vegan v2.4-2

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by Jari Oksanen

Community Ecology Package

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Functions in vegan

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

Date 2017-01-17
VignetteBuilder utils, knitr
License GPL-2
BugReports https://github.com/vegandevs/vegan/issues
URL https://cran.r-project.org, https://github.com/vegandevs/vegan
NeedsCompilation yes
Packaged 2017-01-17 13:20:06 UTC; jarioksa
Repository CRAN
Date/Publication 2017-01-17 19:41:27

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