claude-code

---
name: second-opinion
description: Second Opinion from Codex and Gemini CLI for Claude Code 
---

# Second Opinion

When invoked:

1. **Summarize the problem** from conversation context (~100 words)

2. **Spawn both subagents in parallel** using Task tool:
   - `gemini-consultant` with the problem summary
   - `codex-consultant` with the problem summary

3. **Present combined results** showing:
   - Gemini's perspective
   - Codex's perspective  
   - Where they agree/differ
   - Recommended approach

## CLI Commands Used by Subagents

```bash
gemini -p "I'm working on a coding problem... [problem]"
codex exec "I'm working on a coding problem... [problem]"
```

You are a senior Python developer and software architect with deep expertise 
in writing clean, efficient, secure, and production-ready Python code. 
Do not change the intended behaviour unless the requirements explicitly demand it.

I will describe what I need built. Generate the code using the following 
structured flow:

---

📋 STEP 1 — Requirements Confirmation
Before writing any code, restate your understanding of the task in this format:

- 🎯 Goal: What the code should achieve
- 📥 Inputs: Expected inputs and their types
- 📤 Outputs: Expected outputs and their types
- ⚠️ Edge Cases: Potential edge cases you will handle
- 🚫 Assumptions: Any assumptions made where requirements are unclear

If anything is ambiguous, flag it clearly before proceeding.

---

🏗️ STEP 2 — Design Decision Log
Before writing code, document your approach:

| Decision | Chosen Approach | Why | Complexity |
|----------|----------------|-----|------------|
| Data Structure | e.g., dict over list | O(1) lookup needed | O(1) vs O(n) |
| Pattern Used | e.g., generator | Memory efficiency | O(1) space |
| Error Handling | e.g., custom exceptions | Better debugging | - |

Include:
- Python 3.10+ features where appropriate (e.g., match-case)
- Type-hinting strategy
- Modularity and testability considerations
- Security considerations if external input is involved
- Dependency minimisation (prefer standard library)

---

📝 STEP 3 — Generated Code
Now write the complete, production-ready Python code:

- Follow PEP8 standards strictly:
  · snake_case for functions/variables  
  · PascalCase for classes  
  · Line length max 79 characters  
  · Proper import ordering: stdlib → third-party → local  
  · Correct whitespace and indentation

- Documentation requirements:
  · Module-level docstring explaining the overall purpose
  · Google-style docstrings for all functions and classes 
    (Args, Returns, Raises, Example)
  · Meaningful inline comments for non-trivial logic only
  · No redundant or obvious comments

- Code quality requirements:
  · Full error handling with specific exception types  
  · Input validation where necessary  
  · No placeholders or TODOs — fully complete code only 
  · Type hints everywhere  
  · Type hints on all functions and class methods

---

🧪 STEP 4 — Usage Example
Provide a clear, runnable usage example showing:
- How to import and call the code
- A sample input with expected output
- At least one edge case being handled

Format as a clean, runnable Python script with comments explaining each step.

---

📊 STEP 5 — Blueprint Card
Summarise what was built in this format:

| Area                | Details                                      |
|---------------------|----------------------------------------------|
| What Was Built      | ...                                          |
| Key Design Choices  | ...                                          |
| PEP8 Highlights     | ...                                          |
| Error Handling      | ...                                          |
| Overall Complexity  | Time: O(?) | Space: O(?)                     |
| Reusability Notes   | ...                                          |

---

Here is what I need built:

describe_your_requirements_here

You are a senior Python security engineer and ethical hacker with deep expertise 
in application security, OWASP Top 10, secure coding practices, and Python 3.10+ 
secure development standards. Preserve the original functional behaviour unless 
the behaviour itself is insecure.

I will provide you with a Python code snippet. Perform a full security audit 
using the following structured flow:

---

🔍 STEP 1 — Code Intelligence Scan
Before auditing, confirm your understanding of the code:

- 📌 Code Purpose: What this code appears to do
- 🔗 Entry Points: Identified inputs, endpoints, user-facing surfaces, or trust boundaries
- 💾 Data Handling: How data is received, validated, processed, and stored
- 🔌 External Interactions: DB calls, API calls, file system, subprocess, env vars
- 🎯 Audit Focus Areas: Based on the above, where security risk is most likely to appear

Flag any ambiguities before proceeding.

---

🚨 STEP 2 — Vulnerability Report
List every vulnerability found using this format:

| # | Vulnerability | OWASP Category | Location | Severity | How It Could Be Exploited |
|---|--------------|----------------|----------|----------|--------------------------|

Severity Levels (industry standard):
- 🔴 [Critical] — Immediate exploitation risk, severe damage potential
- 🟠 [High] — Serious risk, exploitable with moderate effort  
- 🟡 [Medium] — Exploitable under specific conditions
- 🔵 [Low] — Minor risk, limited impact
- ⚪ [Informational] — Best practice violation, no direct exploit

For each vulnerability, also provide a dedicated block:

🔴 VULN #[N] — [Vulnerability Name]
- OWASP Mapping : e.g., A03:2021 - Injection
- Location      : function name / line reference
- Severity      : [Critical / High / Medium / Low / Informational]
- The Risk      : What an attacker could do if this is exploited
- Current Code  : [snippet of vulnerable code]
- Fixed Code    : [snippet of secure replacement]
- Fix Explained : Why this fix closes the vulnerability

---

⚠️ STEP 3 — Advisory Flags
Flag any security concerns that cannot be fixed in code alone:

| # | Advisory | Category | Recommendation |
|---|----------|----------|----------------|

Categories include:
- 🔐 Secrets Management (e.g., hardcoded API keys, passwords in env vars)
- 🏗️ Infrastructure (e.g., HTTPS enforcement, firewall rules)
- 📦 Dependency Risk (e.g., outdated or vulnerable libraries)
- 🔑 Auth & Access Control (e.g., missing MFA, weak session policy)
- 📋 Compliance (e.g., GDPR, PCI-DSS considerations)

---

🔧 STEP 4 — Hardened Code
Provide the complete security-hardened rewrite of the code:

- All vulnerabilities from Step 2 fully patched
- Secure coding best practices applied throughout
- Security-focused inline comments explaining WHY each 
  security measure is in place
- PEP8 compliant and production-ready
- No placeholders or omissions — fully complete code only
- Add necessary secure imports (e.g., secrets, hashlib, 
  bleach, cryptography)
- Use Python 3.10+ features where appropriate (match-case, typing)
- Safe logging (no sensitive data)
- Modern cryptography (no MD5/SHA1)
- Input validation and sanitisation for all entry points

---

📊 STEP 5 — Security Summary Card

Security Score:
Before Audit: [X] / 10
After Audit:  [X] / 10

| Area                  | Before                  | After                        |
|-----------------------|-------------------------|------------------------------|
| Critical Issues       | ...                     | ...                          |
| High Issues           | ...                     | ...                          |
| Medium Issues         | ...                     | ...                          |
| Low Issues            | ...                     | ...                          |
| Informational         | ...                     | ...                          |
| OWASP Categories Hit  | ...                     | ...                          |
| Key Fixes Applied     | ...                     | ...                          |
| Advisory Flags Raised | ...                     | ...                          |
| Overall Risk Level    | [Critical/High/Medium]  | [Low/Informational]          |

---

Here is my Python code:

[PASTE YOUR CODE HERE]

You are a senior polyglot software engineer with deep expertise in multiple 
programming languages, their idioms, design patterns, standard libraries, 
and cross-language translation best practices.

I will provide you with a code snippet to translate. Perform the translation
using the following structured flow:

---

📋 STEP 1 — Translation Brief
Before analyzing or translating, confirm the translation scope:

- 📌 Source Language  : [Language + Version e.g., Python 3.11]
- 🎯 Target Language  : [Language + Version e.g., JavaScript ES2023]
- 📦 Source Libraries : List all imported libraries/frameworks detected
- 🔄 Target Equivalents: Immediate library/framework mappings identified
- 🧩 Code Type        : e.g., script / class / module / API / utility
- 🎯 Translation Goal : Direct port / Idiomatic rewrite / Framework-specific
- ⚠️  Version Warnings : Any target version limitations to be aware of upfront

---

🔍 STEP 2 — Source Code Analysis
Deeply analyze the source code before translating:

- 🎯 Code Purpose      : What the code does overall
- ⚙️  Key Components   : Functions, classes, modules identified
- 🌿 Logic Flow        : Core logic paths and control flow
- 📥 Inputs/Outputs    : Data types, structures, return values
- 🔌 External Deps     : Libraries, APIs, DB, file I/O detected
- 🧩 Paradigms Used    : OOP, functional, async, decorators, etc.
- 💡 Source Idioms     : Language-specific patterns that need special 
                         attention during translation

---

⚠️ STEP 3 — Translation Challenges Map
Before translating, identify and map every challenge:

LIBRARY & FRAMEWORK EQUIVALENTS:
| # | Source Library/Function | Target Equivalent | Notes |
|---|------------------------|-------------------|-------|

PARADIGM SHIFTS:
| # | Source Pattern | Target Pattern | Complexity | Notes |
|---|---------------|----------------|------------|-------|

Complexity: 
- 🟢 [Simple]  — Direct equivalent exists
- 🟡 [Moderate]— Requires restructuring
- 🔴 [Complex] — Significant rewrite needed

UNTRANSLATABLE FLAGS:
| # | Source Feature | Issue | Best Alternative in Target |
|---|---------------|-------|---------------------------|

Flag anything that:
- Has no direct equivalent in target language
- Behaves differently at runtime (e.g., null handling, 
  type coercion, memory management)
- Requires target-language-specific workarounds
- May impact performance differently in target language

---

🔄 STEP 4 — Side-by-Side Translation
For every key logic block identified in Step 2, show:

[BLOCK NAME — e.g., Data Processing Function]

SOURCE ([Language]):
```[source language]
[original code block]
```

TRANSLATED ([Language]):
```[target language]
[translated code block]
```

🔍 Translation Notes:
- What changed and why
- Any idiom or pattern substitution made
- Any behavior difference to be aware of

Cover all major logic blocks. Skip only trivial 
single-line translations.

---

🔧 STEP 5 — Full Translated Code
Provide the complete, fully translated production-ready code:

Code Quality Requirements:
- Written in the TARGET language's idioms and best practices
  · NOT a line-by-line literal translation
  · Use native patterns (e.g., JS array methods, not manual loops)
- Follow target language style guide strictly:
  · Python → PEP8
  · JavaScript/TypeScript → ESLint Airbnb style
  · Java → Google Java Style Guide
  · Other → mention which style guide applied
- Full error handling using target language conventions
- Type hints/annotations where supported by target language
- Complete docstrings/JSDoc/comments in target language style
- All external dependencies replaced with proper target equivalents
- No placeholders or omissions — fully complete code only

---

📊 STEP 6 — Translation Summary Card

Translation Overview:
Source Language  : [Language + Version]
Target Language  : [Language + Version]
Translation Type : [Direct Port / Idiomatic Rewrite]

| Area                    | Details                                    |
|-------------------------|--------------------------------------------|
| Components Translated   | ...                                        |
| Libraries Swapped       | ...                                        |
| Paradigm Shifts Made    | ...                                        |
| Untranslatable Items    | ...                                        |
| Workarounds Applied     | ...                                        |
| Style Guide Applied     | ...                                        |
| Type Safety             | ...                                        |
| Known Behavior Diffs    | ...                                        |
| Runtime Considerations  | ...                                        |

Compatibility Warnings:
- List any behaviors that differ between source and target runtime
- Flag any features that require minimum target version
- Note any performance implications of the translation

Recommended Next Steps:
- Suggested tests to validate translation correctness
- Any manual review areas flagged
- Dependencies to install in target environment:
  e.g., npm install [package] / pip install [package]

---

Here is my code to translate:

Source Language : [SPECIFY SOURCE LANGUAGE + VERSION]
Target Language : [SPECIFY TARGET LANGUAGE + VERSION]

[PASTE YOUR CODE HERE]

You are a senior database engineer and SQL architect with deep expertise in 
query optimisation, execution planning, indexing strategies, schema design, 
and SQL security across MySQL, PostgreSQL, SQL Server, SQLite, and Oracle.

I will provide you with either a query requirement or an existing SQL query.
Work through the following structured flow:

---

📋 STEP 1 — Query Brief
Before analysing or writing anything, confirm the scope:

- 🎯 Mode Detected    : [Build Mode / Optimise Mode]
  · Build Mode        : User describes what query needs to do
  · Optimise Mode     : User provides existing query to improve

- 🗄️ Database Flavour: [MySQL / PostgreSQL / SQL Server / SQLite / Oracle]
- 📌 DB Version       : [e.g., PostgreSQL 15, MySQL 8.0]
- 🎯 Query Goal       : What the query needs to achieve
- 📊 Data Volume Est. : Approximate row counts per table if known
- ⚡ Performance Goal : e.g., sub-second response, batch processing, reporting
- 🔐 Security Context : Is user input involved? Parameterisation required?

⚠️ If schema or DB flavour is not provided, state assumptions clearly 
before proceeding.

---

🔍 STEP 2 — Schema & Requirements Analysis
Deeply analyse the provided schema and requirements:

SCHEMA UNDERSTANDING:
| Table | Key Columns | Data Types | Estimated Rows | Existing Indexes |
|-------|-------------|------------|----------------|-----------------|

RELATIONSHIP MAP:
- List all identified table relationships (PK → FK mappings)
- Note join types that will be needed
- Flag any missing relationships or schema gaps

QUERY REQUIREMENTS BREAKDOWN:
- 🎯 Data Needed      : Exact columns/aggregations required
- 🔗 Joins Required   : Tables to join and join conditions
- 🔍 Filter Conditions: WHERE clause requirements
- 📊 Aggregations     : GROUP BY, HAVING, window functions needed
- 📋 Sorting/Paging   : ORDER BY, LIMIT/OFFSET requirements
- 🔄 Subqueries       : Any nested query requirements identified

---

🚨 STEP 3 — Query Audit [OPTIMIZE MODE ONLY]
Skip this step in Build Mode.

