 50 → 51**), a **reframe / headline-change survivor scan** (`--retired-term` / `--old-value`, finds stale framing or superseded values left in the body, supplement, and figure legends after a reframe), a pre-drafting **backbone full-text readiness gate** for `/write-paper` (the backbone article is *used*, not merely detected), a **skill-registry consistency validator** (`capabilities.yml` ⇄ `skill.yml`, CI-enforced), AI-tool **citation-framing** guidance for `/academic-aio`, and **Demo 4** (PneumoniaMNIST CNN, the model-engineering lane end to end). Additive and backward-compatible; **55 skills / 46 guidelines / 51 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.17.)
 
-**v5.15** — model-engineering produce-side depth. Two new skills that *produce* what the review lane previously only audited: **`preprocess-imaging`** (DICOM/NIfTI data prep + a `check_preprocessing_leakage` gate that extends the split-leakage moat upstream to the data stage) and **`explainability`** (Grad-CAM / saliency held to the reviewer bar — Adebayo sanity checks, quantitative localisation vs ground truth, attribution-not-validation framing, via `check_explainability_report`). Plus a by-stage skill index, multi-host README/About (Claude Code · Codex · Cursor · Copilot), copy-paste citation ergonomics, and a real-project precision fix. Additive and backward-compatible; **53 skills / 44 guidelines / 48 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.14.)
+**v5.17** — model-engineering produce-side depth, **completion**. Deployment safety + the final roadmap/candidate items: a new **`uncertainty-imaging`** skill + `check_uncertainty_reporting` gate (calibrated per-case uncertainty / OOD guard on a held-out set / abstention at a pre-specified target / calibration-under-shift — for a deployment-framed model), an **MLOps wiring reference** for `model-scaffold` (experiment tracking, config/data/environment versioning, CI-for-ML — pointing to W&B / MLflow / nnU-Net, reimplementing nothing), and an **`architecture-zoo` graph-neural-net family card** (GCN / GraphSAGE / GAT / GIN / BrainGNN for brain connectomes) that closes the last candidate gap. The six-item produce-side depth roadmap and its candidate list are now complete. Additive and backward-compatible; **55 skills / 46 guidelines / 50 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.16.)
 
-**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):
+**v5.16** — model-engineering produce-side depth, clinical fine-tuning focus (Items 3–4 of the [produce-side depth roadmap](docs/roadmap_model_engineering_depth.md)). A new **`radiomics-ml`** skill + `check_radiomics_ml` gate for the most common solo-doable clinical-ML workflow — radiomics / tabular features → any classical learner (LASSO / SVM / random forest / XGBoost / …) → a clinical outcome, no GPU — with a learner-agnostic nested-CV / calibration / stability gate; plus a **`model-scaffold` fine-tuning mode** (`--task finetune` + `--from-pretrained`) that adapts a pretrained backbone on collected clinical data with a frozen→unfrozen schedule, discriminative learning rates, and a pretrained-weight provenance record (`PRETRAINED.md` + a `PRETRAINED_PROVENANCE_MISSING` verdict on the existing `check_training_hygiene`, plus a MedSAM-adaptation + train-only diffusion-augmentation guide). Additive and backward-compatible; **54 skills / 46 guidelines / 49 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.15.)
+
+**v5.15** — model-engineering produce-side depth. Two new skills that *produce* what the review lane previously only audited: **`preprocess-imaging`** (DICOM/NIfTI data prep + a `check_preprocessing_leakage` gate that extends the split-leakage moat upstream to the data stage) and **`explainability`** (Grad-CAM / saliency held to the reviewer bar — Adebayo sanity checks, quantitative localisation vs ground truth, attribution-not-validation framing, via `check_explainability_report`). Plus a by-stage skill index, multi-host README/About (Claude Code · Codex · Cursor · Copilot), copy-paste citation ergonomics, and a real-project precision fix. Additive and backward-compatible; **53 skills / 46 guidelines / 48 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.14.)
