egtplot: A Python Package for Three-Strategy Evolutionary Games

This is a software package for plotting and animating three-strategy evolutionary games on a triangular simplex.

• The package can be used to create phase portraits of 3-strategy games

• It can also be used to animate transient behavior of the game

Use Cases

While there are many use cases for this software, our group's particular focus is on the mathematical modeling of cancer and cancer therapies through evolutionary game theory [@kaznatcheev2017cancer, @kaznatcheev2015edge, @Kaznatcheev179259]. For details on analytical treatments of evolutionary games, please see Artem Kaznatcheev's blog at Theory, Evolution, and Games Group.

Authorship

Inom Mirzaev and Drew FK Williamson contributed equally to this work.

Dependencies

The program is written and tested on Python >=3.5. This software package depends on the following libraries:

• numpy>=1.13, scipy, shapely for computations
• matplotlib for static plots
• imageio, moviepy for animations
• tqdm for progress bar

Installing the package from PyPi will take care of all the dependencies

pip install egtplot

Installation

• Easiest way to install the package is through PyPi

pip install egtplot

• You can clone this repository using git software and run setup.

git clone https://github.com/mirzaevinom/egtplot.git
cd egtplot
python setup.py install

• Alternatively you can download and extract a zip file of this repo:

cd egtplot-master
python setup.py install

• Finally, we also have created a Docker container for running a jupyter notebook with egtplot: drewfkw/egtplot

Specific Usage

• This software has two main functions: plot_static for plotting static simplex figures and plot_animated for generating simplex animations.
• For detailed usage of these functions we refer to our interactive jupyter notebook: egtplot_demonstration.ipynb
• We also welcome comments and questions regarding our whitepaper on bioRxiv which describes the package and its usage. The content is nearly identical to the jupyter notebook linked above.

Citation

If you use this program to do research that leads to publication, we ask that you acknowledge use of this program by citing the following in your publication:

Mirzaev I., Williamson D. and Scott J., egtplot: A Python Package for 3-Strategy Evolutionary Games, https://doi.org/10.1101/300004

Acknowledgements

• The authors would like to thank Mathematical Biosciences Institue (MBI) at Ohio State University, for partially supporting this research. MBI receives its funding through the National Science Foundation grant DMS 1440386.
• We gratefully acknowledge the work of Hanna Schenk whose code on her github inspired this project.

Contributing and Issues

Please use GitHub Issues for issue tracking and bugs. Feel free to contact Drew and Inom if you would like to contribute to egtplot or with questions and comments.