{
  "_id": "6af5f1f3f58eaab79920c368",
  "Package": "ResistanceGA2",
  "Title": "Optimize Resistance Surfaces Using Genetic Algorithms",
  "Version": "1.2.0",
  "Authors@R": "person(given = \"Bill\", family = \"Peterman\", role = c(\"aut\", \"cre\"), email = \"peterman.73@osu.edu\")",
  "Description": "Optimizes resistance surfaces using genetic algorithms.\nContinuous and categorical surfaces can be optimized\nindividually or jointly to create composite resistance\nsurfaces. Resistance distances can be calculated using\n'Circuitscape' through 'Julia' or with the 'gdistance' package.\nThe framework extends Peterman (2018)\n<doi:10.1111/2041-210X.12984>.",
  "URL": "https://github.com/wpeterman/ResistanceGA2",
  "BugReports": "https://github.com/wpeterman/ResistanceGA2/issues",
  "VignetteBuilder": "knitr",
  "License": "GPL (>= 3)",
  "LazyData": "true",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "Config/roxygen2/version": "8.0.0",
  "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev make libuv1-dev libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev zlib1g-dev",
  "Repository": "https://wpeterman.r-universe.dev",
  "Date/Publication": "2026-09-10 02:51:55 UTC",
  "RemoteUrl": "https://github.com/wpeterman/ResistanceGA2",
  "RemoteRef": "HEAD",
  "RemoteSha": "65a1a428ef13b95fdf50ba691e0433e368af9253",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-11-12 16:47:07 UTC",
    "User": "root"
  },
  "Author": "Bill Peterman [aut, cre]",
  "Maintainer": "Bill Peterman <peterman.73@osu.edu>",
  "_user": "wpeterman",
  "_type": "src",
  "_file": "ResistanceGA2_1.2.0.tar.gz",
  "_fileid": "https://r2.ropensci.org/b4e16d60a828c718f589e0f471e81b8e0d81d4d84e871ae4b7db406b167aff7e",
  "_filesize": 7047715,
  "_sha256": "b4e16d60a828c718f589e0f471e81b8e0d81d4d84e871ae4b7db406b167aff7e",
  "_expires": "2027-02-20T17:05:52.000Z",
  "_created": "2026-11-12T16:47:07.000Z",
  "_published": "2026-11-12T17:05:55.170Z",
  "_upstream": "https://github.com/wpeterman/ResistanceGA2",
  "_status": "success",
  "_maintainer": {
    "name": "Bill Peterman",
    "email": "peterman.73@osu.edu",
    "login": "wpeterman",
    "description": "",
    "uuid": 4634705
  },
  "_jobs": [
    {
      "job": 131337519583,
      "time": 478,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13965460947"
    },
    {
      "job": 131337519569,
      "time": 400,
      "config": "linux-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13965206031"
    },
    {
      "job": 131337519483,
      "time": 285,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13964832372"
    },
    {
      "job": 131337519550,
      "time": 356,
      "config": "macos-release-arm64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13964268322"
    },
    {
      "job": 131334328489,
      "time": 300,
      "config": "source",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13965065574"
    },
    {
      "job": 131337519892,
      "time": 166,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "13963839362"
    },
    {
      "job": 131337519808,
      "time": 1054,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "13964609878"
    },
    {
      "job": 131337519963,
      "time": 1027,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "13966655081"
    },
    {
      "job": 131337519741,
      "time": 975,
      "config": "windows-release-x86_64",
      "r": "4.6.2",
      "check": "OK",
      "artifact": "13965417303"
    }
  ],
  "_buildurl": "https://github.com/r-universe/wpeterman/actions/runs/43261617841",
  "_commit": {
    "id": "65a1a428ef13b95fdf50ba691e0433e368af9253",
    "author": "Bill Peterman <peterman.73@osu.edu>",
    "committer": "Bill Peterman <peterman.73@osu.edu>",
    "message": "Release ResistanceGA2 1.2.0\n",
    "time": 1789008715
  },
  "_distro": "resolute",
  "_host": "GitHub-Actions",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1",
      "role": "Depends"
    },
    {
      "package": "terra",
      "version": ">= 1.7-0",
      "role": "Depends"
    },
    {
      "package": "ggExtra",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "plyr",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "gdistance",
