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vegan (version 1.17-6)

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

1.17-6

License

GPL-2

Maintainer

Jari Oksanen

Last Published

January 10th, 2011

Functions in vegan (1.17-6)

contribdiv

Contribution Diversity Approach
envfit

Fits an Environmental Vector or Factor onto an Ordination
make.cepnames

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

Renyi and Hill Diversities and Corresponding Accumulation Curves
radfit

Rank -- Abundance or Dominance / Diversity Models
specpool

Extrapolated Species Richness in a Species Pool
ordilabel

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

Oribatid Mite Data with Explanatory Variables
mso

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

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

Multivariate homogeneity of groups dispersions (variances)
bgdispersal

Coefficients of Biogeographical Dispersal Direction
ordixyplot

Trellis (Lattice) Plots for Ordination
anosim

Analysis of Similarities
add1.cca

Add or Drop Single Terms to a Constrained Ordination Model
dispindmorisita

Morisita index of intraspecific aggregation
adonis

Permutational Multivariate Analysis of Variance Using Distance Matrices
varespec

Vegetation and environment in lichen pastures
kendall.global

Kendall coefficient of concordance
permuted.index2

Unrestricted and restricted permutations
predict.cca

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

Indicator Power of Species
goodness.cca

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

Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
betadiver

Indices of beta Diversity
ordisurf

Fit and Plot Smooth Surfaces of Variables on Ordination.
permutations

Permutation tests in Vegan
orditkplot

Ordination Plot with Movable Labels
MOStest

Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
vegan-internal

Internal vegan functions
adipart

Additive Diversity Partitioning and Hierarchical Null Model Testing
designdist

Design your own Dissimilarities
cca

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

Matrix Permutation Algorithms for Presence-Absence and Count Data
fisherfit

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

Procrustes Rotation of Two Configurations and PROTEST
as.mlm.cca

Refit Constrained Ordination as a Multiple Response Linear Model
cca.object

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

Isometric Feature Mapping Ordination
dune.taxon

Taxonomic Classification of Dune Meadow Species
plot.cca

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

Principal Response Curves for Treatments with Repeated Observations
oecosimu

Null Models for Biological Communities
deviance.cca

Statistics Resembling Deviance and AIC for Constrained Ordination
ordiresids

Plots of Residuals and Fitted Values for Constrained Ordination
permCheck

Utility functions for permutation schemes
CCorA

Canonical Correlation Analysis
RsquareAdj

Adjusted R-square
mantel

Mantel and Partial Mantel Tests for Dissimilarity Matrices
biplot.rda

PCA biplot
orditorp

Add Text or Points to Ordination Plots
capscale

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

Stepacross as Flexible Shortest Paths or Extended Dissimilarities
simulate.rda

Simulate Responses with Gaussian Error for Redundancy Analysis
bioenv

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

Principal Coordinates of Neighbourhood Matrix
ordistep

Choose a Model by Permutation Tests in Constrained Ordination
distconnected

Connectedness of Dissimilarities
eigenvals

Extract Eigenvalues from an Ordination Object
ordipointlabel

Ordination Plots with Points and Optimized Locations for Text
ordiplot

Alternative plot and identify Functions for Ordination
vegandocs

Display Package Documentation
anova.cca

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

Standardization Methods for Community Ecology
multipart

Multiplicative Diversity Partitioning
dune

Vegetation and Environment in Dutch Dune Meadows.
linestack

Plots One-dimensional Diagrams without Overwriting Labels
vegemite

Prints a Compact, Ordered Vegetation Table
sipoo

Birds in the Archipelago of Sipoo (Sibbo)
treedive

Functional Diversity estimated from a Species Dendrogram
vegan-package

Community Ecology Package: Ordination, Diversity and Dissimilarities
taxondive

Indices of Taxonomic Diversity and Distinctness
diversity

Ecological Diversity Indices and Rarefaction Species Richness
metaMDS

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

Screeplots for Ordination Results and Broken Stick Distributions
varpart

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

Reads a CEP (Canoco) data file
nestedtemp

Nestedness Indices for Communities of Islands or Patches
mantel.correlog

Mantel Correlogram
rankindex

Compares Dissimilarity Indices for Gradient Detection
vegdist

Dissimilarity Indices for Community Ecologists
wascores

Weighted Averages Scores for Species
ordihull

Add Graphical Items to Ordination Diagrams
model.matrix.cca

Reconstruct Model Frame and Model Matrices of Constrained Ordination
ordiplot3d

Three-Dimensional and Dynamic Ordination Graphics
specaccum

Species Accumulation Curves
wcmdscale

Weighted Classical (Metric) Multidimensional Scaling
beals

Beals Smoothing and Degree of Absence
cascadeKM

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

Tsallis Diversity and Corresponding Accumulation Curves
decorana

Detrended Correspondence Analysis and Basic Reciprocal Averaging
mrpp

Multi Response Permutation Procedure and Mean Dissimilarity Matrix
BCI

Barro Colorado Island Tree Counts
permutest.betadisper

Permutation test of multivariate homogeneity of groups dispersions (variances)
scores

Get Species or Site Scores from an Ordination
pyrifos

Response of Aquatic Invertebrates to Insecticide Treatment
spantree

Minimum Spanning Tree