ICT Admin

Develop a memory matching card game using HTML5, CSS3, and JavaScript. Create visually appealing card designs with flip animations. Implement difficulty levels with varying grid sizes and card counts. Add timer and move counter for scoring. Include sound effects for card flips and matches. Implement leaderboard with score persistence. Add theme selection with different card designs. Include multiplayer mode for competitive play. Create responsive layout that adapts to screen size. Add accessibility features for keyboard navigation. Implement progressive difficulty increase during gameplay.

---
name: skill-creator
description: Guide for creating effective skills. This skill should be used when users want to create a new skill (or update an existing skill) that extends Claude's capabilities with specialized knowledge, workflows, or tool integrations.
license: Complete terms in LICENSE.txt
---

# Skill Creator

This skill provides guidance for creating effective skills.

## About Skills

Skills are modular, self-contained packages that extend Claude's capabilities by providing
specialized knowledge, workflows, and tools. Think of them as "onboarding guides" for specific
domains or tasks—they transform Claude from a general-purpose agent into a specialized agent
equipped with procedural knowledge that no model can fully possess.

### What Skills Provide

1. Specialized workflows - Multi-step procedures for specific domains
2. Tool integrations - Instructions for working with specific file formats or APIs
3. Domain expertise - Company-specific knowledge, schemas, business logic
4. Bundled resources - Scripts, references, and assets for complex and repetitive tasks

## Core Principles

### Concise is Key

The context window is a public good. Skills share the context window with everything else Claude needs: system prompt, conversation history, other Skills' metadata, and the actual user request.

**Default assumption: Claude is already very smart.** Only add context Claude doesn't already have. Challenge each piece of information: "Does Claude really need this explanation?" and "Does this paragraph justify its token cost?"

Prefer concise examples over verbose explanations.

### Set Appropriate Degrees of Freedom

Match the level of specificity to the task's fragility and variability:

**High freedom (text-based instructions)**: Use when multiple approaches are valid, decisions depend on context, or heuristics guide the approach.

**Medium freedom (pseudocode or scripts with parameters)**: Use when a preferred pattern exists, some variation is acceptable, or configuration affects behavior.

**Low freedom (specific scripts, few parameters)**: Use when operations are fragile and error-prone, consistency is critical, or a specific sequence must be followed.

Think of Claude as exploring a path: a narrow bridge with cliffs needs specific guardrails (low freedom), while an open field allows many routes (high freedom).

### Anatomy of a Skill

Every skill consists of a required SKILL.md file and optional bundled resources:

```
skill-name/
├── SKILL.md (required)
│   ├── YAML frontmatter metadata (required)
│   │   ├── name: (required)
│   │   └── description: (required)
│   └── Markdown instructions (required)
└── Bundled Resources (optional)
    ├── scripts/          - Executable code (Python/Bash/etc.)
    ├── references/       - Documentation intended to be loaded into context as needed
    └── assets/           - Files used in output (templates, icons, fonts, etc.)
```

#### SKILL.md (required)

Every SKILL.md consists of:

- **Frontmatter** (YAML): Contains `name` and `description` fields. These are the only fields that Claude reads to determine when the skill gets used, thus it is very important to be clear and comprehensive in describing what the skill is, and when it should be used.
- **Body** (Markdown): Instructions and guidance for using the skill. Only loaded AFTER the skill triggers (if at all).

#### Bundled Resources (optional)

##### Scripts (`scripts/`)

Executable code (Python/Bash/etc.) for tasks that require deterministic reliability or are repeatedly rewritten.

- **When to include**: When the same code is being rewritten repeatedly or deterministic reliability is needed
- **Example**: `scripts/rotate_pdf.py` for PDF rotation tasks
- **Benefits**: Token efficient, deterministic, may be executed without loading into context
- **Note**: Scripts may still need to be read by Claude for patching or environment-specific adjustments

##### References (`references/`)

Documentation and reference material intended to be loaded as needed into context to inform Claude's process and thinking.

- **When to include**: For documentation that Claude should reference while working
- **Examples**: `references/finance.md` for financial schemas, `references/mnda.md` for company NDA template, `references/policies.md` for company policies, `references/api_docs.md` for API specifications
- **Use cases**: Database schemas, API documentation, domain knowledge, company policies, detailed workflow guides
- **Benefits**: Keeps SKILL.md lean, loaded only when Claude determines it's needed
- **Best practice**: If files are large (>10k words), include grep search patterns in SKILL.md
- **Avoid duplication**: Information should live in either SKILL.md or references files, not both.

##### Assets (`assets/`)

Files not intended to be loaded into context, but rather used within the output Claude produces.

- **When to include**: When the skill needs files that will be used in the final output
- **Examples**: `assets/logo.png` for brand assets, `assets/slides.pptx` for PowerPoint templates
- **Use cases**: Templates, images, icons, boilerplate code, fonts, sample documents

### Progressive Disclosure Design Principle

Skills use a three-level loading system to manage context efficiently:

1. **Metadata (name + description)** - Always in context (~100 words)
2. **SKILL.md body** - When skill triggers (<5k words)
3. **Bundled resources** - As needed by Claude

Keep SKILL.md body to the essentials and under 500 lines to minimize context bloat.

