ebm-calculator

# EBM Calculator Evidence-Based Medicine diagnostic test calculator. ## Features - Sensitivity / Specificity calculation - PPV / NPV with prevalence adjustment - Likelihood ratios (LR+ / LR-) - Number Needed to Treat (NNT) - Pre/post-test probability conversion ## Parameters | Parameter | Type | Default | Required | Description | |-----------|------|---------|----------|-------------| | `--mode`, `-m` | string | diagnostic | No | Calculation mode (diagnostic, nnt, probability) | | `--tp`, `--true-pos` | int | - | * | True positives (diagnostic mode) | | `--fn`, `--false-neg` | int | - | * | False negatives (diagnostic mode) | | `--tn`, `--true-neg` | int | - | * | True negatives (diagnostic mode) | | `--fp`, `--false-pos` | int | - | * | False positives (diagnostic mode) | | `--prevalence`, `-p` | float | - | No | Disease prevalence 0-1 (diagnostic mode) | | `--control-rate` | float | - | ** | Control event rate 0-1 (nnt mode) | | `--experimental-rate` | float | - | ** | Experimental event rate 0-1 (nnt mode) | | `--pretest` | float | - | *** | Pre-test probability 0-1 (probability mode) | | `--lr` | float | - | *** | Likelihood ratio (probability mode) | | `--output`, `-o` | string | stdout | No | Output file path | \* Required for diagnostic mode \** Required for nnt mode \*** Required for probability mode ## Output Format ```json { "sensitivity": "float", "specificity": "float", "ppv": "float", "npv": "float", "lr_positive": "float", "lr_negative": "float", "interpretation": "string" } ``` ## Risk Assessment | Risk Indicator | Assessment | Level | |----------------|------------|-------| | Code Execution | Python/R scripts executed locally | Medium | | Network Access | No external API calls | Low | | File System Access | Read input files, write output files | Medium | | Instruction Tampering | Standard prompt guidelines | Low | | Data Exposure | Output files saved to workspace | Low | ## Security Checklist - [ ] No hardcoded credentials or API keys - [ ] No unauthorized file system access (../) - [ ] Output does not expose sensitive information - [ ] Prompt injection protections in place - [ ] Input file paths validated (no ../ traversal) - [ ] Output directory restricted to workspace - [ ] Script execution in sandboxed environment - [ ] Error messages sanitized (no stack traces exposed) - [ ] Dependencies audited ## Prerequisites No additional Python packages required. ## Evaluation Criteria ### Success Metrics - [ ] Successfully executes main functionality - [ ] Output meets quality standards - [ ] Handles edge cases gracefully - [ ] Performance is acceptable ### Test Cases 1. **Basic Functionality**: Standard input → Expected output 2. **Edge Case**: Invalid input → Graceful error handling 3. **Performance**: Large dataset → Acceptable processing time ## Lifecycle Status - **Current Stage**: Draft - **Next Review Date**: 2026-03-06 - **Known Issues**: None - **Planned Improvements**: - Performance optimization - Additional feature support