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vegan (version 1.17-7)
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
147,599
Version
1.17-7
License
GPL-2
Homepage
http://cran.r-project.org/
Maintainer
Jari Oksanen
Last Published
February 16th, 2011
Functions in vegan (1.17-7)
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model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
designdist
Design your own Dissimilarities
BCI
Barro Colorado Island Tree Counts
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
kendall.global
Kendall coefficient of concordance
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
specpool
Extrapolated Species Richness in a Species Pool
permutations
Permutation tests in Vegan
rankindex
Compares Dissimilarity Indices for Gradient Detection
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
pcnm
Principal Coordinates of Neighbourhood Matrix
betadiver
Indices of beta Diversity
MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
radfit
Rank -- Abundance or Dominance / Diversity Models
bgdispersal
Coefficients of Biogeographical Dispersal Direction
taxondive
Indices of Taxonomic Diversity and Distinctness
mantel.correlog
Mantel Correlogram
oecosimu
Null Models for Biological Communities
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
permuted.index2
Unrestricted and restricted permutations
biplot.rda
PCA biplot
betadisper
Multivariate homogeneity of groups dispersions (variances)
isomap
Isometric Feature Mapping Ordination
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
distconnected
Connectedness of Dissimilarities
spantree
Minimum Spanning Tree
linestack
Plots One-dimensional Diagrams without Overwriting Labels
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
procrustes
Procrustes Rotation of Two Configurations and PROTEST
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
ordihull
Add Graphical Items to Ordination Diagrams
nestedtemp
Nestedness Indices for Communities of Islands or Patches
cascadeKM
K-means partitioning using a range of values of K
eigenvals
Extract Eigenvalues from an Ordination Object
vegdist
Dissimilarity Indices for Community Ecologists
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
treedive
Functional Diversity estimated from a Species Dendrogram
dispindmorisita
Morisita index of intraspecific aggregation
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
dune
Vegetation and Environment in Dutch Dune Meadows.
orditorp
Add Text or Points to Ordination Plots
contribdiv
Contribution Diversity Approach
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
read.cep
Reads a CEP (Canoco) data file
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
orditkplot
Ordination Plot with Movable Labels
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
vegandocs
Display Package Documentation
dune.taxon
Taxonomic Classification of Dune Meadow Species
multipart
Multiplicative Diversity Partitioning
prc
Principal Response Curves for Treatments with Repeated Observations
specaccum
Species Accumulation Curves
mite
Oribatid Mite Data with Explanatory Variables
beals
Beals Smoothing and Degree of Absence
diversity
Ecological Diversity Indices and Rarefaction Species Richness
permCheck
Utility functions for permutation schemes
wascores
Weighted Averages Scores for Species
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
vegemite
Prints a Compact, Ordered Vegetation Table
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
anosim
Analysis of Similarities
decostand
Standardization Methods for Community Ecology
varespec
Vegetation and environment in lichen pastures
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
scores
Get Species or Site Scores from an Ordination
CCorA
Canonical Correlation Analysis
RsquareAdj
Adjusted R-square
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
envfit
Fits an Environmental Vector or Factor onto an Ordination
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
ordixyplot
Trellis (Lattice) Plots for Ordination
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
vegan-internal
Internal vegan functions
indpower
Indicator Power of Species
ordiplot
Alternative plot and identify Functions for Ordination