Ecosystem Health Check

You are conducting a comprehensive health check of the MediationVerse R package ecosystem.

MediationVerse Packages

Package	Path	Purpose
medfit	~/R-packages/active/medfit	Foundation (fitting, extraction, bootstrap)
probmed	~/R-packages/active/probmed	P_med probabilistic effect size
rmediation	~/R-packages/active/rmediation	Confidence intervals (PRODCLIN)
medrobust	~/R-packages/active/medrobust	Sensitivity analysis
medsim	~/R-packages/active/medsim	Simulation infrastructure
mediationverse	~/R-packages/active/mediationverse	Meta-package

Health Check Process

Step 1: Package Status

For each package, check:

• R CMD check status (use r_check tool if available)
• Test coverage (aim for >80%)
• Documentation completeness
• DESCRIPTION version and dependencies

Step 2: Dependency Analysis

• Check inter-package dependencies
• Identify version conflicts
• Verify dependency chain is correct:

  medfit (foundation)
    ├── probmed (depends on medfit)
    ├── rmediation (standalone, may use medfit)
    ├── medrobust (depends on medfit)
    └── medsim (depends on medfit, probmed)
  mediationverse (imports all)
  

Step 3: API Consistency

• Are S7 class definitions consistent across packages?
• Do function signatures follow conventions?
• Is documentation style consistent?

Step 4: Test Integration

• Do cross-package workflows work?
• Are integration tests passing?

Step 5: Documentation

• Are pkgdown sites building?
• Is the ecosystem navigation correct?
• Are vignettes up to date?

Output Format

## MediationVerse Ecosystem Health Report
**Date**: [Date]

### Summary Dashboard
| Package | R CMD Check | Coverage | Docs | Version |
|---------|-------------|----------|------|---------|
| medfit  | ✓/⚠/✗      | XX%      | ✓/⚠  | X.Y.Z   |
| probmed | ...         | ...      | ...  | ...     |
| ...     | ...         | ...      | ...  | ...     |

### Overall Status: 🟢 Healthy / 🟡 Needs Attention / 🔴 Issues

### Detailed Findings

#### medfit
- **Status**: [Summary]
- **Issues**: [List any problems]
- **Action needed**: [Recommended fixes]

[Repeat for each package]

### Dependency Graph
[ASCII or description of current dependency state]

### Cross-Package Issues
[Any issues that span multiple packages]

### Recommendations
1. **Immediate**: [Urgent fixes]
2. **Short-term**: [Should address soon]
3. **Long-term**: [Future improvements]

### Next Steps
[Specific action items with priorities]

Skills to Apply

• r-package-development
• statistical-research-workflow

Tools to Use

• r_check (for each package)
• r_test (for each package)
• Read (for DESCRIPTION files)
• Glob (for finding test files)