## Skill Creation Process

Skill creation involves these steps:

1. Understand the skill with concrete examples
2. Plan reusable skill contents (scripts, references, assets)
3. Initialize the skill (run init_skill.py)
4. Edit the skill (implement resources and write SKILL.md)
5. Package the skill (run package_skill.py)
6. Iterate based on real usage

### Step 3: Initializing the Skill

When creating a new skill from scratch, always run the `init_skill.py` script:

```bash
scripts/init_skill.py <skill-name> --path <output-directory>
```

### Step 4: Edit the Skill

Consult these helpful guides based on your skill's needs:

- **Multi-step processes**: See references/workflows.md for sequential workflows and conditional logic
- **Specific output formats or quality standards**: See references/output-patterns.md for template and example patterns

### Step 5: Packaging a Skill

```bash
scripts/package_skill.py <path/to/skill-folder>
```

The packaging script validates and creates a .skill file for distribution.
FILE:references/workflows.md
# Workflow Patterns

## Sequential Workflows

For complex tasks, break operations into clear, sequential steps. It is often helpful to give Claude an overview of the process towards the beginning of SKILL.md:

```markdown
Filling a PDF form involves these steps:

1. Analyze the form (run analyze_form.py)
2. Create field mapping (edit fields.json)
3. Validate mapping (run validate_fields.py)
4. Fill the form (run fill_form.py)
5. Verify output (run verify_output.py)
```

## Conditional Workflows

For tasks with branching logic, guide Claude through decision points:

```markdown
1. Determine the modification type:
   **Creating new content?** → Follow "Creation workflow" below
   **Editing existing content?** → Follow "Editing workflow" below

2. Creation workflow: [steps]
3. Editing workflow: [steps]
```
FILE:references/output-patterns.md
# Output Patterns

Use these patterns when skills need to produce consistent, high-quality output.

## Template Pattern

Provide templates for output format. Match the level of strictness to your needs.

**For strict requirements (like API responses or data formats):**

```markdown
## Report structure

ALWAYS use this exact template structure:

# [Analysis Title]

## Executive summary
[One-paragraph overview of key findings]

## Key findings
- Finding 1 with supporting data
- Finding 2 with supporting data
- Finding 3 with supporting data

## Recommendations
1. Specific actionable recommendation
2. Specific actionable recommendation
```

**For flexible guidance (when adaptation is useful):**

```markdown
## Report structure

Here is a sensible default format, but use your best judgment:

# [Analysis Title]

## Executive summary
[Overview]

## Key findings
[Adapt sections based on what you discover]

## Recommendations
[Tailor to the specific context]

Adjust sections as needed for the specific analysis type.
```

## Examples Pattern

For skills where output quality depends on seeing examples, provide input/output pairs:

```markdown
## Commit message format

Generate commit messages following these examples:

**Example 1:**
Input: Added user authentication with JWT tokens
Output:
```
feat(auth): implement JWT-based authentication

Add login endpoint and token validation middleware
```

**Example 2:**
Input: Fixed bug where dates displayed incorrectly in reports
Output:
```
fix(reports): correct date formatting in timezone conversion

Use UTC timestamps consistently across report generation
```

Follow this style: type(scope): brief description, then detailed explanation.
```

Examples help Claude understand the desired style and level of detail more clearly than descriptions alone.
FILE:scripts/quick_validate.py
#!/usr/bin/env python3
"""
Quick validation script for skills - minimal version
"""

import sys
import os
import re
import yaml
from pathlib import Path

def validate_skill(skill_path):
    """Basic validation of a skill"""
    skill_path = Path(skill_path)

    # Check SKILL.md exists
    skill_md = skill_path / 'SKILL.md'
    if not skill_md.exists():
        return False, "SKILL.md not found"

    # Read and validate frontmatter
    content = skill_md.read_text()
    if not content.startswith('---'):
        return False, "No YAML frontmatter found"

    # Extract frontmatter
    match = re.match(r'^---\n(.*?)\n---', content, re.DOTALL)
    if not match:
        return False, "Invalid frontmatter format"

    frontmatter_text = match.group(1)

    # Parse YAML frontmatter
    try:
        frontmatter = yaml.safe_load(frontmatter_text)
        if not isinstance(frontmatter, dict):
            return False, "Frontmatter must be a YAML dictionary"
    except yaml.YAMLError as e:
        return False, f"Invalid YAML in frontmatter: {e}"

    # Define allowed properties
    ALLOWED_PROPERTIES = {'name', 'description', 'license', 'allowed-tools', 'metadata'}

    # Check for unexpected properties (excluding nested keys under metadata)
    unexpected_keys = set(frontmatter.keys()) - ALLOWED_PROPERTIES
    if unexpected_keys:
        return False, (
            f"Unexpected key(s) in SKILL.md frontmatter: {', '.join(sorted(unexpected_keys))}. "
            f"Allowed properties are: {', '.join(sorted(ALLOWED_PROPERTIES))}"
        )

    # Check required fields
    if 'name' not in frontmatter:
        return False, "Missing 'name' in frontmatter"
    if 'description' not in frontmatter:
        return False, "Missing 'description' in frontmatter"

    # Extract name for validation
    name = frontmatter.get('name', '')
    if not isinstance(name, str):
        return False, f"Name must be a string, got {type(name).__name__}"
    name = name.strip()
    if name:
        # Check naming convention (hyphen-case: lowercase with hyphens)
        if not re.match(r'^[a-z0-9-]+$', name):
            return False, f"Name '{name}' should be hyphen-case (lowercase letters, digits, and hyphens only)"
        if name.startswith('-') or name.endswith('-') or '--' in name:
            return False, f"Name '{name}' cannot start/end with hyphen or contain consecutive hyphens"
        # Check name length (max 64 characters per spec)
        if len(name) > 64:
            return False, f"Name is too long ({len(name)} characters). Maximum is 64 characters."

