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vegan (version 2.6-10)
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
88,026
Version
2.6-10
License
GPL-2
Issues
38
Pull Requests
1
Stars
467
Forks
97
Repository
https://github.com/vegandevs/vegan
Maintainer
Jari Oksanen
Last Published
January 29th, 2025
Functions in vegan (2.6-10)
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BCI
Barro Colorado Island Tree Counts
CCorA
Canonical Correlation Analysis
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
betadiver
Indices of beta Diversity
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cascadeKM
K-means partitioning using a range of values of K
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
beals
Beals Smoothing and Degree of Absence
biplot.rda
PCA biplot
betadisper
Multivariate homogeneity of groups dispersions (variances)
avgdist
Averaged Subsampled Dissimilarity Matrices
bgdispersal
Coefficients of Biogeographical Dispersal Direction
decostand
Standardization Methods for Community Ecology
clamtest
Multinomial Species Classification Method (CLAM)
dbrda
Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysis
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
designdist
Design your own Dissimilarities
contribdiv
Contribution Diversity Approach
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
dispindmorisita
Morisita index of intraspecific aggregation
cca.object
Result Object from Constrained Ordination
commsim
Create an Object for Null Model Algorithms
dune.taxon
Taxonomic Classification and Phylogeny of Dune Meadow Species
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
envfit
Fits an Environmental Vector or Factor onto an Ordination
diversity
Ecological Diversity Indices
dispweight
Dispersion-based weighting of species counts
distconnected
Connectedness of Dissimilarities
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
dune
Vegetation and Environment in Dutch Dune Meadows.
eigenvals
Extract Eigenvalues from an Ordination Object
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
mantel.correlog
Mantel Correlogram
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
kendall.global
Kendall coefficient of concordance
influence.cca
Linear Model Diagnostics for Constrained Ordination
isomap
Isometric Feature Mapping Ordination
linestack
Plots One-dimensional Diagrams without Overwriting Labels
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
indpower
Indicator Power of Species
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
multipart
Multiplicative Diversity Partitioning
nobs.cca
Extract the Number of Observations from a vegan Fit.
mite
Oribatid Mite Data with Explanatory Variables
ordiArrowTextXY
Support Functions for Drawing Vectors
nestedtemp
Nestedness Indices for Communities of Islands or Patches
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
nullmodel
Null Model and Simulation
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
oecosimu
Evaluate Statistics with Null Models of Biological Communities
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
ordihull
Display Groups or Factor Levels in Ordination Diagrams
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
orditorp
Add Text or Points to Ordination Plots
ordiplot
Alternative plot and identify Functions for Ordination
ordixyplot
Trellis (Lattice) Plots for Ordination
procrustes
Procrustes Rotation of Two Configurations and PROTEST
prc
Principal Response Curves for Treatments with Repeated Observations
pcnm
Principal Coordinates of Neighbourhood Matrix
permustats
Extract, Analyse and Display Permutation Results
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
permutations
Permutation tests in Vegan
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
simper
Similarity Percentages
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
radfit
Rank -- Abundance or Dominance / Diversity Models
read.cep
Reads a CEP (Canoco) data file
reorder.hclust
Reorder a Hierarchical Clustering Tree
scores
Get Species or Site Scores from an Ordination
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
rankindex
Compares Dissimilarity Indices for Gradient Detection
rarefy
Rarefaction Species Richness
specpool
Extrapolated Species Richness in a Species Pool
sppscores
Add or Replace Species Scores in Distance-Based Ordination
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
stressplot.wcmdscale
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
spantree
Minimum Spanning Tree
tolerance
Species tolerances and sample heterogeneities
taxondive
Indices of Taxonomic Diversity and Distinctness
specaccum
Species Accumulation Curves
sipoo
Birds in the Archipelago of Sipoo (Sibbo and Borgå)
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
vegan-internal
Internal vegan functions
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
treedive
Functional Diversity and Community Distances from Species Trees
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
vegdist
Dissimilarity Indices for Community Ecologists
vegan-defunct
Defunct Functions in Package
vegan
vegan-deprecated
Deprecated Functions in vegan package
vegemite
Display Compact Ordered Community Tables
varespec
Vegetation and environment in lichen pastures
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
wascores
Weighted Averages Scores for Species
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
RsquareAdj
Adjusted R-square
MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
SSarrhenius
Self-Starting nls Species-Area Models
MOStest
Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
anosim
Analysis of Similarities