{
  "_id": "6acf5d86e2d863f662951420",
  "Package": "GDRarity",
  "Title": "Implementation of the global model of discretized rarity and its\nrestrictions",
  "Version": "1.1",
  "RdMacros": "Rdpack",
  "Authors@R": "person(\"Alivia\", \"Nytko\", , \"anytko@vols.utk.edu\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0003-4499-4839\"))",
  "Description": "GDRarity outlines the global model of discretized rarity\nand its various restrictions. By integrating geographic,\nfunctional trait-based, and phylogenetic dimensions of rarity\nacross regional and local spatial scales, GDRarity\ncharacterizes 57 restrictionary frameworks drawn from a global\nmodel - some of which include the widely used Rabinowitz\nrarity, functional rarity, and eco-evolutionary rarity.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "DataImport": "species_data.csv",
  "URL": "https://anytko.github.io/GDRarity/",
  "Config/pak/sysreqs": "libabsl-dev cmake libfreetype6-dev libgdal-dev\ngdal-bin libgeos-dev libglpk-dev libglu1-mesa-dev make texlive\nlibicu-dev libjpeg-dev libjq-dev libpng-dev libprotobuf-dev\nlibuv1-dev libxml2-dev libgl1-mesa-dev libssl-dev libproj-dev\nprotobuf-compiler libprotoc-dev libsqlite3-dev libudunits2-dev\nlibnode-dev libx11-dev zlib1g-dev",
  "Repository": "https://bomeara.r-universe.dev",
  "Date/Publication": "2025-09-27 13:07:49 UTC",
  "RemoteUrl": "https://github.com/anytko/GDRarity",
  "RemoteRef": "HEAD",
  "RemoteSha": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-10-14 10:40:14 UTC",
    "User": "root"
  },
  "Author": "Alivia Nytko [aut, cre] (ORCID:\n<https://orcid.org/0000-0003-4499-4839>)",
  "Maintainer": "Alivia Nytko <anytko@vols.utk.edu>",
  "_user": "bomeara",
  "_type": "src",
  "_file": "GDRarity_1.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/6bc1b91611f4c47158290ea6e371f68d99e675ab941e8c5ccbb5e0c8b1605ffb",
  "_filesize": 2408943,
  "_sha256": "6bc1b91611f4c47158290ea6e371f68d99e675ab941e8c5ccbb5e0c8b1605ffb",
  "_expires": "2027-01-22T10:46:28.000Z",
  "_created": "2026-10-14T10:40:14.000Z",
  "_published": "2026-10-14T10:46:30.174Z",
  "_buildurl": "https://github.com/r-universe/bomeara/actions/runs/38549959769",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_jobs": [
    {
      "job": 115809557686,
      "time": 308,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11886597899"
    },
    {
      "job": 115809557674,
      "time": 307,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11886807428"
    },
    {
      "job": 115809557742,
      "time": 164,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11886334234"
    },
    {
      "job": 115809557918,
      "time": 172,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11887241161"
    },
    {
      "job": 115805354865,
      "time": 654,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11886557298"
    },
    {
      "job": 115809557702,
      "time": 211,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11887201334"
    },
    {
      "job": 115809557985,
      "time": 224,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "11886214979"
    },
    {
      "job": 115809558009,
      "time": 219,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "11887300810"
    },
    {
      "job": 115809558130,
      "time": 230,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "ERROR",
      "artifact": "11886568070"
    }
  ],
  "_upstream": "https://github.com/anytko/GDRarity",
  "_commit": {
    "id": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
    "author": "anytko <anytko@vols.utk.edu>",
    "committer": "anytko <anytko@vols.utk.edu>",
    "message": "\"Added zenodo badge with new minor version 1.1.0\"\n",
    "time": 1758978469
  },
  "_maintainer": {
    "name": "Alivia Nytko",
    "email": "anytko@vols.utk.edu",
    "login": "anytko",
    "description": "",
    "uuid": 124749198,
    "orcid": "0000-0003-4499-4839"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "Rdpack",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "tidyr",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "rgbif",
      "role": "Imports"
    },
    {
      "package": "rgl",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "purrr",
      "role": "Imports"
    },
    {
      "package": "treeio",
      "role": "Imports"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "datasets",
      "role": "Imports"
    },
    {
      "package": "base",
      "role": "Imports"
    },
    {
      "package": "dbscan",
      "role": "Imports"
    },
    {
      "package": "foreach",
      "role": "Imports"
    },
    {
      "package": "doParallel",
      "role": "Imports"
    },
    {
