{
  "_id": "6a1688faacfb0bcc41d76205",
  "Package": "geohabnet",
  "Title": "Geographical Risk Analysis Based on Habitat Connectivity",
  "Version": "2.3",
  "Date": "2026-05-25",
  "Authors@R": "c(\nperson(\"Krishna\", \"Keshav\", , \"krishnakeshav.pes@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Aaron\", \"Plex\", , \"plexaaron@ufl.edu\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-7317-3090\")),\nperson(\"Garrett\", \"Lab\", , \"karengarrett@ufl.edu\", role = \"ctb\",\ncomment = \"https://garrettlab.com\"),\nperson(\"Karen\", \"Garrett\", , \"karengarrett@ufl.edu\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-6578-1616\")),\nperson(\"University of Florida\", role = c(\"cph\", \"fnd\"),\ncomment = \"https://www.ufl.edu\")\n)",
  "Description": "The 'geohabnet' package is designed to perform a\ngeographically or spatially explicit risk analysis of habitat\nconnectivity. Xing et al (2021) <doi:10.1093/biosci/biaa067>\nproposed the concept of cropland connectivity as a risk factor\nfor plant pathogen or pest invasions. As the functions in\n'geohabnet' were initially developed thinking on cropland\nconnectivity, users are recommended to first be familiar with\nthe concept by looking at the Xing et al paper. In a nutshell,\na habitat connectivity analysis combines information from maps\nof host density, estimates the relative likelihood of pathogen\nmovement between habitat locations in the area of interest, and\napplies network analysis to calculate the connectivity of\nhabitat locations. The functions of 'geohabnet' are built to\nconduct a habitat connectivity analysis relying on geographic\nparameters (spatial resolution and spatial extent), dispersal\nparameters (in two commonly used dispersal kernels: inverse\npower law and negative exponential models), and network\nparameters (link weight thresholds and network metrics). The\nfunctionality and main extensions provided by the functions in\n'geohabnet' to habitat connectivity analysis are a) Capability\nto easily calculate the connectivity of locations in a\nlandscape using a single function, such as\nsensitivity_analysis() or msean(). b) As backbone datasets, the\n'geohabnet' package supports the use of two publicly available\nglobal datasets to calculate cropland density. The backbone\ndatasets in the 'geohabnet' package include crop distribution\nmaps from Monfreda, C., N. Ramankutty, and J. A. Foley (2008)\n<doi:10.1029/2007gb002947> \"Farming the planet: 2. Geographic\ndistribution of crop areas, yields, physiological types, and\nnet primary production in the year 2000, Global Biogeochem.\nCycles, 22, GB1022\" and International Food Policy Research\nInstitute (2019) <doi:10.7910/DVN/PRFF8V> \"Global\nSpatially-Disaggregated Crop Production Statistics Data for\n2010 Version 2.0, Harvard Dataverse, V4\". Users can also\nprovide any other geographic dataset that represents host\ndensity. c) Because the 'geohabnet' package allows R users to\nprovide maps of host density (as originally in Xing et al\n(2021)), host landscape density (representing the geographic\ndistribution of either crops or wild species), or habitat\ndistribution (such as host landscape density adjusted by\nclimate suitability) as inputs, we propose the term habitat\nconnectivity. d) The 'geohabnet' package allows R users to\ncustomize parameter values in the habitat connectivity\nanalysis, facilitating context-specific (pathogen- or\npest-specific) analyses. e) The 'geohabnet' package allows\nusers to automatically visualize maps of the habitat\nconnectivity of locations resulting from a sensitivity analysis\nacross all customized parameter combinations. The primary\nfunctions are msean() and sensitivity analysis(). Most\nfunctions in 'geohabnet' provide three main outcomes: i) A map\nof mean habitat connectivity across parameters selected by the\nuser, ii) a map of variance of habitat connectivity across the\nselected parameters, and iii) a map of the difference between\nthe ranks of habitat connectivity and habitat density. Each\nfunction can be used to generate these maps as 'final'\noutcomes. Each function can also provide intermediate outcomes,\nsuch as the adjacency matrices built to perform the analysis,\nwhich can be used in other network analysis. Refer to article\nat\n<https://garrettlab.github.io/HabitatConnectivity/articles/analysis.html>\nto see examples of each function and how to access each of\nthese outcome types. To change parameter values, the file\ncalled 'parameters.yaml' stores the parameters and their\nvalues, can be accessed using 'get_parameters()' and set new\nparameter values with 'set_parameters()'. Users can modify up\nto ten parameters.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.3.2",
  "URL": "https://garrettlab.github.io/HabitatConnectivity/,\nhttps://CRAN.R-project.org/package=geohabnet/,\nhttps://github.com/GarrettLab/HabitatConnectivity/tree/main/geohabnet/,\nhttps://www.garrettlab.com/",
  "BugReports": "https://github.com/GarrettLab/HabitatConnectivity/issues",
  "Config/pak/sysreqs": "libabsl-dev cmake libgdal-dev gdal-bin libgeos-dev\nlibglpk-dev libicu-dev libxml2-dev libssl-dev libproj-dev\nlibsqlite3-dev libudunits2-dev",
  "Repository": "https://garrettlab.r-universe.dev",
  "Date/Publication": "2026-05-27 03:24:47 UTC",
  "RemoteUrl": "https://github.com/garrettlab/habitatconnectivity",
  "RemoteRef": "HEAD",
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  "Packaged": {
    "Date": "2026-05-27 05:59:12 UTC",
    "User": "root"
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  "Author": "Krishna Keshav [aut, cre],\nAaron Plex [aut] (ORCID: <https://orcid.org/0000-0001-7317-3090>),\nGarrett Lab [ctb] (https://garrettlab.com),\nKaren Garrett [aut] (ORCID: <https://orcid.org/0000-0002-6578-1616>),\nUniversity of Florida [cph, fnd] (https://www.ufl.edu)",
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    "nn_sum",
    "node_strength",
    "pagerank",
    "reset_params",
    "reso",
    "risk_indices",
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    "sa_onrasters",
