├── .Rbuildignore ├── .gitignore ├── DESCRIPTION ├── NAMESPACE ├── NEWS ├── R ├── Bootstrap_function.R ├── CS_prep.R ├── Combine_Surfaces.R ├── Combine_Surfaces_scale.R ├── Diagnostic_Plots.R ├── GA_prep.R ├── Grid_Search.R ├── MLPE.R ├── MS_optim.R ├── MS_optim_scale.R ├── OptimFunction_Multi.R ├── OptimFunction_Multi_covariate.R ├── OptimFunction_Multi_scale.R ├── OptimFunction_Single.R ├── OptimFunction_Single_covariate.R ├── OptimFunction_Single_scale.R ├── Plot_trans.R ├── ResistanceGA.R ├── Resistance_transform.R ├── Run_CS.R ├── Run_gdistance.R ├── Run_julia.R ├── SHNe.R ├── SS_optim.R ├── SS_optim_scale.R ├── Transformation_functions.R ├── all_comb.R ├── gdistance.R ├── internal_helper_functions.R ├── julia_prep.R ├── k_smooth.R ├── lower_matrix.R ├── rga_mlpe.R ├── to_from.R ├── utils-pipe.R └── write_CS_file.R ├── README.md ├── ResistanceGA.Rproj ├── data ├── Dc_list.rda ├── jl_out.rda ├── raster_orig.rda ├── raster_true.rda ├── resist_list.rda ├── resistance_surfaces.rda ├── sample_pops.rda └── samples.rda ├── figure ├── Grid.Surface.png ├── Grid.Surface.svg ├── Grid_Search_example.png ├── RickerPlot.png ├── RickerPlot2.png ├── Transformations.png ├── Transformations.svg ├── Transformations_ORIG.svg ├── combine_surfaces.png ├── combined_plots.png ├── combined_plots1.png ├── combined_plots2.png ├── combined_plots3.png ├── correlation_plot.png ├── cs_resposne_multi.png ├── feature_sim.png ├── inverse-reverse_mono.png ├── monomolec_plot.png ├── multi_surface_sim1.png ├── multi_surface_sim2.png ├── plot_trans_demo1.png ├── plot_trans_demo2.png ├── single_surface_plot.png ├── trans_plots.png ├── unnamed-chunk-5.png └── unnamed-chunk-6.png ├── inst └── CITATION ├── man ├── CS.prep.Rd ├── Combine_Surfaces.Rd ├── Dc_list.Rd ├── Diagnostic.Plots.Rd ├── GA.prep.Rd ├── Grid.Search.Rd ├── MLPE.lmm.Rd ├── MS_optim.Rd ├── Plot.trans.Rd ├── Resist.boot.Rd ├── Resistance.tran.Rd ├── ResistanceGA-package.Rd ├── Run_CS.Rd ├── Run_CS.jl.Rd ├── Run_gdistance.Rd ├── SHNe.Rd ├── SS_optim.Rd ├── To.From.ID.Rd ├── all_comb.Rd ├── gdist.prep.Rd ├── jl.prep.Rd ├── jl_out.Rd ├── k.smooth.Rd ├── lower.Rd ├── mlpe_rga.Rd ├── pipe.Rd ├── raster_orig.Rd ├── raster_true.Rd ├── resist_list.Rd ├── resistance_surfaces.Rd ├── sample_pops.Rd └── samples.Rd └── vignettes ├── GettingStarted.R ├── GettingStarted.Rmd ├── GettingStarted.html ├── Julia_Guide.R ├── Julia_Guide.Rmd ├── Julia_Guide.html ├── ResistanceGA.R ├── ResistanceGA.Rmd ├── ResistanceGA.html ├── ResistanceGA.pdf ├── ResistanceGA_files └── figure-latex │ ├── Plot.trans.demo-1.pdf │ ├── Plot.trans.demo-2.pdf │ ├── feature.sim-1.pdf │ ├── feature.sim-2.pdf │ ├── feature.sim-3.pdf │ └── single.surface.plot-1.pdf ├── _SYNCAPP └── metadata.xml └── figure ├── CS_corr.png ├── FlowChart_Narrow2.png ├── FlowChart_Narrow2.tif ├── FlowChart_Narrow2b.png ├── Grid.Surface.png ├── Grid.Surface.svg ├── IR_Mono.png ├── Plot.trans.demo-1.png ├── Plot.trans.demo-2.png ├── Raindow_Surface.png ├── RickerPlot.png ├── RickerPlot2.png ├── Transformations.png ├── Transformations.svg ├── Transformations_ORIG.svg ├── combine.surfaces.png ├── combine_cs.png ├── combine_surfaces.png ├── combined.plots.png ├── combined_plots.png ├── combined_plots1.png ├── combined_plots2.png ├── correlation_plot.png ├── example_analysis.png ├── example_demo_pair.png ├── feature.sim-1.png ├── feature.sim-2.png ├── feature.sim-3.png ├── feature.sim.png ├── feature.sim1.png ├── feature.sim2.png ├── feature.sim3.png ├── feature_sim.png ├── grid1.png ├── grid2.png ├── grid_topo.png ├── monomolec.plot-1.png ├── monomolec.plot.png ├── monomolec_plot.png ├── multi_surface.sim1.png ├── multi_surface.sim2.png ├── multi_surface_sim1.png ├── multi_surface_sim2.png ├── noisy_genetic.png ├── plot.trans.demo1.png ├── plot.trans.demo2.png ├── plot_trans_demo1.png ├── plot_trans_demo2.png ├── plotcorrelation_plot.png ├── pre.smooth_plot.png ├── response_dist.png ├── reverse.ricker-1.png ├── reverse.ricker.png ├── reverse_ricker.png ├── 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