+
+**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 / **46 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 / 44 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 / 46 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 / 44 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 / 46 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 / 44 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 / 46 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 / 44 guidelines; analysis-integrity detectors **28 → 30**, domain probes 11 → 12:
+**v4.6** is a maintainability, governance, and review-depth release — still 45 skills / 46 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 / 44 guidelines); analysis-integrity detectors **27 → 28**:
+**v4.5** deepens the review + submission surface with no new skill or reporting-guideline count (still 45 skills / 46 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 / 44 guidelines / 27 detectors):
+**v4.4** adds reviewer/analysis depth with no new skill or reporting-guideline count (still 45 skills / 46 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 / 44 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 / 46 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 / 44 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 / 46 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.
@@ -484,7 +488,7 @@ All 55 skills, grouped by where they fit in the clinical-manuscript and medical-
 | **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 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. |
+| **check-reporting** | Manuscript compliance audit against 46 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. |
@@ -657,8 +661,8 @@ 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).
 
-### 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.
+### 46 Reporting Guidelines & RoB Tools Built-in
+`check-reporting` includes bundled checklists for 46 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.

package/metadata/distribution_files.json

@@ -573,8 +573,8 @@
     },
     {
       "path": "skills/check-reporting/SKILL.md",
-      "size": 39223,
-      "sha256": "2dec1d994bb37fb6091f755ab51b2f890eca2b3299e18ca247ae3c7e45be86bb"
+      "size": 40628,
+      "sha256": "ad375c3cc13ab13172c9e65af2a4afbb25278d0c8b56461e079b10a086ae8bde"
     },
     {
       "path": "skills/check-reporting/references/LICENSES.md",
@@ -721,6 +721,11 @@
       "size": 6530,
       "sha256": "186000d9cd72e025ce483995735c05400450d9356f89f8f95b855d5815e925fa"
     },
+    {
+      "path": "skills/check-reporting/references/checklists/REMARK.md",
+      "size": 6020,
+      "sha256": "bfe8781663c33fc8a906d2d07f790f7237012ca100351bf2676e0d1f7ec89e11"
+    },
     {
       "path": "skills/check-reporting/references/checklists/ROBINS_E.md",
       "size": 8206,
@@ -796,6 +801,11 @@
       "size": 3516,
       "sha256": "118171e304491812709ee2311b1b968f8caac92e689431622a8fb81b2684e970"
     },
+    {
+      "path": "skills/check-reporting/references/checklists/TARGET.md",
+      "size": 7406,
+      "sha256": "0ddbbe10245d902a191a23a5832d24ada3515314e3b08ce562dd12200356f452"
+    },
     {
       "path": "skills/check-reporting/references/checklists/TRIPOD.md",
       "size": 8625,
@@ -813,8 +823,8 @@
     },
     {
       "path": "skills/check-reporting/references/critical_item_floor.md",
-      "size": 4565,
-      "sha256": "f955a0479da6474e43ece05361838f8db95923ec9f7dc56863afbf4cba66174d"
