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

REGIONAL CLIMATE AFFECTS SALMON LICE DYNAMICS, STAGE STRUCTURE, AND MANAGEMENT
by Amy Hurford, Xiunan Wang, and Xiao-Qiang Zhao

Contact: Amy Hurford, [e-mail]

Several 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.

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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