| c.permustats |
Extract, Analyse and Display Permutation Results |
| calibrate |
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| calibrate.cca |
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| calibrate.ordisurf |
Fit and Plot Smooth Surfaces of Variables on Ordination. |
| capscale |
[Partial] Distance-based Redundancy Analysis |
| cascadeKM |
K-means partitioning using a range of values of K |
| cca |
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis |
| cca.default |
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis |
| cca.formula |
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis |
| cca.object |
Result Object from Constrained Ordination |
| CCorA |
Canonical Correlation Analysis |
| chaodist |
Design your own Dissimilarities |
| cIndexKM |
K-means partitioning using a range of values of K |
| clamtest |
Multinomial Species Classification Method (CLAM) |
| coef.cca |
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| coef.radfit |
Rank - Abundance or Dominance / Diversity Models |
| coef.radfit.frame |
Rank - Abundance or Dominance / Diversity Models |
| coef.rda |
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| commsim |
Create an Object for Null Model Algorithms |
| confint.MOStest |
Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme |
| contribdiv |
Contribution Diversity Approach |
| cooks.distance.cca |
Linear Model Diagnostics for Constrained Ordination |
| cophenetic.spantree |
Minimum Spanning Tree |
| coverscale |
Display Compact Ordered Community Tables |
| cutreeord |
Reorder a Hierarchical Clustering Tree |
| make.cepnames |
Abbreviates a Botanical or Zoological Latin Name into an Eight-character Name |
| make.commsim |
Create an Object for Null Model Algorithms |
| mantel |
Mantel and Partial Mantel Tests for Dissimilarity Matrices |
| mantel.correlog |
Mantel Correlogram |
| mantel.partial |
Mantel and Partial Mantel Tests for Dissimilarity Matrices |
| MDSrotate |
Rotate First MDS Dimension Parallel to an External Variable |
| meandist |
Multi Response Permutation Procedure and Mean Dissimilarity Matrix |
| metaMDS |
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores |
| metaMDSdist |
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores |
| metaMDSiter |
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores |
| metaMDSredist |
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores |
| mite |
Oribatid Mite Data with Explanatory Variables |
| mite.env |
Oribatid Mite Data with Explanatory Variables |
| mite.pcnm |
Oribatid Mite Data with Explanatory Variables |
| mite.xy |
Oribatid Mite Data with Explanatory Variables |
| model.frame.cca |
Result Object from Constrained Ordination |
| model.matrix.cca |
Result Object from Constrained Ordination |
| model.matrix.rda |
Result Object from Constrained Ordination |
| monoMDS |
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling |
| MOStest |
Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme |
| mrpp |
Multi Response Permutation Procedure and Mean Dissimilarity Matrix |
| mso |
Functions for performing and displaying a spatial partitioning of cca or rda results |
| msoplot |
Functions for performing and displaying a spatial partitioning of cca or rda results |
| multipart |
Multiplicative Diversity Partitioning |
| multipart.default |
Multiplicative Diversity Partitioning |
| multipart.formula |
Multiplicative Diversity Partitioning |
| oecosimu |
Evaluate Statistics with Null Models of Biological Communities |
| ordConstrained |
Result Object from Constrained Ordination |
| orderingKM |
K-means partitioning using a range of values of K |
| ordiareatest |
Display Groups or Factor Levels in Ordination Diagrams |
| ordiArrowMul |
Support Functions for Drawing Vectors |
| ordiarrows |
Add Arrows and Line Segments to Ordination Diagrams |
| ordiArrowTextXY |
Support Functions for Drawing Vectors |
| ordibar |
Display Groups or Factor Levels in Ordination Diagrams |
| ordicloud |
Trellis (Lattice) Plots for Ordination |
| ordicluster |
Display Groups or Factor Levels in Ordination Diagrams |
| ordiellipse |
Display Groups or Factor Levels in Ordination Diagrams |
| ordigrid |
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. |
| ordilattice.getEnvfit |
Trellis (Lattice) Plots for Ordination |
| ordimedian |
Multivariate homogeneity of groups dispersions (variances) |
| ordiplot |
Alternative plot and identify Functions for Ordination |
| ordipointlabel |
Ordination Plots with Points and Optimized Locations for Text |