      "version": ">= 1.6",
      "role": "Imports"
    },
    {
      "package": "raster",
      "role": "Imports"
    },
    {
      "package": "reformulas",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "GA",
      "version": ">= 3.2.1",
      "role": "Imports"
    },
    {
      "package": "lme4",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "MuMIn",
      "role": "Imports"
    },
    {
      "package": "spdep",
      "role": "Imports"
    },
    {
      "package": "JuliaConnectoR",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Suggests"
    },
    {
      "package": "igraph",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "pkgload",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "wpeterman",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2026-14",
      "n": 13
    },
    {
      "week": "2026-15",
      "n": 3
    },
    {
      "week": "2026-18",
      "n": 1
    },
    {
      "week": "2026-22",
      "n": 3
    },
    {
      "week": "2026-24",
      "n": 3
    },
    {
      "week": "2026-37",
      "n": 1
    }
  ],
  "_tags": [],
  "_stars": 5,
  "_contributors": [
    {
      "user": "wpeterman",
      "count": 48,
      "uuid": 4634705
    }
  ],
  "_userbio": {
    "uuid": 4634705,
    "type": "user",
    "name": "Bill Peterman",
    "followers": 22
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/ResistanceGA2"
  },
  "_devurl": "https://github.com/wpeterman/resistancega2",
  "_searchresults": 11,
  "_rbuild": "4.6.2",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/ResistanceGA2.html"
  ],
  "_cranurl": false,
  "_exports": [
    "%>%",
    "all_comb",
    "Combine_Surfaces",
    "Diagnostic.Plots",
    "GA.prep",
    "gdist.prep",
    "graph_to_keep",
    "jl.prep",
    "lower",
    "mlpe",
    "mlpe_data",
    "mlpe_rga",
    "MLPE.lmm",
    "MS_optim",
    "Plot.trans",
    "recommend_commute_settings",
    "Resist.boot",
    "Resistance.tran",
    "Run_CS.ini",
    "Run_CS.jl",
    "Run_gdistance",
    "SHNe",
    "site_pairwise_diff",
    "site_pairwise_dist",
    "SS_optim",
    "To.From.ID"
  ],
  "_datasets": [
    {
      "name": "Dc_list",
      "title": "Data file. A list of three matrices",
      "object": "Dc_list",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "jl_out",
      "title": "Data file. Example raster output from CIRCUITSCAPE Julia",
      "object": "jl_out",
      "class": [
        "PackedSpatRaster"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "raster_orig",
      "title": "Data file. Simulated original resistance surfaces",
      "object": "raster_orig",
      "class": [
        "PackedSpatRaster"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "raster_true",
      "title": "Data file. Simulated true resistance surfaces",
      "object": "raster_true",
      "class": [
        "PackedSpatRaster"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "resist_list",
      "title": "Data file. A list of three matrices",
      "object": "resist_list",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "resistance_surfaces",
      "title": "Data file. Simulated resistance surfaces",
      "object": "resistance_surfaces",
      "class": [
        "PackedSpatRaster"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "rga2_demo",
      "title": "Data file. Idaho demo data for joint IBR/IBE examples",
      "object": "rga2_demo",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rga2_demo_covariates",
      "title": "Data file. Idaho demo raster covariates",
      "object": "rga2_demo_covariates",
      "class": [
        "PackedSpatRaster"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "rga2_demo_genetic",
      "title": "Data file. Idaho demo genetic distance matrix",
      "object": "rga2_demo_genetic",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Airplane",
        "Bachelor",
        "BarkingFox",
        "Bob",
        "Cache",
        "Egg",
        "Frog",
        "GentianL",
        "ParagonL",
        "Pothole",
        "ShipIsland",
        "Skyhigh"
      ],