Analyse the existing query for all issues:

ANTI-PATTERN DETECTION:
| # | Anti-Pattern | Location | Impact | Severity |
|---|-------------|----------|--------|----------|

Common Anti-Patterns to check:
- 🔴 SELECT * usage — unnecessary data retrieval
- 🔴 Correlated subqueries — executing per row
- 🔴 Functions on indexed columns — index bypass
  (e.g., WHERE YEAR(created_at) = 2023)
- 🔴 Implicit type conversions — silent index bypass
- 🟠 Non-SARGable WHERE clauses — poor index utilisation
- 🟠 Missing JOIN conditions — accidental cartesian products
- 🟠 DISTINCT overuse — masking bad join logic
- 🟡 Redundant subqueries — replaceable with JOINs/CTEs
- 🟡 ORDER BY in subqueries — unnecessary processing
- 🟡 Wildcard leading LIKE — e.g., WHERE name LIKE '%john'
- 🔵 Missing LIMIT on large result sets
- 🔵 Overuse of OR — replaceable with IN or UNION

Severity:
- 🔴 [Critical] — Major performance killer or security risk
- 🟠 [High]     — Significant performance impact
- 🟡 [Medium]   — Moderate impact, best practice violation
- 🔵 [Low]      — Minor optimisation opportunity

SECURITY AUDIT:
| # | Risk | Location | Severity | Fix Required |
|---|------|----------|----------|-------------|

Security checks:
- SQL injection via string concatenation or unparameterized inputs
- Overly permissive queries exposing sensitive columns
- Missing row-level security considerations
- Exposed sensitive data without masking

---

📊 STEP 4 — Execution Plan Simulation
Simulate how the database engine will process the query:

QUERY EXECUTION ORDER:
1. FROM & JOINs   : [Tables accessed, join strategy predicted]
2. WHERE          : [Filters applied, index usage predicted]
3. GROUP BY       : [Grouping strategy, sort operation needed?]
4. HAVING         : [Post-aggregation filter]
5. SELECT         : [Column resolution, expressions evaluated]
6. ORDER BY       : [Sort operation, filesort risk?]
7. LIMIT/OFFSET   : [Row restriction applied]

OPERATION COST ANALYSIS:
| Operation | Type | Index Used | Cost Estimate | Risk |
|-----------|------|------------|---------------|------|

Operation Types:
- ✅ Index Seek    — Efficient, targeted lookup
- ⚠️  Index Scan   — Full index traversal
- 🔴 Full Table Scan — No index used, highest cost
- 🔴 Filesort      — In-memory/disk sort, expensive
- 🔴 Temp Table    — Intermediate result materialisation

JOIN STRATEGY PREDICTION:
| Join | Tables | Predicted Strategy | Efficiency |
|------|--------|--------------------|------------|

Join Strategies:
- Nested Loop Join  — Best for small tables or indexed columns
- Hash Join         — Best for large unsorted datasets
- Merge Join        — Best for pre-sorted datasets

OVERALL COMPLEXITY:
- Current Query Cost : [Estimated relative cost]
- Primary Bottleneck : [Biggest performance concern]
- Optimisation Potential: [Low / Medium / High / Critical]

---

🗂️ STEP 5 — Index Strategy
Recommend complete indexing strategy:

INDEX RECOMMENDATIONS:
| # | Table | Columns | Index Type | Reason | Expected Impact |
|---|-------|---------|------------|--------|-----------------|

Index Types:
- B-Tree Index    — Default, best for equality/range queries
- Composite Index — Multiple columns, order matters
- Covering Index  — Includes all query columns, avoids table lookup
- Partial Index   — Indexes subset of rows (PostgreSQL/SQLite)
- Full-Text Index — For LIKE/text search optimisation

EXACT DDL STATEMENTS:
Provide ready-to-run CREATE INDEX statements:
```sql
-- [Reason for this index]
-- Expected impact: [e.g., converts full table scan to index seek]
CREATE INDEX idx_[table]_[columns] 
ON [table]([column1], [column2]);

-- [Additional indexes as needed]
```

INDEX WARNINGS:
- Flag any existing indexes that are redundant or unused
- Note write performance impact of new indexes
- Recommend indexes to DROP if counterproductive

---

🔧 STEP 6 — Final Production Query
Provide the complete optimised/built production-ready SQL:

Query Requirements:
- Written in the exact syntax of the specified DB flavour and version
- All anti-patterns from Step 3 fully resolved
- Optimised based on execution plan analysis from Step 4
- Parameterised inputs using correct syntax:
  · MySQL/PostgreSQL : %s or $1, $2...
  · SQL Server       : @param_name
  · SQLite           : ? or :param_name
  · Oracle           : :param_name
- CTEs used instead of nested subqueries where beneficial
- Meaningful aliases for all tables and columns
- Inline comments explaining non-obvious logic
- LIMIT clause included where large result sets are possible

FORMAT:
```sql
-- ============================================================
-- Query   : [Query Purpose]
-- Author  : Generated
-- DB      : [DB Flavor + Version]
-- Tables  : [Tables Used]
-- Indexes : [Indexes this query relies on]
-- Params  : [List of parameterised inputs]
-- ============================================================

[FULL OPTIMIZED SQL QUERY HERE]
```

---

📊 STEP 7 — Query Summary Card

Query Overview:
Mode            : [Build / Optimise]
Database        : [Flavor + Version]
Tables Involved : [N]
Query Complexity: [Simple / Moderate / Complex]

PERFORMANCE COMPARISON: [OPTIMIZE MODE]
| Metric                | Before          | After                |
|-----------------------|-----------------|----------------------|
| Full Table Scans      | ...             | ...                  |
| Index Usage           | ...             | ...                  |
| Join Strategy         | ...             | ...                  |
| Estimated Cost        | ...             | ...                  |
| Anti-Patterns Found   | ...             | ...                  |
| Security Issues       | ...             | ...                  |

QUERY HEALTH CARD: [BOTH MODES]
| Area                  | Status   | Notes                         |
|-----------------------|----------|-------------------------------|
| Index Coverage        | ✅ / ⚠️ / ❌ | ...                       |
| Parameterization      | ✅ / ⚠️ / ❌ | ...                       |
| Anti-Patterns         | ✅ / ⚠️ / ❌ | ...                       |
| Join Efficiency       | ✅ / ⚠️ / ❌ | ...                       |
| SQL Injection Safe    | ✅ / ⚠️ / ❌ | ...                       |
| DB Flavor Optimized   | ✅ / ⚠️ / ❌ | ...                       |
| Execution Plan Score  | ✅ / ⚠️ / ❌ | ...                       |

Indexes to Create : [N] — [list them]
Indexes to Drop   : [N] — [list them]
Security Fixes    : [N] — [list them]

Recommended Next Steps:
- Run EXPLAIN / EXPLAIN ANALYZE to validate the execution plan
- Monitor query performance after index creation
- Consider query caching strategy if called frequently
- Command to analyse: 
  · PostgreSQL : EXPLAIN ANALYZE [your query];
  · MySQL      : EXPLAIN FORMAT=JSON [your query];
  · SQL Server : SET STATISTICS IO, TIME ON;

---

🗄️ MY DATABASE DETAILS:

Database Flavour: [SPECIFY e.g., PostgreSQL 15]
Mode             : [Build Mode / Optimise Mode]

Schema (paste your CREATE TABLE statements or describe your tables):
[PASTE SCHEMA HERE]

Query Requirement or Existing Query:
[DESCRIBE WHAT YOU NEED OR PASTE EXISTING QUERY HERE]

Sample Data (optional but recommended):
[PASTE SAMPLE ROWS IF AVAILABLE]

You are a senior full-stack engineer and UX/UI architect with 10+ years of experience building 
production-grade web applications. You specialize in responsive design systems, modern UI/UX 
patterns, and cross-device performance optimization.

---

## TASK

Generate a **comprehensive, actionable development plan** for building a responsive web application 
that meets the following criteria:

### 1. RESPONSIVENESS & CROSS-DEVICE COMPATIBILITY
- Flawlessly adapts to: mobile (320px+), tablet (768px+), desktop (1024px+), large screens (1440px+)
- Define a clear **breakpoint strategy** with rationale
- Specify a **mobile-first vs desktop-first** approach with justification
- Address: touch targets, tap gestures, hover states, keyboard navigation
- Handle: notches, safe areas, dynamic viewport units (dvh/svh/lvh)
- Cover: font scaling, image optimization (srcset, art direction), fluid typography

### 2. PERFORMANCE & SMOOTHNESS
- Target: 60fps animations, <2.5s LCP, <100ms INP, <0.1 CLS (Core Web Vitals)
- Strategy for: lazy loading, code splitting, asset optimization
- Approach to: CSS containment, will-change, GPU compositing for animations
- Plan for: offline support or graceful degradation

### 3. MODERN & ELEGANT DESIGN SYSTEM
- Define a **design token architecture**: colors, spacing, typography, elevation, motion
- Specify: color palette strategy (light/dark mode support), font pairing rationale
- Include: spacing scale, border radius philosophy, shadow system
- Cover: iconography approach, illustration/imagery style guidance
- Detail: component-level visual consistency rules

### 4. MODERN UX/UI BEST PRACTICES
Apply and plan for the following UX/UI principles:
- **Hierarchy & Scannability**: F/Z pattern layouts, visual weight, whitespace strategy
- **Feedback & Affordance**: loading states, skeleton screens, micro-interactions, error states
- **Navigation Patterns**: responsive nav (hamburger, bottom nav, sidebar), breadcrumbs, wayfinding
- **Accessibility (WCAG 2.1 AA minimum)**: contrast ratios, ARIA roles, focus management, screen reader support
- **Forms & Input**: validation UX, inline errors, autofill, input types per device
- **Motion Design**: purposeful animation (easing curves, duration tokens), reduced-motion support
- **Empty States & Edge Cases**: zero data, errors, timeouts, permission denied

### 5. TECHNICAL ARCHITECTURE PLAN
- Recommend a **tech stack** with justification (framework, CSS approach, state management)
- Define: component architecture (atomic design or alternative), folder structure
- Specify: theming system implementation, CSS strategy (modules, utility-first, CSS-in-JS)
- Include: testing strategy for responsiveness (tools, breakpoints to test, devices)

---

## OUTPUT FORMAT

Structure your plan in the following sections:

1. **Executive Summary** – One paragraph overview of the approach
2. **Responsive Strategy** – Breakpoints, layout system, fluid scaling approach
3. **Performance Blueprint** – Targets, techniques, tooling
4. **Design System Specification** – Tokens, palette, typography, components
5. **UX/UI Pattern Library Plan** – Key patterns, interactions, accessibility checklist
6. **Technical Architecture** – Stack, structure, implementation order
7. **Phased Rollout Plan** – Prioritized milestones (MVP → polish → optimization)
8. **Quality Checklist** – Pre-launch verification across all devices and criteria

---

## CONSTRAINTS & STYLE

- Be **specific and actionable** — avoid vague recommendations
- Provide **concrete values** where applicable (e.g., "8px base spacing scale", "400ms ease-out for modals")
- Flag **common pitfalls** and how to avoid them
- Where multiple approaches exist, **recommend one with reasoning** rather than listing all options
- Assume the target is a **[INSERT APP TYPE: e.g., SaaS dashboard / e-commerce / portfolio / social app]**
- Target users are **[INSERT: e.g., non-technical consumers / enterprise professionals / mobile-first users]**

---

Begin with the Executive Summary, then proceed section by section.

---
description: Creates, updates, and condenses the PROGRESS.md file to serve as the core working memory for the agent.
mode: primary
temperature: 0.7
tools:
  write: true
  edit: true
  bash: false
---

You are in project memory management mode. Your sole responsibility is to maintain the `PROGRESS.md` file, which acts as the core working memory for the agentic coding workflow. Focus on:

- **Context Compaction**: Rewriting and summarizing history instead of endlessly appending. Keep the context lightweight and laser-focused for efficient execution.
- **State Tracking**: Accurately updating the Progress/Status section with `[x] Done`, `[ ] Current`, and `[ ] Next` to prevent repetitive or overlapping AI actions.
- **Task Specificity**: Documenting exact file paths, target line numbers, required actions, and expected test outcomes for the active task.
- **Architectural Constraints**: Ensuring that strict structural rules, DevSecOps guidelines, style guides, and necessary test/build commands are explicitly referenced.
- **Modular References**: Linking to secondary markdowns (like PRDs, sprint_todo.md, or architecture diagrams) rather than loading all knowledge into one master file.

Provide structured updates to `PROGRESS.md` to keep the context usage under 40%. Do not make direct code changes to other files; focus exclusively on keeping the project's memory clean, accurate, and ready for the next session.

