{
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  "Title": "Univariate and Multivariate Spatial Modeling of Species\nAbundance",
  "Version": "0.2.2",
  "Authors@R": "c(person(\"Jeffrey\", \"Doser\", role=c(\"aut\", \"cre\"), email=\"jwdoser@ncsu.edu\"), person(\"Andrew\", \"Finley\", role = c(\"aut\")))",
  "Description": "Fits single-species (univariate) and multi-species\n(multivariate) non-spatial and spatial abundance models in a\nBayesian framework using Markov Chain Monte Carlo (MCMC).\nSpatial models are fit using Nearest Neighbor Gaussian\nProcesses (NNGPs). Details on NNGP models are given in Datta,\nBanerjee, Finley, and Gelfand (2016)\n<doi:10.1080/01621459.2015.1044091> and Finley, Datta, and\nBanerjee (2022) <doi:10.18637/jss.v103.i05>. Fits\nsingle-species and multi-species spatial and non-spatial\nversions of generalized linear mixed models (Gaussian, Poisson,\nNegative Binomial), N-mixture models (Royle 2004\n<doi:10.1111/j.0006-341X.2004.00142.x>) and hierarchical\ndistance sampling models (Royle, Dawson, Bates (2004)\n<doi:10.1890/03-3127>). Multi-species spatial models are fit\nusing a spatial factor modeling approach with NNGPs for\ncomputational efficiency.",
  "License": "GPL (>= 3)",
  "Encoding": "UTF-8",
  "LazyData": "true",
  "URL": "https://www.doserlab.com/files/spabundance-web\nhttps://groups.google.com/g/spocc-spabund-users",
  "BugReports": "https://github.com/biodiverse/spAbundance/issues",
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  "Repository": "https://ecoverser.r-universe.dev",
  "Date/Publication": "2026-01-15 17:55:44 UTC",
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    "Date": "2026-05-15 08:14:38 UTC",
    "User": "root"
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  "Author": "Jeffrey Doser [aut, cre],\nAndrew Finley [aut]",
  "Maintainer": "Jeffrey Doser <jwdoser@ncsu.edu>",
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    "spNMix",
    "svcAbund",
    "svcMsAbund",
    "svcTIntAbund",
    "waicAbund"
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      "object": "bbsData",
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      "fields": [],
      "table": false,
      "tojson": true
    },
    {
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        "y"
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      "table": false,
      "tojson": true
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    {
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      "title": "Count data of 12 foliage gleaning bird species in 2015 in the Hubbard Brook Experimental Forest",
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      "class": [
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      ],
      "fields": [],
      "table": false,
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    },
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      "title": "Distance sampling data of 16 bird species observed in the Disney Wilderness Preserve in 2018 in Florida, USA",
      "object": "neonDWP",
      "class": [
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      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "neonPredData",
      "title": "Land cover covariates and coordinates at a 1ha resolution across Disney Wilderness Preserve",
      "object": "neonPredData",
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      ],
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        "grass",
        "easting",
        "northing"
      ],
      "rows": 4838,
      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "abund",
      "title": "Function for Fitting Univariate Abundance GLMMs",
      "topics": [
        "abund"
      ]
    },
    {
      "page": "bbsData.rda",
      "title": "Count data for six warbler species in Pennsylvania, USA",
      "topics": [
        "bbsData"
      ]
    },
    {
      "page": "bbsPredData.rda",
      "title": "Covariates and coordinates for prediction of relative warbler abundance in Pennsylvania, USA",
      "topics": [
        "bbsPredData"
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    },
    {
      "page": "dataNMixSim.rda",
      "title": "Simulated repeated count data of 6 species across 225 sites",
      "topics": [
        "dataNMixSim"
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    },
    {
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      "title": "Function for Fitting Single-Species Hierarchical Distance Sampling Models",
      "topics": [
        "DS"
      ]
    },
    {
      "page": "fitted.abund",
      "title": "Extract Model Fitted Values for abund Object",
      "topics": [
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      "page": "fitted.DS",
      "title": "Extract Model Fitted Values for DS Object",
      "topics": [
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    },
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      "title": "Extract Model Fitted Values for lfMsAbund Object",
      "topics": [
