├── .Rbuildignore ├── .Rhistory ├── .gitattributes ├── .gitignore ├── ClinePlotR.Rproj ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── .Rhistory ├── alphaBetaPlot.R ├── combine_bgc_output.R ├── genind2bgc.R ├── genind2introgress.R ├── genomicClinesXenvironment.R ├── get_bgc_outliers.R ├── get_important_rasters.R ├── join_bgc_gff.R ├── parseGFF.R ├── phiPlot.R ├── plot_outlier_ideogram.R └── plot_traces.R ├── README.md ├── data └── README ├── docker ├── .env ├── Dockerfile ├── build_docker.sh ├── docker-compose.yml └── entrypoint.sh ├── environment.yml ├── img ├── alphaBetaContourPlot.png ├── alphaTrace.png ├── bad_LnL_convergence.png ├── code_for_flow_diagram_config_mermaid8.7.0.txt ├── code_for_flow_diagram_mermaid8.7.0.txt ├── docker_install_image.png ├── eatt_full_bgc_LnL_convergence.png ├── eatt_genes_hiXphi_alphaAndBeta.png ├── flowchart_ClinePlotR.png ├── genomicClineXlongitude.png ├── genomicClineXraster_bioclim1.png ├── hybridIndexXLongitude.png ├── hybridIndexXraster_bioClim1.png ├── ideogram_EATT.png ├── jupyter_notebook_screenshot.png ├── jupyter_notebook_screenshot_choosekernel.png └── permutationImportance_plot.png ├── man ├── alphaBetaPlot.Rd ├── clinesXenvironment.Rd ├── combine_bgc_output.Rd ├── extractPointValues.Rd ├── genind2bgc.Rd ├── genind2introgress.Rd ├── get_bgc_outliers.Rd ├── join_bgc_gff.Rd ├── parseGFF.Rd ├── partition_raster_bg.Rd ├── phiPlot.Rd ├── plot_outlier_ideogram.Rd ├── plot_traces.Rd ├── prepare_rasters.Rd ├── runENMeval.Rd ├── runIntrogress.Rd ├── subsetIndividuals.Rd └── summarize_ENMeval.Rd ├── scripts ├── .Rhistory ├── bgc_settings.txt ├── introgressPipeline.R ├── prepareDifferentRasters.R ├── run_bgc.sh ├── run_bgcPlotter.R ├── run_docker.sh ├── run_enmevalPipeline.R └── vcf2bgc.py └── tutorials ├── .ipynb_checkpoints ├── ClineHelpR_Tutorial-checkpoint.ipynb ├── ClineHelpR_tutorial_bgc-checkpoint.ipynb └── ClineHelpR_tutorial_introgress-checkpoint.ipynb ├── ClineHelpR_tutorial_bgc.ipynb ├── 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