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vegan (version 2.3-2)
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
110,476
Version
2.3-2
License
GPL-2
Issues
30
Pull Requests
0
Stars
491
Forks
101
Repository
https://github.com/vegandevs/vegan
Homepage
http://cran.r-project.org
Maintainer
Jari Oksanen
Last Published
November 19th, 2015
Functions in vegan (2.3-2)
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betadisper
Multivariate homogeneity of groups dispersions (variances)
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
cascadeKM
K-means partitioning using a range of values of K
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
linestack
Plots One-dimensional Diagrams without Overwriting Labels
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
SSarrhenius
Self-Starting nls Species-Area Models
dispindmorisita
Morisita index of intraspecific aggregation
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
RsquareAdj
Adjusted R-square
nestedtemp
Nestedness Indices for Communities of Islands or Patches
isomap
Isometric Feature Mapping Ordination
beals
Beals Smoothing and Degree of Absence
designdist
Design your own Dissimilarities
envfit
Fits an Environmental Vector or Factor onto an Ordination
ordiplot
Alternative plot and identify Functions for Ordination
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
ordihull
Display Groups or Factor Levels in Ordination Diagrams
orditkplot
Ordination Plot with Movable Labels
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
mantel.correlog
Mantel Correlogram
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
dispweight
Dispersion-based weighting of species counts
ordiArrowTextXY
Support Functions for Drawing Vectors
prc
Principal Response Curves for Treatments with Repeated Observations
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
read.cep
Reads a CEP (Canoco) data file
MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
eigenvals
Extract Eigenvalues from an Ordination Object
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
reorder.hclust
Reorder a Hierarchical Clustering Tree
spantree
Minimum Spanning Tree
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
clamtest
Multinomial Species Classification Method (CLAM)
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
rankindex
Compares Dissimilarity Indices for Gradient Detection
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
biplot.rda
PCA biplot
bgdispersal
Coefficients of Biogeographical Dispersal Direction
wascores
Weighted Averages Scores for Species
nobs.adonis
Extract the Number of Observations from a vegan Fit.
simper
Similarity Percentages
betadiver
Indices of beta Diversity
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
vegandocs
Display Package Documentation
rarefy
Rarefaction Species Richness
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
distconnected
Connectedness of Dissimilarities
vegan-internal
Internal vegan functions
orditorp
Add Text or Points to Ordination Plots
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
nullmodel
Null Model and Simulation
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
mite
Oribatid Mite Data with Explanatory Variables
multipart
Multiplicative Diversity Partitioning
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
vegan-defunct
Defunct Functions in Package
vegan
treedive
Functional Diversity and Community Distances from Species Trees
varespec
Vegetation and environment in lichen pastures
specpool
Extrapolated Species Richness in a Species Pool
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
BCI
Barro Colorado Island Tree Counts
vegdist
Dissimilarity Indices for Community Ecologists
CCorA
Canonical Correlation Analysis
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
dune
Vegetation and Environment in Dutch Dune Meadows.
decostand
Standardization Methods for Community Ecology
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
contribdiv
Contribution Diversity Approach
scores
Get Species or Site Scores from an Ordination
ordixyplot
Trellis (Lattice) Plots for Ordination
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
taxondive
Indices of Taxonomic Diversity and Distinctness
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
vegan-deprecated
Deprecated Functions in vegan package
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
procrustes
Procrustes Rotation of Two Configurations and PROTEST
tolerance
Species tolerances and sample heterogeneities
radfit
Rank -- Abundance or Dominance / Diversity Models
permustats
Extract, Analyse and Display Permutation Results
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
vegemite
Display Compact Ordered Community Tables
anosim
Analysis of Similarities
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
diversity
Ecological Diversity Indices
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
oecosimu
Evaluate Statistics with Null Models of Biological Communities
specaccum
Species Accumulation Curves
pcnm
Principal Coordinates of Neighbourhood Matrix
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
commsim
Create a Object for Null Model Algorithms
dune.taxon
Taxonomic Classification and Phylogeny of Dune Meadow Species
kendall.global
Kendall coefficient of concordance
indpower
Indicator Power of Species
permutations
Permutation tests in Vegan
stressplot.wcmdscale
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations