{
  "_id": "6a101675acfb0bcc41c84645",
  "Package": "vegclust",
  "Type": "Package",
  "Title": "Fuzzy Clustering of Vegetation Data",
  "Version": "2.0.3",
  "Date": "2025-05-19",
  "Authors@R": "c(\nperson('Miquel', 'De Cáceres', role=c('aut','cre'),\nemail='miquelcaceres@gmail.com'))",
  "Description": "A set of functions to: (1) perform fuzzy clustering of\nvegetation data (De Caceres et al, 2010)\n<doi:10.1111/j.1654-1103.2010.01211.x>; (2) to assess\necological community similarity on the basis of structure and\ncomposition (De Caceres et al, 2013)\n<doi:10.1111/2041-210X.12116>.",
  "License": "GPL (>= 2)",
  "URL": "https://emf-creaf.github.io/vegclust/",
  "BugReports": "https://github.com/emf-creaf/vegclust/issues",
  "LazyLoad": "yes",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "VignetteBuilder": "utils, knitr",
  "Config/testthat/edition": "3",
  "Repository": "https://emf-creaf.r-universe.dev",
  "Date/Publication": "2025-05-19 16:19:11 UTC",
  "RemoteUrl": "https://github.com/emf-creaf/vegclust",
  "RemoteRef": "HEAD",
  "RemoteSha": "59a4b4d59cd4217966e5c0e60545b584077b9497",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-14 07:06:10 UTC",
    "User": "root"
  },
  "Author": "Miquel De Cáceres [aut, cre]",
  "Maintainer": "Miquel De Cáceres <miquelcaceres@gmail.com>",
  "MD5sum": "496ea7a8cfa369e73d727c297e4e1691",
  "_user": "emf-creaf",
  "_type": "src",
  "_file": "vegclust_2.0.3.tar.gz",
  "_fileid": "9c001b12ab3a167780523c0eece5b9ea2474f25e935abb4b4a3f78195e69271a",
  "_filesize": 1214653,
  "_sha256": "9c001b12ab3a167780523c0eece5b9ea2474f25e935abb4b4a3f78195e69271a",
  "_created": "2026-05-14T07:06:10.000Z",
  "_published": "2026-05-22T08:40:21.836Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 77345505286,
      "time": 146,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6989107141"
    },
    {
      "job": 77345504979,
      "time": 143,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6989108265"
    },
    {
      "job": 77345505224,
      "time": 88,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7010889989"
    },
    {
      "job": 77345505045,
      "time": 132,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6989103447"
    },
    {
      "job": 77345504752,
      "time": 199,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6989067143"
    },
    {
      "job": 77345504640,
      "time": 95,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7156361717"
    },
    {
      "job": 77345505416,
      "time": 120,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "6989100806"
    },
    {
      "job": 77345505530,
      "time": 92,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "6989093696"
    },
    {
      "job": 77345505419,
      "time": 110,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "6989099177"
    }
  ],
  "_buildurl": "https://github.com/r-universe/emf-creaf/actions/runs/25846786849",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/emf-creaf/vegclust",
  "_commit": {
    "id": "59a4b4d59cd4217966e5c0e60545b584077b9497",
    "author": "Miquel De Cáceres <miquelcaceres@gmail.com>",
    "committer": "Miquel De Cáceres <miquelcaceres@gmail.com>",
    "message": "update bibentry\n",
    "time": 1747671551
  },
  "_maintainer": {
    "name": "Miquel De Cáceres",
    "email": "miquelcaceres@gmail.com",
    "login": "miquelcaceres",
    "uuid": 25384629
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 3.4.0",
      "role": "Depends"
    },
    {
      "package": "vegan",
      "role": "Imports"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "emf-creaf",
  "_selfowned": true,
  "_usedby": 7,
  "_updates": [
    {
      "week": "2025-20",
      "n": 1
    },
    {
      "week": "2025-21",
      "n": 12
    }
  ],
  "_tags": [
    {
      "name": "v.2.0.3",
      "date": "2025-05-19"
    }
  ],
  "_stars": 2,
  "_contributors": [
    {
      "user": "miquelcaceres",
      "count": 151,
      "uuid": 25384629
    },
    {
      "user": "sturboisa",
      "count": 4,
      "uuid": 64250016
    }
  ],
  "_userbio": {
    "uuid": 80052794,
    "type": "organization",
    "name": "Ecosystem Modelling Facility (CREAF)"
  },
  "_downloads": {
    "count": 1316,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/vegclust"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/emf-creaf/vegclust",
  "_pkgdown": "https://emf-creaf.github.io/vegclust/",
  "_searchresults": 67,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/vegclust.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/emf-creaf/vegclust",
  "_realowner": "emf-creaf",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.5.1",
      "date": "2012-10-29"
    },
    {
      "version": "1.6.0",
      "date": "2013-03-06"
    },
    {
      "version": "1.6.3",
      "date": "2013-11-19"
    },
    {
      "version": "1.6.4",
      "date": "2016-05-19"
    },
    {
      "version": "1.6.5",
      "date": "2016-12-21"
    },
    {
      "version": "1.7.1",
      "date": "2017-09-17"
    },
    {
      "version": "1.7.4",
      "date": "2018-05-29"
    },
    {
      "version": "1.7.7",
      "date": "2019-01-08"
    },
    {
      "version": "2.0.0",
      "date": "2021-06-01"
    },
    {
      "version": "2.0.2",
      "date": "2022-08-25"
    },
    {
      "version": "2.0.3",
      "date": "2025-05-19"
    }
  ],
  "_exports": [
    "as.memb",
    "as.stratifiedvegdata",
    "as.vegclust",
    "CAP",
    "CAP2matrix",
    "CAPcenters",
    "CAPquantile",
    "CAS",
    "CAS2matrix",
    "CAScenters",
    "CASmargin",
    "CASquantile",
    "clustcentroid",
    "clustconst",
    "clustmedoid",
    "clustvar",
    "concordance",
    "conformveg",
    "crossmemb",
    "defuzzify",
    "hcr",
    "hier.vegclust",
    "hier.vegclustdist",
    "incr.vegclust",
    "interclustdist",
    "random.vegclust",
    "random.vegclustdist",
    "relate.levels",
    "stratifyvegdata",
    "vegclass",
    "vegclust",
    "vegclust2kmeans",
    "vegclustdist",
    "vegclustIndex",
    "vegdiststruct"
  ],
  "_datasets": [
    {
      "name": "medreg",
      "title": "Regeneration of Mediterranean vegetation data set",
      "object": "medreg",
      "file": "medreg.rda",
      "class": [
        "stratifiedvegdata",
        "list"
      ],
      "fields": [],
      "table": true,
      "tojson": true
    },
    {
      "name": "treedata",
      "title": "Synthetic vegetation data set with tree data",
      "object": "treedata",
      "file": "treedata.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "plotID",
        "species",
        "height",
        "cover",
        "diam"
      ],
      "rows": 33,
      "table": true,
      "tojson": true
    },
    {
      "name": "wetland",
      "title": "Wetland vegetation data set Vegetation of the Adelaide river alluvial plain (Australia). This data set was published by Bowman & Wilson (1987) and used in Dale (1988) to compare fuzzy classification approaches.",
      "object": "wetland",
      "file": "wetland.rda",
      "class": [
        "data.frame"
      ],
      "fields": [
        "Abefic",
        "Merhed",
        "Alyvag",
        "Pancam",
        "Abemos",
        "Melcor",
        "Ludoct",
        "Eupvac",
        "Echpas",
        "Passcr",
        "Poa2",
        "Carhal",
        "Dendio",
        "Casobt",
        "Aesind",
        "Cyprot",
        "Ipocop",
        "Cynarc",
        "Walind",
        "Sessp.",
        "Phynod",
        "Echell",
        "Helind",
        "Ipoaqu",
        "Orysp.",
        "Elesp.",
        "Psespi",
        "Ludads",
        "Polatt",
        "Poa1",
        "Helcri",
        "Physp.",
        "Goopur"
      ],
      "rows": 41,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "as.memb",
      "title": "Turns into membership matrix",
      "topics": [
        "as.memb"
      ]
    },
    {
      "page": "as.vegclust",
      "title": "Turns into vegclust objects",
      "topics": [
        "as.vegclust"
      ]
    },
    {
      "page": "CAP",
      "title": "Cumulative abundance profile (CAP)",
      "topics": [
        "CAP",
        "CAP2matrix",
        "CAPcenters",
        "CAPquantile"
      ]
    },
    {
      "page": "CAS",
      "title": "Cumulative abundance surface (CAS)",
      "topics": [
        "CAS",
        "CAS2matrix",
        "CAScenters",
        "CASmargin",
        "CASquantile"
      ]
    },
    {
      "page": "clustcentroid",
      "title": "Cluster centers of a classification",
      "topics": [
        "clustcentroid",
        "clustmedoid"
      ]
    },
    {
      "page": "clustconst",
      "title": "Constancy table of a classification",
      "topics": [
        "clustconst",
        "summary.clustconst"
      ]
    },
    {
      "page": "clustvar",
      "title": "Cluster variance",
      "topics": [
        "clustvar"
      ]
    },
    {
      "page": "concordance",
      "title": "Concordance between two classifications",
      "topics": [
        "concordance"
      ]
    },
    {
      "page": "conformveg",
      "title": "Conform two community data tables",
      "topics": [
        "conformveg"
      ]
    },
    {
      "page": "crossmemb",
      "title": "Cross-table of two fuzzy classifications",
      "topics": [
        "crossmemb"
      ]
    },
    {
      "page": "defuzzify",
      "title": "Defuzzifies a fuzzy partition",
      "topics": [
        "defuzzify"
      ]
    },
    {
      "page": "hcr",
      "title": "Heterogeneity-constrained random resampling (HCR)",
      "topics": [
        "hcr"
      ]
    },
    {
      "page": "hier.vegclust",
      "title": "Clustering with several number of clusters",
      "topics": [
        "hier.vegclust",
        "hier.vegclustdist",
        "random.vegclust",
        "random.vegclustdist"
      ]
    },
    {
      "page": "incr.vegclust",
      "title": "Noise clustering with increasing number of clusters",
      "topics": [
        "incr.vegclust"
      ]
    },
    {
      "page": "interclustdist",
      "title": "Distance between pairs of cluster centroids",
      "topics": [
        "interclustdist"
      ]
    },
    {
      "page": "medreg",
      "title": "Regeneration of Mediterranean vegetation data set",
      "topics": [
        "medreg"
      ]
    },
    {
      "page": "plot.CAP",
      "title": "Draws cummulative abundance profiles",
      "topics": [
        "plot.CAP",
        "plot.stratifiedvegdata"
      ]
    },
    {
      "page": "plot.CAS",
      "title": "Draws a cummulative abundance surface",
      "topics": [
        "plot.CAS"
      ]
    },
    {
      "page": "plot.mvegclust",
      "title": "Plots clustering results",
      "topics": [
        "plot.mvegclust"
      ]
    },
    {
      "page": "relate.levels",
      "title": "Relates two clustering level results",
      "topics": [
        "relate.levels"
      ]
    },
    {
      "page": "stratifyvegdata",
      "title": "Reshapes community data from individual into stratified form",
      "topics": [
        "as.stratifiedvegdata",
        "stratifyvegdata"
      ]
    },
    {
      "page": "treedata",
      "title": "Synthetic vegetation data set with tree data",
      "topics": [
        "treedata"
      ]
    },
    {
      "page": "vegclass",
      "title": "Classifies vegetation communities",
      "topics": [
        "vegclass"
      ]
    },
    {
      "page": "vegclust",
      "title": "Vegetation clustering methods",
      "topics": [
        "vegclust",
        "vegclustdist"
      ]
    },
    {
      "page": "vegclust2kmeans",
      "title": "Reshapes as kmeans object",
      "topics": [
        "vegclust2kmeans"
      ]
    },
    {
      "page": "vegclustIndex",
      "title": "Fuzzy evaluation statistics",
      "topics": [
        "vegclustIndex"
      ]
    },
    {
      "page": "vegdiststruct",
      "title": "Structural and compositional dissimilarity",
      "topics": [
        "vegdiststruct"
      ]
    },
    {
      "page": "wetland",
      "title": "Wetland vegetation data set Vegetation of the Adelaide river alluvial plain (Australia). This data set was published by Bowman & Wilson (1987) and used in Dale (1988) to compare fuzzy classification approaches.",
      "topics": [
        "wetland"
      ]
    }
  ],
  "_pkglogo": "https://github.com/emf-creaf/vegclust/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/emf-creaf/vegclust/raw/HEAD/README.md",
  "_rundeps": [
    "cluster",
    "lattice",
    "MASS",
    "Matrix",
    "mgcv",
    "nlme",
    "permute",
    "vegan"
  ],
  "_vignettes": [
    {
      "source": "MedRegExample.Rmd",
      "filename": "MedRegExample.html",
      "title": "Describing vegetation in terms of structure and composition",
      "author": "Miquel De Cáceres",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Post-fire vegetation regeneration data",
        "Cumulative abundance profiles",
        "Cumulative abundance surfaces",
        "Dissimilarities in structure and composition",
        "Classification of vegetation stands",
        "References"
      ],
      "created": "2018-05-03 08:26:32",
      "modified": "2020-06-10 14:17:28",
      "commits": 3
    },
    {
      "source": "VegetationClassification.Rmd",
      "filename": "VegetationClassification.html",
      "title": "How to use the vegclust package",
      "author": "Miquel De Cáceres, CREAF, Barcelona, Spain, Susan Wiser, Landcare Research, Lincoln, New Zealand",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "What is this tutorial about?",
