178 lines
9.9 KiB
Plaintext
178 lines
9.9 KiB
Plaintext
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BCI Barro Colorado Island Tree Counts
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CCorA Canonical Correlation Analysis
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MDSrotate Rotate First MDS Dimension Parallel to an
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External Variable
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MOStest Mitchell-Olds and Shaw Test for the Location of
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Quadratic Extreme
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RsquareAdj Adjusted R-square
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SSarrhenius Self-Starting nls Species-Area Models
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add1.cca Add or Drop Single Terms to a Constrained
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Ordination Model
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adipart Additive Diversity Partitioning and
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Hierarchical Null Model Testing
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adonis2 Permutational Multivariate Analysis of Variance
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Using Distance Matrices
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anosim Analysis of Similarities
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anova.cca Permutation Test for Constrained Correspondence
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Analysis, Redundancy Analysis and Constrained
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Analysis of Principal Coordinates
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avgdist Averaged Subsampled Dissimilarity Matrices
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beals Beals Smoothing and Degree of Absence
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betadisper Multivariate homogeneity of groups dispersions
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(variances)
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betadiver Indices of beta Diversity
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bgdispersal Coefficients of Biogeographical Dispersal
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Direction
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bioenv Best Subset of Environmental Variables with
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Maximum (Rank) Correlation with Community
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Dissimilarities
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biplot.rda PCA biplot
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cascadeKM K-means partitioning using a range of values of
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K
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cca [Partial] [Constrained] Correspondence Analysis
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and Redundancy Analysis
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cca.object Result Object from Constrained Ordination
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clamtest Multinomial Species Classification Method
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(CLAM)
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commsim Create an Object for Null Model Algorithms
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contribdiv Contribution Diversity Approach
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dbrda Principal Coordinates Analysis and [Partial]
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Distance-based Redundancy Analysis
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decorana Detrended Correspondence Analysis and Basic
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Reciprocal Averaging
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decostand Standardization Methods for Community Ecology
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designdist Design your own Dissimilarities
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deviance.cca Statistics Resembling Deviance and AIC for
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Constrained Ordination
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dispindmorisita Morisita index of intraspecific aggregation
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dispweight Dispersion-based weighting of species counts
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distconnected Connectedness of Dissimilarities
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diversity Ecological Diversity Indices
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dune Vegetation and Environment in Dutch Dune
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Meadows.
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dune.taxon Taxonomic Classification and Phylogeny of Dune
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Meadow Species
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eigenvals Extract Eigenvalues from an Ordination Object
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envfit Fits an Environmental Vector or Factor onto an
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Ordination
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eventstar Scale Parameter at the Minimum of the Tsallis
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Evenness Profile
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fisherfit Fit Fisher's Logseries and Preston's Lognormal
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Model to Abundance Data
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goodness.cca Diagnostic Tools for [Constrained] Ordination
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(CCA, RDA, DCA, CA, PCA)
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goodness.metaMDS Goodness of Fit and Shepard Plot for Nonmetric
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Multidimensional Scaling
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hatvalues.cca Linear Model Diagnostics for Constrained
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Ordination
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indpower Indicator Power of Species
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isomap Isometric Feature Mapping Ordination
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kendall.global Kendall coefficient of concordance
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linestack Plots One-dimensional Diagrams without
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Overwriting Labels
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make.cepnames Abbreviates a Botanical or Zoological Latin
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Name into an Eight-character Name
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mantel Mantel and Partial Mantel Tests for
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Dissimilarity Matrices
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mantel.correlog Mantel Correlogram
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metaMDS Nonmetric Multidimensional Scaling with Stable
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Solution from Random Starts, Axis Scaling and
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Species Scores
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mite Oribatid Mite Data with Explanatory Variables
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monoMDS Global and Local Non-metric Multidimensional
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Scaling and Linear and Hybrid Scaling
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mrpp Multi Response Permutation Procedure and Mean
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Dissimilarity Matrix
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mso Functions for performing and displaying a
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spatial partitioning of cca or rda results
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multipart Multiplicative Diversity Partitioning
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nestedtemp Nestedness Indices for Communities of Islands
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or Patches
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nobs.cca Extract the Number of Observations from a vegan
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Fit.
