R: Community Ecology Package

# Community Ecology Package

## Documentation for package ‘vegan’ version 2.7-3

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

A B C D E F G H I K L M N O P Q R S T U V W

vegan-package | Community Ecology Package: Ordination, Diversity and Dissimilarities

## -- A --

add1.cca | Add or Drop Single Terms to a Constrained Ordination Model
adipart | Additive Diversity Partitioning and Hierarchical Null Model Testing
adipart.default | Additive Diversity Partitioning and Hierarchical Null Model Testing
adipart.formula | Additive Diversity Partitioning and Hierarchical Null Model Testing
adonis2 | Permutational Multivariate Analysis of Variance Using Distance Matrices
AIC.fitspecaccum | Species Accumulation Curves
AIC.radfit | Rank - Abundance or Dominance / Diversity Models
AIC.radfit.frame | Rank - Abundance or Dominance / Diversity Models
alias.cca | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
anosim | Analysis of Similarities
anova.betadisper | Multivariate homogeneity of groups dispersions (variances)
anova.cca | Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
as.fisher | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
as.hclust.spantree | Minimum Spanning Tree
as.mcmc.oecosimu | Deprecated Functions in vegan package
as.mcmc.permat | Deprecated Functions in vegan package
as.preston | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
as.rad | Rank - Abundance or Dominance / Diversity Models
as.ts.oecosimu | Evaluate Statistics with Null Models of Biological Communities
as.ts.permat | Matrix Permutation Algorithms for Presence-Absence and Count Data
avgdist | Averaged Subsampled Dissimilarity Matrices

## -- B --

BCI | Barro Colorado Island Tree Counts
BCI.env | Barro Colorado Island Tree Counts
beals | Beals Smoothing and Degree of Absence
betadisper | Multivariate homogeneity of groups dispersions (variances)
betadistances | Multivariate homogeneity of groups dispersions (variances)
betadiver | Indices of beta Diversity
bgdispersal | Coefficients of Biogeographical Dispersal Direction
bioenv | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
bioenv.default | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
bioenv.formula | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
bioenvdist | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
biplot.cca | PCA biplot
biplot.CCorA | Canonical Correlation Analysis
biplot.rda | PCA biplot
boxplot.betadisper | Multivariate homogeneity of groups dispersions (variances)
boxplot.permustats | Extract, Analyse and Display Permutation Results
boxplot.specaccum | Species Accumulation Curves
bstick | Screeplots for Ordination Results and Broken Stick Distributions
bstick.cca | Screeplots for Ordination Results and Broken Stick Distributions
bstick.decorana | Screeplots for Ordination Results and Broken Stick Distributions
bstick.default | Screeplots for Ordination Results and Broken Stick Distributions
bstick.prcomp | Screeplots for Ordination Results and Broken Stick Distributions
bstick.princomp | Screeplots for Ordination Results and Broken Stick Distributions

## -- C --

c.permustats | Extract, Analyse and Display Permutation Results
ca | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
calibrate | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
calibrate.cca | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
calibrate.ordisurf | Fit and Plot Smooth Surfaces of Variables on Ordination.
capscale | Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysis
cascadeKM | K-means partitioning using a range of values of K
cca | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cca.default | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cca.formula | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cca.object | Result Object from Constrained Ordination
CCorA | Canonical Correlation Analysis
chaodist | Design your own Dissimilarities
cIndexKM | K-means partitioning using a range of values of K
clamtest | Multinomial Species Classification Method (CLAM)
coef.cca | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
coef.radfit | Rank - Abundance or Dominance / Diversity Models
coef.radfit.frame | Rank - Abundance or Dominance / Diversity Models
coef.rda | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
commsim | Create an Object for Null Model Algorithms
confint.MOStest | Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme
contribdiv | Contribution Diversity Approach
cooks.distance.cca | Linear Model Diagnostics for Constrained Ordination
cophenetic.spantree | Minimum Spanning Tree
coverscale | Display Compact Ordered Community Tables
cutreeord | Reorder a Hierarchical Clustering Tree

## -- D --

dbrda | Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysis
decobackstand | Standardization Methods for Community Ecology
decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
decostand | Standardization Methods for Community Ecology
density.permustats | Extract, Analyse and Display Permutation Results
densityplot.permustats | Deprecated lattice Functions in vegan
designdist | Design your own Dissimilarities
designdist2 | Design your own Dissimilarities
deviance.cca | Statistics Resembling Deviance and AIC for Constrained Ordination
deviance.fitspecaccum | Species Accumulation Curves
deviance.radfit | Rank - Abundance or Dominance / Diversity Models
deviance.radfit.frame | Rank - Abundance or Dominance / Diversity Models
deviance.rda | Statistics Resembling Deviance and AIC for Constrained Ordination
df.residual.cca | Linear Model Diagnostics for Constrained Ordination
dispindmorisita | Morisita index of intraspecific aggregation
dispweight | Dispersion-based weighting of species counts
dist2xy | Add New Points to NMDS ordination
distconnected | Connectedness of Dissimilarities
diversity | Ecological Diversity Indices
downweight | Detrended Correspondence Analysis and Basic Reciprocal Averaging
drarefy | Rarefaction Species Richness
drop1.cca | Add or Drop Single Terms to a Constrained Ordination Model
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

## -- E --

eigengrad | Weighted Averages Scores for Species
eigenvals | Extract Eigenvalues from an Ordination Object
eigenvals.betadisper | Multivariate homogeneity of groups dispersions (variances)
eigenvals.cca | Extract Eigenvalues from an Ordination Object
eigenvals.decorana | Extract Eigenvalues from an Ordination Object
eigenvals.default | Extract Eigenvalues from an Ordination Object
eigenvals.dudi | Extract Eigenvalues from an Ordination Object
eigenvals.pca | Extract Eigenvalues from an Ordination Object
eigenvals.pcnm | Extract Eigenvalues from an Ordination Object
eigenvals.pco | Extract Eigenvalues from an Ordination Object
eigenvals.prcomp | Extract Eigenvalues from an Ordination Object
eigenvals.princomp | Extract Eigenvalues from an Ordination Object
eigenvals.wcmdscale | Extract Eigenvalues from an Ordination Object
envfit | Fits an Environmental Vector or Factor onto an Ordination
envfit.default | Fits an Environmental Vector or Factor onto an Ordination
envfit.formula | Fits an Environmental Vector or Factor onto an Ordination
estaccumR | Extrapolated Species Richness in a Species Pool
estimateR | Extrapolated Species Richness in a Species Pool
estimateR.data.frame | Extrapolated Species Richness in a Species Pool
estimateR.default | Extrapolated Species Richness in a Species Pool
estimateR.matrix | Extrapolated Species Richness in a Species Pool
eventstar | Scale Parameter at the Minimum of the Tsallis Evenness Profile
extractAIC.cca | Statistics Resembling Deviance and AIC for Constrained Ordination

## -- F --

factorfit | Fits an Environmental Vector or Factor onto an Ordination
fieller.MOStest | Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme
fisher.alpha | Ecological Diversity Indices
fisherfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
fitspecaccum | Species Accumulation Curves
fitted.capscale | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
fitted.cca | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
fitted.dbrda | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
fitted.procrustes | Procrustes Rotation of Two Configurations and PROTEST
fitted.radfit | Rank - Abundance or Dominance / Diversity Models
fitted.radfit.frame | Rank - Abundance or Dominance / Diversity Models
fitted.rda | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)

## -- G --

gdispweight | Dispersion-based weighting of species counts
goodness | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
goodness.cca | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
goodness.metaMDS | Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
goodness.monoMDS | Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling

## -- H --

hatvalues.cca | Linear Model Diagnostics for Constrained Ordination
hatvalues.rda | Linear Model Diagnostics for Constrained Ordination
hiersimu | Additive Diversity Partitioning and Hierarchical Null Model Testing
hiersimu.default | Additive Diversity Partitioning and Hierarchical Null Model Testing
hiersimu.formula | Additive Diversity Partitioning and Hierarchical Null Model Testing

## -- I --

identify.ordiplot | Alternative plot and identify Functions for Ordination
indpower | Indicator Power of Species
inertcomp | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
initMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
intersetcor | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
isomap | Isometric Feature Mapping Ordination
isomapdist | Isometric Feature Mapping Ordination

## -- K --

kendall.global | Kendall coefficient of concordance
kendall.post | Kendall coefficient of concordance

