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vegan (version 2.0-6)
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
113,195
Version
2.0-6
License
GPL-2
Homepage
http://cran.r-project.org
Maintainer
Jari Oksanen
Last Published
February 11th, 2013
Functions in vegan (2.0-6)
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BCI
Barro Colorado Island Tree Counts
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
kendall.global
Kendall coefficient of concordance
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
dune
Vegetation and Environment in Dutch Dune Meadows.
radfit
Rank -- Abundance or Dominance / Diversity Models
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
decostand
Standardization Methods for Community Ecology
anosim
Analysis of Similarities
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
nestedtemp
Nestedness Indices for Communities of Islands or Patches
MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
clamtest
Multinomial Species Classification Method (CLAM)
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
mite
Oribatid Mite Data with Explanatory Variables
beals
Beals Smoothing and Degree of Absence
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
orditkplot
Ordination Plot with Movable Labels
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
diversity
Ecological Diversity Indices and Rarefaction Species Richness
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
SSarrhenius
Self-Starting nls Species-Area Models
nobs.adonis
Extract the Number of Observations from a vegan Fit.
cascadeKM
K-means partitioning using a range of values of K
RsquareAdj
Adjusted R-square
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
vegan-defunct
Defunct Functions in Package
vegan
spantree
Minimum Spanning Tree
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
envfit
Fits an Environmental Vector or Factor onto an Ordination
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
vegan-internal
Internal vegan functions
CCorA
Canonical Correlation Analysis
vegemite
Prints a Compact, Ordered Vegetation Table
designdist
Design your own Dissimilarities
isomap
Isometric Feature Mapping Ordination
density.adonis
Kernel Density Estimation for Permutation Results in Vegan
eigenvals
Extract Eigenvalues from an Ordination Object
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
rankindex
Compares Dissimilarity Indices for Gradient Detection
linestack
Plots One-dimensional Diagrams without Overwriting Labels
distconnected
Connectedness of Dissimilarities
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
specpool
Extrapolated Species Richness in a Species Pool
dune.taxon
Taxonomic Classification of Dune Meadow Species
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
indpower
Indicator Power of Species
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
read.cep
Reads a CEP (Canoco) data file
ordixyplot
Trellis (Lattice) Plots for Ordination
dispindmorisita
Morisita index of intraspecific aggregation
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
ordiplot
Alternative plot and identify Functions for Ordination
oecosimu
Null Models for Biological Communities
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
orditorp
Add Text or Points to Ordination Plots
taxondive
Indices of Taxonomic Diversity and Distinctness
mantel.correlog
Mantel Correlogram
tolerance
Species tolerances and sample heterogeneities
procrustes
Procrustes Rotation of Two Configurations and PROTEST
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
multipart
Multiplicative Diversity Partitioning
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
pcnm
Principal Coordinates of Neighbourhood Matrix
treedive
Functional Diversity estimated from a Species Dendrogram
biplot.rda
PCA biplot
vegdist
Dissimilarity Indices for Community Ecologists
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
ordihull
Display Groups or Factor Levels in Ordination Diagrams
permutations
Permutation tests in Vegan
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
bgdispersal
Coefficients of Biogeographical Dispersal Direction
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
varespec
Vegetation and environment in lichen pastures
simper
Similarity Percentages
specaccum
Species Accumulation Curves
wascores
Weighted Averages Scores for Species
vegan-deprecated
Deprecated Functions in vegan package
prc
Principal Response Curves for Treatments with Repeated Observations
vegandocs
Display Package Documentation
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
betadisper
Multivariate homogeneity of groups dispersions (variances)
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
scores
Get Species or Site Scores from an Ordination
contribdiv
Contribution Diversity Approach
betadiver
Indices of beta Diversity
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling