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.

Ecologists now recognize that the dynamics of populations, communities, and ecosystems are strongly affected by adaptive individual behaviors. Yet until now, we have lacked effective and flexible methods for modeling such dynamics. Traditional ecological models become impractical with the inclusion of behavior, and the optimization approaches of be