BCI Barro Colorado Island Tree Counts CCorA Canonical Correlation Analysis MDSrotate Rotate First MDS Dimension Parallel to an External Variable MOStest Mitchell-Olds and 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 adonis2 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 avgdist Averaged Subsampled Dissimilarity Matrices 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 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 clamtest Multinomial Species Classification Method (CLAM) commsim Create an Object for Null Model Algorithms contribdiv Contribution Diversity Approach dbrda Principal Coordinates Analysis and [Partial] Distance-based Redundancy Analysis decorana Detrended Correspondence Analysis and Basic Reciprocal Averaging decostand Standardization Methods for Community Ecology designdist Design your own Dissimilarities deviance.cca Statistics Resembling Deviance and AIC for Constrained Ordination dispindmorisita Morisita index of intraspecific aggregation dispweight Dispersion-based weighting of species counts distconnected Connectedness of Dissimilarities diversity Ecological Diversity Indices dune Vegetation and Environment in Dutch Dune Meadows. dune.taxon Taxonomic Classification and Phylogeny 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 hatvalues.cca Linear Model Diagnostics for Constrained Ordination 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 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.cca Extract the Number of Observations from a vegan Fit. nullmodel Null Model and Simulation oecosimu Evaluate Statistics with Null Models of Biological Communities ordiArrowTextXY Support Functions for Drawing Vectors 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 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. 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 permustats Extract, Analyse and Display Permutation Results 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 rarefy Rarefaction Species Richness 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 reorder.hclust Reorder a Hierarchical Clustering Tree 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 and Borgå) spantree Minimum Spanning Tree specaccum Species Accumulation Curves specpool Extrapolated Species Richness in a Species Pool sppscores Add or Replace Species Scores in Distance-Based Ordination stepacross Stepacross as Flexible Shortest Paths or Extended Dissimilarities stressplot.wcmdscale Display Ordination Distances Against Observed Distances in Eigenvector Ordinations taxondive Indices of Taxonomic Diversity and Distinctness tolerance Species tolerances and sample heterogeneities treedive Functional Diversity and Community Distances from Species Trees 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 vegdist Dissimilarity Indices for Community Ecologists vegemite Display Compact Ordered Community Tables wascores Weighted Averages Scores for Species wcmdscale Weighted Classical (Metric) Multidimensional Scaling