      "rows": 12,
      "table": true,
      "tojson": true
    },
    {
      "name": "sample_pops",
      "title": "Data file. A list of three coordinate matrices",
      "object": "sample_pops",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "samples",
      "title": "Data file. Example sample location file",
      "object": "samples",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "pop",
        "x",
        "y"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "vignette_current_map",
      "title": "Data file. Precomputed Circuitscape current map used in vignette examples",
      "object": "vignette_current_map",
      "class": [
        "PackedSpatRaster"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "vignette_pairwise_outputs",
      "title": "Data file. Precomputed pairwise outputs used in vignette examples",
      "object": "vignette_pairwise_outputs",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "all_comb",
      "title": "Analyze all combinations",
      "topics": [
        "all_comb"
      ]
    },
    {
      "page": "Combine_Surfaces",
      "title": "Combine multiple resistance surfaces into a composite surface",
      "topics": [
        "Combine_Surfaces"
      ]
    },
    {
      "page": "Dc_list",
      "title": "Data file. A list of three matrices",
      "topics": [
        "Dc_list"
      ]
    },
    {
      "page": "Diagnostic.Plots",
      "title": "Diagnose an MLPE resistance-distance model",
      "topics": [
        "Diagnostic.Plots"
      ]
    },
    {
      "page": "GA.prep",
      "title": "Prepare resistance surfaces and genetic-algorithm settings",
      "topics": [
        "GA.prep"
      ]
    },
    {
      "page": "gdist.prep",
      "title": "Prepare data for optimization using 'gdistance'",
      "topics": [
        "gdist.prep"
      ]
    },
    {
      "page": "graph_to_keep",
      "title": "Convert graph topology to a pair-selection keep vector",
      "topics": [
        "graph_to_keep"
      ]
    },
    {
      "page": "jl_out",
      "title": "Data file. Example raster output from CIRCUITSCAPE Julia",
      "topics": [
        "jl_out"
      ]
    },
    {
      "page": "jl.prep",
      "title": "Prepare inputs for running Circuitscape via Julia",
      "topics": [
        "jl.prep"
      ]
    },
    {
      "page": "lower",
      "title": "Extract the lower triangle of a square matrix",
      "topics": [
        "lower"
      ]
    },
    {
      "page": "mlpe",
      "title": "Fit MLPE Models With an lme4-Style Formula",
      "topics": [
        "mlpe"
      ]
    },
    {
      "page": "mlpe_data",
      "title": "Build Long-Form Data for MLPE Models",
      "topics": [
        "mlpe_data"
      ]
    },
    {
      "page": "mlpe_rga",
      "title": "Legacy MLPE wrapper with an explicit ZZ-matrix interface",
      "topics": [
        "mlpe_rga"
      ]
    },
    {
      "page": "MLPE.lmm",
      "title": "Legacy convenience wrapper for a single MLPE resistance predictor",
      "topics": [
        "MLPE.lmm"
      ]
    },
    {
      "page": "MS_optim",
      "title": "Simultaneous optimization of multiple resistance surfaces",
      "topics": [
        "MS_optim"
      ]
    },
    {
      "page": "Plot.trans",
      "title": "Plot continuous surface transformation",
      "topics": [
        "Plot.trans"
      ]
    },
    {
      "page": "raster_orig",
      "title": "Data file. Simulated original resistance surfaces",
      "topics": [
        "raster_orig"
      ]
    },
    {
      "page": "raster_true",
      "title": "Data file. Simulated true resistance surfaces",
      "topics": [
        "raster_true"
      ]
    },
    {
      "page": "recommend_commute_settings",
      "title": "Recommend Commute-Distance Settings",
      "topics": [
        "recommend_commute_settings"
      ]
    },
    {
      "page": "resist_list",
      "title": "Data file. A list of three matrices",
      "topics": [
        "resist_list"
      ]
    },
    {
      "page": "Resist.boot",
      "title": "Assess optimized resistance surfaces by population subsampling",
      "topics": [
        "Resist.boot"
