vegan v2.4-2
0
Monthly downloads
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 |
imports | cluster , MASS , mgcv |
suggests | knitr , parallel , tcltk |
depends | lattice , permute (>= 0.9-0) , R (>= 3.0.0) |
Contributors | Gavin Simpson, Helene Wagner, Dan Mcglinn, Jari Oksanen, Pierre Legendre, Michael Friendly, Peter Solymos, Eduard Szoecs, F. Blanchet, Roeland Kindt, Peter Minchin, R. O'Hara, M. H. Stevens |
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