| ordiR2step |
Choose a Model by Permutation Tests in Constrained Ordination |
| ordiresids |
Plots of Residuals and Fitted Values for Constrained Ordination |
| ordisegments |
Add Arrows and Line Segments to Ordination Diagrams |
| ordispider |
Display Groups or Factor Levels in Ordination Diagrams |
| ordisplom |
Trellis (Lattice) Plots for Ordination |
| ordistep |
Choose a Model by Permutation Tests in Constrained Ordination |
| ordisurf |
Fit and Plot Smooth Surfaces of Variables on Ordination. |
| ordisurf.default |
Fit and Plot Smooth Surfaces of Variables on Ordination. |
| ordisurf.formula |
Fit and Plot Smooth Surfaces of Variables on Ordination. |
| orditkplot |
Deprecated Functions in vegan package |
| orditorp |
Add Text or Points to Ordination Plots |
| ordixyplot |
Trellis (Lattice) Plots for Ordination |
| ordiYbar |
Result Object from Constrained Ordination |
| pairs.permustats |
Extract, Analyse and Display Permutation Results |
| panel.ordi |
Trellis (Lattice) Plots for Ordination |
| panel.ordi3d |
Trellis (Lattice) Plots for Ordination |
| panel.ordiarrows |
Trellis (Lattice) Plots for Ordination |
| pcnm |
Principal Coordinates of Neighbourhood Matrix |
| permatfull |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
| permatswap |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
| permustats |
Extract, Analyse and Display Permutation Results |
| permustats.anosim |
Extract, Analyse and Display Permutation Results |
| permustats.anova.cca |
Extract, Analyse and Display Permutation Results |
| permustats.CCorA |
Extract, Analyse and Display Permutation Results |
| permustats.envfit |
Extract, Analyse and Display Permutation Results |
| permustats.factorfit |
Extract, Analyse and Display Permutation Results |
| permustats.mantel |
Extract, Analyse and Display Permutation Results |
| permustats.mrpp |
Extract, Analyse and Display Permutation Results |
| permustats.mso |
Extract, Analyse and Display Permutation Results |
| permustats.oecosimu |
Extract, Analyse and Display Permutation Results |
| permustats.ordiareatest |
Extract, Analyse and Display Permutation Results |
| permustats.permutest.betadisper |
Extract, Analyse and Display Permutation Results |
| permustats.permutest.cca |
Extract, Analyse and Display Permutation Results |
| permustats.protest |
Extract, Analyse and Display Permutation Results |
| permustats.vectorfit |
Extract, Analyse and Display Permutation Results |
| permutations |
Permutation tests in Vegan |
| permutest |
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates |
| permutest.betadisper |
Permutation test of multivariate homogeneity of groups dispersions (variances) |
| permutest.cca |
Permutation Test for Constrained Correspondence Analysis, Redundancy Analysis and Constrained Analysis of Principal Coordinates |
| persp.renyiaccum |
Renyi and Hill Diversities and Corresponding Accumulation Curves |
| persp.tsallisaccum |
Tsallis Diversity and Corresponding Accumulation Curves |
| plot.anosim |
Analysis of Similarities |
| plot.betadisper |
Multivariate homogeneity of groups dispersions (variances) |
| plot.betadiver |
Indices of beta Diversity |
| plot.cascadeKM |
K-means partitioning using a range of values of K |
| plot.cca |
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis |
| plot.clamtest |
Multinomial Species Classification Method (CLAM) |
| plot.contribdiv |
Contribution Diversity Approach |
| plot.decorana |
Detrended Correspondence Analysis and Basic Reciprocal Averaging |
| plot.envfit |
Fits an Environmental Vector or Factor onto an Ordination |
| plot.fisher |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
| plot.fisherfit |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
| plot.fitspecaccum |
Species Accumulation Curves |
| plot.isomap |
Isometric Feature Mapping Ordination |
| plot.mantel.correlog |
Mantel Correlogram |
| plot.meandist |
Multi Response Permutation Procedure and Mean Dissimilarity Matrix |
| plot.metaMDS |
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores |
| plot.monoMDS |
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling |
| plot.MOStest |
Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme |
| plot.nestednodf |
Nestedness Indices for Communities of Islands or Patches |
| plot.nestedtemp |
Nestedness Indices for Communities of Islands or Patches |
| plot.ordipointlabel |
Ordination Plots with Points and Optimized Locations for Text |
| plot.ordisurf |
Fit and Plot Smooth Surfaces of Variables on Ordination. |