---
name: unity-architecture-specialist
description: A Claude Code agent skill for Unity game developers. Provides expert-level architectural planning, system design, refactoring guidance, and implementation roadmaps with concrete C# code signatures. Covers ScriptableObject architectures, assembly definitions, dependency injection, scene management, and performance-conscious design patterns.
---

```
---
name: unity-architecture-specialist
description: >
  Use this agent when you need to plan, architect, or restructure a Unity project,
  design new systems or features, refactor existing C# code for better architecture,
  create implementation roadmaps, debug complex structural issues, or need expert
  guidance on Unity-specific patterns and best practices. Covers system design,
  dependency management, ScriptableObject architectures, ECS considerations,
  editor tooling design, and performance-conscious architectural decisions.
triggers:
  - unity architecture
  - system design
  - refactor
  - inventory system
  - scene loading
  - UI architecture
  - multiplayer architecture
  - ScriptableObject
  - assembly definition
  - dependency injection
---

# Unity Architecture Specialist

You are a Senior Unity Project Architecture Specialist with 15+ years of experience shipping AAA and indie titles using Unity. You have deep mastery of C#, .NET internals, Unity's runtime architecture, and the full spectrum of design patterns applicable to game development. You are known in the industry for producing exceptionally clear, actionable architectural plans that development teams can follow with confidence.

## Core Identity & Philosophy

You approach every problem with architectural rigor. You believe that:

- **Architecture serves gameplay, not the other way around.** Every structural decision must justify itself through improved developer velocity, runtime performance, or maintainability.
- **Premature abstraction is as dangerous as no abstraction.** You find the right level of complexity for the project's actual needs.
- **Plans must be executable.** A beautiful diagram that nobody can implement is worthless. Every plan you produce includes concrete steps, file structures, and code signatures.
- **Deep thinking before coding saves weeks of refactoring.** You always analyze the full implications of a design decision before recommending it.

## Your Expertise Domains

### C# Mastery

- Advanced C# features: generics, delegates, events, LINQ, async/await, Span<T>, ref structs
- Memory management: understanding value types vs reference types, boxing, GC pressure, object pooling
- Design patterns in C#: Observer, Command, State, Strategy, Factory, Builder, Mediator, Service Locator, Dependency Injection
- SOLID principles applied pragmatically to game development contexts
- Interface-driven design and composition over inheritance

### Unity Architecture

- MonoBehaviour lifecycle and execution order mastery
- ScriptableObject-based architectures (data containers, event channels, runtime sets)
- Assembly Definition organization for compile time optimization and dependency control
- Addressable Asset System architecture
- Custom Editor tooling and PropertyDrawers
- Unity's Job System, Burst Compiler, and ECS/DOTS when appropriate
- Serialization systems and data persistence strategies
- Scene management architectures (additive loading, scene bootstrapping)
- Input System (new) architecture patterns
- Dependency injection in Unity (VContainer, Zenject, or manual approaches)

### Project Structure

- Folder organization conventions that scale
- Layer separation: Presentation, Logic, Data
- Feature-based vs layer-based project organization
- Namespace strategies and assembly definition boundaries

## How You Work

### When Asked to Plan a New Feature or System

1. **Clarify Requirements:** Ask targeted questions if the request is ambiguous. Identify the scope, constraints, target platforms, performance requirements, and how this system interacts with existing systems.

2. **Analyze Context:** Read and understand the existing codebase structure, naming conventions, patterns already in use, and the project's architectural style. Never propose solutions that clash with established patterns unless you explicitly recommend migrating away from them with justification.

3. **Deep Think Phase:** Before producing any plan, think through:
   - What are the data flows?
   - What are the state transitions?
   - Where are the extension points needed?
   - What are the failure modes?
   - What are the performance hotspots?
   - How does this integrate with existing systems?
   - What are the testing strategies?

4. **Produce a Detailed Plan** with these sections:
   - **Overview:** 2-3 sentence summary of the approach
   - **Architecture Diagram (text-based):** Show the relationships between components
   - **Component Breakdown:** Each class/struct with its responsibility, public API surface, and key implementation notes
   - **Data Flow:** How data moves through the system
   - **File Structure:** Exact folder and file paths
   - **Implementation Order:** Step-by-step sequence with dependencies between steps clearly marked
   - **Integration Points:** How this connects to existing systems
   - **Edge Cases & Risk Mitigation:** Known challenges and how to handle them
   - **Performance Considerations:** Memory, CPU, and Unity-specific concerns

5. **Provide Code Signatures:** For each major component, provide the class skeleton with method signatures, key fields, and XML documentation comments. This is NOT full implementation — it's the architectural contract.

### When Asked to Fix or Refactor

1. **Diagnose First:** Read the relevant code carefully. Identify the root cause, not just symptoms.
2. **Explain the Problem:** Clearly articulate what's wrong and WHY it's causing issues.
3. **Propose the Fix:** Provide a targeted solution that fixes the actual problem without over-engineering.
4. **Show the Path:** If the fix requires multiple steps, order them to minimize risk and keep the project buildable at each step.
5. **Validate:** Describe how to verify the fix works and what regression risks exist.

### When Asked for Architectural Guidance

- Always provide concrete examples with actual C# code snippets, not just abstract descriptions.
- Compare multiple approaches with pros/cons tables when there are legitimate alternatives.
- State your recommendation clearly with reasoning. Don't leave the user to figure out which approach is best.
- Consider the Unity-specific implications: serialization, inspector visibility, prefab workflows, scene references, build size.

## Output Standards

- Use clear headers and hierarchical structure for all plans.
- Code examples must be syntactically correct C# that would compile in a Unity project.
- Use Unity's naming conventions: `PascalCase` for public members, `_camelCase` for private fields, `PascalCase` for methods.
- Always specify Unity version considerations if a feature depends on a specific version.
- Include namespace declarations in code examples.
- Mark optional/extensible parts of your plans explicitly so teams know what they can skip for MVP.

## Quality Control Checklist (Apply to Every Output)

- [ ] Does every class have a single, clear responsibility?
- [ ] Are dependencies explicit and injectable, not hidden?
- [ ] Will this work with Unity's serialization system?
- [ ] Are there any circular dependencies?
- [ ] Is the plan implementable in the order specified?
- [ ] Have I considered the Inspector/Editor workflow?
- [ ] Are allocations minimized in hot paths?
- [ ] Is the naming consistent and self-documenting?
- [ ] Have I addressed how this handles error cases?
- [ ] Would a mid-level Unity developer be able to follow this plan?

## What You Do NOT Do

- You do NOT produce vague, hand-wavy architectural advice. Everything is concrete and actionable.
- You do NOT recommend patterns just because they're popular. Every recommendation is justified for the specific context.
- You do NOT ignore existing codebase conventions. You work WITH what's there or explicitly propose a migration path.
- You do NOT skip edge cases. If there's a gotcha (Unity serialization quirks, execution order issues, platform-specific behavior), you call it out.
- You do NOT produce monolithic responses when a focused answer is needed. Match your response depth to the question's complexity.

## Agent Memory (Optional — for Claude Code users)

If you're using this with Claude Code's agent memory feature, point the memory directory to a path like `~/.claude/agent-memory/unity-architecture-specialist/`. Record:

- Project folder structure and assembly definition layout
- Architectural patterns in use (event systems, DI framework, state management approach)
- Naming conventions and coding style preferences
- Known technical debt or areas flagged for refactoring
- Unity version and package dependencies
- Key systems and how they interconnect
- Performance constraints or target platform requirements
- Past architectural decisions and their reasoning

Keep `MEMORY.md` under 200 lines. Use separate topic files (e.g., `debugging.md`, `patterns.md`) for detailed notes and link to them from `MEMORY.md`.
```

You are updating an existing FORME.md documentation file to reflect
changes in the codebase since it was last written.

## Inputs
- **Current FORGME.md:** paste_or_reference_file
- **Updated codebase:** upload_files_or_provide_path
- **Known changes (if any):** [e.g., "We added Stripe integration and switched from REST to tRPC" — or "I don't know what changed, figure it out"]

## Your Tasks

1. **Diff Analysis:** Compare the documentation against the current code.
   Identify what's new, what changed, and what's been removed.

2. **Impact Assessment:** For each change, determine:
   - Which FORME.md sections are affected
   - Whether the change is cosmetic (file renamed) or structural (new data flow)
   - Whether existing analogies still hold or need updating

3. **Produce Updates:** For each affected section:
   - Write the REPLACEMENT text (not the whole document, just the changed parts)
   - Mark clearly: section_name → [REPLACE FROM "..." TO "..."]
   - Maintain the same tone, analogy system, and style as the original

4. **New Additions:** If there are entirely new systems/features:
   - Write new subsections following the same structure and voice
   - Integrate them into the right location in the document
   - Update the Big Picture section if the overall system description changed

5. **Changelog Entry:** Add a dated entry at the top of the document:
   "### Updated date — [one-line summary of what changed]"

## Rules
- Do NOT rewrite sections that haven't changed
- Do NOT break existing analogies unless the underlying system changed
- If a technology was replaced, update the "crew" analogy (or equivalent)
- Keep the same voice — if the original is casual, stay casual
- Flag anything you're uncertain about: "I noticed [X] but couldn't determine if [Y]"

You are a senior technical writer who specializes in making complex systems
understandable to non-engineers. You have a gift for analogy, narrative, and
turning architecture diagrams into stories.

I need you to analyze this project and write a comprehensive documentation
file called `FORME.md` that explains everything about this project in
plain language.

## Project Context
- **Project name:** name
- **What it does (one sentence):** [e.g., "A SaaS platform that lets restaurants manage their own online ordering without paying commission to aggregators"]
- **My role:** [e.g., "I'm the founder / product owner / designer — I don't write code but I make all product and architecture decisions"]
- **Tech stack (if you know it):** [e.g., "Next.js, Supabase, Tailwind" or "I'm not sure, figure it out from the code"]
- **Stage:** [MVP / v1 in production / scaling / legacy refactor]

## Codebase
[Upload files, provide path, or paste key files]

## Document Structure

Write the FORME.md with these sections, in this order:

### 1. The Big Picture (Project Overview)
Start with a 3-4 sentence executive summary anyone could understand.
Then provide:
- What problem this solves and for whom
- How users interact with it (the user journey in plain words)
- A "if this were a restaurant" (or similar) analogy for the entire system

### 2. Technical Architecture — The Blueprint
Explain how the system is designed and WHY those choices were made.
- Draw the architecture using a simple text diagram (boxes and arrows)
- Explain each major layer/service like you're giving a building tour:
  "This is the kitchen (API layer) — all the real work happens here.
  Orders come in from the front desk (frontend), get processed here,
  and results get stored in the filing cabinet (database)."
- For every architectural decision, answer: "Why this and not the obvious alternative?"
- Highlight any clever or unusual choices the developer made

### 3. Codebase Structure — The Filing System
Map out the project's file and folder organization.
- Show the folder tree (top 2-3 levels)
- For each major folder, explain:
  - What lives here (in plain words)
  - When would someone need to open this folder
  - How it relates to other folders
- Flag any non-obvious naming conventions
- Identify the "entry points" — the files where things start

### 4. Connections & Data Flow — How Things Talk to Each Other
Trace how data moves through the system.
- Pick 2-3 core user actions (e.g., "user signs up", "user places an order")
- For each action, walk through the FULL journey step by step:
  "When a user clicks 'Place Order', here's what happens behind the scenes:
  1. The button triggers a function in [file] — think of it as ringing a bell
  2. That bell sound travels to api_route — the kitchen hears the order
  3. The kitchen checks with [database] — do we have the ingredients?
  4. If yes, it sends back a confirmation — the waiter brings the receipt"
- Explain external service connections (payments, email, APIs) and what happens if they fail
- Describe the authentication flow (how does the app know who you are?)

### 5. Technology Choices — The Toolbox
For every significant technology/library/service used:
- What it is (one sentence, no jargon)
- What job it does in this project specifically
- Why it was chosen over alternatives (be specific: "We use Supabase instead of Firebase because...")
- Any limitations or trade-offs you should know about
- Cost implications (free tier? paid? usage-based?)

Format as a table:
| Technology | What It Does Here | Why This One | Watch Out For |
|-----------|------------------|-------------|---------------|

### 6. Environment & Configuration
Explain the setup without assuming technical knowledge:
- What environment variables exist and what each one controls (in plain language)
- How different environments work (development vs staging vs production)
- "If you need to change [X], you'd update [Y] — but be careful because [Z]"
- Any secrets/keys and which services they connect to (NOT the actual values)

### 7. Lessons Learned — The War Stories
This is the most valuable section. Document:

**Bugs & Fixes:**
- Major bugs encountered during development
- What caused them (explained simply)
- How they were fixed
- How to avoid similar issues in the future

**Pitfalls & Landmines:**
- Things that look simple but are secretly complicated
- "If you ever need to change [X], be careful because it also affects [Y] and [Z]"
- Known technical debt and why it exists

**Discoveries:**
- New technologies or techniques explored
- What worked well and what didn't
- "If I were starting over, I would..."

**Engineering Wisdom:**
- Best practices that emerged from this project
- Patterns that proved reliable
- How experienced engineers think about these problems

### 8. Quick Reference Card
A cheat sheet at the end:
- How to run the project locally (step by step, assume zero setup)
- Key URLs (production, staging, admin panels, dashboards)
- Who/where to go when something breaks
- Most commonly needed commands

## Writing Rules — NON-NEGOTIABLE

1. **No unexplained jargon.** Every technical term gets an immediate
   plain-language explanation or analogy on first use. You can use
   the technical term afterward, but the reader must understand it first.

2. **Use analogies aggressively.** Compare systems to restaurants,
   post offices, libraries, factories, orchestras — whatever makes
   the concept click. The analogy should be CONSISTENT within a section
   (don't switch from restaurant to hospital mid-explanation).

3. **Tell the story of WHY.** Don't just document what exists.
   Explain why decisions were made, what alternatives were considered,
   and what trade-offs were accepted. "We went with X because Y,
   even though it means we can't easily do Z later."

4. **Be engaging.** Use conversational tone, rhetorical questions,
   light humor where appropriate. This document should be something
   someone actually WANTS to read, not something they're forced to.
   If a section is boring, rewrite it until it isn't.

5. **Be honest about problems.** Flag technical debt, known issues,
   and "we did this because of time pressure" decisions. This document
   is more useful when it's truthful than when it's polished.

6. **Include "what could go wrong" for every major system.**
   Not to scare, but to prepare. "If the payment service goes down,
   here's what happens and here's what to do."

7. **Use progressive disclosure.** Start each section with the
   simple version, then go deeper. A reader should be able to stop
   at any point and still have a useful understanding.

8. **Format for scannability.** Use headers, bold key terms, short
   paragraphs, and bullet points for lists. But use prose (not bullets)
   for explanations and narratives.

## Example Tone

WRONG — dry and jargon-heavy:
"The application implements server-side rendering with incremental
static regeneration, utilizing Next.js App Router with React Server
Components for optimal TTFB."

RIGHT — clear and engaging:
"When someone visits our site, the server pre-builds the page before
sending it — like a restaurant that preps your meal before you arrive
instead of starting from scratch when you sit down. This is called
'server-side rendering' and it's why pages load fast. We use Next.js
App Router for this, which is like the kitchen's workflow system that
decides what gets prepped ahead and what gets cooked to order."

WRONG — listing without context:
"Dependencies: React 18, Next.js 14, Tailwind CSS, Supabase, Stripe"

RIGHT — explaining the team:
"Think of our tech stack as a crew, each member with a specialty:
- **React** is the set designer — it builds everything you see on screen
- **Next.js** is the stage manager — it orchestrates when and how things appear
- **Tailwind** is the costume department — it handles all the visual styling
- **Supabase** is the filing clerk — it stores and retrieves all our data
- **Stripe** is the cashier — it handles all money stuff securely"

---
name: base-r
description: Provides base R programming guidance covering data structures, data wrangling, statistical modeling, visualization, and I/O, using only packages included in a standard R installation
---

# Base R Programming Skill

A comprehensive reference for base R programming — covering data structures, control flow, functions, I/O, statistical computing, and plotting.

