Introduction of ICoMo#

This toolbox aims to simplify the construction of compartmental models and the inference of their parameters.

The aim isn’t to provide a complete package that will build models from A to Z, but rather provide different helper functions examples and guidelines to help leverage modern python packages like JAX, Diffrax and PyMC to build, automatically differentiate and fit compartmental models.

A central part of the toolbox is the possibility to wrap JAX functions to be used in PyMC models (see here), which is used tro wrap the Diffrax ODE solvers, but might be also useful for other projects.

Features#

Facilitate the construction of compartmental models by only defining flow between compartments, and automatically generating the corresponding ODEs.
Plot the graph of the compartmental model to verify the correctness of the model.
Integrate the ODEs using diffrax, automatically generating the Jacobian of the parameters of the ODE
Fit the parameters using minimization algorithms or build a Bayesian model using PyMC.