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vegan (version 2.7-2)

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

113,195

Version

2.7-2

License

GPL-2

Issues

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Repository

https://github.com/vegandevs/vegan

Homepage

https://vegandevs.github.io/vegan/

Maintainer

Jari Oksanen

Last Published

October 8th, 2025

Functions in vegan (2.7-2)

Analysis of Similarities

Indices of beta Diversity

Averaged Subsampled Dissimilarity Matrices

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

Coefficients of Biogeographical Dispersal Direction

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

Beals Smoothing and Degree of Absence

K-means partitioning using a range of values of K

Multivariate homogeneity of groups dispersions (variances)

Design your own Dissimilarities

Detrended Correspondence Analysis and Basic Reciprocal Averaging

Statistics Resembling Deviance and AIC for Constrained Ordination

[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis

Standardization Methods for Community Ecology

Result Object from Constrained Ordination

Contribution Diversity Approach

Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysis

Multinomial Species Classification Method (CLAM)

Create an Object for Null Model Algorithms

Fits an Environmental Vector or Factor onto an Ordination

Taxonomic Classification and Phylogeny of Dune Meadow Species

Vegetation and Environment in Dutch Dune Meadows.

Scale Parameter at the Minimum of the Tsallis Evenness Profile

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

dispindmorisita

Morisita index of intraspecific aggregation

Ecological Diversity Indices

Connectedness of Dissimilarities

Extract Eigenvalues from an Ordination Object

Dispersion-based weighting of species counts

Abbreviates a Two-Part Botanical or Zoological Latin Name into Character String

Indicator Power of Species

mantel.correlog

Mantel Correlogram

Plots One-dimensional Diagrams without Overwriting Labels

Linear Model Diagnostics for Constrained Ordination

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

goodness.metaMDS

Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling

Isometric Feature Mapping Ordination

Mantel and Partial Mantel Tests for Dissimilarity Matrices

Kendall coefficient of concordance

Null Model and Simulation

Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling

Multiplicative Diversity Partitioning

Nestedness Indices for Communities of Islands or Patches

Multi Response Permutation Procedure and Mean Dissimilarity Matrix

Evaluate Statistics with Null Models of Biological Communities

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

Oribatid Mite Data with Explanatory Variables

Extract the Number of Observations from a vegan Fit.

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

Display Groups or Factor Levels in Ordination Diagrams

Add Arrows and Line Segments to Ordination Diagrams

Choose a Model by Permutation Tests in Constrained Ordination

Ordination Plots with Points and Optimized Locations for Text

optspace: algorithm for matrix reconstruction from a partially revealed set

Add Text or Points to Ordination Plots

ordiArrowTextXY

Support Functions for Drawing Vectors

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

Alternative plot and identify Functions for Ordination

Fit and Plot Smooth Surfaces of Variables on Ordination.

Principal Response Curves for Treatments with Repeated Observations

Permutation tests in Vegan

Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis

Extract, Analyse and Display Permutation Results

Matrix Permutation Algorithms for Presence-Absence and Count Data

Principal Coordinates of Neighbourhood Matrix

Procrustes Rotation of Two Configurations and PROTEST

Trellis (Lattice) Plots for Ordination

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

permutest.betadisper

Permutation test of multivariate homogeneity of groups dispersions (variances)

Raup-Crick Dissimilarity with Unequal Sampling Densities of Species

Rank -- Abundance or Dominance / Diversity Models

Get Species or Site Scores from an Ordination

Renyi and Hill Diversities and Corresponding Accumulation Curves

Rarefaction Species Richness

Screeplots for Ordination Results and Broken Stick Distributions

Reads a CEP (Canoco) data file

Response of Aquatic Invertebrates to Insecticide Treatment

Reorder a Hierarchical Clustering Tree

Compares Dissimilarity Indices for Gradient Detection

Extrapolated Species Richness in a Species Pool

Similarity Percentages

stressplot.wcmdscale

Display Ordination Distances Against Observed Distances in Eigenvector Ordinations

Indices of Taxonomic Diversity and Distinctness

Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination

Stepacross as Flexible Shortest Paths or Extended Dissimilarities

Add or Replace Species Scores in Distance-Based Ordination

Birds in the Archipelago of Sipoo (Sibbo and Borgå)

Minimum Spanning Tree

Species Accumulation Curves

Internal vegan functions

vegan-deprecated-lattice

Deprecated lattice Functions in vegan

Species tolerances and sample heterogeneities

Tsallis Diversity and Corresponding Accumulation Curves

Vegetation and environment in lichen pastures

Functional Diversity and Community Distances from Species Trees

Community Ecology Package: Ordination, Diversity and Dissimilarities

vegan-deprecated

Deprecated Functions in vegan package

Defunct Functions in Package vegan

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

Weighted Averages Scores for Species

Dissimilarity Indices for Community Ecologists

Weighted Classical (Metric) Multidimensional Scaling

Display Compact Ordered Community Tables

Add or Drop Single Terms to a Constrained Ordination Model

Add New Points to NMDS ordination

Barro Colorado Island Tree Counts

Additive Diversity Partitioning and Hierarchical Null Model Testing

Rotate First MDS Dimension Parallel to an External Variable

Self-Starting nls Species-Area Models

Canonical Correlation Analysis

Adjusted R-square

Permutational Multivariate Analysis of Variance Using Distance Matrices

Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme