Community Ecology Package

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Accompanying documentation is available in the subdirectory "doc" of the installed package.

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

-- A --

AIC.radfit Rank - Abundance or Dominance / Diversity Models
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
boxplot.specaccum Species Accumulation Curves

-- C --

capscale [Partial] Constrained Analysis of Principal Coordinates
cca [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
centroids.cca Internal vegan functions
coef.radfit Rank - Abundance or Dominance / Diversity Models
coverscale Prints a Compact, Ordered Vegetation Table

-- D --

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

-- 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.procrustes Procrustes Rotation of Two Configurations
fitted.radfit Rank - Abundance or Dominance / Diversity Models

-- I --

identify.ordiplot Alternative plot and identify Functions for Ordination
initMDS Random Start and Axis Scaling for isoMDS

-- L --

lines.prestonfit Fit Fisher's Logseries and Preston's Lognormal model to Abundance Data
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 Test for Two Dissimilarity Matrices

-- 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
ordiParseFormula Internal vegan functions
ordiplot Alternative plot and identify Functions for Ordination
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.

-- P --

permuted.index Internal vegan functions
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.prestonfit Fit Fisher's Logseries and Preston's Lognormal model to Abundance Data
plot.procrustes Procrustes Rotation of Two Configurations
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.ordiplot Alternative plot and identify Functions for Ordination
points.radline Rank - Abundance or Dominance / Diversity Models
postMDS Random Start and Axis Scaling for isoMDS
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.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.mantel Mantel Test for Two Dissimilarity Matrices
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.cca [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
print.summary.decorana Detrended Correspondence Analysis and Basic Reciprocal Averaging
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
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.procrustes Procrustes Rotation of Two Configurations

-- 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.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
spider.cca Internal vegan functions
stepacross Stepacross as Flexible Shortest Paths or Extended Dissimilarities
summary.anosim Analysis of Similarities
summary.cca [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
summary.decorana Detrended Correspondence Analysis and Basic Reciprocal Averaging
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.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

-- 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