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

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