{
  "_id": "6a1693edacfb0bcc41d799ee",
  "Package": "recluster",
  "Type": "Package",
  "Title": "Ordination Methods for the Analysis of Beta-Diversity Indices",
  "Version": "3.4",
  "Date": "2026-01-25",
  "Authors@R": "c(\nperson(given = \"Leonardo\", family = \"Dapporto\",\nrole = c(\"aut\", \"cre\"),\nemail = \"leondap@gmail.com\"),\nperson(given = \"Matteo\", family = \"Ramazzotti\",\nrole = \"aut\"),\nperson(given = \"Simone\", family = \"Fattorini\",\nrole = \"aut\"),\nperson(given = \"Roger\", family = \"Vila\",\nrole = \"aut\"),\nperson(given = \"Gerard\", family = \"Talavera\",\nrole = \"aut\"),\nperson(given = c(\"Roger\", \"H.L.\"), family = \"Dennis\",\nrole = \"aut\")\n)",
  "Maintainer": "Leonardo Dapporto <leondap@gmail.com>",
  "Description": "The analysis of different aspects of biodiversity requires\nspecific algorithms. For example, in regionalisation analyses,\nthe high frequency of ties and zero values in dissimilarity\nmatrices produced by Beta-diversity turnover produces\nhierarchical cluster dendrograms whose topology and bootstrap\nsupports are affected by the order of rows in the original\nmatrix. Moreover, visualisation of biogeographical\nregionalisation can be facilitated by a combination of\nhierarchical clustering and multi-dimensional scaling. The\nrecluster package provides robust techniques to visualise and\nanalyse patterns of biodiversity and to improve occurrence data\nfor cryptic taxa.",
  "License": "GPL (>= 2.0)",
  "LazyLoad": "yes",
  "URL": "https://github.com/leondap/recluster",
  "NeedsCompilation": "no",
  "Encoding": "UTF-8",
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  "Repository": "https://leondap.r-universe.dev",
  "Date/Publication": "2026-01-27 13:37:09 UTC",
  "RemoteUrl": "https://github.com/leondap/recluster",
  "RemoteRef": "HEAD",
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  "Packaged": {
    "Date": "2026-05-27 06:44:54 UTC",
    "User": "root"
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  "Author": "Leonardo Dapporto [aut, cre],\nMatteo Ramazzotti [aut],\nSimone Fattorini [aut],\nRoger Vila [aut],\nGerard Talavera [aut],\nRoger H.L. Dennis [aut]",
  "MD5sum": "e2adddf0408941fd40106330a16fe724",
  "_user": "leondap",
  "_type": "src",
  "_file": "recluster_3.4.tar.gz",
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  "_created": "2026-05-27T06:44:54.000Z",
  "_published": "2026-05-27T06:49:17.094Z",
  "_distro": "noble",
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    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.json",
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    "extra/readme.md",
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  "_homeurl": "https://github.com/leondap/recluster",
  "_realowner": "leondap",
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  "_releases": [
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      "date": "2013-03-01"
    },
    {
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      "date": "2013-03-27"
    },
    {
      "version": "1.9",
      "date": "2013-03-29"
    },
    {
      "version": "2.1",
      "date": "2013-05-22"
    },
    {
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      "date": "2013-07-31"
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    {
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      "date": "2014-12-17"
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  "_exports": [
    "biodecrypt",
    "biodecrypt.cross",
    "biodecrypt.optimise",
    "biodecrypt.plot",
    "biodecrypt.view",
    "biodecrypt.wrap",
    "recluster.boot",
    "recluster.col",
    "recluster.cons",
    "recluster.dist",
    "recluster.expl",
    "recluster.expl.diss",
    "recluster.fst",
    "recluster.fst.pair",
    "recluster.group.col",
    "recluster.hist",
    "recluster.identify.nodes",
    "recluster.line",
    "recluster.multi",
    "recluster.node.strength",
    "recluster.plot",
    "recluster.plot.col",
    "recluster.plot.matrix",
    "recluster.plot.pie",
    "recluster.plot.sites.col",
    "recluster.procrustes",
    "recluster.region",
    "recluster.rotate",
    "recluster.test.dist"
  ],
  "_datasets": [
    {
      "name": "dataisl",
      "title": "West Mediterranean island butterflies provided with the package recluster",
      "object": "dataisl",
      "file": "dataisl.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "Pyrgus_malvoides",
        "Pyrgus_armoricanus",
        "Spialia_sertorius",
        "Spialia_orbifer",
        "Spialia_therapne",
        "Muschampia_proto",
        "Carcharodus_alceae",
        "Carcharodus_baeticus",
        "Carcharodus_flocciferus",
        "Erynnis_tages",
        "Thymelicus_acteon",
        "Thymelicus_lineola",
        "Thymelicus_sylvestris",
        "Hesperia_comma",
        "Ochlodes_sylvanus",
        "Gegenes_nostrodamus",
        "Gegenes_pumilio",
        "Papilio_machaon",
        "Papilio_hospiton",
        "Papilio_alexanor",
        "Iphiclides_podalirius",
        "Zerynthia_cassandra",
        "Parnassius_apollo",
        "Parnassius_mnemosyne",