| plot.orditkplot |
Deprecated Functions in vegan package |
| plot.permat |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
| plot.poolaccum |
Extrapolated Species Richness in a Species Pool |
| plot.prc |
Principal Response Curves for Treatments with Repeated Observations |
| plot.preston |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
| plot.prestonfit |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
| plot.procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
| plot.rad |
Rank - Abundance or Dominance / Diversity Models |
| plot.radfit |
Rank - Abundance or Dominance / Diversity Models |
| plot.radfit.frame |
Rank - Abundance or Dominance / Diversity Models |
| plot.radline |
Rank - Abundance or Dominance / Diversity Models |
| plot.renyi |
Renyi and Hill Diversities and Corresponding Accumulation Curves |
| plot.renyiaccum |
Renyi and Hill Diversities and Corresponding Accumulation Curves |
| plot.spantree |
Minimum Spanning Tree |
| plot.specaccum |
Species Accumulation Curves |
| plot.taxondive |
Indices of Taxonomic Diversity and Distinctness |
| plot.varpart |
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices |
| plot.varpart234 |
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices |
| plot.wcmdscale |
Weighted Classical (Metric) Multidimensional Scaling |
| points.cca |
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis |
| points.decorana |
Detrended Correspondence Analysis and Basic Reciprocal Averaging |
| points.metaMDS |
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores |
| points.monoMDS |
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling |
| points.ordiplot |
Alternative plot and identify Functions for Ordination |
| points.orditkplot |
Deprecated Functions in vegan package |
| points.procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
| points.radfit |
Rank - Abundance or Dominance / Diversity Models |
| points.radline |
Rank - Abundance or Dominance / Diversity Models |
| poolaccum |
Extrapolated Species Richness in a Species Pool |
| postMDS |
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores |
| prc |
Principal Response Curves for Treatments with Repeated Observations |
| predict.cca |
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| predict.dbrda |
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| predict.decorana |
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| predict.fitspecaccum |
Species Accumulation Curves |
| predict.procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
| predict.radfit |
Rank - Abundance or Dominance / Diversity Models |
| predict.radfit.frame |
Rank - Abundance or Dominance / Diversity Models |
| predict.radline |
Rank - Abundance or Dominance / Diversity Models |
| predict.rda |
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| predict.specaccum |
Species Accumulation Curves |
| pregraphKM |
K-means partitioning using a range of values of K |
| prepanel.ordi3d |
Trellis (Lattice) Plots for Ordination |
| prestondistr |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
| prestonfit |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
| print.betadisper |
Multivariate homogeneity of groups dispersions (variances) |
| print.cca |
Result Object from Constrained Ordination |
| print.commsim |
Create an Object for Null Model Algorithms |
| print.nullmodel |
Null Model and Simulation |
| print.permat |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
| print.simmat |
Null Model and Simulation |
| print.specaccum |
Species Accumulation Curves |
| print.summary.cca |
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis |
| print.summary.decorana |
Detrended Correspondence Analysis and Basic Reciprocal Averaging |
| print.summary.permat |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
| procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
| profile.MOStest |
Mitchell-Olds and Shaw Test for the Location of Quadratic Extreme |
| protest |
Procrustes Rotation of Two Configurations and PROTEST |
| pyrifos |
Response of Aquatic Invertebrates to Insecticide Treatment |
| rad.lognormal |
Rank - Abundance or Dominance / Diversity Models |
| rad.null |
Rank - Abundance or Dominance / Diversity Models |
| rad.preempt |
Rank - Abundance or Dominance / Diversity Models |
| rad.zipf |
Rank - Abundance or Dominance / Diversity Models |
| rad.zipfbrot |
Rank - Abundance or Dominance / Diversity Models |
| radfit |
Rank - Abundance or Dominance / Diversity Models |
| radfit.data.frame |
