{
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  "Package": "prabclus",
  "Title": "Functions for Clustering and Testing of Presence-Absence,\nAbundance and Multilocus Genetic Data",
  "Version": "2.3-5",
  "Date": "2026-01-14",
  "Authors@R": "c(person(\"Christian\", \"Hennig\", role = c(\"aut\", \"cre\"),\nemail = \"christian.hennig@unibo.it\"),\nperson(\"Bernhard\", \"Hausdorf\", role = \"aut\",\nemail = \"Hausdorf@zoologie.uni-hamburg.de\"))",
  "Description": "Distance-based parametric bootstrap tests for clustering\nwith spatial neighborhood information. Some distance measures,\nClustering of presence-absence, abundance and multilocus\ngenetic data for species delimitation, nearest neighbor based\nnoise detection. Genetic distances between communities. Tests\nwhether various distance-based regressions are equal. Try\npackage?prabclus for on overview.",
  "License": "GPL",
  "URL": "https://www.unibo.it/sitoweb/christian.hennig/en/",
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  "Author": "Christian Hennig [aut, cre], Bernhard Hausdorf [aut]",
  "Maintainer": "Christian Hennig <christian.hennig@unibo.it>",
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    "allele2zeroone",
    "alleleconvert",
    "alleledist",
    "alleleinit",
    "allelepaircomp",
    "autoconst",
    "autoreg",
    "build.charmatrix",
    "build.ext.nblist",
    "build.nblist",
    "cfchord",
    "cluspop.nb",
    "communities",
    "communitydist",
    "comp.test",
    "con.comp",
    "con.regmat",
    "coord2dist",
    "crmatrix",
    "dicedist",
    "diploidcomlist",
    "distratio",
    "geco",
    "geo2neighbor",
    "homogen.test",
    "hprabclust",
    "incmatrix",
    "jaccard",
    "kulczynski",
    "lcomponent",
    "lociplots",
    "nastats",
    "nbtest",
    "nn",
    "NNclean",
    "phipt",
    "piecewiselin",
    "plotdistreg",
    "pop.sim",
    "prab.sarestimate",
    "prabclust",
    "prabinit",
    "prabtest",
    "print.alleleobject",
    "print.comprabclust",
    "print.nnclean",
    "print.prab",
    "print.prabclust",
    "print.regdistbetween",
    "print.regeqdist",
    "print.summary.prabtest",
    "qkulczynski",
    "randpop.nb",
    "regdist",
    "regdistbetween",
    "regdistbetweenone",
    "regdistdiff",
    "regdistdiffone",
    "regeqdist",
    "regpop.sar",
    "shared.problist",
    "specgroups",
    "stressvals",
    "summary.prabtest",
    "toprab",
    "unbuild.charmatrix"
  ],
  "_datasets": [
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      "name": "kykladspecreg",
      "title": "Snail presence-absence data from Aegean sea",
      "object": "kykladspecreg",
      "file": "kykladspecreg.rda",
      "class": [
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      "fields": [
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        "V2",
        "V3",
        "V4",
        "V5",
        "V6",
        "V7",
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        "V16",
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        "V19",
        "V20",
        "V21",
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        "V26",
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        "V28",
        "V29",
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        "V31",
        "V32",
        "V33",
        "V34"
      ],
      "rows": 80,
      "table": true,
      "tojson": true
    },
    {
      "name": "nb",
      "title": "Neighborhood list for Aegean islands",
      "object": "nb",
      "file": "nb.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "siskiyou",
      "title": "Herbs of the Siskiyou Mountains",
      "object": "siskiyou",
      "file": "siskiyou.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
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        "V2",
        "V3",
        "V4",
        "V5",
        "V6"
      ],
      "rows": 144,
      "table": true,
      "tojson": true
    },
    {
      "name": "siskiyou.groups",
      "title": "Herbs of the Siskiyou Mountains",
      "object": "siskiyou",
      "file": "siskiyou.rda",
      "class": [
        "numeric"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "siskiyou.nb",
      "title": "Herbs of the Siskiyou Mountains",
      "object": "siskiyou",
      "file": "siskiyou.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "tetragonula",
      "title": "Microsatellite genetic data of Tetragonula bees",
      "object": "tetragonula",
