Supplement 1. Details of the analysis of pink salmon population data, including spawner and catch data and R code for compiling spawner-recruit pairs and fitting the Ricker model.

<h2>File List</h2><div> <p> <a href="nuSEDS_PINK.csv">nuSEDS_PINK.csv</a> (md5: 817593c4467c074239177e92379db2bd)<br> <a href="Catch_PINK.csv">Catch_PINK.csv</a> (md5: a9442b3ebafbf77d5437e36b6b0faad3)<br> <a href="1_DataCompilation.R">1_DataCompilation.R</a> (md5: 1eb5bac1081e5ac2f307b00e4a75c8ef)<br> <a href="2_PopulationAnalysis.R">2_PopulationAnalysis.R</a> (md5: 017c4ea62556877b4b028bb2b4dc947d) </p> </div><h2>Description</h2><div> <p>The following files are made available with the intention of ensuring our manipulation of data and analysis of pink salmon populations is entirely transparent. We assume that the reader is familiar with the program R, which can be downloaded from the web at <a href="http://cran.r-project.org">cran.r-project.org</a>. Any errors in transcribing and manipulating the data are the sole responsibility of the authors. Additional data and code for the analysis of farm treatments and lice on wild salmon are available upon email request to Stephanie Peacock [<a href="mailto:stephanie.peacock@ualberta.ca">stephanie.peacock@ualberta.ca</a>].</p> <p>nuSEDS_PINK.csv contains spawner data for pink salmon populations in British Columbia, Canada from 1950–2010, provided by Fisheries and Oceans Canada (contact: Bruce Baxter [<a href="mailto:bruce.baxter@dfo-mpo.gc.ca">bruce.baxter@dfo-mpo.gc.ca</a>]). These data include the following columns:</p> <p>Area: Fisheries management area, the spatial scale at which catch data are reported.<br> River: The river at which spawners were enumerated, the finest scale at which spawner data are available.<br> Yr: The year spawners were enumerated.<br> Escapement: The estimated number of spawners in that river in that year, from the nuSEDS database.</p> <p>Catch_PINK.csv contains catch data for pink salmon by management area, provided by different area managers at Fisheries and Oceans Canada (contacts: Pieter VanWill [<a href="mailto:pieter.vanwill@dfo-mpo.gc.ca">pieter.vanwill@dfo-mpo.gc.ca</a>] and David Peacock [<a href="mailto:david.peacock@dfo-mpo.gc.ca>">david.peacock@dfo-mpo.gc.ca</a>]). These data include the following columns:</p> <p>Area: Fisheries management area, the spatial scale at which catch data are reported.<br> Odd_Even: Integer indicated whether the catch was of an odd-year population (= 1) or even year (= 2).<br> Year: The year of the catch.<br> Catch: The number of pieces of pink salmon caught in all fisheries for the given year and area.</p> <p>1_DataCompilation.R is R code that calls the previous two data files and calculates the number of recruits per spawner.</p> <p>2_PopulationAnalysis.R is R code that fits the linearized Ricker model to the spawner recruit data, and tests for an effect of sea lice on wild salmon. </p> </div>