medsci-skills 5.7.0 → 5.9.0

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 — 42 reporting guidelines and risk-of-bias tools, reference/citation verification, and deterministic integrity gates before peer review — now extended by a model-engineering lane that scaffolds reproducible, leakage-safe training repos and audits model validation. Clinical AI model research engineering is in scope; a general AI-scientist platform is not. It competes on clinical submission reliability, not skill count.*
+*MedSci Skills is an end-to-end research tool for physician and medical-engineering researchers — design → scaffold → validate → publish — for the clinical manuscript and the medical-AI model behind it. Its moat is the compliance layer — 44 reporting guidelines and risk-of-bias tools, reference/citation verification, and deterministic integrity gates before peer review — now extended by a model-engineering lane that scaffolds reproducible, leakage-safe training repos and audits model validation. Clinical AI model research engineering is in scope; a general AI-scientist platform is not. It competes on clinical submission reliability, not skill count.*
 
 [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
 [![Release](https://img.shields.io/github/v/release/Aperivue/medsci-skills?style=flat-square&color=blue)](https://github.com/Aperivue/medsci-skills/releases/latest)
@@ -51,7 +51,9 @@ integrity gates** for submission-grade biomedical research. As of **v5.0** it ad
 **model-engineering lane**: choose a paper-grounded architecture, scaffold a
 reproducible, leakage-safe PyTorch training repo, and validate, document, and
 evaluate a medical-imaging or LLM/MLLM model so the work reaches a paper — it
-**integrates** MONAI / nnU-Net, never reimplements them. Clinical AI model research
+ships a minimal runnable default model for a forward-pass smoke test and
+**integrates** MONAI / nnU-Net / timm / torchvision for production-grade models,
+rather than reimplementing the ecosystem. Clinical AI model research
 engineering is in scope; it is **not** a diagnostic tool, an autonomous author, or a
 general AI-scientist platform, and every output requires human-expert verification.
 New here? See the [3 workflows below](#start-here-3-workflows), the
@@ -281,54 +283,54 @@ 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 / **42 guidelines** / 36 detectors / **15 domain-probe modules** (was 12):
+**v4.10** — reviewer-coverage expansion reverse-engineered from high-IF, CC-BY papers (learn-only under the `reverse_engineer/` license firewall), plus a clinician-friendly update path. Additive and backward-compatible; 45 skills / **44 guidelines** / 36 detectors / **15 domain-probe modules** (was 12):
 
 - **Three new reviewer domain-probe modules** (`/peer-review` + `/self-review`, vendored byte-identical): **Mendelian randomization** (MR1–MR8 — IV assumptions, pleiotropy-robust sensitivity suite, Steiger, sample overlap, NLMR, drug-target colocalization), **polygenic risk score** (PG1–PG8 — ancestry portability, base/target leakage, incremental value over the clinical model, screening-vs-discrimination, calibration), and **network meta-analysis** (NM1–NM8 — transitivity, incoherence, SUCRA over-interpretation, CINeMA/GRADE-NMA, component-NMA additivity). Plus observational **O17** (agnostic many-exposure-scan multiplicity: ExWAS/EWAS/MWAS).
 - **Two reporting-guideline checklists** (36 → 38): **STROBE-MR** and **PGS-RS / PRS-RS**, with study-type routing. Four new `/analyze-stats` analysis guides (multiplicity, MR, PRS, NMA) and a `/clean-data` implausible-value + cross-field validity reference.
 - **Clinician-friendly update reminders** — the classroom installers enable the in-app "update available" notice + one-click Desktop updater by default; the `npx`/manual paths print how to turn it on; the install guide recommends `npx medsci-skills install --enable-update-notify`.
 
-**v4.9** — analysis-integrity hardening promoted from real review cycles, plus journal-mechanics additions. Additive and backward-compatible; still 45 skills / 42 guidelines, analysis-integrity detectors **32 → 36**:
+**v4.9** — analysis-integrity hardening promoted from real review cycles, plus journal-mechanics additions. Additive and backward-compatible; still 45 skills / 44 guidelines, analysis-integrity detectors **32 → 36**:
 
 - **Four new gates** — a **duplicate-bibliography** check (`check_reference_duplication.py`) for the hybrid `[@key]` + hand-typed `## References` build that renders the list twice; a **cross-script binning / composite-indicator** consistency check (`check_binning_consistency.py`, `BINNING_DRIFT` / `DERIVED_DEF_DRIFT`) for a derived categorical or composite indicator defined inconsistently across analysis scripts; a **float citation-order** check (`check_citation_order.py`) for numbered Tables/Figures not first cited in ascending order per series; and an **audit-dump leak** gate (`/sync-submission`) that blocks a `/check-reporting` output mistakenly attached as a submission file.
 - **KJR technical-check conventions + percentage-decimal style**, reader-allocation-under-burden and generative-image-as-study-object reporting (`/design-ai-benchmarking`, `/check-reporting`), and a **Liver International** CSL with that journal's submission mechanics (`/manage-refs`).
 