      "package": "sf",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "future",
      "role": "Imports"
    },
    {
      "package": "future.apply",
      "role": "Imports"
    },
    {
      "package": "geojsonio",
      "role": "Imports"
    },
    {
      "package": "ggplot2",
      "role": "Imports"
    },
    {
      "package": "leaflet",
      "role": "Imports"
    },
    {
      "package": "picante",
      "role": "Imports"
    },
    {
      "package": "rmapshaper",
      "role": "Imports"
    },
    {
      "package": "DT",
      "role": "Imports"
    },
    {
      "package": "phytools",
      "role": "Imports"
    },
    {
      "package": "treemapify",
      "role": "Imports"
    },
    {
      "package": "BIEN",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "funrar",
      "role": "Imports"
    },
    {
      "package": "phylolm",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "anytko",
  "_selfowned": false,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_stars": 0,
  "_contributors": [
    {
      "user": "anytko",
      "count": 27,
      "uuid": 124749198
    }
  ],
  "_userbio": {
    "uuid": 1612612,
    "type": "user",
    "name": "Brian O'Meara",
    "followers": 112
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/GDRarity"
  },
  "_devurl": "https://github.com/anytko/gdrarity",
  "_pkgdown": "https://anytko.github.io/GDRarity/",
  "_searchresults": 5,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/GDRarity.html",
    "extra/manual.pdf",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_cranurl": false,
  "_exports": [
    "assign_rarity_types",
    "avg_evol_dist",
    "build_trait_data_BIEN",
    "build_trait_data_LEDA",
    "calc_range_size",
    "calculate_phylo_mpd",
    "check_biomes",
    "check_continents",
    "clean_trait_data_BIEN",
    "clip_polygons_to_land",
    "collapse_BIEN_traits",
    "compute_mean_si",
    "compute_wcss",
    "eval_restriction_performance",
    "find_optimal_k",
    "fun_dist",
    "gdrare_pipeline",
    "get_best_methods",
    "get_continent_sf",
    "get_phy_angio",
    "get_range_convex_hulls",
    "map_est_types",
    "prepare_gdrarity_axes",
    "prepare_gdrarity_models",
    "range_sizes",
    "rename_model_code",
    "rename_model_columns",
    "restriction_performance_pipeline",
    "run_all_gdrare_combos",
    "scale_by_median"
  ],
  "_help": [
    {
      "page": "assign_rarity_types",
      "title": "Assign rarity types based on rarity restriction",
      "topics": [
        "assign_rarity_types"
      ]
    },
    {
      "page": "avg_evol_dist",
      "title": "Calculate average evolutionary distinctiveness (ED) for a set of species",
      "topics": [
        "avg_evol_dist"
      ]
    },
    {
      "page": "build_trait_data_BIEN",
      "title": "Retrieve and Clean BIEN Trait Data for a Species",
      "topics": [
        "build_trait_data_BIEN"
      ]
    },
    {
      "page": "build_trait_data_LEDA",
      "title": "Build Trait Data from the LEDA Traitbase",
      "topics": [
        "build_trait_data_LEDA"
      ]
    },
    {
      "page": "calc_range_size",
      "title": "Calculate range sizes for multiple species",
      "topics": [
        "calc_range_size"
      ]
    },
    {
      "page": "calculate_phylo_mpd",
      "title": "Calculate Phylogenetic Mean Pairwise Distance (MPD) per Species per Site",
      "topics": [
        "calculate_phylo_mpd"
      ]
    },
    {
      "page": "check_biomes",
      "title": "Analyze Species Convex Hulls Against Biome Data",
      "topics": [
        "check_biomes"
      ]
    },
    {
      "page": "check_continents",
      "title": "Check Range Intersections with Continent Polygons",
      "topics": [
        "check_continents"
      ]
    },
    {
      "page": "clean_trait_data_BIEN",
      "title": "Clean BIEN Trait Data",
      "topics": [
        "clean_trait_data_BIEN"
      ]
    },
    {
      "page": "clip_polygons_to_land",
      "title": "Clip species range polygons to land boundaries",
      "topics": [
        "clip_polygons_to_land"
      ]
    },
    {
      "page": "collapse_BIEN_traits",
      "title": "Collapse BIEN Trait Data by Species",
      "topics": [
        "collapse_BIEN_traits"
      ]
    },
    {
      "page": "compute_mean_si",
      "title": "Compute Mean Scarcity Index (Si) for Each Species",
      "topics": [
        "compute_mean_si"
      ]
    },
    {
      "page": "compute_wcss",
      "title": "Compute Within-Cluster Sum of Squares (WCSS)",
      "topics": [
        "compute_wcss"
      ]
    },
    {
      "page": "eval_restriction_performance",
      "title": "Evaluate Restriction Performance Using ANOVA",
      "topics": [
