medsci-skills 5.19.0 → 5.20.1

package/README.md

@@ -288,6 +288,10 @@ The E2E pipeline (`orchestrate --e2e`) produces everything up to `qc/`. The `sub
 
 ## What's New
 
+**v5.20.1** — audit-driven coherence fixes. A real `/orchestrate --e2e` state-transition bug (the pipeline halted at step 3 because it required a DOCX that is only rendered at step 7), all 55 skills made routable from the single entry point with a CI reachability gate, and a README plugin-count that had drifted from the marketplace SSOT (now gated). No skill/detector change.
+
+**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.)
+
 **v5.19** — 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.)
 
 **v5.18** — 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.)
@@ -354,7 +358,7 @@ The E2E pipeline (`orchestrate --e2e`) produces everything up to `qc/`. The `sub
 
 **v4.1** ships distribution levers and a submission pre-flight gate — analysis-integrity detectors **24 → 25** (still 43 skills):
 
-- **Claude Code plugin marketplace** — `/plugin marketplace add Aperivue/medsci-skills`, then `/plugin` discovery of eight `medsci-*` category plugins generated from the catalog SSOT (`.claude-plugin/marketplace.json`).
+- **Claude Code plugin marketplace** — `/plugin marketplace add Aperivue/medsci-skills`, then `/plugin` discovery of nine `medsci-*` category plugins generated from the catalog SSOT (`.claude-plugin/marketplace.json`).
 - **MedSci-Audit detector registry** — the deterministic verification layer is now a named, enumerated, citable suite ([`MEDSCI_AUDIT.md`](MEDSCI_AUDIT.md) + generated `metadata/detectors_catalog.json`, six audit families).
 - **Hero-skill standalone mirrors** — `scripts/sync_hero_skill.py` mirrors a focused skill to its own star-funnel repo; first two live: [`Aperivue/verify-refs`](https://github.com/Aperivue/verify-refs) and [`Aperivue/check-reporting`](https://github.com/Aperivue/check-reporting).
 - **Placeholder/marker gate** — `check_placeholders.py` flags leftover `[@NEW:]` / `[version]` / `TODO` / template-URL markers before submission (the 25th detector).

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package/metadata/distribution_manifest.json

@@ -1,6 +1,6 @@
 {
   "schema_version": 1,
-  "version": "5.19.0",
+  "version": "5.20.1",
   "owned_skills": [
     "academic-aio",
     "add-journal",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "medsci-skills",
-  "version": "5.19.0",
+  "version": "5.20.1",
   "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/orchestrate/SKILL.md