-**v4.8** is the **review-harvest batch** — deterministic detector hardening promoted from real-manuscript review cycles. Additive and backward-compatible; still 45 skills / 42 guidelines, analysis-integrity detectors **30 → 32**:
+**v4.8** is the **review-harvest batch** — deterministic detector hardening promoted from real-manuscript review cycles. Additive and backward-compatible; still 45 skills / 44 guidelines, analysis-integrity detectors **30 → 32**:
 
 - **Two new gates** — `check_supplement_hygiene.py` lints the rendered supplement / tables / caption files (not just the manuscript) for §-labels, placeholders, build markers, response-letter framing, and unresolved body↔supplement cross-references; `check_null_calibration.py` flags a headline negative/equivalence claim made without a minimum-detectable-effect / power / equivalence statement.
 - **Four detector false-positive fixes** — gates no longer fire on a recommended colorblind-safe palette, author-footnote `§` daggers, a correctly-hedged disclaimer, or a tier-label digit; each with a regression fixture and three newly CI-wired test suites.
 - **Nine reviewer-side domain probes** (SR/MA, observational, diagnostic, AI-overclaiming, survival) plus a `/design-study` design-stage ceiling gate for perceptual/reader-AI studies and a reusable confidence-weighted-rating→AUC monotonicity template.
 
-**v4.7** is the **self-update foundation** — physician-researchers stay current without GitHub, git, or a terminal. Additive and backward-compatible; still 45 skills / 42 guidelines / 30 detectors:
+**v4.7** is the **self-update foundation** — physician-researchers stay current without GitHub, git, or a terminal. Additive and backward-compatible; still 45 skills / 44 guidelines / 30 detectors:
 
 - **Transactional, crash-recoverable installer.** Each install runs through a durable journal state machine recovered on the next run (roll back / forward-clean / fail-closed), with per-target SHA-256 inventories — your modified or third-party skills are backed up and never clobbered or auto-deleted.
 - **One-click self-updater** (`~/.medsci-skills/updater/`, `install.py --check-update`). Verifies the download against the github.com API digest and **never `extractall()`s** (per-entry rejection of traversal / symlink / duplicate / zip-bomb + an allowlist & per-file hash). The release pipeline injects a verified `provenance.json`, attests build provenance, runs on a protected `release` environment, and verifies each ZIP round-trips through the updater's own safe-extract before publishing.
 - **Opt-in update notice (off by default):** `install.py --enable-update-notify` shows a one-line "update available" message at Claude Code session start — no telemetry, reads nothing about your session, installs nothing. `--disable-update-notify` / `MEDSCI_NO_UPDATE_CHECK=1` turn it off. *(Honest scope: the digest/attestation detect transport tampering, not a compromised publisher account — see `SECURITY.md`.)*
 
-**v4.6** is a maintainability, governance, and review-depth release — still 45 skills / 42 guidelines; analysis-integrity detectors **28 → 30**, domain probes 11 → 12:
+**v4.6** is a maintainability, governance, and review-depth release — still 45 skills / 44 guidelines; analysis-integrity detectors **28 → 30**, domain probes 11 → 12:
 
 - **Fairness / equity / subgroup-performance probe (EQ0–EQ6)** for AI/prediction/diagnostic studies that claim cross-population performance, plus two new detectors: an **AI-disclosure + data/code-availability** check (`/sync-submission`) and a **structured-summary-box conformance** check (`/academic-aio`).
 - **Governance + answer-engine layer:** `ROADMAP.md`, `MAINTAINERS.md`, `SECURITY.md`, a maintainer workflow + release checklist, an AEO/GEO `docs/faq.md`, a "Start here: 3 workflows" + "Validation status" section in this README, and a new `maturity` field (official / experimental / community) on every skill.
 - **Token diet (pilot):** `write-paper` Phase 7 integrity audits moved to a load-on-demand reference (~2,559 tokens saved per invocation). Positioning now leads with the compliance moat rather than skill count.
 
-**v4.5** deepens the review + submission surface with no new skill or reporting-guideline count (still 45 skills / 42 guidelines); analysis-integrity detectors **27 → 28**:
+**v4.5** deepens the review + submission surface with no new skill or reporting-guideline count (still 45 skills / 44 guidelines); analysis-integrity detectors **27 → 28**:
 
 - **`/clean-data` + `/analyze-stats` — reverse-coded-item / negative-alpha detector.** A multi-item Likert scale with a negatively-worded item must be recoded `(min+max) − x` before the scale total or Cronbach's alpha is computed; left un-recoded, the item correlates negatively with the rest of the scale and alpha collapses (often negative). A negative alpha is a coding bug, not a "multidimensional construct." New stdlib-only `check_reverse_coding.py` returns `REVERSE_CODING_LIKELY` / `REVERSE_CODING_SUSPECT` / `OK` from per-item item-rest correlations + raw alpha; the Likert summary template gains a `--reverse-items` recode flag.
 - **`/peer-review` + `/self-review` — SR/MA + DTA + prediction-model probe batch.** `sr_ma.md` **P12** risk-of-bias table row-sum ↔ traffic-light figure-matrix reconciliation and **P13** included-study ↔ reference-list completeness; `diagnostic_accuracy.md` **D7** index-test-as-enrollment-criterion circularity; `clinical_prediction_model.md` **CP5** intended-use horizon leakage and **CP6** development/CV vs held-out/external validation-nomenclature conflation. Vendored byte-identical into `/self-review`.
 - **`/sync-submission` — embedded absolute-path leak scan.** A `word/*.xml` attribute (e.g. a pandoc-embedded image's `<pic:cNvPr descr="…">`) carrying an absolute home-dir path (`/Users/…`, `/home/…`) is a username leak invisible to a rendered-text scan; now flagged as `docx_embedded_abs_path` under `check_asset_anonymization.py`.
 
-**v4.4** adds reviewer/analysis depth with no new skill or reporting-guideline count (still 45 skills / 42 guidelines / 27 detectors):
+**v4.4** adds reviewer/analysis depth with no new skill or reporting-guideline count (still 45 skills / 44 guidelines / 27 detectors):
 
 - **`/author-strategy` — trajectory-archetype classification (optional).** Classifies a queried author's PubMed trajectory into abstract career archetypes (A1 infrastructure builder, A2 methodology rule-maker, A3 clinical→AI hybrid, A4 SR/MA volume engine, A5 large-consortium participation, A6 device/technique depth, + a computed composite) as an **explainable, multi-label, confidence-scored heuristic — not an objective verdict**. The rubric is a single canonical YAML (the narrative doc is generated from it); scores exclude `unavailable` signals (h-index/citation/venue-tier → `[VERIFY]`, never fabricated); a **disambiguation gate** binds an approved `corpus_manifest.json` to the CSV (csv + PMID-set hashes) so a surname alone never classifies, and target-author attribution never borrows a co-author's ORCID/affiliation.
 - **`/peer-review` + `/self-review` — Image-Synthesis / cross-modality probe (IS1–IS4)** for studies that synthesize one imaging modality from another and claim the output carries the target's information, plus a reviewer-side reference-integrity spot-check.
 - **`/verify-refs` — OpenAlex tertiary index** recovers conference-proceedings / non-DOI citations (NeurIPS/ICLR/ACL) that fall through PubMed and CrossRef, the free analogue of a portal's second index.
 
-**v4.3** hardens the **cross-sectional / observational cohort** review surface end-to-end, much of it reverse-engineered from real CC-BY cohort papers (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 42 guidelines); analysis-integrity detectors **25 → 27**:
+**v4.3** hardens the **cross-sectional / observational cohort** review surface end-to-end, much of it reverse-engineered from real CC-BY cohort papers (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 44 guidelines); analysis-integrity detectors **25 → 27**:
 
 - **Observational probes O1 → O14** (`/peer-review` + `/self-review`, vendored) — over-adjustment / analysis-unit clustering / outcome construct-validity (O7–O9), overlapping-subset gradient (O10), **complex-survey design & weighting** for NHANES/KNHANES (O11), **data-driven threshold / "inflection-point" mining** (O12), **cross-sectional mediation** temporal-order & sequential-ignorability (O13), and **interaction scale** — additive RERI/AP/S vs multiplicative (O14). Plus a new **clinical-prediction-model** probe module **CP1–CP4** and survival **S9** (panel-data / multistate variance).
 - **Two new detectors (25 → 27)** — `check_wordcount_cap.py` (the revision-inflation trap: body vs journal cap) and `check_paren_spans.py` (em-dash→paren conversions that wrap a whole sentence). Plus a `check_confounding_completeness.py` upgrade (DB-code↔prose alias map, SMD-from-mean±SD, exposure-defining-covariate exemption), a `check_cohort_arithmetic.py` `ANALYSIS_UNIT_UNDISCLOSED` check, a `check_scope_coherence.py` cross-sectional-yield lexicon, and a verify-refs corporate/collective-author render-abort fix.
 - **Analysis & submission tooling** — `/analyze-stats` gains **mediation** and **interaction & effect-modification** guides; `/sync-submission` gains `assemble_supplement.py` (S{N} index↔file integrity) and a `/revise` body-word-count exit gate; `/render-pdf-doc` gains a `scan_glyph_coverage.py` xelatex silent-glyph-drop scan.
 
-**v4.2** builds out the case-report capability end-to-end, grounded in real CC-BY case reports (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 42 guidelines); journal profiles **68 → 73**:
+**v4.2** builds out the case-report capability end-to-end, grounded in real CC-BY case reports (learn-only under the license firewall) — no new skill or reporting-guideline count (still 45 skills / 44 guidelines); journal profiles **68 → 73**:
 
 - **Case-report + case-series writing** — `/write-paper` gains a CARE narrative + 150-word-abstract case-report exemplar, a **case-series** paper type (methods-light mini-cohort, all-cases summary table, counts-not-rates), and **adverse-event/pharmacovigilance** (Naranjo/WHO-UMC causality) and **diagnostic-pitfall/mimic** subtypes.
 - **Radiology / imaging-led track** — a dedicated `exemplar_case_report_radiology.md` (per-modality technique→findings→impression, structured-reporting lexicons BI-RADS/LI-RADS/PI-RADS/TI-RADS/Lung-RADS/O-RADS, quantitative threshold honesty, an interventional-radiology procedure/complication subtype, DICOM de-identification) plus a `/make-figures` annotated multimodality imaging-panel exemplar.
@@ -452,14 +454,14 @@ 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 42 reporting guidelines and risk of bias tools (STROBE, STROBE-MR, RECORD, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, CROSS, PRISMA, PRISMA-DTA, PRISMA-P, 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 44 reporting guidelines and risk of bias tools (STROBE, STROBE-MR, RECORD, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, CROSS, SRQR, COREQ, PRISMA, PRISMA-DTA, PRISMA-P, PRISMA-ScR, MOOSE, ARRIVE, CONSORT, CONSORT-AI, CARE, SPIRIT, SPIRIT-AI, CLAIM, DECIDE-AI, SQUIRE 2.0, CLEAR, GRRAS, MI-CLEAR-LLM, SWiM, AMSTAR 2, QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA). Machine-readable JSON summary with `compliance_pct` and `fixable_by_ai` flags for automated pipeline integration. |
 | **analyze-stats** | Statistical analysis code generation (Python/R) for diagnostic accuracy, DTA meta-analysis (bivariate/HSROC), inter-rater agreement, survival analysis, demographics tables, regression (logistic/linear), propensity score (matching/IPTW/overlap weighting), and repeated measures (RM ANOVA/GEE/mixed models). Calibration mandatory for prediction models. |
 | **meta-analysis** | Full systematic review and meta-analysis pipeline (8 phases). DTA (bivariate/HSROC) and intervention meta-analysis. Protocol to submission-ready manuscript with PRISMA-DTA compliance. |
 | **make-figures** | Publication-ready figures and visual abstracts: ROC curves, forest plots, PRISMA/CONSORT/STARD flow diagrams, Kaplan-Meier curves, Bland-Altman plots, confusion matrices, and journal-specific visual/graphical abstracts (python-pptx template-based). Communication-first design principles (Nat Hum Behav 2026 — key message, audience, cognitive load, figure-vs-table decision) and five flow-diagram production lessons (official-template fidelity, VML fallback PDF export, docx XML escape, sequential placeholder mapping, version freeze); critic rubric Section G adds 5 communication-first checks. `--study-type` auto-generates the full required figure set; structured `_figure_manifest.md` output for downstream pipeline consumption; D2 enforced as default for flow diagrams. |
 | **design-study** | Study design review: identifies analysis unit, cohort logic, data leakage risks, comparator design, validation strategy, and reporting guideline fit. |
 | **design-ai-benchmarking** | Design and validity review for benchmarking AI system(s) against a human-expert panel: evaluation-question and arm definition, decoupled multi-dimensional rubrics with anchors, planted calibration probes (positive-control / known-bad / instability / mechanism-contradiction), reviewer-panel construction with per-reviewer randomization, inter-rater reliability targets with separate control-item reliability, LLM-as-judge vs human-as-judge adjudication, construct-independence guards, and a structured JSON rating-export schema. Locks the rubric before data collection. |
 | **model-validation** | Design or audit the clinical-validation study for an engineer-built medical-imaging model (segmentation / classification / detection): patient-level split disjointness and the data-leakage taxonomy, tuning-on-test, internal vs genuine external validation, comparator design, single-run vs multi-seed variance, task-correct metric selection (Metrics Reloaded), test-set sizing, and CLAIM 2024 / TRIPOD+AI / STARD-AI reporting fit. Ships a deterministic split-leakage gate that proves patient disjointness by set arithmetic on the emitted split table. Integrates with MONAI / nnU-Net — does not replace them. |
-| **model-scaffold** | Generate a reproducible, runnable PyTorch training repo for a medical-imaging task — segmentation (U-Net), classification, detection, image-to-image synthesis, or self-supervised pretraining — the missing middle link between choosing an architecture and validating a trained model. Emits a patient-level seed-locked split as an auditable artifact, a task-appropriate model, train/evaluate scripts that seed every RNG and infer under eval mode, a config, requirements, a reproducibility record, and a Methods stub with VERIFY placeholders (no fabricated numbers). Reproducibility holds by construction; ships a `check_training_hygiene` AST gate + a network-free build→validate challenge. Integrates with MONAI / nnU-Net / TorchIO / timm / torchvision — does not reimplement them. |
+| **model-scaffold** | Generate a reproducible, runnable PyTorch training repo for a medical-imaging task — segmentation (U-Net), classification, detection, image-to-image synthesis, or self-supervised pretraining — the missing middle link between choosing an architecture and validating a trained model. Emits a patient-level seed-locked split as an auditable artifact, a task-appropriate model, train/evaluate scripts that seed every RNG and infer under eval mode, a config, requirements, a reproducibility record, and a Methods stub with VERIFY placeholders (no fabricated numbers). Reproducibility holds by construction; ships a `check_training_hygiene` AST gate + a network-free build→validate challenge. Emits a minimal runnable default model for a forward-pass smoke test, and integrates with MONAI / nnU-Net / TorchIO / timm / torchvision for production-grade models. |
 | **architecture-zoo** | "Which architecture for which research question" decision tool: maps task (classification / segmentation / detection / transfer), modality, data scale, and class imbalance to a paper-grounded architecture shortlist. Curates the foundational curriculum (ResNet / DenseNet / EfficientNet / ViT / Swin; U-Net / 3-D U-Net / Attention & Residual U-Net / nnU-Net / Mask R-CNN; SAM/MedSAM / TotalSegmentator / BiomedCLIP / DINO / MAE / SimCLR) — each with core idea, when-to-use, medical-imaging use, reference implementation, validation setup, and the matching model-scaffold template. Advisory; teaches archetypes, not a live SOTA leaderboard. |
 | **model-card** | Generate the documentation an engineer-built medical-imaging model must carry — a Model Card (Mitchell et al. 2019), a Datasheet for its dataset (Gebru et al. 2021), and a METRIC-informed data-quality pass — filled from user-supplied facts (never fabricated), then verify every required section is present and non-empty with a deterministic completeness gate (`check_model_card_complete`). Model Card / Datasheet are documentation standards vendored as templates, not counted reporting checklists. |
 | **model-evaluation** | Compute and report task-correct held-out metrics for a trained medical-imaging model — segmentation (Dice + a boundary metric HD95/NSD, per structure), classification (AUROC + AUPRC + sensitivity/specificity with bootstrap CIs at the deployment prevalence), or detection (FROC/mAP with a stated IoU criterion) — plus calibration and subgroup slices. Emits a per-case table for analyze-stats and gates the metric choice against Metrics Reloaded / CLAIM 2024 (`check_metric_reporting`). Numbers come only from executed code. |
@@ -621,8 +623,8 @@ 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).
 
-### 42 Reporting Guidelines & RoB Tools Built-in
-`check-reporting` includes bundled checklists for 42 guidelines and risk-of-bias tools: STROBE, STROBE-MR, RECORD, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, CROSS, PRISMA 2020, PRISMA-DTA, PRISMA-P, 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.
+### 44 Reporting Guidelines & RoB Tools Built-in
+`check-reporting` includes bundled checklists for 44 guidelines and risk-of-bias tools: STROBE, STROBE-MR, RECORD, STARD, STARD-AI, TRIPOD, TRIPOD+AI, TRIPOD-LLM, PGS-RS, CHEERS 2022, CROSS, SRQR, COREQ, PRISMA 2020, PRISMA-DTA, PRISMA-P, PRISMA-ScR, MOOSE, ARRIVE, CONSORT, CONSORT-AI, CARE, SPIRIT, SPIRIT-AI, CLAIM, DECIDE-AI, SQUIRE 2.0, CLEAR, GRRAS, MI-CLEAR-LLM, SWiM, AMSTAR 2, QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA. Includes Results/Discussion section boundary checks and machine-readable JSON summary for pipeline integration.
 
 ### Publication-Ready Output
 `analyze-stats` generates reproducible Python/R code for 13 analysis types -- including regression, propensity score, and repeated measures -- with mandatory calibration for prediction models. `make-figures` produces journal-specification figures (300 DPI, colorblind-safe palettes, proper dimensions), visual/graphical abstracts, and a tool selection guide (D2 for flow diagrams, matplotlib for data plots). `--study-type` auto-generates the complete figure set for each study design.

package/installers/install.py

@@ -167,10 +167,23 @@ def run_self_test() -> int:
     return 0
 
 
+LOG_DIR = REPO_ROOT / "installers" / ".logs"
+LOG_KEEP = 10  # retain the most recent N install logs; prune older
+
+
 def write_log(log_lines: list[str]) -> Path:
+    """Write the timestamped install log to installers/.logs/ (gitignored) and keep only
+    the most recent LOG_KEEP — logs used to accumulate in the repo root."""
+    LOG_DIR.mkdir(parents=True, exist_ok=True)
     stamp = dt.datetime.now().strftime("%Y%m%d-%H%M%S")
-    log_path = REPO_ROOT / f"{stamp}-{LOG_NAME}"
+    log_path = LOG_DIR / f"{stamp}-{LOG_NAME}"
     log_path.write_text("\n".join(log_lines) + "\n", encoding="utf-8")
+    old = sorted(LOG_DIR.glob(f"*-{LOG_NAME}"))
+    for stale in old[:-LOG_KEEP]:
+        try:
+            stale.unlink()
+        except OSError:
+            pass
     return log_path
 
 

package/metadata/distribution_files.json

@@ -23,8 +23,8 @@
     },
     {
       "path": "installers/install.py",
-      "size": 14230,
-      "sha256": "f1a092bbc5ea676a3bfca3dcb724e9e64a07dc1e1e2414ff696fc21cf4f7f8c0"
+      "size": 14720,
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       "path": "installers/medsci_txn.py",
@@ -153,8 +153,8 @@
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-      "size": 54473,
-      "sha256": "6f7a194db60588e84ddf8e62e80d6e143d14265e21bdac35efa6efbbdd5d5ffc"
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       "path": "skills/analyze-stats/references/analysis_guides/health_economic_evaluation.md",
@@ -513,8 +513,8 @@
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-      "size": 20967,
-      "sha256": "da3427c78bf251def5433b5ffad106e9069770be347668e6b14bb3ce8e925d40"
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       "path": "skills/calc-sample-size/references/formulas.md",
@@ -531,6 +531,11 @@
       "size": 2142,
       "sha256": "97062f5aa63ce8f5b5e340e6b65683720b3ce1d94e34d201977d9a2601293038"
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+    {
+      "path": "skills/calc-sample-size/references/prediction_model_sample_size.md",
+      "size": 5074,
+      "sha256": "bf3d42ad59d2a3b3abc2f00db9559de671514b7b64bd4cf44ec53717966dc635"
+    },
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       "size": 2958,
@@ -538,8 +543,8 @@
     },
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       "path": "skills/check-reporting/references/LICENSES.md",
@@ -596,6 +601,11 @@
       "size": 4376,
       "sha256": "e923b3d2f550351f952334053978d5f0ca726ddb4798f3c1e4adba36939bd662"
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+      "size": 6809,
+      "sha256": "9a8c10db7fa2859ab4d9b26e01a4a15b134e6b5f76c338911a5be118d41e8f98"
+    },
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@@ -726,6 +736,11 @@
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+      "size": 6930,
+      "sha256": "27ecdb3835e122566b113dc9afc1de6d1a988820f45dabc34a9d56f4658016fd"
+    },
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       "path": "skills/check-reporting/references/checklists/STARD.md",
       "size": 6440,
@@ -788,8 +803,8 @@
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       "path": "skills/check-reporting/scripts/check_checklist_version.py",
@@ -798,8 +813,8 @@
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-      "size": 7719,
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       "path": "skills/check-reporting/scripts/check_prisma_figure.py",
@@ -993,13 +1008,58 @@
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-      "size": 18282,
-      "sha256": "dfd73871102af6beab3d21f60f650db41ec2e4025d6ee19eae8de61b17851fd4"
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+    },
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+      "path": "skills/design-study/references/dag_adjustment.md",
+      "size": 4390,
+      "sha256": "8b6c9d2b2d4e79652b355cf30f0d56f4232619cad8589489707107f85bef9de3"
+    },
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+      "path": "skills/design-study/references/target_trial_emulation.md",
+      "size": 6025,
+      "sha256": "3f3b8aa8256689a2109e06b0eaa92f0e793869838711c19f0b2d9e9e01dcb0ff"
+    },
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+      "path": "skills/design-study/scripts/adjustment_set_challenge/fixture/confounder.json",
+      "size": 111,
+      "sha256": "3d1c43f40a41e91f674cca1d47fd9bb8566e9d74f9ebb18aa097a41fbf0b11ff"
+    },
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+      "path": "skills/design-study/scripts/adjustment_set_challenge/fixture/instrument.json",
+      "size": 199,
+      "sha256": "5a99731963404b122cb3e233cc5c850885fe42cc49c9b1cfbac0206ea936703b"
+    },
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+      "size": 182,
+      "sha256": "b05f7d537b9a25841172d4325fba858933aedab20718ac78e58547d11f8b6561"
+    },
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+      "size": 106,
+      "sha256": "9e3fe1ed554a115058e9d7916856eaeca4d666c00741282960320cb87e1cfe91"
+    },
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+      "size": 2264,
+      "sha256": "79cba6ed5f3259a9e633c88d7a4d6d08994fff5f4f8461482dd86bcd2c7239ab"
+    },
+    {
+      "path": "skills/design-study/scripts/adjustment_set_challenge/verify.sh",
+      "size": 2672,
+      "sha256": "87349a1eb69b1c5e1b6120c6e5b1269bc830ef91803e7f09219da2285451bb76"
+    },
+    {
+      "path": "skills/design-study/scripts/adjustment_set_helper.py",
+      "size": 8231,
+      "sha256": "239948c31d513f95f834fdf2d48e9938f7e585a2ebb12387a5abf3b06305dca0"
     },
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       "path": "skills/design-study/skill.yml",
-      "size": 1357,
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     {
       "path": "skills/fill-icmje-coi/SKILL.md",
@@ -1943,8 +2003,8 @@
     },
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       "path": "skills/make-figures/references/exemplar_plots/README.md",
-      "size": 4913,
-      "sha256": "a5a320c785154ec73e41863302c2b625c9a24aeb213cfac0f195414aa1570f01"
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@@ -2029,7 +2089,7 @@
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       "path": "skills/make-figures/references/reporting_guideline_figure_map.md",
       "size": 7149,
-      "sha256": "f56ed1e6c77209cef20e82d1caa99aa65d7f41aac074198e217025f183bdee5d"
+      "sha256": "81f2eff4969e055d886976f4c9e26bf20f1946048c2b61563a7c95b7ebec1d86"
     },
     {
       "path": "skills/make-figures/references/visual_abstract_templates/european_radiology.pptx",
@@ -2106,6 +2166,26 @@
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       "sha256": "88c5e0829bb7c6d1fb6d6e1f45e1ce61bccdd91a7ed9a153623e51d8bc30b651"
     },
+    {
+      "path": "skills/make-figures/scripts/render_core_figures.py",
+      "size": 14436,
+      "sha256": "35f91147d51dd73b75dc116be9e0a80588fe1daf502966e82468d3c62b12f25d"
+    },
+    {
+      "path": "skills/make-figures/scripts/render_core_figures_challenge/fixture/synthetic_inputs.json",
+      "size": 1429,
+      "sha256": "24c0944fcb1384f073988d0f6e28b8f375ba4a7eff62fb4e21bc7066726d5ebc"
+    },
+    {
+      "path": "skills/make-figures/scripts/render_core_figures_challenge/problem.md",
+      "size": 2485,
+      "sha256": "a4e62161806d95b637d9ce984541190e5e9e213e2522d1f8740d847ee10c1a30"
+    },
+    {
+      "path": "skills/make-figures/scripts/render_core_figures_challenge/verify.sh",
+      "size": 1907,
+      "sha256": "7f05fd9cd4e2bfdf6c5b7e8e2a61bee5f8fd44d7d2746e29e2ae77adec84b9c0"
+    },
     {
       "path": "skills/make-figures/scripts/validate_pptx_mac_compat.py",
       "size": 8662,
@@ -2113,8 +2193,8 @@
     },
     {
       "path": "skills/make-figures/skill.yml",
-      "size": 2146,
-      "sha256": "bc6f4a4d47ea7a53b733733ee356337edb8803a76fc0d2deb1d889f5931a7b1d"
+      "size": 2205,
+      "sha256": "b973c376998b15cefe9bffdf580889f905b60ddc2dead00cc5cbc900a6fd50f5"
     },
     {
       "path": "skills/make-figures/templates/official/NOTES.md",
@@ -2763,13 +2843,13 @@
     },
     {
       "path": "skills/model-validation/SKILL.md",
-      "size": 9810,
-      "sha256": "1a75a5a1f21f5a8778d0b77db2e99574bf37edda2a291d8dde6aafea4a207ff0"
+      "size": 10836,
+      "sha256": "5cfd4ac6d75b3a474408b10d8eead3fdf7be8a44e1578dcac332cc2203ae75fe"
     },
     {
       "path": "skills/model-validation/references/validation_design.md",
-      "size": 11427,
-      "sha256": "16d43b688ea63745174c7ca8fafd78a7342b26c34ad1e10e1fdbc117cceafb2e"
+      "size": 13780,
+      "sha256": "c7ad02c2679b241d94af70c05f22740a6ad75c61c0c70d71ba2e48c4f3d64bf5"
     },
     {
       "path": "skills/model-validation/scripts/check_split_leakage.py",
@@ -2819,7 +2899,7 @@
     {
       "path": "skills/orchestrate/SKILL.md",
       "size": 35203,
-      "sha256": "78920458eece7f1d65bd376595f0c5f7a6d199514554da517242aff0837b62e5"
+      "sha256": "7197cb70e6f8940653ab9adaad158167111a0478edad8a972e7cc8816ca85123"
     },
     {
       "path": "skills/orchestrate/references/dialogue_nodes.md",
@@ -2843,8 +2923,8 @@
     },
     {
       "path": "skills/peer-review/SKILL.md",
-      "size": 66025,
-      "sha256": "811ebdfbe6ddb04748cc57fd3e02922d07b3f508ec6307e0790f3b3793a0b827"
+      "size": 68213,
+      "sha256": "51feccb82dca34a28a0b9ace5467d23ddc654056af2cd9e152a4559cf074cfc3"
     },
     {
       "path": "skills/peer-review/references/aczel_2021_reviewer2_patterns.md",
@@ -2921,6 +3001,11 @@
       "size": 9718,
       "sha256": "2e383fec4cf2034c62f9e1a419a0ff61e27bc5b3c132f7115b2335bd72472452"
     },
+    {
+      "path": "skills/peer-review/references/domain-probes/qualitative_research.md",
+      "size": 7014,
+      "sha256": "fd82024939bbfc7f30f284a85a06712b69a269b89a2c8e3752484fb6fb23ebea"
+    },
     {
       "path": "skills/peer-review/references/domain-probes/radiomics.md",
       "size": 5344,
@@ -3403,8 +3488,8 @@
     },
     {
       "path": "skills/self-review/SKILL.md",
-      "size": 104929,
-      "sha256": "085c13cd04dae19970ebb2de239fb6d1de9829ba95847e0e18c1e0bbea1e5edf"
+      "size": 102413,
+      "sha256": "97219c57684d4eaced9e35b0968ca09da7731095c186a4e97757b4039f43f2f6"
     },
     {
       "path": "skills/self-review/references/domain-probes/ai_overclaiming.md",
@@ -3476,6 +3561,11 @@
       "size": 9718,
       "sha256": "2e383fec4cf2034c62f9e1a419a0ff61e27bc5b3c132f7115b2335bd72472452"
     },
+    {
+      "path": "skills/self-review/references/domain-probes/qualitative_research.md",
+      "size": 7014,
+      "sha256": "fd82024939bbfc7f30f284a85a06712b69a269b89a2c8e3752484fb6fb23ebea"
+    },
     {
       "path": "skills/self-review/references/domain-probes/radiomics.md",
       "size": 5344,
@@ -3553,8 +3643,13 @@
     },
     {
       "path": "skills/self-review/references/panel_review_template.md",
-      "size": 14863,
-      "sha256": "a44567b5ea0c47971bcc75b0e6c46f3846d687240b0607ded07183d6fbaad86f"
+      "size": 15095,
+      "sha256": "f9c084e950602ec88f7465dc953ed2309148cab37a3bef5f1b4c80deca2707a4"
+    },
+    {
+      "path": "skills/self-review/references/phases/confounding_completeness.md",
+      "size": 5344,
+      "sha256": "051f2b066d2d708b161c1e97d666d9e214d128f1413a9c4822f0333e748bda14"
     },
     {
       "path": "skills/self-review/scripts/check_artifact_coverage.py",
@@ -3573,8 +3668,8 @@
     },
     {
       "path": "skills/self-review/scripts/check_claim_artifact.py",
-      "size": 10757,
-      "sha256": "2cc6690c917ecb064c9e6834fce6162787881599ba845f8cb6ecddd4d65520b6"
+      "size": 13065,
+      "sha256": "ac29a7e8145152e6641fce8eaf98766cfc943a034db72252cc38538d7ab59db2"
     },
     {
       "path": "skills/self-review/scripts/check_classical_style.py",

