In this repository you will find code to simulate unapproximated growth and competition dynamics for Mediterannean annual plant species under water limitation. This simulator is based off the ecophysiological model in Levine et al. 2022, “Competition and coexistence in phenologically structured annual plant communities”, presented primarily in Appendix 1. This simulator does not include the step-function approximation for growth under water limitation described in Appendix 1.3, but rather calculates plant growth rates explicitly at each time point in a growing season from soil water availability. This simulator can be used to explore the population dynamics of competing species and water availability dynamics within and across seasons.
All of the functions necessary to use the simulator are contained in simulator.R. Specifically, the function simulate_dynamics() is used to simulate a system of species with user-specified characteristics across years. By default, the function runs until either a) the system reaches a quasi-equilibrium defined when each species’ delta \(= \left|\frac{N_T - NT-1}{NT-1}\right|\) is less than a specified threshold, delta_tol, or b) the simulator runs for Tmax years. Both delta_tol and Tmax are user-supplied variables with default values of 0.0001 and 100 respectively.
The function simulate_year() is used to simulate the dynamics within a single growing season, and is repeatedly called by simulate_dynamics(). In both functions, evaporation can be added through the variable evap. The user must specify a function to calculate evaporation at each within-season timestep. For example, if the user wishes evaporation to be proportional to current water availability they could write evap = function(W) 0.01*W.
The file, simulator_example.org, contains annotated declarations of the functions and variables in simulator.R as well as scripts demonstrating how to use those functions to simulate a systems of plants. The examples are in fact the analyses performed in Appendix 9.3 of the manuscript, but serve the dual purpose of illustrating the use of the simulator. This file is a .org file, a form of markdown that integrates code and stylized annotations using Org Mode. This filetype is primarily supported by GNU emacs, of which I (Jacob) am a user. The code can be copied and run in RStudio or whatever your preferred IDE or text editor is (though you should consider switching to emacs).