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  "Title": "Ellipsoid-Based Virtual Niches and Visualization",
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  "Authors@R": "c(\nperson(\n\"Mariana\", \"Castaneda-Guzman\",\nemail = \"marianacg@vt.edu\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-6106-4284\")\n),\nperson(\n\"Connor\", \"Hughes\",\nemail = \"connorjh@vt.edu\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-3720-0837\")\n),\nperson(\n\"Paanwaris\", \"Paansri\",\nemail = \"paanwaris@vt.edu\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-9992-098X\")\n),\nperson(\n\"Marlon E.\", \"Cobos\",\nemail = \"manubio13@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0002-2611-1767\")\n)\n)",
  "Description": "Provides a robust set of tools for researchers and\nmodelers to construct and define virtual ecological niches\nusing ellipsoid geometries. It enables the identification and\nextraction of suitable environmental areas, simulation of\nspecies occurrence points with various sampling strategies, and\nvisualization of niche boundaries and simulated occurrences in\nboth environmental and geographic space. Inspired by\nmethodologies in 'NicheA' and the 'virtualspecies' R package,\n'nicheR' aims to streamline the process of niche\nconceptualization and data generation for ecological studies.\nMethodological and theoretical foundations are described in\nPeterson et al. (2011, ISBN:9780691136882), Etherington et al.\n(2009) <doi:10.1111/j.1365-2699.2008.02041.x>, Qiao et al.\n(2015) <doi:10.1111/ecog.01961>, Nunez-Penichet et al. (2021)\n<doi:10.21425/F5FBG52142>, Cobos and Peterson (2022)\n<doi:10.17161/bi.v17i.15985>, Alkishe et al. (2022)\n<doi:10.5194/we-22-33-2022>, and Leroy et al. (2015)\n<doi:10.1111/ecog.01388>.",
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  "Repository": "https://castanedam.r-universe.dev",
  "Date/Publication": "2026-06-08 16:02:48 UTC",
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  "Author": "Mariana Castaneda-Guzman [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-6106-4284>),\nConnor Hughes [aut] (ORCID: <https://orcid.org/0000-0002-3720-0837>),\nPaanwaris Paansri [aut] (ORCID:\n<https://orcid.org/0000-0001-9992-098X>),\nMarlon E. Cobos [aut] (ORCID: <https://orcid.org/0000-0002-2611-1767>)",
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    "add_ellipsoid",
    "add_ellipsoid_3d",
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    "build_ellipsoid",
    "conserved_ellipses",
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    "plot_ellipsoid",
    "plot_ellipsoid_3d",
    "plot_ellipsoid_pairs",
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    "random_ellipses",
    "ranges_from_data",
    "ranges_from_stats",
    "read_nicheR",
    "sample_biased_data",
    "sample_data",
    "save_nicheR",
    "update_covariance",
    "update_ellipsoid_covariance",
    "virtual_data"
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      "title": "Background environmental data for examples",
      "object": "back_data",
      "class": [
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        "y",
        "bio_1",
        "bio_5",
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        "bio_14",
        "bio_15"
      ],
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      "table": true,
      "tojson": true
    },
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      "title": "Example niche ellipsoid objects for virtual communities",
      "object": "example_sp_1",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
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      "title": "Example niche ellipsoid objects for virtual communities",
      "object": "example_sp_2",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_sp_3",
      "title": "Example niche ellipsoid objects for virtual communities",
      "object": "example_sp_3",
      "class": [
        "nicheR_ellipsoid"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "example_sp_4",
      "title": "Example niche ellipsoid objects for virtual communities",
      "object": "example_sp_4",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "ref_ellipse",
      "title": "Reference ellipse for virtual community examples",
      "object": "ref_ellipse",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
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  "_help": [
    {
      "page": "add_data",
      "title": "Add occurrence points or other data to an existing E-space plot",
      "topics": [
        "add_data"
      ]
    },
    {
      "page": "add_data_3d",
      "title": "Add data to an existing 3D E-space plot",
      "topics": [
        "add_data_3d"
      ]
    },
    {
      "page": "add_ellipsoid",
      "title": "Add an ellipsoid boundary to an existing E-space plot",
      "topics": [
        "add_ellipsoid"
      ]
    },
    {
      "page": "add_ellipsoid_3d",
      "title": "Add an ellipsoid to an existing 3D E-space plot",
      "topics": [
        "add_ellipsoid_3d"
      ]
    },
    {
      "page": "apply_bias",
      "title": "Apply sampling bias to suitability surfaces",
      "topics": [
        "apply_bias"
      ]
    },
    {
      "page": "back_data",
      "title": "Background environmental data for examples",
      "topics": [
        "back_data"
      ]
    },
    {
      "page": "build_ellipsoid",
      "title": "Build a probabilistic ellipsoidal niche from ranges",
      "topics": [
        "build_ellipsoid"
      ]
    },
    {
      "page": "conserved_ellipses",
      "title": "Generate ellipses via multivariate normal biased sampling",
      "topics": [
        "conserved_ellipses"
      ]
    },
    {
      "page": "covariance_limits",
      "title": "Calculate safe covariance ranges for positive definiteness",
      "topics": [
        "covariance_limits"
      ]
    },
    {
      "page": "ellipsoid_calculator",
      "title": "Calculate n-dimensional ellipsoid metrics",
      "topics": [
        "ellipsoid_calculator"
      ]
    },
    {
      "page": "ellipsoid_volume",
      "title": "Compute ellipsoid hypervolume",
      "topics": [
        "ellipsoid_volume"
      ]
    },
    {
      "page": "example_ellipsoids",
      "title": "Example niche ellipsoid objects for virtual communities",
      "topics": [
        "example_ellipsoids",
        "example_sp_1",
        "example_sp_2",
        "example_sp_3",
        "example_sp_4"
      ]
    },
    {
      "page": "ma_bios",
      "title": "Bioclimatic variables for part of the Americas",
      "topics": [
        "ma_bios"
      ]
    },
    {
      "page": "nested_ellipses",
      "title": "Generate nested ellipses based on a reference ellipse",
      "topics": [
        "nested_ellipses"
      ]
    },
    {
      "page": "plot_community",
      "title": "Plot a nicheR Community of Ellipses",
      "topics": [
        "plot_community"
      ]
    },
    {
      "page": "plot_ellipsoid",
      "title": "Plot a nicheR ellipsoid in environmental space",
      "topics": [
        "plot_ellipsoid"
      ]
    },
    {
      "page": "plot_ellipsoid_3d",
      "title": "Plot a nicheR ellipsoid in 3D environmental space",
      "topics": [
        "plot_ellipsoid_3d"
      ]
    },
    {
      "page": "plot_ellipsoid_pairs",
      "title": "Plot all pairwise 2D ellipsoid projections",
      "topics": [
        "plot_ellipsoid_pairs"
      ]
    },
    {
      "page": "predict",
      "title": "Predict suitability and Mahalanobis distance from a nicheR ellipsoid",
      "topics": [
        "predict",
        "predict,nicheR_nicheR_community-method",
        "predict,nicheR_nicheR_ellipsoid-method",
        "predict.nicheR_community",
        "predict.nicheR_ellipsoid"
      ]
    },
    {
      "page": "prepare_bias",
      "title": "Prepare sampling bias surfaces",
      "topics": [
        "prepare_bias"
      ]
    },
    {
      "page": "print",
      "title": "Print method for nicheR objects",
      "topics": [
        "print",
        "print,nicheR_nicheR_community-method",
        "print,nicheR_nicheR_ellipsoid-method",
        "print.nicheR_community",
        "print.nicheR_ellipsoid"
      ]
    },
    {
      "page": "random_ellipses",
      "title": "Generate random ellipses constrained by a point cloud and a reference ellipse",
      "topics": [
        "random_ellipses"
      ]
    },
    {
      "page": "range_utilities",
      "title": "Compute variable ranges from data or statistics with optional expansion",
      "topics": [
        "ranges_from_data",
        "ranges_from_stats",
        "range_utilities"
      ]
    },
    {
      "page": "read_nicheR",
      "title": "Read a nicheR object from disk",
      "topics": [
        "read_nicheR"
      ]
    },
    {
      "page": "ref_ellipse",
      "title": "Reference ellipse for virtual community examples",
      "topics": [
        "ref_ellipse"
      ]
    },
    {
      "page": "sample_biased_data",
      "title": "Sample occurrence data from a bias-weighted prediction surface",
      "topics": [
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      ]
    },
    {
      "page": "sample_data",
      "title": "Sample occurrence data from a prediction surface",
      "topics": [
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      ]
    },
    {
      "page": "save_nicheR",
      "title": "Save a nicheR object to disk",
      "topics": [
        "save_nicheR"
      ]
    },
    {
      "page": "update_covariance",
      "title": "Update covariance values and calculate remaining safe limits",
      "topics": [
        "update_covariance"
      ]
    },
    {
      "page": "update_ellipsoid_covariance",
      "title": "Update covariances in a nicheR ellipsoid and recompute metrics",
      "topics": [
        "update_ellipsoid_covariance"
      ]
    },
    {
      "page": "virtual_data",
      "title": "Generate data based on a ellipsoidal niche",
      "topics": [
        "virtual_data"
      ]
    }
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