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    },
    {
      "page": "fitted.lfMsDS",
      "title": "Extract Model Fitted Values for lfMsDS Object",
      "topics": [
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    },
    {
      "page": "fitted.lfMsNMix",
      "title": "Extract Model Fitted Values for lfMsNMix Object",
      "topics": [
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    },
    {
      "page": "fitted.msAbund",
      "title": "Extract Model Fitted Values for msAbund Object",
      "topics": [
        "fitted.msAbund"
      ]
    },
    {
      "page": "fitted.msDS",
      "title": "Extract Model Fitted Values for msDS Object",
      "topics": [
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    },
    {
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      "title": "Extract Model Fitted Values for msNMix Object",
      "topics": [
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      ]
    },
    {
      "page": "fitted.NMix",
      "title": "Extract Model Fitted Values for NMix Object",
      "topics": [
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      ]
    },
    {
      "page": "fitted.sfMsAbund",
      "title": "Extract Model Fitted Values for sfMsAbund Object",
      "topics": [
        "fitted.sfMsAbund"
      ]
    },
    {
      "page": "fitted.sfMsDS",
      "title": "Extract Model Fitted Values for sfMsDS Object",
      "topics": [
        "fitted.sfMsDS"
      ]
    },
    {
      "page": "fitted.sfMsNMix",
      "title": "Extract Model Fitted Values for sfMsNMix Object",
      "topics": [
        "fitted.sfMsNMix"
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    },
    {
      "page": "fitted.spAbund",
      "title": "Extract Model Fitted Values for spAbund Object",
      "topics": [
        "fitted.spAbund"
      ]
    },
    {
      "page": "fitted.spDS",
      "title": "Extract Model Fitted Values for spDS Object",
      "topics": [
        "fitted.spDS"
      ]
    },
    {
      "page": "fitted.spNMix",
      "title": "Extract Model Fitted Values for spNMix Object",
      "topics": [
        "fitted.spNMix"
      ]
    },
    {
      "page": "fitted.svcAbund",
      "title": "Extract Model Fitted Values for svcAbund Object",
      "topics": [
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      ]
    },
    {
      "page": "fitted.svcMsAbund",
      "title": "Extract Model Fitted Values for svcMsAbund Object",
      "topics": [
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      ]
    },
    {
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      "title": "Count data of 12 foliage gleaning bird species in 2015 in the Hubbard Brook Experimental Forest",
      "topics": [
        "hbefCount2015"
      ]
    },
    {
      "page": "lfMsAbund",
      "title": "Function for Fitting Latent Factor Multivariate Abundance GLMMs",
      "topics": [
        "lfMsAbund"
      ]
    },
    {
      "page": "lfMsDS",
      "title": "Function for Fitting Latent Factor Multi-Species Hierarchical Distance Sampling Models",
      "topics": [
        "lfMsDS"
      ]
    },
    {
      "page": "lfMsNMix",
      "title": "Function for Fitting Latent Factor Multi-species N-mixture Models",
      "topics": [
        "lfMsNMix"
      ]
    },
    {
      "page": "msAbund",
      "title": "Function for Fitting Multivariate Abundance GLMMs",
      "topics": [
        "msAbund"
      ]
    },
    {
      "page": "msDS",
      "title": "Function for Fitting Multi-Species Hierarchical Distance Sampling Models",
      "topics": [
        "msDS"
      ]
    },
    {
      "page": "msNMix",
      "title": "Function for Fitting Multi-species N-mixture Models",
      "topics": [
        "msNMix"
      ]
    },
    {
      "page": "neonDWP.rda",
      "title": "Distance sampling data of 16 bird species observed in the Disney Wilderness Preserve in 2018 in Florida, USA",
      "topics": [
        "neonDWP"
      ]
    },
    {
      "page": "neonPredData.rda",
      "title": "Land cover covariates and coordinates at a 1ha resolution across Disney Wilderness Preserve",
      "topics": [
        "neonPredData"
      ]
    },
    {
      "page": "NMix",
      "title": "Function for Fitting Single-Species N-mixture Models",
      "topics": [
        "NMix"
      ]
    },
    {
      "page": "ppcAbund",
      "title": "Function for performing posterior predictive checks",
      "topics": [
        "ppcAbund"
      ]
    },
    {
      "page": "predict.abund",
      "title": "Function for prediction at new locations for univariate GLMMs",
      "topics": [
        "predict.abund"
      ]
    },
    {
      "page": "predict.DS",
      "title": "Function for prediction at new locations for single-species hierarchical distance sampling models",
      "topics": [
        "predict.DS"
      ]
    },
    {
      "page": "predict.lfMsAbund",
      "title": "Function for prediction at new locations for latent factor multivariate GLMMs",
      "topics": [
        "predict.lfMsAbund"
      ]
