{
  "_id": "6a10abd9acfb0bcc41cbf91a",
  "Package": "pdindicatoR",
  "Title": "Calculate and visualize a phylogenetic diversity indicators\nbased on species occurrence data cubes",
  "Version": "0.1.0",
  "Authors@R": "c(\nperson(\"Lissa\", \"Breugelmans\", , \"lissa.breugelmans@plantentuinmeise.be\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-8472-3577\", affiliation = \"Meise Botanic Garden\")),\nperson(\"Maarten\", \"Trekels\", , \"maarten.trekels@plantentuinmeise.be\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-8282-8765\", affiliation = \"Meise Botanic Garden\")),\nperson(\"Louise\", \"Hendrickx\", , \"louise.hendrickx@plantentuinmeise.be\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-9317-7862\", affiliation = \"Meise Botanic Garden\")),\nperson(\"Ward\", \"Langeraert\", , \"ward.langeraert@inbo.be\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-5900-8109\", affiliation = \"Research Institute for Nature and Forest (INBO)\")),\nperson(\"Meise Botanic Garden\", , , \"b-cubedsupport@meisebotanicgarden.be\", role = \"cph\"),\nperson(\"European Union's Horizon Europe Research and Innovation Programme (ID No 101059592)\", role = \"fnd\")\n)",
  "Description": "A package to calculate and produce a map of phylogenetic\ndiversity scores for each grid cell in the input species\noccurrences data cube, and calculate the percentage of high PD\ncells within currently protected areas.  You provide a\nphylogenetic tree, the datacube for the corresponding species\nis downloaded from GBIF (or user-uploaded), and the package\ndoes the rest.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/b-cubed-eu/pdindicatoR,\nhttps://b-cubed-eu.github.io/pdindicatoR/,\nhttps://doi.org/10.5281/zenodo.14237551",
  "BugReports": "https://github.com/b-cubed-eu/pdindicatoR/issues",
  "Config/checklist/communities": "b3",
  "Config/checklist/keywords": "phylogenetic diversity; data cubes; B-Cubed;\nbiodiversity",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "Language": "en-GB",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nmake libicu-dev libuv1-dev libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev zlib1g-dev",
  "Repository": "https://b-cubed-eu.r-universe.dev",
  "Date/Publication": "2026-03-23 10:24:51 UTC",
  "RemoteUrl": "https://github.com/b-cubed-eu/pdindicatoR",
  "RemoteRef": "HEAD",
  "RemoteSha": "5bbd91d03800357d5c0bff8092d8204c42e82fda",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-22 18:54:34 UTC",
    "User": "root"
  },
  "Author": "Lissa Breugelmans [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-8472-3577>, affiliation: Meise Botanic\nGarden),\nMaarten Trekels [aut] (ORCID: <https://orcid.org/0000-0001-8282-8765>,\naffiliation: Meise Botanic Garden),\nLouise Hendrickx [aut] (ORCID: <https://orcid.org/0000-0002-9317-7862>,\naffiliation: Meise Botanic Garden),\nWard Langeraert [ctb] (ORCID: <https://orcid.org/0000-0002-5900-8109>,\naffiliation: Research Institute for Nature and Forest (INBO)),\nMeise Botanic Garden [cph],\nEuropean Union's Horizon Europe Research and Innovation Programme (ID\nNo 101059592) [fnd]",
  "Maintainer": "Lissa Breugelmans <lissa.breugelmans@plantentuinmeise.be>",
  "MD5sum": "1e6969f07a5763a835a3e0670345d89b",
  "_user": "b-cubed-eu",
  "_type": "src",
  "_file": "pdindicatoR_0.1.0.tar.gz",
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  "_filesize": 1494770,
  "_sha256": "0c5513ccf67d86045156488b838f5082b0377daa9344842364f57a358311e7e4",
  "_created": "2026-05-22T18:54:34.000Z",
  "_published": "2026-05-22T19:17:45.096Z",
  "_distro": "noble",
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  "_buildurl": "https://github.com/r-universe/b-cubed-eu/actions/runs/26277300607",
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  "_host": "GitHub-Actions",
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    "author": "Lissa Breugelmans <117663331+LBreugelmans@users.noreply.github.com>",
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    "message": "Merge pull request #51 from b-cubed-eu/logo-link\n\nAdd link to pkgdown website in logo",
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  "_maintainer": {
    "name": "Lissa Breugelmans",
    "email": "lissa.breugelmans@plantentuinmeise.be",
    "login": "lbreugelmans",
    "orcid": "0000-0002-8472-3577",
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  "_owner": "b-cubed-eu",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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      "week": "2026-06",
      "n": 1
    },
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      "week": "2026-07",
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  ],
  "_tags": [],
  "_topics": [
    "biodiversity",
    "conservation",
    "datacube",
    "indicator",
    "phylogenetic-diversity"
  ],
  "_stars": 0,
  "_contributors": [
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    "name": "B-Cubed",
    "description": "Biodiversity Building Blocks for Policy"
  },
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  "_cranurl": false,
  "_exports": [
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    "append_ott_id",
    "calculate_faithpd",
    "check_completeness",
    "convert_multipolygons",
    "generate_map_and_indicator",
    "get_pd_cube",
    "make_shiny_maps",
    "retrieve_example_data",
    "taxonmatch"
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  "_help": [
    {
      "page": "aggregate_cube",
      "title": "Aggregate datacube over grid cell to create new dataframe with species list per grid",
      "topics": [
        "aggregate_cube"
      ]
    },
    {
      "page": "append_ott_id",
      "title": "Append ott id's to cube",
      "topics": [
        "append_ott_id"
      ]
    },
    {
      "page": "calculate_faithpd",
      "title": "Calculation of Faith's PD",
      "topics": [
        "calculate_faithpd"
      ]
    },
    {
      "page": "check_completeness",
      "title": "Check if provided phylogenetic tree is complete and covers all species in occurrence cube",
      "topics": [
        "check_completeness"
      ]
    },
    {
      "page": "convert_multipolygons",
      "title": "Convert multisurface object to multipolygon object",
      "topics": [
        "convert_multipolygons"
      ]
    },
    {
      "page": "generate_map_and_indicator",
      "title": "Mapping PD and calculating indicator",
      "topics": [
        "generate_map_and_indicator"
      ]
    },
    {
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      "title": "Find MRCA for data cube and call function to calculate PD metrics",
      "topics": [
        "get_pd_cube"
      ]
    },
    {
      "page": "make_shiny_maps",
      "title": "Visualizing PD maps for time periods in tabs",
      "topics": [
        "make_shiny_maps"
      ]
    },
    {
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      "title": "Retrieve example data",
      "topics": [
        "retrieve_example_data"
      ]
    },
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      "title": "Taxon matching",
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      ]
    }
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