      ]
    },
    {
      "page": "resistance_surfaces",
      "title": "Data file. Simulated resistance surfaces",
      "topics": [
        "resistance_surfaces"
      ]
    },
    {
      "page": "Resistance.tran",
      "title": "Apply a transformation to a continuous resistance surface",
      "topics": [
        "Resistance.tran"
      ]
    },
    {
      "page": "ResistanceGA2-result-methods",
      "title": "S3 methods for ResistanceGA2 result objects",
      "topics": [
        "plot.resga_all_comb",
        "plot.resga_bootstrap",
        "plot.resga_ms_optim",
        "plot.resga_ss_optim",
        "print.resga_all_comb",
        "print.resga_bootstrap",
        "print.resga_ms_optim",
        "print.resga_ss_optim",
        "print.summary.resga_all_comb",
        "print.summary.resga_bootstrap",
        "print.summary.resga_ms_optim",
        "print.summary.resga_ss_optim",
        "ResistanceGA2-result-methods",
        "summary.resga_all_comb",
        "summary.resga_bootstrap",
        "summary.resga_ms_optim",
        "summary.resga_ss_optim"
      ]
    },
    {
      "page": "rga2_demo",
      "title": "Data file. Idaho demo data for joint IBR/IBE examples",
      "topics": [
        "rga2_demo"
      ]
    },
    {
      "page": "rga2_demo_covariates",
      "title": "Data file. Idaho demo raster covariates",
      "topics": [
        "rga2_demo_covariates"
      ]
    },
    {
      "page": "rga2_demo_genetic",
      "title": "Data file. Idaho demo genetic distance matrix",
      "topics": [
        "rga2_demo_genetic"
      ]
    },
    {
      "page": "Run_CS.ini",
      "title": "Run Circuitscape via Julia with direct INI-style options",
      "topics": [
        "Run_CS.ini"
      ]
    },
    {
      "page": "Run_CS.jl",
      "title": "Run Circuitscape via Julia",
      "topics": [
        "Run_CS.jl"
      ]
    },
    {
      "page": "Run_gdistance",
      "title": "Run gdistance cost/commute distance calculation",
      "topics": [
        "Run_gdistance"
      ]
    },
    {
      "page": "sample_pops",
      "title": "Data file. A list of three coordinate matrices",
      "topics": [
        "sample_pops"
      ]
    },
    {
      "page": "samples",
      "title": "Data file. Example sample location file",
      "topics": [
        "samples"
      ]
    },
    {
      "page": "SHNe",
      "title": "Calculate pairwise spatial heterogeneity in effective population size",
      "topics": [
        "SHNe"
      ]
    },
    {
      "page": "site_pairwise_diff",
      "title": "Build Pairwise Environmental-Difference Covariates",
      "topics": [
        "site_pairwise_diff"
      ]
    },
    {
      "page": "site_pairwise_dist",
      "title": "Build Pairwise Environmental-Distance Covariates",
      "topics": [
        "site_pairwise_dist"
      ]
    },
    {
      "page": "SS_optim",
      "title": "Single surface optimization",
      "topics": [
        "SS_optim"
      ]
    },
    {
      "page": "vignette_current_map",
      "title": "Data file. Precomputed Circuitscape current map used in vignette examples",
      "topics": [
        "vignette_current_map"
      ]
    },
    {
      "page": "vignette_pairwise_outputs",
      "title": "Data file. Precomputed pairwise outputs used in vignette examples",
      "topics": [
        "vignette_pairwise_outputs"
      ]
    }
  ],
  "_pkglogo": "https://github.com/wpeterman/ResistanceGA2/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/wpeterman/ResistanceGA2/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "boot",
    "bslib",
    "cachem",
    "class",
    "classInt",
    "cli",
    "codetools",
    "colourpicker",
    "commonmark",
    "cpp11",
    "crayon",
    "DBI",
    "deldir",
    "digest",
    "dplyr",
    "e1071",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "foreach",
    "fs",
    "GA",
    "gdistance",
    "generics",
    "ggExtra",
    "ggplot2",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "httpuv",
    "igraph",
    "insight",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "JuliaConnectoR",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lifecycle",
