medsci-skills 4.1.0

package/skills/calc-sample-size/skill.yml

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+schema_version: 2
+name: calc-sample-size
+layer: A
+owner_domain: study_design
+when_to_use:
+  - User asks for a sample size, power calculation, or "how many patients/subjects do I need"
+  - Drafting an IRB sample size justification before /write-protocol Methods
+  - Re-deriving N when a reviewer challenges the original power assumption
+  - Estimating events-per-variable (EPV) for survival or logistic regression
+when_NOT_to_use:
+  - Statistical analysis of collected data (use /analyze-stats)
+  - Choosing the test itself rather than its N (use /design-study)
+  - Replicating a prior study's reported N without recomputation (still re-derive)
+inputs:
+  - study_design (proportions, continuous, agreement, survival, ANOVA, logistic, NI/equivalence, diagnostic accuracy, repeated measures, Cox EPV)
+  - parameters (effect size, alpha, power, attrition rate, etc.)
+outputs:
+  - protocol/sample_size_justification.md  # IRB-ready prose, Output Format §"IRB Justification Text"
+  - protocol/sample_size_calc.R  # reproducible R script
+  - protocol/sample_size_calc.py  # alternative reproducible Python script
+deterministic_scripts:
+  - inline R/Python code blocks (skill-emitted, not packaged)
+side_effects:
+  - none  # no external API calls; pure computation + literature anchoring
+downstream_consumers:
+  - write-protocol  # embeds Output §"IRB Justification Text" verbatim into Methods §Sample Size
+  - write-paper  # embeds same text into Methods (post-IRB)
+  - design-study  # cross-reference for analysis-unit / cohort-logic alignment
+ssot_boundary:
+  - protocol/sample_size_justification.md is the canonical sample size text. write-protocol and write-paper EMBED VERBATIM; do not rephrase numbers.
+quality_gates:
+  - parameters_documented: every parameter has a Source column entry (user / literature / convention)
+  - effect_size_interpretation: Cohen's benchmark classification present
+  - methodological_reference: cited (e.g., "Schoenfeld, 1981" for survival)
+  - reproducible_code: both R and Python emitted (skill default), runnable standalone
+forbidden_actions:
+  - fabricate_effect_size_from_unverified_assumption
+  - omit_attrition_or_loss_to_followup
+  - silent_protocol_modification  # changes to N must update both justification.md and protocol Methods
+
+# v2.1 quality card
+purpose: "Compute sample size / power with decision-tree test selection and reproducible R/Python code plus IRB-ready justification."
+safety_boundaries:
+  - "Effect-size assumptions are justified and sourced, not fabricated; attrition/loss is accounted for."
+  - "Any change to N updates both the justification and the protocol Methods (no silent change)."
+known_limitations:
+  - "Emits inline R/Python, not a packaged script; the user runs it."
+  - "Output is only as valid as the assumed effect size and design."
+validation_commands:
+  - "re-run the emitted power code and confirm N matches the justification"
+evidence_surface: manual_workflow

package/skills/check-reporting/SKILL.md

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+---
+name: check-reporting
+description: Check manuscript compliance with medical research reporting guidelines. Supports 32 guidelines including STROBE, CONSORT, STARD, STARD-AI, TRIPOD, TRIPOD+AI, ARRIVE, PRISMA, PRISMA-DTA, PRISMA-P, CARE, SPIRIT, CLAIM, MI-CLEAR-LLM, SQUIRE 2.0, CLEAR, MOOSE, GRRAS, SWiM, AMSTAR 2, and risk of bias tools (QUADAS-2, QUADAS-C, RoB 2, ROBINS-I, ROBINS-E, ROBIS, ROB-ME, PROBAST, PROBAST+AI, NOS, COSMIN, RoB NMA). Generates item-by-item assessment with PRESENT/MISSING/PARTIAL status.
+triggers: checklist, reporting guideline, STROBE, CONSORT, STARD, STARD-AI, TRIPOD, PRISMA, PRISMA-DTA, PRISMA-P, ARRIVE, CARE, CLAIM, MI-CLEAR-LLM, SPIRIT, QUADAS, QUADAS-C, RoB, ROBINS, ROBINS-E, ROBIS, ROB-ME, PROBAST, NOS, COSMIN, AMSTAR, SWiM, risk of bias, compliance check, LLM accuracy
+tools: Read, Write, Edit, Bash, Grep, Glob
+model: inherit
+---
+
+# Check-Reporting Skill
+
+You are helping a medical researcher verify that their manuscript complies with the appropriate
+medical research reporting guideline. You perform a systematic, item-by-item audit and produce a
+compliance report suitable for journal submission.
+
+## Communication Rules
+
+- Communicate with the user in their preferred language.
+- Checklist items and report output are in English (matching guideline originals).
+- Medical terminology is always in English.
+
+## Reference Files
+
+- **Checklists (bundled, open license)**: `${CLAUDE_SKILL_DIR}/references/checklists/`
+  - `STROBE.md` -- observational studies (CC BY)
+  - `STARD.md` -- diagnostic accuracy studies (CC BY 4.0)
+  - `STARD_AI.md` -- AI diagnostic accuracy studies (CC BY, Sounderajah et al. Nat Med 2025)
+  - `TRIPOD.md` -- prediction models, classic 2015 version (CC BY, Moons et al. Ann Intern Med 2015)
+  - `TRIPOD_AI.md` -- prediction models with AI/ML (CC BY 4.0, Collins et al. BMJ 2024)
+  - `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)
+  - `QUADAS2.md` -- diagnostic accuracy risk of bias (CC BY, Whiting et al. Ann Intern Med 2011)
+  - `RoB2.md` -- RCT risk of bias (CC BY, Sterne et al. BMJ 2019)
+  - `ROBINS_I.md` -- non-randomised studies risk of bias (CC BY, Sterne et al. BMJ 2016)
+  - `PROBAST.md` -- prediction model risk of bias (CC BY, Wolff et al. Ann Intern Med 2019)
+  - `NOS.md` -- observational study quality (public domain, Ottawa Hospital)
+  - `CONSORT.md` -- randomised controlled trials, CONSORT 2025 (CC BY 4.0, Hopewell et al. BMJ 2025)
+  - `CARE.md` -- case reports, CARE 2013 (CC BY-NC 4.0, Gagnier et al. J Clin Epidemiol 2014)
+  - `SPIRIT.md` -- clinical trial protocols, SPIRIT 2025 (CC BY 4.0, Chan et al. BMJ 2025)
+  - `CLAIM_2024.md` -- AI/ML in clinical imaging, CLAIM 2024 Update (RSNA open access, Tejani et al. Radiol Artif Intell 2024)
+  - `MI_CLEAR_LLM.md` -- LLM accuracy studies in healthcare (CC BY-NC 4.0, Park et al. KJR 2024; 2025 update)
+  - `SQUIRE_2.md` -- quality improvement in healthcare/education (CC BY, Ogrinc et al. BMJ Qual Saf 2016)
+  - `CLEAR.md` -- radiomics studies (CC BY 4.0, Kocak et al. Insights Imaging 2023)
+  - `MOOSE.md` -- meta-analysis of observational studies (Stroup et al. JAMA 2000)
+  - `GRRAS.md` -- reliability and agreement studies (Kottner et al. J Clin Epidemiol 2011)
+  - `QUADAS_C.md` -- comparative DTA risk of bias, extension to QUADAS-2 (CC BY 4.0, Yang et al. 2021)
+  - `ROBINS_E.md` -- non-randomised exposure studies risk of bias (CC BY-NC-ND 4.0, Higgins et al. Environ Int 2024)
+  - `ROBIS.md` -- risk of bias in systematic reviews (Whiting et al. J Clin Epidemiol 2016)
+  - `ROB_ME.md` -- risk of bias due to missing evidence in meta-analysis (CC BY-NC-ND 4.0, Page et al. BMJ 2023)
+  - `PROBAST_AI.md` -- prediction model risk of bias, updated for AI/ML (Moons et al. BMJ 2025)
+  - `COSMIN_RoB.md` -- reliability/measurement error risk of bias (Mokkink et al. BMC Med Res Methodol 2020)
+  - `RoB_NMA.md` -- risk of bias in network meta-analysis (Lunny et al. 2024)
+  - `AMSTAR2.md` -- quality of systematic reviews (Shea et al. BMJ 2017)
+  - `PRISMA_P.md` -- systematic review protocols (Shamseer et al. BMJ 2015)
+  - `SWiM.md` -- synthesis without meta-analysis reporting (Campbell et al. BMJ 2020)
+- Fail-fast contract: if a routed guideline has no vendored checklist file, the skill does **not** silently construct items from memory. It halts with a `MISSING_CHECKLIST_CONTRACT_VIOLATION` and surfaces the gap. A from-memory assessment is allowed only with the explicit `--allow-from-memory` opt-in, and that report must be clearly labelled NON-AUTHORITATIVE. See Step 2 and `scripts/check_checklist_exists.py`.
