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vegan (version 2.4-0)
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
115,039
Version
2.4-0
License
GPL-2
Issues
35
Pull Requests
0
Stars
481
Forks
100
Repository
https://github.com/vegandevs/vegan
Homepage
https://cran.r-project.org
Maintainer
Jari Oksanen
Last Published
June 15th, 2016
Functions in vegan (2.4-0)
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add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
betadiver
Indices of beta Diversity
beals
Beals Smoothing and Degree of Absence
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
bgdispersal
Coefficients of Biogeographical Dispersal Direction
BCI
Barro Colorado Island Tree Counts
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
betadisper
Multivariate homogeneity of groups dispersions (variances)
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
clamtest
Multinomial Species Classification Method (CLAM)
cascadeKM
K-means partitioning using a range of values of K
capscale
[Partial] Distance-based Redundancy Analysis
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
commsim
Create an Object for Null Model Algorithms
CCorA
Canonical Correlation Analysis
biplot.rda
PCA biplot
contribdiv
Contribution Diversity Approach
designdist
Design your own Dissimilarities
eigenvals
Extract Eigenvalues from an Ordination Object
dispindmorisita
Morisita index of intraspecific aggregation
distconnected
Connectedness of Dissimilarities
dispweight
Dispersion-based weighting of species counts
decostand
Standardization Methods for Community Ecology
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
diversity
Ecological Diversity Indices
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
dune.taxon
Taxonomic Classification and Phylogeny of Dune Meadow Species
isomap
Isometric Feature Mapping Ordination
linestack
Plots One-dimensional Diagrams without Overwriting Labels
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
indpower
Indicator Power of Species
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
kendall.global
Kendall coefficient of concordance
envfit
Fits an Environmental Vector or Factor onto an Ordination
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
mantel.correlog
Mantel Correlogram
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
MOStest
Mitchell-Olds \& Shaw Test for the Location of Quadratic Extreme
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
mite
Oribatid Mite Data with Explanatory Variables
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
multipart
Multiplicative Diversity Partitioning
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
nullmodel
Null Model and Simulation
nestedtemp
Nestedness Indices for Communities of Islands or Patches
nobs.adonis
Extract the Number of Observations from a vegan Fit.
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
ordiArrowTextXY
Support Functions for Drawing Vectors
ordihull
Display Groups or Factor Levels in Ordination Diagrams
oecosimu
Evaluate Statistics with Null Models of Biological Communities
pcnm
Principal Coordinates of Neighbourhood Matrix
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
ordiplot
Alternative plot and identify Functions for Ordination
orditkplot
Ordination Plot with Movable Labels
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
orditorp
Add Text or Points to Ordination Plots
ordixyplot
Trellis (Lattice) Plots for Ordination
procrustes
Procrustes Rotation of Two Configurations and PROTEST
prc
Principal Response Curves for Treatments with Repeated Observations
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
permustats
Extract, Analyse and Display Permutation Results
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
radfit
Rank -- Abundance or Dominance / Diversity Models
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
permutations
Permutation tests in Vegan
rankindex
Compares Dissimilarity Indices for Gradient Detection
reorder.hclust
Reorder a Hierarchical Clustering Tree
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
simper
Similarity Percentages
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
scores
Get Species or Site Scores from an Ordination
read.cep
Reads a CEP (Canoco) data file
RsquareAdj
Adjusted R-square
rarefy
Rarefaction Species Richness
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
tolerance
Species tolerances and sample heterogeneities
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
SSarrhenius
Self-Starting nls Species-Area Models
treedive
Functional Diversity and Community Distances from Species Trees
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
spantree
Minimum Spanning Tree
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
specpool
Extrapolated Species Richness in a Species Pool
vegan-deprecated
Deprecated Functions in vegan package
vegan-defunct
Defunct Functions in Package
vegan
stressplot.wcmdscale
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
specaccum
Species Accumulation Curves
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
vegan-internal
Internal vegan functions
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
vegemite
Display Compact Ordered Community Tables
wascores
Weighted Averages Scores for Species
varespec
Vegetation and environment in lichen pastures
vegandocs
Display vegan Documentation
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
vegdist
Dissimilarity Indices for Community Ecologists