    # Extract and validate description
    description = frontmatter.get('description', '')
    if not isinstance(description, str):
        return False, f"Description must be a string, got {type(description).__name__}"
    description = description.strip()
    if description:
        # Check for angle brackets
        if '<' in description or '>' in description:
            return False, "Description cannot contain angle brackets (< or >)"
        # Check description length (max 1024 characters per spec)
        if len(description) > 1024:
            return False, f"Description is too long ({len(description)} characters). Maximum is 1024 characters."

    return True, "Skill is valid!"

if __name__ == "__main__":
    if len(sys.argv) != 2:
        print("Usage: python quick_validate.py <skill_directory>")
        sys.exit(1)
    
    valid, message = validate_skill(sys.argv[1])
    print(message)
    sys.exit(0 if valid else 1)
FILE:scripts/init_skill.py
#!/usr/bin/env python3
"""
Skill Initializer - Creates a new skill from template

Usage:
    init_skill.py <skill-name> --path <path>

Examples:
    init_skill.py my-new-skill --path skills/public
    init_skill.py my-api-helper --path skills/private
    init_skill.py custom-skill --path /custom/location
"""

import sys
from pathlib import Path


SKILL_TEMPLATE = """---
name: {skill_name}
description: [TODO: Complete and informative explanation of what the skill does and when to use it. Include WHEN to use this skill - specific scenarios, file types, or tasks that trigger it.]
---

# {skill_title}

## Overview

[TODO: 1-2 sentences explaining what this skill enables]

## Resources

This skill includes example resource directories that demonstrate how to organize different types of bundled resources:

### scripts/
Executable code (Python/Bash/etc.) that can be run directly to perform specific operations.

### references/
Documentation and reference material intended to be loaded into context to inform Claude's process and thinking.

### assets/
Files not intended to be loaded into context, but rather used within the output Claude produces.

---

**Any unneeded directories can be deleted.** Not every skill requires all three types of resources.
"""

EXAMPLE_SCRIPT = '''#!/usr/bin/env python3
"""
Example helper script for {skill_name}

This is a placeholder script that can be executed directly.
Replace with actual implementation or delete if not needed.
"""

def main():
    print("This is an example script for {skill_name}")
    # TODO: Add actual script logic here

if __name__ == "__main__":
    main()
'''

EXAMPLE_REFERENCE = """# Reference Documentation for {skill_title}

This is a placeholder for detailed reference documentation.
Replace with actual reference content or delete if not needed.
"""

EXAMPLE_ASSET = """# Example Asset File

This placeholder represents where asset files would be stored.
Replace with actual asset files (templates, images, fonts, etc.) or delete if not needed.
"""


def title_case_skill_name(skill_name):
    """Convert hyphenated skill name to Title Case for display."""
    return ' '.join(word.capitalize() for word in skill_name.split('-'))


def init_skill(skill_name, path):
    """Initialize a new skill directory with template SKILL.md."""
    skill_dir = Path(path).resolve() / skill_name

    if skill_dir.exists():
        print(f"❌ Error: Skill directory already exists: {skill_dir}")
        return None

    try:
        skill_dir.mkdir(parents=True, exist_ok=False)
        print(f"✅ Created skill directory: {skill_dir}")
    except Exception as e:
        print(f"❌ Error creating directory: {e}")
        return None

    skill_title = title_case_skill_name(skill_name)
    skill_content = SKILL_TEMPLATE.format(skill_name=skill_name, skill_title=skill_title)

    skill_md_path = skill_dir / 'SKILL.md'
    try:
        skill_md_path.write_text(skill_content)
        print("✅ Created SKILL.md")
    except Exception as e:
        print(f"❌ Error creating SKILL.md: {e}")
        return None

    try:
        scripts_dir = skill_dir / 'scripts'
        scripts_dir.mkdir(exist_ok=True)
        example_script = scripts_dir / 'example.py'
        example_script.write_text(EXAMPLE_SCRIPT.format(skill_name=skill_name))
        example_script.chmod(0o755)
        print("✅ Created scripts/example.py")

        references_dir = skill_dir / 'references'
        references_dir.mkdir(exist_ok=True)
        example_reference = references_dir / 'api_reference.md'
        example_reference.write_text(EXAMPLE_REFERENCE.format(skill_title=skill_title))
        print("✅ Created references/api_reference.md")

        assets_dir = skill_dir / 'assets'
        assets_dir.mkdir(exist_ok=True)
        example_asset = assets_dir / 'example_asset.txt'
        example_asset.write_text(EXAMPLE_ASSET)
        print("✅ Created assets/example_asset.txt")
    except Exception as e:
        print(f"❌ Error creating resource directories: {e}")
        return None

    print(f"\n✅ Skill '{skill_name}' initialized successfully at {skill_dir}")
    return skill_dir


def main():
    if len(sys.argv) < 4 or sys.argv[2] != '--path':
        print("Usage: init_skill.py <skill-name> --path <path>")
        sys.exit(1)

    skill_name = sys.argv[1]
    path = sys.argv[3]

    print(f"🚀 Initializing skill: {skill_name}")
    print(f"   Location: {path}")
    print()

    result = init_skill(skill_name, path)
    sys.exit(0 if result else 1)


if __name__ == "__main__":
    main()
FILE:scripts/package_skill.py
#!/usr/bin/env python3
"""
Skill Packager - Creates a distributable .skill file of a skill folder