+
+---
+
+## Workflow
+
+### Step 0: Existing-checklist staleness pre-check
+
+If a checklist already exists for this project (`qc/reporting_checklist.json` or a prior `.md` report), verify it targets the **current** manuscript before reusing it — a checklist generated against an older version carries stale section/line references and a stale version label that a reviewer who cross-checks will catch:
+
+```bash
+python3 "${CLAUDE_SKILL_DIR}/scripts/check_checklist_version.py" \
+  --checklist qc/reporting_checklist.json --manuscript manuscript_v8.md
+```
+
+A non-zero exit means the existing checklist is stale (older `target_version`, changed `source_sha256`, different `target_manuscript`) or pre-dates the version contract — regenerate it against the current manuscript (Steps 1–5) rather than reusing it. Every report you generate must carry the `target_manuscript` / `target_version` / `source_sha256` fields (Part A header + Part D JSON) so this check works next round.
+
+### Step 1: Select Guideline
+
+Determine the appropriate reporting guideline. Auto-detect from the manuscript type or accept
+user specification.
+
+**Auto-detection mapping:**
+
+| Study Type | Primary Guideline | AI Extension |
+|------------|------------------|--------------|
+| Observational study | STROBE | -- |
+| Randomized controlled trial | CONSORT 2025 | CONSORT-AI |
+| Diagnostic accuracy study | STARD 2015 | STARD-AI |
+| Prediction model (development/validation) | TRIPOD | TRIPOD+AI |
+| Systematic review / meta-analysis | PRISMA 2020 | -- |
+| DTA systematic review / meta-analysis | PRISMA-DTA | -- |
+| Meta-analysis of observational studies | MOOSE | PRISMA 2020 (use both) |
+| Risk of bias (DTA studies) | QUADAS-2 | -- |
+| Risk of bias (RCTs) | RoB 2 | -- |
+| Risk of bias (non-randomised intervention studies) | ROBINS-I | -- |
+| Risk of bias (non-randomised exposure studies) | ROBINS-E | -- |
+| Risk of bias (comparative DTA studies) | QUADAS-C | QUADAS-2 (use both) |
+| Risk of bias (prediction models) | PROBAST | PROBAST+AI |
+| Risk of bias (systematic reviews) | ROBIS | AMSTAR 2 |
+| Risk of bias (missing evidence in MA) | ROB-ME | -- |
+| Risk of bias (network meta-analysis) | RoB NMA | -- |
+| Risk of bias (measurement properties) | COSMIN RoB | -- |
+| Quality assessment (observational) | NOS | -- |
+| Case report | CARE | -- |
+| Study protocol | SPIRIT 2025 | SPIRIT-AI |
+| Animal study | ARRIVE 2.0 | -- |
+| AI/ML study in clinical imaging | CLAIM 2024 | -- |
+| LLM accuracy evaluation in healthcare | MI-CLEAR-LLM | STARD-AI or CLAIM 2024 (use alongside) |
+| Reliability / agreement study | GRRAS | -- |
+| SR protocol | PRISMA-P | -- |
+| Synthesis without meta-analysis | SWiM | PRISMA 2020 (use both) |
+| Quality of systematic reviews | AMSTAR 2 | ROBIS |
+| Radiomics study | CLEAR | CLAIM 2024 (if deep learning component) |
+| Educational / QI study | SQUIRE 2.0 | -- |
+
+**Rules:**
+- If the study involves AI/ML, always apply the AI extension in addition to the base guideline.
+  - **Exception — TRIPOD**: TRIPOD+AI 2024 (Collins et al., BMJ 2024) is a complete rewrite, not an addendum to TRIPOD 2015 (Moons et al., Ann Intern Med 2015). For non-AI prediction models, use TRIPOD 2015 only. For AI/ML prediction models, use TRIPOD+AI 2024 only. Do NOT apply both simultaneously.
+- **STARD-AI** (Sounderajah et al., Nat Med 2025) extends STARD 2015 with 14 new and 4 modified items (40 total). For AI diagnostic accuracy studies, use STARD-AI (which incorporates all STARD 2015 items). Do NOT apply both STARD 2015 and STARD-AI simultaneously — STARD-AI supersedes STARD 2015 for AI studies.
+- **MI-CLEAR-LLM** is a supplementary checklist (6 items), not a standalone reporting guideline. Always pair it with the study's primary guideline (e.g., STARD-AI for AI diagnostic accuracy, CLAIM for imaging AI). Apply MI-CLEAR-LLM whenever the study evaluates LLM accuracy as an outcome — do NOT apply it merely because the manuscript was written with LLM assistance.
+- If multiple guidelines apply (e.g., a diagnostic accuracy study that is also an AI study), check against all relevant guidelines and merge into one report.
+- If the user requests a specific guideline, use that one regardless of auto-detection.
+
+### Step 2: Load Checklist
+
+1. **Run the fail-fast guard first** for every guideline you intend to apply:
+
+   ```bash
+   python "${CLAUDE_SKILL_DIR}/scripts/check_checklist_exists.py" --guideline "STARD-AI"
+   ```
+
+   - Exit 0 → the vendored checklist exists; read it from
+     `${CLAUDE_SKILL_DIR}/references/checklists/` and proceed.
+   - Exit 1 (`MISSING_CHECKLIST_CONTRACT_VIOLATION`) → the guideline is routed
+     but no checklist file is vendored. **Do not construct items from memory.**
+     Halt, report the violation to the user, and stop unless they explicitly
+     opt in (next bullet).
+   - Exit 2 (`UNKNOWN_GUIDELINE`) → the name is not recognised; confirm the
+     correct guideline with the user.
+
+2. **No silent fallback.** A from-memory checklist is permitted only when the
+   user explicitly accepts it — re-run the guard with `--allow-from-memory`
+   (exit 0 + a NON-AUTHORITATIVE warning). In that case the output report MUST
+   carry a prominent banner that the assessment was constructed from model
+   knowledge and is not backed by a vendored checklist, and `submission_safe`
+   must not be asserted on its basis.
+
+### Step 3: Scan Manuscript
+
+Read all sections of the manuscript thoroughly:
+1. Title and abstract
+2. Introduction
+3. Methods (all subsections)
+4. Results (all subsections)
+5. Discussion
+6. Tables, figures, and their captions
+7. Supplemental materials (if available)
+8. References (for registration numbers, protocol references)
+
+Gather context from the full document before starting the item-by-item assessment.
+
+### Step 4: Assess Each Item
+
+For every checklist item, determine:
+
+| Status | Criteria |
+|--------|----------|
+| **PRESENT** | The item is fully addressed with sufficient detail. |
+| **PARTIAL** | The item is mentioned or partially addressed but lacks required detail. |
+| **MISSING** | The item is not found anywhere in the manuscript. |
+| **N/A** | The item does not apply to this particular study (justify why). |
+
+For each item, record:
+- **Status**: PRESENT / PARTIAL / MISSING / N/A
+- **Location**: Section name and paragraph or approximate position (e.g., "Methods, paragraph 3")
+- **Notes**: What was found (if PRESENT/PARTIAL) or what should be added (if MISSING)
+
+### Step 4b: Section Boundary Check
+
+In addition to checklist items, verify that:
+- **Results section** contains only factual findings: no interpretation, no "why" explanations,
+  no prior literature comparisons, no evaluative adjectives without numbers.
+- **Discussion section** does not introduce new data not presented in Results.
+- Flag any boundary violation as a separate finding in Part C Action Items with the label
+  `[BOUNDARY]`.
+
+### Step 4c: Registration / Protocol Timing Consistency Check
+
+**Applies to:** systematic reviews, meta-analyses, and intervention studies with
+prospective registration (PRISMA 2020, PRISMA-DTA, PRISMA-P, MOOSE, CONSORT, SPIRIT).
+
+**Why this step exists:** the registration identifier is a single checklist item and can
+pass Step 4 even when the manuscript is internally inconsistent about *when* the
+registration or its amendments occurred relative to the analysis. An undisclosed
+post-hoc amendment is a common rejection trigger.
+
+**Five audit items (summary):** (1) registration identifier present in Methods, Abstract,
+and cover letter; (2) initial registration date precedes — or is explicitly disclosed as
+post-dating — the extraction milestone; (3) amendment dates appear in Methods, the
+described change is visible in Methods, analysis was re-run if amendment post-dates the
+lock, and no amendment post-dates submission; (4) cross-artifact agreement between
+Methods and the registry record (PROSPERO PDF, ClinicalTrials.gov export) — silent
+discrepancy is a finding; (5) retrospective-registration disclosure paragraph when
+evidence suggests post-extraction filing.
+
+**Registration-ID format gate:** a PROSPERO ID is `CRD42` + 9 digits = 14 characters
+(`^CRD42\d{9}$`, e.g. `CRD42024500001`). Run `grep -oE 'CRD42[0-9]+' manuscript.md` and
+assert each match is 14 characters long; a 15-character ID (a stray inserted digit) is a
+transcription error logged as `[REGISTRATION-TIMING]` (`fixable_by_ai: false` — verify against
+the live PROSPERO record, do not guess the correct digit).
+
+**Flagging:** any failure is logged in Part C Action Items with label
+`[REGISTRATION-TIMING]`. `fixable_by_ai: false` when reconciliation requires an external
+amendment filing; `true` only when the fix is a Methods-text insertion of a date already
+disclosed elsewhere. Part D JSON includes a `registration_timing` object
+(registry, id, initial_registration_date, amendments[], timing_consistency, findings[]).
+
+**Load-on-demand procedural detail** (exact item-by-item procedure, JSON schema,
+flagging edge cases): `${CLAUDE_SKILL_DIR}/references/step4c_registration_timing.md`.
