comod

Compartmental modelling Python package

Preview

Check the docs to see more.

Features

• Define a model with simple rules as strings or with custom functions.
• Pre-defined models like SIR, SIS, SEIR, ...
• Community-extensions of models.
• Solve numerically for fixed or time-dependent parameters.
• Best-fit to existing data, posibly using time windows.
• Create compartment graphs.
• Export LaTeX.
• Export to Wolfram Language (Mathematica).

Installation

Assuming you have a Python3 distribution with pip, the latest pypi release can be installed with:

pip3 install comod

To install the optional dependencies you can run

pip3 install 'comod[extras]'

Mind the quotes.

Developer information

Instalation

To install a development version, cd to the directory with this file and:

pip3 install -e '.[test]'

As an alternative, a virtualenv might be used to install the package:

# Prepare a clean virtualenv and activate it
virtualenv -p /usr/bin/python3.6 venv
source venv/bin/activate
# Install the package
pip3 install -e '.[test]'

Documentation

To generate the documentation, the docs extra dependencies must be installed.

To generate an html documentation with sphinx run:

make docs

To generate a PDF documentation using LaTeX:

make pdf

Test

To run the unitary tests:

make test