    "lme4",
    "magrittr",
    "MASS",
    "Matrix",
    "memoise",
    "mime",
    "miniUI",
    "minqa",
    "MuMIn",
    "nlme",
    "nloptr",
    "otel",
    "pillar",
    "pkgconfig",
    "plyr",
    "promises",
    "proxy",
    "R6",
    "rappdirs",
    "raster",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "reformulas",
    "rlang",
    "rmarkdown",
    "s2",
    "S7",
    "sass",
    "scales",
    "sf",
    "shiny",
    "shinyjs",
    "sourcetools",
    "sp",
    "spData",
    "spdep",
    "terra",
    "tibble",
    "tidyselect",
    "tinytex",
    "units",
    "utf8",
    "vctrs",
    "viridisLite",
    "withr",
    "wk",
    "xfun",
    "xtable",
    "yaml"
  ],
  "_vignettes": [
    {
      "source": "Circuitscape_INI.Rmd",
      "filename": "Circuitscape_INI.html",
      "title": "Direct Circuitscape Runs from R",
      "author": "Bill Peterman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Julia Setup",
        "Example Inputs",
        "Pairwise Circuitscape with INI-Style Options",
        "Working from R Objects Instead of Manual Files",
        "Advanced mode with source and ground rasters",
        "Included pairs from an R table",
        "Reclassification tables from R",
        "Existing Paths Still Work",
        "Inspecting the Generated INI",
        "Return Modes",
        "Relationship to the Optimization Workflow",
        "Quick reference: direct Circuitscape control",
        "Summary of key functions",
        "See also"
      ],
      "created": "2026-04-03 11:19:16",
      "modified": "2026-09-10 02:51:55",
      "commits": 4
    },
    {
      "source": "GettingStarted.Rmd",
      "filename": "GettingStarted.html",
      "title": "Getting Started with ResistanceGA2",
      "author": "Bill Peterman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Key Changes from ResistanceGA",
        "Spatial classes: terra only",
        "Removed features",
        "New features in ResistanceGA2",
        "What Is ResistanceGA2?",
        "Isolation by Distance, Resistance, and Environment",
        "The Conceptual Workflow",
        "Installation",
        "Package Data Overview",
        "Resistance Surfaces",
        "Sample Locations",
        "The raster_orig Dataset",
        "Precomputed Pairwise Outputs",
        "The Four-Step Workflow",
        "Step 1: Prepare Genetic Algorithm Settings with GA.prep()",
        "Step 2: Prepare Distance Engine Inputs",
        "Using gdistance",
        "Using Julia / Circuitscape",
        "Step 3: Run Optimization",
        "Multisurface optimization",
        "All-combinations analysis",
        "Step 4: Interpret and Compare Results",
        "Transformations and Inspection",
        "Visualizing Transformations",
        "Quick reference: first complete workflow",
        "Summary of key functions",
        "Key Terms Glossary",
        "See also",
        "Tips for New Users",
        "References"
      ],
      "created": "2026-03-30 12:12:57",
      "modified": "2026-09-10 02:51:55",
      "commits": 9
    },
    {
      "source": "IBE_IBR_Framework.Rmd",
      "filename": "IBE_IBR_Framework.html",
      "title": "Joint Isolation by Environment and Isolation by Resistance",
      "author": "Bill Peterman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Design Choices",
        "Demo Data",
        "Step 1: Build Pairwise Geographic and Environmental Covariates",
        "Step 1a: Check Predictor Overlap Before Fitting Models",
        "Step 2: Fit Baseline MLPE Models Before Optimization",
        "Optional: Multiple Dyadic Random Effects",
        "Step 3: Prepare the Conditional IBR Workflow",
        "Step 4: Run Single-Surface IBR Models Conditional on IBE",
        "Step 5: Run a Multi-Surface IBR Model Conditional on IBE",
        "Step 6: Generate Full Analysis Outputs Outside the Vignette",
        "Step 7: Load and Explore Saved Outputs",
        "Interpretation",
        "Quick reference: conditional IBE and IBR workflow",
        "Summary of key functions",
        "See also"
      ],
      "created": "2026-04-04 17:56:04",
