Code for simultaneous branching project

This repository contains the code to generate data and to generate the figures for the simultaneous branching project.

Code to generate data

Code to generate simulations can be found in the folder code_for_submission:

• IBS_code.cpp: generates IBS
• ibs_random.cpp: generates IBS with a random game (for the section on asymmetric games)
• OSS_code.R: generates OSS
• PDE_code.R: code for PDE model; to run PDE use run_PDE_code.R (same folder).

Analysing data and generating figures

The other folders contain R code to analyse data and create figures.

Raw data files generated from OSS simulations are included as RDS files. Raw data files generated frm IBS and PDE are not included because they are too large, but they can be generated by running the code in code_for_submission. However, the repository includes the IBS summary data generated from the raw data (as well as the R files used to generate summary data), in the form of RDS files. All figures can be generated using the included R code and the summary data (in the IBS case) or raw data (in the OSS/PDE case).

The figure of the fitness landscape was generated in Mathematica using the file fitness_landscape.nb.

More

The derivations for Appendix F (stability to large mutations) are in the Mathematica notebook AppendixF.nb; a pdf version of the same file, AppendixF.pdf, is also included.

Feel free to email me at gilhenris-at-gmail-dot-com for any questions.