## -- L --

labels.cca | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
labels.envfit | Fits an Environmental Vector or Factor onto an Ordination
labels.ordipointlabel | Ordination Plots with Points and Optimized Locations for Text
lines.fitspecaccum | Species Accumulation Curves
lines.permat | Matrix Permutation Algorithms for Presence-Absence and Count Data
lines.preston | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
lines.prestonfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
lines.procrustes | Procrustes Rotation of Two Configurations and PROTEST
lines.radfit | Rank - Abundance or Dominance / Diversity Models
lines.radline | Rank - Abundance or Dominance / Diversity Models
lines.spantree | Minimum Spanning Tree
lines.specaccum | Species Accumulation Curves
linestack | Plots One-dimensional Diagrams without Overwriting Labels
logLik, radfit | Rank - Abundance or Dominance / Diversity Models
logLik, radfit.frame | Rank - Abundance or Dominance / Diversity Models
logLik.fitspecaccum | Species Accumulation Curves

## -- M --

make.cepnames | Abbreviates a Two-Part Botanical or Zoological Latin Name into Character String
make.commsim | Create an Object for Null Model Algorithms
mantel | Mantel and Partial Mantel Tests for Dissimilarity Matrices
mantel.correlog | Mantel Correlogram
mantel.partial | Mantel and Partial Mantel Tests for Dissimilarity Matrices
MDSaddpoints | Add New Points to NMDS ordination
MDSrotate | Rotate First MDS Dimension Parallel to an External Variable
meandist | Multi Response Permutation Procedure and Mean Dissimilarity Matrix
metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
metaMDSdist | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
metaMDSiter | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
metaMDSredist | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
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
model.frame.cca | Result Object from Constrained Ordination
model.matrix.cca | Result Object from Constrained Ordination
model.matrix.rda | Result Object from Constrained Ordination
monoMDS | Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
MOStest | Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme
mrpp | Multi Response Permutation Procedure and Mean Dissimilarity Matrix
mso | Functions for performing and displaying a spatial partitioning of cca or rda results
msoplot | Functions for performing and displaying a spatial partitioning of cca or rda results
multipart | Multiplicative Diversity Partitioning
multipart.default | Multiplicative Diversity Partitioning
multipart.formula | Multiplicative Diversity Partitioning

## -- N --

nestedbetajac | Nestedness Indices for Communities of Islands or Patches
nestedbetasor | Nestedness Indices for Communities of Islands or Patches
nestedchecker | Nestedness Indices for Communities of Islands or Patches
nesteddisc | Nestedness Indices for Communities of Islands or Patches
nestedn0 | Nestedness Indices for Communities of Islands or Patches
nestednodf | Nestedness Indices for Communities of Islands or Patches
nestedtemp | Nestedness Indices for Communities of Islands or Patches
no.shared | Connectedness of Dissimilarities
nobs.betadisper | Extract the Number of Observations from a vegan Fit.
nobs.cca | Extract the Number of Observations from a vegan Fit.
nobs.CCorA | Extract the Number of Observations from a vegan Fit.
nobs.decorana | Extract the Number of Observations from a vegan Fit.
nobs.fitspecaccum | Species Accumulation Curves
nobs.isomap | Extract the Number of Observations from a vegan Fit.
nobs.metaMDS | Extract the Number of Observations from a vegan Fit.
nobs.pcnm | Extract the Number of Observations from a vegan Fit.
nobs.procrustes | Extract the Number of Observations from a vegan Fit.
nobs.rad | Extract the Number of Observations from a vegan Fit.
nobs.varpart | Extract the Number of Observations from a vegan Fit.
nobs.wcmdscale | Extract the Number of Observations from a vegan Fit.
nullmodel | Null Model and Simulation

