These are the codes in R accompanying the manuscript Integrating coexistence and invasion theories under a probabilistic framework written by Jie Deng, Washington Taylor, Simon A. Levin, and Serguei Saavedra. The codes are well commented with simple examples.

Specifically, toolbox.R provides the functions to calculate the probabilistic measures (Figs. 2 & 3 in the manuscript) of simultaneous assembly outcomes (i.e., individual survival, community persistence, competitor exclusion) and sequential assembly outcomes (i.e., invader colonization, invader-resident augmentation, resident replacement). Also, example.R illustrates an example of how to use the functions in toolbox.R.