{
  "_id": "6ab2457b3d719c1f8408b1fe",
  "Package": "picante",
  "Type": "Package",
  "Title": "Integrating Phylogenies and Ecology",
  "Version": "1.8.4",
  "Date": "2026-08-23",
  "Authors@R": "c(person(given = c(\"Steven\", \"W.\"),\nfamily = \"Kembel\",\nrole = c(\"aut\", \"cre\"),\nemail = \"steve.kembel@gmail.com\"),\nperson(given = c(\"David\", \"D.\"),\nfamily = \"Ackerly\",\nrole = \"aut\",\nemail = \"dackerly@berkeley.edu\"),\nperson(given = c(\"Simone\", \"P.\"),\nfamily = \"Blomberg\",\nrole = \"aut\",\nemail = \"s.blomberg1@uq.edu.au\"),\nperson(given = c(\"Will\", \"K.\"),\nfamily = \"Cornwell\",\nrole = \"aut\",\nemail = \"cornwell@zoology.ubc.ca\"),\nperson(given = c(\"Peter\", \"D.\"),\nfamily = \"Cowan\",\nrole = \"aut\",\nemail = \"pdc@berkeley.edu\"),\nperson(given = c(\"Matthew\", \"R.\"),\nfamily = \"Helmus\",\nrole = \"aut\",\nemail = \"mrhelmus@wisc.edu\"),\nperson(given = \"Helene\",\nfamily = \"Morlon\",\nrole = \"aut\",\nemail = \"morlon.helene@gmail.com\"),\nperson(given = c(\"Campbell\", \"O.\"),\nfamily = \"Webb\",\nrole = \"aut\",\nemail = \"cwebb@oeb.harvard.edu\"))",
  "Description": "Functions for phylocom integration, community analyses,\nnull-models, traits and evolution. Implements numerous\necophylogenetic approaches including measures of community\nphylogenetic and trait diversity, phylogenetic signal,\nestimation of trait values for unobserved taxa, null models for\ncommunity and phylogeny randomizations, and utility functions\nfor data input/output and phylogeny plotting. A full\ndescription of package functionality and methods are provided\nby Kembel et al. (2010) <doi:10.1093/bioinformatics/btq166>.",
  "License": "GPL-2",
  "Config/roxygen2/version": "8.0.0",
  "Repository": "https://phylotastic.r-universe.dev",
  "Date/Publication": "2026-08-23 13:24:48 UTC",
  "RemoteUrl": "https://github.com/skembel/picante",
  "RemoteRef": "HEAD",
  "RemoteSha": "a5979444a42c1d045ce0a2ede01c71b3d56e89c0",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-09-22 09:02:24 UTC",
    "User": "root"
  },
  "Author": "Steven W. Kembel [aut, cre],\nDavid D. Ackerly [aut],\nSimone P. Blomberg [aut],\nWill K. Cornwell [aut],\nPeter D. Cowan [aut],\nMatthew R. Helmus [aut],\nHelene Morlon [aut],\nCampbell O. Webb [aut]",
  "Maintainer": "Steven W. Kembel <steve.kembel@gmail.com>",
  "_user": "phylotastic",
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  "_expires": "2026-12-31T09:08:09.000Z",
  "_created": "2026-09-22T09:02:24.000Z",
  "_published": "2026-09-22T09:08:11.250Z",
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    "author": "skembel <steve.kembel@gmail.com>",
    "committer": "skembel <steve.kembel@gmail.com>",
    "message": "Updating NAMESPACE to fix list of exported names, to address CRAN build issue. Bump date for v1.8.4 build.\n",
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  "_homeurl": "https://github.com/skembel/picante",
  "_realowner": "skembel",
  "_cranurl": true,
  "_releases": [
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      "date": "2010-04-10"
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      "version": "1.1-1",
      "date": "2010-05-22"
    },
    {
      "version": "1.2-0",
      "date": "2010-07-24"
    },
    {
      "version": "1.3-0",
      "date": "2011-04-24"
    },
    {
      "version": "1.4-1",
      "date": "2012-09-04"
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    {
      "version": "1.4-2",
      "date": "2012-09-22"
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    {
      "version": "1.5-1",
      "date": "2012-10-02"
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    {
      "version": "1.5-2",
      "date": "2012-10-09"
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    {
      "version": "1.6-0",
      "date": "2013-05-31"
    },
    {
      "version": "1.6-1",
      "date": "2013-11-01"
    },
    {
      "version": "1.6-2",
      "date": "2014-03-05"
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    {
      "version": "1.7",
      "date": "2018-05-14"
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    {
      "version": "1.8",
      "date": "2019-03-21"
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      "version": "1.8.1",
      "date": "2020-02-13"
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      "version": "1.8.2",
      "date": "2020-06-10"
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    {
      "version": "1.8.4",
