Modeling the Survival of Chinook Salmon Smolts Outmigrating Through the Lower Sacramento River System
Journal of the American Statistical Association
A quasi-likelihood model with a ridge parameter was developed to understand the factors possibly associated with the survival of juvenile chinook salmon smolts outmigrating through the lower portions of the Sacramento river system. Coded-wire-tagged (CWT) chinook salmon smolts were released at various locations within the river between the years 1979 and 1995. Recoveries of these juvenile salmon in a lower river trawl fishery and later recoveries of adults from samples of ocean catches provided
... the basic data. Due to the number of interested parties with differing a priori opinions as to which factors most affected survival, a large number of covariates were required relative to the number of cases. To stabilize the parameter estimates and to improve predictive ability, a ridge parameter was included. Given the complexity of the processes generating recoveries, including possible dependencies between fish, and the additional sources of variation experienced by ocean recoveries relative to river recoveries, separate dispersion parameters were applied to the river and ocean recoveries. Interpretation of estimated coefficients was delicate given correlation between some of the covariates, the biases introduced by the ridge parameter, and possible confounding factors. With these caveats in mind, we found the most influential covariates to be the water temperature covariates and a measure of regional pesticide application, with increasing temperatures and increasing pesticide levels having a negative association with recoveries. Two covariates were of particular interest to the biologists and water managers: the position of a water diversion gate (open or closed) separating the mainstem from the central delta and the relative fraction of water exported for irrigation and urban consumption. Of these two, only gate position suggested a strong effect. When the gate was open, fish released upstream of the gate suffered increased mortality but survival increased for fish released in the central delta region (on the other side of the gate). Over the range of export levels observed, there was no strong evidence for either adverse or beneficial effects of increasing water exports.