Metadata-Version: 2.2
Name: icomo
Version: 1.0.3
Summary: This toolbox aims to simplify the construction of compartmental models and the inference of their parameters
Author-email: Jonas Dehning <jonas.dehning@ds.mpg.de>
Project-URL: Homepage, https://github.com/Priesemann-Group/icomo
Project-URL: Bug Tracker, https://github.com/Priesemann-Group/icomo/issues
Project-URL: Discussions, https://github.com/Priesemann-Group/icomo/discussions
Project-URL: Changelog, https://github.com/Priesemann-Group/icomo/releases
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: pymc==5.*
Requires-Dist: equinox
Requires-Dist: diffrax
Requires-Dist: pytensor
Requires-Dist: graphviz
Requires-Dist: jax
Requires-Dist: numpy
Provides-Extra: opt
Requires-Dist: numpyro; extra == "opt"
Requires-Dist: optax; extra == "opt"
Requires-Dist: jaxopt; extra == "opt"
Requires-Dist: equinox; extra == "opt"
Requires-Dist: jaxtyping; extra == "opt"
Requires-Dist: optimistix; extra == "opt"
Provides-Extra: dev
Requires-Dist: icomo[opt]; extra == "dev"
Requires-Dist: pytest>=7.3.2; extra == "dev"
Requires-Dist: pytest-xdist; extra == "dev"
Requires-Dist: pre-commit>=3.3.2; extra == "dev"
Requires-Dist: ruff>=0.0.272; extra == "dev"
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Requires-Dist: sphinx-book-theme; extra == "dev"
Requires-Dist: importlib-metadata>=6.5.1; extra == "dev"
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Requires-Dist: pandoc>=2.3; extra == "dev"
Requires-Dist: pytest-beartype; extra == "dev"
Requires-Dist: sphinx-autodoc-typehints; extra == "dev"

<div align="center">
<img src="https://raw.githubusercontent.com/Priesemann-Group/icomo/main/docs/images/icomo_logo250px.png" width="550" alt="logo"></img>
</div>


# Inference of Compartmental Models toolbox

## Leverage the power of JAX libraries for PyMC models

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](https://jax.readthedocs.io/en/latest/),
[Diffrax](https://docs.kidger.site/diffrax/) and
[PyMC](https://www.pymc.io/welcome.html) 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](https://icomo.readthedocs.
io/en/stable/api/jax2pytensor.html)), which
is used tro wrap the [Diffrax ODE solvers](https://docs.kidger.site/diffrax/api/diffeqsolve/), but might be also useful for other
projects.

* Documentation: https://icomo.readthedocs.io.

### 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.

### Credits

Logo by [Fabian Mikulasch](https://scholar.google.com/citations?user=ZWWBIoUAAAAJ&hl=en)