## -- O --

oecosimu | Evaluate Statistics with Null Models of Biological Communities
optspace | optspace: algorithm for matrix reconstruction from a partially revealed set
ordConstrained | Result Object from Constrained Ordination
orderingKM | K-means partitioning using a range of values of K
ordiareatest | Display Groups or Factor Levels in Ordination Diagrams
ordiArrowMul | Support Functions for Drawing Vectors
ordiarrows | Add Arrows and Line Segments to Ordination Diagrams
ordiArrowTextXY | Support Functions for Drawing Vectors
ordibar | Display Groups or Factor Levels in Ordination Diagrams
ordicloud | Deprecated lattice Functions in vegan
ordicluster | Display Groups or Factor Levels in Ordination Diagrams
ordiellipse | Display Groups or Factor Levels in Ordination Diagrams
ordigrid | Add Arrows and Line Segments to Ordination Diagrams
ordihull | Display Groups or Factor Levels in Ordination Diagrams
ordilabel | Add Text on Non-transparent Label to an Ordination Plot.
ordilattice.getEnvfit | Deprecated lattice Functions in vegan
ordimedian | Multivariate homogeneity of groups dispersions (variances)
ordiplot | Alternative plot and identify Functions for Ordination
ordipointlabel | Ordination Plots with Points and Optimized Locations for Text
ordiR2step | Choose a Model by Permutation Tests in Constrained Ordination
ordiresids | Deprecated lattice Functions in vegan
ordisegments | Add Arrows and Line Segments to Ordination Diagrams
ordispider | Display Groups or Factor Levels in Ordination Diagrams
ordisplom | Deprecated lattice Functions in vegan
ordistep | Choose a Model by Permutation Tests in Constrained Ordination
ordisurf | Fit and Plot Smooth Surfaces of Variables on Ordination.
ordisurf.default | Fit and Plot Smooth Surfaces of Variables on Ordination.
ordisurf.formula | Fit and Plot Smooth Surfaces of Variables on Ordination.
orditorp | Add Text or Points to Ordination Plots
ordixyplot | Deprecated lattice Functions in vegan
ordiYbar | Result Object from Constrained Ordination