+      "size": 5323,
+      "sha256": "2c8aaf303bda8c5295ea13d3a41f3318ccbe65e053d23dcadc06f7fa5148e8fb"
     },
     {
       "path": "skills/check-reporting/references/genai_image_study_object_decision_aid.md",
@@ -833,8 +843,8 @@
     },
     {
       "path": "skills/check-reporting/scripts/check_checklist_exists.py",
-      "size": 6886,
-      "sha256": "c2ffe9761b4580e43a9ea7889b124a6591a6687c3cf939bc3ae1aad051e3040c"
+      "size": 7051,
+      "sha256": "0fdefb2deb36ba3774d7255aa020e10409484be10113cdc16779fc95786abaf3"
     },
     {
       "path": "skills/check-reporting/scripts/check_checklist_version.py",
@@ -2169,7 +2179,7 @@
     {
       "path": "skills/make-figures/references/reporting_guideline_figure_map.md",
       "size": 7149,
-      "sha256": "81f2eff4969e055d886976f4c9e26bf20f1946048c2b61563a7c95b7ebec1d86"
+      "sha256": "a5883b85fc772c0365137264ecc98c06cb9fb084f3cd2011d4c0f87324cf6fc1"
     },
     {
       "path": "skills/make-figures/references/visual_abstract_templates/european_radiology.pptx",
@@ -3014,7 +3024,7 @@
     {
       "path": "skills/orchestrate/SKILL.md",
       "size": 35203,
-      "sha256": "7197cb70e6f8940653ab9adaad158167111a0478edad8a972e7cc8816ca85123"
+      "sha256": "ef8b919606efbf794d7ebe67b011bd676c129cd1d9d51bac16d85dcaaae5e12e"
     },
     {
       "path": "skills/orchestrate/references/dialogue_nodes.md",
@@ -3038,8 +3048,8 @@
     },
     {
       "path": "skills/peer-review/SKILL.md",
-      "size": 70338,
-      "sha256": "246beb8a3c3c6eef78180a6ab1d87fa49db4f98d55964af5b3ab0ce5d0e7e3b0"
+      "size": 75710,
+      "sha256": "484a289ceb990a3301fc3a8093c1e5fae2e8fb00e267d774e4d7df4e0591a748"
     },
     {
       "path": "skills/peer-review/references/aczel_2021_reviewer2_patterns.md",
@@ -3063,8 +3073,8 @@
     },
     {
       "path": "skills/peer-review/references/domain-probes/diagnostic_accuracy.md",
-      "size": 11967,
-      "sha256": "8c0a8bd30fe16507e2997ddba1bbcfb4ee7eade7df44f1981e1427cd3a28d233"
+      "size": 12675,
+      "sha256": "06f8a8e6fcfaf00f25d04e98b58ddf3344ddc1d772057c401a83ef71d012be90"
     },
     {
       "path": "skills/peer-review/references/domain-probes/equity_fairness.md",
@@ -3108,8 +3118,8 @@
     },
     {
       "path": "skills/peer-review/references/domain-probes/observational_confounding.md",
-      "size": 34795,
-      "sha256": "ff8cb910c7fb83ec08a04ba88866bdf1e0d2f43d972e2861b825595a85b035ee"
+      "size": 35839,
+      "sha256": "32343fb2ed0d20cb76593c8d07842d0628ce363a7c24a6739f10fa29b37e6398"
     },
     {
       "path": "skills/peer-review/references/domain-probes/polygenic_risk_score.md",
@@ -3236,10 +3246,50 @@
       "size": 3171,
       "sha256": "2f548ccbe1ee101bf6630b4d363f15e4df0750a350788b26f177490496be74f6"
     },
+    {
+      "path": "skills/peer-review/scripts/check_pdf_injection.py",
+      "size": 10870,
+      "sha256": "fcf33336f16dbfa92a0b5bbd5588b4026d3c89f21041733099d7a028e16e6bd3"
+    },
+    {
+      "path": "skills/peer-review/scripts/check_pdf_injection_challenge/expected/clean.txt",
+      "size": 113,
+      "sha256": "9f37abe54221df614502f460030e15d30fd3d0573fcc5f3af47feac736614a8b"
+    },
+    {
+      "path": "skills/peer-review/scripts/check_pdf_injection_challenge/expected/inject.txt",
+      "size": 1228,
+      "sha256": "bd5788f40f87e599caa5e9883fe1374b204008fb8de89a4781068a74a08ddb3b"
+    },
+    {
+      "path": "skills/peer-review/scripts/check_pdf_injection_challenge/fixture/manifest_clean.json",
+      "size": 553,
+      "sha256": "bb67c4f241be5603b70743a2f443c8221ad69f48433ad4fa846845eaea70737d"
+    },
+    {
+      "path": "skills/peer-review/scripts/check_pdf_injection_challenge/fixture/manifest_inject.json",
+      "size": 1042,
+      "sha256": "b77379a0e3ae35914528f8a0905bdaee887bcf5cce6913872c1d343d68da168b"
+    },
+    {
+      "path": "skills/peer-review/scripts/check_pdf_injection_challenge/problem.md",
+      "size": 2614,
+      "sha256": "409bf859e9fafd5121ff5d7fb02c9e0b2bfcf818b8976acca1d0ab30b64ab1c6"
+    },
+    {
+      "path": "skills/peer-review/scripts/check_pdf_injection_challenge/verify.sh",
+      "size": 2187,
+      "sha256": "6d149ab8d6737430937a0424dd4c66ea9332f25d83d1eca8e37104db33e97b0d"
+    },
+    {
+      "path": "skills/peer-review/scripts/scan_pdf_layers.py",
+      "size": 6216,
+      "sha256": "0bccc9b86e6e8caa47cb7e1897618459abe376aef8264114d7c4795c358fe2c3"
+    },
     {
       "path": "skills/peer-review/skill.yml",
-      "size": 1628,
-      "sha256": "e8022ffd3a2716f27dff881915b166c9423bc343de99ef7a84c8b14584c7041b"
+      "size": 2346,
+      "sha256": "42bd6cc388a3802960ddf3e46b2ca226926bd4c9a779e6802b43e9fbb4172bac"
     },
     {
       "path": "skills/polish-language/SKILL.md",
@@ -3728,8 +3778,8 @@
     },
     {
       "path": "skills/self-review/references/domain-probes/diagnostic_accuracy.md",
-      "size": 11967,
-      "sha256": "8c0a8bd30fe16507e2997ddba1bbcfb4ee7eade7df44f1981e1427cd3a28d233"
+      "size": 12675,
+      "sha256": "06f8a8e6fcfaf00f25d04e98b58ddf3344ddc1d772057c401a83ef71d012be90"
     },
     {
       "path": "skills/self-review/references/domain-probes/equity_fairness.md",
@@ -3773,8 +3823,8 @@
     },
     {
       "path": "skills/self-review/references/domain-probes/observational_confounding.md",
-      "size": 34795,
-      "sha256": "ff8cb910c7fb83ec08a04ba88866bdf1e0d2f43d972e2861b825595a85b035ee"
+      "size": 35839,
+      "sha256": "32343fb2ed0d20cb76593c8d07842d0628ce363a7c24a6739f10fa29b37e6398"
     },
     {
       "path": "skills/self-review/references/domain-probes/polygenic_risk_score.md",
@@ -3911,6 +3961,41 @@
       "size": 6349,
       "sha256": "431c5f14ad2c4f59e85b2a5e86150ac708d476e8f2f1da859d81953f522b2117"
     },
+    {
+      "path": "skills/self-review/scripts/check_dta_denominators.py",
+      "size": 7798,
+      "sha256": "98c116aa7c42f045565e6e8a24df2b15751aef4a5e7e012ec7e5b5ec17a73850"
+    },
+    {
+      "path": "skills/self-review/scripts/check_dta_denominators_challenge/expected/bad.txt",
+      "size": 506,
+      "sha256": "c784ee7acd5521c7789b6893f4b86deb5c9401e1b1195dc1b77be088af2dda96"
+    },
+    {
+      "path": "skills/self-review/scripts/check_dta_denominators_challenge/expected/ok.txt",
+      "size": 119,
+      "sha256": "875e7cfd99ff0c4e2daa1270f9a5dce30597cc2e58e50c085b7c30d843d57fda"
+    },
+    {
+      "path": "skills/self-review/scripts/check_dta_denominators_challenge/fixture/dta_bad.md",
+      "size": 281,
+      "sha256": "49ed72428ff7cbcc16470fad4f7e63ef20c529fff6a0866d26003cc6cb3f75c7"
+    },
+    {
+      "path": "skills/self-review/scripts/check_dta_denominators_challenge/fixture/dta_ok.md",
+      "size": 280,
+      "sha256": "3ed363e1a00af0db022c522254788d76c3618becff8479b91e98fab52fa77760"
+    },
+    {
+      "path": "skills/self-review/scripts/check_dta_denominators_challenge/problem.md",
