This repository contains the code to perform simualtions and analysis for Lechón et al. The role of competition versus cooperation in microbial community coalescence (2021).

The repository contains three folders: code which contains the code to generate communities, run simualtions and plot figures, data which is used to store simulation results and sandbox which contains...

In order to run the simulations in the manuscript you'll need to run two scripts. First run code/assembly_clean.py which generates parent communities, simulates till equilibrium and saves the output in the data folder. To run the coalescence simualtions run code/coalescence_clean.py which will simulate community coalescence and save the output to data.

To plot the simualtion results as seen in the manuscript run any of the respective R scripts in the code folder:

├── figure_2.R
├── figure_3.R
├── figure_4.R
├── figure_S3.R
├── figure_S4.R
├── figure_S6.R

which will save the figures in the sandbox folder.