PyRossTSI: Time since infection models in Python

About

PyRoss is a companion library that offers tools for both deterministic and stochastic simulation of macroscopic compartmental models, as well as a complete suite of inference and optimal control tools.
PyRossGeo is another companion library that supports spatially resolved compartment models with explicit commuting networks.

You can take PyRossTSI for a spin without installation: . Please be patient while Binder loads.

PyRossTSI requires the following software

Python 2.6+ or Python 3.4+
Cython | Matplotlib | NumPy | SciPy | cma | NLopt
Optional: integrators (OdesPy) | parallelizing inference (pathos) | data files (Pandas, xlrd)

Clone (or download) the repository and use a terminal to install PyRoss (above requirements need to be satisfied)

>> git clone https://github.com/rajeshrinet/pyrosstsi.git
>> cd pyrosstsi
>> python setup.py install

Alternatively, use anaconda to install PyRossTSI and its dependencies in a pyrosstsi environment

>> git clone https://github.com/rajeshrinet/pyrosstsi.git
>> cd pyrosstsi
>> make env
>> conda activate pyrosstsi
>> make

pip install -e git+https://github.com/rajeshrinet/pyrosstsi.git#egg=pyrosstsi