@@ -73,6 +73,26 @@ You do NOT do the work yourself. You classify, plan, and delegate.
 | **fill-icmje-coi** | Form filling | Batch ICMJE COI Disclosure Form generation per author from a synthetic seed |
 | **sync-submission** | Submission | SSOT-to-submission drift audit; journal-specific submission manifest creation from canonical manuscript artifacts |
 | **peer-review** | Review | External manuscript peer review draft generation (journal-specific formatting). Use ONLY for reviewing other authors' work, never for self-review |
+| **review-paper** | Writing | Scaffold/draft a literature review (narrative / scoping PRISMA-ScR / systematic); reuses the self-review narrative-review probes for QC. Distinct from `write-paper` (original research) and `meta-analysis` (pooling) |
+| **polish-language** | Quality | Academic-English consistency lint + non-native clarity polish (abbreviation define-once, US/UK spelling drift, hyphen/en-dash ranges, P/p case, value/unit spacing). Style-only; distinct from `humanize` (AI-tell removal) and `check-reporting` (guideline items) |
+| **author-strategy** | Analysis | PubMed author-profile analysis: study-type classification, trajectory-archetype, publication-strategy report from a name |
+| **batch-cohort** | Analysis | Generate N analysis scripts from one validated methodology template × many exposure/outcome combinations (same method, swap variables) + summary matrix |
+| **replicate-study** | Analysis | Replicate an existing cohort study's methodology on a different database: design extraction, variable-harmonization table, replication-difference report |
+| **cross-national** | Analysis | Cross-national comparison study (KNHANES + NHANES + CHNS or parallel surveys): variable harmonization + parallel weighted analysis |
+| **ma-scout** | Systematic review | Meta-analysis topic discovery + feasibility (professor-first profile→gap, or topic-first question→gap→co-author) before a protocol exists |
+| **find-cohort-gap** | Methodology | Research-gap discovery from a longitudinal cohort DB: profile strengths, match PI expertise, literature-saturation scan, ranked topic proposals |
+| **design-ai-benchmarking** | Methodology | Design/validity review for benchmarking one or more AI systems against a human-expert reference panel (decoupled rubrics, planted calibration probes, reviewer-panel construction, IRR targets, rating-export schema) — before data collection |
+| **architecture-zoo** | Modeling | Choose a medical-imaging model architecture (classification / segmentation / detection / transfer) before scaffolding — maps task + modality + labelled-data scale + imbalance to a paper-grounded shortlist |
+| **preprocess-imaging** | Modeling | Design/audit DICOM/NIfTI intake, resampling, normalisation, and augmentation so the pipeline is leakage-safe before `model-scaffold`; emits a preprocessing manifest + data-stage leakage gate |
+| **model-scaffold** | Modeling | Generate a reproducible runnable PyTorch training repo (patient-level seed-locked split, task model, train/eval scripts, repro record) — the link between choosing an architecture and validating a trained model |
+| **radiomics-ml** | Modeling | Produce/audit a radiomics / tabular-ML study (imaging or clinical features → penalised logistic / SVM / RF / gradient-boosting / MLP → outcome) with a learner-agnostic nested-CV / feature-stability / calibration / external-validation gate (no GPU) |
+| **model-validation** | Validation | Design/audit the clinical-validation study for an engineer-built imaging model (segmentation / classification / detection): patient-level split disjointness, internal-vs-external validation, comparator, metric fit — with a deterministic split-leakage gate |
+| **model-evaluation** | Evaluation | Compute task-correct held-out metrics for a trained imaging model (segmentation Dice + boundary; classification AUROC + AUPRC + Se/Sp with bootstrap CIs; detection FROC/mAP; calibration; subgroup slices) → per-case results table |
+| **mllm-eval** | Evaluation | Design/audit a model-agnostic evaluation harness for an LLM/MLLM clinical task (report generation, VQA, extraction/classification): adjudicated reference, clinical-efficacy metrics beyond BLEU/ROUGE, hallucination, contamination, prompt-sensitivity, reader study |
+| **explainability** | Modeling | Produce/audit a medical-imaging model's interpretability analysis (Grad-CAM / saliency / integrated-gradients) held to the reviewer bar — Adebayo sanity checks, quantitative localisation vs ground truth, cohort-level results, attribution-not-validation framing |
+| **uncertainty-imaging** | Modeling | Design/audit the uncertainty-quantification / OOD-detection / selective-prediction layer of a deployment-framed imaging model (MC-dropout / ensemble / conformal, held-out OOD set, abstention at a pre-specified point) + deployment-claim gate |
+| **model-card** | Documentation | Generate a Model Card + Datasheet + METRIC-informed data-quality pass for an engineer-built imaging model, filled from user-supplied facts, with a completeness gate (never fabricates numbers/provenance/licence) |
+| **setup-medsci** | Setup | Diagnostic checklist for the runtime (Python, R, Node, Claude Code, Git, Zotero, MCP servers) — read-only pass/fail table pointing to the right setup doc for any missing component |
 
 ---
 
@@ -287,7 +307,7 @@ After each skill completes, verify that expected output files exist. If validati
 |-------|-----------------|------------|
 | `/analyze-stats` | At least one file in `analysis/tables/*.csv` OR `analysis/_analysis_outputs.md` | Check file existence and non-empty |
 | `/make-figures` | `analysis/figures/_figure_manifest.md` with at least 1 entry | Parse manifest, verify listed files exist |
-| `/write-paper` | `manuscript/manuscript.md` (required), `manuscript/manuscript_final.docx` (required in --e2e) | Check file existence and non-empty |
+| `/write-paper` | `manuscript/manuscript.md` (required) | Check file existence and non-empty. Do NOT require the DOCX here — `manuscript_final.docx` is rendered later by `/manage-refs` (step 7); requiring it at this step would halt an `--e2e` run before the DOCX exists |
 | `/check-reporting` | `qc/reporting_checklist.md` or inline report | Check file existence |
 | `/verify-refs` | `qc/reference_audit.json` (sole output) | Parse JSON; halt if `submission_safe == false` (i.e., `FABRICATED` / `MISMATCH` count > 0 OR `duplicate_findings[]` nonempty) |
 | `/self-review` | Review report with JSON block (when --json) | Check JSON block is parseable. In `--panel` mode each issue may carry an additional optional `consensus` array plus R1/R2/R3 attribution annotations on the `M`/`m` comments — these are additive and backwards-compatible; accept them |

package/skills/peer-review/SKILL.md

@@ -368,6 +368,13 @@ calibration, optimistic validation reporting, selective outcome reporting). Each
 it as a partner (Aczel-compliant), and calibrate severity (design-level → Major #1). Model
 the anchoring and phrasing; do not copy — they are synthetic teaching examples.
 
+**Request-type discipline (classify every Major's ask before it ships).** Sort each request into two kinds:
+
+- **Disclosure** — the study already holds the answer and has not printed it (the analysis unit; the subset's characteristics; a CI already computed; whether the model was trained on this cohort; the reading order). It costs the authors nothing to produce and *surfaces* errors; the highest-value comments are almost always this kind, including one that forces an over-claiming title to be softened.
+- **Computation** — the authors must produce a number that does not yet exist (test this difference; bootstrap a CI; give an effect size). It creates a **new, unreviewed error surface** produced under revision deadline by authors who will not re-check it and accepted next round by a reviewer who reads its existence as compliance.
+
+A computation request must carry an explicit justification that the existing tables cannot answer the question; otherwise reword it as disclosure or drop it. Prefer **naming the estimator** you want (e.g. *Hodges–Lehmann pseudomedian*) over a loose phrase (*"paired median differences"*), which authors adopt verbatim (an odd-n integer-scale "median difference" is impossible — `check_paired_difference_estimator.py`). A comment may be **both** — split it: never *request* a subset-vs-parent-cohort P value, because the groups are nested and the test is invalid (`check_nested_group_comparison.py`, and the observational/DTA domain probes); ask for the subset's characteristics (disclosure) and judge representativeness by magnitude. This is not "ask for less" — a short review with two computation requests is worse than a long one with ten disclosure requests.
+
 Generate `{manuscript_id}_review_draft.md`:
 
 ```markdown
@@ -468,7 +475,7 @@ After drafting, verify mechanically:
     Comments contain no Reject-grade language (including value-judgment deferral to the board) left
     inconsistent with a softer recommendation.
 13. **Observational-confounding QC** (if Phase 2E applied): For any covariate imbalanced by exposure in Table 1 but absent from the adjustment set (O1), confirm the comment requests a concrete extended-adjustment sensitivity model, not a vague "adjust for more confounders." Confirm a selection/collider structure (O3) or an undisclosed complete-case collapse from a structural-zero dose covariate (O5) is raised at design-level severity, and that any E-value request (O6) targets the declared primary estimate rather than a supporting one.
-14. **Verify-your-own-criticism** (all reviews): For each Major framed as a technical inaccuracy or a citation–claim mismatch, confirm the reviewer's own assertion was checked against a current authoritative source (full paper, CrossRef, arXiv). Downgrade unverified technical claims to a hedged "Please verify…"; keep confirmed ones firm. Watch for status drift (a "preprint" since published; a method since adapted) before asserting the manuscript is wrong.
+14. **Verify-your-own-criticism** (all reviews): For each Major framed as a technical inaccuracy or a citation–claim mismatch, confirm the reviewer's own assertion was checked against a current authoritative source (full paper, CrossRef, arXiv). Downgrade unverified technical claims to a hedged "Please verify…"; keep confirmed ones firm. Watch for status drift (a "preprint" since published; a method since adapted) before asserting the manuscript is wrong. **This extends to any assertion of arithmetic or statistical *impossibility* derived from the manuscript's own summary statistics** — the highest-embarrassment class, asserted with certainty and trivially falsified by the authors. Any claim containing *requires / cannot / impossible / must / contradicts* must be restated as an explicit premise→conclusion pair and stress-tested for a counterexample before submission. Two recurring traps: **a quantile or IQR statement does not constrain the tail**, and **an agreement coefficient (κ, ICC) does not constrain the marginal distribution.** Separately, for a **reviewer-requested** new statistic that appears Resolved at revision, re-derive it from the manuscript's own cells before accepting — its existence is not evidence of its correctness, and a requested analysis is the highest-prior-probability location for error in the revision (`~/.claude/rules/peer-review-response-verification.md`).
 15. **Image-synthesis QC** (if Phase 2K applied): Confirm the determinism/information-ceiling point (IS1) is raised whenever the manuscript reads a same-reader source→source+synthetic gain as added diagnostic information without a source→label baseline, that undescribed slice/mask provenance (IS2) is surfaced as a leakage/circularity concern rather than a reporting nicety, that quantitative agreement is checked at the lesion/target level not only globally (IS3), and that a biological-information claim built on image similarity alone is tempered (IS4). Per Phase 2F, confirm IS2/IS4 were treated as unfixable-in-current-form when present.
 16. **Reference-integrity QC** (all original-research reviews): Confirm the load-bearing Introduction/Discussion citations (those used as evidence the method or premise works) were spot-checked — a cited paper doing a different task, a duplicate reference, or a wrong year/author is a Minor (Major if the premise rests on it), and any unconfirmed suspicion is phrased "please verify" rather than asserted.
 
@@ -494,6 +501,8 @@ Fix all issues found, then present to user.
 - [ ] Reference-baseline ratio (`wc / 545w`) reported; ratio > 2.0 trimmed
 - [ ] Hard cap 1400 words not exceeded
 - [ ] AI pattern density within thresholds (em-dash ≤2/1000w; structural rule-of-three ≤2/Major; significance inflation 0/Major; hedged Minor ≥50%)
+- [ ] Every Major's ask classified disclosure vs computation; each computation request justified (existing tables cannot answer it) and its estimator named; no subset-vs-parent-cohort P value requested
+- [ ] Impossibility claims (requires/cannot/impossible/must/contradicts) restated as premise→conclusion + counterexample-tested; reviewer-requested new statistics re-derived from the manuscript's own cells (correctness ≠ presence)
 - [ ] Fatal flaw hierarchy stated in Confidential Comments (if applicable)
 - [ ] Reject recommendations (if used): §1C condition checklist (design-level flaw + speculative practical value 3-trigger + novelty gap) explicitly verified — at least 2 of 3 conditions met
 - [ ] AI/method/review Major Revision (or Reconsider) recommendations: Phase 2F contribution/value gate checked; weak novelty + weak utility not silently softened; for review articles, weak-novelty/no-distinct-contribution treated as unfixable-in-current-form (escalate toward Reject); unfixable defects govern tier over fixable list; confidential note carries no Reject-grade language left inconsistent with a softer recommendation

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

@@ -17,6 +17,7 @@ A checklist for **diagnostic test accuracy (DTA) primary studies** — an index
 **D2 — Spectrum + sampling design**:
 - How were participants sampled — a **single-gate** consecutive/random series of those with the target condition suspected (preserves spectrum and prevalence), or a **two-gate** case-control design (known cases vs healthy controls)? Two-gate sampling **overestimates** accuracy and distorts spectrum; it is a MAJOR interpretive limit when the headline is clinical accuracy, not just proof-of-concept.
 - Is the study **prospective** with a pre-specified index threshold, or retrospective with a threshold chosen on the same data (D-linked to optimism)? Spectrum (disease severity, comorbid mimics) should match the intended-use population.
+- **Representativeness-of-the-analysed-subset table**: when the analysed subset (e.g. the pathology-correlated cases) is compared with the parent cohort that *contains* it, a reported P value is **invalid** — nested groups, no valid null (`check_nested_group_comparison.py`). Judge representativeness by magnitude; the valid contrast is subset vs remainder. Separately, the sensitivity a/(a+c) and specificity d/(b+d) **denominators must equal the reference-standard positive / negative counts** in the characteristics table — grand-total agreement does **not** license a per-category split mismatch, which is exactly what lets it survive review under an Abstract headline (`check_dta_denominators.py`).
 
 **D3 — Blinding of index and reference interpretation**:
 - Was the **index test** interpreted blind to the reference standard and to clinical information that would not be available at the point of use, and vice versa? Unblinded interpretation (review bias) inflates agreement.

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

@@ -67,6 +67,7 @@ A 17-probe checklist for observational studies (cohort, case-control, cross-sect
 - When a manuscript reports an effect-size **gradient or trend across nested / overlapping cohorts or subsets** — a "comparator-refinement gradient" where the exposed arm is held fixed and only the reference group is progressively refined (Frame A ⊃ B ⊃ C; e.g. 144 → 119 → 84 events as competing-cause cases are removed from the reference) — the across-frame shift is **attributable by construction**: the reference changed, not the exposure. The estimates are not independent and there is no contrast being tested.
 - Inferential language for that gradient — "the association **attenuated significantly** across frames", "the [confounder] **largely accounted for** the effect", "a **stepwise reduction**" — is unsupported without a formal **difference / interaction test**. Two acceptable resolutions: (a) keep the gradient **descriptive** (report each frame's estimate and state that the shift follows by construction from refining the reference, not from a tested difference), or (b) fit **one model** with a frame-membership × exposure interaction (or a formally nested-model comparison) and report that interaction term.
 - This is the cohort comparator-refinement analogue of the sensitivity-envelope rule in `~/.claude/rules/scope-coherence-gate.md` (a numeric analysis introduced as if estimable/tested without the supporting test). An inferential "attenuated/accounted-for/reduced across overlapping subsets" claim with no difference/interaction test → MAJOR; downgrade to descriptive or add the interaction model.
+- **A P value comparing an analysed subset with the parent cohort that contains it is invalid, not merely uninformative** — the groups are nested (the subset's patients are *inside* the "full cohort"), so the two-group test has no valid null. This is the RC5 baseline-testing failure's observational sibling, and here it is worse than uninformative. The shape appears when authors answer a selection-bias comment with a "representativeness of the analysed subset" table (full cohort n vs subset n, with P values). Judge representativeness by the **magnitude** of the difference; if a test is genuinely wanted, the valid contrast is **subset vs remainder** (n_full − n_subset), which is disjoint. Flag any subset-vs-parent P as MAJOR (the reported P is uninterpretable). The self-review sibling automates this as a deterministic gate (`scripts/check_nested_group_comparison.py`); on the reviewer side, do not *request* such a table either — ask for the subset's characteristics (disclosure) and read representativeness off the magnitudes.
 
 **O11 — Complex-survey design & weighting (NHANES / KNHANES / CHNS and other multistage probability samples)**:
 - When the data are a **complex probability survey** (NHANES, KNHANES, CHNS, BRFSS, national health-examination surveys), unweighted or naively-weighted analysis is wrong. Check that the analysis is **design-based**: the **sampling weight** is applied AND the **stratification** (e.g. NHANES `SDMVSTRA`) and **primary sampling unit / cluster** (`SDMVPSU`) are declared so that variances use Taylor linearization or replicate weights — a weighted point estimate with **model-based (unclustered) standard errors** still understates uncertainty.

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

@@ -17,6 +17,7 @@ A checklist for **diagnostic test accuracy (DTA) primary studies** — an index
 **D2 — Spectrum + sampling design**:
 - How were participants sampled — a **single-gate** consecutive/random series of those with the target condition suspected (preserves spectrum and prevalence), or a **two-gate** case-control design (known cases vs healthy controls)? Two-gate sampling **overestimates** accuracy and distorts spectrum; it is a MAJOR interpretive limit when the headline is clinical accuracy, not just proof-of-concept.