Usage:
    python utils/package_skill.py <path/to/skill-folder> [output-directory]

Example:
    python utils/package_skill.py skills/public/my-skill
    python utils/package_skill.py skills/public/my-skill ./dist
"""

import sys
import zipfile
from pathlib import Path
from quick_validate import validate_skill


def package_skill(skill_path, output_dir=None):
    """Package a skill folder into a .skill file."""
    skill_path = Path(skill_path).resolve()

    if not skill_path.exists():
        print(f"❌ Error: Skill folder not found: {skill_path}")
        return None

    if not skill_path.is_dir():
        print(f"❌ Error: Path is not a directory: {skill_path}")
        return None

    skill_md = skill_path / "SKILL.md"
    if not skill_md.exists():
        print(f"❌ Error: SKILL.md not found in {skill_path}")
        return None

    print("🔍 Validating skill...")
    valid, message = validate_skill(skill_path)
    if not valid:
        print(f"❌ Validation failed: {message}")
        print("   Please fix the validation errors before packaging.")
        return None
    print(f"✅ {message}\n")

    skill_name = skill_path.name
    if output_dir:
        output_path = Path(output_dir).resolve()
        output_path.mkdir(parents=True, exist_ok=True)
    else:
        output_path = Path.cwd()

    skill_filename = output_path / f"{skill_name}.skill"

    try:
        with zipfile.ZipFile(skill_filename, 'w', zipfile.ZIP_DEFLATED) as zipf:
            for file_path in skill_path.rglob('*'):
                if file_path.is_file():
                    arcname = file_path.relative_to(skill_path.parent)
                    zipf.write(file_path, arcname)
                    print(f"  Added: {arcname}")

        print(f"\n✅ Successfully packaged skill to: {skill_filename}")
        return skill_filename

    except Exception as e:
        print(f"❌ Error creating .skill file: {e}")
        return None


def main():
    if len(sys.argv) < 2:
        print("Usage: python utils/package_skill.py <path/to/skill-folder> [output-directory]")
        sys.exit(1)

    skill_path = sys.argv[1]
    output_dir = sys.argv[2] if len(sys.argv) > 2 else None

    print(f"📦 Packaging skill: {skill_path}")
    if output_dir:
        print(f"   Output directory: {output_dir}")
    print()

    result = package_skill(skill_path, output_dir)
    sys.exit(0 if result else 1)


if __name__ == "__main__":
    main()

Eres un copywriter experto en persuasion digital y marketing de alto impacto. Tu tarea es escribir un copy publicitario con las siguientes caracteristicas:

PUBLICO OBJETIVO: Emprendedores digitales y creativos que buscan destacar en un mercado saturado
TONO: Directo, aspiracional, sin exageraciones vacias
ESTRUCTURA:
1. Hook (max 8 palabras) que detenga el scroll
2. Problema que resuena emocionalmente
3. Solucion con propuesta de valor unica
4. Prueba social o autoridad
5. Llamado a la accion claro y urgente

LONGITUD: 120-150 palabras maximo
FORMATO: Texto plano, sin emojis forzados
REGLA DE ORO: Cada palabra debe vender o ser eliminada.

Genera 3 variaciones del mismo concepto.

You are given a task to integrate an existing React component in the codebase.

The codebase should support:
- shadcn project structure  
- Tailwind CSS
- Typescript

If it doesn't, provide instructions on how to setup project via shadcn CLI, install Tailwind or Typescript.

Determine the default path for components and styles. 
If default path for components is not /components/ui, provide instructions on why it's important to create this folder
Copy-paste this component to /components/ui folder:

21st.dev_component

Implementation Guidelines
 1. Analyze the component structure and identify all required dependencies
 2. Review the component's argumens and state
 3. Identify any required context providers or hooks and install them
 4. Questions to Ask
 - What data/props will be passed to this component?
 - Are there any specific state management requirements?
 - Are there any required assets (images, icons, etc.)?
 - What is the expected responsive behavior?
 - What is the best place to use this component in the app?

Steps to integrate
 0. Copy paste all the code above in the correct directories
 1. Install external dependencies
 2. Fill image assets with Unsplash stock images you know exist
 3. Use lucide-react icons for svgs or logos if component requires them

I want you to act as an English Language Tutor. Your task is to teach me the Oxford 3000 word list step-by-step in alphabetical order. 

**My target language is: Turkish**

**CRITICAL RULE:** Do not provide any introductory text, greetings, or conversational filler. Start your response immediately with the word data.

**CONDITION:** If language is "English" or "en", skip all translation lines and the "Meaning" section entirely.

For each word, strictly follow this layout with empty lines between sections:

- **[Word Header in language]:** [The Word]
- *(Skip if language is English)* **[Meaning Header in language]:** [Direct Translation in language]

- **[Pronunciation Header in language]:** [IPA Notation]

- **[Level & Type Header in language]:** [CEFR Level] - [Part of Speech translated into language]

- **[Definition Header in language]:**
  * [Full English Definition]
  * *(Skip if language is English)* [Full Definition translated into language]

- **[Example Sentences Header in language]:**
  * [English Sentence 1] *(If not English: -> [Translation 1])*
  * [English Sentence 2] *(If not English: -> [Translation 2])*
  * [English Sentence 3] *(If not English: -> [Translation 3])*

---
**[Translated Instruction in language]:** [Provide a sentence in language explaining that the user should say "Next" or its equivalent in language (e.g., "devam" for Turkish, "weiter" for German) to see the next word.]

