{
  "_id": "6acec1e0d9de2f3f33fc790e",
  "Package": "OccurrenceCleaner",
  "Title": "Fast Quality Checks for Species Occurrence Records",
  "Version": "0.2.0",
  "Authors@R": "person(\"Gilles\", \"Colling\", , \"gilles.colling051@gmail.com\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0003-3070-6066\"))",
  "Description": "An extension of 'CoordinateCleaner' (Zizka et al. 2019\n<doi:10.1111/2041-210X.13152>) tailored to large-scale species\noccurrence data. Flags common problems in occurrence records,\nsuch as coordinates at country centroids, capitals or\nbiodiversity institutions, zero or equal coordinates, records\nat sea, in the wrong country or outside the species range,\nduplicates, outliers within a species, and datasets with\nconverted or gridded coordinates, with the test definitions and\ndefault buffers of 'CoordinateCleaner' apart from documented\ndifferences. It also reads the quality warnings GBIF attaches\nto each record, the basis of record and the establishment\nmeans, and checks records at sea or on land against the habitat\nof their genus from the Interim Register of Marine and\nNonmarine Genera. Records are flagged and kept, and users\nchoose afterwards which flags to filter on. Data frames of a\nfew million records are flagged in seconds, and GBIF snapshots\nof billions of records are processed by reading Parquet files\nin chunks.",
  "License": "MIT + file LICENSE",
  "URL": "https://gillescolling.com/OccurrenceCleaner/,\nhttps://github.com/gcol33/OccurrenceCleaner",
  "BugReports": "https://github.com/gcol33/OccurrenceCleaner/issues",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Roxygen": "list(markdown = TRUE)",
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  "Collate": "'OccurrenceCleaner-package.R' 'RcppExports.R' 'group.R'\n'flag.R' 'clean.R' 'columns.R' 'data.R' 'flag_tests.R'\n'habitat.R' 'methods.R' 'progress.R' 'pyrate.R' 'reference.R'\n'shapefile.R' 'spatialvalid.R' 'store.R' 'stream.R' 'tally.R'\n'test-docs.R'",
  "Repository": "https://gcol33.r-universe.dev",
  "Date/Publication": "2026-10-13 15:49:31 UTC",
  "RemoteUrl": "https://github.com/gcol33/OccurrenceCleaner",
  "RemoteRef": "HEAD",
  "RemoteSha": "dea3bc9b977c64bd8515da497392743973ef4a6e",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-10-13 23:28:50 UTC",
    "User": "root"
  },
  "Author": "Gilles Colling [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0003-3070-6066>)",
  "Maintainer": "Gilles Colling <gilles.colling051@gmail.com>",
  "_user": "gcol33",
  "_type": "src",
  "_file": "OccurrenceCleaner_0.2.0.tar.gz",
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  "_sha256": "fc01fc767f648e1a52fea64d4137526623dc6a0a062ba727d6cbba4a83bad24b",
  "_expires": "2027-01-21T23:42:22.000Z",
  "_created": "2026-10-13T23:28:50.000Z",
  "_published": "2026-10-13T23:42:24.653Z",
  "_buildurl": "https://github.com/r-universe/gcol33/actions/runs/38484092428",
  "_status": "success",
  "_host": "GitHub-Actions",
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    "author": "Gilles Colling <gilles.colling051@gmail.com>",
    "committer": "Gilles Colling <gilles.colling051@gmail.com>",
    "message": "Docs: threads article intro rewritten, speedup line labelled in the plot, site rebuilt\n\nCo-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>\n",
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    "description": "Building tools for ecology in R, C++, and Rust.\nWhy did Microsoft have to buy it. Sadge :(",
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  "_tags": [
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  "_topics": [
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    "data-cleaning",
    "gbif",
    "occurrence-data",
    "rcpp",
    "cpp",
    "openmp"
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  "_pkgdown": "https://gillescolling.com/OccurrenceCleaner/",
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  "_rbuild": "4.6.1",
  "_assets": [
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    "extra/citation.json",
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    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
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    "clean_age_equal",
    "clean_age_outlier",
    "clean_age_range_outlier",
    "clean_aohi",
    "clean_basis_fossil",
    "clean_basis_living",
    "clean_capital",
    "clean_centroid",
    "clean_country_mismatch",
    "clean_dataset_ddmm",
    "clean_dataset_rounded",
    "clean_duplicate",
    "clean_equal",
    "clean_establishment_introduced",
    "clean_establishment_managed",
    "clean_gbif_headquarters",
    "clean_institution",
    "clean_invalid",
    "clean_issue_coordinate",
    "clean_issue_date",
    "clean_issue_rounded",
    "clean_issue_taxon",
    "clean_land_marine",
    "clean_outlier",
    "clean_range",
    "clean_sea",
    "clean_sea_nonmarine",
    "clean_spatiotemporal_outlier",
    "clean_urban",
    "clean_zero",
    "download_reference",
    "export_pyrate",
    "flag_mask",
    "flag_occurrences",
    "flag_reference",
    "flag_tests",
    "flagged_table",
    "has_flag",
    "keep_unflagged",
    "occ_columns",
    "read_flagged",
    "reference_habitat",
    "reference_info",
    "reference_points",
    "tally_flags",
    "test_plan"
  ],
  "_datasets": [
    {
      "name": "gentiana",
      "title": "GBIF records of gentians in Austria",
      "object": "gentiana",
      "class": [
        "data.frame"
      ],
      "fields": [
        "gbifid",
        "datasetkey",
        "kingdom",
        "genus",
        "species",
        "countrycode",
        "decimallongitude",
        "decimallatitude",
        "coordinateuncertaintyinmeters",
        "year",
        "basisofrecord",
        "institutioncode",
        "establishmentmeans",
        "issue",
        "license"
      ],
      "rows": 33025,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "as_spatialvalid",
      "title": "Convert flags to CoordinateCleaner's spatialvalid format",
      "topics": [
        "as_spatialvalid"
      ]
    },
    {
      "page": "test_age_equal",
      "title": "Test: fossil age range",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_age_equal",
        "test_age_equal"
      ]
    },
    {
      "page": "test_age_outlier",
      "title": "Test: fossil age outliers",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_age_outlier",
        "test_age_outlier"
      ]
    },
    {
      "page": "test_age_range_outlier",
      "title": "Test: fossil age-range outliers",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_age_range_outlier",
        "test_age_range_outlier"
      ]
    },
    {
      "page": "test_aohi",
      "title": "Test: artificial hotspots",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_aohi",
        "test_aohi"
      ]
    },
    {
      "page": "test_basis",
      "title": "Tests: basis of record",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_basis_fossil",
        "clean_basis_living",
        "test_basis"
      ]
    },
    {
      "page": "test_capital",
      "title": "Test: country capitals",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_capital",
        "test_capital"
      ]
    },
    {
      "page": "test_centroid",
      "title": "Test: country and province centroids",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_centroid",
        "test_centroid"
      ]
    },
    {
      "page": "test_country_mismatch",
      "title": "Test: country code mismatch",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_country_mismatch",
        "test_country_mismatch"
      ]
    },
    {
      "page": "test_dataset_ddmm",
      "title": "Test: degree-minute conversion errors in a dataset",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_dataset_ddmm",
        "test_dataset_ddmm"
      ]
    },
    {
      "page": "test_dataset_rounded",
      "title": "Test: rasterised datasets",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_dataset_rounded",
        "test_dataset_rounded"
      ]
    },
    {
      "page": "test_duplicate",
      "title": "Test: duplicates",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_duplicate",
        "test_duplicate"
      ]
    },
    {
      "page": "test_equal",
      "title": "Test: equal coordinates",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_equal",
        "test_equal"
      ]
    },
    {
      "page": "test_establishment",
      "title": "Tests: establishment means",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_establishment_introduced",
        "clean_establishment_managed",
        "test_establishment"
      ]
    },
    {
      "page": "test_gbif_headquarters",
      "title": "Test: GBIF headquarters",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_gbif_headquarters",
        "test_gbif_headquarters"
      ]
    },
    {
      "page": "test_institution",
      "title": "Test: biodiversity institutions",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_institution",
        "test_institution"
      ]
    },
    {
      "page": "test_invalid",
      "title": "Test: invalid coordinates",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_invalid",
        "test_invalid"
      ]
    },
    {
      "page": "test_gbif_issue",
      "title": "Tests: GBIF issue flags",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_issue_coordinate",
        "clean_issue_date",
        "clean_issue_rounded",
