Vertical and Oblique Transmission under Fluctuating Selection

Yoav Ram, Uri Liberman, and Marcus W. Feldman, PNAS 2018

This repository contains supporting material for

Ram, Liberman & Feldman (2018) Vertical and Oblique Transmission under Fluctuating Selection, Proc Natl Acad Sci USA. DOI: 10.1073/pnas.1719171115

The notebook file figures.ipynb includes Python source code for reproduction of the manuscript figures.

Run the notebook

You can interact with the notebooks on your own machine.

Install dependencies

The easiest way to install the dependencies is to install Anaconda. You should use Python 3, preferably with version 3.5 or higher. The notebook will probably not work on Python 2.

All required packages should then be available. However, if you get an ImportError due to a package not being installed, the following command will install all requirements using conda:

conda install jupyter numpy scipy matplotlib pandas seaborn sympy numba 

You also need to install rakott and matplotlib_colorbar:

pip install https://github.com/yoavram/rakott.git
pip install matplotlib_colorbar

Get the source code repository

You can download all the source code by clicking the Clone or Download button and choosing Download ZIP. Then extract the ZIP to a folder on your machine.

If you use git you can clone the repo using:

git clone https://github.com/yoavram/Milpitas.git

Run the notebook

Start a Jupyter notebook server inside the repo folder:

cd <path to folder>
jupyter notebook

Your browser should open automatically. Open the notebooks folder and choose the notebook file figures.ipynb file.

Troubleshooting

Use the Issues page to report problems or suggest improvements or contact Yoav Ram.

License

This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License.