Optimal adaptation model

Introduction

Code for the manuscript "A prediction of optimal timescales for niche construction" by Edward D. Lee, Jessica C. Flack, and David C. Krakauer.

Preprint located at https://arxiv.org/abs/2209.00476.

Code is written by Eddie Lee.

Instructions

Functions for reproducing figures are in the file "pipeline.py". The specification of the Python 3 environment used to generate the results are in "adaptation.yml".

First clone the repository using

git clone https://github.com/eltrompetero/adaptation.git

After navigating into the directory of the repository, install the conda environment.

conda env create -f pyutils/adaptation.yml

Create the cache folder to store results.

mkdir cache

You should be able to run some of the pipeline code as, for example,

from pyutils import *

pipe.tau_range()

System specification

This code runs using Python 3.11 and was run on a 64-bit Ubuntu system. Note that some of the simulations require a substantial amount of RAM, so the recommendation is to have at least 128GB and additional 64-128GB of swap space to run all the pipeline code.

Troubleshooting

For any questions about the code and results, please open an issue on the GitHub page [https://github.com/eltrompetero/adaptation].