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vegan (version 2.0-4)
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
88,429
Version
2.0-4
License
GPL-2
Homepage
http://cran.r-project.org
Maintainer
Jari Oksanen
Last Published
June 19th, 2012
Functions in vegan (2.0-4)
Search functions
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
CCorA
Canonical Correlation Analysis
clamtest
Multinomial Species Classification Method (CLAM)
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
anosim
Analysis of Similarities
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
mantel.correlog
Mantel Correlogram
distconnected
Connectedness of Dissimilarities
indpower
Indicator Power of Species
betadiver
Indices of beta Diversity
multipart
Multiplicative Diversity Partitioning
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
designdist
Design your own Dissimilarities
BCI
Barro Colorado Island Tree Counts
eigenvals
Extract Eigenvalues from an Ordination Object
decostand
Standardization Methods for Community Ecology
ordixyplot
Trellis (Lattice) Plots for Ordination
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
mite
Oribatid Mite Data with Explanatory Variables
MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
envfit
Fits an Environmental Vector or Factor onto an Ordination
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
ordiplot
Alternative plot and identify Functions for Ordination
contribdiv
Contribution Diversity Approach
linestack
Plots One-dimensional Diagrams without Overwriting Labels
biplot.rda
PCA biplot
MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
SSarrhenius
Self-Starting nls Species-Area Models
cascadeKM
K-means partitioning using a range of values of K
kendall.global
Kendall coefficient of concordance
oecosimu
Null Models for Biological Communities
dune
Vegetation and Environment in Dutch Dune Meadows.
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
prc
Principal Response Curves for Treatments with Repeated Observations
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
spantree
Minimum Spanning Tree
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
orditkplot
Ordination Plot with Movable Labels
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
read.cep
Reads a CEP (Canoco) data file
betadisper
Multivariate homogeneity of groups dispersions (variances)
specaccum
Species Accumulation Curves
nobs.adonis
Extract the Number of Observations from a vegan Fit.
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
bgdispersal
Coefficients of Biogeographical Dispersal Direction
tolerance
Species tolerances and sample heterogeneities
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
RsquareAdj
Adjusted R-square
procrustes
Procrustes Rotation of Two Configurations and PROTEST
simper
Similarity Percentages
vegan-internal
Internal vegan functions
nestedtemp
Nestedness Indices for Communities of Islands or Patches
diversity
Ecological Diversity Indices and Rarefaction Species Richness
vegandocs
Display Package Documentation
treedive
Functional Diversity estimated from a Species Dendrogram
beals
Beals Smoothing and Degree of Absence
permutations
Permutation tests in Vegan
pcnm
Principal Coordinates of Neighbourhood Matrix
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
dispindmorisita
Morisita index of intraspecific aggregation
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
orditorp
Add Text or Points to Ordination Plots
isomap
Isometric Feature Mapping Ordination
rankindex
Compares Dissimilarity Indices for Gradient Detection
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
vegdist
Dissimilarity Indices for Community Ecologists
scores
Get Species or Site Scores from an Ordination
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
varespec
Vegetation and environment in lichen pastures
vegemite
Prints a Compact, Ordered Vegetation Table
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
radfit
Rank -- Abundance or Dominance / Diversity Models
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
specpool
Extrapolated Species Richness in a Species Pool
vegan-deprecated
Deprecated Functions in vegan package
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
taxondive
Indices of Taxonomic Diversity and Distinctness
wascores
Weighted Averages Scores for Species
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
vegan-defunct
Defunct Functions in Package
vegan
dune.taxon
Taxonomic Classification of Dune Meadow Species
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
ordihull
Display Groups or Factor Levels in Ordination Diagrams