      "date": "2026-08-23"
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  ],
  "_exports": [
    "color.plot.phylo",
    "comdist",
    "comdistnt",
    "comm.phylo.cor",
    "comm.phylo.qr",
    "cor.table",
    "df2vec",
    "ead",
    "evol.distinct",
    "expected.pd",
    "internal2tips",
    "Kcalc",
    "match.comm.dist",
    "match.phylo.comm",
    "match.phylo.data",
    "matrix2sample",
    "mntd",
    "mpd",
    "multiPhylosignal",
    "node.age",
    "pblm",
    "pblmpredict",
    "pcd",
    "pd",
    "phyEstimate",
    "phyEstimateDisc",
    "phylosignal",
    "phylosor",
    "phylosor.rnd",
    "phylostruct",
    "pic.variance",
    "prune.missing",
    "prune.sample",
    "psc",
    "psd",
    "pse",
    "psr",
    "psv",
    "psv.spp",
    "randomizeMatrix",
    "raoD",
    "readsample",
    "sample2matrix",
    "ses.mntd",
    "ses.mpd",
    "ses.pd",
    "sortColumns",
    "sortRows",
    "specaccum.psr",
    "species.dist",
    "sppregs",
    "sppregs.plot",
    "tax.distinctiveness",
    "taxaShuffle",
    "tipShuffle",
    "traitgram",
    "unifrac",
    "variance.pd",
    "writesample",
    "writetraits"
  ],
  "_datasets": [
    {
      "name": "IvesGodfray",
      "title": "Host-parasitoid food web data",
      "object": "IvesGodfray",
      "file": "IvesGodfray.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "phylocom",
      "title": "Phylocom default data",
      "object": "phylocom",
      "file": "phylocom.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "picante-package",
      "title": "picante: Integrating Phylogenies and Ecology",
      "topics": [
        "picante-package",
        "picante"
      ]
    },
    {
      "page": "color.plot.phylo",
      "title": "Color tip labels based on trait",
      "topics": [
        "color.plot.phylo"
      ]
    },
    {
      "page": "comdist",
      "title": "Calculates inter-community mean pairwise distance",
      "topics": [
        "comdist"
      ]
    },
    {
      "page": "comdistnt",
      "title": "Calculates inter-community mean nearest taxon distance",
      "topics": [
        "comdistnn",
        "comdistnt"
      ]
    },
    {
      "page": "comm.phylo.cor",
      "title": "Correlations between species co-occurrence and phylogenetic distances",
      "topics": [
        "comm.phylo.cor"
      ]
    },
    {
      "page": "comm.phylo.qr",
      "title": "Quantile regression slopes between species co-occurrence and phylogenetic distances",
      "topics": [
        "comm.phylo.qr"
      ]
    },
    {
      "page": "cor.table",
      "title": "Table of correlations and P-values",
      "topics": [
        "cor.table"
      ]
    },
    {
      "page": "evol.distinct",
      "title": "Species' evolutionary distinctiveness",
      "topics": [
        "evol.distinct"
      ]
    },
    {
      "page": "expected.pd",
      "title": "Expected PD, PD Variance, and Edge Abundance Distribution of a phylogeny",
      "topics": [
        "ead",
        "expected.pd",
        "variance.pd"
      ]
    },
    {
      "page": "IvesGodfray",
      "title": "Host-parasitoid food web data",
      "topics": [
        "IvesGodfray"
      ]
    },
    {
      "page": "Kcalc",
      "title": "K statistic of phylogenetic signal",
      "topics": [
        "Kcalc"
      ]
    },
    {
      "page": "data.checking",
      "title": "Match taxa in phylogeny and data",
      "topics": [
        "match.comm.dist",
        "match.phylo.comm",
        "match.phylo.data"
      ]
    },
    {
      "page": "matrix2sample",
      "title": "Convert community data matrix to Phylocom sample",
      "topics": [
        "matrix2sample"
      ]
    },
    {
      "page": "mntd",
      "title": "Mean nearest taxon distance",
      "topics": [
        "mnnd",
        "mntd"
      ]
    },
    {
      "page": "mpd",
      "title": "Mean pairwise distance",
      "topics": [
        "mpd"
      ]
    },
    {
      "page": "multiPhylosignal",
      "title": "Calculates phylogenetic signal for data.frame of traits",
      "topics": [
        "multiPhylosignal"
      ]
    },
    {
      "page": "pblm",
      "title": "Phylogenetic Bipartite Linear Model",
      "topics": [
        "pblm",
        "pblmpredict"
      ]
    },
    {
      "page": "pcd",
      "title": "Phylogenetic Community Dissimilarity",
      "topics": [
        "PCD",
        "pcd"
      ]
    },
    {
      "page": "pd",
      "title": "Calculate Faith's Phylogenetic Diversity",