+
+### Step 4d: PRISMA Figure 1 Arithmetic & Cross-Reference Audit
+
+**Applies to:** systematic reviews and meta-analyses using PRISMA 2020 / PRISMA-DTA /
+PRISMA-P. Triggers when Item 16a (flow diagram) is PRESENT.
+
+**Why this step exists:** the flow diagram is a single checklist item and can pass Step 4
+visually while still containing arithmetic errors (records screened ≠ identified − duplicates;
+sought-for-retrieval ≠ screened − excluded) or text↔figure number disagreements. Senior
+MA reviewers commonly require strict PRISMA 2020 diagram conformance and explicit body↔
+figure number agreement; reviewers who detect these mismatches lose confidence in the
+study's data integrity immediately.
+
+**Four arithmetic checks:**
+1. records screened = records identified − duplicates removed
+2. records sought-for-retrieval = records screened − records excluded (screening)
+3. reports retrieved = sought − reports not retrieved
+4. studies included = reports assessed for eligibility − reports excluded (with reasons)
+
+**Two cross-reference checks:**
+- Body text PRISMA numbers (e.g., "315 records identified, 122 duplicates removed,
+  186 records screened") match Figure 1 box labels 1:1.
+- Reasons for exclusion (Methods + Figure legend) agree on counts and category names.
+
+**Procedure:**
+1. Extract numbers from manuscript Results / PRISMA flow paragraph (regex: integers near
+   keywords `identified`, `duplicates`, `screened`, `excluded`, `sought`, `retrieved`,
+   `assessed`, `included`).
+2. Extract numbers from Figure 1 source — preferred order: (a) `analysis/figures/Figure1_PRISMA.md`
+   markdown manifest, (b) caption text in `manuscript.md`, (c) PPTX text run if `.pptx`
+   exists, (d) manual entry from PNG/SVG.
+3. **Cross-check `analysis/figures/_figure_manifest.md`** (produced by `/make-figures`):
+   verify that the row whose `Type = prisma` (or `Type = prisma-dta`) points at the same
+   file path used as the audit source, and that the row's `Critic` field is `yes` or
+   `partial` (not `no`). A missing manifest row, mismatched path, or `Critic = no` flag
+   logs `[MANIFEST-XREF]` (advisory) — the arithmetic check still runs against the source
+   identified in step 2. Skip this sub-step if `_figure_manifest.md` does not exist (older
+   projects).
+4. Run 4 arithmetic checks; emit PRESENT / MISSING / MISMATCH per equation.
+5. Run 2 cross-reference checks; emit PRESENT / MISSING / MISMATCH per number.
+6. Output `qc/prisma_figure_audit.json` and a short table.
+
+**Flagging:** any MISMATCH or arithmetic failure logs a Part C Action Item with label
+`[PRISMA-FIGURE]`. `fixable_by_ai: false` (numbers must be reconciled by the author).
+
+**Load-on-demand procedural detail** (exact regex set, JSON schema, edge cases —
+duplicates handled across databases, citation searching strand, dual-reviewer screening):
+`${CLAUDE_SKILL_DIR}/references/step4d_prisma_figure_audit.md`.
+
+**Cross-cutting**: integrates with `~/.claude/rules/numerical-safety.md` (PRISMA 5-way
+consistency: text ↔ Figure ↔ extraction CSV ↔ analysis script ↔ supplementary).
+
+### Step 4e: Reporting-Framework Naming Audit
+
+**Applies to:** any manuscript that invokes an AI/extension reporting framework
+(PROBAST+AI, STARD-AI, TRIPOD+AI, TRIPOD-LLM, CONSORT-AI, SPIRIT-AI, PRISMA-DTA, QUADAS-C).
+
+**Why this step exists:** a base reporting tool and its extension are distinct instruments
+with separate citations (manuscript-style-classical §14). Step 1 routes to the right
+checklist but does not police how the framework is *named* in prose. The recurring failures
+are: invoking an extension without ever naming or citing the base instrument it extends;
+mixing `+AI` and `-AI` hyphenation for one family within a single document; coining item
+labels like "12-AI"; and waving at "recent guidance" instead of naming the framework.
+
+**Run the deterministic gate:**
+
+```bash
+python3 "${CLAUDE_SKILL_DIR}/scripts/check_framework_naming.py" \
+  --manuscript manuscript.md --out qc/framework_naming.json --strict
+```
+
+**Verdicts:** `BASE_MISSING` (extension used, base instrument never named standalone) is a
+Major and logs `[FRAMEWORK-NAMING]` in Part C with `fixable_by_ai: true` (insert the base
+name + its citation). `HYPHEN_MIX`, `CITE_MISSING`, `SELF_COINED_LABEL`, and `VAGUE_GUIDANCE`
+are Minor (`fixable_by_ai: true`). Part D JSON includes a `framework_naming` object mirroring
+the script's `claims[]`.
