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vegan (version 1.13-0)
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
1.13-0
License
GPL-2
Maintainer
Jari Oksanen
Last Published
January 29th, 2025
Functions in vegan (1.13-0)
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capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
adonis
Multivariate Analysis of Variance Using Distance Matrices
orditkplot
Ordination Plot with Movable Labels
varespec
Vegetation and environment in lichen pastures
dune
Vegetation and Environment in Dutch Dune Meadows.
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
distconnected
Connectedness of Dissimilarities
betadiver
Indices of beta Diversity
scores
Get Species or Site Scores from an Ordination
diversity
Ecological Diversity Indices and Rarefaction Species Richness
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
isomap
Isometric Feature Mapping Ordination
mite
Oribatid Mite Data with Explanatory Variables
permCheck
Utility functions for permutation schemes
read.cep
Reads a CEP (Canoco) data file
ordihull
Add Graphical Items to Ordination Diagrams
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
oecosimu
Nestedness and Null Models for Islands or Patches
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
vegdist
Dissimilarity Indices for Community Ecologists
ordiplot
Alternative plot and identify Functions for Ordination
dune.taxon
Taxonomic Classification of Dune Meadow Species
permutest.betadisper
Permutation test of ultivariate homogeneity of groups dispersions (variances)
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
radfit
Rank -- Abundance or Dominance / Diversity Models
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
prc
Principal Response Curves for Treatments with Repeated Observations
specpool
Extrapolated Species Richness in a Species Pool
vegan-internal
Internal vegan functions
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
CCorA
Canonical Correlation Analysis
designdist
Design your own Dissimilarities
decostand
Standardization Methods for Community Ecology
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
rankindex
Compares Dissimilarity Indices for Gradient Detection
biplot.rda
PCA biplot
linestack
Plots One-dimensional Diagrams without Overwriting Labels
cascadeKM
K-means partitioning using a range of values of K
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
beals
Beals Smoothing and Degree of Absence
envfit
Fits an Environmental Vector or Factor onto an Ordination
betadisper
Multivariate homogeneity of groups dispersions (variances)
bgdispersal
Coefficients of Biogeographical Dispersal Direction
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
procrustes
Procrustes Rotation of Two Configurations and PROTEST
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
spantree
Minimum Spanning Tree
specaccum
Species Accumulation Curves
wascores
Weighted Averages Scores for Species
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
vegandocs
Display Package Documentation
taxondive
Indices of Taxonomic Diversity and Distinctness
BCI
Barro Colorado Island Tree Counts
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
anosim
Analysis of Similarities
mrpp
Multi Response Permutation Procedure of Within- versus Among-Group Dissimilarities
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
ordixyplot
Trellis (Lattice) Plots for Ordination
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
orditorp
Add Text or Points to Ordination Plots
permuted.index2
Unrestricted and restricted permutations
vegemite
Prints a Compact, Ordered Vegetation Table