Code to run closed-loop simulations of Kukskokwim "like" system to evaluate the performance of alternative management procedures in the face of environmental stochasticity and uncertainty in drivers of recruitment:

Connors B.M., Staton B., Coggins L., Walters C., Jones M., Gwinn D., Catalano M. and S. Fleischman. In press. Incorporating harvest – population diversity trade-offs into harvest policy analyses of salmon management in large river basins. Canadian Journal of Fisheries and Aquatic Sciences.

Posterior samples required to condition the operating model in the closed loop simulations are available upon request from brendan.connors@dfo-mpo.gc.ca and are from analyses described in:

Staton B., M. Catalano, B.M. Connors, L. Coggins, M. Jones, C. Walters, S. Fleischman and D. Gwinn. In press. Evaluation of methods for quantifying population diversity in mixed-stock Pacific salmon fisheries. Canadian Journal of Fisheries and Aquatic Sciences.

Project made possible by grant 1503 from the Arctic-Yukon-Kuskokwim Sustainable Salmon Initiative

Files

• make.R: All code required to reproduce current set of simulations and figures.

• load.R: Loads packages and scripts necessary for analysis. This file should be sourced prior to running other scripts.

• functions.R: All functions written for the analysis should be placed in this file.

• close_loop_sims.R: Run closed loop forwad simulations.

• figures.R: Generate figures not associated with simulations (e.g., equilibrium trade-offs, populaiton diversity; in figures folder)

• simulation_summary.Rmd: R Markdown doc that summarizes simulations, and generates figures for manuscript (in images folder)

• appendix_A.R: R Markdown doc that details the stationary Ricker to time-varying Beverton-Holt formulation we used, and simulations to justify its parameterization in our closed-loop simulations.