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Railsback, Steven F.; Harvey, Bret C.; Jackson, Stephen K.; Lamberson, Roland H. 2009. InSTREAM: the individual-based stream trout research and environmental assessment model. Gen. Tech. Rep. PSW-GTR-218. Albany, CA: U.S. Department of Agriculture, Forest Service, Pacific Southwest Research Station. 254 p. This report documents Version 4.2 of InSTREAM, including its formulation, software, and application to research and management problems. InSTREAM is a simulation model designed to understand how stream and river salmonid populations respond to habitat alteration, including altered flow, temperature, and turbidity regimes and changes in channel morphology. The model represents individual fish at a daily time step, with population responses emerging from how individuals are affected by their habitat and by each other (especially, via competition for food). Key individual behaviors include habitat selection (movement to the best available foraging location), feeding and growth, mortality, and spawning. Fish growth depends on prey availability and hydraulic conditions. Mortality risks due to terrestrial predators, piscivorous fish, and extreme conditions are functions of habitat and fish variables. Field and analysis techniques for applying InSTREAM are based in part on extensive analysis of the model’s sensitivities and uncertainties. The model’s software provides graphical displays to observe fish behavior, detailed output files, and a tool to automate simulation experiments.