scoping

# Scoping Conducts a focused conversation to establish the research scope, then generates a scope document that guides all subsequent writing. ## Prerequisites - `inventory.md` must exist (from context-ingestion step) - `notes/irb-summary.md` may exist (if IRB document was provided) - Review inventory before starting conversation ## Workflow ``` [Read inventory.md and notes/irb-summary.md] │ ▼ [Ask: Research Question] │ ▼ [Ask: Key Findings] ─── Cross-reference with data inventory │ ▼ [Confirm: Constraints] ─── From config.md │ ▼ [Ask: Additional Context] │ ▼ [IRB Scope Comparison] ─── If IRB exists, compare and confirm discrepancies │ ▼ [Generate scope.md and notes/irb-scope-comparison.md] ``` ## Step 1: Review Inventory and IRB Before asking questions, read `inventory.md` to understand: - How many papers are available for literature context - What data files exist (this informs what results are possible) - What figures are already generated - Whether code repository is available Also check if `notes/irb-summary.md` exists. If it does, read it to understand: - IRB-approved population and inclusion/exclusion criteria - Approved procedures and endpoints - Sample size justification - Study design This context helps ask informed questions and validate user responses. Note that IRB scope is often broader than actual research scope. ## Step 2: Scoping Conversation Ask questions **one at a time**. Wait for response before proceeding. ### Question 1: Research Question > "What research question does this study address? > > Try to frame it as a specific, answerable question. For example: > - 'Can MR fingerprinting differentiate tumor recurrence from treatment effect?' > - 'Does quantitative T1 mapping predict treatment response in glioblastoma?'" **Good research questions have:** - Specific population/context - Clear intervention or exposure - Measurable outcome If vague, ask follow-up to clarify. ### Question 2: Key Findings > "What are the key findings from your analysis? > > I can see from your data that you have [summarize data files from inventory]. > What were the main results?" **Cross-check with inventory:** - If user mentions statistics, verify data files could support them - If user mentions figures, check they exist in `figures/` - If claims seem inconsistent with available data, ask for clarification Ask for: 1. Primary finding (the main result) 2. Secondary findings (supporting results) 3. Any unexpected or negative results ### Question 3: Constraints > "I see from your config that you're targeting [journal] with a [word_limit] word limit. > > Are there any other constraints I should know about? > - Specific formatting requirements? > - Required sections or subsections? > - Exclusions (topics to avoid)?" ### Question 4: Additional Context (Optional) > "Is there anything else I should know about this study? > > For example: > - Study limitations you want to acknowledge > - Specific papers you want to cite or respond to > - Clinical implications to emphasize" ## Step 3: IRB Scope Comparison (If IRB Exists) **Skip this step if `notes/irb-summary.md` does not exist.** After gathering user's stated scope, compare it against IRB document and present discrepancies for confirmation. ### Comparison Table Present to user: > "I've compared your stated research scope with the IRB document. > > | Aspect | IRB Document | Your Stated Scope | > |--------|--------------|-------------------| > | Population | [from IRB] | [from user] | > | Sample size | [from IRB] | [from user] | > | Endpoints | [from IRB] | [from user] | > | Procedures | [from IRB] | [from user] | > > **Please confirm:** > 1. Are these differences intentional? (subset of approved protocol) > 2. Any context for the narrower scope? (e.g., 'questionnaire data not yet analyzed') > 3. Anything I've misunderstood?" ### Document User Responses Create `notes/irb-scope-comparison.md`: ```markdown # IRB vs Actual Scope Comparison **Generated**: [timestamp] **IRB Source**: [filename from irb-summary.md] ## Comparison | Aspect | IRB Document | Actual Scope | Explanation | |--------|--------------|--------------|-------------| | Population | [from IRB] | [from user] | [user explanation] | | Sample size | [from IRB] | [from user] | [user explanation] | | Endpoints | [from IRB] | [from user] | [user explanation] | | Procedures | [from IRB] | [from user] | [user explanation] | ## User Confirmation - **Differences intentional?**: [yes/no + explanation] - **Context for narrower scope**: [user response] - **Clarifications**: [any corrections to understanding] ## Implications for Manuscript - [Note any elements from IRB that should NOT appear in manuscript] - [Note any elements that need careful framing] ``` This document provides audit trail and guides later steps when they need to understand why IRB and manuscript scope differ. ## Step 4: Generate scope.md After conversation, generate structured scope document: ```markdown # Manuscript Scope Generated: [timestamp] ## Research Question [User's research question, cleaned up if needed] ## Hypothesis [Inferred or stated hypothesis] ## Key Findings ### Primary Finding [Main result with expected statistics] ### Secondary Findings 1. [Finding 2] 2. [Finding 3] ### Negative/Null Results - [If any] ## Target Publication - **Journal**: [from config] - **Word Limit**: [from config] - **Citation Style**: [from config] ## Constraints - [Any additional constraints from conversation] ## Study Context ### Population [Inferred from data/conversation] ### Methods Overview [Brief summary based on code inventory] ### Limitations to Address - [User-specified limitations] ## Materials Available ### Literature - [n] PDFs in papers/ folder - Key papers to emphasize: [if mentioned] ### Data - [List key data files and what they contain] ### Figures - [List figures and what they show] ### Code - Repository: [url] - Analysis approach: [inferred from code inventory] ### IRB Document - **Available**: [yes/no] - **Ethics Approval Number**: [from irb-summary.md or "to be added manually"] - **Scope Notes**: [see notes/irb-scope-comparison.md for differences] ## Writing Guidance ### Tone [Infer from journal: clinical, technical, etc.] ### Emphasis [What to highlight based on conversation] ### Avoid [What to minimize or exclude] ``` ## Validation Checklist Before saving scope.md, verify: - [ ] Research question is specific and answerable - [ ] Key findings are supported by available data - [ ] Word limit is realistic for content - [ ] All necessary context is captured - [ ] If IRB exists: discrepancies documented and confirmed by user ## Output Save to: - `project/scope.md` - Main scope document - `notes/irb-scope-comparison.md` - IRB comparison (if IRB exists) Summarize back to user: > "I've created the scope document. Here's the summary: > > **Research Question**: [question] > **Primary Finding**: [finding] > **Target**: [journal], [word_limit] words > > Ready to proceed with literature review?" Return to parent skill.