{ "_id": "6a1df8e01d7bb097a0a5d053", "Package": "vegan", "Title": "Community Ecology Package", "Version": "2.8-0", "Authors@R": "c(person(\"Jari\", \"Oksanen\", role=c(\"aut\",\"cre\"),\nemail=\"jhoksane@gmail.com\",\ncomment = c(ORCID=\"0000-0001-7102-9626\")),\nperson(\"Gavin L.\", \"Simpson\", role=\"aut\",\nemail=\"ucfagls@gmail.com\",\ncomment = c(ORCID = \"0000-0002-9084-8413\")),\nperson(\"F. Guillaume\", \"Blanchet\", role=\"aut\"),\nperson(\"Roeland\", \"Kindt\", role=\"aut\"),\nperson(\"Pierre\", \"Legendre\", role=\"aut\"),\nperson(\"Peter R.\", \"Minchin\", role=\"aut\"),\nperson(\"R.B.\", \"O'Hara\", role=\"aut\"),\nperson(\"Peter\", \"Solymos\", role=\"aut\"),\nperson(\"M. Henry H.\", \"Stevens\", role=\"aut\"),\nperson(\"Eduard\", \"Szoecs\", role=\"aut\"),\nperson(\"Helene\", \"Wagner\", role=\"aut\"),\nperson(\"Matt\", \"Barbour\", role=\"ctb\"),\nperson(\"Michael\", \"Bedward\", role=\"aut\"),\nperson(\"Henrik\", \"Bengtsson\", role=\"ctb\"),\nperson(\"Ben\", \"Bolker\", role=\"aut\"),\nperson(\"Daniel\", \"Borcard\", role=\"aut\"),\nperson(\"Tuomas\", \"Borman\", role=\"ctb\"),\nperson(\"Gustavo\", \"Carvalho\", role=\"aut\"),\nperson(\"Michael\", \"Chirico\", role=\"ctb\"),\nperson(\"Miquel\", \"De Caceres\", role=\"aut\"),\nperson(\"Sebastien\", \"Durand\", role=\"aut\"),\nperson(\"Heloisa Beatriz Antoniazi\", \"Evangelista\", role=\"aut\"),\nperson(\"Rich\", \"FitzJohn\", role=\"ctb\"),\nperson(\"Michael\", \"Friendly\", role=\"ctb\"),\nperson(\"Brendan\",\"Furneaux\", role=\"ctb\"),\nperson(\"Geoffrey\", \"Hannigan\", role=\"aut\"),\nperson(\"Isaac\", \"Heida\", role=\"ctb\"),\nperson(\"Mark O.\", \"Hill\", role=\"aut\"),\nperson(\"Leo\", \"Lahti\", role=\"aut\"),\nperson(\"Cameron\", \"Martino\", role=\"aut\"),\nperson(\"Dan\", \"McGlinn\", role=\"ctb\"),\nperson(\"Marie-Helene\", \"Ouellette\", role=\"aut\"),\nperson(\"Eduardo\", \"Ribeiro Cunha\", role=\"aut\"),\nperson(\"Tyler\", \"Smith\", role=\"aut\"),\nperson(\"Adrian\", \"Stier\", role=\"aut\"),\nperson(\"Cajo J.F.\", \"Ter Braak\", role=\"aut\"),\nperson(\"James\", \"Weedon\", role=\"aut\"))", "VignetteBuilder": "utils, knitr", "Description": "Ordination methods, diversity analysis and other functions\nfor community and vegetation ecologists.", "License": "GPL-2", "BugReports": "https://github.com/vegandevs/vegan/issues", "URL": "https://vegandevs.github.io/vegan/,\nhttps://github.com/vegandevs/vegan", "Repository": "https://vegandevs.r-universe.dev", "Date/Publication": "2026-06-01 17:41:46 UTC", "RemoteUrl": "https://github.com/vegandevs/vegan", "RemoteRef": "HEAD", "RemoteSha": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "NeedsCompilation": "yes", "Packaged": { "Date": "2026-06-01 21:13:05 UTC", "User": "root" }, "Author": "Jari Oksanen [aut, cre] (ORCID:\n),\nGavin L. Simpson [aut] (ORCID: ),\nF. Guillaume Blanchet [aut],\nRoeland Kindt [aut],\nPierre Legendre [aut],\nPeter R. Minchin [aut],\nR.B. O'Hara [aut],\nPeter Solymos [aut],\nM. Henry H. Stevens [aut],\nEduard Szoecs [aut],\nHelene Wagner [aut],\nMatt Barbour [ctb],\nMichael Bedward [aut],\nHenrik Bengtsson [ctb],\nBen Bolker [aut],\nDaniel Borcard [aut],\nTuomas Borman [ctb],\nGustavo Carvalho [aut],\nMichael Chirico [ctb],\nMiquel De Caceres [aut],\nSebastien Durand [aut],\nHeloisa Beatriz Antoniazi Evangelista [aut],\nRich FitzJohn [ctb],\nMichael Friendly [ctb],\nBrendan Furneaux [ctb],\nGeoffrey Hannigan [aut],\nIsaac Heida [ctb],\nMark O. Hill [aut],\nLeo Lahti [aut],\nCameron Martino [aut],\nDan McGlinn [ctb],\nMarie-Helene Ouellette [aut],\nEduardo Ribeiro Cunha [aut],\nTyler Smith [aut],\nAdrian Stier [aut],\nCajo J.F. Ter Braak [aut],\nJames Weedon [aut]", "Maintainer": "Jari Oksanen ", "MD5sum": "b9b46c062ad77af27442725a468d5760", "_user": "vegandevs", "_type": "src", "_file": "vegan_2.8-0.tar.gz", "_fileid": "793a7676ee877d840a17506665e4eb94b93e481ed20ec592e80c2fc81335f33d", "_filesize": 3232985, "_sha256": "793a7676ee877d840a17506665e4eb94b93e481ed20ec592e80c2fc81335f33d", "_created": "2026-06-01T21:13:05.000Z", "_published": "2026-06-01T21:25:52.445Z", "_distro": "noble", "_jobs": [ { "job": 78950025269, "time": 193, "config": "linux-devel-arm64", "r": "4.7.0", "check": "NOTE", "artifact": "7343196924" }, { "job": 78950025300, "time": 206, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7343200303" }, { "job": 78950025240, "time": 202, "config": "linux-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7343199798" }, { "job": 78950025354, "time": 176, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7343189651" }, { "job": 78950025299, "time": 174, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7343293782" }, { "job": 78950025342, "time": 427, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "NOTE", "artifact": "7343375315" }, { "job": 78950025370, "time": 200, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7343311555" }, { "job": 78950025406, "time": 288, "config": "macos-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7343315637" }, { "job": 78949158298, "time": 290, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7343123738" }, { "job": 78950025243, "time": 104, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7343162988" }, { "job": 78950025260, "time": 162, "config": "windows-devel", "r": "4.7.0", "check": "OK", "artifact": "7343184282" }, { "job": 78950025246, "time": 232, "config": "windows-oldrel", "r": "4.5.3", "check": "OK", "artifact": "7343208944" }, { "job": 78950025229, "time": 209, "config": "windows-release", "r": "4.6.0", "check": "OK", "artifact": "7343201318" } ], "_buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/vegandevs/vegan", "_commit": { "id": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "author": "Jari Oksanen ", "committer": "Jari Oksanen ", "message": "fix role\n", "time": 1780335706 }, "_maintainer": { "name": "Jari Oksanen", "email": "jhoksane@gmail.com", "login": "jarioksa", "description": "", "uuid": 1432933, "orcid": "0000-0001-7102-9626" }, "_registered": true, "_dependencies": [ { "package": "permute", "version": ">= 0.9-0", "role": "Depends" }, { "package": "R", "version": ">= 4.1.0", "role": "Depends" }, { "package": "MASS", "role": "Imports" }, { "package": "cluster", "role": "Imports" }, { "package": "lattice", "role": "Imports" }, { "package": "mgcv", "role": "Imports" }, { "package": "parallel", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "markdown", "role": "Suggests" } ], "_owner": "vegandevs", "_selfowned": true, "_usedby": 504, "_updates": [ { "week": "2025-22", "n": 1 }, { "week": "2025-23", "n": 11 }, { "week": "2025-24", "n": 4 }, { "week": "2025-25", "n": 2 }, { "week": "2025-29", "n": 7 }, { "week": "2025-30", "n": 4 }, { "week": "2025-31", "n": 5 }, { "week": "2025-32", "n": 1 }, { "week": "2025-33", "n": 5 }, { "week": "2025-34", "n": 3 }, { "week": "2025-35", "n": 1 }, { "week": "2025-36", "n": 2 }, { "week": "2025-38", "n": 1 }, { "week": "2025-39", "n": 4 }, { "week": "2025-40", "n": 2 }, { "week": "2025-41", "n": 