+      "size": 1584,
+      "sha256": "fcb419b743fa08256f3098c9a96ee7277819e8b769732d7f4763053535af61a5"
+    },
+    {
+      "path": "skills/self-review/scripts/check_dta_denominators_challenge/verify.sh",
+      "size": 1410,
+      "sha256": "3d6582b582ab5fef657dbb1e8b75a5d478669ccd88fff52e7ebe644ce5ba51f4"
+    },
     {
       "path": "skills/self-review/scripts/check_editorial_impression.py",
       "size": 22032,
@@ -3926,11 +4011,81 @@
       "size": 5298,
       "sha256": "342bc1126a420111da9c0fe38c6cd68cc45542b0e485202689d7219de9d80712"
     },
+    {
+      "path": "skills/self-review/scripts/check_nested_group_comparison.py",
+      "size": 6351,
+      "sha256": "44a7d7ce9913dcf33386de3fae510bc2f1e388c59d338ae482028920b327b37a"
+    },
+    {
+      "path": "skills/self-review/scripts/check_nested_group_comparison_challenge/expected/clean.txt",
+      "size": 104,
+      "sha256": "de4af34352139fba95d091bd65da9c34ffba15d205c1f5ebe53bf1eb23dbe01d"
+    },
+    {
+      "path": "skills/self-review/scripts/check_nested_group_comparison_challenge/expected/nested.txt",
+      "size": 301,
+      "sha256": "497f6f5ce6604a8cce134a165d72768d5bb724458912f926a5cbfbbb22243671"
+    },
+    {
+      "path": "skills/self-review/scripts/check_nested_group_comparison_challenge/fixture/clean.md",
+      "size": 328,
+      "sha256": "882880e171b845160d2f228a45d74fbab55ad9c65aa5ef0f19fc53ff5f4dbb92"
+    },
+    {
+      "path": "skills/self-review/scripts/check_nested_group_comparison_challenge/fixture/nested.md",
+      "size": 243,
+      "sha256": "40d41141e8c60a8338f8e33ac2a597ec2ee4f42fa92ce3cc94cee7be20f52b2d"
+    },
+    {
+      "path": "skills/self-review/scripts/check_nested_group_comparison_challenge/problem.md",
+      "size": 1494,
+      "sha256": "f02cff50c0c86f28ea144cb06b190420d9a02f2217d15c271157943b3f6a4984"
+    },
+    {
+      "path": "skills/self-review/scripts/check_nested_group_comparison_challenge/verify.sh",
+      "size": 1478,
+      "sha256": "c84ba913c3ba0f4d9ecc9bf84a77836513314c967491c2bb0d8666b1baf0281e"
+    },
     {
       "path": "skills/self-review/scripts/check_null_calibration.py",
       "size": 8585,
       "sha256": "e5bd71c515554b3acbaefd3807e584364a536dc6e1101bec5b524bc26b341309"
     },
+    {
+      "path": "skills/self-review/scripts/check_paired_difference_estimator.py",
+      "size": 6612,
+      "sha256": "e4a4c4c59b7dc50a8eeace2a9dfa7ba988120b4ede5f307d9836c37b40a2b76f"
+    },
+    {
+      "path": "skills/self-review/scripts/check_paired_difference_estimator_challenge/expected/bad.txt",
+      "size": 550,
+      "sha256": "3f9204146334e1f18c67997cb208d1e3702e9f2c7ed865f31f342c03ca962935"
+    },
+    {
+      "path": "skills/self-review/scripts/check_paired_difference_estimator_challenge/expected/ok.txt",
+      "size": 111,
+      "sha256": "4706dc20a9e9391a032acf5b91ce71b6ec619174ffc7e676eee4fc2cf91d4e40"
+    },
+    {
+      "path": "skills/self-review/scripts/check_paired_difference_estimator_challenge/fixture/paired_bad.md",
+      "size": 257,
+      "sha256": "a268c335cc776f26f6b366044d40d75538fba87e2730c58cc8cbeb66780f44eb"
+    },
+    {
+      "path": "skills/self-review/scripts/check_paired_difference_estimator_challenge/fixture/paired_ok.md",
+      "size": 287,
+      "sha256": "0be43e775f0e6d45162c9d0dd23e591b916992f2abd041ff71483920cb4d8a90"
+    },
+    {
+      "path": "skills/self-review/scripts/check_paired_difference_estimator_challenge/problem.md",
