R Specialized Applications Tutorial Generator

Generate comprehensive R tutorials for specialized domain applications with proper academic structure, terminology, and visual assets.

Purpose

This skill creates detailed R tutorials (.rmd/.qmd files) for specialized applications including:

Each tutorial follows a "Domain Background → Terminology → Theory → Practice → Interpretation" workflow with minimum 300 lines of content.

Workflow

Step 1: Generate Tutorial Content and Cover Image

**Read Template Structure:**

**Create Tutorial File:**

Create `doc/[number]-[topic].rmd` with the following structure:

1. **YAML Frontmatter**: Include title, subtitle, author, date, output format

2. **Domain Background**: Explain the application domain and its importance

3. **Core Concepts**: Define key terms with Chinese-English bilingual terminology

4. **Method Theory**: Explain the statistical/computational principles

5. **Detailed Practice**: Provide step-by-step R code workflow (30% of content)

6. **Domain Interpretation**: Interpret results from domain perspective (clinical significance, policy implications)

7. **Ethical Considerations**: Address data ethics where applicable

8. **Reporting Standards**: Reference domain-specific reporting guidelines

**Content Requirements:**

**Generate Cover Image (MANDATORY):**

Create `doc/images/[number]-[topic]-cover.svg` following visual templates

**Generate Diagram Images (if needed):**

For complex logic or structures that code cannot easily demonstrate, create `doc/images/diagrams/stat-[topic].svg` (or .png) using AI image generation. Reference in markdown using standard image syntax.

Step 2: Validate Rendering (CRITICAL)

Before committing, validate that the tutorial renders correctly:

```bash

Render the single file to verify content

quarto render doc/[number]-[topic].rmd

Ensure no errors, missing packages, or formatting issues

```

Step 3: Update Navigation System (CRITICAL)

The new article will not appear on the website sidebar or category pages unless these steps are completed:

**1. Update `doc/_quarto.yml`:**

```yaml

- text: "Article Title"

href: "[number]-[topic].rmd"

```

**2. Update `doc/0001-guide.rmd`:**

```markdown

| [Topic Name] | [Article Title]([number]-[topic].html) | [Brief description] |

```

**3. Run Auto-Generation Script (MANDATORY):**

This script updates `sections/special.qmd` and other category index pages based on `_quarto.yml`:

```bash

Run from project root directory

workdir="doc" Rscript doc/generate_sections.R

```

**4. Update `README.md`:**

Step 4: Final Rendering and Commit

**Re-render Affected Pages:**

```bash

quarto render doc/sections/special.qmd

quarto render doc/index.qmd

```

**Commit Changes:**

```bash

git add doc/[number]-[topic].rmd doc/images/[number]-[topic]-cover.svg

git add doc/_quarto.yml doc/0001-guide.rmd README.md doc/sections/special.qmd

git commit -m "feat(spc): Add [domain-method] specialized application tutorial"

```

Quality Standards

Reference Files

Before starting, read these reference documents in the `doc/references/` directory:

Example Usage

User: "Create a tutorial on cost-effectiveness analysis in health economics"

Agent should:

1. Read reference documents to understand structure and terminology

2. Generate comprehensive `doc/[number]-cea-health-economics.rmd` with 300+ lines

3. Create cover image `doc/images/[number]-cea-health-economics-cover.svg`

4. Validate rendering with `quarto render`

5. Update all navigation files (`_quarto.yml`, `0001-guide.rmd`, `README.md`)

6. Run `generate_sections.R` script

7. Re-render affected pages and commit all changes