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vegan (version 1.17-8)
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
1.17-8
License
GPL-2
Homepage
http://cran.r-project.org/
Maintainer
Jari Oksanen
Last Published
March 2nd, 2011
Functions in vegan (1.17-8)
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MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
contribdiv
Contribution Diversity Approach
anosim
Analysis of Similarities
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
mantel.correlog
Mantel Correlogram
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
RsquareAdj
Adjusted R-square
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
CCorA
Canonical Correlation Analysis
diversity
Ecological Diversity Indices and Rarefaction Species Richness
isomap
Isometric Feature Mapping Ordination
pcnm
Principal Coordinates of Neighbourhood Matrix
linestack
Plots One-dimensional Diagrams without Overwriting Labels
betadiver
Indices of beta Diversity
designdist
Design your own Dissimilarities
dispindmorisita
Morisita index of intraspecific aggregation
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
envfit
Fits an Environmental Vector or Factor onto an Ordination
kendall.global
Kendall coefficient of concordance
dune.taxon
Taxonomic Classification of Dune Meadow Species
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
ordihull
Add Graphical Items to Ordination Diagrams
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
orditorp
Add Text or Points to Ordination Plots
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
permuted.index2
Unrestricted and restricted permutations
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
orditkplot
Ordination Plot with Movable Labels
ordixyplot
Trellis (Lattice) Plots for Ordination
betadisper
Multivariate homogeneity of groups dispersions (variances)
permutations
Permutation tests in Vegan
nestedtemp
Nestedness Indices for Communities of Islands or Patches
ordiplot
Alternative plot and identify Functions for Ordination
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
indpower
Indicator Power of Species
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
permCheck
Utility functions for permutation schemes
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
multipart
Multiplicative Diversity Partitioning
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
eigenvals
Extract Eigenvalues from an Ordination Object
radfit
Rank -- Abundance or Dominance / Diversity Models
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
cascadeKM
K-means partitioning using a range of values of K
scores
Get Species or Site Scores from an Ordination
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
oecosimu
Null Models for Biological Communities
taxondive
Indices of Taxonomic Diversity and Distinctness
rankindex
Compares Dissimilarity Indices for Gradient Detection
wascores
Weighted Averages Scores for Species
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
prc
Principal Response Curves for Treatments with Repeated Observations
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
BCI
Barro Colorado Island Tree Counts
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
varespec
Vegetation and environment in lichen pastures
biplot.rda
PCA biplot
specpool
Extrapolated Species Richness in a Species Pool
vegdist
Dissimilarity Indices for Community Ecologists
mite
Oribatid Mite Data with Explanatory Variables
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
treedive
Functional Diversity estimated from a Species Dendrogram
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
specaccum
Species Accumulation Curves
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
vegandocs
Display Package Documentation
dune
Vegetation and Environment in Dutch Dune Meadows.
vegan-internal
Internal vegan functions
vegemite
Prints a Compact, Ordered Vegetation Table
read.cep
Reads a CEP (Canoco) data file
beals
Beals Smoothing and Degree of Absence
bgdispersal
Coefficients of Biogeographical Dispersal Direction
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
distconnected
Connectedness of Dissimilarities
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
procrustes
Procrustes Rotation of Two Configurations and PROTEST
spantree
Minimum Spanning Tree
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
decostand
Standardization Methods for Community Ecology