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vegan (version 2.7-1)
Community Ecology Package
Description
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
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Install
install.packages('vegan')
Monthly Downloads
110,476
Version
2.7-1
License
GPL-2
Issues
34
Pull Requests
0
Stars
489
Forks
101
Repository
https://github.com/vegandevs/vegan
Homepage
https://vegandevs.github.io/vegan/
Maintainer
Jari Oksanen
Last Published
June 5th, 2025
Functions in vegan (2.7-1)
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anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
betadiver
Indices of beta Diversity
biplot.rda
PCA biplot
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
cascadeKM
K-means partitioning using a range of values of K
bgdispersal
Coefficients of Biogeographical Dispersal Direction
betadisper
Multivariate homogeneity of groups dispersions (variances)
anosim
Analysis of Similarities
avgdist
Averaged Subsampled Dissimilarity Matrices
beals
Beals Smoothing and Degree of Absence
contribdiv
Contribution Diversity Approach
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
dbrda
Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysis
clamtest
Multinomial Species Classification Method (CLAM)
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
cca.object
Result Object from Constrained Ordination
commsim
Create an Object for Null Model Algorithms
designdist
Design your own Dissimilarities
decostand
Standardization Methods for Community Ecology
distconnected
Connectedness of Dissimilarities
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
dune.taxon
Taxonomic Classification and Phylogeny of Dune Meadow Species
diversity
Ecological Diversity Indices
dispweight
Dispersion-based weighting of species counts
dune
Vegetation and Environment in Dutch Dune Meadows.
eigenvals
Extract Eigenvalues from an Ordination Object
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
envfit
Fits an Environmental Vector or Factor onto an Ordination
dispindmorisita
Morisita index of intraspecific aggregation
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
make.cepnames
Abbreviates a Two-Part Botanical or Zoological Latin Name into Character String
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
indpower
Indicator Power of Species
influence.cca
Linear Model Diagnostics for Constrained Ordination
isomap
Isometric Feature Mapping Ordination
mantel.correlog
Mantel Correlogram
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
linestack
Plots One-dimensional Diagrams without Overwriting Labels
kendall.global
Kendall coefficient of concordance
nestedtemp
Nestedness Indices for Communities of Islands or Patches
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
nobs.cca
Extract the Number of Observations from a vegan Fit.
nullmodel
Null Model and Simulation
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
oecosimu
Evaluate Statistics with Null Models of Biological Communities
multipart
Multiplicative Diversity Partitioning
mite
Oribatid Mite Data with Explanatory Variables
orditorp
Add Text or Points to Ordination Plots
ordiArrowTextXY
Support Functions for Drawing Vectors
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
ordihull
Display Groups or Factor Levels in Ordination Diagrams
ordiplot
Alternative plot and identify Functions for Ordination
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
optspace
optspace: algorithm for matrix reconstruction from a partially revealed set
permutations
Permutation tests in Vegan
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
prc
Principal Response Curves for Treatments with Repeated Observations
pcnm
Principal Coordinates of Neighbourhood Matrix
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
procrustes
Procrustes Rotation of Two Configurations and PROTEST
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
permustats
Extract, Analyse and Display Permutation Results
ordixyplot
Trellis (Lattice) Plots for Ordination
rarefy
Rarefaction Species Richness
reorder.hclust
Reorder a Hierarchical Clustering Tree
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
rankindex
Compares Dissimilarity Indices for Gradient Detection
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
scores
Get Species or Site Scores from an Ordination
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
read.cep
Reads a CEP (Canoco) data file
radfit
Rank -- Abundance or Dominance / Diversity Models
sppscores
Add or Replace Species Scores in Distance-Based Ordination
stressplot.wcmdscale
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
simper
Similarity Percentages
spantree
Minimum Spanning Tree
sipoo
Birds in the Archipelago of Sipoo (Sibbo and Borgå)
specpool
Extrapolated Species Richness in a Species Pool
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
taxondive
Indices of Taxonomic Diversity and Distinctness
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
specaccum
Species Accumulation Curves
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
vegan-deprecated-lattice
Deprecated lattice Functions in vegan
tolerance
Species tolerances and sample heterogeneities
vegan-deprecated
Deprecated Functions in vegan package
varespec
Vegetation and environment in lichen pastures
treedive
Functional Diversity and Community Distances from Species Trees
vegan-defunct
Defunct Functions in Package
vegan
vegan-internal
Internal vegan functions
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
wascores
Weighted Averages Scores for Species
vegdist
Dissimilarity Indices for Community Ecologists
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
vegemite
Display Compact Ordered Community Tables