Community Ecology Package


[Up] [Top]

Documentation for package ‘vegan’ version 2.6-2

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
adonis Deprecated Functions in vegan package
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 Evaluate Statistics with Null Models of Biological Communities
as.mcmc.permat Matrix Permutation Algorithms for Presence-Absence and Count Data
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)
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
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 [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 & 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 [Partial] Distance-based Redundancy Analysis
decorana Detrended Correspondence Analysis and Basic Reciprocal Averaging
decostand Standardization Methods for Community Ecology
density.permustats Extract, Analyse and Display Permutation Results
densityplot.permustats Extract, Analyse and Display Permutation Results
designdist 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
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.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 & 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
head.summary.cca Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
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
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 Botanical or Zoological Latin Name into an Eight-character Name
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
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 & 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
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 Trellis (Lattice) Plots for Ordination
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 Trellis (Lattice) Plots for Ordination
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 Plots of Residuals and Fitted Values for Constrained Ordination
ordisegments Add Arrows and Line Segments to Ordination Diagrams
ordispider Display Groups or Factor Levels in Ordination Diagrams
ordisplom Trellis (Lattice) Plots for Ordination
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.
orditkplot Ordination Plot with Movable Labels
orditorp Add Text or Points to Ordination Plots
ordixyplot Trellis (Lattice) Plots for Ordination
ordiYbar Result Object from Constrained Ordination

-- P --

pairs.permustats Extract, Analyse and Display Permutation Results
panel.ordi Trellis (Lattice) Plots for Ordination
panel.ordi3d Trellis (Lattice) Plots for Ordination
panel.ordiarrows Trellis (Lattice) Plots for Ordination
pcnm Principal Coordinates of Neighbourhood Matrix
permatfull Matrix Permutation Algorithms for Presence-Absence and Count Data
permatswap Matrix Permutation Algorithms for Presence-Absence and Count Data
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 & 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.orditkplot Ordination Plot with Movable Labels
plot.permat Matrix Permutation Algorithms for Presence-Absence and Count Data
plot.poolaccum Extrapolated Species Richness in a Species Pool
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 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
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.orditkplot Ordination Plot with Movable Labels
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.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 Trellis (Lattice) Plots for Ordination
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.decorana Detrended Correspondence Analysis and Basic Reciprocal Averaging
print.summary.permat Matrix Permutation Algorithms for Presence-Absence and Count Data
procrustes Procrustes Rotation of Two Configurations and PROTEST
profile.MOStest Mitchell-Olds & 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 Extract, Analyse and Display Permutation Results
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.orditkplot Ordination Plot with Movable Labels
scores.pcnm Principal Coordinates of Neighbourhood Matrix
scores.rda Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
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 BorgÄ)
sipoo.map Birds in the Archipelago of Sipoo (Sibbo and BorgÄ)
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
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.meandist Multi Response Permutation Procedure and Mean Dissimilarity Matrix
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
swan Beals Smoothing and Degree of Absence

-- T --

tabasco Display Compact Ordered Community Tables
tail.summary.cca Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
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.orditkplot Ordination Plot with Movable Labels
text.procrustes Procrustes Rotation of Two Configurations and PROTEST
tolerance Species tolerances and sample heterogeneities
tolerance.cca 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