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vegan (version 2.4-2)
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
87,996
Version
2.4-2
License
GPL-2
Issues
76
Pull Requests
1
Stars
423
Forks
94
Repository
https://github.com/vegandevs/vegan
Homepage
https://cran.r-project.org
Maintainer
Jari Oksanen
Last Published
January 17th, 2017
Functions in vegan (2.4-2)
Search functions
beals
Beals Smoothing and Degree of Absence
betadiver
Indices of beta Diversity
betadisper
Multivariate homogeneity of groups dispersions (variances)
BCI
Barro Colorado Island Tree Counts
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
bgdispersal
Coefficients of Biogeographical Dispersal Direction
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
biplot.rda
PCA biplot
CCorA
Canonical Correlation Analysis
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
clamtest
Multinomial Species Classification Method (CLAM)
capscale
[Partial] Distance-based Redundancy Analysis
commsim
Create an Object for Null Model Algorithms
cascadeKM
K-means partitioning using a range of values of K
contribdiv
Contribution Diversity Approach
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
linestack
Plots One-dimensional Diagrams without Overwriting Labels
indpower
Indicator Power of Species
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
oecosimu
Evaluate Statistics with Null Models of Biological Communities
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
permutations
Permutation tests in Vegan
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
dispindmorisita
Morisita index of intraspecific aggregation
dispweight
Dispersion-based weighting of species counts
MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
ordihull
Display Groups or Factor Levels in Ordination Diagrams
ordiArrowTextXY
Support Functions for Drawing Vectors
decostand
Standardization Methods for Community Ecology
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
kendall.global
Kendall coefficient of concordance
isomap
Isometric Feature Mapping Ordination
mantel.correlog
Mantel Correlogram
dune
Vegetation and Environment in Dutch Dune Meadows.
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
envfit
Fits an Environmental Vector or Factor onto an Ordination
eigenvals
Extract Eigenvalues from an Ordination Object
dune.taxon
Taxonomic Classification and Phylogeny of Dune Meadow Species
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
mite
Oribatid Mite Data with Explanatory Variables
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
read.cep
Reads a CEP (Canoco) data file
distconnected
Connectedness of Dissimilarities
stressplot.wcmdscale
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
diversity
Ecological Diversity Indices
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
MOStest
Mitchell-Olds \& Shaw Test for the Location of Quadratic Extreme
simper
Similarity Percentages
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
nobs.adonis
Extract the Number of Observations from a vegan Fit.
specpool
Extrapolated Species Richness in a Species Pool
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
SSarrhenius
Self-Starting nls Species-Area Models
varespec
Vegetation and environment in lichen pastures
orditkplot
Ordination Plot with Movable Labels
orditorp
Add Text or Points to Ordination Plots
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
prc
Principal Response Curves for Treatments with Repeated Observations
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
multipart
Multiplicative Diversity Partitioning
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
nestedtemp
Nestedness Indices for Communities of Islands or Patches
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
ordiplot
Alternative plot and identify Functions for Ordination
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
designdist
Design your own Dissimilarities
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
procrustes
Procrustes Rotation of Two Configurations and PROTEST
ordixyplot
Trellis (Lattice) Plots for Ordination
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
pcnm
Principal Coordinates of Neighbourhood Matrix
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
vegan-defunct
Defunct Functions in Package
vegan
wascores
Weighted Averages Scores for Species
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
nullmodel
Null Model and Simulation
permustats
Extract, Analyse and Display Permutation Results
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
rarefy
Rarefaction Species Richness
rankindex
Compares Dissimilarity Indices for Gradient Detection
specaccum
Species Accumulation Curves
spantree
Minimum Spanning Tree
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
radfit
Rank -- Abundance or Dominance / Diversity Models
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
reorder.hclust
Reorder a Hierarchical Clustering Tree
tolerance
Species tolerances and sample heterogeneities
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
treedive
Functional Diversity and Community Distances from Species Trees
vegandocs
Display vegan Documentation
vegdist
Dissimilarity Indices for Community Ecologists
vegemite
Display Compact Ordered Community Tables
RsquareAdj
Adjusted R-square
scores
Get Species or Site Scores from an Ordination
vegan-internal
Internal vegan functions
vegan-deprecated
Deprecated Functions in vegan package