Supplement 1. Matlab code to run the simulation/site-selection model and GAUSS code to estimate the stock–recruitment parameters, plus all input files.

File List SALMON.m Main MATLAB program—running this program with current parameter settings will reproduce all of the main results presented in the paper.<br> SALMON_BH_graphs.m MATLAB sub-program, called by SALMON.m<br> SALMON_concentrations.m MATLAB sub-program, called by SALMON.m<br> SALMON_ext_probs_fast.m MATLAB sub-program, called by SALMON.m<br> SALMON_forecast.m MATLAB sub-program, called by SALMON.m<br> SALMON_forecast_Ricker.m MATLAB sub-program, called by SALMON.m<br> SALMON_graph.m MATLAB sub-program, called by SALMON.m<br> SALMON_header.m MATLAB sub-program, called by SALMON.m<br> SALMON_pva_function.m MATLAB sub-program, called by SALMON.m<br> SALMON_pva_graph.m MATLAB sub-program, called by SALMON.m<br> SALMON_pva_graph_Ricker.m MATLAB sub-program, called by SALMON.m<br> SALMON_raw_graph.m MATLAB sub-program, called by SALMON.m<br> SALMON_save.m MATLAB sub-program, called by SALMON.m<br> SALMON_set_parameters.m MATLAB sub-program, called by SALMON.m<br> SALMON_wild_graph.m MATLAB sub-program, called by SALMON.m<br> Entiat_boot.txt Input file for MATLAB programs, called by SALMON_set_parameters.m<br> Methow_boot.txt Input file for MATLAB programs, called by SALMON_set_parameters.m<br> SalmonML.prg GAUSS code for estimating stock-recruitment parameters for each sub-stock<br> SalmonRawSpawners.txt Input file for MATLAB programs, called by SALMON_set_parameters.m<br> SalmonWildSpawners.txt Input file for MATLAB programs, called by SALMON_set_parameters.m<br> WatershedAttributesAndRanks.txt description<br> WatershedAttributes.txt Input file for MATLAB programs, called by SALMON_set_parameters.m<br> Wenatchee_boot.txt Input file for MATLAB programs, called by SALMON_set_parameters.m<br> SALMONsupplement.zip All supplemental files at once Description To reproduce the main results given in the paper, copy all files in the list above to the same folder. Then use Matlab to run SALMON.m, from that folder, which will call the other Matlab subroutines (.m files) and input files (.txt files) as needed. Most of the input parameters can be found in SALMON_set_parameters.m, so that file can be modified to conduct further sensitivity analyses. To re-estimate the stock-recruitment parameters, use GAUSS to run SalmonML.prg.