Package: vegan 2.7-0

Jari Oksanen

vegan: Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Authors:Jari Oksanen [aut, cre], Gavin L. Simpson [aut], F. Guillaume Blanchet [aut], Roeland Kindt [aut], Pierre Legendre [aut], Peter R. Minchin [aut], R.B. O'Hara [aut], Peter Solymos [aut], M. Henry H. Stevens [aut], Eduard Szoecs [aut], Helene Wagner [aut], Matt Barbour [aut], Michael Bedward [aut], Ben Bolker [aut], Daniel Borcard [aut], Tuomas Borman [aut], Gustavo Carvalho [aut], Michael Chirico [aut], Miquel De Caceres [aut], Sebastien Durand [aut], Heloisa Beatriz Antoniazi Evangelista [aut], Rich FitzJohn [aut], Michael Friendly [aut], Brendan Furneaux [aut], Geoffrey Hannigan [aut], Mark O. Hill [aut], Leo Lahti [aut], Dan McGlinn [aut], Marie-Helene Ouellette [aut], Eduardo Ribeiro Cunha [aut], Tyler Smith [aut], Adrian Stier [aut], Cajo J.F. Ter Braak [aut], James Weedon [aut]

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vegan.pdf |vegan.html
vegan/json (API)
NEWS

# Install 'vegan' in R:
install.packages('vegan', repos = c('https://vegandevs.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/vegandevs/vegan/issues

Uses libs:
  • openblas– Optimized BLAS
  • fortran– Runtime library for GNU Fortran applications
Datasets:
  • BCI - Barro Colorado Island Tree Counts
  • BCI.env - Barro Colorado Island Tree Counts
  • dune - Vegetation and Environment in Dutch Dune Meadows.
  • dune.env - Vegetation and Environment in Dutch Dune Meadows.
  • dune.phylodis - Taxonomic Classification and Phylogeny of Dune Meadow Species
  • dune.taxon - Taxonomic Classification and Phylogeny of Dune Meadow Species
  • mite - Oribatid Mite Data with Explanatory Variables
  • mite.env - Oribatid Mite Data with Explanatory Variables
  • mite.pcnm - Oribatid Mite Data with Explanatory Variables
  • mite.xy - Oribatid Mite Data with Explanatory Variables
  • pyrifos - Response of Aquatic Invertebrates to Insecticide Treatment
  • sipoo - Birds in the Archipelago of Sipoo
  • sipoo.map - Birds in the Archipelago of Sipoo
  • varechem - Vegetation and environment in lichen pastures
  • varespec - Vegetation and environment in lichen pastures

On CRAN:

ecological-modellingecologyordination

19.23 score 452 stars 434 packages 14k scripts 107k downloads 6.9k mentions 202 exports 7 dependencies

Last updated 3 days agofrom:3621a97f20. Checks:OK: 8 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 05 2024
R-4.5-win-x86_64OKNov 05 2024
R-4.5-linux-x86_64NOTENov 05 2024
R-4.4-win-x86_64OKNov 05 2024
R-4.4-mac-x86_64OKNov 05 2024
R-4.4-mac-aarch64OKNov 05 2024
R-4.3-win-x86_64OKNov 05 2024
R-4.3-mac-x86_64OKNov 05 2024
R-4.3-mac-aarch64OKNov 05 2024

Exports:adipartadonisadonis2anosimanova.ccaas.fisheras.mcmc.oecosimuas.mcmc.permatas.mlmas.prestonas.radavgdistbealsbetadisperbetadiverbgdispersalbioenvbioenvdistbstickcacalibratecapscalecascadeKMccaCCorAcenterdistcentredistchaodistcIndexKMclamtestcommsimcommsimulatorcontribdivcoverscalecutreeorddbrdadecobackstanddecoranadecostanddesigndistdesigndist2dispindmorisitadispweightdist2xydistconnecteddiversitydownweightdrarefyeigengradeigenvalsenvfitestaccumRestimateReventstarfactorfitfieller.MOStestfisher.alphafisherfitfitspecaccumgdispweightgoodnesshiersimuindpowerinertcompinitMDSintersetcorisomapisomapdistkendall.globalkendall.postlinestackmake.cepnamesmake.commsimmantelmantel.correlogmantel.partialMDSaddpointsMDSrotatemeandistmetaMDSmetaMDSdistmetaMDSitermetaMDSredistmonoMDSMOStestmrppmsomsoplotmultipartnestedbetajacnestedbetasornestedcheckernesteddiscnestedn0nestednodfnestedtempno.sharednullmodeloecosimuordiareatestordiArrowMulordiarrowsordiArrowTextXYordibarordicloudordiclusterordiellipseordigridordihullordilabelordiplotordipointlabelordiR2stepordiresidsordisegmentsordispiderordisplomordistepordisurforditkplotorditorpordixyplotordiYbarpanel.ordipanel.ordi3dpanel.ordiarrowspasteCallpcapcnmpcopermatfullpermatswappermustatspermutestpoolaccumpostMDSprcprepanel.ordi3dprestondistrprestonfitprocrustesprotestrad.lognormalrad.nullrad.preemptrad.zipfrad.zipfbrotradfitradlatticerankindexrarecurverarefyraresloperaupcrickrdaread.ceprenyirenyiaccumrrarefyRsquareAdjscoresshowvarpartssimpersimpson.unbsmbindspandepthspantreespecaccumspecnumberspecpoolspecpool2vectspecslopespenvcorsppscoressppscores<-SSarrheniusSSgitaySSgleasonSSlomolinostepacrossstressplotswantabascotaxa2disttaxondivetoCodatolerancetreedisttreedivetreeheighttsallistsallisaccumvarpartvectorfitvegandocsvegdistvegemiteveiledspecvif.ccawascoreswcmdscalewisconsin

