Function reference

All functions

BCI BCI.env

Barro Colorado Island Tree Counts

CCorA() biplot(<CCorA>)

Canonical Correlation Analysis

MDSrotate()

Rotate First MDS Dimension Parallel to an External Variable

MOStest() plot(<MOStest>) fieller.MOStest() profile(<MOStest>) confint(<MOStest>)

Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme

RsquareAdj(<default>) RsquareAdj(<rda>) RsquareAdj(<cca>)

Adjusted R-square

SSarrhenius() SSgleason() SSgitay() SSlomolino()

Self-Starting nls Species-Area Models

add1(<cca>) drop1(<cca>)

Add or Drop Single Terms to a Constrained Ordination Model

adipart() hiersimu()

Additive Diversity Partitioning and Hierarchical Null Model Testing

adonis2()

Permutational Multivariate Analysis of Variance Using Distance Matrices

anosim()

Analysis of Similarities

anova(<cca>) permutest(<cca>)

Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates

avgdist()

Averaged Subsampled Dissimilarity Matrices

beals() swan()

Beals Smoothing and Degree of Absence

betadisper() anova(<betadisper>) scores(<betadisper>) eigenvals(<betadisper>) plot(<betadisper>) boxplot(<betadisper>) TukeyHSD(<betadisper>) print(<betadisper>)

Multivariate homogeneity of groups dispersions (variances)

betadiver() plot(<betadiver>) scores(<betadiver>)

Indices of beta Diversity

bgdispersal()

Coefficients of Biogeographical Dispersal Direction

bioenv(<default>) bioenv(<formula>) bioenvdist()

Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities

biplot(<rda>)

PCA biplot

cascadeKM() cIndexKM() plot(<cascadeKM>)

K-means partitioning using a range of values of K

cca(<formula>) rda(<formula>) cca(<default>) rda(<default>)

[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis

ordiYbar() model.frame(<cca>) model.matrix(<cca>) weights(<cca>)

Result Object from Constrained Ordination

clamtest() summary(<clamtest>) plot(<clamtest>)

Multinomial Species Classification Method (CLAM)

commsim() make.commsim() print(<commsim>)

Create an Object for Null Model Algorithms

contribdiv() plot(<contribdiv>)

Contribution Diversity Approach

dbrda() capscale()

[Partial] Distance-based Redundancy Analysis

decorana() plot(<decorana>) text(<decorana>) points(<decorana>) summary(<decorana>) print(<summary.decorana>) downweight() scores(<decorana>)

Detrended Correspondence Analysis and Basic Reciprocal Averaging

decostand() wisconsin() decobackstand()

Standardization Methods for Community Ecology

designdist() chaodist()

Design your own Dissimilarities

deviance(<cca>) extractAIC(<cca>)

Statistics Resembling Deviance and AIC for Constrained Ordination

dispindmorisita()

Morisita index of intraspecific aggregation

dispweight() gdispweight() summary(<dispweight>)

Dispersion-based weighting of species counts

distconnected() no.shared()

Connectedness of Dissimilarities

diversity() simpson.unb() fisher.alpha() specnumber()

Ecological Diversity Indices

dune dune.env

Vegetation and Environment in Dutch Dune Meadows.

dune.taxon dune.phylodis

Taxonomic Classification and Phylogeny of Dune Meadow Species

eigenvals() summary(<eigenvals>)

Extract Eigenvalues from an Ordination Object

envfit(<default>) envfit(<formula>) plot(<envfit>) scores(<envfit>) vectorfit() factorfit()

Fits an Environmental Vector or Factor onto an Ordination

eventstar()

Scale Parameter at the Minimum of the Tsallis Evenness Profile

fisherfit() prestonfit() prestondistr() plot(<prestonfit>) lines(<prestonfit>) veiledspec() as.fisher() plot(<fisher>) as.preston() plot(<preston>) lines(<preston>)

Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data

goodness(<cca>) inertcomp() spenvcor() intersetcor() vif.cca() alias(<cca>)

Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)

goodness(<metaMDS>) stressplot(<default>)

Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling

indpower()

Indicator Power of Species

hatvalues(<cca>) rstandard(<cca>) rstudent(<cca>) cooks.distance(<cca>) sigma(<cca>) vcov(<cca>) SSD(<cca>) qr(<cca>) df.residual(<cca>)