        "Aporia_crataegi",
        "Pieris_brassicae",
        "Pieris_rapae",
        "Pieris_mannii",
        "Pieris_napi_",
        "Pontia_daplidice",
        "Pontia_edusa",
        "Euchloe_ausonia",
        "Euchloe_insularis",
        "Anthocharis_cardamines",
        "Anthocharis_damone",
        "Colias_crocea",
        "Gonepteryx_cleopatra",
        "Gonepteryx_rhamni",
        "Leptidea_sinapis",
        "Neozephyrus_quercus",
        "Satyrium_ilicis",
        "Satyrium_w.album",
        "Callophrys_rubi",
        "Lycaena_phlaeas",
        "Lycaena_tityrus",
        "Lycaena_alciphron",
        "Lampides_boeticus",
        "Leptotes_pirithous",
        "Zizeeria_karsandra",
        "Cupido_minimus",
        "Celastrina_argiolus",
        "Glaucopsyche_alexis",
        "Phengaris_arion",
        "Pseudophilotes_baton",
        "Pseudophilotes_barbagiae",
        "Plebejus_argus",
        "Plebejus_bellieri",
        "Eumedonia_eumedon",
        "Aricia_agestis",
        "Aricia_cramera",
        "Aricia_artaxerxes",
        "Cyaniris_semiargus",
        "Polyommatus_amandus",
        "Polyommatus_celina",
        "Polyommatus_icarus",
        "Polyommatus_daphnis",
        "Lysandra_coridon",
        "Lysandra_bellargus",
        "Libythea_celtis",
        "Danaus_chrysippus",
        "Charaxes_jasius",
        "Limenitis_reducta",
        "Nymphalis_polychloros",
        "Inachis_io",
        "Aglais_urticae",
        "Aglais_ichnusae",
        "Vanessa_atalanta",
        "Vanessa_cardui",
        "Polygonia_c.album",
        "Polygonia_egea",
        "Issoria_lathonia",
        "Argynnis_pandora",
        "Argynnis_paphia",
        "Argynnis_elisa",
        "Argynnis_aglaja",
        "Argynnis_niobe",
        "Argynnis_adippe",
        "Brenthis_daphne",
        "Boloria_euphrosyne",
        "Melitaea_cinxia",
        "Melitaea_phoebe",
        "Melitaea_aetherie",
        "Melitaea_didyma",
        "Melitaea_celadussa",
        "Melanargia_galathea",
        "Melanargia_russiae",
        "Melanargia_pherusa",
        "Melanargia_arge",
        "Hipparchia_fagi",
        "Hipparchia_hermione",
        "Hipparchia_aristaeus",
        "Hipparchia_blachieri",
        "Hipparchia_neapolitana",
        "Hipparchia_leighebi",
        "Hipparchia_sbordonii",
        "Hipparchia_semele",
        "Hipparchia_neomiris",
        "Hipparchia_statilinus",
        "Hipparchia_fidia",
        "Chazara_briseis",
        "Brintesia_circe",
        "Maniola_jurtina",
        "Maniola_nurag",
        "Hyponephele_lycaon",
        "Hyponephele_lupina",
        "Pyronia_cecilia",
        "Pyronia_tithonus",
        "Coenonympha_pamphilus",
        "Coenonympha_lyllus",
        "Coenonympha_corinna",
        "Pararge_aegeria",
        "Lasiommata_megera",
        "Lasiommata_paramegaera",
        "Lasiommata_maera"
      ],
      "rows": 31,
      "table": true,
      "tojson": true
    },
    {
      "name": "datamod",
      "title": "Virtual island faunas provided with the package recluster",
      "object": "datamod",
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      ],
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    },
    {
      "name": "multiboot",
      "title": "A multiboot result obtained with the dataisl dataset.",
      "object": "multiboot",
      "file": "multiboot.rda",
      "class": [
        "data.frame"
      ],
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        "V2",
        "V3",
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        "V10",
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        "V27",
        "V28",
        "V29",
        "V30"
      ],
      "rows": 29,
      "table": true,
      "tojson": true
    },
    {
      "name": "treebut",
      "title": "Phylogenetic tree for the butterfly species included in dataisl dataset",
      "object": "treebut",
      "file": "treebut.rda",
      "class": [
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      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "treemod",
      "title": "Hypothetical phylogenetic tree for the virtual island faunas provided with the package recluster",
      "object": "treemod",
      "file": "treemod.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "biodecrypt",
      "title": "An algorithm to attribute unidentified occurrence data based on a subset of identified records",
      "topics": [
        "biodecrypt"
      ]
    },
    {
      "page": "biodecrypt.cross",
      "title": "Perform a cross validation analysis to test the attribution of biodecrypt on attributed records",
      "topics": [
        "biodecrypt.cross"
      ]
    },
    {
      "page": "biodecrypt.optimise",
      "title": "Comparing the values obtained by biodecrypt.wrap, it optimises the combination of alpha, buffer and ratio values to be used with biodecrypt function.",
      "topics": [
        "biodecrypt.optimise"
      ]
    },
    {
      "page": "biodecrypt.plot",
      "title": "Plotting biodecrypt and biodecrypt.cross results.",
      "topics": [
        "biodecrypt.plot"
      ]
    },
    {
      "page": "biodecrypt.view",
