Generalized Compartmental Modeling Framework

A flexible Python framework for simulating, fitting, and visualizing epidemiological compartmental models such as SIR, SEIR, SIS, and custom user-defined models.

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Features

• Define models entirely via a YAML configuration file
• Supports ODE-based simulations for arbitrary compartment structures
• Built-in noise injection and subset sampling for fitting
• Parameter estimation with:
  • Nelder-Mead
  • BFGS
  • L-BFGS-B
  • MCMC (via emcee)
• Automatic plot generation for:
  • Clean simulations
  • Noisy data
  • Model fit comparisons
  • Parameter estimation results
  • MCMC posterior distributions

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Installation

The source code is available on GitHub at:
https://github.com/dsih-artpark/infectious-disease-models

git clone https://github.com/dsih-artpark/infectious-disease-models.git
cd infectious-disease-models
uv pip install -r requirements.txt