/usr/lib/R/site-library/vegan/INDEX is in r-cran-vegan 2.4-2-1.
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CCorA Canonical Correlation Analysis
MDSrotate Rotate First MDS Dimension Parallel to an
External Variable
MOStest Mitchell-Olds & Shaw Test for the Location of
Quadratic Extreme
RsquareAdj Adjusted R-square
SSarrhenius Self-Starting nls Species-Area Models
add1.cca Add or Drop Single Terms to a Constrained
Ordination Model
adipart Additive Diversity Partitioning and
Hierarchical Null Model Testing
adonis Permutational Multivariate Analysis of Variance
Using Distance Matrices
anosim Analysis of Similarities
anova.cca Permutation Test for Constrained Correspondence
Analysis, Redundancy Analysis and Constrained
Analysis of Principal Coordinates
as.mlm.cca Refit Constrained Ordination as a Multiple
Response Linear Model
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
biplot.rda PCA biplot
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.object Result Object from Constrained Ordination with
cca, rda or capscale
clamtest Multinomial Species Classification Method
(CLAM)
commsim Create an Object for Null Model Algorithms
contribdiv Contribution Diversity Approach
decorana Detrended Correspondence Analysis and Basic
Reciprocal Averaging
decostand Standardization Methods for Community Ecology
designdist Design your own Dissimilarities
deviance.cca Statistics Resembling Deviance and AIC for
Constrained Ordination
dispindmorisita Morisita index of intraspecific aggregation
dispweight Dispersion-based weighting of species counts
distconnected Connectedness of Dissimilarities
diversity Ecological Diversity Indices
dune Vegetation and Environment in Dutch Dune
Meadows.
dune.taxon Taxonomic Classification and Phylogeny of Dune
Meadow Species
eigenvals Extract Eigenvalues from an Ordination Object
envfit Fits an Environmental Vector or Factor onto an
Ordination
eventstar Scale Parameter at the Minimum of the Tsallis
Evenness Profile
fisherfit Fit Fisher's Logseries and Preston's Lognormal
Model to Abundance Data
goodness.cca Diagnostic Tools for [Constrained] Ordination
(CCA, RDA, DCA, CA, PCA)
goodness.metaMDS Goodness of Fit and Shepard Plot for Nonmetric
Multidimensional Scaling
humpfit No-interaction Model for Hump-backed Species
Richness vs. Biomass
indpower Indicator Power of Species
isomap Isometric Feature Mapping Ordination
kendall.global Kendall coefficient of concordance
linestack Plots One-dimensional Diagrams without
Overwriting Labels
make.cepnames Abbreviates a Botanical or Zoological Latin
Name into an Eight-character Name
mantel Mantel and Partial Mantel Tests for
Dissimilarity Matrices
mantel.correlog Mantel Correlogram
metaMDS Nonmetric Multidimensional Scaling with Stable
Solution from Random Starts, Axis Scaling and
Species Scores
mite Oribatid Mite Data with Explanatory Variables
model.matrix.cca Reconstruct Model Frame and Model Matrices of
Constrained Ordination
monoMDS Global and Local Non-metric Multidimensional
Scaling and Linear and Hybrid Scaling
mrpp Multi Response Permutation Procedure and Mean
Dissimilarity Matrix
mso Functions for performing and displaying a
spatial partitioning of cca or rda results
multipart Multiplicative Diversity Partitioning
nestedtemp Nestedness Indices for Communities of Islands
or Patches
nobs.adonis Extract the Number of Observations from a vegan
Fit.
nullmodel Null Model and Simulation
oecosimu Evaluate Statistics with Null Models of
Biological Communities
ordiArrowTextXY Support Functions for Drawing Vectors
ordiarrows 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.
ordiplot Alternative plot and identify Functions for
Ordination
ordipointlabel Ordination Plots with Points and Optimized
Locations for Text
ordiresids Plots of Residuals and Fitted Values for
Constrained Ordination
ordistep Choose a Model by Permutation Tests in
Constrained Ordination
ordisurf 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
pcnm Principal Coordinates of Neighbourhood Matrix
permatfull Matrix Permutation Algorithms for
Presence-Absence and Count Data
permustats Extract, Analyse and Display Permutation
Results
permutations Permutation tests in Vegan
permutest.betadisper Permutation test of multivariate homogeneity of
groups dispersions (variances)
plot.cca Plot or Extract Results of Constrained
Correspondence Analysis or Redundancy Analysis
prc Principal Response Curves for Treatments with
Repeated Observations
predict.cca Prediction Tools for [Constrained] Ordination
(CCA, RDA, DCA, CA, PCA)
procrustes Procrustes Rotation of Two Configurations and
PROTEST
pyrifos Response of Aquatic Invertebrates to
Insecticide Treatment
radfit Rank - Abundance or Dominance / Diversity
Models
rankindex Compares Dissimilarity Indices for Gradient
Detection
rarefy Rarefaction Species Richness
raupcrick Raup-Crick Dissimilarity with Unequal Sampling
Densities of Species
read.cep Reads a CEP (Canoco) data file
renyi Renyi and Hill Diversities and Corresponding
Accumulation Curves
reorder.hclust Reorder a Hierarchical Clustering Tree
scores Get Species or Site Scores from an Ordination
screeplot.cca Screeplots for Ordination Results and Broken
Stick Distributions
simper Similarity Percentages
simulate.rda Simulate Responses with Gaussian Error or
Permuted Residuals for Constrained Ordination
sipoo Birds in the Archipelago of Sipoo (Sibbo)
spantree Minimum Spanning Tree
specaccum Species Accumulation Curves
specpool Extrapolated Species Richness in a Species Pool
stepacross Stepacross as Flexible Shortest Paths or
Extended Dissimilarities
stressplot.wcmdscale Display Ordination Distances Against Observed
Distances in Eigenvector Ordinations
taxondive Indices of Taxonomic Diversity and Distinctness
tolerance Species tolerances and sample heterogeneities
treedive Functional Diversity and Community Distances
from Species Trees
tsallis Tsallis Diversity and Corresponding
Accumulation Curves
varespec Vegetation and environment in lichen pastures
varpart Partition the Variation of Community Matrix by
2, 3, or 4 Explanatory Matrices
vegan-deprecated Deprecated Functions in vegan package
vegan-package Community Ecology Package: Ordination,
Diversity and Dissimilarities
vegandocs Display vegan Documentation
vegdist Dissimilarity Indices for Community Ecologists
vegemite Display Compact Ordered Community Tables
wascores Weighted Averages Scores for Species
wcmdscale Weighted Classical (Metric) Multidimensional
Scaling
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