vegan2.6-8 package

Community Ecology Package

nobs.cca

Extract the Number of Observations from a vegan Fit.

nullmodel

Null Model and Simulation

oecosimu

Evaluate Statistics with Null Models of Biological Communities

ordiarrows

Add Arrows and Line Segments to Ordination Diagrams

ordiArrowTextXY

Support Functions for Drawing Vectors

ordihull

Display Groups or Factor Levels in Ordination Diagrams

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

kendall.global

Kendall coefficient of concordance

multipart

Multiplicative Diversity Partitioning

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...

biplot.rda

PCA biplot

cascadeKM

K-means partitioning using a range of values of K

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 Matrice...

anosim

Analysis of Similarities

anova.cca

Permutation Test for Constrained Correspondence Analysis, Redundancy A...

avgdist

Averaged Subsampled Dissimilarity Matrices

beals

Beals Smoothing and Degree of Absence

cca.object

Result Object from Constrained Ordination

cca

[Partial] [Constrained] Correspondence Analysis and Redundancy Analysi...

CCorA

Canonical Correlation Analysis

clamtest

Multinomial Species Classification Method (CLAM)

commsim

Create an Object for Null Model Algorithms

contribdiv

Contribution Diversity Approach

dbrda

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

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

nestedtemp

Nestedness Indices for Communities of Islands or Patches

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 Scalin...

indpower

Indicator Power of Species

influence.cca

Linear Model Diagnostics for Constrained Ordination

isomap

Isometric Feature Mapping Ordination

predict.cca

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

linestack

Plots One-dimensional Diagrams without Overwriting Labels

make.cepnames

Abbreviates a Botanical or Zoological Latin Name into an Eight-charact...

mantel.correlog

Mantel Correlogram

mantel

Mantel and Partial Mantel Tests for Dissimilarity Matrices

MDSrotate

Rotate First MDS Dimension Parallel to an External Variable

metaMDS

Nonmetric Multidimensional Scaling with Stable Solution from Random St...

monoMDS

Global and Local Non-metric Multidimensional Scaling and Linear and Hy...

MOStest

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

mrpp

Multi Response Permutation Procedure and Mean Dissimilarity Matrix

mso

Functions for performing and displaying a spatial partitioning of cca ...

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.

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 (va...

plot.cca

Plot or Extract Results of Constrained Correspondence Analysis or Redu...

prc

Principal Response Curves for Treatments with Repeated Observations

procrustes

Procrustes Rotation of Two Configurations and PROTEST

RsquareAdj

Adjusted R-square

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 Const...

spantree

Minimum Spanning Tree

specaccum

Species Accumulation Curves

specpool

Extrapolated Species Richness in a Species Pool

sppscores

Add or Replace Species Scores in Distance-Based Ordination

SSarrhenius

Self-Starting nls Species-Area Models

stepacross

Stepacross as Flexible Shortest Paths or Extended Dissimilarities

stressplot.wcmdscale

Display Ordination Distances Against Observed Distances in Eigenvector...

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

varpart

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

vegan-defunct

Defunct Functions in Package vegan

vegan-deprecated

Deprecated Functions in vegan package

vegan-internal

Internal vegan functions

vegan-package

Community Ecology Package: Ordination, Diversity and Dissimilarities

vegdist

Dissimilarity Indices for Community Ecologists

vegemite

Display Compact Ordered Community Tables

wascores

Weighted Averages Scores for Species

wcmdscale

Weighted Classical (Metric) Multidimensional Scaling

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

  • Maintainer: Jari Oksanen
  • License: GPL-2
  • Last published: 2024-08-28