+
+### Step 5: Generate Report
+
+Produce a structured compliance report in two parts.
+
+#### Part A: Summary
+
+```
+## Reporting Guideline Compliance Report
+
+Manuscript: {title}
+Target manuscript file: {manuscript filename, e.g. manuscript_v8.md}
+Target version: {version token from the filename or frontmatter, e.g. v8}
+Guideline: {name and version}
+Date: {YYYY-MM-DD}
+Assessed by: Claude (automated pre-screening)
+
+### Summary
+
+| Status | Count | Percentage |
+|--------|-------|------------|
+| PRESENT | {n} | {%} |
+| PARTIAL | {n} | {%} |
+| MISSING | {n} | {%} |
+| N/A | {n} | {%} |
+| **Total** | **{n}** | **100%** |
+
+Overall compliance: {PRESENT count}/{applicable count} ({%})
+```
+
+#### Part B: Item-by-Item Checklist
+
+```
+### Detailed Checklist
+
+| # | Section | Item | Status | Location | Notes |
+|---|---------|------|--------|----------|-------|
+| 1 | Title/Abstract | {item text} | PRESENT | Title | {notes} |
+| 2 | Introduction | {item text} | MISSING | -- | {suggestion} |
+| ... | ... | ... | ... | ... | ... |
+```
+
+#### Part C: Action Items (for MISSING and PARTIAL)
+
+```
+### Action Items (Priority Order)
+
+1. **[MISSING] Item {N}: {item name}**
+   - Required: {what needs to be added}
+   - Suggested location: {section, paragraph}
+   - Example text: "{draft sentence or phrase}"
+
+2. **[PARTIAL] Item {N}: {item name}**
+   - Current: {what was found}
+   - Needed: {what additional detail is required}
+   - Suggested revision: "{draft revision}"
+```
+
+Order action items by:
+1. Items most journals enforce strictly (e.g., ethics approval, registration, sample size)
+2. Items in the Methods section (easiest to fix)
+3. Items in other sections
+
+#### Part D: Machine-Readable JSON Summary
+
+Append a fenced JSON block at the end of the report. This enables `/write-paper` Phase 7 and `/orchestrate` to parse compliance results programmatically. This block **MUST** be present when invoked with `--json` flag or when called from `/write-paper` Phase 7. It SHOULD also be present in standard invocations (appended after Part C).
+
+```json
+{
+  "check_reporting_version": "1.1",
+  "manuscript_title": "...",
+  "target_manuscript": "manuscript_v8.md",
+  "target_version": "v8",
+  "source_sha256": "<first 12 hex chars of sha256 of the manuscript file bytes>",
+  "guideline": "STARD-AI",
+  "guideline_version": "2025",
+  "date": "YYYY-MM-DD",
+  "total_items": 40,
+  "present": 32,
+  "partial": 4,
+  "missing": 3,
+  "na": 1,
+  "compliance_pct": 88.9,
+  "action_items": [
+    {
+      "item_number": 12,
+      "section": "Methods",
+      "item_name": "Sample size justification",
+      "status": "MISSING",
+      "suggested_location": "Methods, after participant description",
+      "suggested_fix": "Add: 'The sample size was determined based on [rationale]. A minimum of [N] cases was required to achieve [target] precision for the primary endpoint.'",
+      "fixable_by_ai": true
+    },
+    {
+      "item_number": 7,
+      "section": "Methods",
+      "item_name": "Blinding of index test to reference standard",
+      "status": "PARTIAL",
+      "current_text": "Readers were blinded",
+      "needed": "Specify what readers were blinded to (reference standard results, clinical information, other reader results)",
+      "suggested_fix": "Expand to: 'Readers interpreted [index test] images blinded to the reference standard results, clinical information, and other readers' assessments.'",
+      "fixable_by_ai": true
+    }
+  ]
+}
+```
+
+**Field definitions:**
+- `compliance_pct`: `present / (total_items - na) * 100`, rounded to one decimal
+- `action_items`: Array of MISSING and PARTIAL items only (PRESENT and N/A excluded)
+- `fixable_by_ai`: `true` if the fix involves inserting or expanding text with information available in the manuscript or inferable from context; `false` if it requires external information (e.g., registration number, IRB approval number, specific protocol details only the author knows)
+- `suggested_fix`: Concrete draft text that can be inserted or used to expand an existing sentence
+
+---
+
+## Assessment Standards
+
+### Be Strict
+
+- PARTIAL means the item is mentioned but lacks specificity. For example:
+  - "We used appropriate statistical tests" = PARTIAL (which tests?)
+  - "We used the Mann-Whitney U test for continuous variables and Fisher's exact test for categorical variables" = PRESENT
+- A vague reference does not count as PRESENT. The detail level must match what the guideline expects.
+
+### Be Specific in Suggestions
+
+- For MISSING items, provide a draft sentence the user can insert.
+- For PARTIAL items, point to the exact gap and suggest specific additions.
+- Reference the specific manuscript section where the addition should go.
+
+### Common Gaps to Watch For
+
+These items are frequently missing in medical manuscripts:
+
+1. **Study registration number** (CONSORT, PRISMA, STARD)
+2. **Registration / amendment date consistency** (PRISMA 2020, PRISMA-DTA, CONSORT, SPIRIT) — run Step 4c whenever a registration identifier is present
+3. **Sample size justification** (CONSORT, STROBE, STARD)
+4. **Missing data handling** (all guidelines)
+5. **Blinding details** (CONSORT, STARD)
+6. **Funding and conflicts of interest** (all guidelines)
+7. **Ethics approval with committee name and approval number** (all guidelines)
+8. **Data availability statement** (increasingly required)
+9. **AI-specific: training/validation/test split details** (TRIPOD+AI, CLAIM, STARD-AI)
+10. **AI-specific: model architecture and hyperparameters** (TRIPOD+AI, CLAIM, STARD-AI)
+11. **AI-specific: failure mode analysis** (CLAIM, STARD-AI)
+12. **AI-specific: fairness/bias assessment** (STARD-AI)
+13. **AI-specific: commercial interests and data/code availability** (STARD-AI)
+
+---
+
+## PRISMA Cascade Arithmetic Auto-Verify
+
+PRISMA 2020 flow diagrams chain a cascade of subtractions (database
+records → after dedup → title/abstract screened → full-text reviewed →
+included in synthesis). Off-by-one errors in the prose cascade are a
+high-frequency reviewer red flag (e.g., `151 + 108 + 39 + 1 + 1 + 4 =
+304` followed by a prose summary "305" four lines later).
+
+When PRISMA 2020 or PRISMA-DTA is selected and round-by-round
+screening TSV artifacts are available, run the cascade auto-verify:
+
+```bash
+python "${CLAUDE_SKILL_DIR}/scripts/prisma_cascade_check.py" \
+    --round1 2_Screening/round1.tsv \
+    --round2 2_Screening/round2.tsv \
+    --round3 2_Screening/round3_adjudication.tsv \
+    --manuscript manuscript.md \
+    --out qc/prisma_cascade.json
+```
+
+The script:
+1. Reads the round TSVs and counts `INCLUDE` / `EXCLUDE` / `MAYBE`
+   decisions per round.
+2. Computes the cascade arithmetic from raw decisions (no prose).
+3. Optionally grep the manuscript for matching stage-count claims and
+   emits per-stage drift when the prose disagrees.
+
+Treat any `manuscript_drift` entry as a P0 blocker — fix the prose to
+match the computed cascade and re-run.
+
+## Submission Checklist Export
+
+Many journals require a filled reporting checklist to be submitted alongside the manuscript.
+When the user asks for a submission-ready checklist, format the output as:
+
+```
+{Guideline Name} Checklist
+
+Manuscript title: {title}
+Date: {YYYY-MM-DD}
+
+| Item # | Checklist Item | Reported on Page # | Reported in Section |
+|--------|---------------|-------------------|-------------------|
+| 1 | {item text} | {page or N/A} | {section} |
+| 2 | {item text} | {page or N/A} | {section} |
+| ... | ... | ... | ... |
+```
+
+Page numbers should be filled in by the user after final formatting. Use section names as placeholders.
+
+---
+
+## Skill Interactions
+
+| When | Call | Purpose |
+|------|------|---------|
+| During manuscript writing | `/write-paper` Phase 7 | Final compliance check |
+| Need to add Methods text | `/write-paper` Phase 3 | Draft missing Methods content |
+| Need statistical details | `/analyze-stats` | Generate missing statistical reporting |
+| Need flow diagram | `/make-figures` | Generate CONSORT/STARD/PRISMA diagram |
+
+---
+
+## Error Handling
+
+- If the manuscript file cannot be read, ask the user for the correct path.
+- If the study type is ambiguous, ask the user to confirm before selecting a guideline.
+- If a checklist item is genuinely unclear in its applicability, mark as N/A with justification.
+- This is a pre-screening tool. Always remind the user that final compliance should be verified by all co-authors and ideally by a methodologist.
+
+## Language
+
+- Checklist content and compliance report: English
+- Communication with user: Match user's preferred language
+- Medical terms: English only
+
+## Anti-Hallucination
+
+- **Never fabricate references.** All citations must be verified via `/search-lit` with confirmed DOI or PMID. Mark unverified references as `[UNVERIFIED - NEEDS MANUAL CHECK]`.