        "Example vegetation data",
        "Clustering methods in vegclust",
        "Resemblance space",
        "Prototype-based clustering",
        "Clustering models",
        "Hard (crisp) or fuzzy memberships",
        "Centroids or medoids",
        "Partitive clustering",
        "Noise clustering",
        "Possibilistic clustering",
        "Dissimilarity-based duals",
        "Medoid-based clustering and dissimilarity matrices",
        "Centroid-based clustering and dissimilarity matrices",
        "Managing vegetation classifications",
        "Creating classifications: vegclust and vegclustdist()",
        "The K-means model",
        "The Fuzzy C-means model",
        "The Noise clustering model",
        "Medoid-based clustering",
        "Supervised classification: as.vegclust() and vegclass()",
        "Extending vegetation classifications",
        "Conforming vegetation data sets",
        "Re-calculating the centroids of the initial classification",
        "Calling vegclust with fixed prototypes",
        "Extending or refining classifications?",
        "Using vegclustdist() with fixed prototypes",
        "Cluster characterization",
        "Cluster prototypes: clustcentroid() and clustmedoid()",
        "Cluster internal variability: clustvar()",
        "Distance between clusters: interclustdist()",
        "Constancy classes: clustconst()",
        "Bibliography"
      ],
      "created": "2021-06-04 15:05:16",
      "modified": "2021-06-08 10:03:38",
      "commits": 2
    }
  ],
  "_score": 6.869609978040645,
  "_indexed": true,
  "_nocasepkg": "vegclust",
  "_universes": [
    "emf-creaf",
    "miquelcaceres"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.0.3",
      "date": "2026-05-14T07:08:17.000Z",
      "distro": "noble",
      "commit": "59a4b4d59cd4217966e5c0e60545b584077b9497",
      "fileid": "e056c043444b79dfc7cffc3c0b6b430f288f7aa0017125ca2dadd4e4f08f681a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emf-creaf/actions/runs/25846786849"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.0.3",
      "date": "2026-05-14T07:08:23.000Z",
      "distro": "noble",
      "commit": "59a4b4d59cd4217966e5c0e60545b584077b9497",
      "fileid": "c14bd4ef5305371353c091ceb4c4f58f168de856be57948f4c0894ee9618291a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emf-creaf/actions/runs/25846786849"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.0.3",
      "date": "2026-05-15T05:45:56.000Z",
      "commit": "59a4b4d59cd4217966e5c0e60545b584077b9497",
      "fileid": "c2abb9901b9ffabb144eaff9e7c3ecbf4f765e44a7f45bd7dc4edc211bec07dd",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emf-creaf/actions/runs/25846786849"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.0.3",
      "date": "2026-05-14T07:08:07.000Z",
      "commit": "59a4b4d59cd4217966e5c0e60545b584077b9497",
      "fileid": "1dc06e0da80232da90ae57b77fa06ab0f67340135042a71224f2be1f355833b3",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emf-creaf/actions/runs/25846786849"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.0.3",
      "date": "2026-05-14T07:07:41.000Z",
      "commit": "59a4b4d59cd4217966e5c0e60545b584077b9497",
      "fileid": "342f69aa07ce13ef71747c63f226d133615167b41599c1ab2421240bc7821f6f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emf-creaf/actions/runs/25846786849"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.0.3",
      "date": "2026-05-14T07:07:19.000Z",
      "commit": "59a4b4d59cd4217966e5c0e60545b584077b9497",
      "fileid": "745bbbac8f61e67938966fd7a3f3479dc8bf8cb38fb129e8dae4ba447c8be3de",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emf-creaf/actions/runs/25846786849"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.0.3",
      "date": "2026-05-14T07:07:41.000Z",
      "commit": "59a4b4d59cd4217966e5c0e60545b584077b9497",
      "fileid": "bac1275710d492414e3aa84fb436bbec92b1071d5088b5da556572ceb6d75abe",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/emf-creaf/actions/runs/25846786849"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.0.3",
      "date": "2026-05-22T08:40:03.000Z",
      "commit": "59a4b4d59cd4217966e5c0e60545b584077b9497",
      "fileid": "fe12eba25ffa2176db66b2c5cb2455a383b5b96e6da18de99dd81473a1a2c695",
      "status": "success",
      "buildurl": "https://github.com/r-universe/emf-creaf/actions/runs/25846786849"
    }
  ]
}