All chapters of this dissertation share two central themes: understanding predator–prey dynamics between kangaroo rats and rattlesnakes and developing standardized computational methods that are generalizable to other biological systems. In Chapter 1, I develop a game-theoretic agent-based model to simulate microhabitat use strategies in the kangaroo rat-rattlesnake system. Microhabitat choice shapes predator-prey interactions through differential selection pressures from aerial predators and sit-and-wait predators, as well as physical structure for refuge and camouflage. The results of our analysis show that when specialist predators occur at higher densities than generalist predators, both generalist predators and prey shift toward habitat specialization due to competition. In Chapter 2, I simulate microhabitat use from the perspective of an ectothermic predator that is thermoregulating to compare computational approaches to standard thermal ecology metrics used for determining...