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vegan (version 1.15-0)

Community Ecology Package

Description

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

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Version

Install

install.packages('vegan')

Monthly Downloads

108,498

Version

1.15-0

License

GPL-2

Maintainer

Jari Oksanen

Last Published

June 6th, 2025

Functions in vegan (1.15-0)

screeplot.cca

Screeplots for Ordination Results and Broken Stick Distributions
anosim

Analysis of Similarities
fisherfit

Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
bgdispersal

Coefficients of Biogeographical Dispersal Direction
beals

Beals Smoothing and Degree of Absence
envfit

Fits an Environmental Vector or Factor onto an Ordination
bioenv

Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
vegdist

Dissimilarity Indices for Community Ecologists
deviance.cca

Statistics Resembling Deviance and AIC for Constrained Ordination
orditorp

Add Text or Points to Ordination Plots
ordilabel

Add Text on Non-transparent Label to an Ordination Plot
cca.object

Result Object from Constrained Ordination with cca, rda or capscale
betadisper

Multivariate homogeneity of groups dispersions (variances)
permutest.betadisper

Permutation test of ultivariate homogeneity of groups dispersions (variances)
specaccum

Species Accumulation Curves
read.cep

Reads a CEP (Canoco) data file
tsallis

Tsallis Diversity and Corresponding Accumulation Curves
permuted.index2

Unrestricted and restricted permutations
dune

Vegetation and Environment in Dutch Dune Meadows.
diversity

Ecological Diversity Indices and Rarefaction Species Richness
distconnected

Connectedness of Dissimilarities
oecosimu

Null Models for Biological Communities
add1.cca

Add or Drop Single Terms to a Constrained Ordination Model
goodness.metaMDS

Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
decostand

Standardization Methods for Community Ecology
mantel

Mantel and Partial Mantel Tests for Dissimilarity Matrices
decorana

Detrended Correspondence Analysis and Basic Reciprocal Averaging
renyi

Renyi and Hill Diversities and Corresponding Accumulation Curves
ordiplot3d

Three-Dimensional and Dynamic Ordination Graphics
ordiplot

Alternative plot and identify Functions for Ordination
prc

Principal Response Curves for Treatments with Repeated Observations
metaMDS

Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
rankindex

Compares Dissimilarity Indices for Gradient Detection
radfit

Rank -- Abundance or Dominance / Diversity Models
mrpp

Multi Response Permutation Procedure of Within- versus Among-Group Dissimilarities
stepacross

Stepacross as Flexible Shortest Paths or Extended Dissimilarities
wcmdscale

Weighted Classical (Metric) Multidimensional Scaling
linestack

Plots One-dimensional Diagrams without Overwriting Labels
make.cepnames

Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
pyrifos

Response of Aquatic Invertebrates to Insecticide Treatment
procrustes

Procrustes Rotation of Two Configurations and PROTEST
varespec

Vegetation and environment in lichen pastures
mite

Oribatid Mite Data with Explanatory Variables
plot.cca

Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
spantree

Minimum Spanning Tree
anova.cca

Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
biplot.rda

PCA biplot
taxondive

Indices of Taxonomic Diversity and Distinctness
vegandocs

Display Package Documentation
permCheck

Utility functions for permutation schemes
CCorA

Canonical Correlation Analysis
varpart

Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
scores

Get Species or Site Scores from an Ordination
betadiver

Indices of beta Diversity
dune.taxon

Taxonomic Classification of Dune Meadow Species
vegemite

Prints a Compact, Ordered Vegetation Table
permat

Matrix Permutation Algorithms for Presence-Absence and Count Data
treedive

Functional Diversity estimated from a Species Dendrogram
humpfit

No-interaction Model for Hump-backed Species Richness vs. Biomass
ordixyplot

Trellis (Lattice) Plots for Ordination
capscale

[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
as.mlm.cca

Refit Constrained Ordination as a Multiple Response Linear Model
cascadeKM

K-means partitioning using a range of values of K
vegan-internal

Internal vegan functions
designdist

Design your own Dissimilarities
BCI

Barro Colorado Island Tree Counts
adonis

Permutational Multivariate Analysis of Variance Using Distance Matrices
goodness.cca

Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
isomap

Isometric Feature Mapping Ordination
nestedtemp

Nestedness Indices for Communities of Islands or Patches
ordipointlabel

Ordination Plots with Points and Optimized Locations for Text
ordisurf

Fit and Plot Smooth Surfaces of Variables on Ordination.
cca

[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
orditkplot

Ordination Plot with Movable Labels
mso

Functions for performing and displaying a spatial partitioning of cca or rda results
predict.cca

Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
ordihull

Add Graphical Items to Ordination Diagrams
specpool

Extrapolated Species Richness in a Species Pool
ordiresids

Plots of Residuals and Fitted Values for Constrained Ordination
sipoo

Birds in the Archipelago of Sipoo (Sibbo)
wascores

Weighted Averages Scores for Species