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vegan (version 1.15-2)

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

147,599

Version

1.15-2

License

GPL-2

Maintainer

Jari Oksanen

Last Published

April 15th, 2009

Functions in vegan (1.15-2)

anova.cca

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

Standardization Methods for Community Ecology
kendall.global

Kendall coefficient of concordance
vegemite

Prints a Compact, Ordered Vegetation Table
contribdiv

Contribution Diversity Approach
metaMDS

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

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

Procrustes Rotation of Two Configurations and PROTEST
nestedtemp

Nestedness Indices for Communities of Islands or Patches
orditkplot

Ordination Plot with Movable Labels
stepacross

Stepacross as Flexible Shortest Paths or Extended Dissimilarities
betadiver

Indices of beta Diversity
wcmdscale

Weighted Classical (Metric) Multidimensional Scaling
oecosimu

Null Models for Biological Communities
permat

Matrix Permutation Algorithms for Presence-Absence and Count Data
fisherfit

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

PCA biplot
varpart

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

Add Graphical Items to Ordination Diagrams
vegan-internal

Internal vegan functions
taxondive

Indices of Taxonomic Diversity and Distinctness
mso

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

Ordination Plots with Points and Optimized Locations for Text
tsallis

Tsallis Diversity and Corresponding Accumulation Curves
ordilabel

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

Fits an Environmental Vector or Factor onto an Ordination
orditorp

Add Text or Points to Ordination Plots
renyi

Renyi and Hill Diversities and Corresponding Accumulation Curves
dispindmorisita

Morisita index of intraspecific aggregation
wascores

Weighted Averages Scores for Species
CCorA

Canonical Correlation Analysis
bgdispersal

Coefficients of Biogeographical Dispersal Direction
beals

Beals Smoothing and Degree of Absence
decorana

Detrended Correspondence Analysis and Basic Reciprocal Averaging
cascadeKM

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

Trellis (Lattice) Plots for Ordination
prc

Principal Response Curves for Treatments with Repeated Observations
make.cepnames

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

Oribatid Mite Data with Explanatory Variables
ordiresids

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

Screeplots for Ordination Results and Broken Stick Distributions
distconnected

Connectedness of Dissimilarities
permCheck

Utility functions for permutation schemes
cca

[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cca.object

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

Response of Aquatic Invertebrates to Insecticide Treatment
goodness.cca

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

Functional Diversity estimated from a Species Dendrogram
permuted.index2

Unrestricted and restricted permutations
anosim

Analysis of Similarities
read.cep

Reads a CEP (Canoco) data file
varespec

Vegetation and environment in lichen pastures
BCI

Barro Colorado Island Tree Counts
bioenv

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

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

Display Package Documentation
isomap

Isometric Feature Mapping Ordination
mantel

Mantel and Partial Mantel Tests for Dissimilarity Matrices
sipoo

Birds in the Archipelago of Sipoo (Sibbo)
specaccum

Species Accumulation Curves
radfit

Rank -- Abundance or Dominance / Diversity Models
deviance.cca

Statistics Resembling Deviance and AIC for Constrained Ordination
add1.cca

Add or Drop Single Terms to a Constrained Ordination Model
ordiplot3d

Three-Dimensional and Dynamic Ordination Graphics
dune.taxon

Taxonomic Classification of Dune Meadow Species
betadisper

Multivariate homogeneity of groups dispersions (variances)
scores

Get Species or Site Scores from an Ordination
linestack

Plots One-dimensional Diagrams without Overwriting Labels
diversity

Ecological Diversity Indices and Rarefaction Species Richness
dune

Vegetation and Environment in Dutch Dune Meadows.
ordiplot

Alternative plot and identify Functions for Ordination
as.mlm.cca

Refit Constrained Ordination as a Multiple Response Linear Model
mrpp

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

Compares Dissimilarity Indices for Gradient Detection
specpool

Extrapolated Species Richness in a Species Pool
permutest.betadisper

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

Permutational Multivariate Analysis of Variance Using Distance Matrices
predict.cca

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

Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
ordisurf

Fit and Plot Smooth Surfaces of Variables on Ordination.
vegdist

Dissimilarity Indices for Community Ecologists
plot.cca

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

Design your own Dissimilarities
spantree

Minimum Spanning Tree