 - Is the study **prospective** with a pre-specified index threshold, or retrospective with a threshold chosen on the same data (D-linked to optimism)? Spectrum (disease severity, comorbid mimics) should match the intended-use population.
+- **Representativeness-of-the-analysed-subset table**: when the analysed subset (e.g. the pathology-correlated cases) is compared with the parent cohort that *contains* it, a reported P value is **invalid** — nested groups, no valid null (`check_nested_group_comparison.py`). Judge representativeness by magnitude; the valid contrast is subset vs remainder. Separately, the sensitivity a/(a+c) and specificity d/(b+d) **denominators must equal the reference-standard positive / negative counts** in the characteristics table — grand-total agreement does **not** license a per-category split mismatch, which is exactly what lets it survive review under an Abstract headline (`check_dta_denominators.py`).
 
 **D3 — Blinding of index and reference interpretation**:
 - Was the **index test** interpreted blind to the reference standard and to clinical information that would not be available at the point of use, and vice versa? Unblinded interpretation (review bias) inflates agreement.

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

@@ -67,6 +67,7 @@ A 17-probe checklist for observational studies (cohort, case-control, cross-sect
 - When a manuscript reports an effect-size **gradient or trend across nested / overlapping cohorts or subsets** — a "comparator-refinement gradient" where the exposed arm is held fixed and only the reference group is progressively refined (Frame A ⊃ B ⊃ C; e.g. 144 → 119 → 84 events as competing-cause cases are removed from the reference) — the across-frame shift is **attributable by construction**: the reference changed, not the exposure. The estimates are not independent and there is no contrast being tested.
 - Inferential language for that gradient — "the association **attenuated significantly** across frames", "the [confounder] **largely accounted for** the effect", "a **stepwise reduction**" — is unsupported without a formal **difference / interaction test**. Two acceptable resolutions: (a) keep the gradient **descriptive** (report each frame's estimate and state that the shift follows by construction from refining the reference, not from a tested difference), or (b) fit **one model** with a frame-membership × exposure interaction (or a formally nested-model comparison) and report that interaction term.
 - This is the cohort comparator-refinement analogue of the sensitivity-envelope rule in `~/.claude/rules/scope-coherence-gate.md` (a numeric analysis introduced as if estimable/tested without the supporting test). An inferential "attenuated/accounted-for/reduced across overlapping subsets" claim with no difference/interaction test → MAJOR; downgrade to descriptive or add the interaction model.
+- **A P value comparing an analysed subset with the parent cohort that contains it is invalid, not merely uninformative** — the groups are nested (the subset's patients are *inside* the "full cohort"), so the two-group test has no valid null. This is the RC5 baseline-testing failure's observational sibling, and here it is worse than uninformative. The shape appears when authors answer a selection-bias comment with a "representativeness of the analysed subset" table (full cohort n vs subset n, with P values). Judge representativeness by the **magnitude** of the difference; if a test is genuinely wanted, the valid contrast is **subset vs remainder** (n_full − n_subset), which is disjoint. Flag any subset-vs-parent P as MAJOR (the reported P is uninterpretable). The self-review sibling automates this as a deterministic gate (`scripts/check_nested_group_comparison.py`); on the reviewer side, do not *request* such a table either — ask for the subset's characteristics (disclosure) and read representativeness off the magnitudes.
 