Dependencies:clusterlatticeMASSMatrixmgcvnlmepermute

Design decisions and implementation

Rendered fromdecision-vegan.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2017-09-18
Started: 2013-08-28

Diversity analysis in vegan

Rendered fromdiversity-vegan.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2018-01-11
Started: 2013-08-28

Introduction to ordination in vegan

Rendered fromintro-vegan.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2024-04-09
Started: 2013-08-28

Partition of Variation

Rendered frompartitioning.Rnwusingutils::Sweaveon Nov 05 2024.

Last update: 2016-02-28
Started: 2016-02-25

vegan FAQ

Rendered fromFAQ-vegan.Rmdusingknitr::knitron Nov 05 2024.

Last update: 2024-04-09
Started: 2016-02-25

Readme and manuals

Help Manual

Help pageTopics
Community Ecology Package: Ordination, Diversity and Dissimilaritiesvegan-package vegan
Add or Drop Single Terms to a Constrained Ordination Modeladd1.cca drop1.cca
Additive Diversity Partitioning and Hierarchical Null Model Testingadipart adipart.default adipart.formula hiersimu hiersimu.default hiersimu.formula
Permutational Multivariate Analysis of Variance Using Distance Matricesadonis2
Analysis of Similaritiesanosim plot.anosim summary.anosim
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinatesanova.cca permutest permutest.cca
Averaged Subsampled Dissimilarity Matricesavgdist
Barro Colorado Island Tree CountsBCI BCI.env
Beals Smoothing and Degree of Absencebeals swan
Multivariate homogeneity of groups dispersions (variances)anova.betadisper betadisper boxplot.betadisper eigenvals.betadisper ordimedian plot.betadisper print.betadisper scores.betadisper TukeyHSD.betadisper
Indices of beta Diversitybetadiver plot.betadiver scores.betadiver
Coefficients of Biogeographical Dispersal Directionbgdispersal
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilaritiesbioenv bioenv.default bioenv.formula bioenvdist summary.bioenv
PCA biplotbiplot.cca biplot.rda
K-means partitioning using a range of values of KcascadeKM cIndexKM orderingKM plot.cascadeKM pregraphKM
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysisca cca cca.default cca.formula pca rda rda.default rda.formula
Result Object from Constrained Ordinationcca.object model.frame.cca model.matrix.cca model.matrix.rda ordConstrained ordiYbar print.cca weights.cca weights.decorana weights.rda
Canonical Correlation Analysisbiplot.CCorA CCorA
Distances of Points to Class Centroidscenterdist centredist centredist.betadisper centredist.cca centredist.dbrda centredist.default centredist.rda centredist.wcmdscale
Multinomial Species Classification Method (CLAM)clamtest plot.clamtest summary.clamtest
Create an Object for Null Model Algorithmscommsim make.commsim print.commsim
Contribution Diversity Approachcontribdiv plot.contribdiv
Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysiscapscale dbrda pco
Detrended Correspondence Analysis and Basic Reciprocal Averagingdecorana downweight plot.decorana points.decorana scores.decorana summary.decorana text.decorana
Standardization Methods for Community Ecologydecobackstand decostand wisconsin
Design your own Dissimilaritieschaodist designdist designdist2
Statistics Resembling Deviance and AIC for Constrained Ordinationdeviance.cca deviance.rda extractAIC.cca
Morisita index of intraspecific aggregationdispindmorisita
Dispersion-based weighting of species countsdispweight gdispweight summary.dispweight
Connectedness of Dissimilaritiesdistconnected no.shared
Ecological Diversity Indicesdiversity fisher.alpha simpson.unb specnumber
Vegetation and Environment in Dutch Dune Meadows.dune dune.env
Taxonomic Classification and Phylogeny of Dune Meadow Speciesdune.phylodis dune.taxon
Extract Eigenvalues from an Ordination Objecteigenvals eigenvals.cca eigenvals.decorana eigenvals.default eigenvals.dudi eigenvals.pca eigenvals.pcnm eigenvals.pco eigenvals.prcomp eigenvals.princomp eigenvals.wcmdscale summary.eigenvals
Fits an Environmental Vector or Factor onto an Ordinationenvfit envfit.default envfit.formula factorfit labels.envfit plot.envfit scores.envfit vectorfit
Scale Parameter at the Minimum of the Tsallis Evenness Profileeventstar
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Dataas.fisher as.preston fisherfit lines.preston lines.prestonfit plot.fisher plot.fisherfit plot.preston plot.prestonfit prestondistr prestonfit veiledspec
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)alias.cca goodness goodness.cca inertcomp intersetcor spenvcor vif.cca
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scalinggoodness.metaMDS goodness.monoMDS stressplot stressplot.default stressplot.monoMDS
Indicator Power of Speciesindpower
Linear Model Diagnostics for Constrained Ordinationcooks.distance.cca df.residual.cca hatvalues.cca hatvalues.rda qr.cca rstandard.cca rstudent.cca sigma.cca SSD.cca vcov.cca
Isometric Feature Mapping Ordinationisomap isomapdist plot.isomap summary.isomap
Kendall coefficient of concordancekendall.global kendall.post
Plots One-dimensional Diagrams without Overwriting Labelslinestack
Abbreviates a Two-Part Botanical or Zoological Latin Name into Character Stringmake.cepnames
Mantel and Partial Mantel Tests for Dissimilarity Matricesmantel mantel.partial
Mantel Correlogrammantel.correlog plot.mantel.correlog
Add New Points to NMDS ordinationdist2xy MDSaddpoints
Rotate First MDS Dimension Parallel to an External VariableMDSrotate
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species ScoresinitMDS metaMDS metaMDSdist metaMDSiter metaMDSredist plot.metaMDS points.metaMDS postMDS scores.metaMDS text.metaMDS
Oribatid Mite Data with Explanatory Variablesmite mite.env mite.pcnm mite.xy
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid ScalingmonoMDS plot.monoMDS points.monoMDS scores.monoMDS text.monoMDS
Mitchell-Olds and Shaw Test for the Location of Quadratic Extremeconfint.MOStest fieller.MOStest MOStest plot.MOStest profile.MOStest
Multi Response Permutation Procedure and Mean Dissimilarity Matrixmeandist mrpp plot.meandist summary.meandist
Functions for performing and displaying a spatial partitioning of cca or rda resultsmso msoplot
Multiplicative Diversity Partitioningmultipart multipart.default multipart.formula
Nestedness Indices for Communities of Islands or Patchesnestedbetajac nestedbetasor nestedchecker nesteddisc nestedn0 nestednodf nestedtemp plot.nestednodf plot.nestedtemp
Extract the Number of Observations from a vegan Fit.nobs.betadisper nobs.cca nobs.CCorA nobs.decorana nobs.isomap nobs.metaMDS nobs.pcnm nobs.procrustes nobs.rad nobs.varpart nobs.wcmdscale
Null Model and Simulationnullmodel print.nullmodel print.simmat simmat simulate.nullmodel smbind str.nullmodel update.nullmodel
Evaluate Statistics with Null Models of Biological Communitiesas.ts.oecosimu oecosimu toCoda toCoda.oecosimu
Add Arrows and Line Segments to Ordination Diagramsordiarrows ordigrid ordisegments
Support Functions for Drawing VectorsordiArrowMul ordiArrowTextXY
Display Groups or Factor Levels in Ordination Diagramsordiareatest ordibar ordicluster ordiellipse ordihull ordispider scores.ordihull summary.ordiellipse summary.ordihull
Add Text on Non-transparent Label to an Ordination Plot.ordilabel
Alternative plot and identify Functions for Ordinationidentify.ordiplot ordiplot points.ordiplot scores.ordiplot text.ordiplot
Ordination Plots with Points and Optimized Locations for Textlabels.ordipointlabel ordipointlabel plot.ordipointlabel
Plots of Residuals and Fitted Values for Constrained Ordinationordiresids
Choose a Model by Permutation Tests in Constrained OrdinationordiR2step ordistep
Fit and Plot Smooth Surfaces of Variables on Ordination.calibrate.ordisurf ordisurf ordisurf.default ordisurf.formula plot.ordisurf
Add Text or Points to Ordination Plotsorditorp
Trellis (Lattice) Plots for Ordinationordicloud ordilattice.getEnvfit ordisplom ordixyplot panel.ordi panel.ordi3d panel.ordiarrows prepanel.ordi3d
Principal Coordinates of Neighbourhood Matrixpcnm scores.pcnm
Matrix Permutation Algorithms for Presence-Absence and Count Dataas.ts.permat lines.permat permatfull permatswap plot.permat print.permat print.summary.permat summary.permat toCoda.permat
Extract, Analyse and Display Permutation Resultsboxplot.permustats c.permustats density.permustats densityplot.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 qqmath.permustats qqnorm.permustats summary.permustats
Permutation tests in Veganpermutations
Permutation test of multivariate homogeneity of groups dispersions (variances)permutest.betadisper
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysislabels.cca plot.cca points.cca print.summary.cca scores.cca scores.rda summary.cca text.cca
Principal Response Curves for Treatments with Repeated Observationsplot.prc prc summary.prc
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)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
Procrustes Rotation of Two Configurations and PROTESTfitted.procrustes lines.procrustes plot.procrustes points.procrustes predict.procrustes procrustes protest residuals.procrustes summary.procrustes text.procrustes
Response of Aquatic Invertebrates to Insecticide Treatmentpyrifos
Rank - Abundance or Dominance / Diversity ModelsAIC.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
Compares Dissimilarity Indices for Gradient Detectionrankindex
Rarefaction Species Richnessdrarefy rarecurve rarefy rareslope rrarefy
Raup-Crick Dissimilarity with Unequal Sampling Densities of Speciesraupcrick
Reads a CEP (Canoco) data fileread.cep
Renyi and Hill Diversities and Corresponding Accumulation Curvespersp.renyiaccum plot.renyi plot.renyiaccum renyi renyiaccum
Reorder a Hierarchical Clustering Treecutreeord reorder.hclust rev.hclust scores.hclust
Adjusted R-squareRsquareAdj RsquareAdj.cca RsquareAdj.default RsquareAdj.glm RsquareAdj.lm RsquareAdj.rda
Get Species or Site Scores from an Ordinationscores scores.default scores.lda
Screeplots for Ordination Results and Broken Stick Distributionsbstick bstick.cca bstick.decorana bstick.default bstick.prcomp bstick.princomp screeplot.cca screeplot.decorana screeplot.prcomp screeplot.princomp
Similarity Percentagessimper summary.simper
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordinationsimulate.capscale simulate.cca simulate.rda
Birds in the Archipelago of Sipoo (Sibbo and Borgå)sipoo sipoo.map
Minimum Spanning Treeas.hclust.spantree cophenetic.spantree lines.spantree plot.spantree spandepth spantree
Species Accumulation CurvesAIC.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
Extrapolated Species Richness in a Species PoolestaccumR estimateR estimateR.data.frame estimateR.default estimateR.matrix plot.poolaccum poolaccum specpool specpool2vect summary.poolaccum
Add or Replace Species Scores in Distance-Based Ordinationsppscores sppscores<- sppscores<-.capscale sppscores<-.dbrda sppscores<-.metaMDS sppscores<-.monoMDS sppscores<-.wcmdscale
Self-Starting nls Species-Area ModelsSSarrhenius SSgitay SSgleason SSlomolino
Stepacross as Flexible Shortest Paths or Extended Dissimilaritiesstepacross
Display Ordination Distances Against Observed Distances in Eigenvector Ordinationsstressplot.capscale stressplot.cca stressplot.dbrda stressplot.prcomp stressplot.princomp stressplot.rda stressplot.wcmdscale
Indices of Taxonomic Diversity and Distinctnessplot.taxondive summary.taxondive taxa2dist taxondive
Species tolerances and sample heterogeneitiestolerance tolerance.cca tolerance.decorana
Functional Diversity and Community Distances from Species Treestreedist treedive treeheight
Tsallis Diversity and Corresponding Accumulation Curvespersp.tsallisaccum tsallis tsallisaccum
Vegetation and environment in lichen pasturesvarechem varespec
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matricesplot.varpart plot.varpart234 showvarparts simpleDBRDA simpleRDA2 summary.varpart varpart varpart2 varpart3 varpart4
Deprecated Functions in vegan packageas.mcmc.oecosimu as.mcmc.permat orditkplot vegan-deprecated
Dissimilarity Indices for Community Ecologistsvegdist
Display Compact Ordered Community Tablescoverscale tabasco vegemite
Weighted Averages Scores for Specieseigengrad scores.wascores wascores
Weighted Classical (Metric) Multidimensional Scalingplot.wcmdscale scores.wcmdscale wcmdscale