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 | |
| No Results! | ||
Last month downloads
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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