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vegan (version 1.15-3)

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

115,039

Version

1.15-3

License

GPL-2

Maintainer

Jari Oksanen

Last Published

June 17th, 2009

Functions in vegan (1.15-3)

vegdist

Dissimilarity Indices for Community Ecologists
ordihull

Add Graphical Items to Ordination Diagrams
oecosimu

Null Models for Biological Communities
dune

Vegetation and Environment in Dutch Dune Meadows.
ordisurf

Fit and Plot Smooth Surfaces of Variables on Ordination.
BCI

Barro Colorado Island Tree Counts
betadisper

Multivariate homogeneity of groups dispersions (variances)
permuted.index2

Unrestricted and restricted permutations
permutest.betadisper

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

Weighted Averages Scores for Species
vegan-internal

Internal vegan functions
capscale

[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
treedive

Functional Diversity estimated from a Species Dendrogram
vegemite

Prints a Compact, Ordered Vegetation Table
cascadeKM

K-means partitioning using a range of values of K
eigenvals

Extract Eigenvalues from an Ordination Object
goodness.cca

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

Morisita index of intraspecific aggregation
adonis

Permutational Multivariate Analysis of Variance Using Distance Matrices
ordiresids

Plots of Residuals and Fitted Values for Constrained Ordination
deviance.cca

Statistics Resembling Deviance and AIC for Constrained Ordination
taxondive

Indices of Taxonomic Diversity and Distinctness
isomap

Isometric Feature Mapping Ordination
designdist

Design your own Dissimilarities
bioenv

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

Principal Response Curves for Treatments with Repeated Observations
ordixyplot

Trellis (Lattice) Plots for Ordination
vegandocs

Display Package Documentation
mrpp

Multi Response Permutation Procedure of Within- versus Among-Group Dissimilarities
cca.object

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

Coefficients of Biogeographical Dispersal Direction
wcmdscale

Weighted Classical (Metric) Multidimensional Scaling
ordiplot

Alternative plot and identify Functions for Ordination
add1.cca

Add or Drop Single Terms to a Constrained Ordination Model
radfit

Rank -- Abundance or Dominance / Diversity Models
cca

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

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

Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
permat

Matrix Permutation Algorithms for Presence-Absence and Count Data
stepacross

Stepacross as Flexible Shortest Paths or Extended Dissimilarities
anosim

Analysis of Similarities
read.cep

Reads a CEP (Canoco) data file
biplot.rda

PCA biplot
ordilabel

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

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

Response of Aquatic Invertebrates to Insecticide Treatment
kendall.global

Kendall coefficient of concordance
scores

Get Species or Site Scores from an Ordination
decostand

Standardization Methods for Community Ecology
ordiplot3d

Three-Dimensional and Dynamic Ordination Graphics
betadiver

Indices of beta Diversity
CCorA

Canonical Correlation Analysis
decorana

Detrended Correspondence Analysis and Basic Reciprocal Averaging
linestack

Plots One-dimensional Diagrams without Overwriting Labels
make.cepnames

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

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

Contribution Diversity Approach
anova.cca

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

Species Accumulation Curves
procrustes

Procrustes Rotation of Two Configurations and PROTEST
specpool

Extrapolated Species Richness in a Species Pool
beals

Beals Smoothing and Degree of Absence
distconnected

Connectedness of Dissimilarities
varespec

Vegetation and environment in lichen pastures
envfit

Fits an Environmental Vector or Factor onto an Ordination
dune.taxon

Taxonomic Classification of Dune Meadow Species
fisherfit

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

Screeplots for Ordination Results and Broken Stick Distributions
orditorp

Add Text or Points to Ordination Plots
humpfit

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

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

Birds in the Archipelago of Sipoo (Sibbo)
as.mlm.cca

Refit Constrained Ordination as a Multiple Response Linear Model
orditkplot

Ordination Plot with Movable Labels
renyi

Renyi and Hill Diversities and Corresponding Accumulation Curves
predict.cca

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

Oribatid Mite Data with Explanatory Variables
spantree

Minimum Spanning Tree
permCheck

Utility functions for permutation schemes
tsallis

Tsallis Diversity and Corresponding Accumulation Curves
mantel

Mantel and Partial Mantel Tests for Dissimilarity Matrices
ordipointlabel

Ordination Plots with Points and Optimized Locations for Text
rankindex

Compares Dissimilarity Indices for Gradient Detection
diversity

Ecological Diversity Indices and Rarefaction Species Richness
nestedtemp

Nestedness Indices for Communities of Islands or Patches