Modeling juvenile salmon migration using a simple Markov chain

We describe movement patterns of hatchery-raised, juvenile, spring chinook salmon, Oncorhynchus tshawytscha, using a two-state Markov chain model. The existence of two states, moving and holding, is suggested by anecdotal information from a large radio telemetry study; yet adequate observations of these small-scale fish behaviors are not available for estimating transition probabilities directly. Instead, we estimate the transition probability matrix from travel times within each of II river segments using a method of moments approach. Bootstrapped confidence intervals are presented. Results suggest that fish behavior in the region of the confluence between the Grande Ronde and Snake Rivers includes many transitions between moving and staying while fish behavior in the Snake River is more likely to include long periods of staying.