The potential effects of conservation actions on threatened species can be predicted using ensemble ecosystem models. These model ensembles commonly assume stable coexistence of species in the absence of available data. However, existing ensemble-generation methods become computationally inefficient as the size of the ecosystem network increases, preventing larger networks from being studied. We present a novel sequential Monte Carlo sampling approach for ensemble generation that is orders of magnitude faster than existing approaches. We demonstrate that the methods produce equivalent parameter inferences, model predictions, and tightly constrained parameter combinations using a novel sensitivity analysis method. For one case study, we demonstrate a speed-up from 108 days to 6 hours, while maintaining equivalent ensembles. Now, for the first time, larger and more realistic networks can be practically simulated.

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