# Community Ecology Package

## Documentation for package `vegan' version 1.8-8

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

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

## -- A --

adonis | Multivariate Analysis of Variance Using Distance Matrices
AIC.radfit | Rank - Abundance or Dominance / Diversity Models
alias.cca | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
anosim | Analysis of Similarities
anova.cca | Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
anova.ccabyaxis | Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
anova.ccabyterm | 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.mlm | Refit Constrained Ordination as a Multiple Response Linear Model
as.preston | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
as.rad | Rank - Abundance or Dominance / Diversity Models

## -- B --

BCI | Barro Colorado Island Tree Counts
beals | Beals Smoothing and Degree of Absence
bgdispersal | Coefficients of Biogeographical Dispersal Direction
bioenv | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
boxplot.specaccum | Species Accumulation Curves
bstick | Screeplots for Ordination Results and Broken Stick Distributions

## -- C --

calibrate.cca | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
capscale | [Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
cascadeKM | K-means partitioning using a range of values of K
cca | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cca.object | Result Object from Constrained Ordination with cca, rda or capscale
cIndexKM | K-means partitioning using a range of values of K
coef.cca | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
coef.radfit | Rank - Abundance or Dominance / Diversity Models
coef.rda | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
confint.fisherfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
cophenetic.spantree | Minimum Spanning Tree
coverscale | Prints a Compact, Ordered Vegetation Table

## -- D --

decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
decostand | Standardizaton Methods for Community Ecology
designdist | Design your own Dissimilarities
deviance.capscale | Statistics Resembling Deviance and AIC for Constrained Ordination
deviance.cca | Statistics Resembling Deviance and AIC for Constrained Ordination
deviance.rda | Statistics Resembling Deviance and AIC for Constrained Ordination
distconnected | Connectedness of Dissimilarities
diversity | Ecological Diversity Indices and Rarefaction Species Richness
downweight | Detrended Correspondence Analysis and Basic Reciprocal Averaging
dune | Vegetation and Environment in Dutch Dune Meadows.
dune.taxon | Taxonomic Classification of Dune Meadow Species

## -- E --

eigengrad | Weighted Averages Scores for Species
envfit | Fits an Environmental Vector or Factor onto an Ordination
estimateR | Extrapolated Species Richness in a Species Pool
extractAIC.cca | Statistics Resembling Deviance and AIC for Constrained Ordination

## -- F --

factorfit | Fits an Environmental Vector or Factor onto an Ordination
fisher.alpha | Ecological Diversity Indices and Rarefaction Species Richness
fisherfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
fitted.cca | 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.rda | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)

## -- G --

goodness | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
goodness.metaMDS | Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
goodness.rda | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)

## -- H --

humpfit | No-interaction Model for Hump-backed Species Richness vs. Biomass

## -- I --

identify.ordiplot | Alternative plot and identify Functions for Ordination
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

## -- L --

lines.humpfit | No-interaction Model for Hump-backed Species Richness vs. Biomass
lines.prestonfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
lines.procrustes | Procrustes Rotation of Two Configurations and PROTEST
lines.radline | Rank - Abundance or Dominance / Diversity Models
lines.spantree | Minimum Spanning Tree
linestack | Plots One-dimensional Diagrams without Overwriting Labels

## -- M --

make.cepnames | Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
mantel | Mantel and Partial Mantel Tests for Dissimilarity Matrices
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
mrpp | Multi Response Permutation Procedure of Within- versus Among-Group Dissimilarities

## -- N --

no.shared | Connectedness of Dissimilarities

## -- O --

orderingKM | K-means partitioning using a range of values of K
ordiarrows | Add Graphical Items to Ordination Diagrams
ordicluster | Add Graphical Items to Ordination Diagrams
ordiellipse | Add Graphical Items to Ordination Diagrams
ordigrid | Add Graphical Items to Ordination Diagrams
ordihull | Add Graphical Items to Ordination Diagrams
ordiplot | Alternative plot and identify Functions for Ordination
ordiplot3d | Three-Dimensional and Dynamic Ordination Graphics
ordirgl | Three-Dimensional and Dynamic Ordination Graphics
ordisegments | Add Graphical Items to Ordination Diagrams
ordispider | Add Graphical Items to Ordination Diagrams
ordisurf | Fit and Plot Smooth Surfaces of Variables on Ordination.
orditorp | Add Text or Points to Ordination Plots
orglpoints | Three-Dimensional and Dynamic Ordination Graphics
orglsegments | Three-Dimensional and Dynamic Ordination Graphics
orglspider | Three-Dimensional and Dynamic Ordination Graphics
orgltext | Three-Dimensional and Dynamic Ordination Graphics

## -- P --

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
plot.anosim | Analysis of Similarities
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.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
plot.envfit | Fits an Environmental Vector or Factor onto an Ordination
plot.fisherfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
plot.humpfit | No-interaction Model for Hump-backed Species Richness vs. Biomass
plot.isomap | Isometric Feature Mapping Ordination
plot.metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
plot.prc | Principal Response Curves for Treatments with Repeated Observations
plot.prestonfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
plot.procrustes | Procrustes Rotation of Two Configurations and PROTEST
plot.profile.fisherfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
plot.rad | Rank - Abundance or Dominance / Diversity Models
plot.radfit | Rank - Abundance or Dominance / Diversity Models
plot.radline | Rank - Abundance or Dominance / Diversity Models
plot.renyi | Renyi and Hill Diversities and Corresponding Accumulation Curves
plot.renyiaccum | Renyi and Hill Diversities and Corresponding Accumulation Curves
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
points.cca | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
points.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
points.humpfit | No-interaction Model for Hump-backed Species Richness vs. Biomass
points.metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
points.ordiplot | Alternative plot and identify Functions for Ordination
points.procrustes | Procrustes Rotation of Two Configurations and PROTEST
points.radline | Rank - Abundance or Dominance / Diversity Models
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.decorana | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
predict.humpfit | No-interaction Model for Hump-backed Species Richness vs. Biomass
predict.rda | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
pregraphKM | K-means partitioning using a range of values of K
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.adonis | Multivariate Analysis of Variance Using Distance Matrices
print.anosim | Analysis of Similarities
print.anova.cca | Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
print.bioenv | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
print.cca | [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
print.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
print.envfit | Fits an Environmental Vector or Factor onto an Ordination
print.factorfit | Fits an Environmental Vector or Factor onto an Ordination
print.fisherfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
print.humpfit | No-interaction Model for Hump-backed Species Richness vs. Biomass
print.isomap | Isometric Feature Mapping Ordination
print.mantel | Mantel and Partial Mantel Tests for Dissimilarity Matrices
print.metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
print.mrpp | Multi Response Permutation Procedure of Within- versus Among-Group Dissimilarities
print.permutest.cca | Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
print.prestonfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
print.procrustes | Procrustes Rotation of Two Configurations and PROTEST
print.protest | Procrustes Rotation of Two Configurations and PROTEST
print.radfit | Rank - Abundance or Dominance / Diversity Models
print.radline | Rank - Abundance or Dominance / Diversity Models
print.specaccum | Species Accumulation Curves
print.summary.bioenv | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
print.summary.cca | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
print.summary.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
print.summary.humpfit | No-interaction Model for Hump-backed Species Richness vs. Biomass
print.summary.isomap | Isometric Feature Mapping Ordination
print.summary.prc | Principal Response Curves for Treatments with Repeated Observations
print.summary.procrustes | Procrustes Rotation of Two Configurations and PROTEST
print.summary.taxondive | Indices of Taxonomic Diversity and Distinctness
print.taxondive | Indices of Taxonomic Diversity and Distinctness
print.varpart | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
print.varpart234 | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
print.vectorfit | Fits an Environmental Vector or Factor onto an Ordination
procrustes | Procrustes Rotation of Two Configurations and PROTEST
profile.fisherfit | Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
profile.humpfit | No-interaction Model for Hump-backed Species Richness vs. Biomass
protest | Procrustes Rotation of Two Configurations and PROTEST
pyrifos | Response of Aquatic Invertebrates to Insecticide Treatment

## -- 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
rankindex | Compares Dissimilarity Indices for Gradient Detection
rarefy | Ecological Diversity Indices and Rarefaction Species Richness
rda | [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
residuals.cca | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
residuals.procrustes | Procrustes Rotation of Two Configurations and PROTEST
residuals.rda | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
rgl.renyiaccum | Renyi and Hill Diversities and Corresponding Accumulation Curves
ripley.subs | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
ripley.subsets | Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
RsquareAdj | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices

## -- S --

scores | Get Species or Site Scores from an Ordination
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.metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
scores.ordiplot | Alternative plot and identify Functions for Ordination
scores.rda | Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
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
simpleRDA2 | Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
spantree | Minimum Spanning Tree
specaccum | Species Accumulation Curves
specnumber | Ecological Diversity Indices and Rarefaction Species Richness
specpool | Extrapolated Species Richness in a Species Pool
specpool2vect | Extrapolated Species Richness in a Species Pool
spenvcor | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
stepacross | Stepacross as Flexible Shortest Paths or Extended Dissimilarities
stressplot | Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
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.decorana | Detrended Correspondence Analysis and Basic Reciprocal Averaging
summary.humpfit | No-interaction Model for Hump-backed Species Richness vs. Biomass
summary.isomap | Isometric Feature Mapping Ordination
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.specaccum | Species Accumulation Curves
summary.taxondive | Indices of Taxonomic Diversity and Distinctness
swan | Beals Smoothing and Degree of Absence

## -- T --

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.ordiplot | Alternative plot and identify Functions for Ordination

## -- 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
vectorfit | Fits an Environmental Vector or Factor onto an Ordination
vegandocs | Display Package Documentation
vegdist | Dissimilarity Indices for Community Ecologists
vegemite | Prints a Compact, Ordered Vegetation Table
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
weights.cca | Add Graphical Items to Ordination Diagrams
weights.decorana | Add Graphical Items to Ordination Diagrams
weights.rda | Add Graphical Items to Ordination Diagrams
wisconsin | Standardizaton Methods for Community Ecology