+      "size": 1505,
+      "sha256": "ede7ecbef797e18958abd037d3534f11b71e1027f87a3a99c310a24484da69ed"
+    },
+    {
+      "path": "skills/self-review/scripts/check_paired_difference_estimator_challenge/verify.sh",
+      "size": 1531,
+      "sha256": "b3172bbdc15868b8d4f16534e1c0049ec8b694ac864f22a989ee00aa84d218e4"
+    },
     {
       "path": "skills/self-review/scripts/check_panel_diversity.py",
       "size": 15324,
@@ -3946,6 +4101,41 @@
       "size": 17564,
       "sha256": "007100ed2ec23d01a9352feae10c5af23e7b3e88d91bb7fda7c3c899772aaa85"
     },
+    {
+      "path": "skills/self-review/scripts/check_reported_p_from_counts.py",
+      "size": 8813,
+      "sha256": "86771e8dfbad9d9680fa7cfd15cc98b63a247a318cd86c4162d852359c82a252"
+    },
+    {
+      "path": "skills/self-review/scripts/check_reported_p_from_counts_challenge/expected/bad.txt",
+      "size": 308,
+      "sha256": "b9d0da79b8eedda2c8a17ef6852400e6b7adb5e556d561cf544c8a5e5a8fb875"
+    },
+    {
+      "path": "skills/self-review/scripts/check_reported_p_from_counts_challenge/expected/ok.txt",
+      "size": 112,
+      "sha256": "cddb1acfec3c0a27e18c24755373a0bcb5521eae3d6ad6e97b06a03eabfafdbc"
+    },
+    {
+      "path": "skills/self-review/scripts/check_reported_p_from_counts_challenge/fixture/p_bad.md",
+      "size": 206,
+      "sha256": "b22b3cae304a8986a9b9ec49377601dc96f791fbbc0e04cd8adaf7c9952707dc"
+    },
+    {
+      "path": "skills/self-review/scripts/check_reported_p_from_counts_challenge/fixture/p_ok.md",
+      "size": 205,
+      "sha256": "15546bf0a9be157265dd3ec80be46d32b7fbe5386ad6e31ea6c16ea669abf3ac"
+    },
+    {
+      "path": "skills/self-review/scripts/check_reported_p_from_counts_challenge/problem.md",
+      "size": 1572,
+      "sha256": "e2df6d50acbce0da65f1af6f767a63e7007a855f40e5ef7b549d8348bd830133"
+    },
+    {
+      "path": "skills/self-review/scripts/check_reported_p_from_counts_challenge/verify.sh",
+      "size": 1509,
+      "sha256": "1a1fddcdef6d23a3c6e2f83c924180c2703355953223d5d82cd89e01615e436d"
+    },
     {
       "path": "skills/self-review/scripts/check_reviewer_team_consistency.py",
       "size": 15481,
@@ -3966,10 +4156,45 @@
       "size": 13579,
       "sha256": "c61bd5e485d2bce4a6efd7bf2a7980aa0d31ebecb876a7c6895fd12cb6bf7f1c"
     },
+    {
+      "path": "skills/self-review/scripts/check_table_percentages.py",
+      "size": 8674,
+      "sha256": "102cc795660fd41c40219b006dc657edd8d77f9195cf5b8fd2e5e470d3c28f3a"
+    },
+    {
+      "path": "skills/self-review/scripts/check_table_percentages_challenge/expected/bad.txt",
+      "size": 301,
+      "sha256": "6fed046d75f3a02818e0a3ac4aa0ad907b17eab7e05e9629467e1d54bea51856"
+    },
+    {
+      "path": "skills/self-review/scripts/check_table_percentages_challenge/expected/ok.txt",
+      "size": 112,
+      "sha256": "2fb34506bf65909fdb040acf085c4c18810b52497b6b1a53a2e08509a4465fd8"
+    },
+    {
+      "path": "skills/self-review/scripts/check_table_percentages_challenge/fixture/table_bad.md",
+      "size": 121,
+      "sha256": "841bcb7d75c8e51512c59de171d82c9959b72976eef29f631ba9440c873357d6"
+    },
+    {
+      "path": "skills/self-review/scripts/check_table_percentages_challenge/fixture/table_ok.md",
+      "size": 235,
+      "sha256": "ea5999c08b15a928606ca154c504545ed5804e45bade45ffca4d12b5849cc0bc"
+    },
+    {
+      "path": "skills/self-review/scripts/check_table_percentages_challenge/problem.md",
