Community Ecology Package

add1.cca | Add or Drop Single Terms to a Constrained Ordination Model |

adipart | Additive Diversity Partitioning and Hierarchical Null Model... |

adonis | Permutational Multivariate Analysis of Variance Using... |

anosim | Analysis of Similarities |

anova.cca | Permutation Test for Constrained Correspondence Analysis,... |

as.mlm | Refit Constrained Ordination as a Multiple Response Linear... |

BCI | Barro Colorado Island Tree Counts |

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)... |

biplot.rda | PCA biplot |

capscale | [Partial] Constrained Analysis of Principal Coordinates or... |

cascadeKM | K-means partitioning using a range of values of K |

cca | [Partial] [Constrained] Correspondence Analysis and... |

cca.object | Result Object from Constrained Ordination with cca, rda or... |

CCorA | Canonical Correlation Analysis |

clamtest | Multinomial Species Classification Method (CLAM) |

commsim | Create a Object for Null Model Algorithms |

contribdiv | Contribution Diversity Approach |

decorana | Detrended Correspondence Analysis and Basic Reciprocal... |

decostand | Standardization Methods for Community Ecology |

designdist | Design your own Dissimilarities |

deviance.cca | Statistics Resembling Deviance and AIC for Constrained... |

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... |

fisherfit | Fit Fisher's Logseries and Preston's Lognormal Model to... |

goodness.cca | Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA,... |

goodness.metaMDS | Goodness of Fit and Shepard Plot for Nonmetric... |

humpfit | No-interaction Model for Hump-backed Species Richness vs.... |

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... |

mantel | Mantel and Partial Mantel Tests for Dissimilarity Matrices |

mantel.correlog | Mantel Correlogram |

MDSrotate | Rotate First MDS Dimension Parallel to an External Variable |

metaMDS | Nonmetric Multidimensional Scaling with Stable Solution from... |

mite | Oribatid Mite Data with Explanatory Variables |

model.matrix.cca | Reconstruct Model Frame and Model Matrices of Constrained... |

monoMDS | Global and Local Non-metric Multidimensional Scaling and... |

MOStest | Mitchell-Olds & Shaw Test for the Location of Quadratic... |

mrpp | Multi Response Permutation Procedure and Mean Dissimilarity... |

mso | Functions for performing and displaying a spatial... |

multipart | Multiplicative Diversity Partitioning |

nestedtemp | Nestedness Indices for Communities of Islands or Patches |

nobs.adonis | Extract the Number of Observations from a vegan Fit. |

nullmodel | Null Model and Simulation |

oecosimu | Evaluate Statistics with Null Models of Biological... |

ordiarrows | Add Arrows and Line Segments to Ordination Diagrams |

ordiArrowTextXY | Support Functions for Drawing Vectors |

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... |

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... |

permustats | Extract, Analyse and Display Permutation Results |

permutations | Permutation tests in Vegan |

permutest.betadisper | Permutation test of multivariate homogeneity of groups... |

plot.cca | Plot or Extract Results of Constrained Correspondence... |

prc | Principal Response Curves for Treatments with Repeated... |

predict.cca | Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA,... |

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... |

read.cep | Reads a CEP (Canoco) data file |

renyi | Renyi and Hill Diversities and Corresponding Accumulation... |

reorder.hclust | Reorder a Hierarchical Clustering Tree |

RsquareAdj | Adjusted R-square |

scores | Get Species or Site Scores from an Ordination |

screeplot.cca | Screeplots for Ordination Results and Broken Stick... |

simper | Similarity Percentages |

simulate.rda | Simulate Responses with Gaussian Error or Permuted Residuals... |

sipoo | Birds in the Archipelago of Sipoo (Sibbo) |

spantree | Minimum Spanning Tree |

specaccum | Species Accumulation Curves |

specpool | Extrapolated Species Richness in a Species Pool |

SSarrhenius | Self-Starting nls Species-Area Models |

stepacross | Stepacross as Flexible Shortest Paths or Extended... |

stressplot.wcmdscale | Display Ordination Distances Against Observed Distances in... |

taxondive | Indices of Taxonomic Diversity and Distinctness |

tolerance | Species tolerances and sample heterogeneities |

treedive | Functional Diversity and Community Distances from Species... |

tsallis | Tsallis Diversity and Corresponding Accumulation Curves |

varechem | Vegetation and environment in lichen pastures |

varpart | Partition the Variation of Community Matrix by 2, 3, or 4... |

vegan-defunct | Defunct Functions in Package 'vegan' |

vegan-deprecated | Deprecated Functions in vegan package |

vegandocs | Display vegan Documentation |

vegan-internal | Internal vegan functions |

vegan-package | Community Ecology Package: Ordination, Diversity and... |

vegdist | Dissimilarity Indices for Community Ecologists |

vegemite | Display Compact Ordered Community Tables |

wascores | Weighted Averages Scores for Species |

wcmdscale | Weighted Classical (Metric) Multidimensional Scaling |

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