2 }, { "week": "2025-42", "n": 9 }, { "week": "2025-43", "n": 1 }, { "week": "2025-44", "n": 7 }, { "week": "2025-45", "n": 2 }, { "week": "2025-46", "n": 6 }, { "week": "2025-47", "n": 7 }, { "week": "2025-48", "n": 1 }, { "week": "2026-09", "n": 2 }, { "week": "2026-10", "n": 3 }, { "week": "2026-11", "n": 6 }, { "week": "2026-12", "n": 1 }, { "week": "2026-13", "n": 3 }, { "week": "2026-14", "n": 3 }, { "week": "2026-15", "n": 2 }, { "week": "2026-16", "n": 1 }, { "week": "2026-17", "n": 1 }, { "week": "2026-18", "n": 6 }, { "week": "2026-19", "n": 2 }, { "week": "2026-20", "n": 2 }, { "week": "2026-21", "n": 4 }, { "week": "2026-22", "n": 1 }, { "week": "2026-23", "n": 1 } ], "_tags": [ { "name": "v2.7-1", "date": "2025-06-05" }, { "name": "2.8-0", "date": "2025-06-06" }, { "name": "v2.7-2", "date": "2025-10-08" }, { "name": "v2.7-3", "date": "2026-03-03" }, { "name": "v2.7-5", "date": "2026-05-25" } ], "_topics": [ "ecological-modelling", "ecology", "ordination", "openblas", "fortran" ], "_stars": 533, "_contributors": [ { "user": "jarioksa", "count": 3815, "uuid": 1432933 }, { "user": "gavinsimpson", "count": 402, "uuid": 514696 }, { "user": "antagomir", "count": 65, "uuid": 1228382 }, { "user": "psolymos", "count": 56, "uuid": 831636 }, { "user": "j-tweed", "count": 16, "uuid": 1643942 }, { "user": "eduardszoecs", "count": 14, "uuid": 849616 }, { "user": "olivroy", "count": 9, "uuid": 52606734 }, { "user": "michaelchirico", "count": 7, "uuid": 7606389 }, { "user": "dmcglinn", "count": 6, "uuid": 1190381 }, { "user": "o957", "count": 4, "uuid": 127630341 }, { "user": "legendre", "count": 4, "uuid": 1571740 }, { "user": "zhilongjia", "count": 3, "uuid": 1230436 }, { "user": "tuomasborman", "count": 2, "uuid": 60338854 }, { "user": "prminchin", "count": 2, "uuid": 67326049 }, { "user": "henrikbengtsson", "count": 2, "uuid": 1616850 }, { "user": "friendly", "count": 2, "uuid": 456353 }, { "user": "bbolker", "count": 2, "uuid": 78918 }, { "user": "danielborcard", "count": 1, "uuid": 1561952 }, { "user": "fvd", "count": 1, "uuid": 2441145 }, { "user": "microbiology", "count": 1, "uuid": 6383687 }, { "user": "adrianstier", "count": 1, "uuid": 4541503 }, { "user": "kasperskytte", "count": 1, "uuid": 23030537 }, { "user": "richfitz", "count": 1, "uuid": 1558093 }, { "user": "salix-d", "count": 1, "uuid": 31168746 }, { "user": "norival", "count": 1, "uuid": 11806113 }, { "user": "brendanf", "count": 1, "uuid": 16835777 }, { "user": "hezibu", "count": 1, "uuid": 44232295 } ], "_userbio": { "uuid": 8548207, "type": "organization", "name": "vegandevs" }, "_downloads": { "count": 146563, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/vegan" }, "_mentions": 6903, "_devurl": "https://github.com/vegandevs/vegan", "_pkgdown": "https://vegandevs.github.io/vegan/", "_searchresults": 24704, "_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/vegan.html", "manual.pdf" ], "_homeurl": "https://github.com/vegandevs/vegan", "_realowner": "vegandevs", "_cranurl": true, "_releases": [ { "version": "1.0-1", "date": "2001-09-06" }, { "version": "1.2-0", "date": "2001-11-19" }, { "version": "1.2-1", "date": "2001-12-18" }, { "version": "1.4-0", "date": "2002-05-03" }, { "version": "1.4-1", "date": "2002-10-04" }, { "version": "1.4-2", "date": "2003-02-07" }, { "version": "1.4-3", "date": "2003-04-22" }, { "version": "1.4-4", "date": "2003-05-19" }, { "version": "1.6-0", "date": "2003-10-20" }, { "version": "1.6-1", "date": "2003-12-12" }, { "version": "1.6-2", "date": "2004-01-22" }, { "version": "1.6-3", "date": "2004-03-22" }, { "version": "1.6-4", "date": "2004-06-11" }, { "version": "1.6-5", "date": "2004-10-13" }, { "version": "1.6-6", "date": "2005-01-09" }, { "version": "1.6-7", "date": "2005-01-25" }, { "version": "1.6-8", "date": "2005-04-18" }, { "version": "1.6-9", "date": "2005-04-22" }, { "version": "1.6-10", "date": "2005-09-26" }, { "version": "1.8-1", "date": "2006-06-12" }, { "version": "1.8-2", "date": "2006-06-14" }, { "version": "1.8-3", "date": "2006-09-29" }, { "version": "1.8-4", "date": "2007-01-08" }, { "version": "1.8-5", "date": "2007-01-11" }, { "version": "1.8-6", "date": "2007-05-10" }, { "version": "1.8-7", "date": "2007-08-25" }, { "version": "1.8-8", "date": "2007-10-03" }, { "version": "1.11-0", "date": "2008-02-21" }, { "version": "1.11-2", "date": "2008-03-21" }, { "version": "1.11-3", "date": "2008-04-10" }, { "version": "1.11-4", "date": "2008-04-24" }, { "version": "1.13-0", "date": "2008-05-21" }, { "version": "1.13-1", "date": "2008-06-11" }, { "version": "1.13-2", "date": "2008-08-20" }, { "version": "1.15-0", "date": "2008-09-30" }, { "version": "1.15-1", "date": "2008-12-19" }, { "version": "1.15-2", "date": "2009-04-15" }, { "version": "1.15-3", "date": "2009-06-17" }, { "version": "1.15-4", "date": "2009-09-07" }, { "version": "1.17-0", "date": "2010-01-11" }, { "version": "1.17-1", "date": "2010-02-18" }, { "version": "1.17-2", "date": "2010-03-08" }, { "version": "1.17-3", "date": "2010-06-16" }, { "version": "1.17-4", "date": "2010-08-20" }, { "version": "1.17-5", "date": "2010-12-18" }, { "version": "1.17-6", "date": "2011-01-10" }, { "version": "1.17-7", "date": "2011-02-16" }, { "version": "1.17-8", "date": "2011-03-02" }, { "version": "1.17-9", "date": "2011-03-31" }, { "version": "1.17-10", "date": "2011-04-27" }, { "version": "1.17-11", "date": "2011-06-15" }, { "version": "1.17-12", "date": "2011-08-17" }, { "version": "2.0-0", "date": "2011-09-08" }, { "version": "2.0-1", "date": "2011-10-20" }, { "version": "2.0-2", "date": "2011-11-15" }, { "version": "2.0-3", "date": "2012-03-03" }, { "version": "2.0-4", "date": "2012-06-19" }, { "version": "2.0-5", "date": "2012-10-08" }, { "version": "2.0-6", "date": "2013-02-11" }, { "version": "2.0-7", "date": "2013-03-19" }, { "version": "2.0-8", "date": "2013-07-10" }, { "version": "2.0-9", "date": "2013-09-25" }, { "version": "2.0-10", "date": "2013-12-12" }, { "version": "2.2-0", "date": "2014-11-17" }, { "version": "2.2-1", "date": "2015-01-12" }, { "version": "2.3-0", "date": "2015-05-26" }, { "version": "2.3-1", "date": "2015-09-25" }, { "version": "2.3-2", "date": "2015-11-19" }, { "version": "2.3-3", "date": "2016-01-12" }, { "version": "2.3-4", "date": "2016-02-26" }, { "version": "2.3-5", "date": "2016-04-08" }, { "version": "2.4-0", "date": "2016-06-15" }, { "version": "2.4-1", "date": "2016-09-07" }, { "version": "2.4-2", "date": "2017-01-17" }, { "version": "2.4-3", "date": "2017-04-07" }, { "version": "2.4-4", "date": "2017-08-24" }, { "version": "2.4-5", "date": "2017-12-01" }, { "version": "2.4-6", "date": "2018-01-24" }, { "version": "2.5-1", "date": "2018-04-14" }, { "version": "2.5-2", "date": "2018-05-17" }, { "version": "2.5-3", "date": "2018-10-25" }, { "version": "2.5-4", "date": "2019-02-04" }, { "version": "2.5-5", "date": "2019-05-12" }, { "version": "2.5-6", "date": "2019-09-01" }, { "version": "2.5-7", "date": "2020-11-28" }, { "version": "2.6-2", "date": "2022-04-17" }, { "version": "2.6-4", "date": "2022-10-11" }, { "version": "2.6-6", "date": "2024-05-14" }, { "version": "2.6-6.1", "date": "2024-05-21" }, { "version": "2.6-8", "date": "2024-08-28" }, { "version": "2.6-10", "date": "2025-01-29" }, { "version": "2.7-1", "date": "2025-06-05" }, { "version": "2.7-2", "date": "2025-10-08" }, { "version": "2.7-3", "date": "2026-03-04" }, { "version": "2.7-5", "date": "2026-05-25" } ], "_exports": [ "adipart", "adonis", "adonis2", "anosim", "anova.cca", "as.fisher", "as.mcmc.oecosimu", "as.mcmc.permat", "as.mlm", "as.preston", "as.rad", "avgdist", "beals", "betadisper", "betadistances", "betadiver", "bgdispersal", "bioenv", "bioenvdist", "bstick", "ca", "calibrate", "capscale", "cascadeKM", "cca", "CCorA", "chaodist", "cIndexKM", "clamtest", "commsim", "commsimulator", "contribdiv", "coverscale", "cutreeord", "dbrda", "decobackstand", "decorana", "decostand", "designdist", "designdist2", "dispindmorisita", "dispweight", "dist2xy", "distconnected", "diversity", "downweight", "drarefy", "eigengrad", "eigenvals", "envfit", "estaccumR", "estimateR", "eventstar", "factorfit", "fieller.MOStest", "fisher.alpha", "fisherfit", "fitspecaccum", "gdispweight", "goodness", "hiersimu", "indpower", "inertcomp", "initMDS", "intersetcor", "isomap", "isomapdist", "kendall.global", "kendall.post", "linestack", "make.cepnames", "make.commsim", "mantel", "mantel.correlog", "mantel.partial", "MDSaddpoints", "MDSrotate", "meandist", "metaMDS", "metaMDSdist", "metaMDSiter", "metaMDSredist", "monoMDS", "MOStest", "mrpp", "mso", "msoplot", "multipart", "nestedbetajac", "nestedbetasor", "nestedchecker", "nesteddisc", "nestedn0", "nestednodf", "nestedtemp", "no.shared", "nullmodel", "oecosimu", "optspace", "ordConstrained", "ordiareatest", "ordiArrowMul", "ordiarrows", "ordiArrowTextXY", "ordibar", "ordicloud", "ordicluster", "ordiellipse", "ordigrid", "ordihull", "ordilabel", "ordiplot", "ordipointlabel", "ordiR2step", "ordiresids", "ordisegments", "ordispider", "ordisplom", "ordistep", "ordisurf", "orditorp", "ordixyplot", "ordiYbar", "pasteCall", "pca", "pcnm", "pco", "permatfull", "permatswap", "permulattice", "permustats", "permutest", "poolaccum", "postMDS", "prc", "prestondistr", "prestonfit", "procrustes", "protest", "rad.lognormal", "rad.null", "rad.preempt", "rad.zipf", "rad.zipfbrot", "radfit", "radlattice", "rankindex", "rarecurve", "rarefy", "rareslope", "raupcrick", "rda", "read.cep", "renyi", "renyiaccum", "rrarefy", "RsquareAdj", "scores", "showvarparts", "simper", "simpson.unb", "smbind", "spandepth", "spantree", "specaccum", "specnumber", "specpool", "specpool2vect", "specslope", "spenvcor", "sppscores", "sppscores<-", "SSarrhenius", "SSgitay", "SSgleason", "SSlomolino", "stepacross", "stressplot", "swan", "tabasco", "taxa2dist", "taxondive", "toCoda", "tolerance", "treedist", "treedive", "treeheight", "tsallis", "tsallisaccum", "varpart", "vectorfit", "vegandocs", "vegdist", "vegemite", "veiledspec", "vif.cca", "wascores", "wcmdscale", "wisconsin" ], "_datasets": [ { "name": "BCI", "title": "Barro Colorado Island Tree Counts", "object": "BCI", "file": "BCI.env.rda", "class": [ "data.frame" ], "fields": [ "Abarema.macradenia", "Vachellia.melanoceras", "Acalypha.diversifolia", "Acalypha.macrostachya", "Adelia.triloba", "Aegiphila.panamensis", "Alchornea.costaricensis", "Alchornea.latifolia", "Alibertia.edulis", "Allophylus.psilospermus", "Alseis.blackiana", "Amaioua.corymbosa", "Anacardium.excelsum", "Andira.inermis", "Annona.spraguei", "Apeiba.glabra", "Apeiba.tibourbou", "Aspidosperma.desmanthum", "Astrocaryum.standleyanum", "Astronium.graveolens", "Attalea.butyracea", "Banara.guianensis", "Beilschmiedia.pendula", "Brosimum.alicastrum", "Brosimum.guianense", "Calophyllum.longifolium", "Casearia.aculeata", "Casearia.arborea", "Casearia.commersoniana", "Casearia.guianensis", "Casearia.sylvestris", "Cassipourea.guianensis", "Cavanillesia.platanifolia", "Cecropia.insignis", "Cecropia.obtusifolia", "Cedrela.odorata", "Ceiba.pentandra", "Celtis.schippii", "Cespedesia.spathulata", "Chamguava.schippii", "Chimarrhis.parviflora", "Maclura.tinctoria", "Chrysochlamys.eclipes", "Chrysophyllum.argenteum", "Chrysophyllum.cainito", "Coccoloba.coronata", "Coccoloba.manzinellensis", "Colubrina.glandulosa", "Cordia.alliodora", "Cordia.bicolor", "Cordia.lasiocalyx", "Coussarea.curvigemma", "Croton.billbergianus", "Cupania.cinerea", "Cupania.latifolia", "Cupania.rufescens", "Cupania.seemannii", "Dendropanax.arboreus", "Desmopsis.panamensis", "Diospyros.artanthifolia", "Dipteryx.oleifera", "Drypetes.standleyi", "Elaeis.oleifera", "Enterolobium.schomburgkii", "Erythrina.costaricensis", "Erythroxylum.macrophyllum", "Eugenia.florida", "Eugenia.galalonensis", "Eugenia.nesiotica", "Eugenia.oerstediana", "Faramea.occidentalis", "Ficus.colubrinae", "Ficus.costaricana", "Ficus.insipida", "Ficus.maxima", "Ficus.obtusifolia", "Ficus.popenoei", "Ficus.tonduzii", "Ficus.trigonata", "Ficus.yoponensis", "Garcinia.intermedia", "Garcinia.madruno", "Genipa.americana", "Guapira.myrtiflora", "Guarea.fuzzy", "Guarea.grandifolia", "Guarea.guidonia", "Guatteria.dumetorum", "Guazuma.ulmifolia", "Guettarda.foliacea", "Gustavia.superba", "Hampea.appendiculata", "Hasseltia.floribunda", "Heisteria.acuminata", "Heisteria.concinna", "Hirtella.americana", "Hirtella.triandra", "Hura.crepitans", "Hieronyma.alchorneoides", "Inga.acuminata", "Inga.cocleensis", "Inga.goldmanii", "Inga.laurina", "Inga.semialata", "Inga.nobilis", "Inga.oerstediana", "Inga.pezizifera", "Inga.punctata", "Inga.ruiziana", "Inga.sapindoides", "Inga.spectabilis", "Inga.umbellifera", "Jacaranda.copaia", "Lacistema.aggregatum", "Lacmellea.panamensis", "Laetia.procera", "Laetia.thamnia", "Lafoensia.punicifolia", "Licania.hypoleuca", "Licania.platypus", "Lindackeria.laurina", "Lonchocarpus.heptaphyllus", "Luehea.seemannii", "Macrocnemum.roseum", "Maquira.guianensis.costaricana", "Margaritaria.nobilis", "Marila.laxiflora", "Maytenus.schippii", "Miconia.affinis", "Miconia.argentea", "Miconia.elata", "Miconia.hondurensis", "Mosannona.garwoodii", "Myrcia.gatunensis", "Myrospermum.frutescens", "Nectandra.cissiflora", "Nectandra.lineata", "Nectandra.purpurea", "Ochroma.pyramidale", "Ocotea.cernua", "Ocotea.oblonga", "Ocotea.puberula", "Ocotea.whitei", "Oenocarpus.mapora", "Ormosia.amazonica", "Ormosia.coccinea", "Ormosia.macrocalyx", "Pachira.quinata", "Pachira.sessilis", "Perebea.xanthochyma", "Cinnamomum.triplinerve", "Picramnia.latifolia", "Piper.reticulatum", "Platymiscium.pinnatum", "Platypodium.elegans", "Posoqueria.latifolia", "Poulsenia.armata", "Pourouma.bicolor", "Pouteria.fossicola", "Pouteria.reticulata", "Pouteria.stipitata", "Prioria.copaifera", "Protium.costaricense", "Protium.panamense", "Protium.tenuifolium", "Pseudobombax.septenatum", "Psidium.friedrichsthalianum", "Psychotria.grandis", "Pterocarpus.rohrii", "Quararibea.asterolepis", "Quassia.amara", "Randia.armata", "Sapium.broadleaf", "Sapium.glandulosum", "Schizolobium.parahyba", "Senna.dariensis", "Simarouba.amara", "Siparuna.guianensis", "Siparuna.pauciflora", "Sloanea.terniflora", "Socratea.exorrhiza", "Solanum.hayesii", "Sorocea.affinis", "Spachea.membranacea", "Spondias.mombin", "Spondias.radlkoferi", "Sterculia.apetala", "Swartzia.simplex.var.grandiflora", "Swartzia.simplex.continentalis", "Symphonia.globulifera", "Handroanthus.guayacan", "Tabebuia.rosea", "Tabernaemontana.arborea", "Tachigali.versicolor", "Talisia.nervosa", "Talisia.princeps", "Terminalia.amazonia", "Terminalia.oblonga", "Tetragastris.panamensis", "Tetrathylacium.johansenii", "Theobroma.cacao", "Thevetia.ahouai", "Tocoyena.pittieri", "Trattinnickia.aspera", "Trema.micrantha", "Trichanthera.gigantea", "Trichilia.pallida", "Trichilia.tuberculata", "Trichospermum.galeottii", "Triplaris.cumingiana", "Trophis.caucana", "Trophis.racemosa", "Turpinia.occidentalis", "Unonopsis.pittieri", "Virola.multiflora", "Virola.sebifera", "Virola.surinamensis", "Vismia.baccifera", "Vochysia.ferruginea", "Xylopia.macrantha", "Zanthoxylum.ekmanii", "Zanthoxylum.juniperinum", "Zanthoxylum.panamense", "Zanthoxylum.setulosum", "Zuelania.guidonia" ], "rows": 50, "table": true, "tojson": true }, { "name": "BCI.env", "title": "Barro Colorado Island Tree Counts", "object": "BCI.env", "file": "BCI.env.rda", "class": [ "data.frame" ], "fields": [ "UTM.EW", "UTM.NS", "Precipitation", "Elevation", "Age.cat", "Geology", "Habitat", "Stream", "EnvHet" ], "rows": 50, "table": true, "tojson": true }, { "name": "dune", "title": "Vegetation and Environment in Dutch Dune Meadows.", "object": "dune", "file": "dune.env.rda", "class": [ "data.frame" ], "fields": [ "Achimill", "Agrostol", "Airaprae", "Alopgeni", "Anthodor", "Bellpere", "Bromhord", "Chenalbu", "Cirsarve", "Comapalu", "Eleopalu", "Elymrepe", "Empenigr", "Hyporadi", "Juncarti", "Juncbufo", "Lolipere", "Planlanc", "Poaprat", "Poatriv", "Ranuflam", "Rumeacet", "Sagiproc", "Salirepe", "Scorautu", "Trifprat", "Trifrepe", "Vicilath", "Bracruta", "Callcusp" ], "rows": 20, "table": true, "tojson": true }, { "name": "dune.env", "title": "Vegetation and Environment in Dutch Dune Meadows.", "object": "dune.env", "file": "dune.env.rda", "class": [ "data.frame" ], "fields": [ "A1", "Moisture", "Management", "Use", "Manure" ], "rows": 20, "table": true, "tojson": true }, { "name": "dune.phylodis", "title": "Taxonomic Classification and Phylogeny of Dune Meadow Species", "object": "dune.phylodis", "file": "dune.phylodis.rda", "class": [ "dist" ], "fields": [], "table": false, "tojson": false }, { "name": "dune.taxon", "title": "Taxonomic Classification and Phylogeny of Dune Meadow Species", "object": "dune.taxon", "file": "dune.taxon.rda", "class": [ "data.frame" ], "fields": [ "Genus", "Family", "Order", "Superorder", "Subclass" ], "rows": 30, "table": true, "tojson": true }, { "name": "mite", "title": "Oribatid Mite Data with Explanatory Variables", "object": "mite", "file": "mite.env.rda", "class": [ "data.frame" ], "fields": [ "Brachy", "PHTH", "HPAV", "RARD", "SSTR", "Protopl", "MEGR", "MPRO", "TVIE", "HMIN", "HMIN2", "NPRA", "TVEL", "ONOV", "SUCT", "LCIL", "Oribatl1", "Ceratoz1", "PWIL", "Galumna1", "Stgncrs2", "HRUF", "Trhypch1", "PPEL", "NCOR", "SLAT", "FSET", "Lepidzts", "Eupelops", "Miniglmn", "LRUG", "PLAG2", "Ceratoz3", "Oppiminu", "Trimalc2" ], "rows": 70, "table": true, "tojson": true }, { "name": "mite.env", "title": "Oribatid Mite Data with Explanatory Variables", "object": "mite.env", "file": "mite.env.rda", "class": [ "data.frame" ], "fields": [ "SubsDens", "WatrCont", "Substrate", "Shrub", "Topo" ], "rows": 70, "table": true, "tojson": true }, { "name": "mite.pcnm", "title": "Oribatid Mite Data with Explanatory Variables", "object": "mite.pcnm", "file": "mite.pcnm.rda", "class": [ "data.frame" ], "fields": [ "V1", "V2", "V3", "V4", "V5", "V6", "V7", "V8", "V9", "V10", "V11", "V12", "V13", "V14", "V15", "V16", "V17", "V18", "V19", "V20", "V21", "V22" ], "rows": 70, "table": true, "tojson": true }, { "name": "mite.xy", "title": "Oribatid Mite Data with Explanatory Variables", "object": "mite.xy", "file": "mite.xy.rda", "class": [ "data.frame" ], "fields": [ "x", "y" ], "rows": 70, "table": true, "tojson": true }, { "name": "pyrifos", "title": "Response of Aquatic Invertebrates to Insecticide Treatment", "object": "pyrifos", "file": "pyrifos.rda", "class": [ "data.frame" ], "fields": [ "Simve", "Daplo", "Cerpu", "Alogu", "Aloco", "Alore", "Aloaf", "Copsp", "Ostsp", "Slyla", "Acrha", "Aloex", "Chysp", "Alona", "Plead", "Oxyte", "Grate", "Copdi", "NauLa", "CilHa", "Strvi", "amosp", "Ascmo", "Synsp", "Squro", "Squmu", "Polar", "Kerqu", "Anufi", "Mytve", "Mytvi", "Mytmu", "Lepsp", "Leppa", "Colob", "Colbi", "Colun", "Lecsp", "Lecqu", "Lecco", "Leclu", "Lecfl", "Tripo", "Cepsp", "Monlo", "Monae", "Scalo", "Trilo", "Tripo.1", "Tricy", "Trisp", "Tepat", "Rotne", "Notla", "Filsp", "Lopox", "hydrspec", "bothrosp", "olchaeta", "erpoocto", "glsicomp", "alglhete", "hebdstag", "sphidae", "ansuvote", "armicris", "bathcont", "binitent", "gyraalbu", "hippcomp", "lymnstag", "lymnaes7", "physfont", "plbacorn", "popyanti", "radiovat", "radipere", "valvcris", "valvpisc", "hycarina", "gammpule", "aselaqua", "proameri", "collembo", "caenhora", "caenluct", "caenrobu", "cloedipt", "cloesimi", "aeshniae", "libellae", "conagrae", "corident", "coripanz", "coripunc", "cymabons", "hesplinn", "hespsahl", "notoglau", "notomacu", "notoobli", "notoviri", "pacoconc", "pleaminu", "sigadist", "sigafall", "sigastri", "sigarasp", "colyfusc", "donacis6", "gyrimari", "haliconf", "haliflav", "haligruf", "haliobli", "herubrev", "hya_herm", "hyglpusi", "hyhyovat", "hypoplan", "hyporusp", "hytuinae", "hytuvers", "laphminu", "noteclav", "rhantusp", "sialluta", "ablalong", "ablaphmo", "cltanerv", "malopisp", "mopetenu", "prdiussp", "pstavari", "chironsp", "crchirsp", "crclglat", "ditendsp", "mitegchl", "pachgarc", "pachgvit", "popegnub", "popedisp", "acriluce", "chclpige", "conescut", "cricotsp", "liesspec", "psclbarb", "psclgsli", "psclobvi", "psclplat", "psclpsil", "pscladsp", "cladotsp", "laa_spec", "patanysp", "tatarssp", "zaa_spec", "anopmacu", "cepogoae", "chaoobsc", "cucidae4", "tabanusp", "agdasphr", "athrater", "cyrncren", "holodubi", "holopici", "leceriae", "lilurhom", "monaangu", "mystazur", "mystloni", "oecefurv", "oecelacu", "triabico", "paponysp" ], "rows": 132, "table": true, "tojson": true }, { "name": "sipoo", "title": "Birds in the Archipelago of Sipoo (Sibbo and Borgå)", "object": "sipoo", "file": "sipoo.map.rda", "class": [ "data.frame" ], "fields": [ "Pandhali", "Falcsubb", "Tetrtetr", "Scolrust", "Colupalu", "Cucucano", "Apusapus", "Picucanu", "Dryomart", "Jynxtorq", "Deliurbi", "Hirurust", "Motaalba", "Anthtriv", "Trogtrog", "Prunmodu", "Turdpila", "Turdphil", "Turdmeru", "Turdilia", "Eritrube", "Oenaoena", "Phoephoe", "Acroarun", "Acroscir", "Hippicte", "Sylvatri", "Sylvbori", "Sylvcurr", "Sylvcomm", "Phylsibi", "Phyltrocs", "Phyltrocd", "Reguregu", "Muscstri", "Ficehypo", "Parumajo", "Parucaer", "Paruater", "Parumont", "Cardchlo", "Cardspin", "Pyrrpyrr", "Loxicurv", "Frincoel", "Sturvulg", "Orioorio", "Corvcoro", "Corvcora", "Garrglan" ], "rows": 18, "table": true, "tojson": true }, { "name": "sipoo.map", "title": "Birds in the Archipelago of Sipoo (Sibbo and Borgå)", "object": "sipoo.map", "file": "sipoo.map.rda", "class": [ "data.frame" ], "fields": [ "N", "E", "area" ], "rows": 18, "table": true, "tojson": true }, { "name": "varechem", "title": "Vegetation and environment in lichen pastures", "object": "varechem", "file": "varechem.rda", "class": [ "data.frame" ], "fields": [ "N", "P", "K", "Ca", "Mg", "S", "Al", "Fe", "Mn", "Zn", "Mo", "Baresoil", "Humdepth", "pH" ], "rows": 24, "table": true, "tojson": true }, { "name": "varespec", "title": "Vegetation and environment in lichen pastures", "object": "varespec", "file": "varespec.rda", "class": [ "data.frame" ], "fields": [ "Callvulg", "Empenigr", "Rhodtome", "Vaccmyrt", "Vaccviti", "Pinusylv", "Descflex", "Betupube", "Vacculig", "Diphcomp", "Dicrsp", "Dicrfusc", "Dicrpoly", "Hylosple", "Pleuschr", "Polypili", "Polyjuni", "Polycomm", "Pohlnuta", "Ptilcili", "Barbhatc", "Cladarbu", "Cladrang", "Cladstel", "Cladunci", "Cladcocc", "Cladcorn", "Cladgrac", "Cladfimb", "Cladcris", "Cladchlo", "Cladbotr", "Cladamau", "Cladsp", "Cetreric", "Cetrisla", "Flavniva", "Nepharct", "Stersp", "Peltapht", "Icmaeric", "Cladcerv", "Claddefo", "Cladphyl" ], "rows": 24, "table": true, "tojson": true } ], "_help": [ { "page": "vegan-package", "title": "Community Ecology Package: Ordination, Diversity and Dissimilarities", "topics": [ "vegan-package", "vegan" ] }, { "page": "add1.cca", "title": "Add or Drop Single Terms to a Constrained Ordination Model", "topics": [ "add1.cca", "drop1.cca" ] }, { "page": "adipart", "title": "Additive Diversity Partitioning and Hierarchical Null Model Testing", "topics": [ "adipart", "adipart.default", "adipart.formula", "hiersimu", "hiersimu.default", "hiersimu.formula" ] }, { "page": "adonis", "title": "Permutational Multivariate Analysis of Variance Using Distance Matrices", "topics": [ "adonis2" ] }, { "page": "anosim", "title": "Analysis of Similarities", "topics": [ "anosim", "plot.anosim", "summary.anosim" ] }, { "page": "anova.cca", "title": "Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates", "topics": [ "anova.cca", "permutest", "permutest.cca" ] }, { "page": "avgdist", "title": "Averaged Subsampled Dissimilarity Matrices", "topics": [ "avgdist" ] }, { "page": "BCI", "title": "Barro Colorado Island Tree Counts", "topics": [ "BCI", "BCI.env" ] }, { "page": "beals", "title": "Beals Smoothing and Degree of Absence", "topics": [ "beals", "swan" ] }, { "page": "betadisper", "title": "Multivariate homogeneity of groups dispersions (variances)", "topics": [ "anova.betadisper", "betadisper", "betadistances", "boxplot.betadisper", "eigenvals.betadisper", "ordimedian", "plot.betadisper", "print.betadisper", "scores.betadisper", "TukeyHSD.betadisper" ] }, { "page": "betadiver", "title": "Indices of beta Diversity", "topics": [ "betadiver", "plot.betadiver", "scores.betadiver" ] }, { "page": "bgdispersal", "title": "Coefficients of Biogeographical Dispersal Direction", "topics": [ "bgdispersal" ] }, { "page": "bioenv", "title": "Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities", "topics": [ "bioenv", "bioenv.default", "bioenv.formula", "bioenvdist", "summary.bioenv" ] }, { "page": "biplot.rda", "title": "PCA biplot", "topics": [ "biplot.cca", "biplot.rda" ] }, { "page": "cascadeKM", "title": "K-means partitioning using a range of values of K", "topics": [ "cascadeKM", "cIndexKM", "orderingKM", "plot.cascadeKM", "pregraphKM" ] }, { "page": "cca", "title": "[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis", "topics": [ "ca", "cca", "cca.default", "cca.formula", "pca", "rda", "rda.default", "rda.formula" ] }, { "page": "cca.object", "title": "Result Object from Constrained Ordination", "topics": [ "cca.object", "model.frame.cca", "model.matrix.cca", "model.matrix.rda", "ordConstrained", "ordiYbar", "print.cca", "weights.cca", "weights.decorana", "weights.rda" ] }, { "page": "CCorA", "title": "Canonical Correlation Analysis", "concept": [ "ordination" ], "topics": [ "biplot.CCorA", "CCorA" ] }, { "page": "clamtest", "title": "Multinomial Species Classification Method (CLAM)", "topics": [ "clamtest", "plot.clamtest", "summary.clamtest" ] }, { "page": "commsim", "title": "Create an Object for Null Model Algorithms", "topics": [ "commsim", "make.commsim", "print.commsim" ] }, { "page": "contribdiv", "title": "Contribution Diversity Approach", "topics": [ "contribdiv", "plot.contribdiv" ] }, { "page": "dbrda", "title": "Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysis", "topics": [ "capscale", "dbrda", "pco" ] }, { "page": "decorana", "title": "Detrended Correspondence Analysis and Basic Reciprocal Averaging", "topics": [ "decorana", "downweight", "plot.decorana", "points.decorana", "scores.decorana", "summary.decorana", "text.decorana" ] }, { "page": "decostand", "title": "Standardization Methods for Community Ecology", "topics": [ "decobackstand", "decostand", "wisconsin" ] }, { "page": "designdist", "title": "Design your own Dissimilarities", "topics": [ "chaodist", "designdist", "designdist2" ] }, { "page": "deviance.cca", "title": "Statistics Resembling Deviance and AIC for Constrained Ordination", "topics": [ "deviance.cca", "deviance.rda", "extractAIC.cca" ] }, { "page": "dispindmorisita", "title": "Morisita index of intraspecific aggregation", "topics": [ "dispindmorisita" ] }, { "page": "dispweight", "title": "Dispersion-based weighting of species counts", "topics": [ "dispweight", "gdispweight", "summary.dispweight" ] }, { "page": "distconnected", "title": "Connectedness of Dissimilarities", "topics": [ "distconnected", "no.shared" ] }, { "page": "diversity", "title": "Ecological Diversity Indices", "topics": [ "diversity", "fisher.alpha", "simpson.unb", "specnumber" ] }, { "page": "dune", "title": "Vegetation and Environment in Dutch Dune Meadows.", "topics": [ "dune", "dune.env" ] }, { "page": "dune.taxon", "title": "Taxonomic Classification and Phylogeny of Dune Meadow Species", "topics": [ "dune.phylodis", "dune.taxon" ] }, { "page": "eigenvals", "title": "Extract Eigenvalues from an Ordination Object", "topics": [ "eigenvals", "eigenvals.cca", "eigenvals.decorana", "eigenvals.default", "eigenvals.dudi", "eigenvals.pca", "eigenvals.pcnm", "eigenvals.pco", "eigenvals.prcomp", "eigenvals.princomp", "eigenvals.wcmdscale", "summary.eigenvals" ] }, { "page": "envfit", "title": "Fits an Environmental Vector or Factor onto an Ordination", "topics": [ "envfit", "envfit.default", "envfit.formula", "factorfit", "labels.envfit", "names<-.envfit", "plot.envfit", "scores.envfit", "vectorfit" ] }, { "page": "eventstar", "title": "Scale Parameter at the Minimum of the Tsallis Evenness Profile", "topics": [ "eventstar" ] }, { "page": "fisherfit", "title": "Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data", "topics": [ "as.fisher", "as.preston", "fisherfit", "lines.preston", "lines.prestonfit", "plot.fisher", "plot.fisherfit", "plot.preston", "plot.prestonfit", "prestondistr", "prestonfit", "veiledspec" ] }, { "page": "goodness.cca", "title": "Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)", "topics": [ "alias.cca", "goodness", "goodness.cca", "inertcomp", "intersetcor", "spenvcor", "vif.cca" ] }, { "page": "goodness.metaMDS", "title": "Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling", "topics": [ "goodness.metaMDS", "goodness.monoMDS", "stressplot", "stressplot.default", "stressplot.monoMDS" ] }, { "page": "indpower", "title": "Indicator Power of Species", "topics": [ "indpower" ] }, { "page": "influence.cca", "title": "Linear Model Diagnostics for Constrained Ordination", "topics": [ "cooks.distance.cca", "df.residual.cca", "hatvalues.cca", "hatvalues.rda", "influence.cca", "qr.cca", "rstandard.cca", "rstudent.cca", "sigma.cca", "SSD.cca", "vcov.cca" ] }, { "page": "isomap", "title": "Isometric Feature Mapping Ordination", "topics": [ "isomap", "isomapdist", "plot.isomap", "summary.isomap" ] }, { "page": "kendall.global", "title": "Kendall coefficient of concordance", "topics": [ "kendall.global", "kendall.post" ] }, { "page": "linestack", "title": "Plots One-dimensional Diagrams without Overwriting Labels", "topics": [ "linestack" ] }, { "page": "make.cepnames", "title": "Abbreviates a Two-Part Botanical or Zoological Latin Name into Character String", "topics": [ "make.cepnames" ] }, { "page": "mantel", "title": "Mantel and Partial Mantel Tests for Dissimilarity Matrices", "topics": [ "mantel", "mantel.partial", "summary.mantel" ] }, { "page": "mantel.correlog", "title": "Mantel Correlogram", "topics": [ "mantel.correlog", "plot.mantel.correlog" ] }, { "page": "MDSaddpoints", "title": "Add New Points to NMDS ordination", "topics": [ "dist2xy", "MDSaddpoints" ] }, { "page": "MDSrotate", "title": "Rotate First MDS Dimension Parallel to an External Variable", "topics": [ "MDSrotate" ] }, { "page": "metaMDS", "title": "Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores", "topics": [ "initMDS", "metaMDS", "metaMDSdist", "metaMDSiter", "metaMDSredist", "plot.metaMDS", "points.metaMDS", "postMDS", "scores.metaMDS", "text.metaMDS" ] }, { "page": "mite", "title": "Oribatid Mite Data with Explanatory Variables", "topics": [ "mite", "mite.env", "mite.pcnm", "mite.xy" ] }, { "page": "monoMDS", "title": "Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling", "topics": [ "monoMDS", "plot.monoMDS", "points.monoMDS", "scores.monoMDS", "text.monoMDS" ] }, { "page": "MOStest", "title": "Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme", "topics": [ "confint.MOStest", "fieller.MOStest", "MOStest", "plot.MOStest", "profile.MOStest" ] }, { "page": "mrpp", "title": "Multi Response Permutation Procedure and Mean Dissimilarity Matrix", "topics": [ "meandist", "mrpp", "plot.meandist", "summary.meandist", "summary.mrpp" ] }, { "page": "mso", "title": "Functions for performing and displaying a spatial partitioning of cca or rda results", "topics": [ "mso", "msoplot" ] }, { "page": "multipart", "title": "Multiplicative Diversity Partitioning", "topics": [ "multipart", "multipart.default", "multipart.formula" ] }, { "page": "nestedtemp", "title": "Nestedness Indices for Communities of Islands or Patches", "topics": [ "nestedbetajac", "nestedbetasor", "nestedchecker", "nesteddisc", "nestedn0", "nestednodf", "nestedtemp", "plot.nestednodf", "plot.nestedtemp" ] }, { "page": "nobs.cca", "title": "Extract the Number of Observations from a vegan Fit.", "topics": [ "nobs.betadisper", "nobs.cca", "nobs.CCorA", "nobs.decorana", "nobs.isomap", "nobs.metaMDS", "nobs.pcnm", "nobs.procrustes", "nobs.rad", "nobs.varpart", "nobs.wcmdscale" ] }, { "page": "nullmodel", "title": "Null Model and Simulation", "topics": [ "nullmodel", "print.nullmodel", "print.simmat", "simmat", "simulate.nullmodel", "smbind", "str.nullmodel", "update.nullmodel" ] }, { "page": "oecosimu", "title": "Evaluate Statistics with Null Models of Biological Communities", "topics": [ "as.ts.oecosimu", "oecosimu", "summary.oecosimu", "toCoda", "toCoda.oecosimu" ] }, { "page": "optspace", "title": "optspace: algorithm for matrix reconstruction from a partially revealed set", "topics": [ "optspace" ] }, { "page": "ordiarrows", "title": "Add Arrows and Line Segments to Ordination Diagrams", "topics": [ "ordiarrows", "ordigrid", "ordisegments" ] }, { "page": "ordiArrowTextXY", "title": "Support Functions for Drawing Vectors", "topics": [ "ordiArrowMul", "ordiArrowTextXY" ] }, { "page": "ordihull", "title": "Display Groups or Factor Levels in Ordination Diagrams", "topics": [ "ordiareatest", "ordibar", "ordicluster", "ordiellipse", "ordihull", "ordispider", "scores.ordihull", "summary.ordiareatest", "summary.ordiellipse", "summary.ordihull" ] }, { "page": "ordilabel", "title": "Add Text on Non-transparent Label to an Ordination Plot.", "topics": [ "ordilabel" ] }, { "page": "ordiplot", "title": "Alternative plot and identify Functions for Ordination", "topics": [ "identify.ordiplot", "ordiplot", "points.ordiplot", "scores.ordiplot", "text.ordiplot" ] }, { "page": "ordipointlabel", "title": "Ordination Plots with Points and Optimized Locations for Text", "topics": [ "labels.ordipointlabel", "ordipointlabel", "plot.ordipointlabel" ] }, { "page": "ordistep", "title": "Choose a Model by Permutation Tests in Constrained Ordination", "topics": [ "ordiR2step", "ordistep" ] }, { "page": "ordisurf", "title": "Fit and Plot Smooth Surfaces of Variables on Ordination.", "topics": [ "calibrate.ordisurf", "ordisurf", "ordisurf.default", "ordisurf.formula", "plot.ordisurf" ] }, { "page": "orditorp", "title": "Add Text or Points to Ordination Plots", "topics": [ "orditorp" ] }, { "page": "pcnm", "title": "Principal Coordinates of Neighbourhood Matrix", "topics": [ "pcnm", "scores.pcnm" ] }, { "page": "permatfull", "title": "Matrix Permutation Algorithms for Presence-Absence and Count Data", "topics": [ "as.ts.permat", "lines.permat", "permatfull", "permatswap", "plot.permat", "print.permat", "print.summary.permat", "summary.permat", "toCoda.permat" ] }, { "page": "permustats", "title": "Extract, Analyse and Display Permutation Results", "topics": [ "boxplot.permustats", "c.permustats", "density.permustats", "pairs.permustats", "permustats", "permustats.anosim", "permustats.anova.cca", "permustats.CCorA", "permustats.envfit", "permustats.factorfit", "permustats.mantel", "permustats.mrpp", "permustats.mso", "permustats.oecosimu", "permustats.ordiareatest", "permustats.permutest.betadisper", "permustats.permutest.cca", "permustats.protest", "permustats.vectorfit", "qqnorm.permustats", "summary.permustats" ] }, { "page": "permutations", "title": "Permutation tests in Vegan", "topics": [ "permutations" ] }, { "page": "permutest.betadisper", "title": "Permutation test of