 **O11 — Complex-survey design & weighting (NHANES / KNHANES / CHNS and other multistage probability samples)**:
 - When the data are a **complex probability survey** (NHANES, KNHANES, CHNS, BRFSS, national health-examination surveys), unweighted or naively-weighted analysis is wrong. Check that the analysis is **design-based**: the **sampling weight** is applied AND the **stratification** (e.g. NHANES `SDMVSTRA`) and **primary sampling unit / cluster** (`SDMVPSU`) are declared so that variances use Taylor linearization or replicate weights — a weighted point estimate with **model-based (unclustered) standard errors** still understates uncertainty.

package/skills/self-review/scripts/check_dta_denominators.py

@@ -0,0 +1,182 @@
+#!/usr/bin/env python3
+"""check_dta_denominators.py — cross-check diagnostic-accuracy sensitivity /
+specificity denominators against the reference-standard category counts in the
+characteristics table.
+
+Sensitivity is a/(a+c) over the disease-positive patients; specificity is d/(b+d)
+over the disease-negative patients. Those denominators must equal the reference-
+standard positive / negative counts printed in the characteristics table. When
+they disagree while the grand total still matches (e.g. table 14/19, Results
+15/18, both summing to 33), a totals check passes and the split-level error — which
+sits under an Abstract headline — survives multiple review rounds. This detector
+recovers both category counts and both denominators and asserts equality per
+category, refusing to accept grand-total agreement as passing.
+
+Also `STAGE_ROWSUM`: a staging-confusion breakdown must satisfy
+correctly-staged + over-staged + under-staged == n.
+
+Runs on FIRST submissions, not only revisions — the source incident had both
+numbers on the page from submission one.
+
+Stdlib-only. Reads the manuscript, never writes it.
+
+Usage:
+  python3 check_dta_denominators.py --manuscript paper.md [--strict] [--quiet] [--json]
+Exit: 0 clean; with --strict, 1 on any mismatch; 2 on input/usage error.
+"""
+from __future__ import annotations
+
+import argparse
+import json
+import re
+import sys
+from dataclasses import dataclass, field, asdict
+
+SEP_RE = re.compile(r"^\s*\|?[\s:|-]*-[\s:|-]*\|?\s*$")
+NEG_LABEL_RE = re.compile(r"\b(p?N\s*0|node[- ]negative|disease[- ](?:free|negative)|absent|benign|non-?malignant)\b", re.I)
+POS_LABEL_RE = re.compile(r"\b(p?N\s*[1-9]|node[- ]positive|disease[- ]positive|present|malignant|metasta\w+)\b", re.I)
+# "sensitivity ... 13/18" or "13 of 18"; bounded gap so it does not cross a
+# sentence boundary but tolerates a decimal percentage (e.g. "72.2% (13/18)").
+SENS_RE = re.compile(r"sensitivit\w*[^\n]{0,40}?\b(\d+)\s*(?:/|of)\s*(\d+)", re.I)
+SPEC_RE = re.compile(r"specificit\w*[^\n]{0,40}?\b(\d+)\s*(?:/|of)\s*(\d+)", re.I)
+CORRECT_RE = re.compile(r"correctl\w*[^.\n]*?\b(\d+)", re.I)
+OVER_RE = re.compile(r"over[- ]?stag\w*[^.\n]*?\b(\d+)", re.I)
+UNDER_RE = re.compile(r"under[- ]?stag\w*[^.\n]*?\b(\d+)", re.I)
+STAGE_N_RE = re.compile(r"\b(?:in|of|among)\s+(\d+)\s+(?:patients|exams|cases|lesions)\b", re.I)
+
+
+@dataclass
+class Finding:
+    kind: str
+    severity: str
+    detail: str
+
+
+@dataclass
+class Report:
+    source: str
+    findings: list[Finding] = field(default_factory=list)
+
+    @property
+    def n_flag(self) -> int:
+        return sum(1 for f in self.findings if f.severity == "MAJOR")
+
+    @property
+    def verdict(self) -> str:
+        return "DENOMINATOR MISMATCH" if self.n_flag else "OK"
+
+
+def _split_row(line: str) -> list[str]:
+    s = line.strip()
+    if s.startswith("|"):
+        s = s[1:]
+    if s.endswith("|"):
+        s = s[:-1]
+    return [c.strip() for c in s.split("|")]
+
+
+def _reference_counts(text: str):
+    """Return (neg_total, pos_total) summed over reference-standard rows, or None."""
+    neg = pos = 0
+    seen = False
+    lines = text.splitlines()
+    i, n = 0, len(lines)
+    while i < n:
+        if "|" in lines[i] and i + 1 < n and SEP_RE.match(lines[i + 1]) and "-" in lines[i + 1]:
+            j = i + 2
+            while j < n and "|" in lines[j] and lines[j].strip():
+                cells = _split_row(lines[j])
+                if cells:
+                    label = cells[0]
+                    cm = re.search(r"\b(\d[\d,]*)\b", " ".join(cells[1:]))
+                    if cm:
+                        cnt = int(cm.group(1).replace(",", ""))
