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vegan (version 1.17-9)
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
79,999
Version
1.17-9
License
GPL-2
Homepage
http://cran.r-project.org/
Maintainer
Jari Oksanen
Last Published
March 31st, 2011
Functions in vegan (1.17-9)
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cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
CCorA
Canonical Correlation Analysis
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
prc
Principal Response Curves for Treatments with Repeated Observations
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
anosim
Analysis of Similarities
envfit
Fits an Environmental Vector or Factor onto an Ordination
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
RsquareAdj
Adjusted R-square
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
ordihull
Add Graphical Items to Ordination Diagrams
betadisper
Multivariate homogeneity of groups dispersions (variances)
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
indpower
Indicator Power of Species
multipart
Multiplicative Diversity Partitioning
BCI
Barro Colorado Island Tree Counts
cascadeKM
K-means partitioning using a range of values of K
dune.taxon
Taxonomic Classification of Dune Meadow Species
isomap
Isometric Feature Mapping Ordination
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
specaccum
Species Accumulation Curves
mantel.correlog
Mantel Correlogram
eigenvals
Extract Eigenvalues from an Ordination Object
rankindex
Compares Dissimilarity Indices for Gradient Detection
kendall.global
Kendall coefficient of concordance
decostand
Standardization Methods for Community Ecology
contribdiv
Contribution Diversity Approach
dispindmorisita
Morisita index of intraspecific aggregation
distconnected
Connectedness of Dissimilarities
treedive
Functional Diversity estimated from a Species Dendrogram
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
orditkplot
Ordination Plot with Movable Labels
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
nestedtemp
Nestedness Indices for Communities of Islands or Patches
mite
Oribatid Mite Data with Explanatory Variables
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
beals
Beals Smoothing and Degree of Absence
taxondive
Indices of Taxonomic Diversity and Distinctness
designdist
Design your own Dissimilarities
orditorp
Add Text or Points to Ordination Plots
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
spantree
Minimum Spanning Tree
betadiver
Indices of beta Diversity
dune
Vegetation and Environment in Dutch Dune Meadows.
scores
Get Species or Site Scores from an Ordination
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
oecosimu
Null Models for Biological Communities
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
pcnm
Principal Coordinates of Neighbourhood Matrix
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
permutations
Permutation tests in Vegan
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
specpool
Extrapolated Species Richness in a Species Pool
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
bgdispersal
Coefficients of Biogeographical Dispersal Direction
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
procrustes
Procrustes Rotation of Two Configurations and PROTEST
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
vegandocs
Display Package Documentation
radfit
Rank -- Abundance or Dominance / Diversity Models
vegemite
Prints a Compact, Ordered Vegetation Table
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
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
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
permCheck
Utility functions for permutation schemes
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
varespec
Vegetation and environment in lichen pastures
wascores
Weighted Averages Scores for Species
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
biplot.rda
PCA biplot
diversity
Ecological Diversity Indices and Rarefaction Species Richness
read.cep
Reads a CEP (Canoco) data file
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
ordixyplot
Trellis (Lattice) Plots for Ordination
linestack
Plots One-dimensional Diagrams without Overwriting Labels
permuted.index2
Unrestricted and restricted permutations
ordiplot
Alternative plot and identify Functions for Ordination
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
vegan-internal
Internal vegan functions
vegdist
Dissimilarity Indices for Community Ecologists