    },
    {
      "page": "predict.lfMsDS",
      "title": "Function for prediction at new locations for latent factor multi-species hierarchical distance sampling models",
      "topics": [
        "predict.lfMsDS"
      ]
    },
    {
      "page": "predict.lfMsNMix",
      "title": "Function for prediction at new locations for latent factor multi-species N-mixture models",
      "topics": [
        "predict.lfMsNMix"
      ]
    },
    {
      "page": "predict.msAbund",
      "title": "Function for prediction at new locations for multivariate GLMMs",
      "topics": [
        "predict.msAbund"
      ]
    },
    {
      "page": "predict.msDS",
      "title": "Function for prediction at new locations for multi-species hierarchical distance sampling models",
      "topics": [
        "predict.msDS"
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    },
    {
      "page": "predict.msNMix",
      "title": "Function for prediction at new locations for multi-species N-mixture models",
      "topics": [
        "predict.msNMix"
      ]
    },
    {
      "page": "predict.NMix",
      "title": "Function for prediction at new locations for single-species N-mixture models",
      "topics": [
        "predict.NMix"
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    },
    {
      "page": "predict.sfMsAbund",
      "title": "Function for prediction at new locations for spatial factor multivariate GLMMs",
      "topics": [
        "predict.sfMsAbund"
      ]
    },
    {
      "page": "predict.sfMsDS",
      "title": "Function for prediction at new locations for spatial factor multi-species hierarchical distance sampling models",
      "topics": [
        "predict.sfMsDS"
      ]
    },
    {
      "page": "predict.sfMsNMix",
      "title": "Function for prediction at new locations for spatial factor multi-species N-mixture models",
      "topics": [
        "predict.sfMsNMix"
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    },
    {
      "page": "predict.spAbund",
      "title": "Function for prediction at new locations for univariate spatial GLMMs",
      "topics": [
        "predict.spAbund"
      ]
    },
    {
      "page": "predict.spDS",
      "title": "Function for prediction at new locations for single-species spatially-explicit hierarchical distance sampling models",
      "topics": [
        "predict.spDS"
      ]
    },
    {
      "page": "predict.spNMix",
      "title": "Function for prediction at new locations for single-species spatial N-mixture models",
      "topics": [
        "predict.spNMix"
      ]
    },
    {
      "page": "predict.svcAbund",
      "title": "Function for prediction at new locations for univariate Gaussian spatially-varying coefficient models",
      "topics": [
        "predict.svcAbund"
      ]
    },
    {
      "page": "predict.svcMsAbund",
      "title": "Function for prediction at new locations for multivariate spatially-varying coefficient GLMMs",
      "topics": [
        "predict.svcMsAbund"
      ]
    },
    {
      "page": "sfMsAbund",
      "title": "Function for Fitting Spatial Factor Multivariate Abundance GLMMs",
      "topics": [
        "sfMsAbund"
      ]
    },
    {
      "page": "sfMsDS",
      "title": "Function for Fitting Spatial Factor Multi-Species Hierarchical Distance Sampling Models",
      "topics": [
        "sfMsDS"
      ]
    },
    {
      "page": "sfMsNMix",
      "title": "Function for Fitting Spatial Factor Multi-species N-mixture Models",
      "topics": [
        "sfMsNMix"
      ]
    },
    {
      "page": "simAbund",
      "title": "Simulate Univariate Data for Testing GLMMs",
      "topics": [
        "simAbund"
      ]
    },
    {
      "page": "simDS",
      "title": "Simulate Single-Species Distance Sampling Data",
      "topics": [
        "simDS"
      ]
    },
    {
      "page": "simMsAbund",
      "title": "Simulate Multivariate Data for Testing GLMMs",
      "topics": [
        "simMsAbund"
      ]
    },
    {
      "page": "simMsDS",
      "title": "Simulate Multi-Species Distance Sampling Data",
      "topics": [
        "simMsDS"
      ]
    },
    {
      "page": "simMsNMix",
      "title": "Simulate Multi-Species Repeated Count Data with Imperfect Detection",
      "topics": [
        "simMsNMix"
      ]
    },
    {
      "page": "simNMix",
      "title": "Simulate Single-Species Count Data with Imperfect Detection",
      "topics": [
        "simNMix"
      ]
    },
    {
      "page": "spAbund",
      "title": "Function for Fitting Univariate Spatial Abundance GLMs",
      "topics": [
        "spAbund"
      ]
    },
    {
      "page": "spDS",
      "title": "Function for Fitting Single-Species Spatially-Explicit Hierarchical Distance Sampling Models",
      "topics": [
        "spDS"
      ]
    },
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      "page": "spNMix",
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      "title": "Methods for lfMsAbund Object",
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