      "modified": "2026-09-10 02:51:55",
      "commits": 2
    },
    {
      "source": "Surface_Transformations.Rmd",
      "filename": "Surface_Transformations.html",
      "title": "Resistance Surface Transformations",
      "author": "Bill Peterman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Why Transform Resistance Surfaces?",
        "The Transformation Parameter Space",
        "Shape",
        "Max",
        "The Eight Transformation Families",
        "Monomolecular Families",
        "Monomolecular",
        "Reverse Monomolecular",
        "Inverse Monomolecular",
        "Inverse-Reverse Monomolecular",
        "Ricker Families",
        "Ricker",
        "Reverse Ricker",
        "Inverse Ricker",
        "Inverse-Reverse Ricker",
        "Comparing All Eight Families",
        "The Flat Distance Transformation",
        "Choosing Transformation Families",
        "Practical Guidance",
        "The select.trans Argument",
        "Applying Transformations Directly",
        "Resistance.tran()",
        "Plot.trans()",
        "How the GA Searches Transformation Space",
        "Collapsing to the Distance Solution",
        "Overfitting Concerns",
        "Summary of Transformation Families",
        "Quick reference: choosing and applying transformations",
        "Summary of key functions",
        "See also",
        "References"
      ],
      "created": "2026-04-03 15:54:06",
      "modified": "2026-09-10 02:51:55",
      "commits": 6
    },
    {
      "source": "ResistanceGA.Rmd",
      "filename": "ResistanceGA.html",
      "title": "ResistanceGA2: Full Optimization Workflow",
      "author": "Bill Peterman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Background",
        "Resistance Modeling in Landscape Genetics",
        "The Genetic Algorithm Approach",
        "The MLPE Framework",
        "Thoughts on Optimization",
        "Choosing an Objective Function",
        "Counting Parameters: k.value",
        "Transformation Families",
        "Example Data and Preparation",
        "The Dataset",
        "Preparing GA Settings",
        "Preparing gdistance Inputs",
        "Single-Surface Optimization",
        "Running SS_optim",
        "Multi-Surface Optimization",
        "Loading and Displaying Results",
        "Recovered Transformation Parameters",
        "Interpreting SS_optim Output",
        "Running MS_optim",
        "Loading Multi-Surface Results",
        "Percent Contribution",
        "Reconstructing the Composite Surface",
        "All-Combinations Analysis",
        "When to Use all_comb",
        "Setting Up all_comb",
        "Loading all_comb Results",
        "Bootstrap Analysis",
        "Why Bootstrap?",
        "Running Resist.boot",
        "Loading Bootstrap Results",
        "Interpreting Bootstrap Results",
        "Comparing Single-Surface, Multi-Surface, and Null Models",
        "Diagnostic Plots",
        "Quick reference: full optimization workflow",
        "Summary of key functions",
        "See also",
        "Tips for Running Full Analyses",
        "References"
      ],
      "created": "2026-03-30 17:56:26",
      "modified": "2026-09-10 02:51:55",
      "commits": 9
    },
    {
      "source": "Julia_Guide.Rmd",
      "filename": "Julia_Guide.html",
      "title": "Using Julia and Circuitscape with ResistanceGA2",
      "author": "Bill Peterman",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Overview",
        "Step 1: Install Julia",
        "Downloading Julia",
        "Verifying the Julia Installation",
        "Step 2: Install Circuitscape.jl",
        "Installing JuliaConnectoR",
        "Step 3: Configure R to Find Julia",
        "How ResistanceGA2 Manages Julia Paths",
        "Finding Julia's Path Automatically",
        "Step 4: Verify the Connection",
        "Step 5: Prepare a Small Julia Example",
        "Set Up Sample Data",
        "Create Julia Inputs with jl.prep()",
        "jl.prep() Parameter Details",
        "Computing Pairwise Resistance Distances",
        "Run_CS.jl() for Pairwise Distances",
        "Run_CS.jl() Parameter Details",