multivariate homogeneity of groups dispersions (variances)", "topics": [ "permutest.betadisper" ] }, { "page": "plot.cca", "title": "Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis", "topics": [ "labels.cca", "plot.cca", "points.cca", "print.summary.cca", "scores.cca", "scores.rda", "summary.cca", "text.cca" ] }, { "page": "prc", "title": "Principal Response Curves for Treatments with Repeated Observations", "topics": [ "plot.prc", "prc", "summary.prc" ] }, { "page": "predict.cca", "title": "Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)", "topics": [ "calibrate", "calibrate.cca", "coef.cca", "coef.rda", "fitted.capscale", "fitted.cca", "fitted.dbrda", "fitted.rda", "predict.cca", "predict.dbrda", "predict.decorana", "predict.rda", "residuals.cca" ] }, { "page": "procrustes", "title": "Procrustes Rotation of Two Configurations and PROTEST", "topics": [ "fitted.procrustes", "lines.procrustes", "plot.procrustes", "points.procrustes", "predict.procrustes", "procrustes", "protest", "residuals.procrustes", "summary.procrustes", "text.procrustes" ] }, { "page": "pyrifos", "title": "Response of Aquatic Invertebrates to Insecticide Treatment", "topics": [ "pyrifos" ] }, { "page": "radfit", "title": "Rank - Abundance or Dominance / Diversity Models", "topics": [ "AIC.radfit", "AIC.radfit.frame", "as.rad", "coef.radfit", "coef.radfit.frame", "deviance.radfit", "deviance.radfit.frame", "fitted.radfit", "fitted.radfit.frame", "lines.radfit", "lines.radline", "logLik.radfit", "logLik.radfit.frame", "plot.rad", "plot.radfit", "plot.radfit.frame", "plot.radline", "points.radfit", "points.radline", "predict.radfit", "predict.radfit.frame", "predict.radline", "rad.lognormal", "rad.null", "rad.preempt", "rad.zipf", "rad.zipfbrot", "radfit", "radfit.data.frame", "radfit.default", "radlattice", "summary.radfit.frame" ] }, { "page": "rankindex", "title": "Compares Dissimilarity Indices for Gradient Detection", "topics": [ "rankindex" ] }, { "page": "rarefy", "title": "Rarefaction Species Richness", "topics": [ "drarefy", "rarecurve", "rarefy", "rareslope", "rrarefy" ] }, { "page": "raupcrick", "title": "Raup-Crick Dissimilarity with Unequal Sampling Densities of Species", "topics": [ "raupcrick" ] }, { "page": "read.cep", "title": "Reads a CEP (Canoco) data file", "topics": [ "read.cep" ] }, { "page": "renyi", "title": "Renyi and Hill Diversities and Corresponding Accumulation Curves", "topics": [ "lines.renyiaccum", "persp.renyiaccum", "plot.renyi", "plot.renyiaccum", "renyi", "renyiaccum" ] }, { "page": "reorder.hclust", "title": "Reorder a Hierarchical Clustering Tree", "topics": [ "cutreeord", "reorder.hclust", "rev.hclust", "scores.hclust" ] }, { "page": "RsquareAdj", "title": "Adjusted R-square", "topics": [ "RsquareAdj", "RsquareAdj.cca", "RsquareAdj.default", "RsquareAdj.glm", "RsquareAdj.lm", "RsquareAdj.rda" ] }, { "page": "scores", "title": "Get Species or Site Scores from an Ordination", "topics": [ "scores", "scores.default", "scores.lda" ] }, { "page": "screeplot.cca", "title": "Screeplots for Ordination Results and Broken Stick Distributions", "topics": [ "bstick", "bstick.cca", "bstick.decorana", "bstick.default", "bstick.prcomp", "bstick.princomp", "screeplot.cca", "screeplot.decorana", "screeplot.prcomp", "screeplot.princomp" ] }, { "page": "simper", "title": "Similarity Percentages", "topics": [ "simper", "summary.simper" ] }, { "page": "simulate.rda", "title": "Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination", "topics": [ "simulate.capscale", "simulate.cca", "simulate.rda" ] }, { "page": "sipoo", "title": "Birds in the Archipelago of Sipoo (Sibbo and Borgå)", "topics": [ "sipoo", "sipoo.map" ] }, { "page": "spantree", "title": "Minimum Spanning Tree", "topics": [ "as.hclust.spantree", "cophenetic.spantree", "lines.spantree", "plot.spantree", "spandepth", "spantree" ] }, { "page": "specaccum", "title": "Species Accumulation Curves", "topics": [ "AIC.fitspecaccum", "boxplot.specaccum", "deviance.fitspecaccum", "fitspecaccum", "lines.fitspecaccum", "lines.specaccum", "logLik.fitspecaccum", "nobs.fitspecaccum", "plot.fitspecaccum", "plot.specaccum", "predict.fitspecaccum", "predict.specaccum", "print.specaccum", "specaccum", "specslope", "summary.specaccum" ] }, { "page": "specpool", "title": "Extrapolated Species Richness in a Species Pool", "topics": [ "estaccumR", "estimateR", "estimateR.data.frame", "estimateR.default", "estimateR.matrix", "plot.poolaccum", "poolaccum", "specpool", "specpool2vect", "summary.poolaccum" ] }, { "page": "sppscores", "title": "Add or Replace Species Scores in Distance-Based Ordination", "topics": [ "sppscores", "sppscores<-", "sppscores<-.capscale", "sppscores<-.dbrda", "sppscores<-.metaMDS", "sppscores<-.monoMDS", "sppscores<-.wcmdscale" ] }, { "page": "SSarrhenius", "title": "Self-Starting nls Species-Area Models", "topics": [ "SSarrhenius", "SSgitay", "SSgleason", "SSlomolino" ] }, { "page": "stepacross", "title": "Stepacross as Flexible Shortest Paths or Extended Dissimilarities", "topics": [ "stepacross" ] }, { "page": "stressplot.wcmdscale", "title": "Display Ordination Distances Against Observed Distances in Eigenvector Ordinations", "topics": [ "stressplot.capscale", "stressplot.cca", "stressplot.dbrda", "stressplot.prcomp", "stressplot.princomp", "stressplot.rda", "stressplot.wcmdscale" ] }, { "page": "taxondive", "title": "Indices of Taxonomic Diversity and Distinctness", "topics": [ "plot.taxondive", "summary.taxondive", "taxa2dist", "taxondive" ] }, { "page": "tolerance", "title": "Species tolerances and sample heterogeneities", "topics": [ "tolerance", "tolerance.cca", "tolerance.decorana" ] }, { "page": "treedive", "title": "Functional Diversity and Community Distances from Species Trees", "topics": [ "treedist", "treedive", "treeheight" ] }, { "page": "tsallis", "title": "Tsallis Diversity and Corresponding Accumulation Curves", "topics": [ "persp.tsallisaccum", "tsallis", "tsallisaccum" ] }, { "page": "varechem", "title": "Vegetation and environment in lichen pastures", "topics": [ "varechem", "varespec" ] }, { "page": "varpart", "title": "Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices", "topics": [ "plot.varpart", "plot.varpart234", "showvarparts", "simpleDBRDA", "simpleRDA2", "summary.varpart", "varpart", "varpart2", "varpart3", "varpart4" ] }, { "page": "vegan-deprecated", "title": "Deprecated Functions in vegan package", "topics": [ "vegan-deprecated" ] }, { "page": "vegdist", "title": "Dissimilarity Indices for Community Ecologists", "topics": [ "vegdist" ] }, { "page": "vegemite", "title": "Display Compact Ordered Community Tables", "topics": [ "coverscale", "tabasco", "vegemite" ] }, { "page": "wascores", "title": "Weighted Averages Scores for Species", "topics": [ "eigengrad", "scores.wascores", "wascores" ] }, { "page": "wcmdscale", "title": "Weighted Classical (Metric) Multidimensional Scaling", "topics": [ "plot.wcmdscale", "scores.wcmdscale", "wcmdscale" ] } ], "_readme": "https://github.com/vegandevs/vegan/raw/HEAD/README.md", "_rundeps": [ "cluster", "lattice", "MASS", "Matrix", "mgcv", "nlme", "permute" ], "_sysdeps": [ { "shlib": "liblapack", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libblas", "package": "libopenblas0-pthread", "source": "openblas", "version": "0.3.26+ds-1ubuntu0.1", "name": "openblas", "homepage": "https://www.openblas.net/", "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)" }, { "shlib": "libgfortran", "package": "libgfortran5", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "fortran", "homepage": "http://gcc.gnu.org/", "description": "Runtime library for GNU Fortran applications" } ], "_vignettes": [ { "source": "decision-vegan.Rnw", "filename": "decision-vegan.pdf", "title": "Design decisions and implementation", "engine": "utils::Sweave", "headings": [], "created": "2013-08-28 08:56:55", "modified": "2017-09-18 08:57:16", "commits": 8 }, { "source": "diversity-vegan.Rnw", "filename": "diversity-vegan.pdf", "title": "Diversity analysis in vegan", "engine": "utils::Sweave", "headings": [], "created": "2013-08-28 08:56:55", "modified": "2026-04-20 19:32:56", "commits": 12 }, { "source": "intro-vegan.Rnw", "filename": "intro-vegan.pdf", "title": "Introduction to ordination in vegan", "engine": "utils::Sweave", "headings": [], "created": "2013-08-28 08:56:55", "modified": "2026-02-28 16:17:31", "commits": 13 }, { "source": "partitioning.Rnw", "filename": "partitioning.pdf", "title": "Partition of Variation", "engine": "utils::Sweave", "headings": [], "created": "2016-02-25 11:45:11", "modified": "2025-08-11 10:38:49", "commits": 3 }, { "source": "FAQ-vegan.Rmd", "filename": "FAQ-vegan.html", "title": "vegan FAQ", "engine": "knitr::knitr", "headings": [ "vegan FAQ", "Introduction", "What is vegan?", "How to obtain vegan and R?", "What other packages are available for ecologists?", "What other documentation is available for vegan?", "Is there a Graphical User Interface (GUI) for vegan?", "How to cite vegan?", "How to build vegan from sources?", "Are there binaries for devel versions?", "How to report a bug in vegan?", "Is it a bug or a feature?", "Can I contribute to vegan?", "Ordination", "I have only numeric and positive data but vegan still complains", "Can I use tibbles in ordination?", "Can I analyse binary or cover class data?", "Why dissimilarities in vegan differ from other sources?", "I cannot get repeated solutions in metaMDS", "I get zero stress but no repeated solutions in metaMDS", "I have heard that you cannot fit environmental vectors or surfaces to NMDS results which only have rank-order scores", "Why ordiellipses are much smaller than ggplot2 ellipses?", "Where can I find numerical scores of ordination axes?", "How the RDA results are scaled?", "Variance explained by ordination axes.", "Can I have random effects in constrained ordination or in adonis?", "Is it possible to have passive points in ordination?", "Class variables and dummies", "How are environmental arrows scaled?", "I cannot see all variables in constrained ordination", "Plotting aliased variables", "Restricted permutations in vegan", "Why restricted permutation does not influence adonis results?", "How to use different plotting symbols in ordination graphics?", "How to avoid cluttered ordination graphs?", "Can I flip an axis in ordination diagram?", "Can I zoom into an ordination plot?", "Other analysis methods", "Is there TWINSPAN?" ], "created": "2016-02-25 11:45:11", "modified": "2026-05-20 16:43:42", "commits": 20 } ], "_score": 19.857767578101363, "_indexed": true, "_nocasepkg": "vegan", "_universes": [ "vegandevs", "jarioksa" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "2.8-0", "date": "2026-06-01T21:15:36.000Z", "distro": "noble", "arch": "aarch64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "25009d81891dc3d379b2542d99ed024aaaa5c4d9ff90c1fdcca49cfc80779b67", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.7.0", "os": "linux", "version": "2.8-0", "date": "2026-06-01T21:15:35.000Z", "distro": "noble", "arch": "x86_64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "3f3cf50b1c0f70e78420ff5caa17cfedff8c82460b8a938fb592631b13bda123", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.6.0", "os": "linux", "version": "2.8-0", "date": "2026-06-01T21:15:53.000Z", "distro": "noble", "arch": "aarch64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "0294301b91d4dc1e007150c57834b0467ace25ffee478177389863c6c6aba516", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.6.0", "os": "linux", "version": "2.8-0", "date": "2026-06-01T21:15:16.000Z", "distro": "noble", "arch": "x86_64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "ff3917c8346986c9d32c1cdc3db947570fed3c2e49cc1c499e62c5040d4089fa", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.5.3", "os": "mac", "version": "2.8-0", "date": "2026-06-01T21:20:20.000Z", "arch": "aarch64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "26b677e6af72889d45be0f5becec527c565e9c58349c6026eff9c07627583713", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.5.3", "os": "mac", "version": "2.8-0", "date": "2026-06-01T21:22:15.000Z", "arch": "x86_64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "d5f0f5082daed7ca1d1285cf7cbabe657d7413b8dd011b189c106d20fc96c912", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.6.0", "os": "mac", "version": "2.8-0", "date": "2026-06-01T21:20:52.000Z", "arch": "aarch64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "aa6a0f6e5acb06fdc154837c83124dcd50256551e8ac3974f319acc6237a97a6", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.6.0", "os": "mac", "version": "2.8-0", "date": "2026-06-01T21:20:16.000Z", "arch": "x86_64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "cb0cc007a570af0c03a58ad357c44ef813b2a64e014cf8d04a50f72beee86a77", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.6.0", "os": "wasm", "version": "2.8-0", "date": "2026-06-01T21:15:37.000Z", "arch": "emscripten", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "b086717915475029247fb119b21dc4b42dd44edd372eb6464f5327a8d8a56417", "status": "success", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.7.0", "os": "win", "version": "2.8-0", "date": "2026-06-01T21:15:04.000Z", "arch": "x86_64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "008b5afef5a4e4c3008c1577af0c533bad406643da50e25be49b60070835eda3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.5.3", "os": "win", "version": "2.8-0", "date": "2026-06-01T21:15:03.000Z", "arch": "x86_64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "2e1d3fb66689b9ba249a8253bc151e3e9ce9e7587bf666853fc236aff0a9d442", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" }, { "r": "4.6.0", "os": "win", "version": "2.8-0", "date": "2026-06-01T21:14:51.000Z", "arch": "x86_64", "commit": "d43e2b433894e81c56e2a3de03df9eb7a8f46488", "fileid": "1f8fb45227dc31c9d0d205dae4856f843e0e7db44326337e3506e225482a6c82", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/vegandevs/actions/runs/26782194530" } ] }