Regional climate affects salmon lice dynamics, stage structure, and management

REGIONAL CLIMATE AFFECTS SALMON LICE DYNAMICS, STAGE STRUCTURE, AND MANAGEMENT<br>by Amy Hurford, Xiunan Wang, and Xiao-Qiang Zhao<br><br>Contact: Amy Hurford, [e-mail]<br><br>Several of these codes have dependencies on the PBSddesolve package.<br><br>CODE TO MAKE FIGURES (have dependencies on *.Rdata files)<br>(1) Figure1_map.R: makes FIGURE 1: Map and temperature and salinity plots<br>(2) Figure2_R0Graphs.R makes FIGURE 2. This file calls Summary.Rdata, the output of R0Calcs.R. <br>(3) Figure2_R0Calcs.R: performs the calculations underlying FIGURE 2.<br>(4) Figure3_Dynamics: makes FIGURE 3.<br>(5) Figure4_GenerationTime.R: makes FIGURE 4.<br>(6) FigureS1_S2_ParamsFunc.R: makes FIGURES S1 &amp; S2: Figure S.1 shows fits of functions for lab data describing life history parameters as a function of temperature and salinity. The output ParamsFunc.Rdata is called by subsequent codes. Figure S.2 examines evidence for local adaptation.<br>(7) FigureS3_NumericalMethods.R: makes FIGURE S3.<br>(8) SalinityMortalityCaligus.R: runs analyses for Caligus rogercresseyi adult mortality data shown in Figure S1.<br><br>===============<br>DATA FILES<br>(9) Data_Extraction.csv: The raw data extracted from the sources as listed in Section S1 of Hurford et al.<br>Site abbreviations are described in detail in Section S1 of Hurford et al.<br>(10) CH.Rdata: Parameters and data for the site in Chile (CH). This file is called by other codes.<br>(11) IM3.Rdata: Parameters and data for the site a site off the coast of Ireland (IM3).<br>(12) IM4.Rdata: Parameters and data for the site a site off the coast of Ireland (IM4).<br>(13) farm24.Rdata: Parameters and data for the site in the Broughton Archipegalo (BCB).<br>(14) farmWCVI.Rdata: … for a site on the west coast of Vancouver Island (BCV).<br>(15) farmCC.Rdata: … for a site on the central coast of BC (BCC).<br>(16) farmNB.Rdata: … for a site in New Brunswick (NB).<br>(17) farmNS.Rdata: … for a site in Nova Scotia (NS).<br>(18) farmNL.Rdata: ... data is from Newfoundland (NL).<br>(19) farmNLI.Rdata: … for the Lista site in Norway (NLI).<br>(20) farmNIN.Rdata: … for the Ingoy site in Norway (NIN).<br>(21) ParamsFuncs.Rdata: Save parameterized functions (see Figure S1)<br>(22) Summary.Rdata: produced by Figure2_R0Calcs.R and loaded by Figure2_R0Graphs.R