Delta STARS Model

Criterion	Explanation
General Description	STARS = Survival, Travel Time, and Routing Simulation The Delta STARS Model is an individual-based simulation model that predicts survival, travel time, and routing of juvenile salmon migrating through the Delta. The model's structure and parameters are based on a recent analysis (Perry et al. in press) that relates individual survival, travel time, and routing of late-fall Chinook Salmon to daily Sacramento River flows at Freeport and Delta Cross Channel operations.
Model Domain	Eight reaches in the Sacramento-San Joaquin Delta. Simulated fish enter the model at Freeport and exit at Chipps Island.
Developer	USGS, Western Fisheries Research Center, Quantitative Fisheries Ecology Section
Hardware computing requirements	None specified
Code language	R
Original application	The STARS model simulates travel time, routing, and survival of individuals in a daily cohort as they migrate through eight unique reaches of the Delta. A daily cohort is defined as all fish that enter the Delta on a given day at Freeport. Because travel time, routing, and survival depends on river flow when an individual enters a given reach, overall survival of a daily cohort depends on the entire time series of daily flows during their migration time through the Delta. For example, two cohorts may enter the Delta at the same discharge, but their overall survival will differ if one cohort enters during an ascending hydrograph and the other enters when it descending.
Public/proprietary and cost	Model is free to use through web interface (https://oceanview.pfeg.noaa.gov/shiny/FED/CalFishTrack/).
Physically or empirically based	Empirical
Mathematical methods used	The simulation model is based on a Bayesian multistate mark-recapture model with model parameters estimated as a function of time-varying individual covariates.
Input data requirements	Daily time series of discharge and Delta Cross Channel gate operations
Outputs	The Shiny App summarizes the output of each daily cohort for the current water year to display 1) overall survival and median travel time through the Delta between Freeport and Chipps Island, 2) route-specific survival and median travel time, and 3) the proportion of fish using each unique migration route. In addition to median travel time, users may also examine travel time distributions of daily cohorts or animate how travel time distributions change over time. Not currently possible to download outputs in tabular form through web interface; only provided as plots.
Pre-processing and post-processing tools	Web interface is provided as post-processing tool
Representation of uncertainty	Parameter set drawn from the joint posterior parameter distribution. Travel times drawn from a log-normal distribution where the mean of the distribution depends on the parameter set and discharge. Routing probabilities drawn from Bernoulli distributions as a function of discharge on the day each fish arrives at the junction.
Prevalence	One peer-reviewed publication. No known uses in management or policy.
Ease of use for public entities	The web interface makes interacting with the model very easy.
Ease of obtaining information and availability of technical support	No user group or commercial help desk
Source code availability	Source code is not publicly available
Status of model development	Beta version. They plan to continually evolve the Shiny App to improve the user's experience.
Challenges for integration	Model is in early stages of development. Source code is not available. Web interface does not provide outputs in tabular format.

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