package/metadata/distribution_manifest.json

@@ -1,6 +1,6 @@
 {
   "schema_version": 1,
-  "version": "5.7.0",
+  "version": "5.9.0",
   "owned_skills": [
     "academic-aio",
     "add-journal",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "medsci-skills",
-  "version": "5.7.0",
+  "version": "5.9.0",
   "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

@@ -283,9 +283,20 @@ rho = 0.39 between a fasting marker (IQR 0.6 to 3.5 units, SD 3.05) and an index
 marker is associated with about 0.8 index units higher on average (monotonic-linear approximation;
 crude, unadjusted)."
 
-**Output contract**: add a "Real-world translation" line beneath each primary effect size in the
-results table or its footnote. For OR/HR/RR primary outcomes, add an NNT/NNH line with the baseline
-risk stated.
+**Output contract (clinical-utility is a default, not an optional add-on).** Report every
+primary effect in units a clinician acts on, by default — do not leave these as prose to be
+added later:
+- **OR/HR/RR primary outcomes** → report the relative measure **and** the absolute risk at
+  a stated baseline + absolute risk difference + **NNT** (or NNH = 1/ARI), baseline risk
+  explicit. A relative-only headline is incomplete.
+- **Continuous outcomes** → add the IQR/clinically-anchored "Real-world translation" line
+  beneath the effect size.
+- **Prediction / classification (incl. medical-AI) models** → a **decision-curve /
+  net-benefit** pass at the relevant threshold is standard output, not just AUC +
+  calibration. An incremental claim reports added **net benefit / NRI / IDI over the
+  established clinical model**, not the new model's AUC alone. See
+  `references/table-standards/table-types/incremental_value.md` and the `make-figures`
+  `decision_curve` exemplar (and `render_core_figures.py` for the rendered curve).
 
