BCI Barro Colorado Island Tree Counts CCorA Canonical Correlation Analysis MDSrotate Rotate First MDS Dimension Parallel to an External Variable MOStest Mitchell-Olds & Shaw Test for the Location of Quadratic Extreme RsquareAdj Adjusted R-square SSarrhenius Self-Starting nls Species-Area Models add1.cca Add or Drop Single Terms to a Constrained Ordination Model adipart Additive Diversity Partitioning and Hierarchical Null Model Testing adonis Permutational Multivariate Analysis of Variance Using Distance Matrices anosim Analysis of Similarities anova.cca Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates as.mlm.cca Refit Constrained Ordination as a Multiple Response Linear Model beals Beals Smoothing and Degree of Absence betadisper Multivariate homogeneity of groups dispersions (variances) betadiver Indices of beta Diversity bgdispersal Coefficients of Biogeographical Dispersal Direction bioenv Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities biplot.rda PCA biplot capscale [Partial] Constrained Analysis of Principal Coordinates or distance-based RDA cascadeKM K-means partitioning using a range of values of K cca [Partial] [Constrained] Correspondence Analysis and Redundancy Analysis cca.object Result Object from Constrained Ordination with cca, rda or capscale clamtest Multinomial Species Classification Method (CLAM) contribdiv Contribution Diversity Approach decorana Detrended Correspondence Analysis and Basic Reciprocal Averaging decostand Standardization Methods for Community Ecology density.adonis Kernel Density Estimation for Permutation Results in Vegan designdist Design your own Dissimilarities deviance.cca Statistics Resembling Deviance and AIC for Constrained Ordination dispindmorisita Morisita index of intraspecific aggregation distconnected Connectedness of Dissimilarities diversity Ecological Diversity Indices and Rarefaction Species Richness dune Vegetation and Environment in Dutch Dune Meadows. dune.taxon Taxonomic Classification of Dune Meadow Species eigenvals Extract Eigenvalues from an Ordination Object envfit Fits an Environmental Vector or Factor onto an Ordination eventstar Scale Parameter at the Minimum of the Tsallis Evenness Profile fisherfit Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data goodness.cca Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) goodness.metaMDS Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling humpfit No-interaction Model for Hump-backed Species Richness vs. Biomass indpower Indicator Power of Species isomap Isometric Feature Mapping Ordination kendall.global Kendall coefficient of concordance linestack Plots One-dimensional Diagrams without Overwriting Labels make.cepnames Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name mantel Mantel and Partial Mantel Tests for Dissimilarity Matrices mantel.correlog Mantel Correlogram metaMDS Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores mite Oribatid Mite Data with Explanatory Variables model.matrix.cca Reconstruct Model Frame and Model Matrices of Constrained Ordination monoMDS Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling mrpp Multi Response Permutation Procedure and Mean Dissimilarity Matrix mso Functions for performing and displaying a spatial partitioning of cca or rda results multipart Multiplicative Diversity Partitioning nestedtemp Nestedness Indices for Communities of Islands or Patches nobs.adonis Extract the Number of Observations from a vegan Fit. oecosimu Null Models for Biological Communities ordiarrows Add Arrows and Line Segments to Ordination Diagrams ordihull Display Groups or Factor Levels in Ordination Diagrams ordilabel Add Text on Non-transparent Label to an Ordination Plot. ordiplot Alternative plot and identify Functions for Ordination ordiplot3d Three-Dimensional and Dynamic Ordination Graphics ordipointlabel Ordination Plots with Points and Optimized Locations for Text ordiresids Plots of Residuals and Fitted Values for Constrained Ordination ordistep Choose a Model by Permutation Tests in Constrained Ordination ordisurf Fit and Plot Smooth Surfaces of Variables on Ordination. orditkplot Ordination Plot with Movable Labels orditorp Add Text or Points to Ordination Plots ordixyplot Trellis (Lattice) Plots for Ordination pcnm Principal Coordinates of Neighbourhood Matrix permatfull Matrix Permutation Algorithms for Presence-Absence and Count Data permutations Permutation tests in Vegan permutest.betadisper Permutation test of multivariate homogeneity of groups dispersions (variances) plot.cca Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis prc Principal Response Curves for Treatments with Repeated Observations predict.cca Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) procrustes Procrustes Rotation of Two Configurations and PROTEST pyrifos Response of Aquatic Invertebrates to Insecticide Treatment radfit Rank - Abundance or Dominance / Diversity Models rankindex Compares Dissimilarity Indices for Gradient Detection raupcrick Raup-Crick Dissimilarity with Unequal Sampling Densities of Species read.cep Reads a CEP (Canoco) data file renyi Renyi and Hill Diversities and Corresponding Accumulation Curves scores Get Species or Site Scores from an Ordination screeplot.cca Screeplots for Ordination Results and Broken Stick Distributions simper Similarity Percentages simulate.rda Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination sipoo Birds in the Archipelago of Sipoo (Sibbo) spantree Minimum Spanning Tree specaccum Species Accumulation Curves specpool Extrapolated Species Richness in a Species Pool stepacross Stepacross as Flexible Shortest Paths or Extended Dissimilarities taxondive Indices of Taxonomic Diversity and Distinctness tolerance Species tolerances and sample heterogeneities treedive Functional Diversity estimated from a Species Dendrogram tsallis Tsallis Diversity and Corresponding Accumulation Curves varespec Vegetation and environment in lichen pastures varpart Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices vegan-deprecated Deprecated Functions in vegan package vegan-package Community Ecology Package: Ordination, Diversity and Dissimilarities vegandocs Display Package Documentation vegdist Dissimilarity Indices for Community Ecologists vegemite Display Compact Ordered Community Tables wascores Weighted Averages Scores for Species wcmdscale Weighted Classical (Metric) Multidimensional Scaling