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vegan (version 1.11-0)
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
88,429
Version
1.11-0
License
GPL-2
Homepage
http://cran.r-project.org/
Maintainer
Jari Oksanen
Last Published
February 19th, 2008
Functions in vegan (1.11-0)
Search functions
cca.object
Result Object from Constrained Ordination with cca, rda or capscale
dune
Vegetation and Environment in Dutch Dune Meadows.
betadisper
Multivariate homogeneity of groups dispersions (variances)
fisherfit
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data
rankindex
Compares Dissimilarity Indices for Gradient Detection
ordiresids
Plots of Residuals and Fitted Values for Constrained Ordination
mantel
Mantel and Partial Mantel Tests for Dissimilarity Matrices
prc
Principal Response Curves for Treatments with Repeated Observations
vegemite
Prints a Compact, Ordered Vegetation Table
as.mlm.cca
Refit Constrained Ordination as a Multiple Response Linear Model
orditorp
Add Text or Points to Ordination Plots
plot.cca
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis
designdist
Design your own Dissimilarities
anova.cca
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates
pyrifos
Response of Aquatic Invertebrates to Insecticide Treatment
dune.taxon
Taxonomic Classification of Dune Meadow Species
beals
Beals Smoothing and Degree of Absence
vegandocs
Display Package Documentation
predict.cca
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
radfit
Rank -- Abundance or Dominance / Diversity Models
cascadeKM
K-means partitioning using a range of values of K
CCorA
Canonical Correlation Analysis
goodness.cca
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA)
ordihull
Add Graphical Items to Ordination Diagrams
bgdispersal
Coefficients of Biogeographical Dispersal Direction
biplot.rda
PCA biplot
permCheck
Number of possible permutations and checking of permutation schemes
taxondive
Indices of Taxonomic Diversity and Distinctness
adonis
Multivariate Analysis of Variance Using Distance Matrices
metaMDS
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores
scores
Get Species or Site Scores from an Ordination
renyi
Renyi and Hill Diversities and Corresponding Accumulation Curves
permuted.index2
Unrestricted and restricted permutations
screeplot.cca
Screeplots for Ordination Results and Broken Stick Distributions
cca
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis
anosim
Analysis of Similarities
capscale
[Partial] Constrained Analysis of Principal Coordinates or distance-based RDA
bioenv
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities
diversity
Ecological Diversity Indices and Rarefaction Species Richness
deviance.cca
Statistics Resembling Deviance and AIC for Constrained Ordination
make.cepnames
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name
decostand
Standardization Methods for Community Ecology
vegan-internal
Internal vegan functions
decorana
Detrended Correspondence Analysis and Basic Reciprocal Averaging
specaccum
Species Accumulation Curves
ordiplot3d
Three-Dimensional and Dynamic Ordination Graphics
ordixyplot
Trellis (Lattice) Plots for Ordination
oecosimu
Nestedness and Null Models for Islands or Patches
ordisurf
Fit and Plot Smooth Surfaces of Variables on Ordination.
procrustes
Procrustes Rotation of Two Configurations and PROTEST
envfit
Fits an Environmental Vector or Factor onto an Ordination
ordiplot
Alternative plot and identify Functions for Ordination
spantree
Minimum Spanning Tree
mrpp
Multi Response Permutation Procedure of Within- versus Among-Group Dissimilarities
wascores
Weighted Averages Scores for Species
mite
Oribatid Mite Data with Explanatory Variables
read.cep
Reads a CEP (Canoco) data file
vegdist
Dissimilarity Indices for Community Ecologists
specpool
Extrapolated Species Richness in a Species Pool
humpfit
No-interaction Model for Hump-backed Species Richness vs. Biomass
linestack
Plots One-dimensional Diagrams without Overwriting Labels
isomap
Isometric Feature Mapping Ordination
sipoo
Birds in the Archipelago of Sipoo (Sibbo)
goodness.metaMDS
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling
distconnected
Connectedness of Dissimilarities
BCI
Barro Colorado Island Tree Counts
orditkplot
Ordination Plot with Movable Labels
varpart
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices
varespec
Vegetation and environment in lichen pastures
stepacross
Stepacross as Flexible Shortest Paths or Extended Dissimilarities