      "topics": [
        "pd"
      ]
    },
    {
      "page": "phyEstimate",
      "title": "Phylogenetic estimation of traits for unobserved taxa",
      "topics": [
        "phyEstimate",
        "phyEstimateDisc"
      ]
    },
    {
      "page": "phylocom",
      "title": "Phylocom default data",
      "topics": [
        "phylocom"
      ]
    },
    {
      "page": "phylosignal",
      "title": "Measure phylogenetic signal",
      "topics": [
        "phylosignal"
      ]
    },
    {
      "page": "phylosor",
      "title": "Phylogenetic index of beta-diversity PhyloSor",
      "topics": [
        "phylosor"
      ]
    },
    {
      "page": "phylosor.rnd",
      "title": "Null PhyloSor values of phylogenetic beta-diversity",
      "topics": [
        "phylosor.rnd"
      ]
    },
    {
      "page": "phylostruct",
      "title": "Permutations to Test for Phylogenetic Signal in Community Composition",
      "topics": [
        "phylostruct"
      ]
    },
    {
      "page": "pruning",
      "title": "Prune tree to match community data or trait data",
      "topics": [
        "prune.missing",
        "prune.sample"
      ]
    },
    {
      "page": "psd",
      "title": "Phylogenetic Species Diversity Metrics",
      "topics": [
        "psc",
        "psd",
        "pse",
        "psr",
        "psv",
        "psv.spp"
      ]
    },
    {
      "page": "randomizeSample",
      "title": "Null models for community data matrix randomization",
      "topics": [
        "randomizeMatrix"
      ]
    },
    {
      "page": "raoD",
      "title": "Rao's quadratic entropy",
      "topics": [
        "raoD"
      ]
    },
    {
      "page": "readsample",
      "title": "Read Phylocom sample",
      "topics": [
        "readsample"
      ]
    },
    {
      "page": "sample2matrix",
      "title": "Convert Phylocom sample to community data matrix",
      "topics": [
        "sample2matrix"
      ]
    },
    {
      "page": "ses.mntd",
      "title": "Standardized effect size of MNTD",
      "topics": [
        "ses.mnnd",
        "ses.mntd"
      ]
    },
    {
      "page": "ses.mpd",
      "title": "Standardized effect size of MPD",
      "topics": [
        "ses.mpd"
      ]
    },
    {
      "page": "ses.pd",
      "title": "Standardized effect size of PD",
      "topics": [
        "ses.pd"
      ]
    },
    {
      "page": "specaccum.psr",
      "title": "Phylogenetic Species Richness Sample-Based Rarefaction Curve",
      "topics": [
        "specaccum.psr"
      ]
    },
    {
      "page": "species.dist",
      "title": "Species co-occurrence distances",
      "topics": [
        "species.dist"
      ]
    },
    {
      "page": "sppregs",
      "title": "Regressions to Separate Phylogenetic Attraction and Repulsion",
      "topics": [
        "sppregs",
        "sppregs.plot"
      ]
    },
    {
      "page": "tax.distinctiveness",
      "title": "Taxonomic distinctiveness sensu Vane-Wright or May",
      "topics": [
        "tax.distinctiveness"
      ]
    },
    {
      "page": "traitgram",
      "title": "Draw phylogeny with nodes at trait positions",
      "topics": [
        "traitgram"
      ]
    },
    {
      "page": "unifrac",
      "title": "Unweighted UniFrac distance between communities",
      "topics": [
        "unifrac"
      ]
    },
    {
      "page": "utility",
      "title": "Picante utility functions",
      "topics": [
        "df2vec",
        "internal2tips",
        "node.age",
        "pic.variance",
        "sortColumns",
        "sortRows",
        "taxaShuffle",
        "tipShuffle"
      ]
    },
    {
      "page": "writesample",
      "title": "Write a Phylocom community sample file",
      "topics": [
        "writesample"
      ]
    },
    {
      "page": "writetraits",
      "title": "Write a Phylocom traits formatted file",
      "topics": [
        "writetraits"
      ]
    }
  ],
  "_readme": "https://github.com/skembel/picante/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "cluster",
    "digest",
    "lattice",
    "MASS",
    "Matrix",
    "mgcv",
    "nlme",
    "permute",
    "Rcpp",
    "vegan"
  ],
  "_vignettes": [
    {
      "source": "picante-intro.Rnw",
      "filename": "picante-intro.pdf",
      "title": "Data and analysis in picante",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2013-10-29 17:52:57",
      "modified": "2019-03-18 16:27:53",
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