+                        if NEG_LABEL_RE.search(label):
+                            neg += cnt; seen = True
+                        elif POS_LABEL_RE.search(label):
+                            pos += cnt; seen = True
+                j += 1
+            i = j
+        else:
+            i += 1
+    return (neg, pos) if seen else None
+
+
+def audit(text: str, source: str) -> Report:
+    rep = Report(source=source)
+    ref = _reference_counts(text)
+    sens = SENS_RE.search(text)
+    spec = SPEC_RE.search(text)
+
+    if ref and (sens or spec):
+        neg_ct, pos_ct = ref
+        sens_denom = int(sens.group(2)) if sens else None
+        spec_denom = int(spec.group(2)) if spec else None
+        if sens_denom is not None and pos_ct and sens_denom != pos_ct:
+            rep.findings.append(Finding(
+                "DTA_DENOMINATOR_MISMATCH", "MAJOR",
+                f"sensitivity denominator {sens_denom} (disease-positive) ≠ reference-standard "
+                f"positive count {pos_ct} from the characteristics table"))
+        if spec_denom is not None and neg_ct and spec_denom != neg_ct:
+            rep.findings.append(Finding(
+                "DTA_DENOMINATOR_MISMATCH", "MAJOR",
+                f"specificity denominator {spec_denom} (disease-negative) ≠ reference-standard "
+                f"negative count {neg_ct} from the characteristics table"))
+        # note when the grand totals still agree — that is what hides it
+        if rep.n_flag and sens_denom and spec_denom and neg_ct + pos_ct == sens_denom + spec_denom:
+            rep.findings.append(Finding(
+                "GRAND_TOTAL_AGREES", "INFO",
+                f"grand totals agree ({neg_ct}+{pos_ct} = {sens_denom}+{spec_denom} = "
+                f"{neg_ct + pos_ct}), so a totals-only check passes — the split-level "
+                f"mismatch is the defect"))
+
+    c, o, u = CORRECT_RE.search(text), OVER_RE.search(text), UNDER_RE.search(text)
+    sn = STAGE_N_RE.search(text)
+    if c and o and u and sn:
+        s = int(c.group(1)) + int(o.group(1)) + int(u.group(1))
+        tot = int(sn.group(1))
+        if s != tot:
+            rep.findings.append(Finding(
+                "STAGE_ROWSUM", "MAJOR",
+                f"correctly {c.group(1)} + over {o.group(1)} + under {u.group(1)} = {s} ≠ n={tot}"))
+    return rep
+
+
+def format_report(rep: Report, color: bool) -> str:
+    tag = {"OK": "\033[92m", "DENOMINATOR MISMATCH": "\033[91m"}.get(rep.verdict, "") if color else ""
+    end = "\033[0m" if color else ""
+    out = [f"{tag}== {rep.verdict} =={end}  {rep.source}", f"mismatches={rep.n_flag}"]
+    if not rep.findings:
+        out.append("sens/spec denominators reconcile with the reference-standard category counts.")
+        return "\n".join(out)
+    for f in sorted(rep.findings, key=lambda x: (x.severity != "MAJOR", x.kind, x.detail)):
+        out.append(f"[{f.severity:<5}] {f.kind}  {f.detail}")
+    return "\n".join(out)
+
+
+def main(argv: list[str] | None = None) -> int:
+    ap = argparse.ArgumentParser(description=__doc__,
+                                 formatter_class=argparse.RawDescriptionHelpFormatter)
+    ap.add_argument("--manuscript", required=True, help="manuscript markdown/text")
+    ap.add_argument("--strict", action="store_true", help="exit 1 on any mismatch")
+    ap.add_argument("--quiet", action="store_true", help="suppress the report; exit code only")
+    ap.add_argument("--json", action="store_true", help="emit JSON instead of a text report")
+    args = ap.parse_args(argv)
+    try:
+        text = open(args.manuscript, encoding="utf-8").read()
+    except OSError as e:
+        print(f"error: cannot read manuscript: {e}", file=sys.stderr)
+        return 2
+    rep = audit(text, args.manuscript)
+    if not args.quiet:
+        if args.json:
+            print(json.dumps({"source": rep.source, "verdict": rep.verdict,
+                              "findings": [asdict(f) for f in rep.findings]},
+                             ensure_ascii=False, indent=2))
+        else:
+            print(format_report(rep, color=sys.stdout.isatty()))
+    return 1 if (args.strict and rep.n_flag) else 0
+
+
+if __name__ == "__main__":
+    raise SystemExit(main())