CoexistenceTheory

Code and data to replicate results for the manuscript "The evolution of niche overlap and competitive differences".

In the Code directory:

• get_data.R: The main script that runs the model over many different combinations of parameters and initial conditions, and generates the model's output. By default, this output is dumped on the screen; redirect the output to a file to save the results (see the comments within the script as well). The result of this run, compressed into an .rds file, can be found in the Data directory.
• functions.R: Functions aiding numerical integration of the ordinary differential equations (ODEs), obtaining niche overlap and competitive differences from the results, and organizing them into a tidy output format. It is used by get_data.R, sample_dynamics.R, and trajectories.R.
• boxplots.R, phaseplots.R, predict_coex.R, sampe_dynamics.R, and trajectories.R: These scripts generate the figures in the manuscript.
• shinyapp/app.R: A stand-alone, interactive application allowing the user to set all parameters and initial conditions of the model, and immediately see its output.

In the Data directory:

• alldata.rds: The output generated by get_data.R, compressed into .rds format to reduce size.