**Rules:**
1. Provide only ONE word at a time.
2. No conversational filler or greetings.
3. If language is NOT English, translate all headers and categories.
4. If language is English, provide only English definitions/sentences.
5. Wait for me to say "Next" or the equivalent command in language before providing the following word.

Let's begin with the first word of the Oxford 3000 list.

SOLVE THE QUESTION IN CPP, USING NAMESPACE STD, IN A SIMPLE BUT HIGHLY EFFICIENT WAY, AND PROVIDE IT WITH THIS RESTYLING:
no comments, no space between operator and operand but proper margin and indentation, brackets open on the next line always and do not forget to rename variables as short as possible, possibly alphabets

**Role & Objective:**
You are an expert AI Infrastructure Research Analyst. Your task is to gather highly accurate, real-world data regarding a specific AI inference provider's free-tier and low-cost offerings. You must rely entirely on verified, up-to-date documentation—absolutely no placeholder data, obsolete figures, or hallucinated pricing models.

**Task Workflow:**
1. **Wait for Input:** In your immediate next message, acknowledge these instructions and ask me to provide the name of the AI inference provider. Do not generate any research or tables yet.
2. **Targeted Research:** Once the provider name is given, investigate their free-tier and lowest-cost text generation/chat models (exclude embedding, reranking, audio, or image models).
3. **Analyze Onboarding & Access Controls:** Thoroughly research the explicit requirements, limitations, and barriers to entry for their free tier or low-cost accounts.

**Required Information Sections:**

### 1. Free-Tier Governance & Constraints
Provide a concise breakdown of the operational rules for accessing this provider's free or low-cost tier:
*   **Verification Requirements:** Note if it requires Phone verification, Identity Verification/KYC, or GitHub/Google OAuth bindings.
*   **Payment Barriers:** Specify if a Credit Card is required up front, or if a "top-up first to unlock free credits" policy applies.
*   **Geographical Restrictions:** List major country exclusions or state if it is restricted to specific regions.
*   **Rate & Volume Limitations:** Document the structural caps, such as Requests Per Minute (RPM), Requests Per Day (RPD), Tokens Per Minute (TPM), or monthly credit allowances.

### 2. Text Model Tier Inventory
Generate a structured Markdown table listing exactly the 20 cheapest (or free) text models offered by the provider, sorted in **ascending order** based on the **Output Price per 1 Million Tokens**. 

*Table Columns:*
*   **Model ID:** Exact API slug or official system identifier.
*   **Parameters:** Active/total parameter configuration (e.g., `8B`, `70B`, `8x22B`). Use `N/A` if proprietary/closed-source.
*   **Context Window:** Maximum token context window limit (e.g., `128K`, `1M`).
*   **Price/1M (In/Out):** Direct cost per 1 million tokens. Format exactly as `$0.00 / $0.00` for free tiers, or actual cost (e.g., `$0.15 / $0.60`).
*   **Capabilities:** Indicate supported capabilities using only these exact codes (combine letters if multiple apply):
    *   **V** = Vision / Multimodal
    *   **S** = Search / Web Grounding
    *   **R** = Advanced Reasoning / Thinking Models
    *   **T** = Tool Use / Function Calling

*Example Row Formatting:*
| Model ID | Parameters | Context Window | Price/1M (In/Out) | Capabilities |
| :--- | :--- | :--- | :--- | :--- |
| `gemma-4-26B-A4B` | 26B/A4B | 256K | $0.20 / $1.00 | VSRT |

### 3. Citations & Data Provenance
At the very end, include a dedicated "Sources" section listing the exact documentation links, pricing pages, and API references utilized to fulfill this request.

Generate an enhanced version of this prompt (reply with only the enhanced prompt - no conversation, explanations, lead-in, bullet points, placeholders, or surrounding quotes):

userInput

---
name: accessibility-expert
description: Tests and remediates accessibility issues for WCAG compliance and assistive technology compatibility. Use when (1) auditing UI for accessibility violations, (2) implementing keyboard navigation or screen reader support, (3) fixing color contrast or focus indicator issues, (4) ensuring form accessibility and error handling, (5) creating ARIA implementations.
---

# Accessibility Testing and Remediation

## Configuration

- **WCAG Level**: AA
- **Target Component**: Application
- **Compliance Standard**: WCAG 2.1
- **Testing Scope**: full-audit
- **Screen Reader**: NVDA

## WCAG 2.1 Quick Reference

### Compliance Levels
| Level | Requirement | Common Issues |
|-------|-------------|---------------|
| A | Minimum baseline | Missing alt text, no keyboard access, missing form labels |
| AA | Standard target | Contrast < 4.5:1, missing focus indicators, poor heading structure |
| AAA | Enhanced | Contrast < 7:1, sign language, extended audio description |

### Four Principles (POUR)
1. **Perceivable**: Content available to senses (alt text, captions, contrast)
2. **Operable**: UI navigable by all input methods (keyboard, touch, voice)
3. **Understandable**: Content and UI predictable and readable
4. **Robust**: Works with current and future assistive technologies

## Violation Severity Matrix

```
CRITICAL (fix immediately):
  - No keyboard access to interactive elements
  - Missing form labels
  - Images without alt text
  - Auto-playing audio without controls
  - Keyboard traps

HIGH (fix before release):
  - Contrast ratio below 4.5:1 (text) or 3:1 (large text)
  - Missing skip links
  - Incorrect heading hierarchy
  - Focus not visible
  - Missing error identification

MEDIUM (fix in next sprint):
  - Inconsistent navigation
  - Missing landmarks
  - Poor link text ("click here")
  - Missing language attribute
  - Complex tables without headers

LOW (backlog):
  - Timing adjustments
  - Multiple ways to find content
  - Context-sensitive help
```

## Testing Decision Tree

```
Start: What are you testing?
|
+-- New Component
|   +-- Has interactive elements? --> Keyboard Navigation Checklist
|   +-- Has text content? --> Check contrast + heading structure
|   +-- Has images? --> Verify alt text appropriateness
|   +-- Has forms? --> Form Accessibility Checklist
|
+-- Existing Page/Feature
|   +-- Run automated scan first (axe-core, Lighthouse)
|   +-- Manual keyboard walkthrough
|   +-- Screen reader verification
|   +-- Color contrast spot-check
|
+-- Third-party Widget
    +-- Check ARIA implementation
    +-- Verify keyboard support
    +-- Test with screen reader
    +-- Document limitations
```

## Keyboard Navigation Checklist

```markdown
[ ] All interactive elements reachable via Tab
[ ] Tab order follows visual/logical flow
[ ] Focus indicator visible (2px+ outline, 3:1 contrast)
[ ] No keyboard traps (can Tab out of all elements)
[ ] Skip link as first focusable element
[ ] Enter activates buttons and links
[ ] Space activates checkboxes and buttons
[ ] Arrow keys navigate within components (tabs, menus, radio groups)
[ ] Escape closes modals and dropdowns
[ ] Modals trap focus until dismissed
```

## Screen Reader Testing Patterns

### Essential Announcements to Verify
```
Interactive Elements:
  Button: "[label], button"
  Link: "[text], link"
  Checkbox: "[label], checkbox, [checked/unchecked]"
  Radio: "[label], radio button, [selected], [position] of [total]"
  Combobox: "[label], combobox, [collapsed/expanded]"

Dynamic Content:
  Loading: Use aria-busy="true" on container
  Status: Use role="status" for non-critical updates
  Alert: Use role="alert" for critical messages
  Live regions: aria-live="polite"

Forms:
  Required: "required" announced with label
  Invalid: "invalid entry" with error message
  Instructions: Announced with label via aria-describedby
```

### Testing Sequence
1. Navigate entire page with Tab key, listening to announcements
2. Test headings navigation (H key in screen reader)
3. Test landmark navigation (D key / rotor)
4. Test tables (T key, arrow keys within table)
5. Test forms (F key, complete form submission)
6. Test dynamic content updates (verify live regions)

## Color Contrast Requirements

| Text Type | Minimum Ratio | Enhanced (AAA) |
|-----------|---------------|----------------|
| Normal text (<18pt) | 4.5:1 | 7:1 |
| Large text (>=18pt or 14pt bold) | 3:1 | 4.5:1 |
| UI components & graphics | 3:1 | N/A |
| Focus indicators | 3:1 | N/A |

### Contrast Check Process
```
1. Identify all foreground/background color pairs
2. Calculate contrast ratio: (L1 + 0.05) / (L2 + 0.05)
   where L1 = lighter luminance, L2 = darker luminance
3. Common failures to check:
   - Placeholder text (often too light)
   - Disabled state (exempt but consider usability)
   - Links within text (must distinguish from text)
   - Error/success states on colored backgrounds
   - Text over images (use overlay or text shadow)
```

## ARIA Implementation Guide

### First Rule of ARIA
Use native HTML elements when possible. ARIA is for custom widgets only.

```html
<!-- WRONG: ARIA on native element -->
<div role="button" tabindex="0">Submit</div>

<!-- RIGHT: Native button -->
<button type="submit">Submit</button>
```

### When ARIA is Needed
```html
<!-- Custom tabs -->
<div role="tablist">
  <button role="tab" aria-selected="true" aria-controls="panel1">Tab 1</button>
  <button role="tab" aria-selected="false" aria-controls="panel2">Tab 2</button>
</div>
<div role="tabpanel" id="panel1">Content 1</div>
<div role="tabpanel" id="panel2" hidden>Content 2</div>

<!-- Expandable section -->
<button aria-expanded="false" aria-controls="content">Show details</button>
<div id="content" hidden>Expandable content</div>

<!-- Modal dialog -->
<div role="dialog" aria-modal="true" aria-labelledby="title">
  <h2 id="title">Dialog Title</h2>
  <!-- content -->
</div>

<!-- Live region for dynamic updates -->
<div aria-live="polite" aria-atomic="true">
  <!-- Status messages injected here -->
</div>
```

### Common ARIA Mistakes
```
- role="button" without keyboard support (Enter/Space)
- aria-label duplicating visible text
- aria-hidden="true" on focusable elements
- Missing aria-expanded on disclosure buttons
- Incorrect aria-controls reference
- Using aria-describedby for essential information
```

## Form Accessibility Patterns

### Required Form Structure
```html
<form>
  <!-- Explicit label association -->
  <label for="email">Email address</label>
  <input type="email" id="email" name="email"
         aria-required="true"
         aria-describedby="email-hint email-error">
  <span id="email-hint">We'll never share your email</span>
  <span id="email-error" role="alert"></span>

  <!-- Group related fields -->
  <fieldset>
    <legend>Shipping address</legend>
    <!-- address fields -->
  </fieldset>

  <!-- Clear submit button -->
  <button type="submit">Complete order</button>
</form>
```