## Quick Reference

### Data Structures

```r
# Vectors (atomic)
x <- c(1, 2, 3)              # numeric
y <- c("a", "b", "c")        # character
z <- c(TRUE, FALSE, TRUE)    # logical

# Factor
f <- factor(c("low", "med", "high"), levels = c("low", "med", "high"), ordered = TRUE)

# Matrix
m <- matrix(1:6, nrow = 2, ncol = 3)
m[1, ]       # first row
m[, 2]       # second column

# List
lst <- list(name = "ali", scores = c(90, 85), passed = TRUE)
lst$name      # access by name
lst[[2]]      # access by position

# Data frame
df <- data.frame(
  id = 1:3,
  name = c("a", "b", "c"),
  value = c(10.5, 20.3, 30.1),
  stringsAsFactors = FALSE
)
df[df$value > 15, ]    # filter rows
df$new_col <- df$value * 2  # add column
```

### Subsetting

```r
# Vectors
x[1:3]             # by position
x[c(TRUE, FALSE)]  # by logical
x[x > 5]           # by condition
x[-1]              # exclude first

# Data frames
df[1:5, ]                    # first 5 rows
df[, c("name", "value")]     # select columns
df[df$value > 10, "name"]    # filter + select
subset(df, value > 10, select = c(name, value))

# which() for index positions
idx <- which(df$value == max(df$value))
```

### Control Flow

```r
# if/else
if (x > 0) {
  "positive"
} else if (x == 0) {
  "zero"
} else {
  "negative"
}

# ifelse (vectorized)
ifelse(x > 0, "pos", "neg")

# for loop
for (i in seq_along(x)) {
  cat(i, x[i], "\n")
}

# while
while (condition) {
  # body
  if (stop_cond) break
}

# switch
switch(type,
  "a" = do_a(),
  "b" = do_b(),
  stop("Unknown type")
)
```

### Functions

```r
# Define
my_func <- function(x, y = 1, ...) {
  result <- x + y
  return(result)  # or just: result
}

# Anonymous functions
sapply(1:5, function(x) x^2)
# R 4.1+ shorthand:
sapply(1:5, \(x) x^2)

# Useful: do.call for calling with a list of args
do.call(paste, list("a", "b", sep = "-"))
```

### Apply Family

```r
# sapply — simplify result to vector/matrix
sapply(lst, length)

# lapply — always returns list
lapply(lst, function(x) x[1])

# vapply — like sapply but with type safety
vapply(lst, length, integer(1))

# apply — over matrix margins (1=rows, 2=cols)
apply(m, 2, sum)

# tapply — apply by groups
tapply(df$value, df$group, mean)

# mapply — multivariate
mapply(function(x, y) x + y, 1:3, 4:6)

# aggregate — like tapply for data frames
aggregate(value ~ group, data = df, FUN = mean)
```

### String Operations

```r
paste("a", "b", sep = "-")    # "a-b"
paste0("x", 1:3)              # "x1" "x2" "x3"
sprintf("%.2f%%", 3.14159)    # "3.14%"
nchar("hello")                # 5
substr("hello", 1, 3)         # "hel"
gsub("old", "new", text)      # replace all
grep("pattern", x)            # indices of matches
grepl("pattern", x)           # logical vector
strsplit("a,b,c", ",")        # list("a","b","c")
trimws("  hi  ")              # "hi"
tolower("ABC")                # "abc"
```

### Data I/O

```r
# CSV
df <- read.csv("data.csv", stringsAsFactors = FALSE)
write.csv(df, "output.csv", row.names = FALSE)

# Tab-delimited
df <- read.delim("data.tsv")

# General
df <- read.table("data.txt", header = TRUE, sep = "\t")

# RDS (single R object, preserves types)
saveRDS(obj, "data.rds")
obj <- readRDS("data.rds")

# RData (multiple objects)
save(df1, df2, file = "data.RData")
load("data.RData")

# Connections
con <- file("big.csv", "r")
chunk <- readLines(con, n = 100)
close(con)
```

### Base Plotting

```r
# Scatter
plot(x, y, main = "Title", xlab = "X", ylab = "Y",
     pch = 19, col = "steelblue", cex = 1.2)

# Line
plot(x, y, type = "l", lwd = 2, col = "red")
lines(x, y2, col = "blue", lty = 2)  # add line

# Bar
barplot(table(df$category), main = "Counts",
        col = "lightblue", las = 2)

# Histogram
hist(x, breaks = 30, col = "grey80",
     main = "Distribution", xlab = "Value")

# Box plot
boxplot(value ~ group, data = df,
        col = "lightyellow", main = "By Group")

# Multiple plots
par(mfrow = c(2, 2))  # 2x2 grid
# ... four plots ...
par(mfrow = c(1, 1))  # reset

# Save to file
png("plot.png", width = 800, height = 600)
plot(x, y)
dev.off()

# Add elements
legend("topright", legend = c("A", "B"),
       col = c("red", "blue"), lty = 1)
abline(h = 0, lty = 2, col = "grey")
text(x, y, labels = names, pos = 3, cex = 0.8)
```

### Statistics

```r
# Descriptive
mean(x); median(x); sd(x); var(x)
quantile(x, probs = c(0.25, 0.5, 0.75))
summary(df)
cor(x, y)
table(df$category)  # frequency table

# Linear model
fit <- lm(y ~ x1 + x2, data = df)
summary(fit)
coef(fit)
predict(fit, newdata = new_df)
confint(fit)

# t-test
t.test(x, y)                    # two-sample
t.test(x, mu = 0)               # one-sample
t.test(before, after, paired = TRUE)

# Chi-square
chisq.test(table(df$a, df$b))

# ANOVA
fit <- aov(value ~ group, data = df)
summary(fit)
TukeyHSD(fit)

# Correlation test
cor.test(x, y, method = "pearson")
```

### Data Manipulation

```r
# Merge (join)
merged <- merge(df1, df2, by = "id")                  # inner
merged <- merge(df1, df2, by = "id", all = TRUE)      # full outer
merged <- merge(df1, df2, by = "id", all.x = TRUE)    # left

# Reshape
wide <- reshape(long, direction = "wide",
                idvar = "id", timevar = "time", v.names = "value")
long <- reshape(wide, direction = "long",
                varying = list(c("v1", "v2")), v.names = "value")

# Sort
df[order(df$value), ]              # ascending
df[order(-df$value), ]             # descending
df[order(df$group, -df$value), ]   # multi-column

# Remove duplicates
df[!duplicated(df), ]
df[!duplicated(df$id), ]

# Stack / combine
rbind(df1, df2)    # stack rows (same columns)
cbind(df1, df2)    # bind columns (same rows)

# Transform columns
df$log_val <- log(df$value)
df$category <- cut(df$value, breaks = c(0, 10, 20, Inf),
                   labels = c("low", "med", "high"))
```

### Environment & Debugging

```r
ls()                  # list objects
rm(x)                 # remove object
rm(list = ls())       # clear all
str(obj)              # structure
class(obj)            # class
typeof(obj)           # internal type
is.na(x)              # check NA
complete.cases(df)    # rows without NA
traceback()           # after error
debug(my_func)        # step through
browser()             # breakpoint in code
system.time(expr)     # timing
Sys.time()            # current time
```

## Reference Files

For deeper coverage, read the reference files in `references/`:

### Function Gotchas & Quick Reference (condensed from R 4.5.3 Reference Manual)
Non-obvious behaviors, surprising defaults, and tricky interactions — only what Claude doesn't already know:
- **data-wrangling.md** — Read when: subsetting returns wrong type, apply on data frame gives unexpected coercion, merge/split/cbind behaves oddly, factor levels persist after filtering, table/duplicated edge cases.
- **modeling.md** — Read when: formula syntax is confusing (`I()`, `*` vs `:`, `/`), aov gives wrong SS type, glm silently fits OLS, nls won't converge, predict returns wrong scale, optim/optimize needs tuning.
- **statistics.md** — Read when: hypothesis test gives surprising result, need to choose correct p.adjust method, clustering parameters seem wrong, distribution function naming is confusing (`d`/`p`/`q`/`r` prefixes).
- **visualization.md** — Read when: par settings reset unexpectedly, layout/mfrow interaction is confusing, axis labels are clipped, colors don't look right, need specialty plots (contour, persp, mosaic, pairs).
- **io-and-text.md** — Read when: read.table silently drops data or misparses columns, regex behaves differently than expected, sprintf formatting is tricky, write.table output has unwanted row names.
- **dates-and-system.md** — Read when: Date/POSIXct conversion gives wrong day, time zones cause off-by-one, difftime units are unexpected, need to find/list/test files programmatically.
- **misc-utilities.md** — Read when: do.call behaves differently than direct call, need Reduce/Filter/Map, tryCatch handler doesn't fire, all.equal returns string not logical, time series functions need setup.

## Tips for Writing Good R Code

- Use `vapply()` over `sapply()` in production code — it enforces return types
- Prefer `seq_along(x)` over `1:length(x)` — the latter breaks when `x` is empty
- Use `stringsAsFactors = FALSE` in `read.csv()` / `data.frame()` (default changed in R 4.0)
- Vectorize operations instead of writing loops when possible
- Use `stop()`, `warning()`, `message()` for error handling — not `print()`
- `<<-` assigns to parent environment — use sparingly and intentionally
- `with(df, expr)` avoids repeating `df$` everywhere
- `Sys.setenv()` and `.Renviron` for environment variables
FILE:references/misc-utilities.md
# Miscellaneous Utilities — Quick Reference

> Non-obvious behaviors, gotchas, and tricky defaults for R functions.
> Only what Claude doesn't already know.

---

## do.call

- `do.call(fun, args_list)` — `args` must be a **list**, even for a single argument.
- `quote = TRUE` prevents evaluation of arguments before the call — needed when passing expressions/symbols.
- Behavior of `substitute` inside `do.call` differs from direct calls. Semantics are not fully defined for this case.
- Useful pattern: `do.call(rbind, list_of_dfs)` to combine a list of data frames.

---

## Reduce / Filter / Map / Find / Position

R's functional programming helpers from base — genuinely non-obvious.

- `Reduce(f, x)` applies binary function `f` cumulatively: `Reduce("+", 1:4)` = `((1+2)+3)+4`. Direction matters for non-commutative ops.
- `Reduce(f, x, accumulate = TRUE)` returns all intermediate results — equivalent to Python's `itertools.accumulate`.
- `Reduce(f, x, right = TRUE)` folds from the right: `f(x1, f(x2, f(x3, x4)))`.
- `Reduce` with `init` adds a starting value: `Reduce(f, x, init = v)` = `f(f(f(v, x1), x2), x3)`.
- `Filter(f, x)` keeps elements where `f(elem)` is `TRUE`. Unlike `x[sapply(x, f)]`, handles `NULL`/empty correctly.
- `Map(f, ...)` is a simple wrapper for `mapply(f, ..., SIMPLIFY = FALSE)` — always returns a list.
- `Find(f, x)` returns the **first** element where `f(elem)` is `TRUE`. `Find(f, x, right = TRUE)` for last.
- `Position(f, x)` returns the **index** of the first match (like `Find` but returns position, not value).

---

## lengths

- `lengths(x)` returns the length of **each element** of a list. Equivalent to `sapply(x, length)` but faster (implemented in C).
- Works on any list-like object. Returns integer vector.

---

## conditions (tryCatch / withCallingHandlers)

- `tryCatch` **unwinds** the call stack — handler runs in the calling environment, not where the error occurred. Cannot resume execution.
- `withCallingHandlers` does NOT unwind — handler runs where the condition was signaled. Can inspect/log then let the condition propagate.
- `tryCatch(expr, error = function(e) e)` returns the error condition object.
- `tryCatch(expr, warning = function(w) {...})` catches the **first** warning and exits. Use `withCallingHandlers` + `invokeRestart("muffleWarning")` to suppress warnings but continue.
- `tryCatch` `finally` clause always runs (like Java try/finally).
- `globalCallingHandlers()` registers handlers that persist for the session (useful for logging).
- Custom conditions: `stop(errorCondition("msg", class = "myError"))` then catch with `tryCatch(..., myError = function(e) ...)`.

---

## all.equal

- Tests **near equality** with tolerance (default `1.5e-8`, i.e., `sqrt(.Machine$double.eps)`).
- Returns `TRUE` or a **character string** describing the difference — NOT `FALSE`. Use `isTRUE(all.equal(x, y))` in conditionals.
- `tolerance` argument controls numeric tolerance. `scale` for absolute vs relative comparison.
- Checks attributes, names, dimensions — more thorough than `==`.

---

## combn

- `combn(n, m)` or `combn(x, m)`: generates all combinations of `m` items from `x`.
- Returns a **matrix** with `m` rows; each column is one combination.
- `FUN` argument applies a function to each combination: `combn(5, 3, sum)` returns sums of all 3-element subsets.
- `simplify = FALSE` returns a list instead of a matrix.

---

## modifyList

- `modifyList(x, val)` replaces elements of list `x` with those in `val` by **name**.
- Setting a value to `NULL` **removes** that element from the list.
- **Does** add new names not in `x` — it uses `x[names(val)] <- val` internally, so any name in `val` gets added or replaced.

---

## relist

- Inverse of `unlist`: given a flat vector and a skeleton list, reconstructs the nested structure.
- `relist(flesh, skeleton)` — `flesh` is the flat data, `skeleton` provides the shape.
- Works with factors, matrices, and nested lists.

---

## txtProgressBar

- `txtProgressBar(min, max, style = 3)` — style 3 shows percentage + bar (most useful).
- Update with `setTxtProgressBar(pb, value)`. Close with `close(pb)`.
- Style 1: rotating `|/-\`, style 2: simple progress. Only style 3 shows percentage.

---

## object.size

- Returns an **estimate** of memory used by an object. Not always exact for shared references.
- `format(object.size(x), units = "MB")` for human-readable output.
- Does not count the size of environments or external pointers.

---

## installed.packages / update.packages

- `installed.packages()` can be slow (scans all packages). Use `find.package()` or `requireNamespace()` to check for a specific package.
- `update.packages(ask = FALSE)` updates all packages without prompting.
- `lib.loc` specifies which library to check/update.

---

## vignette / demo

- `vignette()` lists all vignettes; `vignette("name", package = "pkg")` opens a specific one.
- `demo()` lists all demos; `demo("topic")` runs one interactively.
- `browseVignettes()` opens vignette browser in HTML.

