The method consists of four main steps: (ⅰ) constructing ecological networks, (ⅱ) assigning assembly processes, (ⅲ) quantifying biotic associations, and (ⅳ) assessing ecological consequence. Each step has been encapsulated as user-friendly functions that could be easily feasible and flexible. Besides, this package is developed based on a series of commonly used and advanced approaches in microbial ecology, for example, Spiec-Easi.