ebm-calculator

Source: https://github.com/aipoch/medical-research-skills

EBM Calculator

Evidence-Based Medicine diagnostic test calculator.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

python -m py_compile scripts/main.py
python scripts/main.py --help

When to Use

• Use this skill when calculating diagnostic test performance (sensitivity, specificity, PPV, NPV, likelihood ratios).
• Use this skill when converting between pre-test and post-test probability or computing NNT.
• Use this skill when the user says "calculate sensitivity", "EBM calculator", "diagnostic accuracy", or "likelihood ratio".

Workflow

1. Identify calculation mode: Determine mode from user request — diagnostic (sensitivity/specificity/PPV/NPV/LR), nnt (number needed to treat), or probability (pre/post-test probability conversion).
2. Collect required parameters:
   • Diagnostic mode: TP, FN, TN, FP counts; optional prevalence for PPV/NPV adjustment
   • NNT mode: control event rate, experimental event rate
   • Probability mode: pre-test probability, likelihood ratio
3. Validate inputs: Check that all counts are non-negative integers, rates are between 0 and 1, and denominators are not zero. If invalid, report exact error and stop.
4. Checkpoint: Display input summary to user for confirmation before computing results.
5. Compute results: Execute calculations per mode. Include interpretation string (e.g., "LR+ of 10 strongly rules in disease").
6. Output: Return structured JSON with computed metrics and interpretation.
7. Fallback: If a required parameter is missing, output a template showing which fields are needed with example values.

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

{
  "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

Output Requirements

Every final response should make these items explicit when they are relevant:

• Objective or requested deliverable
• Inputs used and assumptions introduced
• Workflow or decision path
• Core result, recommendation, or artifact
• Constraints, risks, caveats, or validation needs
• Unresolved items and next-step checks

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
• If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
• Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of ebm-calculator and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

ebm-calculator only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

Response Template

Use the following fixed structure for non-trivial requests:

1. Objective
2. Inputs Received
3. Assumptions
4. Workflow
5. Deliverable
6. Risks and Limits
7. Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.