{
  "_id": "6aaa904fea78b3e62eacdfcd",
  "Package": "xnicher",
  "Type": "Package",
  "Title": "Estimates Ecological Niche Models Using Ellipses",
  "Version": "1.0.0",
  "Authors@R": "c(person(given = \"Angel\",\nfamily = \"Robles\",\nemail = \"a.l.robles.fernandez@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(given = \"Laura\",\nfamily = \"Jimenez\",\ncomment = c(ORCID = \"0000-0002-4674-4270\"),\nemail = \"ljimenez@cmm.uchile.cl\",\nrole = c(\"aut\", \"ctb\"))\n)",
  "Description": "Ecological niche model estimation using ellipsoidal\ngeometry under an M hypothesis.  Fits nine likelihood families\n(presence-only, weighted, inverse-probability-weighted,\nskew-normal, skew-normal-weighted, skew-t, skew-t-weighted,\nncst, and ncst-weighted) via multi-start optimisation with\nSobol sequences. Methods for the optimisation of ellipses\nparameters are as described in Jimenez et al. (2022)\n<doi:10.1016/j.ecolmodel.2021.109823>.",
  "URL": "https://github.com/alrobles/xnicher",
  "BugReports": "https://github.com/alrobles/xnicher/issues",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "Config/testthat/edition": "3",
  "SystemRequirements": "GNU make",
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  "RoxygenNote": "7.1.2",
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  "Repository": "https://alrobles.r-universe.dev",
  "Date/Publication": "2026-09-07 03:43:01 UTC",
  "RemoteUrl": "https://github.com/alrobles/xnicher",
  "RemoteRef": "HEAD",
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  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-09-16 12:39:49 UTC",
    "User": "root"
  },
  "Author": "Angel Robles [aut, cre],\nLaura Jimenez [aut, ctb] (ORCID:\n<https://orcid.org/0000-0002-4674-4270>)",
  "Maintainer": "Angel Robles <a.l.robles.fernandez@gmail.com>",
  "_user": "alrobles",
  "_type": "src",
  "_file": "xnicher_1.0.0.tar.gz",
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  "_expires": "2026-12-25T12:49:17.000Z",
  "_created": "2026-09-16T12:39:49.000Z",
  "_published": "2026-09-16T12:49:19.378Z",
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  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/alrobles/actions/runs/35096813816",
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  "_upstream": "https://github.com/alrobles/xnicher",
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    "author": "Angel Robles <a.l.robles.fernandez@gmail.com>",
    "committer": "Angel Robles <a.l.robles.fernandez@gmail.com>",
    "message": "refactor: replace ucminf R package dependency with ucminfcpp\n\n- Remove ucminf from DESCRIPTION Imports.\n- Replace ucminf::ucminf() calls with ucminfcpp::ucminf() in R/cv.R\n  and R/optimize_niche.R.\n- Update roxygen docs and Rd files to reference ucminfcpp::ucminf().\n- Update convergence-code references from ucminf to ucminfcpp.\n- R CMD check --as-cran still passes; tests pass.\n",
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  "_maintainer": {
    "name": "Angel Robles",
    "email": "a.l.robles.fernandez@gmail.com",
    "login": "alrobles",
    "description": "Postdoctoral Research at University of Kansas",
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  "_assets": [
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  "_exports": [
    "assess",
    "compare_xnicher",
    "cv_xnicher",
    "cvine_cholesky",
    "geom_xnicher_background",
    "geom_xnicher_ellipse",
    "geom_xnicher_isosuitability",
    "geom_xnicher_occ",
    "get_ellipsoid_pars",
    "habitat_suitability",
    "kde_gaussian",
    "loglik_niche",
    "loglik_niche_math_cpp",
    "loglik_niche_math_ip_weighted",
    "loglik_niche_math_ip_weighted_integrated",
    "loglik_niche_math_presence_only",
    "niche_ip_weighted",
    "niche_presence_only",
    "optimize_niche",
    "optimize_niche_xptr",
    "start_theta",
    "start_theta_multiple"
  ],
  "_datasets": [
    {
      "name": "example_env_m_2d",
      "title": "Samples of environmental data from M hypothesis to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with two variables containing points contains 2 bioclimatic variables",
      "object": "example_env_m_2d",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "bio1WH",
        "bio12WH"
      ],
      "rows": 10000,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_env_m_3d",
      "title": "Samples points from M hypothesis to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with three columns containing extracted information from 3 bioclimatic variables",
      "object": "example_env_m_3d",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "bio1WH",
        "bio12WH",
        "bio19WH"
      ],
      "rows": 10000,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_env_occ_2d",
      "title": "Species occurrence points to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with two variables containing points contains 2 bioclimatic variables",
      "object": "example_env_occ_2d",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "bio1WH",