Linear Model Diagnostics for Constrained Ordination

isomap() isomapdist() summary(<isomap>) plot(<isomap>)

Isometric Feature Mapping Ordination

kendall.global() kendall.post()

Kendall coefficient of concordance

linestack()

Plots One-dimensional Diagrams without Overwriting Labels

make.cepnames()

Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name

mantel() mantel.partial()

Mantel and Partial Mantel Tests for Dissimilarity Matrices

mantel.correlog() plot(<mantel.correlog>)

Mantel Correlogram

metaMDS() plot(<metaMDS>) points(<metaMDS>) text(<metaMDS>) scores(<metaMDS>) metaMDSdist() metaMDSiter() initMDS() postMDS() metaMDSredist()

Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores

mite mite.env mite.pcnm mite.xy

Oribatid Mite Data with Explanatory Variables

monoMDS() scores(<monoMDS>) plot(<monoMDS>) points(<monoMDS>) text(<monoMDS>)

Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling

mrpp() meandist() summary(<meandist>) plot(<meandist>)

Multi Response Permutation Procedure and Mean Dissimilarity Matrix

mso() msoplot()

Functions for performing and displaying a spatial partitioning of cca or rda results

multipart()

Multiplicative Diversity Partitioning

nestedchecker() nestedn0() nesteddisc() nestedtemp() nestednodf() nestedbetasor() nestedbetajac() plot(<nestedtemp>) plot(<nestednodf>)

Nestedness Indices for Communities of Islands or Patches

nobs(<cca>)

Extract the Number of Observations from a vegan Fit.

nullmodel() print(<nullmodel>) simulate(<nullmodel>) update(<nullmodel>) print(<simmat>) smbind()

Null Model and Simulation

oecosimu() as.ts(<oecosimu>) toCoda(<oecosimu>)

Evaluate Statistics with Null Models of Biological Communities

ordiArrowTextXY() ordiArrowMul()

Support Functions for Drawing Vectors

ordiarrows() ordisegments() ordigrid()

Add Arrows and Line Segments to Ordination Diagrams

ordihull() ordiellipse() ordibar() ordispider() ordicluster() summary(<ordihull>) summary(<ordiellipse>) ordiareatest()

Display Groups or Factor Levels in Ordination Diagrams

ordilabel()

Add Text on Non-transparent Label to an Ordination Plot.

ordiplot() identify(<ordiplot>) points(<ordiplot>) text(<ordiplot>)

Alternative plot and identify Functions for Ordination

ordipointlabel() plot(<ordipointlabel>)

Ordination Plots with Points and Optimized Locations for Text

ordiresids()

Plots of Residuals and Fitted Values for Constrained Ordination

ordistep() ordiR2step()

Choose a Model by Permutation Tests in Constrained Ordination

ordisurf(<default>) ordisurf(<formula>) calibrate(<ordisurf>) plot(<ordisurf>)

Fit and Plot Smooth Surfaces of Variables on Ordination.

orditorp()

Add Text or Points to Ordination Plots

ordixyplot() ordisplom() ordicloud()

Trellis (Lattice) Plots for Ordination

pcnm()

Principal Coordinates of Neighbourhood Matrix

permatfull() permatswap() print(<permat>) summary(<permat>) print(<summary.permat>) plot(<permat>) lines(<permat>) as.ts(<permat>) toCoda(<permat>)

Matrix Permutation Algorithms for Presence-Absence and Count Data

permustats() summary(<permustats>) densityplot(<permustats>) density(<permustats>) qqnorm(<permustats>) qqmath(<permustats>) boxplot(<permustats>) pairs(<permustats>)

Extract, Analyse and Display Permutation Results

permutations

Permutation tests in Vegan

permutest(<betadisper>)

Permutation test of multivariate homogeneity of groups dispersions (variances)

plot(<cca>) text(<cca>) points(<cca>) scores(<cca>) scores(<rda>) summary(<cca>) labels(<cca>)

Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis

prc() summary(<prc>) plot(<prc>)

Principal Response Curves for Treatments with Repeated Observations

fitted(<cca>) fitted(<capscale>) residuals(<cca>) predict(<cca>) predict(<rda>) predict(<dbrda>) calibrate(<cca>) coef(<cca>) predict(<decorana>)

Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)

procrustes() summary(<procrustes>) plot(<procrustes>) points(<procrustes>) text(<procrustes>) lines(<procrustes>) residuals(<procrustes>) fitted(<procrustes>) predict(<procrustes>) protest()

Procrustes Rotation of Two Configurations and PROTEST

pyrifos

Response of Aquatic Invertebrates to Insecticide Treatment

radfit(<default>) rad.null() rad.preempt() rad.lognormal() rad.zipf() rad.zipfbrot() predict(<radline>) plot(<radfit>) plot(<radfit.frame>) plot(<radline>) radlattice() lines(<radfit>) points(<radfit>) as.rad() plot(<rad>)

Rank -- Abundance or Dominance / Diversity Models

rankindex()

Compares Dissimilarity Indices for Gradient Detection

rarefy() rrarefy() drarefy() rarecurve() rareslope()

Rarefaction Species Richness

raupcrick()

Raup-Crick Dissimilarity with Unequal Sampling Densities of Species

read.cep()

Reads a CEP (Canoco) data file

renyi() plot(<renyi>) renyiaccum() plot(<renyiaccum>) persp(<renyiaccum>)

Renyi and Hill Diversities and Corresponding Accumulation Curves

reorder(<hclust>) rev(<hclust>) scores(<hclust>) cutreeord()

Reorder a Hierarchical Clustering Tree

scores(<default>)

Get Species or Site Scores from an Ordination

screeplot(<cca>) screeplot(<decorana>) screeplot(<prcomp>) screeplot(<princomp>) bstick()

Screeplots for Ordination Results and Broken Stick Distributions

simper() summary(<simper>)

Similarity Percentages

simulate(<rda>)

Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination

sipoo sipoo.map

Birds in the Archipelago of Sipoo (Sibbo and Borgå)

spantree() as.hclust(<spantree>) cophenetic(<spantree>) spandepth() plot(<spantree>) lines(<spantree>)

Minimum Spanning Tree

specaccum() plot(<specaccum>) boxplot(<specaccum>) fitspecaccum() plot(<fitspecaccum>) predict(<specaccum>) predict(<fitspecaccum>) specslope()

Species Accumulation Curves

specpool() estimateR() specpool2vect() poolaccum() estaccumR() summary(<poolaccum>) plot(<poolaccum>)

Extrapolated Species Richness in a Species Pool

`sppscores<-`()

Add or Replace Species Scores in Distance-Based Ordination

stepacross()

Stepacross as Flexible Shortest Paths or Extended Dissimilarities

stressplot(<wcmdscale>)

Display Ordination Distances Against Observed Distances in Eigenvector Ordinations

taxondive() taxa2dist()

Indices of Taxonomic Diversity and Distinctness

tolerance()

Species tolerances and sample heterogeneities

treedive() treeheight() treedist()

Functional Diversity and Community Distances from Species Trees

tsallis() tsallisaccum() persp(<tsallisaccum>)

Tsallis Diversity and Corresponding Accumulation Curves

varechem varespec

Vegetation and environment in lichen pastures

varpart() summary(<varpart>) showvarparts() plot(<varpart234>)

Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices

adonis() orditkplot() plot(<orditkplot>) points(<orditkplot>) text(<orditkplot>) scores(<orditkplot>) as.mcmc.oecosimu() as.mcmc.permat()

Deprecated Functions in vegan package

ordiParseFormula() ordiTerminfo() ordiNAexclude() ordiNApredict() ordiArgAbsorber() centroids.cca() getPermuteMatrix() howHead() pasteCall() veganCovEllipse() veganMahatrans() hierParseFormula() GowerDblcen() addLingoes() addCailliez()

Internal vegan functions

vegan-package vegan

Community Ecology Package: Ordination, Diversity and Dissimilarities

vegdist()

Dissimilarity Indices for Community Ecologists

vegemite() tabasco() coverscale()

Display Compact Ordered Community Tables

wascores() eigengrad()

Weighted Averages Scores for Species

wcmdscale() plot(<wcmdscale>) scores(<wcmdscale>)

Weighted Classical (Metric) Multidimensional Scaling