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vegan (version 1.17-12)
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
1.17-12
License
GPL-2
Homepage
http://cran.r-project.org/
Maintainer
Jari Oksanen
Last Published
August 17th, 2011
Functions in vegan (1.17-12)
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beals
Beals Smoothing and Degree of Absence
betadisper
Multivariate homogeneity of groups dispersions (variances)
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
ordihull
Display Groups or Factor Levels in Ordination Diagrams
contribdiv
Contribution Diversity Approach
BCI
Barro Colorado Island Tree Counts
kendall.global
Kendall coefficient of concordance
biplot.rda
PCA biplot
multipart
Multiplicative Diversity Partitioning
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
decostand
Standardization Methods for Community Ecology
RsquareAdj
Adjusted R-square
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
dune
Vegetation and Environment in Dutch Dune Meadows.
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
anosim
Analysis of Similarities
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
ordiplot
Alternative plot and identify Functions for Ordination
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
bgdispersal
Coefficients of Biogeographical Dispersal Direction
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
scores
Get Species or Site Scores from an Ordination
CCorA
Canonical Correlation Analysis
MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
diversity
Ecological Diversity Indices and Rarefaction Species Richness
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
oecosimu
Null Models for Biological Communities
distconnected
Connectedness of Dissimilarities
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
rankindex
Compares Dissimilarity Indices for Gradient Detection
dispindmorisita
Morisita index of intraspecific aggregation
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
permuted.index2
Unrestricted and restricted permutations
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
taxondive
Indices of Taxonomic Diversity and Distinctness
orditorp
Add Text or Points to Ordination Plots
vegdist
Dissimilarity Indices for Community Ecologists
cascadeKM
K-means partitioning using a range of values of K
linestack
Plots One-dimensional Diagrams without Overwriting Labels
isomap
Isometric Feature Mapping Ordination
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
envfit
Fits an Environmental Vector or Factor onto an Ordination
specaccum
Species Accumulation Curves
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
permCheck
Utility functions for permutation schemes
orditkplot
Ordination Plot with Movable Labels
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
wascores
Weighted Averages Scores for Species
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
pcnm
Principal Coordinates of Neighbourhood Matrix
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
specpool
Extrapolated Species Richness in a Species Pool
tolerance
Species tolerances and sample heterogeneities
eigenvals
Extract Eigenvalues from an Ordination Object
designdist
Design your own Dissimilarities
spantree
Minimum Spanning Tree
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
indpower
Indicator Power of Species
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
mite
Oribatid Mite Data with Explanatory Variables
nobs.adonis
Extract the Number of Observations from a vegan Fit.
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
read.cep
Reads a CEP (Canoco) data file
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
permutations
Permutation tests in Vegan
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
vegemite
Prints a Compact, Ordered Vegetation Table
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
betadiver
Indices of beta Diversity
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
mantel.correlog
Mantel Correlogram
prc
Principal Response Curves for Treatments with Repeated Observations
nestedtemp
Nestedness Indices for Communities of Islands or Patches
procrustes
Procrustes Rotation of Two Configurations and PROTEST
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
ordixyplot
Trellis (Lattice) Plots for Ordination
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
varespec
Vegetation and environment in lichen pastures
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
vegandocs
Display Package Documentation
vegan-internal
Internal vegan functions
treedive
Functional Diversity estimated from a Species Dendrogram
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
dune.taxon
Taxonomic Classification of Dune Meadow Species
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
radfit
Rank -- Abundance or Dominance / Diversity Models