These are the codes in R accompanying the manuscript The development of ecological systems along paths of least resistance written by Jie Deng, Otto X. Cordero, Tadashi Fukami, Simon A. Levin, Robert M. Pringle, Ricard Solé, and Serguei Saavedra. The codes are well commented with simple examples.

Specifically, toolbox.R provides the functions to calculate the developmental probabilities (Fig. 2A) and the optimal path (Fig. 2B, Fig. 3) in our theoretical framework. Also, example.R illustrates an example of how to use the functions in toolbox.R. All codes were executed on the MIT SuperCloud (High-Performance Computing).

The flowchart illustrating the analysis in Figure 2B is presented below.