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This paper introduces MATES: the Macro Agent Transport Event-based Simulator. MATES is a free, open-source simulator intended for efficient comparison of application layer agent algorithms. Existing simulators, both from the networking and artificial intelligence communities, are not adequate to efficiently model the domain of mobile agent systems running atop dynamic, peer-to-peer networks. MATES bridges the gap between the two disciplines by providing macroscopic models for low-layer network processes, allowing for more processing time to be devoted to the agent behavior model. The three principle contributions of this paper are an introduction to the simulator, validation of MATES' models using data from a live wireless network, and explication of a technique for improving simulator transparency through preservation of agent state.