Scripts accompanying Bhat and Guttal 2023

This repository contains scripts and data accompanying Bhat and Guttal 2024, "Eco-evolutionary dynamics for finite populations from first principles and noise-induced reversal of selection". The scripts and data files in this repository can be used to reproduce the plots presented in Box 3 and Supplementary section S12 of the manuscript.

Guide to the repo

This repo contains two folders, box_3_example and supp_LV_example, which contain scripts for reproducing the figures presented in Box 3 and Supplementary section S12 respectively.

Scripts for reproducing the figure in box 3

fast_mechanism.R and slow_mechanism.R are R scripts that reproduce Box Figure IIA and Box Figure IIB in the main text respectively. The plots generated are stored as SVG files in the plots folder. Both scripts plot the quasi-steady state density of the example introduced in Box 3 for various parameter values.

Scripts for reproducing the figure in the Supplementary

The data folder contains CSV files that are output by the scripts presented in the main repository. The plots folder contains plots that make up figure 2 in the manuscript. The plots were arranged into a single figure using Inkscape. The scripts serve the following functions:

• noise_induced_selection_model_SSA.R is an R script that uses Gillespie's stochastic simulation algorithm (SSA) to simulate the exact birth-death process corresponding to the resource competition model we introduce as an example in supplementary section S12. The output of this file is a CSV file stored in the data folder.
• analytical_solution_in_deterministic_limit.ipynb is a Jupyter Notebook in which we use Python code to symbolically find the fixed points of the cubic ODE corresponding to the infinite population (deterministic) limit of our birth-death process.
• compare_SSA_with_numerical_integration.R is an R script that compares the steady state density obtained from the SSA (using noise_induced_selection_model_SSA.R) with the quasi-steady state density obtained by numerically solving the Fokker-Planck equation corresponding to the Ito SDE obtained after a system-size expansion of the exact birth-death process by plotting the two density functions on the same graph. We also plot the infinite population limit prediction obtained in analytical_solution_in_deterministic_limit.ipynb. The output of this file is an SVG file stored in the plots folder. These plots are figure S2A and figure S2B in the manuscript.