+- **Never invent clinical definitions, diagnostic criteria, or guideline recommendations.** If uncertain, flag with `[VERIFY]` and ask the user.
+- **Never fabricate numerical results** — compliance percentages, scores, effect sizes, or sample sizes must come from actual data or analysis output.
+- If a reporting guideline item, journal policy, or clinical standard is uncertain, state the uncertainty rather than guessing.
+
+---
+
+## Gates
+
+| Gate | Severity | Trigger | Action on fail |
+|---|---|---|---|
+| Mandatory items present | ENFORCED at submission | < 100% of guideline-mandatory items marked PRESENT | Auto-fix MISSING items where text exists; otherwise route to `/write-paper` Phase 7 for re-draft |
+| Step 4d PRISMA Figure 1 arithmetic & cross-reference audit (PRISMA / PRISMA-DTA only) | ENFORCED for SR/MA | flow numbers don't sum (e.g., screened ≠ included + excluded), or in-text counts mismatch flow diagram | HALT; reconcile against extraction artifacts |
+| Optional items (e.g., supplementary AI declarations) | ADVISORY | < 80% of optional items present | warn; user accepts |
+| Cross-reporting-guideline routing (study type → guideline) | ENFORCED | study type undeclared or guideline missing | Ask user; do not silently default |

package/skills/check-reporting/references/LICENSES.md

@@ -0,0 +1,41 @@
+# Checklist Licenses
+
+Attribution for bundled reporting guideline checklists.
+
+| File | Guideline | Reference | License |
+|------|-----------|-----------|---------|
+| STROBE.md | STROBE 2007 | von Elm E et al. PLoS Med 2007 | CC BY |
+| STARD.md | STARD 2015 | Bossuyt PM et al. BMJ 2015 | CC BY 4.0 |
+| STARD_AI.md | STARD-AI 2025 | Sounderajah V et al. Nat Med 2025;31:3283-3289 | CC BY |
+| TRIPOD_AI.md | TRIPOD+AI 2024 | Collins GS et al. BMJ 2024 | CC BY 4.0 |
+| PRISMA_2020.md | PRISMA 2020 | Page MJ et al. BMJ 2021 | CC BY |
+| ARRIVE_2.md | ARRIVE 2.0 | Percie du Sert N et al. PLoS Biol 2020 | CC0 |
+| PRISMA_DTA.md | PRISMA-DTA 2018 | McInnes MDF et al. JAMA 2018 | CC BY |
+| QUADAS2.md | QUADAS-2 | Whiting PF et al. Ann Intern Med 2011 | CC BY |
+| RoB2.md | RoB 2 | Sterne JAC et al. BMJ 2019 | CC BY |
+| ROBINS_I.md | ROBINS-I | Sterne JAC et al. BMJ 2016 | CC BY |
+| PROBAST.md | PROBAST | Wolff RF et al. Ann Intern Med 2019 | CC BY |
+| NOS.md | Newcastle-Ottawa Scale | Wells GA et al. Ottawa Hospital Research Institute | Public Domain |
+| MI_CLEAR_LLM.md | MI-CLEAR-LLM 2025 | Park SH et al. Korean J Radiol 2024;25(10):865-868; 2025 update KJR 2025;26(12):1123-1132 | CC BY-NC 4.0 |
+| CONSORT.md | CONSORT 2025 | Hopewell S et al. BMJ 2025;389:e081123 | CC BY 4.0 |
+| SPIRIT.md | SPIRIT 2025 | Chan AW et al. BMJ 2025;389:e081477 | CC BY 4.0 |
+| CARE.md | CARE 2013 | Gagnier JJ et al. J Clin Epidemiol 2014;67(1):46-51 | CC BY-NC 4.0 |
+| CLAIM_2024.md | CLAIM 2024 Update | Tejani AS et al. Radiol Artif Intell 2024;6(4):e240300 | RSNA, open access |
+
+These files are educational summaries of published assessment tools. The original
+checklist documents should be cited in any manuscript that uses them.
+
+## Third-party licenses (NOT covered by the repository MIT license)
+
+Most files above are CC BY / CC0 / public domain and redistribute freely with
+attribution. The following retain their own licenses and are **not** placed under
+this repository's MIT license — downstream use must comply with the original terms:
+
+- **CARE.md** and **MI_CLEAR_LLM.md** are **CC BY-NC 4.0**: free to copy and
+  redistribute **with attribution for non-commercial purposes**. Commercial use
+  requires permission from the original rights holders.
+- **CLAIM_2024.md** is an educational summary of an RSNA open-access checklist
+  (© RSNA). Cite Tejani et al. 2024; consult RSNA for commercial reuse terms.
+
+All files remain educational summaries that cite their source; they do not relicense
+the underlying guidelines.