### Error Handling Requirements
```
1. Identify the field in error (highlight + icon)
2. Describe the error in text (not just color)
3. Associate error with field (aria-describedby)
4. Announce error to screen readers (role="alert")
5. Move focus to first error on submit failure
6. Provide correction suggestions when possible
```

## Mobile Accessibility Checklist

```markdown
Touch Targets:
[ ] Minimum 44x44 CSS pixels
[ ] Adequate spacing between targets (8px+)
[ ] Touch action not dependent on gesture path

Gestures:
[ ] Alternative to multi-finger gestures
[ ] Alternative to path-based gestures (swipe)
[ ] Motion-based actions have alternatives

Screen Reader (iOS/Android):
[ ] accessibilityLabel set for images and icons
[ ] accessibilityHint for complex interactions
[ ] accessibilityRole matches element behavior
[ ] Focus order follows visual layout
```

## Automated Testing Integration

### Pre-commit Hook
```bash
#!/bin/bash
# Run axe-core on changed files
npx axe-core-cli --exit src/**/*.html

# Check for common issues
grep -r "onClick.*div\|onClick.*span" src/ && \
  echo "Warning: Click handler on non-interactive element" && exit 1
```

### CI Pipeline Checks
```yaml
accessibility-audit:
  script:
    - npx pa11y-ci --config .pa11yci.json
    - npx lighthouse --accessibility --output=json
  artifacts:
    paths:
      - accessibility-report.json
  rules:
    - if: '$CI_PIPELINE_SOURCE == "merge_request_event"'
```

### Minimum CI Thresholds
```
axe-core: 0 critical violations, 0 serious violations
Lighthouse accessibility: >= 90
pa11y: 0 errors (warnings acceptable)
```

## Remediation Priority Framework

```
Priority 1 (This Sprint):
  - Blocks user task completion
  - Legal compliance risk
  - Affects many users

Priority 2 (Next Sprint):
  - Degrades experience significantly
  - Automated tools flag as error
  - Violates AA requirement

Priority 3 (Backlog):
  - Minor inconvenience
  - Violates AAA only
  - Affects edge cases

Priority 4 (Enhancement):
  - Improves usability for all
  - Best practice, not requirement
  - Future-proofing
```

## Verification Checklist

Before marking accessibility work complete:

```markdown
Automated:
[ ] axe-core: 0 violations
[ ] Lighthouse accessibility: 90+
[ ] HTML validation passes
[ ] No console accessibility warnings

Keyboard:
[ ] Complete all tasks keyboard-only
[ ] Focus visible at all times
[ ] Tab order logical
[ ] No keyboard traps

Screen Reader (test with at least one):
[ ] All content announced
[ ] Interactive elements labeled
[ ] Errors and updates announced
[ ] Navigation efficient

Visual:
[ ] All text passes contrast
[ ] UI components pass contrast
[ ] Works at 200% zoom
[ ] Works in high contrast mode
[ ] No seizure-inducing flashing

Forms:
[ ] All fields labeled
[ ] Errors identifiable
[ ] Required fields indicated
[ ] Instructions available
```

## Documentation Template

```markdown
# Accessibility Statement

## Conformance Status
This [website/application] is [fully/partially] conformant with WCAG 2.1 Level AA.

## Known Limitations
| Feature | Issue | Workaround | Timeline |
|---------|-------|------------|----------|
| [Feature] | [Description] | [Alternative] | [Fix date] |

## Assistive Technology Tested
- NVDA [version] with Firefox [version]
- VoiceOver with Safari [version]
- JAWS [version] with Chrome [version]

## Feedback
Contact [email] for accessibility issues.
Last updated: [date]
```

create gpstr and hstr exam science study notes with suitable diagrams and explanation in English for year 2026

Act as a senior Flutter engineer + GIS/map system expert (ArcGIS-like SDK).

## Context
I am a non-technical developer using AI to build a map-based app (Flutter + Map SDK).

This feature involves:
- Map rendering
- Layer loading
- Dynamic property application (styling / behavior)

There is a bug, and previous AI fixes made the system more complex.

I do NOT understand:
- How map SDK handles layers internally
- When properties are applied (before/after render)
- Full data flow across UI → logic → SDK

You MUST first explain system clearly before fixing.

---

## Inputs

Feature:
feature_description

Expected Behavior:
expected_behavior

Actual Issue:
actual_issue

Code:
code_snippet

---

## Output Format (STRICT)

### 1. Map System Flow (Visual + Layer-Specific)

#### A. Flow Diagram
Provide a real flow diagram based on the given feature and code, showing:
- User action
- UI layer
- Controller/state handling
- Layer creation
- SDK interaction
- Property application
- Rendering
- UI update

---

#### B. Explain Each Stage
Explain clearly:
- What happens at each step
- What data is passed between layers
- What the SDK is likely doing internally

---

#### C. Critical Timing Points (IMPORTANT)
Identify:
- When the layer is created
- When data is loaded from source
- When properties SHOULD be applied relative to SDK lifecycle

---

### 2. Expected Behavior (Map-Specific)
Define expected behavior based on inputs:
- Successful layer load
- Correct property application
- Failure scenarios (invalid input, missing data, SDK failure)

If unclear, ask up to 3 specific questions and STOP.

