An age- and time-specific space-for-time mark-recapture model

Space-for-time Cormack-Jolly-Seber (CJS) models have been developed to estimate survival of migrating animals that are imperfectly detected at spatially discrete sampling stations. However, space-for-time CJS models typically ignore survival over time and age-specific probability of movement, missing the diversity of life history strategies. To address these limitations, we extended space-for-time Cormack-Jolly-Seber models to explicitly incorporate time, age, and individual-level covariates to account for diverse life history strategies. We incorporate a sub-model that includes uncertainty in individuals age using a finite-mixture model. The detection and transition probabilities were parameterized using generalized linear models, facilitating flexible model specification and inclusion of spatiotemporal and individual covariates. We apply the model to detections of juvenile steelhead (Oncorhynchus mykiss) from two populations in the Snake River Basin in Idaho, USA, to estimate trends in survival with respect to population, age, time, and the length of individuals. Additionally, we generalized the model so that it can be applied to other systems and populations with different life history strategies and monitoring infrastructure.