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vegan (version 2.3-5)
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
2.3-5
License
GPL-2
Issues
35
Pull Requests
0
Stars
483
Forks
100
Repository
https://github.com/vegandevs/vegan
Homepage
https://cran.r-project.org
Maintainer
Jari Oksanen
Last Published
April 8th, 2016
Functions in vegan (2.3-5)
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ordiArrowTextXY
Support Functions for Drawing Vectors
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
CCorA
Canonical Correlation Analysis
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
isomap
Isometric Feature Mapping Ordination
mantel.correlog
Mantel Correlogram
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
dune
Vegetation and Environment in Dutch Dune Meadows.
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
commsim
Create a Object for Null Model Algorithms
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
cascadeKM
K-means partitioning using a range of values of K
anosim
Analysis of Similarities
dispweight
Dispersion-based weighting of species counts
envfit
Fits an Environmental Vector or Factor onto an Ordination
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
permat
Matrix Permutation Algorithms for Presence-Absence and Count Data
clamtest
Multinomial Species Classification Method (CLAM)
adipart
Additive Diversity Partitioning and Hierarchical Null Model Testing
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
permustats
Extract, Analyse and Display Permutation Results
ordixyplot
Trellis (Lattice) Plots for Ordination
distconnected
Connectedness of Dissimilarities
betadisper
Multivariate homogeneity of groups dispersions (variances)
nestedtemp
Nestedness Indices for Communities of Islands or Patches
reorder.hclust
Reorder a Hierarchical Clustering Tree
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
diversity
Ecological Diversity Indices
vegan-defunct
Defunct Functions in Package
vegan
oecosimu
Evaluate Statistics with Null Models of Biological Communities
vegan-internal
Internal vegan functions
taxondive
Indices of Taxonomic Diversity and Distinctness
specaccum
Species Accumulation Curves
dispindmorisita
Morisita index of intraspecific aggregation
beals
Beals Smoothing and Degree of Absence
betadiver
Indices of beta Diversity
designdist
Design your own Dissimilarities
radfit
Rank -- Abundance or Dominance / Diversity Models
varespec
Vegetation and environment in lichen pastures
RsquareAdj
Adjusted R-square
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
MOStest
Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme
decostand
Standardization Methods for Community Ecology
ordipointlabel
Ordination Plots with Points and Optimized Locations for Text
ordihull
Display Groups or Factor Levels in Ordination Diagrams
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
ordiarrows
Add Arrows and Line Segments to Ordination Diagrams
model.matrix.cca
Reconstruct Model Frame and Model Matrices of Constrained Ordination
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
mrpp
Multi Response Permutation Procedure and Mean Dissimilarity Matrix
eventstar
Scale Parameter at the Minimum of the Tsallis Evenness Profile
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
simulate.rda
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination
nullmodel
Null Model and Simulation
mite
Oribatid Mite Data with Explanatory Variables
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
read.cep
Reads a CEP (Canoco) data file
orditorp
Add Text or Points to Ordination Plots
treedive
Functional Diversity and Community Distances from Species Trees
orditkplot
Ordination Plot with Movable Labels
adonis
Permutational Multivariate Analysis of Variance Using Distance Matrices
ordilabel
Add Text on Non-transparent Label to an Ordination Plot.
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
tolerance
Species tolerances and sample heterogeneities
raupcrick
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species
vegemite
Display Compact Ordered Community Tables
stressplot.wcmdscale
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations
permutest.betadisper
Permutation test of multivariate homogeneity of groups dispersions (variances)
vegan-deprecated
Deprecated Functions in vegan package
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
pcnm
Principal Coordinates of Neighbourhood Matrix
prc
Principal Response Curves for Treatments with Repeated Observations
dune.taxon
Taxonomic Classification and Phylogeny of Dune Meadow Species
BCI
Barro Colorado Island Tree Counts
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
vegan-package
Community Ecology Package: Ordination, Diversity and Dissimilarities
rarefy
Rarefaction Species Richness
bgdispersal
Coefficients of Biogeographical Dispersal Direction
specpool
Extrapolated Species Richness in a Species Pool
vegdist
Dissimilarity Indices for Community Ecologists
eigenvals
Extract Eigenvalues from an Ordination Object
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities
tsallis
Tsallis Diversity and Corresponding Accumulation Curves
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
SSarrhenius
Self-Starting nls Species-Area Models
kendall.global
Kendall coefficient of concordance
multipart
Multiplicative Diversity Partitioning
MDSrotate
Rotate First MDS Dimension Parallel to an External Variable
nobs.adonis
Extract the Number of Observations from a vegan Fit.
scores
Get Species or Site Scores from an Ordination
wascores
Weighted Averages Scores for Species
add1.cca
Add or Drop Single Terms to a Constrained Ordination Model
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
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
procrustes
Procrustes Rotation of Two Configurations and PROTEST
rankindex
Compares Dissimilarity Indices for Gradient Detection
vegandocs
Display vegan Documentation
linestack
Plots One-dimensional Diagrams without Overwriting Labels
simper
Similarity Percentages
spantree
Minimum Spanning Tree
wcmdscale
Weighted Classical (Metric) Multidimensional Scaling
biplot.rda
PCA biplot
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
mso
Functions for performing and displaying a spatial partitioning of cca or rda results
ordistep
Choose a Model by Permutation Tests in Constrained Ordination
contribdiv
Contribution Diversity Approach
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
ordiplot
Alternative plot and identify Functions for Ordination
indpower
Indicator Power of Species
permutations
Permutation tests in Vegan