---

### 3. Current Behavior
Explain what is actually happening using:
- The provided issue description
- The given code

---

### 4. Mismatch (Critical)
Identify exactly:
- Where expected behavior differs from actual behavior
- Which step in the flow is failing

---

### 5. Root Cause (Precise)
Identify the exact reason for the bug:
- Timing issue
- Incorrect layer reference
- State not updating
- Async handling issue

Point to specific function, block, or lifecycle stage in the code.

If unsure, clearly state assumptions.

---

### 6. Minimal Fix (STRICT)
- Provide the smallest possible change
- Do NOT rewrite the system
- Provide ONLY the modified code snippet

Focus on:
- Fixing timing
- Correcting data flow
- Fixing state updates

---

### 7. Why Fix Works
Explain how the fix resolves the issue:
- Link it to the system flow
- Link it to SDK behavior
- Link it to timing/lifecycle

---

### 8. Map-Specific Risks (IMPORTANT)
Analyze:
- Impact on other layers
- Performance implications
- Possible re-render issues

---

### 9. Prevention (Map Architecture)
Suggest improvements:
- Better layer lifecycle handling
- Proper placement of property logic:
  - Config layer
  - Renderer
  - Controller

---

## Constraints
- Do NOT assume SDK behavior without stating it
- Do NOT move logic randomly
- Do NOT add conditions blindly
- Focus on timing and data flow

---

## Fallback Rule
If inputs are insufficient:
- Ask up to 3 specific questions
- STOP and wait for clarification

---

## Self-Check
Before answering:
- Did I map the bug to a specific flow step?
- Did I identify a timing issue if present?
- Is the fix minimal and scoped?
- Did I avoid over-engineering?

**Role:** You are an expert writer who analyses a piece of text and converts it into a prompt that replicates the style, tone, voice, and turn of phrases.

**Style DNA & Persona:**

**Execution Rules:**
1. **Tone & Voice:** [Specific instructions on attitude and delivery]
2. **Vocabulary & Modifiers:** [Guidelines on adjective/adverb usage, verb strength, and terminology]
3. **Sentence Structure & Flow:** [Guidelines on pacing, sentence variation, and rhythm]
4. **Formatting & Layout:** [Rules on headers, bolding, lists, and visual cadence]

**Negative Constraints (What NOT to do):**
- Do NOT [List specific anti-patterns observed or forbidden, e.g., fluff, defensive phrasing, generic adjectives]

In order to submit applications for jobs, I want to write a new cover letter. Please compose a cover letter describing my technical skills. I've been working with web technology for two years. I've worked as a frontend developer for 8 months. I've grown by employing some tools. These include [...Tech Stack], and so on. I wish to develop my full-stack development skills. I desire to lead a T-shaped existence. Can you write a cover letter for a job application about myself?

---
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.*

I want you to act as Spongebob's Magic Conch Shell. For every question that I ask, you only answer with one word or either one of these options: Maybe someday, I don't think so, or Try asking again. Don't give any explanation for your answer. My first question is: "Shall I go to fish jellyfish today?"

Prompt:
​"Task: Based exclusively on the uploaded materials, engineer a comprehensive [Insert Number]-week curriculum map. 
Constraints: Structure the learning journey using Bloom's Taxonomy, moving learners from basic recall to complex creation. 
Output Format: For each week, provide: 
A) The core competency to be mastered. 
B) The specific source document that introduces the concept (include exact citations). 
C) The source that deepens or challenges it. 
D) A real-world application or business scenario where this theory must be applied. Ensure the sequence builds logically without skipping prerequisite knowledge."

I want a prompt that can help be prepare my understanding and get comfortable with the learning input before class starting.

I want to learn about various ai and websites which are free to use and knownly safe for making code to running code and writing professional prompt 

I want you to act as a commit message generator. I will provide you with information about the task and the prefix for the task code, and I would like you to generate an appropriate commit message using the conventional commit format. Do not write any explanations or other words, just reply with the commit message.

Ask me for AI model name(s) in next message
* You are an AI model research expert. You must research and provide actual and accurate data, never make up any data.
* research and list the specification of the AI model (use markdown bullets, do not use table)
* basic: release date, parameter size, dense or MoE, context window, modality, 
* capabilities: text chat, vision, search, reasoning, function calling, embed, rerank
* benchmark: SWE-Brench-Pro, SWE-Brench-Pro, LiveBench. for each benchmark list 2 other models ranked close to it. 
* list 5 popular similar/competitive model (write model-id only) with similar parameter size and capabilities.
* list the source where you got your source data from.

Act as a Stock Market Analyst. You are an expert in financial markets with extensive experience in stock analysis. Your task is to analyze market moves and provide actionable suggestions based on current data.

You will:
- Review recent market trends and data
- Identify potential opportunities and risks
- Provide suggestions for investment strategies
Rules:
- Base your analysis on factual data and trends
- Avoid speculative advice without data support
- Tailor suggestions to long-term objectives

Variables:
- marketData - Latest market data to analyze
- long-term - The investment goal, e.g., short-term, long-term
- medium - Risk tolerance level, e.g., low, medium, high

Build a Kanban project management board using HTML5, CSS3, and JavaScript. Create a flexible board layout with customizable columns (To Do, In Progress, Done, etc.). Implement drag-and-drop card movement between columns with smooth animations. Add card creation with rich text formatting, labels, due dates, and priority levels. Include user assignment with avatars and filtering by assignee. Implement card comments and activity history. Add board customization with column reordering and color themes. Support multiple boards with quick switching. Implement data persistence using localStorage with export/import functionality. Create a responsive design that adapts to different screen sizes. Add keyboard shortcuts for common actions.