Community Ecology Package


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Documentation for package `vegan' version 1.6-8

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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
as.fisher Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
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
bioenv Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
boxplot.specaccum Species Accumulation Curves

-- C --

capscale [Partial] Constrained Analysis of Principal Coordinates
cca [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
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
coverscale Prints a Compact, Ordered Vegetation Table

-- D --

decorana Detrended Correspondence Analysis and Basic Reciprocal Averaging
decostand Standardizaton Methods for Community Ecology
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 and Minimum Spanning Tree for 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
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

-- 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
lines.radline Rank - Abundance or Dominance / Diversity Models

-- 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

-- N --

no.shared Connectedness and Minimum Spanning Tree for Dissimilarities

-- O --

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
ordispantree Add Graphical Items to Ordination Diagrams
ordispider Add Graphical Items to Ordination Diagrams
ordisurf Smooths Variables and Plots Contours on Ordination.
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
plot.anosim Analysis of Similarities
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.metaMDS Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
plot.prestonfit Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
plot.procrustes Procrustes Rotation of Two Configurations
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.specaccum Species Accumulation Curves
points.cca Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
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
points.radline Rank - Abundance or Dominance / Diversity Models
postMDS Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
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)
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.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.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
print.protest Procrustes Rotation of Two Configurations
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 [Partial] [Constrained] Correspondence Analysis and 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.procrustes Procrustes Rotation of Two Configurations
print.vectorfit Fits an Environmental Vector or Factor onto an Ordination
procrustes Procrustes Rotation of Two Configurations
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

-- R --

rad.lognormal Rank - Abundance or Dominance / Diversity Models
rad.preempt Rank - Abundance or Dominance / Diversity Models
rad.veil 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 Ecological Diversity Indices and Rarefaction Species Richness
residuals.cca Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
residuals.procrustes Procrustes Rotation of Two Configurations
residuals.rda Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
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

-- 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
spantree Connectedness and Minimum Spanning Tree for Dissimilarities
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 [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
summary.decorana Detrended Correspondence Analysis and Basic Reciprocal Averaging
summary.humpfit No-interaction Model for Hump-backed Species Richness vs. Biomass
summary.procrustes Procrustes Rotation of Two Configurations
summary.rda [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
summary.specaccum Species Accumulation Curves

-- T --

text.cca Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
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
vectorfit Fits an Environmental Vector or Factor onto an Ordination
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