R Code Review

Comprehensive code review for R scripts and packages. This command uses the r-code-reviewer agent (Opus) to perform thorough quality assessment.

Review Scope

Style Review

• Tidyverse style guide compliance
• Naming conventions (snake_case, meaningful names)
• Code formatting and indentation
• Pipe usage and readability

Quality Review

• Function design (single responsibility, pure functions)
• Error handling patterns
• Documentation completeness
• DRY principle adherence

Performance Review

• Vectorization opportunities
• Memory efficiency
• Computational bottlenecks
• Parallel processing opportunities

Security Review

• Input validation
• Credential handling
• SQL injection prevention
• Safe file operations

Testing Review

• Test coverage assessment
• Test quality and patterns
• Edge case coverage
• Mocking practices

TMwR Review (Tidymodels Workflow Review)

• Data Leakage Detection (CRITICAL)
  • Recipe fitted on test data (DL-001)
  • Preprocessing before split (DL-002)
  • Target encoding without CV (DL-003)
  • Feature selection using test data (DL-004)
  • prep() before initial_split() (DL-005)
• Resampling Violations (MAJOR/CRITICAL)
  • Missing stratified sampling (RS-001)
  • Evaluating on training data (RS-002)
  • Tuning without nested CV (RS-003)
  • Missing random seeds (RS-004)
  • Validation set reuse (RS-005)
• Workflow Issues (MINOR/MAJOR)
  • Not using workflows (WF-001)
  • Inconsistent preprocessing train/test (WF-002)
  • Not finalizing workflow after tuning (WF-003)
• Evaluation Issues (MAJOR)
  • Only accuracy for imbalanced data (ME-001)
  • Wrong metrics for model mode (ME-002)
  • Missing calibration assessment (ME-003)
  • Missing confidence intervals (ME-004)
  • Different resamples for comparison (ME-005)
• Reproducibility Issues (MINOR/MAJOR)
  • Missing set.seed() (RP-001)
  • Missing tidymodels_prefer() (RP-002)
  • Hard-coded paths (RP-003)
  • Missing renv (RP-004)
  • Missing session info (RP-005)

Usage

/r-code-review [path] [review_type]

Parameters

• path: Path to R file, directory, or package (default: current directory)
• review_type: One of full, style, performance, security, tests, tmwr (default: full)

Review Types

Type	Description
full	All review types including TMwR
style	Tidyverse style guide compliance only
performance	Vectorization, memory, speed optimization
security	Input validation, credential handling
tests	Test coverage and quality
tmwr	Tidymodels workflow review (data leakage, resampling, evaluation)

Output Location

Review report will be written to:

output/
└── reports/
    └── code_review_[timestamp].md

Review Report Structure

1. Executive Summary

   • Overall assessment
   • Key findings count by severity
   • Recommended priority actions

2. Detailed Findings

   • Each issue with:
     • Severity (Critical, Major, Minor, Suggestion)
     • Location (file:line)
     • Description
     • Recommendation
     • Code example (before/after)

3. Metrics

   • Lines of code
   • Function count and complexity
   • Test coverage (if available)
   • Documentation coverage

4. Positive Observations

   • Well-written code patterns
   • Good practices observed

Examples

/r-code-review R/ full

Performs a comprehensive review of all R files in the R/ directory including TMwR compliance.

/r-code-review scripts/analysis.R tmwr

Performs a focused TMwR review for tidymodels workflow anti-patterns.

TMwR Review Output

TMwR reviews include:

• TMwR Compliance Score: 0-100 based on anti-pattern severity
• Issue Findings: Each with ID, severity, location, description
• Before/After Examples: Remediation code for each issue
• Checklist Summary: Pass/fail for 10-point TMwR compliance checklist

Integration with CI/CD

The review output can be integrated into GitHub Actions or other CI pipelines:

- name: R Code Review
  run: |
    # Generate review report
    # Parse for critical issues
    # Fail if critical issues found

Notes

• Review is read-only - no code modifications are made
• All suggestions are written to the output folder
• Large codebases may be reviewed in sections