        "Direct Circuitscape runs with .ini-style control",
        "Current maps",
        "Computing Current Maps",
        "Julia in Optimization Workflows",
        "Tuning and Troubleshooting",
        "Comparing gdistance and Julia Outputs",
        "Conceptual Similarity",
        "Comparing Outputs",
        "Performance Considerations",
        "Landscape Size",
        "Number of Populations",
        "Environment Management for Julia Packages",
        "Checking Your Julia Environment",
        "Multiple Julia Versions",
        "Updating Circuitscape.jl",
        "Troubleshooting",
        "Julia Not Found",
        "Circuitscape Not Found",
        "Slow Startup",
        "Out of Memory",
        "File Permission Errors on Windows",
        "Connection Drops Mid-Optimization",
        "Summary",
        "Quick reference: the Julia workflow in one block",
        "Summary of key functions",
        "See also",
        "References"
      ],
      "created": "2026-03-30 12:12:57",
      "modified": "2026-09-10 02:51:55",
      "commits": 11
    }
  ],
  "_score": 4.99563519459755,
  "_indexed": true,
  "_nocasepkg": "resistancega2",
  "_universes": [
    "wpeterman"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.2.0",
      "date": "2026-11-12T16:50:08.000Z",
      "distro": "resolute",
      "commit": "65a1a428ef13b95fdf50ba691e0433e368af9253",
      "fileid": "https://r2.ropensci.org/1c1d639489c989f70c541d6aba5c9adfc152b047a074c6226b6f81fa454d7629",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wpeterman/actions/runs/43261617841"
    },
    {
      "r": "4.6.2",
      "os": "linux",
      "version": "1.2.0",
      "date": "2026-11-12T16:50:30.000Z",
      "distro": "resolute",
      "commit": "65a1a428ef13b95fdf50ba691e0433e368af9253",
      "fileid": "https://r2.ropensci.org/2620e1b79f7a702d7e8479a2b7670d0840451045e401a86eb8ef0da37b40ccb4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wpeterman/actions/runs/43261617841"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.2.0",
      "date": "2026-11-12T16:52:08.000Z",
      "commit": "65a1a428ef13b95fdf50ba691e0433e368af9253",
      "fileid": "https://r2.ropensci.org/0d6153eceea23ae545439d59ee24a5fce9580f618ad65ac6e5b3e838aaaa486b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wpeterman/actions/runs/43261617841"
    },
    {
      "r": "4.6.2",
      "os": "mac",
      "version": "1.2.0",
      "date": "2026-11-12T16:52:32.000Z",
      "commit": "65a1a428ef13b95fdf50ba691e0433e368af9253",
      "fileid": "https://r2.ropensci.org/65bf0fafb7901cad7e49f75f10e7f466862de3bfcfcd0171cdacffb064872cb7",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wpeterman/actions/runs/43261617841"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.2.0",
      "date": "2026-11-12T16:50:31.000Z",
      "commit": "65a1a428ef13b95fdf50ba691e0433e368af9253",
      "fileid": "https://r2.ropensci.org/fa9bc38a3a3ffa1d9ef2e887e085fadf294e8973bdf0adaa8033156671f5a0dd",
      "status": "success",
      "buildurl": "https://github.com/r-universe/wpeterman/actions/runs/43261617841"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-11-12T16:50:01.000Z",
      "commit": "65a1a428ef13b95fdf50ba691e0433e368af9253",
      "fileid": "https://r2.ropensci.org/1053ae31348172fd7df6042048bff0afcaab8bd21d72b1f56064f5fc50ae60db",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wpeterman/actions/runs/43261617841"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-11-12T16:50:30.000Z",
      "commit": "65a1a428ef13b95fdf50ba691e0433e368af9253",
      "fileid": "https://r2.ropensci.org/0fc9d34040b1ed22f167b13e37e8419bd3c30db138899b9bd9f7ace6d67c7bba",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wpeterman/actions/runs/43261617841"
    },
    {
      "r": "4.6.2",
      "os": "win",
      "version": "1.2.0",
      "date": "2026-11-12T16:49:52.000Z",
      "commit": "65a1a428ef13b95fdf50ba691e0433e368af9253",
      "fileid": "https://r2.ropensci.org/526c8797f824e129d5539e457b8e01610b902931f3a6df134be999430e2ee26e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/wpeterman/actions/runs/43261617841"
    }
  ]
}