Model Creators:
- Dr. Curry J. Cunningham (University of Alaska Fairbanks, College of Fisheries and Ocean Sciences)
- Dr. Trevor Branch (University of Washington, School of Aquatic and Fishery Sciences)
This run reconstruction model is detailed in A general model for salmon run reconstruction that accounts for interception and and differences in availability to harvest Cunningham et al. (2018).
Original Project Collaborators: Curry J. Cunningham, Trevor A. Branch, Tyler H. Dann, Matt Smith, James E. Seeb, Lisa W. Seeb, Ray Hilborn, Lowell Fair, Tim Baker, Fred West.
A general run reconstruction model for the sockeye salmon fishery in Bristol Bay, Alaska. This model leverages information from age and genetic composition samples to apportion mixed-stock catches and account for interception among terminal fishing districts.
Each year is estimated independently although some information is shared among years.
- R code creates ADMB input files in the /Syrah directory, based on input data in the /R directory.
- Formal run reconstruction model estimation by AD-Model Builder (ADMB) in /Syrah directory.
- Parsing annual ADMB output (.out) files into user-friendly tables and figures in the Syrah/outputFiles directory.
| Name | Description |
|---|---|
| Syrah | Original version. |
| Syrah_v1 | Original model + small update to estimate RunSize in log space. |
| Syrah_v2 | Original model + small update to estimate RunSize in log space + updates from Hamazaki (ADFG) to likelihood formula (and perhaps other changes). |
** NOTE: *** all versions are designed to be backward compatible with input (.dat) and output (.out) files. All upstream data input creation R functions, and output processing and data visualization R functions will operate normally, independent of version.
| Directory | Description |
|---|---|
| R | ageComp.annual.csv |
| R | GeneticsComp_updated_Annual.csv |
| R | qry_Annual_ESCAPEMENT.csv |
| R | qry_Annual_CATCH_updated.csv |
| Syrah/outputFiles/Reallocation | catchAdd.csv |
| Syrah/outputFiles/Reallocation | ageCompAdd.csv |
| Syrah/outputFiles/Reallocation | inshoreTogiak.csv |
| Syrah/outputFiles/Reallocation | offshoreCatchAdd.csv |
| Syrah | Directory for running ADMB estimation model. |
| Syrah/outputFiles | Holds ADMB estimation model output (.out files) and code to generate output figures |