Hepatitis-C Cost Effectiveness

Source Code: https://github.com/SyndemicsLab/hep-ce

HEP-CE is a simulation model written and maintained by the Syndemics Lab at Boston Medical Center. HEP-CE is a Markov chain Monte Carlo state-transition model which simulates the spread and treatment of Hepatitis C Virus (HCV).

The version of HEP-CE you see now is a complete refactor developed with a focus on four goals:

1. Implement the model as a discrete-event simulation
2. Improve the maintainability of the model
3. Make adding/removing events easier
4. Make building the model easier across systems

The old HEP-CE model (HEPCEv1) was written in C++, like this one, but to honor the above goals we did not reuse code from HEPCEv1.

Key Features

• Easy addition and removal of events
• Parallel execution using OpenMP
• Able to be used standalone or as a library in your projects

Installation

Clone the source code and then build:

git clone https://github.com/SyndemicsLab/hep-ce.git
cd hep-ce
cmake --workflow gcc-release

Using the HEP-CE Executable

To use the provided executable, you need data in the correct structure.

Each set of model inputs must be provided in a folder named input<number>, where the <number> is replaced with the identifier of the input. The following depicts a tree of directories in which there are two input sets, numbered 1 and 2, for HEP-CE in the same source directory:

data-source/
├── input1/
│   ├── inputs.db
│   └── sim.conf
└── input2/
    ├── inputs.db
    └── sim.conf

Configuration

The sim.conf uses the .ini configuration format to break down model settings into key-value pairs that are also grouped into sections. For detailed descriptions of these values, reference Managing the Data.

Database Schema

An empty database with the correct structure can be created via the example schema.

Calling the Executable

Once you have model inputs in the correct structure, you can call the executable from the git directory with

build/extras/executable/hepce_exe /path/to/data/source <input_number_start> <input_number_end>

Example

To run the model for the example data-source shown above, you'd use the following command:

build/extras/executable/hepce_exe data-source 1 2

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