 ## Error Handling
 

package/skills/calc-sample-size/SKILL.md

@@ -20,6 +20,7 @@ Python (alternative), interpret effect sizes clinically, and produce IRB-ready j
 
 - **Formulas**: `${CLAUDE_SKILL_DIR}/references/formulas.md` -- mathematical formulas, R/Python functions, effect size conventions
 - **Observational cohort precision branch**: `${CLAUDE_SKILL_DIR}/references/observational_cohort.md`
+- **Prediction-model / medical-AI sample size (Riley)**: `${CLAUDE_SKILL_DIR}/references/prediction_model_sample_size.md` -- the current TRIPOD+AI-aligned standard for a clinical prediction/classification model (development via `pmsampsize`, external validation via `pmvalsampsize`, net-benefit precision). Use this instead of EPV-10 whenever the goal is risk prediction for use rather than a single-predictor hypothesis test (Tests 12-13).
 - **Justification prose exemplars**: `${CLAUDE_SKILL_DIR}/references/justification_examples.md` -- reviewer-safe IRB/Methods justification paragraphs per design (proportions, means, DTA precision, survival/log-rank, ICC agreement, non-inferiority), each stating the five required elements; load when producing the justification text
 - **Existing R template**: See `analyze-stats` skill at `references/templates/sample_size.R` for the 7 original tests
 
@@ -49,7 +50,10 @@ What is your primary outcome?
 |   |   +-- NO  --> How many groups?
 |   |       +-- 2 groups, superiority     --> [4] Two-proportion comparison (chi-square)
 |   |       +-- 2 groups, non-inferiority --> [10] Non-inferiority / equivalence
-|   |       +-- Multivariable model       --> [9] Logistic regression
+|   |       +-- Multivariable model       --> single-predictor hypothesis test? --> [9] Logistic regression
+|   |                                     --> clinical prediction / AI model for use?
+|   |                                         +-- developing the model  --> [12] Prediction-model development (Riley)
+|   |                                         +-- externally validating  --> [13] External-validation (Riley)
 |   |
 +-- Continuous (measurement, score)
 |   |
@@ -242,7 +246,10 @@ What is your primary outcome?
 **Approach A: Peduzzi Rule of Thumb (EPV >= 10)**
 - N_events = 10 * n_predictors
 - N_total = N_events / event_rate
-- Simple, widely cited, conservative. Use as a minimum baseline.
+- Simple, widely cited, conservative. Use as a minimum baseline **for a single-predictor
+  hypothesis test only**. For a **clinical prediction / medical-AI model intended for use**,
+  EPV-10 is outdated and reviewer-vulnerable — use the Riley criteria in Test 12
+  (development) / Test 13 (validation) instead.
 
 **Approach B: Hsieh (1989) Formula**
 - Uses the OR of interest for the primary predictor to calculate a more precise sample size.
@@ -320,6 +327,44 @@ N_adj = N_total / (1 - attrition_rate)
 
 ---
 
+### Test 12: Prediction-Model Development (Riley)
+
+**When to use**: developing a clinical prediction / classification model (including a
+medical-AI model evaluated as one) — the goal is risk prediction *for use*, not a single
+predictor's hypothesis test. EPV-10 (Tests 9/11) is outdated here.
+
+**Approach**: the minimum N is the largest satisfying all four Riley criteria
+simultaneously — global shrinkage ≥ 0.9, apparent–adjusted R² gap ≤ 0.05, precise overall
+risk estimate, and (time-to-event) precise baseline survival. Implemented in R `pmsampsize`.
+
+**Required parameters**: number of **candidate predictor parameters** (count dummy/non-linear
+terms), a conservative expected **C-statistic or Cox-Snell R²** (with its literature source),
+and outcome **prevalence** (binary) or **event rate + mean follow-up** (time-to-event).
+
+Read `${CLAUDE_SKILL_DIR}/references/prediction_model_sample_size.md` for the criteria, the
+`pmsampsize` code, and the reporting requirements. Report N + required events + the binding
+criterion + the assumed C/R² and its source.
+
+---
+
+### Test 13: External-Validation Sample Size (Riley)
+
+**When to use**: sizing an **external validation** of an existing prediction/AI model.
+
+**Approach**: size to estimate the key validation metrics *precisely enough to be
+conclusive* — target the CI width of the **C-statistic**, the **calibration slope**, the
+**calibration-in-the-large / O:E ratio**, and (if a utility claim) **net benefit**.
+Implemented in R `pmvalsampsize`. A floor of ≥ 100 events and ≥ 100 non-events applies, but
+the precise target is usually larger.
+
+**Required parameters**: expected **prevalence**, anticipated **C-statistic**, and the
+target CI widths.
+
+Read `${CLAUDE_SKILL_DIR}/references/prediction_model_sample_size.md` for the `pmvalsampsize`
+code. Report the targeted CI widths and the resulting events / non-events.
+
+---
+
 ## Scope Limitations
 
 ### Supported