        "clean_issue_taxon",
        "test_gbif_issue"
      ]
    },
    {
      "page": "test_outlier",
      "title": "Test: geographic outliers",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_outlier",
        "test_outlier"
      ]
    },
    {
      "page": "test_range",
      "title": "Test: outside the species range",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_range",
        "test_range"
      ]
    },
    {
      "page": "test_sea",
      "title": "Test: records at sea",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_sea",
        "test_sea"
      ]
    },
    {
      "page": "test_habitat",
      "title": "Tests: habitat at sea and on land",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_land_marine",
        "clean_sea_nonmarine",
        "test_habitat"
      ]
    },
    {
      "page": "test_spatiotemporal_outlier",
      "title": "Test: fossil outliers in space and time",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_spatiotemporal_outlier",
        "test_spatiotemporal_outlier"
      ]
    },
    {
      "page": "test_urban",
      "title": "Test: urban areas",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_urban",
        "test_urban"
      ]
    },
    {
      "page": "test_zero",
      "title": "Test: zero coordinates",
      "concept": [
        "tests"
      ],
      "topics": [
        "clean_zero",
        "test_zero"
      ]
    },
    {
      "page": "download_reference",
      "title": "Download the 1:10 million land layer",
      "topics": [
        "download_reference"
      ]
    },
    {
      "page": "export_pyrate",
      "title": "Export fossil records as PyRate input",
      "topics": [
        "export_pyrate"
      ]
    },
    {
      "page": "flag_mask",
      "title": "Bit mask and membership for sets of tests",
      "topics": [
        "flag_mask",
        "has_flag"
      ]
    },
    {
      "page": "flag_occurrences",
      "title": "Flag occurrence records",
      "topics": [
        "flag_occurrences"
      ]
    },
    {
      "page": "flag_reference",
      "title": "Reference data behind a set of flags",
      "topics": [
        "flag_reference"
      ]
    },
    {
      "page": "flag_tests",
      "title": "The flag layout: one bit per test",
      "topics": [
        "flag_tests"
      ]
    },
    {
      "page": "gentiana",
      "title": "GBIF records of gentians in Austria",
      "topics": [
        "gentiana"
      ]
    },
    {
      "page": "keep_unflagged",
      "title": "Keep the records no test flagged",
      "topics": [
        "keep_unflagged"
      ]
    },
    {
      "page": "occ_columns",
      "title": "Name the record fields",
      "topics": [
        "occ_columns"
      ]
    },
    {
      "page": "plot.occ_summary",
      "title": "Plot flag percentages, or map flagged records",
      "topics": [
        "plot.occ_flagged",
        "plot.occ_flags",
        "plot.occ_summary",
        "plot.occ_tally"
      ]
    },
    {
      "page": "read_flagged",
      "title": "Read flag output written by flag_occurrences()",
      "topics": [
        "flagged_table",
        "read_flagged"
      ]
    },
    {
      "page": "reference_habitat",
      "title": "Genus habitats of the habitat tests",
      "topics": [
        "reference_habitat"
      ]
    },
    {
      "page": "reference_info",
      "title": "Reference data: sources and versions",
      "topics": [
        "reference_info"
      ]
    },
    {
      "page": "reference_points",
      "title": "Reference points of a proximity test",
      "topics": [
        "reference_points"
      ]
    },
    {
      "page": "summary.occ_flags",
      "title": "Share of records flagged, per test and rule",
      "topics": [
        "summary.occ_flagged",
        "summary.occ_flags",
        "summary.occ_tally"
      ]
    },
    {
      "page": "tally_flags",
      "title": "Tally flags into a loss table",
      "topics": [
        "tally_flags"
      ]
    },
    {
      "page": "test_plan",
      "title": "Which tests run on an input",
      "topics": [
        "test_plan"
      ]
    }
  ],
  "_pkglogo": "https://github.com/gcol33/OccurrenceCleaner/raw/HEAD/man/figures/logo.svg",
  "_readme": "https://github.com/gcol33/OccurrenceCleaner/raw/HEAD/README.md",
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    "withr"
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  "_sysdeps": [
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      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
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      "name": "c++",
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      "package": "libgomp1",
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