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nullmodel Null Model and Simulation
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oecosimu Evaluate Statistics with Null Models of
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Biological Communities
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ordiArrowTextXY Support Functions for Drawing Vectors
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ordiarrows Add Arrows and Line Segments to Ordination
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Diagrams
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ordihull Display Groups or Factor Levels in Ordination
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Diagrams
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ordilabel Add Text on Non-transparent Label to an
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Ordination Plot.
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ordiplot Alternative plot and identify Functions for
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Ordination
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ordipointlabel Ordination Plots with Points and Optimized
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Locations for Text
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ordiresids Plots of Residuals and Fitted Values for
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Constrained Ordination
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ordistep Choose a Model by Permutation Tests in
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Constrained Ordination
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ordisurf Fit and Plot Smooth Surfaces of Variables on
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Ordination.
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orditorp Add Text or Points to Ordination Plots
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ordixyplot Trellis (Lattice) Plots for Ordination
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pcnm Principal Coordinates of Neighbourhood Matrix
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permatfull Matrix Permutation Algorithms for
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Presence-Absence and Count Data
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permustats Extract, Analyse and Display Permutation
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Results
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permutations Permutation tests in Vegan
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permutest.betadisper Permutation test of multivariate homogeneity of
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groups dispersions (variances)
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plot.cca Plot or Extract Results of Constrained
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Correspondence Analysis or Redundancy Analysis
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prc Principal Response Curves for Treatments with
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Repeated Observations
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predict.cca Prediction Tools for [Constrained] Ordination
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(CCA, RDA, DCA, CA, PCA)
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procrustes Procrustes Rotation of Two Configurations and
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PROTEST
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pyrifos Response of Aquatic Invertebrates to
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Insecticide Treatment
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radfit Rank - Abundance or Dominance / Diversity
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Models
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rankindex Compares Dissimilarity Indices for Gradient
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Detection
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rarefy Rarefaction Species Richness
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raupcrick Raup-Crick Dissimilarity with Unequal Sampling
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Densities of Species
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read.cep Reads a CEP (Canoco) data file
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renyi Renyi and Hill Diversities and Corresponding
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Accumulation Curves
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reorder.hclust Reorder a Hierarchical Clustering Tree
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scores Get Species or Site Scores from an Ordination
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screeplot.cca Screeplots for Ordination Results and Broken
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Stick Distributions
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simper Similarity Percentages
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simulate.rda Simulate Responses with Gaussian Error or
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Permuted Residuals for Constrained Ordination
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sipoo Birds in the Archipelago of Sipoo (Sibbo and
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Borgå)
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spantree Minimum Spanning Tree
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specaccum Species Accumulation Curves
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specpool Extrapolated Species Richness in a Species Pool
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sppscores Add or Replace Species Scores in Distance-Based
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Ordination
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stepacross Stepacross as Flexible Shortest Paths or
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Extended Dissimilarities
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stressplot.wcmdscale Display Ordination Distances Against Observed
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Distances in Eigenvector Ordinations
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taxondive Indices of Taxonomic Diversity and Distinctness
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tolerance Species tolerances and sample heterogeneities
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treedive Functional Diversity and Community Distances
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from Species Trees
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tsallis Tsallis Diversity and Corresponding
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Accumulation Curves
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varespec Vegetation and environment in lichen pastures
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varpart Partition the Variation of Community Matrix by
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2, 3, or 4 Explanatory Matrices
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vegan-deprecated Deprecated Functions in vegan package
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vegan-package Community Ecology Package: Ordination,
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Diversity and Dissimilarities
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vegdist Dissimilarity Indices for Community Ecologists
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vegemite Display Compact Ordered Community Tables
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wascores Weighted Averages Scores for Species
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wcmdscale Weighted Classical (Metric) Multidimensional
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Scaling
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