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vegan (version 2.0-3)
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
115,039
Version
2.0-3
License
GPL-2
Homepage
http://cran.r-project.org
Maintainer
Jari Oksanen
Last Published
March 3rd, 2012
Functions in vegan (2.0-3)
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mite
Oribatid Mite Data with Explanatory Variables
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
clamtest
Multinomial Species Classification Method (CLAM)
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
contribdiv
Contribution Diversity Approach
nobs.adonis
Extract the Number of Observations from a vegan Fit.
dispindmorisita
Morisita index of intraspecific aggregation
designdist
Design your own Dissimilarities
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
anosim
Analysis of Similarities
cascadeKM
K-means partitioning using a range of values of K
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
radfit
Rank -- Abundance or Dominance / Diversity Models
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
vegemite
Prints a Compact, Ordered Vegetation Table
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
envfit
Fits an Environmental Vector or Factor onto an Ordination
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
indpower
Indicator Power of Species
spantree
Minimum Spanning Tree
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
specaccum
Species Accumulation Curves
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
ordixyplot
Trellis (Lattice) Plots for Ordination
orditorp
Add Text or Points to Ordination Plots
procrustes
Procrustes Rotation of Two Configurations and PROTEST
kendall.global
Kendall coefficient of concordance
rankindex
Compares Dissimilarity Indices for Gradient Detection
multipart
Multiplicative Diversity Partitioning
ordihull
Display Groups or Factor Levels in Ordination Diagrams
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
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
dune.taxon
Taxonomic Classification of Dune Meadow Species
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
betadisper
Multivariate homogeneity of groups dispersions (variances)
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
diversity
Ecological Diversity Indices and Rarefaction Species Richness
ordiplot
Alternative plot and identify Functions for Ordination
eigenvals
Extract Eigenvalues from an Ordination Object
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
mantel.correlog
Mantel Correlogram
vegan-internal
Internal vegan functions
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
read.cep
Reads a CEP (Canoco) data file
dune
Vegetation and Environment in Dutch Dune Meadows.
oecosimu
Null Models for Biological Communities
pcnm
Principal Coordinates of Neighbourhood Matrix
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
linestack
Plots One-dimensional Diagrams without Overwriting Labels
BCI
Barro Colorado Island Tree Counts
isomap
Isometric Feature Mapping Ordination
vegan-defunct
Defunct Functions in Package
vegan
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
specpool
Extrapolated Species Richness in a Species Pool
nestedtemp
Nestedness Indices for Communities of Islands or Patches
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
wascores
Weighted Averages Scores for Species
vegandocs
Display Package Documentation
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
tolerance
Species tolerances and sample heterogeneities
biplot.rda
PCA biplot
beals
Beals Smoothing and Degree of Absence
distconnected
Connectedness of Dissimilarities
SSarrhenius
Self-Starting nls Species-Area Models
RsquareAdj
Adjusted R-square
CCorA
Canonical Correlation Analysis
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
varespec
Vegetation and environment in lichen pastures
treedive
Functional Diversity estimated from a Species Dendrogram
MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
permutations
Permutation tests in Vegan
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
bgdispersal
Coefficients of Biogeographical Dispersal Direction
orditkplot
Ordination Plot with Movable Labels
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
scores
Get Species or Site Scores from an Ordination
prc
Principal Response Curves for Treatments with Repeated Observations
simper
Similarity Percentages
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
taxondive
Indices of Taxonomic Diversity and Distinctness
vegdist
Dissimilarity Indices for Community Ecologists
betadiver
Indices of beta Diversity
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
decostand
Standardization Methods for Community Ecology
vegan-deprecated
Deprecated Functions in vegan package