Spatial covariation of fish population vital rates in a stream network

A multi-state Cormack-Jolly-Seber (CJS) model was developed to infer state-specific annual survival, capture and transition probabilities for charr and salmon. States were defined based on age (juveniles and adults) and location (tributary, mainstem connected, and mainstem fragmented). Because locations were considered states, the state-transition probability referred to the movement probability among locations, which varied by age. To account for imperfect recapture of individuals, a state-space model was developed, composed of an ecological model following the state transitions over time and an observation model linking the true states to observed data. Data were formatted in a two-dimensional array (yi,t), where rows indicated individuals (i) and columns indicated annual sampling occasions (t). Elements of the array were observed states defined by age and location. A unique combination of ages (juvenile and adult) and locations (tributary, mainstem connected and mainstem fragmented) resulted in six states (1 = juveniles in tributary; 2 = juveniles in mainstem connected; 3 = juveniles in mainstem fragmented; 4 = adults in tributary; 5 = adults in mainstem connected; and 6 = adults in mainstem fragmented). In addition, sampling occasions on which individuals were not detected were coded as 7. Prior to fitting multi-state CJS models to data, we used the R2ucare package (Gimenez et al. 2018) to confirm that there was no evidence for trap-dependence (p > 0.27), transience (p = 1.00), and memory of past states (p > 0.35) in either charr or salmon.