        "eval_restriction_performance"
      ]
    },
    {
      "page": "find_optimal_k",
      "title": "Find the Optimal Number of Clusters (k) Using the Elbow Method",
      "topics": [
        "find_optimal_k"
      ]
    },
    {
      "page": "fun_dist",
      "title": "Calculate Relative Functional Distinctiveness (FD) from Trait Data",
      "topics": [
        "fun_dist"
      ]
    },
    {
      "page": "gdrare_pipeline",
      "title": "Global Discretized Rarity Pipeline",
      "topics": [
        "gdrare_pipeline"
      ]
    },
    {
      "page": "get_best_methods",
      "title": "Get Best Methods of Applying Each Restriction Per Response Variable Based on AIC",
      "topics": [
        "get_best_methods"
      ]
    },
    {
      "page": "get_continent_sf",
      "title": "Get continent spatial data from a GeoJSON file",
      "topics": [
        "get_continent_sf"
      ]
    },
    {
      "page": "get_phy_angio",
      "title": "Get Phylogeny of Angiosperms",
      "topics": [
        "get_phy_angio"
      ]
    },
    {
      "page": "get_range_convex_hulls",
      "title": "Get Convex Hull Polygons for Species from GBIF Data",
      "topics": [
        "get_range_convex_hulls"
      ]
    },
    {
      "page": "map_est_types",
      "title": "Map Rarity Types to Established Restrictions.",
      "topics": [
        "map_est_types"
      ]
    },
    {
      "page": "prepare_gdrarity_axes",
      "title": "Compute Rarity Dimensions Based on Selected Restrictions",
      "topics": [
        "prepare_gdrarity_axes"
      ]
    },
    {
      "page": "prepare_gdrarity_models",
      "title": "Prepare Restrictions for the Global Model of Discretized Rarity",
      "topics": [
        "prepare_gdrarity_models"
      ]
    },
    {
      "page": "range_sizes",
      "title": "Compute range sizes (sq km) from clipped or raw range polygons",
      "topics": [
        "range_sizes"
      ]
    },
    {
      "page": "rename_model_code",
      "title": "Rename Restriction Codes to Simplified Names",
      "topics": [
        "rename_model_code"
      ]
    },
    {
      "page": "rename_model_columns",
      "title": "Rename Columns in a Data Frame Based on Restriction Names",
      "topics": [
        "rename_model_columns"
      ]
    },
    {
      "page": "restriction_performance_pipeline",
      "title": "Run Full Restriction Performance Pipeline",
      "topics": [
        "restriction_performance_pipeline"
      ]
    },
    {
      "page": "run_all_gdrare_combos",
      "title": "Run All Restrictions of the Global Model of Discretized Rarity",
      "topics": [
        "run_all_gdrare_combos"
      ]
    },
    {
      "page": "scale_by_median",
      "title": "Scale by Median",
      "topics": [
        "scale_by_median"
      ]
    }
  ],
  "_readme": "https://github.com/anytko/GDRarity/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "askpass",
    "base64enc",
    "BIEN",
    "bit",
    "bit64",
    "bslib",
    "cachem",
    "class",
    "classInt",
    "cli",
    "clipr",
    "cluster",
    "clusterGeneration",
    "coda",
    "codetools",
    "combinat",
    "commonmark",
    "cpp11",
    "crayon",
    "crosstalk",
    "crul",
    "curl",
    "data.table",
    "DBI",
    "dbscan",
    "DEoptim",
    "digest",
    "doParallel",
    "dplyr",
    "DT",
    "e1071",
    "evaluate",
    "expm",
    "farver",
    "fastmap",
    "fastmatch",
    "fontawesome",
    "foreach",
    "fs",
    "funrar",
    "future",
    "future.apply",
    "generics",
    "geojson",
    "geojsonio",
    "geojsonsf",
    "geometries",
    "ggfittext",
    "ggplot2",
    "globals",
    "glue",
    "gridtext",
    "gtable",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httpcode",
    "httr",
    "igraph",
    "isoband",
    "iterators",
    "jpeg",
    "jqr",
    "jquerylib",
    "jsonify",
    "jsonlite",
    "KernSmooth",
    "knitr",
    "labeling",
    "later",
    "lattice",
    "lazyeval",
    "leaflet",
    "leaflet.providers",
    "lifecycle",
    "listenv",
    "litedown",
    "magrittr",
    "maps",
    "markdown",
    "MASS",
    "Matrix",
    "memoise",
    "mgcv",
    "mime",
    "mnormt",
    "nlme",
    "numDeriv",
    "oai",
    "openssl",
    "optimParallel",
    "otel",
    "parallelly",
    "permute",
    "phangorn",
    "phylolm",
    "phytools",
    "picante",
    "pillar",
    "pkgconfig",
    "plyr",
    "png",
    "prettyunits",
    "progress",
    "promises",
    "protolite",
    "proxy",
    "purrr",
    "quadprog",
    "R6",
    "rapidjsonr",
    "rappdirs",
    "raster",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "Rdpack",
    "readr",
    "rgbif",
    "rgl",
    "rlang",
    "rmapshaper",
    "rmarkdown",
    "RPostgreSQL",
    "s2",
    "S7",
    "sass",
    "scales",
    "scatterplot3d",
    "sf",
    "sfheaders",
    "shades",
    "sp",
    "stringi",
    "stringr",
    "sys",
    "terra",
    "tibble",
    "tidyr",
    "tidyselect",
    "tidytree",
    "tinytex",
    "treeio",
    "treemapify",
    "triebeard",
    "tzdb",
    "units",
    "urltools",
    "utf8",
    "V8",
    "vctrs",
    "vegan",
    "viridisLite",
    "vroom",
    "whisker",
    "withr",
    "wk",
    "xfun",
    "xml2",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "GDRarity.Rmd",
      "filename": "GDRarity.html",
      "title": "GDRarity",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Vignette Info",
        "Setup",
        "Import Data",
        "Run All Methods on All 63 Restrictions of GDR using Phylogenetic Linear Models",
        "Output Examples",
        "Results from the first combination of methods",
        "Results of Coefficients using every Method and Restriction",
        "Best Restrictions Explaining Flowering Phenology",
        "Parameter Combinations",
        "Threshold Sets",
        "Best Restriction for Flowering Phenology",
        "Methods Used",
        "Thresholds Applied",
        "Incorporating Additional Dimensions",
        "Additional dimensions of rarity can also be incorporated but must be specified by users",
        "Example: Adding Random Habitat Specificity",
        "Re-run Methods with Habitat Specificity using Linear Models",
        "Best Restrictions with Habitat Specificity",
        "Best Restriction for Flowering Phenology Incorporating Habitat Specificity"
      ],
      "created": "2025-09-15 14:50:34",
      "modified": "2025-09-26 19:43:55",
      "commits": 3
    }
  ],
  "_score": 2.6989700043360187,
  "_indexed": false,
  "_nocasepkg": "gdrarity",
  "_universes": [
    "bomeara"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.1",
      "date": "2026-10-14T10:43:53.000Z",
      "distro": "resolute",
      "commit": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
      "fileid": "https://r2.ropensci.org/6430d651790d54a03c4ca4a2c446716abbf13abfe63c6e194fb6bd3a823eae39",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38549959769"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.1",
      "date": "2026-10-14T10:43:52.000Z",
      "distro": "resolute",
      "commit": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
      "fileid": "https://r2.ropensci.org/31689ac6c7da490dc6407b59e003bf57317986ce6ffa40700e30bf8068283ceb",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38549959769"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.1",
      "date": "2026-10-14T10:42:22.000Z",
      "commit": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
      "fileid": "https://r2.ropensci.org/e66d487d1484865a9992588e9673f8b9ff5aa6045ecc30545b272183e601b65e",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38549959769"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.1",
      "date": "2026-10-14T10:42:29.000Z",
      "commit": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
      "fileid": "https://r2.ropensci.org/ea01cbbc8cff53ab6ba792a9977c709845bfe95c801770eaee8f4778f96ade75",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38549959769"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.1",
      "date": "2026-10-14T10:44:21.000Z",
      "commit": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
      "fileid": "https://r2.ropensci.org/00414ee1d300f973cf80de783ac312e4d0e288bd7fc751bf855ed051a22cfb30",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38549959769"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.1",
      "date": "2026-10-14T10:42:06.000Z",
      "commit": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
      "fileid": "https://r2.ropensci.org/a0b8ddea00230955cf3389f56858dc56719a5fcb9ebce576be1deee09c84d319",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38549959769"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.1",
      "date": "2026-10-14T10:42:00.000Z",
      "commit": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
      "fileid": "https://r2.ropensci.org/a7ebbac7303f17dda8dce7d5156eac6669680d04627c7f263c0bb654730797da",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38549959769"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.1",
      "date": "2026-10-14T10:42:10.000Z",
      "commit": "65c567edde3b1b71d97eb62f88452d98dafe3af6",
      "fileid": "https://r2.ropensci.org/18c7a2f8479778230e2b927fd030a8f929ea66a7b18927cd472d56b13c898873",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/bomeara/actions/runs/38549959769"
    }
  ]
}