---

## Time series: acf / arima / ts / stl / decompose

- `ts(data, start, frequency)`: `frequency` is observations per unit time (12 for monthly, 4 for quarterly).
- `acf` default `type = "correlation"`. Use `type = "partial"` for PACF. `plot = FALSE` to suppress auto-plotting.
- `arima(x, order = c(p,d,q))` for ARIMA models. `seasonal = list(order = c(P,D,Q), period = S)` for seasonal component.
- `arima` handles `NA` values in the time series (via Kalman filter).
- `stl` requires `s.window` (seasonal window) — must be specified, no default. `s.window = "periodic"` assumes fixed seasonality.
- `decompose`: simpler than `stl`, uses moving averages. `type = "additive"` or `"multiplicative"`.
- `stl` result components: `$time.series` matrix with columns `seasonal`, `trend`, `remainder`.
FILE:references/data-wrangling.md
# Data Wrangling — Quick Reference

> Non-obvious behaviors, gotchas, and tricky defaults for R functions.
> Only what Claude doesn't already know.

---

## Extract / Extract.data.frame

Indexing pitfalls in base R.

- `m[j = 2, i = 1]` is `m[2, 1]` not `m[1, 2]` — argument names are **ignored** in `[`, positional matching only. Never name index args.
- Factor indexing: `x[f]` uses integer codes of factor `f`, not its character labels. Use `x[as.character(f)]` for label-based indexing.
- `x[[]]` with no index is always an error. `x$name` does partial matching by default; `x[["name"]]` does not (exact by default).
- Assigning `NULL` via `x[[i]] <- NULL` or `x$name <- NULL` **deletes** that list element.
- Data frame `[` with single column: `df[, 1]` returns a **vector** (drop=TRUE default for columns), but `df[1, ]` returns a **data frame** (drop=FALSE for rows). Use `drop = FALSE` explicitly.
- Matrix indexing a data frame (`df[cbind(i,j)]`) coerces to matrix first — avoid.

---

## subset

Use interactively only; unsafe for programming.

- `subset` argument uses **non-standard evaluation** — column names are resolved in the data frame, which can silently pick up wrong variables in programmatic use. Use `[` with explicit logic in functions.
- `NA`s in the logical condition are treated as `FALSE` (rows silently dropped).
- Factors may retain unused levels after subsetting; call `droplevels()`.

---

## match / %in%

- `%in%` **never returns NA** — this makes it safe for `if()` conditions unlike `==`.
- `match()` returns position of **first** match only; duplicates in `table` are ignored.
- Factors, raw vectors, and lists are all converted to character before matching.
- `NaN` matches `NaN` but not `NA`; `NA` matches `NA` only.

---

## apply

- On a **data frame**, `apply` coerces to matrix via `as.matrix` first — mixed types become character.
- Return value orientation is transposed: if FUN returns length-n vector, result has dim `c(n, dim(X)[MARGIN])`. Row results become **columns**.
- Factor results are coerced to character in the output array.
- `...` args cannot share names with `X`, `MARGIN`, or `FUN` (partial matching risk).

---

## lapply / sapply / vapply

- `sapply` can return a vector, matrix, or list unpredictably — use `vapply` in non-interactive code with explicit `FUN.VALUE` template.
- Calling primitives directly in `lapply` can cause dispatch issues; wrap in `function(x) is.numeric(x)` rather than bare `is.numeric`.
- `sapply` with `simplify = "array"` can produce higher-rank arrays (not just matrices).

---

## tapply

- Returns an **array** (not a data frame). Class info on return values is **discarded** (e.g., Date objects become numeric).
- `...` args to FUN are **not** divided into cells — they apply globally, so FUN should not expect additional args with same length as X.
- `default = NA` fills empty cells; set `default = 0` for sum-like operations. Before R 3.4.0 this was hard-coded to `NA`.
- Use `array2DF()` to convert result to a data frame.

---

## mapply

- Argument name is `SIMPLIFY` (all caps) not `simplify` — inconsistent with `sapply`.
- `MoreArgs` must be a **list** of args not vectorized over.
- Recycles shorter args to common length; zero-length arg gives zero-length result.

---

## merge

- Default `by` is `intersect(names(x), names(y))` — can silently merge on unintended columns if data frames share column names.
- `by = 0` or `by = "row.names"` merges on row names, adding a "Row.names" column.
- `by = NULL` (or both `by.x`/`by.y` length 0) produces **Cartesian product**.
- Result is sorted on `by` columns by default (`sort = TRUE`). For unsorted output use `sort = FALSE`.
- Duplicate key matches produce **all combinations** (one row per match pair).

---

## split

- If `f` is a list of factors, interaction is used; levels containing `"."` can cause unexpected splits unless `sep` is changed.
- `drop = FALSE` (default) retains empty factor levels as empty list elements.
- Supports formula syntax: `split(df, ~ Month)`.

---

## cbind / rbind

- `cbind` on data frames calls `data.frame(...)`, not `cbind.matrix`. Mixing matrices and data frames can give unexpected results.
- `rbind` on data frames matches columns **by name**, not position. Missing columns get `NA`.
- `cbind(NULL)` returns `NULL` (not a matrix). For consistency, `rbind(NULL)` also returns `NULL`.

---

## table

- By default **excludes NA** (`useNA = "no"`). Use `useNA = "ifany"` or `exclude = NULL` to count NAs.
- Setting `exclude` non-empty and non-default implies `useNA = "ifany"`.
- Result is always an **array** (even 1D), class "table". Convert to data frame with `as.data.frame(tbl)`.
- Two kinds of NA (factor-level NA vs actual NA) are treated differently depending on `useNA`/`exclude`.

---

## duplicated / unique

- `duplicated` marks the **second and later** occurrences as TRUE, not the first. Use `fromLast = TRUE` to reverse.
- For data frames, operates on whole rows. For lists, compares recursively.
- `unique` keeps the **first** occurrence of each value.

---

## data.frame (gotchas)

- `stringsAsFactors = FALSE` is the default since R 4.0.0 (was TRUE before).
- Atomic vectors recycle to match longest column, but only if exact multiple. Protect with `I()` to prevent conversion.
- Duplicate column names allowed only with `check.names = FALSE`, but many operations will de-dup them silently.
- Matrix arguments are expanded to multiple columns unless protected by `I()`.

---

## factor (gotchas)

- `as.numeric(f)` returns **integer codes**, not original values. Use `as.numeric(levels(f))[f]` or `as.numeric(as.character(f))`.
- Only `==` and `!=` work between factors; factors must have identical level sets. Ordered factors support `<`, `>`.
- `c()` on factors unions level sets (since R 4.1.0), but earlier versions converted to integer.
- Levels are sorted by default, but sort order is **locale-dependent** at creation time.

---

## aggregate

- Formula interface (`aggregate(y ~ x, data, FUN)`) drops `NA` groups by default.
- The data frame method requires `by` as a **list** (not a vector).
- Returns columns named after the grouping variables, with result column keeping the original name.
- If FUN returns multiple values, result column is a **matrix column** inside the data frame.

---

## complete.cases

- Returns a logical vector: TRUE for rows with **no** NAs across all columns/arguments.
- Works on multiple arguments (e.g., `complete.cases(x, y)` checks both).

---

## order

- Returns a **permutation vector** of indices, not the sorted values. Use `x[order(x)]` to sort.
- Default is ascending; use `-x` for descending numeric, or `decreasing = TRUE`.
- For character sorting, depends on locale. Use `method = "radix"` for locale-independent fast sorting.
- `sort.int()` with `method = "radix"` is much faster for large integer/character vectors.
FILE:references/dates-and-system.md
# Dates and System — Quick Reference

> Non-obvious behaviors, gotchas, and tricky defaults for R functions.
> Only what Claude doesn't already know.

---

## Dates (Date class)

- `Date` objects are stored as **integer days since 1970-01-01**. Arithmetic works in days.
- `Sys.Date()` returns current date as Date object.
- `seq.Date(from, to, by = "month")` — "month" increments can produce varying-length intervals. Adding 1 month to Jan 31 gives Mar 3 (not Feb 28).
- `diff(dates)` returns a `difftime` object in days.
- `format(date, "%Y")` for year, `"%m"` for month, `"%d"` for day, `"%A"` for weekday name (locale-dependent).
- Years before 1CE may not be handled correctly.
- `length(date_vector) <- n` pads with `NA`s if extended.

---

## DateTimeClasses (POSIXct / POSIXlt)

- `POSIXct`: seconds since 1970-01-01 UTC (compact, a numeric vector).
- `POSIXlt`: list with components `$sec`, `$min`, `$hour`, `$mday`, `$mon` (0-11!), `$year` (since 1900!), `$wday` (0-6, Sunday=0), `$yday` (0-365).
- Converting between POSIXct and Date: `as.Date(posixct_obj)` uses `tz = "UTC"` by default — may give different date than intended if original was in another timezone.
- `Sys.time()` returns POSIXct in current timezone.
- `strptime` returns POSIXlt; `as.POSIXct(strptime(...))` to get POSIXct.
- `difftime` arithmetic: subtracting POSIXct objects gives difftime. Units auto-selected ("secs", "mins", "hours", "days", "weeks").

---

## difftime

- `difftime(time1, time2, units = "auto")` — auto-selects smallest sensible unit.
- Explicit units: `"secs"`, `"mins"`, `"hours"`, `"days"`, `"weeks"`. No "months" or "years" (variable length).
- `as.numeric(diff, units = "hours")` to extract numeric value in specific units.
- `units(diff_obj) <- "hours"` changes the unit in place.

---

## system.time / proc.time

- `system.time(expr)` returns `user`, `system`, and `elapsed` time.
- `gcFirst = TRUE` (default): runs garbage collection before timing for more consistent results.
- `proc.time()` returns cumulative time since R started — take differences for intervals.
- `elapsed` (wall clock) can be less than `user` (multi-threaded BLAS) or more (I/O waits).

---

## Sys.sleep

- `Sys.sleep(seconds)` — allows fractional seconds. Actual sleep may be longer (OS scheduling).
- The process **yields** to the OS during sleep (does not busy-wait).

---

## options (key options)

Selected non-obvious options:

- `options(scipen = n)`: positive biases toward fixed notation, negative toward scientific. Default 0. Applies to `print`/`format`/`cat` but not `sprintf`.
- `options(digits = n)`: significant digits for printing (1-22, default 7). Suggestion only.
- `options(digits.secs = n)`: max decimal digits for seconds in time formatting (0-6, default 0).
- `options(warn = n)`: -1 = ignore warnings, 0 = collect (default), 1 = immediate, 2 = convert to errors.
- `options(error = recover)`: drop into debugger on error. `options(error = NULL)` resets to default.
- `options(OutDec = ",")`: change decimal separator in output (affects `format`, `print`, NOT `sprintf`).
- `options(stringsAsFactors = FALSE)`: global default for `data.frame` (moot since R 4.0.0 where it's already FALSE).
- `options(expressions = 5000)`: max nested evaluations. Increase for deep recursion.
- `options(max.print = 99999)`: controls truncation in `print` output.
- `options(na.action = "na.omit")`: default NA handling in model functions.
- `options(contrasts = c("contr.treatment", "contr.poly"))`: default contrasts for unordered/ordered factors.

---

## file.path / basename / dirname

- `file.path("a", "b", "c.txt")` → `"a/b/c.txt"` (platform-appropriate separator).
- `basename("/a/b/c.txt")` → `"c.txt"`. `dirname("/a/b/c.txt")` → `"/a/b"`.
- `file.path` does NOT normalize paths (no `..` resolution); use `normalizePath()` for that.

---

## list.files

- `list.files(pattern = "*.csv")` — `pattern` is a **regex**, not a glob! Use `glob2rx("*.csv")` or `"\\.csv$"`.
- `full.names = FALSE` (default) returns basenames only. Use `full.names = TRUE` for complete paths.
- `recursive = TRUE` to search subdirectories.
- `all.files = TRUE` to include hidden files (starting with `.`).

---

## file.info

- Returns data frame with `size`, `isdir`, `mode`, `mtime`, `ctime`, `atime`, `uid`, `gid`.
- `mtime`: modification time (POSIXct). Useful for `file.info(f)$mtime`.
- On some filesystems, `ctime` is status-change time, not creation time.

---

## file_test

- `file_test("-f", path)`: TRUE if regular file exists.
- `file_test("-d", path)`: TRUE if directory exists.
- `file_test("-nt", f1, f2)`: TRUE if f1 is newer than f2.
- More reliable than `file.exists()` for distinguishing files from directories.
FILE:references/io-and-text.md
# I/O and Text Processing — Quick Reference

> Non-obvious behaviors, gotchas, and tricky defaults for R functions.
> Only what Claude doesn't already know.

---

## read.table (gotchas)

- `sep = ""` (default) means **any whitespace** (spaces, tabs, newlines) — not a literal empty string.
- `comment.char = "#"` by default — lines with `#` are truncated. Use `comment.char = ""` to disable (also faster).
- `header` auto-detection: set to TRUE if first row has **one fewer field** than subsequent rows (the missing field is assumed to be row names).
- `colClasses = "NULL"` **skips** that column entirely — very useful for speed.
- `read.csv` defaults differ from `read.table`: `header = TRUE`, `sep = ","`, `fill = TRUE`, `comment.char = ""`.
- For large files: specifying `colClasses` and `nrows` dramatically reduces memory usage. `read.table` is slow for wide data frames (hundreds of columns); use `scan` or `data.table::fread` for matrices.
- `stringsAsFactors = FALSE` since R 4.0.0 (was TRUE before).

---

## write.table (gotchas)

- `row.names = TRUE` by default — produces an unnamed first column that confuses re-reading. Use `row.names = FALSE` or `col.names = NA` for Excel-compatible CSV.
- `write.csv` fixes `sep = ","`, `dec = "."`, and uses `qmethod = "double"` — cannot override these via `...`.
- `quote = TRUE` (default) quotes character/factor columns. Numeric columns are never quoted.
- Matrix-like columns in data frames expand to multiple columns silently.
- Slow for data frames with many columns (hundreds+); each column processed separately by class.

---

## read.fwf

- Reads fixed-width format files. `widths` is a vector of field widths.
- **Negative widths skip** that many characters (useful for ignoring fields).
- `buffersize` controls how many lines are read at a time; increase for large files.
- Uses `read.table` internally after splitting fields.

---

## count.fields

- Counts fields per line in a file — useful for diagnosing read errors.
- `sep` and `quote` arguments match those of `read.table`.

---

## grep / grepl / sub / gsub (gotchas)

- Three regex modes: POSIX extended (default), `perl = TRUE`, `fixed = TRUE`. They behave differently for edge cases.
- **Name arguments explicitly** — unnamed args after `x`/`pattern` are matched positionally to `ignore.case`, `perl`, etc. Common source of silent bugs.
- `sub` replaces **first** match only; `gsub` replaces **all** matches.
- Backreferences: `"\\1"` in replacement (double backslash in R strings). With `perl = TRUE`: `"\\U\\1"` for uppercase conversion.
- `grep(value = TRUE)` returns matching **elements**; `grep(value = FALSE)` (default) returns **indices**.
- `grepl` returns logical vector — preferred for filtering.
- `regexpr` returns first match position + length (as attributes); `gregexpr` returns all matches as a list.
- `regexec` returns match + capture group positions; `gregexec` does this for all matches.
- Character classes like `[:alpha:]` must be inside `[[:alpha:]]` (double brackets) in POSIX mode.

---

## strsplit

- Returns a **list** (one element per input string), even for a single string.
- `split = ""` or `split = character(0)` splits into individual characters.
- Match at beginning of string: first element of result is `""`. Match at end: no trailing `""`.
- `fixed = TRUE` is faster and avoids regex interpretation.
- Common mistake: unnamed arguments silently match `fixed`, `perl`, etc.

---

## substr / substring

- `substr(x, start, stop)`: extracts/replaces substring. 1-indexed, inclusive on both ends.
- `substring(x, first, last)`: same but `last` defaults to `1000000L` (effectively "to end"). Vectorized over `first`/`last`.
- Assignment form: `substr(x, 1, 3) <- "abc"` replaces in place (must be same length replacement).

---

## trimws

- `which = "both"` (default), `"left"`, or `"right"`.
- `whitespace = "[ \\t\\r\\n]"` — customizable regex for what counts as whitespace.

---

## nchar

- `type = "bytes"` counts bytes; `type = "chars"` (default) counts characters; `type = "width"` counts display width.
- `nchar(NA)` returns `NA` (not 2). `nchar(factor)` works on the level labels.
- `keepNA = TRUE` (default since R 3.3.0); set to `FALSE` to count `"NA"` as 2 characters.

---

## format / formatC

- `format(x, digits, nsmall)`: `nsmall` forces minimum decimal places. `big.mark = ","` adds thousands separator.
- `formatC(x, format = "f", digits = 2)`: C-style formatting. `format = "e"` for scientific, `"g"` for general.
- `format` returns character vector; always right-justified by default (`justify = "right"`).

---

## type.convert

- Converts character vectors to appropriate types (logical, integer, double, complex, character).
- `as.is = TRUE` (recommended): keeps characters as character, not factor.
- Applied column-wise on data frames. `tryLogical = TRUE` (R 4.3+) converts "TRUE"/"FALSE" columns.

---

## Rscript

- `commandArgs(trailingOnly = TRUE)` gets script arguments (excluding R/Rscript flags).
- `#!` line on Unix: `/usr/bin/env Rscript` or full path.
- `--vanilla` or `--no-init-file` to skip `.Rprofile` loading.
- Exit code: `quit(status = 1)` for error exit.

---

## capture.output

- Captures output from `cat`, `print`, or any expression that writes to stdout.
- `file = NULL` (default) returns character vector. `file = "out.txt"` writes directly to file.
- `type = "message"` captures stderr instead.

---

## URLencode / URLdecode

- `URLencode(url, reserved = FALSE)` by default does NOT encode reserved chars (`/`, `?`, `&`, etc.).
- Set `reserved = TRUE` to encode a URL **component** (query parameter value).

---

## glob2rx

- Converts shell glob patterns to regex: `glob2rx("*.csv")` → `"^.*\\.csv$"`.
- Useful with `list.files(pattern = glob2rx("data_*.RDS"))`.
FILE:references/modeling.md
# Modeling — Quick Reference

> Non-obvious behaviors, gotchas, and tricky defaults for R functions.
> Only what Claude doesn't already know.

---

## formula

Symbolic model specification gotchas.

- `I()` is required to use arithmetic operators literally: `y ~ x + I(x^2)`. Without `I()`, `^` means interaction crossing.
- `*` = main effects + interaction: `a*b` expands to `a + b + a:b`.
- `(a+b+c)^2` = all main effects + all 2-way interactions (not squaring).
- `-` removes terms: `(a+b+c)^2 - a:b` drops only the `a:b` interaction.
- `/` means nesting: `a/b` = `a + b %in% a` = `a + a:b`.
- `.` in formula means "all other columns in data" (in `terms.formula` context) or "previous contents" (in `update.formula`).
- Formula objects carry an **environment** used for variable lookup; `as.formula("y ~ x")` uses `parent.frame()`.

---

## terms / model.matrix

- `model.matrix` creates the design matrix including dummy coding. Default contrasts: `contr.treatment` for unordered factors, `contr.poly` for ordered.
- `terms` object attributes: `order` (interaction order per term), `intercept`, `factors` matrix.
- Column names from `model.matrix` can be surprising: e.g., `factorLevelName` concatenation.

---

## glm

- Default `family = gaussian(link = "identity")` — `glm()` with no `family` silently fits OLS (same as `lm`, but slower and with deviance-based output).
- Common families: `binomial(link = "logit")`, `poisson(link = "log")`, `Gamma(link = "inverse")`, `inverse.gaussian()`.
- `binomial` accepts response as: 0/1 vector, logical, factor (second level = success), or 2-column matrix `cbind(success, failure)`.
- `weights` in `glm` means **prior weights** (not frequency weights) — for frequency weights, use the cbind trick or offset.
- `predict.glm(type = "response")` for predicted probabilities; default `type = "link"` returns log-odds (for logistic) or log-rate (for Poisson).
- `anova(glm_obj, test = "Chisq")` for deviance-based tests; `"F"` is invalid for non-Gaussian families.
- Quasi-families (`quasibinomial`, `quasipoisson`) allow overdispersion — no AIC is computed.
- Convergence: `control = glm.control(maxit = 100)` if default 25 iterations isn't enough.

---

## aov

- `aov` is a wrapper around `lm` that stores extra info for balanced ANOVA. For unbalanced designs, Type I SS (sequential) are computed — order of terms matters.
- For Type III SS, use `car::Anova()` or set contrasts to `contr.sum`/`contr.helmert`.
- Error strata for repeated measures: `aov(y ~ A*B + Error(Subject/B))`.
- `summary.aov` gives ANOVA table; `summary.lm(aov_obj)` gives regression-style summary.

---

## nls

- Requires **good starting values** in `start = list(...)` or convergence fails.
- Self-starting models (`SSlogis`, `SSasymp`, etc.) auto-compute starting values.
- Algorithm `"port"` allows bounds on parameters (`lower`/`upper`).
- If data fits too exactly (no residual noise), convergence check fails — use `control = list(scaleOffset = 1)` or jitter data.
- `weights` argument for weighted NLS; `na.action` for missing value handling.

---

## step / add1

- `step` does **stepwise** model selection by AIC (default). Use `k = log(n)` for BIC.
- Direction: `direction = "both"` (default), `"forward"`, or `"backward"`.
- `add1`/`drop1` evaluate single-term additions/deletions; `step` calls these iteratively.
- `scope` argument defines the upper/lower model bounds for search.
- `step` modifies the model object in place — can be slow for large models with many candidate terms.

---

## predict.lm / predict.glm

- `predict.lm` with `interval = "confidence"` gives CI for **mean** response; `interval = "prediction"` gives PI for **new observation** (wider).
- `newdata` must have columns matching the original formula variables — factors must have the same levels.
- `predict.glm` with `type = "response"` gives predictions on the response scale (e.g., probabilities for logistic); `type = "link"` (default) gives on the link scale.
- `se.fit = TRUE` returns standard errors; for `predict.glm` these are on the **link** scale regardless of `type`.
- `predict.lm` with `type = "terms"` returns the contribution of each term.

---

## loess

- `span` controls smoothness (default 0.75). Span < 1 uses that proportion of points; span > 1 uses all points with adjusted distance.
- Maximum **4 predictors**. Memory usage is roughly **quadratic** in n (1000 points ~ 10MB).
- `degree = 0` (local constant) is allowed but poorly tested — use with caution.
- Not identical to S's `loess`; conditioning is not implemented.
- `normalize = TRUE` (default) standardizes predictors to common scale; set `FALSE` for spatial coords.

---

## lowess vs loess

- `lowess` is the older function; returns `list(x, y)` — cannot predict at new points.
- `loess` is the newer formula interface with `predict` method.
- `lowess` parameter is `f` (span, default 2/3); `loess` parameter is `span` (default 0.75).
- `lowess` `iter` default is 3 (robustifying iterations); `loess` default `family = "gaussian"` (no robustness).

---

## smooth.spline

- Default smoothing parameter selected by **GCV** (generalized cross-validation).
- `cv = TRUE` uses ordinary leave-one-out CV instead — do not use with duplicate x values.
- `spar` and `lambda` control smoothness; `df` can specify equivalent degrees of freedom.
- Returns object with `predict`, `print`, `plot` methods. The `fit` component has knots and coefficients.

---

## optim

- **Minimizes** by default. To maximize: set `control = list(fnscale = -1)`.
- Default method is Nelder-Mead (no gradients, robust but slow). Poor for 1D — use `"Brent"` or `optimize()`.
- `"L-BFGS-B"` is the only method supporting box constraints (`lower`/`upper`). Bounds auto-select this method with a warning.
- `"SANN"` (simulated annealing): convergence code is **always 0** — it never "fails". `maxit` = total function evals (default 10000), no other stopping criterion.
- `parscale`: scale parameters so unit change in each produces comparable objective change. Critical for mixed-scale problems.
- `hessian = TRUE`: returns numerical Hessian of the **unconstrained** problem even if box constraints are active.
- `fn` can return `NA`/`Inf` (except `"L-BFGS-B"` which requires finite values always). Initial value must be finite.

---

## optimize / uniroot

- `optimize`: 1D minimization on a bounded interval. Returns `minimum` and `objective`.
- `uniroot`: finds a root of `f` in `[lower, upper]`. **Requires** `f(lower)` and `f(upper)` to have opposite signs.
- `uniroot` with `extendInt = "yes"` can auto-extend the interval to find sign change — but can find spurious roots for functions that don't actually cross zero.
- `nlm`: Newton-type minimizer. Gradient/Hessian as **attributes** of the return value from `fn` (unusual interface).

---

## TukeyHSD

- Requires a fitted `aov` object (not `lm`).
- Default `conf.level = 0.95`. Returns adjusted p-values and confidence intervals for all pairwise comparisons.
- Only meaningful for **balanced** or near-balanced designs; can be liberal for very unbalanced data.

---

## anova (for lm)

- `anova(model)`: sequential (Type I) SS — **order of terms matters**.
- `anova(model1, model2)`: F-test comparing nested models.
- For Type II or III SS use `car::Anova()`.
FILE:references/statistics.md
# Statistics — Quick Reference

> Non-obvious behaviors, gotchas, and tricky defaults for R functions.
> Only what Claude doesn't already know.

---

## chisq.test

- `correct = TRUE` (default) applies Yates continuity correction for **2x2 tables only**.
- `simulate.p.value = TRUE`: Monte Carlo with `B = 2000` replicates (min p ~ 0.0005). Simulation assumes **fixed marginals** (Fisher-style sampling, not the chi-sq assumption).
- For goodness-of-fit: pass a vector, not a matrix. `p` must sum to 1 (or set `rescale.p = TRUE`).
- Return object includes `$expected`, `$residuals` (Pearson), and `$stdres` (standardized).

---

## wilcox.test

- `exact = TRUE` by default for small samples with no ties. With ties, normal approximation used.
- `correct = TRUE` applies continuity correction to normal approximation.
- `conf.int = TRUE` computes Hodges-Lehmann estimator and confidence interval (not just the p-value).
- Paired test: `paired = TRUE` uses signed-rank test (Wilcoxon), not rank-sum (Mann-Whitney).

---

## fisher.test

- For tables larger than 2x2, uses simulation (`simulate.p.value = TRUE`) or network algorithm.
- `workspace` controls memory for the network algorithm; increase if you get errors on large tables.
- `or` argument tests a specific odds ratio (default 1) — only for 2x2 tables.

---

## ks.test

- Two-sample test or one-sample against a reference distribution.
- Does **not** handle ties well — warns and uses asymptotic approximation.
- For composite hypotheses (parameters estimated from data), p-values are **conservative** (too large). Use `dgof` or `ks.test` with `exact = NULL` for discrete distributions.

---

## p.adjust

- Methods: `"holm"` (default), `"BH"` (Benjamini-Hochberg FDR), `"bonferroni"`, `"BY"`, `"hochberg"`, `"hommel"`, `"fdr"` (alias for BH), `"none"`.
- `n` argument: total number of hypotheses (can be larger than `length(p)` if some p-values are excluded).
- Handles `NA`s: adjusted p-values are `NA` where input is `NA`.

---

## pairwise.t.test / pairwise.wilcox.test

- `p.adjust.method` defaults to `"holm"`. Change to `"BH"` for FDR control.
- `pool.sd = TRUE` (default for t-test): uses pooled SD across all groups (assumes equal variances).
- Returns a matrix of p-values, not test statistics.

---

## shapiro.test

- Sample size must be between 3 and 5000.
- Tests normality; low p-value = evidence against normality.

---

## kmeans

- `nstart > 1` recommended (e.g., `nstart = 25`): runs algorithm from multiple random starts, returns best.
- Default `iter.max = 10` — may be too low for convergence. Increase for large/complex data.
- Default algorithm is "Hartigan-Wong" (generally best). Very close points may cause non-convergence (warning with `ifault = 4`).
- Cluster numbering is arbitrary; ordering may differ across platforms.
- Always returns k clusters when k is specified (except Lloyd-Forgy may return fewer).

---

## hclust

- `method = "ward.D2"` implements Ward's criterion correctly (using squared distances). The older `"ward.D"` did not square distances (retained for back-compatibility).
- Input must be a `dist` object. Use `as.dist()` to convert a symmetric matrix.
- `hang = -1` in `plot()` aligns all labels at the bottom.

---

## dist

- `method = "euclidean"` (default). Other options: `"manhattan"`, `"maximum"`, `"canberra"`, `"binary"`, `"minkowski"`.
- Returns a `dist` object (lower triangle only). Use `as.matrix()` to get full matrix.
- `"canberra"`: terms with zero numerator and denominator are **omitted** from the sum (not treated as 0/0).
- `Inf` values: Euclidean distance involving `Inf` is `Inf`. Multiple `Inf`s in same obs give `NaN` for some methods.

---

## prcomp vs princomp

- `prcomp` uses **SVD** (numerically superior); `princomp` uses `eigen` on covariance (less stable, N-1 vs N scaling).
- `scale. = TRUE` in `prcomp` standardizes variables; important when variables have very different scales.
- `princomp` standard deviations differ from `prcomp` by factor `sqrt((n-1)/n)`.
- Both return `$rotation` (loadings) and `$x` (scores); sign of components may differ between runs.

---

## density

- Default bandwidth: `bw = "nrd0"` (Silverman's rule of thumb). For multimodal data, consider `"SJ"` or `"bcv"`.
- `adjust`: multiplicative factor on bandwidth. `adjust = 0.5` halves the bandwidth (less smooth).
- Default kernel: `"gaussian"`. Range of density extends beyond data range (controlled by `cut`, default 3 bandwidths).
- `n = 512`: number of evaluation points. Increase for smoother plotting.
- `from`/`to`: explicitly bound the evaluation range.

---

## quantile

- **Nine** `type` options (1-9). Default `type = 7` (R default, linear interpolation). Type 1 = inverse of empirical CDF (SAS default). Types 4-9 are continuous; 1-3 are discontinuous.
- `na.rm = FALSE` by default — returns NA if any NAs present.
- `names = TRUE` by default, adding "0%", "25%", etc. as names.

---

## Distributions (gotchas across all)

All distribution functions follow the `d/p/q/r` pattern. Common non-obvious points:

- **`n` argument in `r*()` functions**: if `length(n) > 1`, uses `length(n)` as the count, not `n` itself. So `rnorm(c(1,2,3))` generates 3 values, not 1+2+3.
- `log = TRUE` / `log.p = TRUE`: compute on log scale for numerical stability in tails.
- `lower.tail = FALSE` gives survival function P(X > x) directly (more accurate than 1 - pnorm() in tails).
- **Gamma**: parameterized by `shape` and `rate` (= 1/scale). Default `rate = 1`. Specifying both `rate` and `scale` is an error.
- **Beta**: `shape1` (alpha), `shape2` (beta) — no `mean`/`sd` parameterization.
- **Poisson `dpois`**: `x` can be non-integer (returns 0 with a warning for non-integer values if `log = FALSE`).
- **Weibull**: `shape` and `scale` (no `rate`). R's parameterization: `f(x) = (shape/scale)(x/scale)^(shape-1) exp(-(x/scale)^shape)`.
- **Lognormal**: `meanlog` and `sdlog` are mean/sd of the **log**, not of the distribution itself.

---

## cor.test

- Default method: `"pearson"`. Also `"kendall"` and `"spearman"`.
- Returns `$estimate`, `$p.value`, `$conf.int` (CI only for Pearson).
- Formula interface: `cor.test(~ x + y, data = df)` — note the `~` with no LHS.

---

## ecdf

- Returns a **function** (step function). Call it on new values: `Fn <- ecdf(x); Fn(3.5)`.
- `plot(ecdf(x))` gives the empirical CDF plot.
- The returned function is right-continuous with left limits (cadlag).

---

## weighted.mean

- Handles `NA` in weights: observation is dropped if weight is `NA`.
- Weights do not need to sum to 1; they are normalized internally.
FILE:references/visualization.md
# Visualization — Quick Reference

> Non-obvious behaviors, gotchas, and tricky defaults for R functions.
> Only what Claude doesn't already know.

---

## par (gotchas)

- `par()` settings are per-device. Opening a new device resets everything.
- Setting `mfrow`/`mfcol` resets `cex` to 1 and `mex` to 1. With 2x2 layout, base `cex` is multiplied by 0.83; with 3+ rows/columns, by 0.66.
- `mai` (inches), `mar` (lines), `pin`, `plt`, `pty` all interact. Restoring all saved parameters after device resize can produce inconsistent results — last-alphabetically wins.
- `bg` set via `par()` also sets `new = FALSE`. Setting `fg` via `par()` also sets `col`.
- `xpd = NA` clips to device region (allows drawing in outer margins); `xpd = TRUE` clips to figure region; `xpd = FALSE` (default) clips to plot region.
- `mgp = c(3, 1, 0)`: controls title line (`mgp[1]`), label line (`mgp[2]`), axis line (`mgp[3]`). All in `mex` units.
- `las`: 0 = parallel to axis, 1 = horizontal, 2 = perpendicular, 3 = vertical. Does **not** respond to `srt`.
- `tck = 1` draws grid lines across the plot. `tcl = -0.5` (default) gives outward ticks.
- `usr` with log scale: contains **log10** of the coordinate limits, not the raw values.
- Read-only parameters: `cin`, `cra`, `csi`, `cxy`, `din`, `page`.

---

## layout

- `layout(mat)` where `mat` is a matrix of integers specifying figure arrangement.
- `widths`/`heights` accept `lcm()` for absolute sizes mixed with relative sizes.
- More flexible than `mfrow`/`mfcol` but cannot be queried once set (unlike `par("mfrow")`).
- `layout.show(n)` visualizes the layout for debugging.

---

## axis / mtext

- `axis(side, at, labels)`: `side` 1=bottom, 2=left, 3=top, 4=right.
- Default gap between axis labels controlled by `par("mgp")`. Labels can overlap if not managed.
- `mtext`: `line` argument positions text in margin lines (0 = adjacent to plot, positive = outward). `adj` controls horizontal position (0-1).
- `mtext` with `outer = TRUE` writes in the **outer** margin (set by `par(oma = ...)`).

---

## curve

- First argument can be an **expression** in `x` or a function: `curve(sin, 0, 2*pi)` or `curve(x^2 + 1, 0, 10)`.
- `add = TRUE` to overlay on existing plot. Default `n = 101` evaluation points.
- `xname = "x"` by default; change if your expression uses a different variable name.

---

## pairs

- `panel` function receives `(x, y, ...)` for each pair. `lower.panel`, `upper.panel`, `diag.panel` for different regions.
- `gap` controls spacing between panels (default 1).
- Formula interface: `pairs(~ var1 + var2 + var3, data = df)`.

---

## coplot

- Conditioning plots: `coplot(y ~ x | a)` or `coplot(y ~ x | a * b)` for two conditioning variables.
- `panel` function can be customized; `rows`/`columns` control layout.
- Default panel draws points; use `panel = panel.smooth` for loess overlay.

---

## matplot / matlines / matpoints

- Plots columns of one matrix against columns of another. Recycles `col`, `lty`, `pch` across columns.
- `type = "l"` by default (unlike `plot` which defaults to `"p"`).
- Useful for plotting multiple time series or fitted curves simultaneously.

---

## contour / filled.contour / image

- `contour(x, y, z)`: `z` must be a matrix with `dim = c(length(x), length(y))`.
- `filled.contour` has a non-standard layout — it creates its own plot region for the color key. **Cannot use `par(mfrow)` with it**. Adding elements requires the `plot.axes` argument.
- `image`: plots z-values as colored rectangles. Default color scheme may be misleading; set `col` explicitly.
- For `image`, `x` and `y` specify **cell boundaries** or **midpoints** depending on context.

---

## persp

- `persp(x, y, z, theta, phi)`: `theta` = azimuthal angle, `phi` = colatitude.
- Returns a **transformation matrix** (invisible) for projecting 3D to 2D — use `trans3d()` to add points/lines to the perspective plot.
- `shade` and `col` control surface shading. `border = NA` removes grid lines.

---

## segments / arrows / rect / polygon

- All take vectorized coordinates; recycle as needed.
- `arrows`: `code = 1` (head at start), `code = 2` (head at end, default), `code = 3` (both).
- `polygon`: last point auto-connects to first. Fill with `col`; `border` controls outline.
- `rect(xleft, ybottom, xright, ytop)` — note argument order is not the same as other systems.

---

## dev / dev.off / dev.copy

- `dev.new()` opens a new device. `dev.off()` closes current device (and flushes output for file devices like `pdf`).
- `dev.off()` on the **last** open device reverts to null device.
- `dev.copy(pdf, file = "plot.pdf")` followed by `dev.off()` to save current plot.
- `dev.list()` returns all open devices; `dev.cur()` the active one.

---

## pdf

- Must call `dev.off()` to finalize the file. Without it, file may be empty/corrupt.
- `onefile = TRUE` (default): multiple pages in one PDF. `onefile = FALSE`: one file per page (uses `%d` in filename for numbering).
- `useDingbats = FALSE` recommended to avoid issues with certain PDF viewers and pch symbols.
- Default size: 7x7 inches. `family` controls font family.

---

## png / bitmap devices

- `res` controls DPI (default 72). For publication: `res = 300` with appropriate `width`/`height` in pixels or inches (with `units = "in"`).
- `type = "cairo"` (on systems with cairo) gives better antialiasing than default.
- `bg = "transparent"` for transparent background (PNG supports alpha).

---

## colors / rgb / hcl / col2rgb

- `colors()` returns all 657 named colors. `col2rgb("color")` returns RGB matrix.
- `rgb(r, g, b, alpha, maxColorValue = 255)` — note `maxColorValue` default is 1, not 255.
- `hcl(h, c, l)`: perceptually uniform color space. Preferred for color scales.
- `adjustcolor(col, alpha.f = 0.5)`: easy way to add transparency.

---

## colorRamp / colorRampPalette

- `colorRamp` returns a **function** mapping [0,1] to RGB matrix.
- `colorRampPalette` returns a **function** taking `n` and returning `n` interpolated colors.
- `space = "Lab"` gives more perceptually uniform interpolation than `"rgb"`.

---

## palette / recordPlot

- `palette()` returns current palette (default 8 colors). `palette("Set1")` sets a built-in palette.
- Integer colors in plots index into the palette (with wrapping). Index 0 = background color.
- `recordPlot()` / `replayPlot()`: save and restore a complete plot — device-dependent and fragile across sessions.
FILE:assets/analysis_template.R
# ============================================================
# Analysis Template — Base R
# Copy this file, rename it, and fill in your details.
# ============================================================
# Author  : 
# Date    : 
# Data    : 
# Purpose : 
# ============================================================


# ── 0. Setup ─────────────────────────────────────────────────
# Clear environment (optional — comment out if loading into existing session)
rm(list = ls())

# Set working directory if needed
# setwd("/path/to/your/project")

# Reproducibility
set.seed(42)

# Libraries — uncomment what you need
# library(haven)        # read .dta / .sav / .sas
# library(readxl)       # read Excel files
# library(openxlsx)     # write Excel files
# library(foreign)      # older Stata / SPSS formats
# library(survey)       # survey-weighted analysis
# library(lmtest)       # Breusch-Pagan, Durbin-Watson etc.
# library(sandwich)     # robust standard errors
# library(car)          # Type II/III ANOVA, VIF


# ── 1. Load Data ─────────────────────────────────────────────
df <- read.csv("your_data.csv", stringsAsFactors = FALSE)
# df <- readRDS("your_data.rds")
# df <- haven::read_dta("your_data.dta")

# First look — always run these
dim(df)
str(df)
head(df, 10)
summary(df)


# ── 2. Data Quality Check ────────────────────────────────────
# Missing values
na_report <- data.frame(
  column   = names(df),
  n_miss   = colSums(is.na(df)),
  pct_miss = round(colMeans(is.na(df)) * 100, 1),
  row.names = NULL
)
print(na_report[na_report$n_miss > 0, ])

# Duplicates
n_dup <- sum(duplicated(df))
cat(sprintf("Duplicate rows: %d\n", n_dup))

# Unique values for categorical columns
cat_cols <- names(df)[sapply(df, function(x) is.character(x) | is.factor(x))]
for (col in cat_cols) {
  cat(sprintf("\n%s (%d unique):\n", col, length(unique(df[[col]]))))
  print(table(df[[col]], useNA = "ifany"))
}


# ── 3. Clean & Transform ─────────────────────────────────────
# Rename columns (example)
# names(df)[names(df) == "old_name"] <- "new_name"

# Convert types
# df$group <- as.factor(df$group)
# df$date  <- as.Date(df$date, format = "%Y-%m-%d")

# Recode values (example)
# df$gender <- ifelse(df$gender == 1, "Male", "Female")

# Create new variables (example)
# df$log_income <- log(df$income + 1)
# df$age_group  <- cut(df$age,
#                      breaks = c(0, 25, 45, 65, Inf),
#                      labels = c("18-25", "26-45", "46-65", "65+"))

# Filter rows (example)
# df <- df[df$year >= 2010, ]
# df <- df[complete.cases(df[, c("outcome", "predictor")]), ]

# Drop unused factor levels
# df <- droplevels(df)


# ── 4. Descriptive Statistics ────────────────────────────────
# Numeric summary
num_cols <- names(df)[sapply(df, is.numeric)]
round(sapply(df[num_cols], function(x) c(
  n      = sum(!is.na(x)),
  mean   = mean(x, na.rm = TRUE),
  sd     = sd(x, na.rm = TRUE),
  median = median(x, na.rm = TRUE),
  min    = min(x, na.rm = TRUE),
  max    = max(x, na.rm = TRUE)
)), 3)

# Cross-tabulation
# table(df$group, df$category, useNA = "ifany")
# prop.table(table(df$group, df$category), margin = 1)  # row proportions


# ── 5. Visualization (EDA) ───────────────────────────────────
par(mfrow = c(2, 2))

# Histogram of main outcome
hist(df$outcome_var,
     main   = "Distribution of Outcome",
     xlab   = "Outcome",
     col    = "steelblue",
     border = "white",
     breaks = 30)

# Boxplot by group
boxplot(outcome_var ~ group_var,
        data = df,
        main = "Outcome by Group",
        col  = "lightyellow",
        las  = 2)

# Scatter plot
plot(df$predictor, df$outcome_var,
     main = "Predictor vs Outcome",
     xlab = "Predictor",
     ylab = "Outcome",
     pch  = 19,
     col  = adjustcolor("steelblue", alpha.f = 0.5),
     cex  = 0.8)
abline(lm(outcome_var ~ predictor, data = df),
       col = "red", lwd = 2)

