Community Ecology Package


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Documentation for package `vegan' version 1.8-6

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

-- A --

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.

-- 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.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.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.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
swan Beals Smoothing and Degree of Absence

-- T --

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