+      "size": 2072,
+      "sha256": "0af0e84599a8ac52a33ce33bc3244803ccc34d6f8f7f8de24234ac3b64a9a61a"
+    },
+    {
+      "path": "skills/self-review/scripts/check_table_percentages_challenge/verify.sh",
+      "size": 2041,
+      "sha256": "b4c9eb16f291841c1d6dc74a5554a49b5dc60d3562d0e328e01a78797f8d32ad"
+    },
     {
       "path": "skills/self-review/skill.yml",
-      "size": 2381,
-      "sha256": "9499a87d985d981eac9418d6cd95ed79c1d9724aba8854b7d6713d89679d9f1d"
+      "size": 3278,
+      "sha256": "84ea9430003ffc8f1b2e009600ac3b4614abb84a697ec1891a39086aa65fe404"
     },
     {
       "path": "skills/setup-medsci/SKILL.md",

package/metadata/distribution_manifest.json

@@ -1,6 +1,6 @@
 {
   "schema_version": 1,
-  "version": "5.18.0",
+  "version": "5.20.0",
   "owned_skills": [
     "academic-aio",
     "add-journal",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "medsci-skills",
-  "version": "5.18.0",
+  "version": "5.20.0",
   "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 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
+description: Check manuscript compliance with medical research reporting guidelines. Supports 46 guidelines including STROBE, STROBE-MR, RECORD, REMARK (prognostic tumor-marker studies), TARGET (target trial emulation), 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, REMARK, tumor marker, prognostic marker, prognostic biomarker, molecular residual disease, TARGET, target trial emulation, target trial, causal inference, estimand, immortal time bias, risk of bias, compliance check, LLM accuracy, large language model, clinical deployment
 tools: Read, Write, Edit, Bash, Grep, Glob
 model: inherit
 ---
@@ -35,6 +35,8 @@ compliance report suitable for journal submission.
   - `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)
+  - `REMARK.md` -- prognostic tumor-marker / biomarker studies (single or multiple markers; e.g., ctDNA / molecular residual disease), REMARK 2005/2012, 20 items (in-house faithful summary of item intents, McShane et al. Br J Cancer 2005 + Altman et al. PLoS Med 2012)
+  - `TARGET.md` -- observational studies emulating a target trial (causal / comparative-effectiveness questions on routinely-collected / registry / EHR data), TARGET 2025, 21 items (in-house faithful summary of item intents, Cashin/Hansford/Hernán et al. JAMA 2025; pairs with the /design-study target-trial-emulation module)
   - `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)
@@ -103,6 +105,8 @@ user specification.
 | Diagnostic accuracy study | STARD 2015 | STARD-AI |
 | Prediction model (development/validation) | TRIPOD | TRIPOD+AI |
 | Polygenic (risk) score prediction study | PGS-RS (with TRIPOD / TRIPOD+AI) | -- |
+| Prognostic tumor-marker / biomarker study (single or multiple markers; e.g., ctDNA / molecular residual disease) | REMARK (pair with STROBE for the observational-design items; TRIPOD / TRIPOD+AI if a prognostic model is developed) | -- |
+| Causal / comparative-effectiveness question emulated on observational data (treatment vs treatment, screening vs none, drug A vs B on registry / EHR / claims data) | TARGET (pair with the /design-study target-trial-emulation module for design; RECORD / STROBE for the routinely-collected-data items) | -- |
 | Systematic review / meta-analysis | PRISMA 2020 | -- |
 | DTA systematic review / meta-analysis | PRISMA-DTA | -- |
 | Meta-analysis of observational studies | MOOSE | PRISMA 2020 (use both) |