      "title": "A function to view the hulls and manually adjust alpha values before applying biodecrypt",
      "topics": [
        "biodecrypt.view"
      ]
    },
    {
      "page": "biodecrypt.wrap",
      "title": "Wraps the biodecrypt.cross analysis to compare the performance of biodecrypt among different parameters.",
      "topics": [
        "biodecrypt.wrap"
      ]
    },
    {
      "page": "dataisl",
      "title": "West Mediterranean island butterflies provided with the package recluster",
      "topics": [
        "dataisl"
      ]
    },
    {
      "page": "datamod",
      "title": "Virtual island faunas provided with the package recluster",
      "topics": [
        "datamod"
      ]
    },
    {
      "page": "multiboot",
      "title": "A multiboot result obtained with the dataisl dataset.",
      "topics": [
        "multiboot"
      ]
    },
    {
      "page": "recluster",
      "title": "Ordination methods for biodiversity patterns.",
      "topics": [
        "reCluster",
        "recluster"
      ]
    },
    {
      "page": "recluster.boot",
      "title": "Bootstrap nodes of consensus trees",
      "topics": [
        "recluster.boot"
      ]
    },
    {
      "page": "recluster.col",
      "title": "Projecting a two dimensional plot in RGB space",
      "topics": [
        "recluster.col"
      ]
    },
    {
      "page": "recluster.cons",
      "title": "Consensus tree among re-sampled trees",
      "topics": [
        "recluster.cons"
      ]
    },
    {
      "page": "recluster.dist",
      "title": "Compute a dissimilarity matrix using a battery of beta-diversity indices",
      "topics": [
        "recluster.dist"
      ]
    },
    {
      "page": "recluster.expl",
      "title": "Computes the dissimilarity contained in a distance matrix which is explained by a clustering solution.",
      "topics": [
        "recluster.expl"
      ]
    },
    {
      "page": "recluster.expl.diss",
      "title": "Cuts a phylogenetic tree and provides cluster membership of areas for custom of all possible clustering solutions and their explained dissimilarity.",
      "topics": [
        "recluster.expl.diss"
      ]
    },
    {
      "page": "recluster.fst",
      "title": "Compute some indexes of genetic differentiation",
      "topics": [
        "recluster.fst"
      ]
    },
    {
      "page": "recluster.fst.pair",
      "title": "Compute pairwise indexes of genetic differentiation among populations",
      "topics": [
        "recluster.fst.pair"
      ]
    },
    {
      "page": "recluster.group.col",
      "title": "Computes mean coordinate values and RGB colours.",
      "topics": [
        "recluster.group.col"
      ]
    },
    {
      "page": "recluster.hist",
      "title": "Histogram of dissimilarity with tied and zero values",
      "topics": [
        "recluster.hist"
      ]
    },
    {
      "page": "recluster.identify.nodes",
      "title": "Evaluating solutions in multiscale bootstrap",
      "topics": [
        "recluster.identify.nodes"
      ]
    },
    {
      "page": "recluster.line",
      "title": "Identifies a line in a configuration and computes its intercept and angular coefficient",
      "topics": [
        "recluster.line"
      ]
    },
    {
      "page": "recluster.multi",
      "title": "Multiscale bootstrap based on a consensus tree",
      "topics": [
        "recluster.multi"
      ]
    },
    {
      "page": "recluster.node.strength",
      "title": "Evaluating order row bias in a cluster",
      "topics": [
        "recluster.node.strength"
      ]
    },
    {
      "page": "recluster.plot",
      "title": "A plotter for recluster bootstrapped objects",
      "topics": [
        "recluster.plot"
      ]
    },
    {
      "page": "recluster.plot.col",
      "title": "Plotting data in RGB space",
      "topics": [
        "recluster.plot.col"
      ]
    },
    {
      "page": "recluster.plot.matrix",
      "title": "Plot the values of the cells of a matrix in grey scale",
      "topics": [
        "recluster.plot.matrix"
      ]
    },
    {
      "page": "recluster.plot.pie",
      "title": "Plotting pies with RGB colours on a custom coordinate space",
      "topics": [
        "recluster.plot.pie"
      ]
    },
    {
      "page": "recluster.plot.sites.col",
      "title": "Plotting RGB dots on a custom coordinate space",
      "topics": [
        "recluster.plot.sites.col"
      ]
    },
    {
      "page": "recluster.procrustes",
      "title": "Computes a procrustes analysis between two matrices even if only a subset of cases are shared.",
      "topics": [
        "recluster.procrustes"
      ]
    },
    {
      "page": "recluster.region",
      "title": "A clustering method based on continuous consensus among clustering solutions after resampling row order.",
      "topics": [
        "recluster.region"
      ]
    },
    {
      "page": "recluster.rotate",
      "title": "Rotates a bidimensional configuration according to a line",
      "topics": [
        "recluster.rotate"
      ]
    },
    {
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