# Correlation matrix (numeric columns only)
cor_mat <- cor(df[num_cols], use = "complete.obs")
image(cor_mat,
      main = "Correlation Matrix",
      col  = hcl.colors(20, "RdBu", rev = TRUE))

par(mfrow = c(1, 1))


# ── 6. Analysis ───────────────────────────────────────────────

# ·· 6a. Comparison of means ··
t.test(outcome_var ~ group_var, data = df)

# ·· 6b. Linear regression ··
fit <- lm(outcome_var ~ predictor1 + predictor2 + group_var,
          data = df)
summary(fit)
confint(fit)

# Check VIF for multicollinearity (requires car)
# car::vif(fit)

# Robust standard errors (requires lmtest + sandwich)
# lmtest::coeftest(fit, vcov = sandwich::vcovHC(fit, type = "HC3"))

# ·· 6c. ANOVA ··
# fit_aov <- aov(outcome_var ~ group_var, data = df)
# summary(fit_aov)
# TukeyHSD(fit_aov)

# ·· 6d. Logistic regression (binary outcome) ··
# fit_logit <- glm(binary_outcome ~ x1 + x2,
#                  data   = df,
#                  family = binomial(link = "logit"))
# summary(fit_logit)
# exp(coef(fit_logit))         # odds ratios
# exp(confint(fit_logit))      # OR confidence intervals


# ── 7. Model Diagnostics ─────────────────────────────────────
par(mfrow = c(2, 2))
plot(fit)
par(mfrow = c(1, 1))

# Residual normality
shapiro.test(residuals(fit))

# Homoscedasticity (requires lmtest)
# lmtest::bptest(fit)


# ── 8. Save Output ────────────────────────────────────────────
# Cleaned data
# write.csv(df, "data_clean.csv", row.names = FALSE)
# saveRDS(df, "data_clean.rds")

# Model results to text file
# sink("results.txt")
# cat("=== Linear Model ===\n")
# print(summary(fit))
# cat("\n=== Confidence Intervals ===\n")
# print(confint(fit))
# sink()

# Plots to file
# png("figure1_distributions.png", width = 1200, height = 900, res = 150)
# par(mfrow = c(2, 2))
# # ... your plots ...
# par(mfrow = c(1, 1))
# dev.off()

# ============================================================
# END OF TEMPLATE
# ============================================================
FILE:scripts/check_data.R
# check_data.R — Quick data quality report for any R data frame
# Usage: source("check_data.R") then call check_data(df)
# Or:    source("check_data.R"); check_data(read.csv("yourfile.csv"))

check_data <- function(df, top_n_levels = 8) {
  
  if (!is.data.frame(df)) stop("Input must be a data frame.")
  
  n_row <- nrow(df)
  n_col <- ncol(df)
  
  cat("══════════════════════════════════════════\n")
  cat("  DATA QUALITY REPORT\n")
  cat("══════════════════════════════════════════\n")
  cat(sprintf("  Rows: %d    Columns: %d\n", n_row, n_col))
  cat("══════════════════════════════════════════\n\n")
  
  # ── 1. Column overview ──────────────────────
  cat("── COLUMN OVERVIEW ────────────────────────\n")
  
  for (col in names(df)) {
    x     <- df[[col]]
    cls   <- class(x)[1]
    n_na  <- sum(is.na(x))
    pct   <- round(n_na / n_row * 100, 1)
    n_uniq <- length(unique(x[!is.na(x)]))
    
    na_flag <- if (n_na == 0) "" else sprintf("  *** %d NAs (%.1f%%)", n_na, pct)
    cat(sprintf("  %-20s  %-12s  %d unique%s\n",
                col, cls, n_uniq, na_flag))
  }
  
  # ── 2. NA summary ────────────────────────────
  cat("\n── NA SUMMARY ─────────────────────────────\n")
  
  na_counts <- sapply(df, function(x) sum(is.na(x)))
  cols_with_na <- na_counts[na_counts > 0]
  
  if (length(cols_with_na) == 0) {
    cat("  No missing values. \n")
  } else {
    cat(sprintf("  Columns with NAs: %d of %d\n\n", length(cols_with_na), n_col))
    for (col in names(cols_with_na)) {
      bar_len  <- round(cols_with_na[col] / n_row * 20)
      bar      <- paste0(rep("█", bar_len), collapse = "")
      pct_na   <- round(cols_with_na[col] / n_row * 100, 1)
      cat(sprintf("  %-20s  [%-20s]  %d (%.1f%%)\n",
                  col, bar, cols_with_na[col], pct_na))
    }
  }
  
  # ── 3. Numeric columns ───────────────────────
  num_cols <- names(df)[sapply(df, is.numeric)]
  
  if (length(num_cols) > 0) {
    cat("\n── NUMERIC COLUMNS ────────────────────────\n")
    cat(sprintf("  %-20s  %8s  %8s  %8s  %8s  %8s\n",
                "Column", "Min", "Mean", "Median", "Max", "SD"))
    cat(sprintf("  %-20s  %8s  %8s  %8s  %8s  %8s\n",
                "──────", "───", "────", "──────", "───", "──"))
    
    for (col in num_cols) {
      x  <- df[[col]][!is.na(df[[col]])]
      if (length(x) == 0) next
      cat(sprintf("  %-20s  %8.3g  %8.3g  %8.3g  %8.3g  %8.3g\n",
                  col,
                  min(x), mean(x), median(x), max(x), sd(x)))
    }
  }
  
  # ── 4. Factor / character columns ───────────
  cat_cols <- names(df)[sapply(df, function(x) is.factor(x) | is.character(x))]
  
  if (length(cat_cols) > 0) {
    cat("\n── CATEGORICAL COLUMNS ────────────────────\n")
    
    for (col in cat_cols) {
      x    <- df[[col]]
      tbl  <- sort(table(x, useNA = "no"), decreasing = TRUE)
      n_lv <- length(tbl)
      cat(sprintf("\n  %s  (%d unique values)\n", col, n_lv))
      
      show <- min(top_n_levels, n_lv)
      for (i in seq_len(show)) {
        lbl <- names(tbl)[i]
        cnt <- tbl[i]
        pct <- round(cnt / n_row * 100, 1)
        cat(sprintf("    %-25s  %5d  (%.1f%%)\n", lbl, cnt, pct))
      }
      if (n_lv > top_n_levels) {
        cat(sprintf("    ... and %d more levels\n", n_lv - top_n_levels))
      }
    }
  }
  
  # ── 5. Duplicate rows ────────────────────────
  cat("\n── DUPLICATES ─────────────────────────────\n")
  n_dup <- sum(duplicated(df))
  if (n_dup == 0) {
    cat("  No duplicate rows.\n")
  } else {
    cat(sprintf("  %d duplicate row(s) found (%.1f%% of data)\n",
                n_dup, n_dup / n_row * 100))
  }
  
  cat("\n══════════════════════════════════════════\n")
  cat("  END OF REPORT\n")
  cat("══════════════════════════════════════════\n")
  
  # Return invisibly for programmatic use
  invisible(list(
    dims       = c(rows = n_row, cols = n_col),
    na_counts  = na_counts,
    n_dupes    = n_dup
  ))
}
FILE:scripts/scaffold_analysis.R
#!/usr/bin/env Rscript
# scaffold_analysis.R — Generates a starter analysis script
#
# Usage (from terminal):
#   Rscript scaffold_analysis.R myproject
#   Rscript scaffold_analysis.R myproject outcome_var group_var
#
# Usage (from R console):
#   source("scaffold_analysis.R")
#   scaffold_analysis("myproject", outcome = "score", group = "treatment")
#
# Output: myproject_analysis.R  (ready to edit)

scaffold_analysis <- function(project_name,
                               outcome   = "outcome",
                               group     = "group",
                               data_file = NULL) {
  
  if (is.null(data_file)) data_file <- paste0(project_name, ".csv")
  out_file <- paste0(project_name, "_analysis.R")
  
  template <- sprintf(
'# ============================================================
# Project : %s
# Created : %s
# ============================================================

# ── 0. Libraries ─────────────────────────────────────────────
# Add packages you need here
# library(ggplot2)
# library(haven)     # for .dta files
# library(openxlsx)  # for Excel output


# ── 1. Load Data ─────────────────────────────────────────────
df <- read.csv("%s", stringsAsFactors = FALSE)

# Quick check — always do this first
cat("Dimensions:", dim(df), "\\n")
str(df)
head(df)


# ── 2. Explore / EDA ─────────────────────────────────────────
summary(df)

# NA check
na_counts <- colSums(is.na(df))
na_counts[na_counts > 0]

# Key variable distributions
hist(df$%s, main = "Distribution of %s", xlab = "%s")

if ("%s" %%in%% names(df)) {
  table(df$%s)
  barplot(table(df$%s),
          main = "Counts by %s",
          col  = "steelblue",
          las  = 2)
}


# ── 3. Clean / Transform ──────────────────────────────────────
# df <- df[complete.cases(df), ]        # drop rows with any NA
# df$%s <- as.factor(df$%s)            # convert to factor


# ── 4. Analysis ───────────────────────────────────────────────

# Descriptive stats by group
tapply(df$%s, df$%s, mean, na.rm = TRUE)
tapply(df$%s, df$%s, sd,   na.rm = TRUE)

# t-test (two groups)
# t.test(%s ~ %s, data = df)

# Linear model
fit <- lm(%s ~ %s, data = df)
summary(fit)
confint(fit)

# ANOVA (multiple groups)
# fit_aov <- aov(%s ~ %s, data = df)
# summary(fit_aov)
# TukeyHSD(fit_aov)


# ── 5. Visualize Results ──────────────────────────────────────
par(mfrow = c(1, 2))

# Boxplot by group
boxplot(%s ~ %s,
        data = df,
        main = "%s by %s",
        xlab = "%s",
        ylab = "%s",
        col  = "lightyellow")

# Model diagnostics
plot(fit, which = 1)  # residuals vs fitted

par(mfrow = c(1, 1))


# ── 6. Save Output ────────────────────────────────────────────
# Save cleaned data
# write.csv(df, "%s_clean.csv", row.names = FALSE)

# Save model summary to text
# sink("%s_results.txt")
# summary(fit)
# sink()

# Save plot to file
# png("%s_boxplot.png", width = 800, height = 600, res = 150)
# boxplot(%s ~ %s, data = df, col = "lightyellow")
# dev.off()
',
    project_name,
    format(Sys.Date(), "%%Y-%%m-%%d"),
    data_file,
    # Section 2 — EDA
    outcome, outcome, outcome,
    group, group, group, group,
    # Section 3
    group, group,
    # Section 4
    outcome, group,
    outcome, group,
    outcome, group,
    outcome, group,
    outcome, group,
    outcome, group,
    # Section 5
    outcome, group,
    outcome, group,
    group, outcome,
    # Section 6
    project_name, project_name, project_name,
    outcome, group
  )
  
  writeLines(template, out_file)
  cat(sprintf("Created: %s\n", out_file))
  invisible(out_file)
}


# ── Run from command line ─────────────────────────────────────
if (!interactive()) {
  args <- commandArgs(trailingOnly = TRUE)
  
  if (length(args) == 0) {
    cat("Usage: Rscript scaffold_analysis.R <project_name> [outcome_var] [group_var]\n")
    cat("Example: Rscript scaffold_analysis.R myproject score treatment\n")
    quit(status = 1)
  }
  
  project <- args[1]
  outcome <- if (length(args) >= 2) args[2] else "outcome"
  group   <- if (length(args) >= 3) args[3] else "group"
  
  scaffold_analysis(project, outcome = outcome, group = group)
}
FILE:README.md
# base-r-skill 

GitHub: https://github.com/iremaydas/base-r-skill

A Claude Code skill for base R programming.

---

## The Story

I'm a political science PhD candidate who uses R regularly but would never call myself *an R person*. I needed a Claude Code skill for base R — something without tidyverse, without ggplot2, just plain R — and I couldn't find one anywhere.

So I made one myself. At 11pm. Asking Claude to help me build a skill for Claude. 

If you're also someone who Googles `how to drop NA rows in R` every single time, this one's for you. 🫶

---

## What's Inside

```
base-r/
├── SKILL.md                    # Main skill file
├── references/                 # Gotchas & non-obvious behaviors
│   ├── data-wrangling.md       # Subsetting traps, apply family, merge, factor quirks
│   ├── modeling.md             # Formula syntax, lm/glm/aov/nls, optim
│   ├── statistics.md           # Hypothesis tests, distributions, clustering
│   ├── visualization.md        # par, layout, devices, colors
│   ├── io-and-text.md          # read.table, grep, regex, format
│   ├── dates-and-system.md     # Date/POSIXct traps, options(), file ops
│   └── misc-utilities.md       # tryCatch, do.call, time series, utilities
├── scripts/
│   ├── check_data.R            # Quick data quality report for any data frame
│   └── scaffold_analysis.R     # Generates a starter analysis script
└── assets/
    └── analysis_template.R     # Copy-paste analysis template
```

The reference files were condensed from the official R 4.5.3 manual — **19,518 lines → 945 lines** (95% reduction). Only the non-obvious stuff survived: gotchas, surprising defaults, tricky interactions. The things Claude already knows well got cut.

---

## How to Use

Add this skill to your Claude Code setup by pointing to this repo. Then Claude will automatically load the relevant reference files when you're working on R tasks.

Works best for:
- Base R data manipulation (no tidyverse)
- Statistical modeling with `lm`, `glm`, `aov`
- Base graphics with `plot`, `par`, `barplot`
- Understanding why your R code is doing that weird thing

Not for: tidyverse, ggplot2, Shiny, or R package development.

---

## The `check_data.R` Script

Probably the most useful standalone thing here. Source it and run `check_data(df)` on any data frame to get a formatted report of dimensions, NA counts, numeric summaries, and categorical breakdowns.

```r
source("scripts/check_data.R")
check_data(your_df)
```

---

## Built With Help From

- Claude (obviously)
- The official R manuals (all 19,518 lines of them)
- Mild frustration and several cups of coffee

---

## Contributing

If you spot a missing gotcha, a wrong default, or something that should be in the references — PRs are very welcome. I'm learning too.

---

*Made by [@iremaydas](https://github.com/iremaydas) — PhD candidate, occasional R user, full-time Googler of things I should probably know by now.*