      "file": "tetragonula.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
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        "V2",
        "V3",
        "V4",
        "V5",
        "V6",
        "V7",
        "V8",
        "V9",
        "V10",
        "V11",
        "V12",
        "V13"
      ],
      "rows": 236,
      "table": true,
      "tojson": true
    },
    {
      "name": "tetragonula.coord",
      "title": "Microsatellite genetic data of Tetragonula bees",
      "object": "tetragonula",
      "file": "tetragonula.rda",
      "class": [
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      ],
      "fields": [
        "V1",
        "V2"
      ],
      "rows": 236,
      "table": true,
      "tojson": true
    },
    {
      "name": "veronica",
      "title": "Genetic AFLP data of Veronica plants",
      "object": "veronica",
      "file": "veronica.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [],
      "rows": 207,
      "table": true,
      "tojson": true
    },
    {
      "name": "veronica.coord",
      "title": "Genetic AFLP data of Veronica plants",
      "object": "veronica",
      "file": "veronica.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "V1",
        "V2"
      ],
      "rows": 207,
      "table": true,
      "tojson": true
    },
    {
      "name": "waterdist",
      "title": "Overwater distances between islands in the Aegean sea",
      "object": "waterdist",
      "file": "waterdist.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "V1",
        "V2",
        "V3",
        "V4",
        "V5",
        "V6",
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        "V25",
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        "V31",
        "V32",
        "V33",
        "V34"
      ],
      "rows": 34,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "prabclus-package",
      "title": "prabclus package overview",
      "topics": [
        "prabclus-package"
      ]
    },
    {
      "page": "abundtest",
      "title": "Parametric bootstrap test for clustering in abundance matrices",
      "topics": [
        "abundtest"
      ]
    },
    {
      "page": "allele2zeroone",
      "title": "Converts alleleobject into binary matrix",
      "topics": [
        "allele2zeroone"
      ]
    },
    {
      "page": "alleleconvert",
      "title": "Format conversion for codominant marker data",
      "topics": [
        "alleleconvert"
      ]
    },
    {
      "page": "alleledist",
      "title": "Shared allele distance for diploid loci",
      "topics": [
        "alleledist"
      ]
    },
    {
      "page": "alleleinit",
      "title": "Diploid loci matrix initialization",
      "topics": [
        "alleleinit",
        "alleleobject",
        "print.alleleobject"
      ]
    },
    {
      "page": "allelepaircomp",
      "title": "Internal: compares two pairs of alleles",
      "topics": [
        "allelepaircomp"
      ]
    },
    {
      "page": "autoconst",
      "title": "Spatial autocorrelation parameter estimation",
      "topics": [
        "autoconst",
        "autoreg"
      ]
    },
    {
      "page": "build.charmatrix",
      "title": "Internal: create character matrix out of allele list",
      "topics": [
        "build.charmatrix"
      ]
    },
    {
      "page": "build.ext.nblist",
      "title": "Internal: generates neighborhood list for diploid loci",
      "topics": [
        "build.ext.nblist"
      ]
    },
    {
      "page": "build.nblist",
      "title": "Generate spatial weights from prabclus neighborhood list",
      "topics": [
        "build.nblist"
      ]
    },
    {
      "page": "cluspop.nb",
      "title": "Simulation of presence-absence matrices (clustered)",
      "topics": [
        "cluspop.nb"
      ]
    },
    {
      "page": "communities",
      "title": "Construct communities from individuals",
      "topics": [
        "communities"
      ]
    },
    {
      "page": "communitydist",
      "title": "Distances between communities",
      "topics": [
        "communitydist"
      ]
    },
    {
      "page": "comp.test",
      "title": "Compare species clustering and species groups",
      "topics": [
        "comp.test"
      ]
    },
    {
      "page": "concomp",
      "title": "Connectivity components of an undirected graph",
      "topics": [
        "con.comp"
      ]
    },
    {
      "page": "conregmat",
      "title": "Connected regions per species",
      "topics": [
        "con.regmat"
      ]
    },
    {
      "page": "coord2dist",
      "title": "Geographical coordinates to distances",
      "topics": [
        "coord2dist"
      ]
    },
    {
      "page": "crmatrix",
      "title": "Region-wise cluster membership",
      "topics": [
        "crmatrix"
      ]
    },
    {
      "page": "dicedist",
      "title": "Dice distance matrix",
      "topics": [
        "dicedist"
      ]
    },
    {
      "page": "distratio",
      "title": "Distance ratio test statistics for distance based clustering",
      "topics": [
        "distratio"
      ]
    },
    {
      "page": "geco",
      "title": "geco distance matrix",
      "topics": [
        "geco"
      ]
    },
    {
      "page": "geo2neighbor",
      "title": "Neighborhood list from geographical distance",
      "topics": [
        "geo2neighbor"
      ]
    },
    {
      "page": "homogen.test",
      "title": "Classical distance-based test for homogeneity against clustering",
      "topics": [
        "homogen.test"
      ]
    },
    {
      "page": "hprabclust",
      "title": "Clustering of species ranges from presence-absence matrices (hierarchical methods)",
      "topics": [
        "hprabclust",
        "print.comprabclust"
      ]
    },
    {
      "page": "incmatrix",
      "title": "Nestedness matrix",
      "topics": [
        "incmatrix"
      ]
    },
    {
      "page": "jaccard",
      "title": "Jaccard distance matrix",
      "topics": [
        "jaccard"
      ]
    },
    {
      "page": "kulczynski",
      "title": "Kulczynski distance matrix",
      "topics": [
        "kulczynski"
      ]
    },
    {
      "page": "kykladspecreg",
      "title": "Snail presence-absence data from Aegean sea",
      "topics": [
        "kykladspecreg"
      ]
    },
    {
      "page": "lcomponent",
      "title": "Largest connectivity component",
      "topics": [
        "lcomponent"
      ]
    },
    {
      "page": "lociplots",
      "title": "Visualises clusters of markers vs. species",
      "topics": [
        "lociplots"
      ]
    },
    {
      "page": "nastats",
      "title": "Missing values statistics for matrix",
      "topics": [
        "nastats"
      ]
    },
    {
      "page": "nb",
      "title": "Neighborhood list for Aegean islands",
      "topics": [
        "nb"
      ]
    },
    {
      "page": "nbtest",
      "title": "Test of neighborhood list",
      "topics": [
        "nbtest"
      ]
    },
    {
      "page": "nn",
      "title": "Mean distance to kth nearest neighbor",
      "topics": [
        "nn"
      ]
    },
    {
      "page": "NNclean",
      "title": "Nearest neighbor based clutter/noise detection",
      "topics": [
        "NNclean",
        "print.nnclean"
      ]
    },
    {
      "page": "phipt",
      "title": "Distances between communities, auxiliary functions",
      "topics": [
        "cfchord",
        "diploidcomlist",
        "phipt",
        "shared.problist"
      ]
    },
    {
      "page": "piecewiselin",
      "title": "Piecewise linear transformation for distance matrices",
      "topics": [
        "piecewiselin"
      ]
    },
    {
      "page": "plotdistreg",
      "title": "Plots for within-groups and between-groups distance regression",
      "topics": [
        "plotdistreg"
      ]
    },
    {
      "page": "pop.sim",
      "title": "p-value simulation for presence-absence matrices clustering test",
      "topics": [
        "pop.sim"
      ]
    },
    {
      "page": "prab.sarestimate",
      "title": "Estimates SAR model from log-abundance matrix of prab-object.",
      "topics": [
        "prab.sarestimate"
      ]
    },
    {
      "page": "prabclust",
      "title": "Clustering for biotic elements or for species delimitation (mixture method)",
      "topics": [
        "prabclust",
        "print.prabclust"
      ]
    },
    {
      "page": "prabinit",
      "title": "Presence-absence/abundance matrix initialization",
      "topics": [
        "prab",
        "prabinit",
        "print.prab"
      ]
    },
    {
      "page": "prabtest",
      "title": "Parametric bootstrap test for clustering in presence-absence matrices",
      "topics": [
        "prabtest",
        "print.summary.prabtest",
        "summary.prabtest"
      ]
    },
    {
      "page": "qkulczynski",
      "title": "Quantitative Kulczynski distance matrix",
      "topics": [
        "qkulczynski"
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