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vegan (version 2.6-6.1)
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
116,062
Version
2.6-6.1
License
GPL-2
Issues
70
Pull Requests
1
Stars
457
Forks
98
Repository
https://github.com/vegandevs/vegan
Maintainer
Jari Oksanen
Last Published
May 21st, 2024
Functions in vegan (2.6-6.1)
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MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
CCorA
Canonical Correlation Analysis
BCI
Barro Colorado Island Tree Counts
anosim
Analysis of Similarities
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
SSarrhenius
Self-Starting nls Species-Area Models
RsquareAdj
Adjusted R-square
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
biplot.rda
PCA biplot
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cascadeKM
K-means partitioning using a range of values of K
beals
Beals Smoothing and Degree of Absence
betadisper
Multivariate homogeneity of groups dispersions (variances)
avgdist
Averaged Subsampled Dissimilarity Matrices
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
designdist
Design your own Dissimilarities
betadiver
Indices of beta Diversity
decostand
Standardization Methods for Community Ecology
bgdispersal
Coefficients of Biogeographical Dispersal Direction
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
dispindmorisita
Morisita index of intraspecific aggregation
cca.object
Result Object from Constrained Ordination
commsim
Create an Object for Null Model Algorithms
contribdiv
Contribution Diversity Approach
dbrda
[Partial] Distance-based Redundancy Analysis
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
clamtest
Multinomial Species Classification Method (CLAM)
dune.taxon
Taxonomic Classification and Phylogeny of Dune Meadow Species
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
eigenvals
Extract Eigenvalues from an Ordination Object
distconnected
Connectedness of Dissimilarities
dispweight
Dispersion-based weighting of species counts
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
envfit
Fits an Environmental Vector or Factor onto an Ordination
isomap
Isometric Feature Mapping Ordination
influence.cca
Linear Model Diagnostics for Constrained Ordination
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
indpower
Indicator Power of Species
mantel.correlog
Mantel Correlogram
dune
Vegetation and Environment in Dutch Dune Meadows.
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
diversity
Ecological Diversity Indices
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
oecosimu
Evaluate Statistics with Null Models of Biological Communities
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
ordiArrowTextXY
Support Functions for Drawing Vectors
mite
Oribatid Mite Data with Explanatory Variables
monoMDS
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
ordihull
Display Groups or Factor Levels in Ordination Diagrams
kendall.global
Kendall coefficient of concordance
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
linestack
Plots One-dimensional Diagrams without Overwriting Labels
nullmodel
Null Model and Simulation
nobs.cca
Extract the Number of Observations from a vegan Fit.
nestedtemp
Nestedness Indices for Communities of Islands or Patches
multipart
Multiplicative Diversity Partitioning
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
ordiplot
Alternative plot and identify Functions for Ordination
ordixyplot
Trellis (Lattice) Plots for Ordination
orditorp
Add Text or Points to Ordination Plots
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
prc
Principal Response Curves for Treatments with Repeated Observations
permustats
Extract, Analyse and Display Permutation Results
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
procrustes
Procrustes Rotation of Two Configurations and PROTEST
permutations
Permutation tests in Vegan
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
pcnm
Principal Coordinates of Neighbourhood Matrix
read.cep
Reads a CEP (Canoco) data file
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
rankindex
Compares Dissimilarity Indices for Gradient Detection
rarefy
Rarefaction Species Richness
radfit
Rank -- Abundance or Dominance / Diversity Models
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
scores
Get Species or Site Scores from an Ordination
reorder.hclust
Reorder a Hierarchical Clustering Tree
simper
Similarity Percentages
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
specpool
Extrapolated Species Richness in a Species Pool
spantree
Minimum Spanning Tree
sipoo
Birds in the Archipelago of Sipoo (Sibbo and Borgå)
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
taxondive
Indices of Taxonomic Diversity and Distinctness
specaccum
Species Accumulation Curves
stressplot.wcmdscale
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
sppscores
Add or Replace Species Scores in Distance-Based Ordination
tolerance
Species tolerances and sample heterogeneities
vegan-defunct
Defunct Functions in Package
vegan
vegemite
Display Compact Ordered Community Tables
vegan-internal
Internal vegan functions
treedive
Functional Diversity and Community Distances from Species Trees
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
vegdist
Dissimilarity Indices for Community Ecologists
vegan-deprecated
Deprecated Functions in vegan package
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
varespec
Vegetation and environment in lichen pastures
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
wascores
Weighted Averages Scores for Species
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
MOStest
Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing