Rdocumentation
powered by
Learn R Programming
⚠️
There's a newer version (2.7-1) of this package.
Take me there.
vegan (version 2.4-1)
Community Ecology Package
Description
Ordination methods, diversity analysis and other functions for community and vegetation ecologists.
Copy Link
Link to current version
Version
Version
2.7-1
2.6-10
2.6-8
2.6-6.1
2.6-6
2.6-4
2.6-2
2.4-2
2.4-1
2.4-0
2.3-5
2.3-4
2.3-3
2.3-2
2.3-1
2.3-0
2.2-1
2.2-0
2.0-10
2.0-9
2.0-8
2.0-7
2.0-6
2.0-5
2.0-4
2.0-3
2.0-2
2.0-1
2.0-0
1.17-12
1.17-11
1.17-10
1.17-9
1.17-8
1.17-7
1.17-6
1.17-5
1.17-4
1.17-3
1.17-2
1.17-1
1.17-0
1.15-4
1.15-3
1.15-2
1.15-1
1.15-0
1.13-2
1.13-1
1.13-0
1.11-4
1.11-3
1.11-2
1.11-0
1.8-8
1.8-7
1.8-6
1.8-5
1.8-4
1.8-3
1.8-2
1.8-1
1.6-10
1.6-9
1.6-8
1.6-7
1.6-6
1.6-5
1.6-4
1.6-3
1.6-2
1.6-1
1.6-0
1.4-4
1.4-3
1.4-2
1.4-1
1.4-0
1.2-1
1.2-0
1.0-1
Install
install.packages('vegan')
Monthly Downloads
79,999
Version
2.4-1
License
GPL-2
Issues
31
Pull Requests
0
Stars
498
Forks
102
Repository
https://github.com/vegandevs/vegan
Homepage
https://cran.r-project.org
Maintainer
Jari Oksanen
Last Published
September 7th, 2016
Functions in vegan (2.4-1)
Search all functions
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
betadisper
Multivariate homogeneity of groups dispersions (variances)
betadiver
Indices of beta Diversity
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
bgdispersal
Coefficients of Biogeographical Dispersal Direction
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
BCI
Barro Colorado Island Tree Counts
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
beals
Beals Smoothing and Degree of Absence
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
contribdiv
Contribution Diversity Approach
cascadeKM
K-means partitioning using a range of values of K
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
clamtest
Multinomial Species Classification Method (CLAM)
CCorA
Canonical Correlation Analysis
biplot.rda
PCA biplot
commsim
Create an Object for Null Model Algorithms
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
capscale
[Partial] Distance-based Redundancy Analysis
distconnected
Connectedness of Dissimilarities
dispindmorisita
Morisita index of intraspecific aggregation
designdist
Design your own Dissimilarities
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
dune.taxon
Taxonomic Classification and Phylogeny of Dune Meadow Species
decostand
Standardization Methods for Community Ecology
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
diversity
Ecological Diversity Indices
dispweight
Dispersion-based weighting of species counts
dune
Vegetation and Environment in Dutch Dune Meadows.
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
eigenvals
Extract Eigenvalues from an Ordination Object
indpower
Indicator Power of Species
kendall.global
Kendall coefficient of concordance
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
isomap
Isometric Feature Mapping Ordination
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
envfit
Fits an Environmental Vector or Factor onto an Ordination
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
linestack
Plots One-dimensional Diagrams without Overwriting Labels
MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
mite
Oribatid Mite Data with Explanatory Variables
MOStest
Mitchell-Olds \& Shaw Test for the Location of Quadratic Extreme
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
mantel.correlog
Mantel Correlogram
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
nobs.adonis
Extract the Number of Observations from a vegan Fit.
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
multipart
Multiplicative Diversity Partitioning
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
nestedtemp
Nestedness Indices for Communities of Islands or Patches
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
ordiArrowTextXY
Support Functions for Drawing Vectors
nullmodel
Null Model and Simulation
ordihull
Display Groups or Factor Levels in Ordination Diagrams
oecosimu
Evaluate Statistics with Null Models of Biological Communities
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
stressplot.wcmdscale
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
prc
Principal Response Curves for Treatments with Repeated Observations
vegan-internal
Internal vegan functions
vegan-deprecated
Deprecated Functions in vegan package
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
read.cep
Reads a CEP (Canoco) data file
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
spantree
Minimum Spanning Tree
specaccum
Species Accumulation Curves
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
wascores
Weighted Averages Scores for Species
varespec
Vegetation and environment in lichen pastures
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
permutations
Permutation tests in Vegan
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
RsquareAdj
Adjusted R-square
scores
Get Species or Site Scores from an Ordination
ordiplot
Alternative plot and identify Functions for Ordination
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
procrustes
Procrustes Rotation of Two Configurations and PROTEST
simper
Similarity Percentages
vegemite
Display Compact Ordered Community Tables
vegdist
Dissimilarity Indices for Community Ecologists
orditkplot
Ordination Plot with Movable Labels
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
orditorp
Add Text or Points to Ordination Plots
radfit
Rank -- Abundance or Dominance / Diversity Models
rarefy
Rarefaction Species Richness
rankindex
Compares Dissimilarity Indices for Gradient Detection
specpool
Extrapolated Species Richness in a Species Pool
pcnm
Principal Coordinates of Neighbourhood Matrix
ordixyplot
Trellis (Lattice) Plots for Ordination
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
permustats
Extract, Analyse and Display Permutation Results
tolerance
Species tolerances and sample heterogeneities
vegandocs
Display vegan Documentation
treedive
Functional Diversity and Community Distances from Species Trees
reorder.hclust
Reorder a Hierarchical Clustering Tree
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
SSarrhenius
Self-Starting nls Species-Area Models
vegan-defunct
Defunct Functions in Package
vegan
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
sipoo
Birds in the Archipelago of Sipoo (Sibbo)