## -- P --

pairs.permustats | Extract, Analyse and Display Permutation Results
panel.ordi | Deprecated lattice Functions in vegan
panel.ordi3d | Deprecated lattice Functions in vegan
panel.ordiarrows | Deprecated lattice Functions in vegan
pca | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
pcnm | Principal Coordinates of Neighbourhood Matrix
pco | Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysis
permatfull | Matrix Permutation Algorithms for Presence-Absence and Count Data
permatswap | Matrix Permutation Algorithms for Presence-Absence and Count Data
permulattice | Deprecated lattice Functions in vegan
permustats | Extract, Analyse and Display Permutation Results
permustats.anosim | Extract, Analyse and Display Permutation Results
permustats.anova.cca | Extract, Analyse and Display Permutation Results
permustats.CCorA | Extract, Analyse and Display Permutation Results
permustats.envfit | Extract, Analyse and Display Permutation Results
permustats.factorfit | Extract, Analyse and Display Permutation Results
permustats.mantel | Extract, Analyse and Display Permutation Results
permustats.mrpp | Extract, Analyse and Display Permutation Results
permustats.mso | Extract, Analyse and Display Permutation Results
permustats.oecosimu | Extract, Analyse and Display Permutation Results
permustats.ordiareatest | Extract, Analyse and Display Permutation Results
permustats.permutest.betadisper | Extract, Analyse and Display Permutation Results
permustats.permutest.cca | Extract, Analyse and Display Permutation Results
permustats.protest | Extract, Analyse and Display Permutation Results
permustats.vectorfit | Extract, Analyse and Display Permutation Results
permutations | Permutation tests in Vegan
permutest | Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
permutest.betadisper | Permutation test of multivariate homogeneity of groups dispersions (variances)
permutest.cca | Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
persp.renyiaccum | Renyi and Hill Diversities and Corresponding Accumulation Curves
persp.tsallisaccum | Tsallis Diversity and Corresponding Accumulation Curves
plot.anosim | Analysis of Similarities
plot.betadisper | Multivariate homogeneity of groups dispersions (variances)
plot.betadiver | Indices of beta Diversity
plot.cascadeKM | K-means partitioning using a range of values of K
plot.cca | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
plot.clamtest | Multinomial Species Classification Method (CLAM)
plot.contribdiv | Contribution Diversity Approach
plot.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
plot.envfit | Fits an Environmental Vector or Factor onto an Ordination
plot.fisher | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
plot.fisherfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
plot.fitspecaccum | Species Accumulation Curves
plot.isomap | Isometric Feature Mapping Ordination
plot.mantel.correlog | Mantel Correlogram
plot.meandist | Multi Response Permutation Procedure and Mean Dissimilarity Matrix
plot.metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
plot.monoMDS | Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
plot.MOStest | Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme
plot.nestednodf | Nestedness Indices for Communities of Islands or Patches
plot.nestedtemp | Nestedness Indices for Communities of Islands or Patches
plot.ordipointlabel | Ordination Plots with Points and Optimized Locations for Text
plot.ordisurf | Fit and Plot Smooth Surfaces of Variables on Ordination.
plot.permat | Matrix Permutation Algorithms for Presence-Absence and Count Data
plot.poolaccum | Deprecated lattice Functions in vegan
plot.prc | Principal Response Curves for Treatments with Repeated Observations
plot.preston | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
plot.prestonfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
plot.procrustes | Procrustes Rotation of Two Configurations and PROTEST
plot.rad | Rank - Abundance or Dominance / Diversity Models
plot.radfit | Rank - Abundance or Dominance / Diversity Models
plot.radfit.frame | Rank - Abundance or Dominance / Diversity Models
plot.radline | Rank - Abundance or Dominance / Diversity Models
plot.renyi | Deprecated lattice Functions in vegan
plot.renyiaccum | Deprecated lattice Functions in vegan
plot.spantree | Minimum Spanning Tree
plot.specaccum | Species Accumulation Curves
plot.taxondive | Indices of Taxonomic Diversity and Distinctness
plot.varpart | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
plot.varpart234 | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
plot.wcmdscale | Weighted Classical (Metric) Multidimensional Scaling
points.cca | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
points.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
points.metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
points.monoMDS | Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
points.ordiplot | Alternative plot and identify Functions for Ordination
points.procrustes | Procrustes Rotation of Two Configurations and PROTEST
points.radfit | Rank - Abundance or Dominance / Diversity Models
points.radline | Rank - Abundance or Dominance / Diversity Models
poolaccum | Extrapolated Species Richness in a Species Pool
postMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
prc | Principal Response Curves for Treatments with Repeated Observations
predict.cca | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
predict.dbrda | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
predict.decorana | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
predict.fitspecaccum | Species Accumulation Curves
predict.procrustes | Procrustes Rotation of Two Configurations and PROTEST
predict.radfit | Rank - Abundance or Dominance / Diversity Models
predict.radfit.frame | Rank - Abundance or Dominance / Diversity Models
predict.radline | Rank - Abundance or Dominance / Diversity Models
predict.rda | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
predict.specaccum | Species Accumulation Curves
pregraphKM | K-means partitioning using a range of values of K
prepanel.ordi3d | Deprecated lattice Functions in vegan
prestondistr | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
prestonfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
print.betadisper | Multivariate homogeneity of groups dispersions (variances)
print.cca | Result Object from Constrained Ordination
print.commsim | Create an Object for Null Model Algorithms
print.nullmodel | Null Model and Simulation
print.permat | Matrix Permutation Algorithms for Presence-Absence and Count Data
print.simmat | Null Model and Simulation
print.specaccum | Species Accumulation Curves
print.summary.cca | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
print.summary.permat | Matrix Permutation Algorithms for Presence-Absence and Count Data
procrustes | Procrustes Rotation of Two Configurations and PROTEST
profile.MOStest | Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme
protest | Procrustes Rotation of Two Configurations and PROTEST
pyrifos | Response of Aquatic Invertebrates to Insecticide Treatment

## -- Q --

qqmath.permustats | Deprecated lattice Functions in vegan
qqnorm.permustats | Extract, Analyse and Display Permutation Results
qr.cca | Linear Model Diagnostics for Constrained Ordination

## -- R --

rad.lognormal | Rank - Abundance or Dominance / Diversity Models
rad.null | Rank - Abundance or Dominance / Diversity Models
rad.preempt | Rank - Abundance or Dominance / Diversity Models
rad.zipf | Rank - Abundance or Dominance / Diversity Models
rad.zipfbrot | Rank - Abundance or Dominance / Diversity Models
radfit | Rank - Abundance or Dominance / Diversity Models
radfit.data.frame | Rank - Abundance or Dominance / Diversity Models
radfit.default | Rank - Abundance or Dominance / Diversity Models
radlattice | Rank - Abundance or Dominance / Diversity Models
rankindex | Compares Dissimilarity Indices for Gradient Detection
rarecurve | Rarefaction Species Richness
rarefy | Rarefaction Species Richness
rareslope | Rarefaction Species Richness
raupcrick | Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
rda | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
rda.default | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
rda.formula | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
read.cep | Reads a CEP (Canoco) data file
renyi | Renyi and Hill Diversities and Corresponding Accumulation Curves
renyiaccum | Renyi and Hill Diversities and Corresponding Accumulation Curves
reorder.hclust | Reorder a Hierarchical Clustering Tree
residuals.cca | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
residuals.procrustes | Procrustes Rotation of Two Configurations and PROTEST
rev.hclust | Reorder a Hierarchical Clustering Tree
rrarefy | Rarefaction Species Richness
RsquareAdj | Adjusted R-square
RsquareAdj.cca | Adjusted R-square
RsquareAdj.default | Adjusted R-square
RsquareAdj.glm | Adjusted R-square
RsquareAdj.lm | Adjusted R-square
RsquareAdj.rda | Adjusted R-square
rstandard.cca | Linear Model Diagnostics for Constrained Ordination
rstudent.cca | Linear Model Diagnostics for Constrained Ordination

## -- S --

scores | Get Species or Site Scores from an Ordination
scores.betadisper | Multivariate homogeneity of groups dispersions (variances)
scores.betadiver | Indices of beta Diversity
scores.cca | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
scores.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
scores.default | Get Species or Site Scores from an Ordination
scores.envfit | Fits an Environmental Vector or Factor onto an Ordination
scores.hclust | Reorder a Hierarchical Clustering Tree
scores.lda | Get Species or Site Scores from an Ordination
scores.metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
scores.monoMDS | Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
scores.ordihull | Display Groups or Factor Levels in Ordination Diagrams
scores.ordiplot | Alternative plot and identify Functions for Ordination
scores.pcnm | Principal Coordinates of Neighbourhood Matrix
scores.rda | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
scores.wascores | Weighted Averages Scores for Species
scores.wcmdscale | Weighted Classical (Metric) Multidimensional Scaling
screeplot.cca | Screeplots for Ordination Results and Broken Stick Distributions
screeplot.decorana | Screeplots for Ordination Results and Broken Stick Distributions
screeplot.prcomp | Screeplots for Ordination Results and Broken Stick Distributions
screeplot.princomp | Screeplots for Ordination Results and Broken Stick Distributions
showvarparts | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
sigma.cca | Linear Model Diagnostics for Constrained Ordination
simmat | Null Model and Simulation
simper | Similarity Percentages
simpleDBRDA | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
simpleRDA2 | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
simpson.unb | Ecological Diversity Indices
simulate.capscale | Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
simulate.cca | Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
simulate.nullmodel | Null Model and Simulation
simulate.rda | Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
sipoo | Birds in the Archipelago of Sipoo (Sibbo and Borgå)
sipoo.map | Birds in the Archipelago of Sipoo (Sibbo and Borgå)
smbind | Null Model and Simulation
spandepth | Minimum Spanning Tree
spantree | Minimum Spanning Tree
specaccum | Species Accumulation Curves
specnumber | Ecological Diversity Indices
specpool | Extrapolated Species Richness in a Species Pool
specpool2vect | Extrapolated Species Richness in a Species Pool
specslope | Species Accumulation Curves
spenvcor | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
sppscores | Add or Replace Species Scores in Distance-Based Ordination
sppscores<- | Add or Replace Species Scores in Distance-Based Ordination
sppscores<-.capscale | Add or Replace Species Scores in Distance-Based Ordination
sppscores<-.dbrda | Add or Replace Species Scores in Distance-Based Ordination
sppscores<-.metaMDS | Add or Replace Species Scores in Distance-Based Ordination
sppscores<-.monoMDS | Add or Replace Species Scores in Distance-Based Ordination
sppscores<-.wcmdscale | Add or Replace Species Scores in Distance-Based Ordination
SSarrhenius | Self-Starting nls Species-Area Models
SSD.cca | Linear Model Diagnostics for Constrained Ordination
SSgitay | Self-Starting nls Species-Area Models
SSgleason | Self-Starting nls Species-Area Models
SSlomolino | Self-Starting nls Species-Area Models
stepacross | Stepacross as Flexible Shortest Paths or Extended Dissimilarities
str.nullmodel | Null Model and Simulation
stressplot | Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
stressplot.capscale | Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
stressplot.cca | Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
stressplot.dbrda | Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
stressplot.default | Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
stressplot.monoMDS | Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
stressplot.prcomp | Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
stressplot.princomp | Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
stressplot.rda | Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
stressplot.wcmdscale | Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
summary.anosim | Analysis of Similarities
summary.bioenv | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
summary.cca | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
summary.clamtest | Multinomial Species Classification Method (CLAM)
summary.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
summary.dispweight | Dispersion-based weighting of species counts
summary.eigenvals | Extract Eigenvalues from an Ordination Object
summary.isomap | Isometric Feature Mapping Ordination
summary.mantel | Mantel and Partial Mantel Tests for Dissimilarity Matrices
summary.meandist | Multi Response Permutation Procedure and Mean Dissimilarity Matrix
summary.mrpp | Multi Response Permutation Procedure and Mean Dissimilarity Matrix
summary.oecosimu | Evaluate Statistics with Null Models of Biological Communities
summary.ordiareatest | Display Groups or Factor Levels in Ordination Diagrams
summary.ordiellipse | Display Groups or Factor Levels in Ordination Diagrams
summary.ordihull | Display Groups or Factor Levels in Ordination Diagrams
summary.permat | Matrix Permutation Algorithms for Presence-Absence and Count Data
summary.permustats | Extract, Analyse and Display Permutation Results
summary.poolaccum | Extrapolated Species Richness in a Species Pool
summary.prc | Principal Response Curves for Treatments with Repeated Observations
summary.procrustes | Procrustes Rotation of Two Configurations and PROTEST
summary.radfit.frame | Rank - Abundance or Dominance / Diversity Models
summary.simper | Similarity Percentages
summary.specaccum | Species Accumulation Curves
summary.taxondive | Indices of Taxonomic Diversity and Distinctness
summary.varpart | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
swan | Beals Smoothing and Degree of Absence

## -- T --

tabasco | Display Compact Ordered Community Tables
taxa2dist | Indices of Taxonomic Diversity and Distinctness
taxondive | Indices of Taxonomic Diversity and Distinctness
text.cca | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
text.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
text.metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
text.monoMDS | Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
text.ordiplot | Alternative plot and identify Functions for Ordination
text.procrustes | Procrustes Rotation of Two Configurations and PROTEST
toCoda | Evaluate Statistics with Null Models of Biological Communities
toCoda.oecosimu | Evaluate Statistics with Null Models of Biological Communities
toCoda.permat | Matrix Permutation Algorithms for Presence-Absence and Count Data
tolerance | Species tolerances and sample heterogeneities
tolerance.cca | Species tolerances and sample heterogeneities
tolerance.decorana | Species tolerances and sample heterogeneities
treedist | Functional Diversity and Community Distances from Species Trees
treedive | Functional Diversity and Community Distances from Species Trees
treeheight | Functional Diversity and Community Distances from Species Trees
tsallis | Tsallis Diversity and Corresponding Accumulation Curves
tsallisaccum | Tsallis Diversity and Corresponding Accumulation Curves
TukeyHSD.betadisper | Multivariate homogeneity of groups dispersions (variances)

## -- U --

update.nullmodel | Null Model and Simulation

## -- V --

varechem | Vegetation and environment in lichen pastures
varespec | Vegetation and environment in lichen pastures
varpart | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
varpart2 | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
varpart3 | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
varpart4 | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
vcov.cca | Linear Model Diagnostics for Constrained Ordination
vectorfit | Fits an Environmental Vector or Factor onto an Ordination
vegan | Community Ecology Package: Ordination, Diversity and Dissimilarities
vegan-deprecated | Deprecated Functions in vegan package
vegdist | Dissimilarity Indices for Community Ecologists
vegemite | Display Compact Ordered Community Tables
veiledspec | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
vif.cca | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)

## -- W --

wascores | Weighted Averages Scores for Species
wcmdscale | Weighted Classical (Metric) Multidimensional Scaling
weights.cca | Result Object from Constrained Ordination
weights.decorana | Result Object from Constrained Ordination
weights.rda | Result Object from Constrained Ordination
wisconsin | Standardization Methods for Community Ecology