CRM

This Repository provides a unified modeling framework for simulating microbial community dynamics using consumer-resource models (CRMs). It begins with classical CRMs, modeling species-resource interactions through fixed consumption and secretion matrices, and explores scenarios such as different resource supply strategies, structured trait-based assembly, and functional convergence. The framework then extends into adaptive CRMs, where species dynamically adjust their uptake strategies, capturing niche shifts and flexible foraging. Inspired by Goldford et al. (2018, Science), the Goldford-style model integrates metabolic family structures through Dirichlet priors, simulates community assembly, and analyzes diversity patterns across replicate simulations. The CommunityModels API unifies MCRM, MiCRM, and Gibbs models for head-to-head comparison under consistent parameter settings, enabling exploration of cross-feeding, leakage, and thermodynamic constraints. Lastly, the framework incorporates parameter estimation modules using optimization and Bayesian inference to infer model parameters from synthetic or experimental data. Together, this pipeline enables comprehensive investigation of microbial community structure, function, and assembly under both controlled and complex ecological scenarios.