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vegan (version 2.0-5)
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
121,787
Version
2.0-5
License
GPL-2
Homepage
http://cran.r-project.org
Maintainer
Jari Oksanen
Last Published
October 8th, 2012
Functions in vegan (2.0-5)
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MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
betadiver
Indices of beta Diversity
decostand
Standardization Methods for Community Ecology
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
distconnected
Connectedness of Dissimilarities
BCI
Barro Colorado Island Tree Counts
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
orditkplot
Ordination Plot with Movable Labels
envfit
Fits an Environmental Vector or Factor onto an Ordination
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
mantel.correlog
Mantel Correlogram
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
designdist
Design your own Dissimilarities
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
dune.taxon
Taxonomic Classification of Dune Meadow Species
dune
Vegetation and Environment in Dutch Dune Meadows.
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
radfit
Rank -- Abundance or Dominance / Diversity Models
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
dispindmorisita
Morisita index of intraspecific aggregation
contribdiv
Contribution Diversity Approach
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
cascadeKM
K-means partitioning using a range of values of K
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
bgdispersal
Coefficients of Biogeographical Dispersal Direction
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
isomap
Isometric Feature Mapping Ordination
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
nestedtemp
Nestedness Indices for Communities of Islands or Patches
scores
Get Species or Site Scores from an Ordination
oecosimu
Null Models for Biological Communities
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
indpower
Indicator Power of Species
density.adonis
Kernel Density Estimation for Permutation Results in Vegan
diversity
Ecological Diversity Indices and Rarefaction Species Richness
treedive
Functional Diversity estimated from a Species Dendrogram
linestack
Plots One-dimensional Diagrams without Overwriting Labels
orditorp
Add Text or Points to Ordination Plots
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
clamtest
Multinomial Species Classification Method (CLAM)
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
permutations
Permutation tests in Vegan
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
taxondive
Indices of Taxonomic Diversity and Distinctness
tolerance
Species tolerances and sample heterogeneities
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
vegemite
Prints a Compact, Ordered Vegetation Table
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
vegan-deprecated
Deprecated Functions in vegan package
read.cep
Reads a CEP (Canoco) data file
mite
Oribatid Mite Data with Explanatory Variables
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
betadisper
Multivariate homogeneity of groups dispersions (variances)
vegan-internal
Internal vegan functions
ordihull
Display Groups or Factor Levels in Ordination Diagrams
ordiplot
Alternative plot and identify Functions for Ordination
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
pcnm
Principal Coordinates of Neighbourhood Matrix
beals
Beals Smoothing and Degree of Absence
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
simper
Similarity Percentages
nobs.adonis
Extract the Number of Observations from a vegan Fit.
RsquareAdj
Adjusted R-square
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
eigenvals
Extract Eigenvalues from an Ordination Object
ordixyplot
Trellis (Lattice) Plots for Ordination
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
SSarrhenius
Self-Starting nls Species-Area Models
CCorA
Canonical Correlation Analysis
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
specaccum
Species Accumulation Curves
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
kendall.global
Kendall coefficient of concordance
vegandocs
Display Package Documentation
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
prc
Principal Response Curves for Treatments with Repeated Observations
varespec
Vegetation and environment in lichen pastures
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
procrustes
Procrustes Rotation of Two Configurations and PROTEST
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
rankindex
Compares Dissimilarity Indices for Gradient Detection
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
wascores
Weighted Averages Scores for Species
specpool
Extrapolated Species Richness in a Species Pool
spantree
Minimum Spanning Tree
vegan-defunct
Defunct Functions in Package
vegan
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
biplot.rda
PCA biplot
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
vegdist
Dissimilarity Indices for Community Ecologists
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
anosim
Analysis of Similarities
multipart
Multiplicative Diversity Partitioning