        "bio12WH"
      ],
      "rows": 73,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_env_occ_3d",
      "title": "Species occurrence points to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with three variables containing points contains 3 bioclimatic variables",
      "object": "example_env_occ_3d",
      "class": [
        "data.frame"
      ],
      "fields": [
        "bio1WH",
        "bio12WH",
        "bio19WH"
      ],
      "rows": 73,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_mu_vec",
      "title": "Example of a vector of the center of an ellipsoid from two environmental variables. vector of length 2 corresponding to the centroid of an ellipsoid",
      "object": "example_mu_vec",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "example_occ_df",
      "title": "Species occurrence points from Abeillia abeillei presence points after download and clean from GBIF. This is a hummingbird example. A dataset with three variables. Contains scientific name, longitude and latitude.",
      "object": "example_occ_df",
      "class": [
        "data.frame"
      ],
      "fields": [
        "species",
        "lon",
        "lat"
      ],
      "rows": 73,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_s_mat",
      "title": "Example of a covariance matrix of an ellipsoid from two environmental variables. The 2 x 2 matrix corresponded to a positive semi-definite matrix. In two dimensions encodes the rotation (orientation) and scaling of an ellipse.",
      "object": "example_s_mat",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "bio1WH",
        "bio12WH"
      ],
      "rows": 2,
      "table": true,
      "tojson": true
    },
    {
      "name": "example_vicugna",
      "title": "Samples of environmental data from M hypothesis to estimate negative log likelihood from Vicugna vicugna.",
      "object": "example_vicugna",
      "class": [
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "rhipicephalus",
      "title": "Rhipicephalus microplus occurrence and background environment data",
      "object": "rhipicephalus",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "rhipicephalus_occ",
      "title": "Rhipicephalus microplus occurrence coordinates",
      "object": "rhipicephalus_occ",
      "class": [
        "data.frame"
      ],
      "fields": [
        "species",
        "lon",
        "lat"
      ],
      "rows": 334,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "AIC.xnicher",
      "title": "Akaike information criterion for a xnicher fit",
      "topics": [
        "AIC.xnicher"
      ]
    },
    {
      "page": "assess",
      "title": "Assess acceptance criteria for an optimization result",
      "topics": [
        "assess"
      ]
    },
    {
      "page": "assess.xnicher",
      "title": "Assess acceptance criteria for a xnicher result",
      "topics": [
        "assess.xnicher"
      ]
    },
    {
      "page": "BIC.xnicher",
      "title": "Bayesian information criterion for a xnicher fit",
      "topics": [
        "BIC.xnicher"
      ]
    },
    {
      "page": "compare_xnicher",
      "title": "Compare xnicher fits side-by-side via AIC and BIC",
      "topics": [
        "compare_xnicher"
      ]
    },
    {
      "page": "cv_xnicher",
      "title": "k-fold (or leave-one-out) cross-validation for a xnicher fit",
      "topics": [
        "cv_xnicher"
      ]
    },
    {
      "page": "cvine_cholesky",
      "title": "Build Cholesky factor of a correlation matrix from C‑vine partial correlations",
      "topics": [
        "cvine_cholesky"
      ]
    },
    {
      "page": "example_env_m_2d",
      "title": "Samples of environmental data from M hypothesis to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with two variables containing points contains 2 bioclimatic variables",
      "topics": [
        "example_env_m_2d"
      ]
    },
    {
      "page": "example_env_m_3d",
      "title": "Samples points from M hypothesis to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with three columns containing extracted information from 3 bioclimatic variables",
      "topics": [
        "example_env_m_3d"
      ]
    },
    {
      "page": "example_env_occ_2d",
      "title": "Species occurrence points to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with two variables containing points contains 2 bioclimatic variables",
      "topics": [
        "example_env_occ_2d"
      ]
    },
    {
      "page": "example_env_occ_3d",
      "title": "Species occurrence points to estimate negative log likelihood from Abeillia abeillei presence points. This is a hummingbird example. A dataset with three variables containing points contains 3 bioclimatic variables",
      "topics": [
        "example_env_occ_3d"
      ]
    },
    {
      "page": "example_mu_vec",
      "title": "Example of a vector of the center of an ellipsoid from two environmental variables. vector of length 2 corresponding to the centroid of an ellipsoid",