    "scales",
    "sean",
    "sensitivity_analysis",
    "set_global_scales",
    "set_parameters",
    "setmaps",
    "setprops",
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    "supported_metrics"
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    {
      "page": "dot-indices",
      "title": "Internal function to extract risk indices from a list of habitat rasters.",
      "topics": [
        ".indices"
      ]
    },
    {
      "page": "connectivity",
      "title": "Calculate and plot maps of habitat connectivity",
      "topics": [
        "connectivity"
      ]
    },
    {
      "page": "dist_methods",
      "title": "Distance methods supported",
      "topics": [
        "dist_methods"
      ]
    },
    {
      "page": "GeoModel-class",
      "title": "GeoModel class",
      "topics": [
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        "GeoModel-class"
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    },
    {
      "page": "GeoNetwork-class",
      "title": "GeoNetwork",
      "topics": [
        "GeoNetwork-class",
        "habitat_density<-,GeoNetwork-method"
      ]
    },
    {
      "page": "GeoRasters-class",
      "title": "GeoRaster class",
      "topics": [
        ".rast_ro",
        "GeoRasters-class"
      ]
    },
    {
      "page": "geoscale_param",
      "title": "Get geographical scales from the parameters",
      "topics": [
        "geoscale_param"
      ]
    },
    {
      "page": "get_parameters",
      "title": "Get Parameters",
      "topics": [
        "get_parameters"
      ]
    },
    {
      "page": "get_rasters",
      "title": "Get rasters object from parameters See host object in 'get_parameters()' or 'load_parameters()'.",
      "topics": [
        "get_rasters"
      ]
    },
    {
      "page": "global_scales",
      "title": "Global geographical extent",
      "topics": [
        "global_scales"
      ]
    },
    {
      "page": "GlobalRast-class",
      "title": "GlobalRast class",
      "topics": [
        ".grast_ro",
        "GlobalRast-class"
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    },
    {
      "page": "Gmap-class",
      "title": "Gmap class",
      "topics": [
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        "setmaps"
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    },
    {
      "page": "gplot",
      "title": "Plot a Raster* object",
      "topics": [
        "gplot"
      ]
    },
    {
      "page": "habitat_density-set",
      "title": "Set the habitat density.",
      "topics": [
        "habitat_density<-"
      ]
    },
    {
      "page": "hci_diff",
      "title": "Calculate difference map",
      "topics": [
        "hci_diff"
      ]
    },
    {
      "page": "hci_mean",
      "title": "Calculate mean of habitat connectivity in a region",
      "topics": [
        "hci_mean"
      ]
    },
    {
      "page": "hci_variance",
      "title": "Calculate variance of habitat connectivity in a region",
      "topics": [
        "hci_variance"
      ]
    },
    {
      "page": "Dispersal-kernels",
      "title": "Dispersal kernels",
      "topics": [
        "inv_powerlaw",
        "neg_expo"
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    },
    {
      "page": "load_parameters",
      "title": "Load Parameters from YAML File",
      "topics": [
        "load_parameters"
      ]
    },
    {
      "page": "ndplot",
      "title": "Network density plot",
      "topics": [
        "ndplot"
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    },
    {
      "page": "ndplot-GeoNetwork-method",
      "title": "Network density",
      "topics": [
        "ndplot,GeoNetwork-method"
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    },
    {
      "page": "nn_sum",
      "title": "Calculation on network metrics a.k.a centralities.",
      "concept": [
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        "degree",
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        "nn_sum",
        "node_strength",
        "pagerank"
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      "page": "reset_params",
      "title": "Reset parameters.yaml",
      "topics": [
        "reset_params"
      ]
    },
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      "page": "reso",
      "title": "Get resolution value",
      "topics": [
        "reso"
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      "page": "risk_indices",
      "title": "Get risk indices",
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        "risk_indices"
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        "RiskMap-class"
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      "title": "Run sensitivity analysis",
      "topics": [
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        "sa_onrasters"
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    },
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      "title": "Sensitivity analysis across maps of habitat connectivity",
      "topics": [
        "msean",
        "sean"
      ]
    },
    {
      "page": "sensitivity_analysis",
      "title": "Sensitivity analysis for habitat connectivity",
      "topics": [
        "sensitivity_analysis"
      ]
    },
    {
      "page": "set_global_scales",
      "title": "Set global geographical extent",
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    },
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      "page": "setprops",
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      "topics": [
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      ]
    },
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      "title": "Set properties of the GeoModel object.",
      "topics": [
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      ]
    },
    {
      "page": "supported_metrics",
      "title": "Returns metrics currently supported in the analysis.",
      "concept": [
        "metrics"
      ],
      "topics": [
        "supported_metrics"
      ]
    }
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