trd-cea-toolkit 0.4.0

Open-source toolkit for health economic evaluation of psychedelic therapies vs ECT for treatment-resistant depression

TRD CEA Toolkit: Health Economic Evaluation Tools

This repository contains a comprehensive toolkit for conducting health economic evaluations comparing psychedelic therapies and other interventions for treatment-resistant depression (TRD).

Overview

The TRD CEA Toolkit provides:

• Cost-Effectiveness Analysis (CEA): Traditional and distributional CEA
• Value of Information (VOI): EVPI, EVPPI, and EVSI analysis
• Budget Impact Analysis (BIA): Multi-year budget projections
• Multiple Criteria Decision Analysis (MCDA): Multi-attribute utility modeling
• Sensitivity Analysis: One-way, multi-way, and probabilistic sensitivity analysis
• Implementation Modeling: Capacity constraints and implementation costs
• Equity Analysis: Distributional cost-effectiveness with population subgroups

Installation

# Clone the repository
git clone https://github.com/your-username/trd-cea-toolkit.git
cd trd-cea-toolkit

# Create conda environment (recommended)
conda env create -f environment.yml
conda activate trd-cea

# Or create environment manually
conda create -n trd-cea python=3.10
conda activate trd-cea
pip install -r requirements.txt

# Install as package in development mode
pip install -e .

Usage

Quick Start with Jupyter Notebooks

The easiest way to get started is using the example notebooks in the analysis/ directory:

# Activate environment
conda activate trd-cea

# Launch Jupyter Lab
jupyter lab

Then navigate to the example notebooks in analysis/cea/, analysis/dcea/, etc.

Command Line Interface

The toolkit includes a command-line interface:

# Run CEA analysis
trd-cea-analyze cea --config config/analysis_config.yaml

# Run Budget Impact Analysis
trd-cea-analyze bia --config config/bia_config.yaml

# Run Value of Information analysis
trd-cea-analyze voi --config config/voi_config.yaml --type evpi

Programmatic Usage

from src.trd_cea.analysis import run_analysis_pipeline

# Run analysis from configuration
results = run_analysis_pipeline(
    config_path="config/analysis_config.yaml",
    analysis_type="cea"
)

Analysis Types

The toolkit provides implementations for:

• CEA: Cost-effectiveness analysis with ICERs and NMB calculations
• DCEA: Distributional CEA incorporating equity considerations
• VOI: Value of information analysis (EVPI, EVPPI, EVSI)
• BIA: Budget impact analysis with multi-year projections
• MCDA: Multi-criteria decision analysis
• PSA: Probabilistic sensitivity analysis
• DSA: Deterministic sensitivity analysis (one-way and multi-way)
• VBP: Value-based pricing calculations
• Headroom: Headroom and pricing threshold analysis
• Subgroup: Subgroup analysis by demographics/clinical characteristics
• Scenario: Scenario analysis for different assumptions
• Capacity: Capacity constraints and implementation modeling
• Policy: Policy realism and implementation feasibility assessment

Project Structure

trd-cea-analysis/
├── analysis/                 # Jupyter notebooks by analysis type
│   ├── cea/                  # Cost-effectiveness analysis examples
│   ├── dcea/                 # Distributional CEA examples  
│   ├── voi/                  # Value of information examples
│   ├── bia/                  # Budget impact analysis examples
│   └── ...                   # Other analysis types
├── src/trd_cea/              # Python package source
│   ├── core/                 # Core utilities and configuration
│   ├── models/               # Analysis engine implementations
│   ├── analysis/             # Analysis execution functions
│   ├── plotting/             # Visualization and plotting utilities
│   └── utils/                # General utility functions
├── config/                   # Configuration files
├── data/                     # Data schemas and sample data structures
├── docs/                     # Documentation
├── tests/                    # Test suite
├── reports/                  # Project reports and documentation
├── development/              # Development tools and configuration
├── archives/                 # Archive files and backups
├── environment.yml           # Conda environment specification
├── requirements.txt          # Python dependencies
├── pyproject.toml            # Python package metadata
├── setup.py                  # Package setup script
├── scripts/                  # Additional scripts (orchestration, etc.)
├── README.md                 # This file
└── LICENSE                   # License information

Configuration

All analyses are configurable through YAML files in the config/ directory. This separates configuration from code, allowing for reproducible analyses with different parameter sets.

Contributing

We welcome contributions! Please see the CONTRIBUTING.md file for details.

License

This project is licensed under the Apache 2.0 License - see the LICENSE file for details.

Citation

If you use this toolkit in your research, please consider citing:

Dylan A Mordaunt (2025). TRD CEA Toolkit: Health Economic Evaluation Tools. Available at https://github.com/edithatogo/ee_trd