      "topics": [
        "example_mu_vec"
      ]
    },
    {
      "page": "example_occ_df",
      "title": "Species occurrence points from Abeillia abeillei presence points after download and clean from GBIF. This is a hummingbird example. A dataset with three variables. Contains scientific name, longitude and latitude.",
      "topics": [
        "example_occ_df"
      ]
    },
    {
      "page": "example_s_mat",
      "title": "Example of a covariance matrix of an ellipsoid from two environmental variables. The 2 x 2 matrix corresponded to a positive semi-definite matrix. In two dimensions encodes the rotation (orientation) and scaling of an ellipse.",
      "topics": [
        "example_s_mat"
      ]
    },
    {
      "page": "example_vicugna",
      "title": "Samples of environmental data from M hypothesis to estimate negative log likelihood from Vicugna vicugna.",
      "topics": [
        "example_vicugna"
      ]
    },
    {
      "page": "geom_xnicher_background",
      "title": "Background environment layer",
      "topics": [
        "geom_xnicher_background"
      ]
    },
    {
      "page": "geom_xnicher_ellipse",
      "title": "Niche-ellipse layer derived from a fitted 'xnicher' model",
      "topics": [
        "geom_xnicher_ellipse"
      ]
    },
    {
      "page": "geom_xnicher_isosuitability",
      "title": "Iso-suitability contour layer derived from a fitted 'xnicher' model",
      "topics": [
        "geom_xnicher_isosuitability"
      ]
    },
    {
      "page": "geom_xnicher_occ",
      "title": "Occurrence-points layer",
      "topics": [
        "geom_xnicher_occ"
      ]
    },
    {
      "page": "get_ellipsoid_pars",
      "title": "Get ellipsoid parameters. A function to compute average and the inverse of covariance matrix from environmental data",
      "topics": [
        "get_ellipsoid_pars"
      ]
    },
    {
      "page": "habitat_suitability",
      "title": "Tiled habitat-suitability map from an environmental 'terra' stack",
      "topics": [
        "habitat_suitability"
      ]
    },
    {
      "page": "kde_gaussian",
      "title": "Multivariate Gaussian KDE with fixed Scott bandwidth",
      "topics": [
        "kde_gaussian"
      ]
    },
    {
      "page": "loglik_niche",
      "title": "Negative log likelihood of an ellipsoid corrected with environmental combinations which come from the area of study (M)",
      "topics": [
        "loglik_niche"
      ]
    },
    {
      "page": "loglik_niche_math_cpp",
      "title": "Negative log-likelihood (M-restricted, math scale, Cholesky version)",
      "topics": [
        "loglik_niche_math_cpp"
      ]
    },
    {
      "page": "loglik_niche_math_ip_weighted",
      "title": "Negative log-likelihood (inverse-probability-weighted normal, math scale)",
      "topics": [
        "loglik_niche_math_ip_weighted"
      ]
    },
    {
      "page": "loglik_niche_math_ip_weighted_integrated",
      "title": "Negative log-likelihood (inverse-probability-weighted normal, integrated C++)",
      "topics": [
        "loglik_niche_math_ip_weighted_integrated"
      ]
    },
    {
      "page": "loglik_niche_math_presence_only",
      "title": "Negative log-likelihood (presence-only, math scale)",
      "topics": [
        "loglik_niche_math_presence_only"
      ]
    },
    {
      "page": "logLik.xnicher",
      "title": "Log-likelihood of a fitted xnicher model",
      "topics": [
        "logLik.xnicher"
      ]
    },
    {
      "page": "niche_ip_weighted",
      "title": "Fit inverse-probability-weighted (IPW) normal niche model",
      "topics": [
        "niche_ip_weighted"
      ]
    },
    {
      "page": "niche_presence_only",
      "title": "Fit presence-only Gaussian niche model",
      "topics": [
        "niche_presence_only"
      ]
    },
    {
      "page": "nobs.xnicher",
      "title": "Number of observations used to fit a xnicher model",
      "topics": [
        "nobs.xnicher"
      ]
    },
    {
      "page": "optimize_niche",
      "title": "Optimize niche model log-likelihood with multi-start Sobol design",
      "topics": [
        "optimize_niche"
      ]
    },
    {
      "page": "optimize_niche_xptr",
      "title": "Optimize niche model using a compiled XPtr backend",
      "topics": [
        "optimize_niche_xptr"
      ]
    },
    {
      "page": "predict.xnicher",
      "title": "Habitat-suitability raster from a fitted 'xnicher' object",
      "topics": [
        "predict.xnicher"
      ]
    },
    {
      "page": "print.xnicher",
      "title": "Print a xnicher object",
      "topics": [
        "print.xnicher"
      ]
    },
    {
      "page": "rhipicephalus",
      "title": "Rhipicephalus microplus occurrence and background environment data",
      "topics": [
        "rhipicephalus"
      ]
    },
    {
      "page": "rhipicephalus_occ",
      "title": "Rhipicephalus microplus occurrence coordinates",
      "topics": [
        "rhipicephalus_occ"
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