Rank - Abundance or Dominance / Diversity Models |
| radfit.default |
Rank - Abundance or Dominance / Diversity Models |
| radlattice |
Rank - Abundance or Dominance / Diversity Models |
| rankindex |
Compares Dissimilarity Indices for Gradient Detection |
| rarecurve |
Rarefaction Species Richness |
| rarefy |
Rarefaction Species Richness |
| rareslope |
Rarefaction Species Richness |
| raupcrick |
Raup-Crick Dissimilarity with Unequal Sampling Densities of Species |
| rda |
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis |
| rda.default |
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis |
| rda.formula |
[Partial] [Constrained] Correspondence Analysis and Redundancy Analysis |
| read.cep |
Reads a CEP (Canoco) data file |
| renyi |
Renyi and Hill Diversities and Corresponding Accumulation Curves |
| renyiaccum |
Renyi and Hill Diversities and Corresponding Accumulation Curves |
| reorder.hclust |
Reorder a Hierarchical Clustering Tree |
| residuals.cca |
Prediction Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| residuals.procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
| rev.hclust |
Reorder a Hierarchical Clustering Tree |
| rrarefy |
Rarefaction Species Richness |
| RsquareAdj |
Adjusted R-square |
| RsquareAdj.cca |
Adjusted R-square |
| RsquareAdj.default |
Adjusted R-square |
| RsquareAdj.glm |
Adjusted R-square |
| RsquareAdj.lm |
Adjusted R-square |
| RsquareAdj.rda |
Adjusted R-square |
| rstandard.cca |
Linear Model Diagnostics for Constrained Ordination |
| rstudent.cca |
Linear Model Diagnostics for Constrained Ordination |
| scores |
Get Species or Site Scores from an Ordination |
| scores.betadisper |
Multivariate homogeneity of groups dispersions (variances) |
| scores.betadiver |
Indices of beta Diversity |
| scores.cca |
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis |
| scores.decorana |
Detrended Correspondence Analysis and Basic Reciprocal Averaging |
| scores.default |
Get Species or Site Scores from an Ordination |
| scores.envfit |
Fits an Environmental Vector or Factor onto an Ordination |
| scores.hclust |
Reorder a Hierarchical Clustering Tree |
| scores.lda |
Get Species or Site Scores from an Ordination |
| scores.metaMDS |
Nonmetric Multidimensional Scaling with Stable Solution from Random Starts, Axis Scaling and Species Scores |
| scores.monoMDS |
Global and Local Non-metric Multidimensional Scaling and Linear and Hybrid Scaling |
| scores.ordihull |
Display Groups or Factor Levels in Ordination Diagrams |
| scores.ordiplot |
Alternative plot and identify Functions for Ordination |
| scores.orditkplot |
Deprecated Functions in vegan package |
| scores.pcnm |
Principal Coordinates of Neighbourhood Matrix |
| scores.rda |
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis |
| scores.wcmdscale |
Weighted Classical (Metric) Multidimensional Scaling |
| screeplot.cca |
Screeplots for Ordination Results and Broken Stick Distributions |
| screeplot.decorana |
Screeplots for Ordination Results and Broken Stick Distributions |
| screeplot.prcomp |
Screeplots for Ordination Results and Broken Stick Distributions |
| screeplot.princomp |
Screeplots for Ordination Results and Broken Stick Distributions |
| showvarparts |
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices |
| sigma.cca |
Linear Model Diagnostics for Constrained Ordination |
| simmat |
Null Model and Simulation |
| simper |
Similarity Percentages |
| simpleDBRDA |
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices |
| simpleRDA2 |
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices |
| simpson.unb |
Ecological Diversity Indices |
| simulate.capscale |
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination |
| simulate.cca |
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination |
| simulate.nullmodel |
Null Model and Simulation |
| simulate.rda |
Simulate Responses with Gaussian Error or Permuted Residuals for Constrained Ordination |
| sipoo |
Birds in the Archipelago of Sipoo (Sibbo and Borgå) |
| sipoo.map |
Birds in the Archipelago of Sipoo (Sibbo and Borgå) |
| smbind |
Null Model and Simulation |
| spandepth |
Minimum Spanning Tree |
| spantree |
Minimum Spanning Tree |
| specaccum |
Species Accumulation Curves |
| specnumber |
Ecological Diversity Indices |
| specpool |
Extrapolated Species Richness in a Species Pool |
| specpool2vect |
Extrapolated Species Richness in a Species Pool |
| specslope |
Species Accumulation Curves |
| spenvcor |
Diagnostic Tools for [Constrained] Ordination (CCA, RDA, DCA, CA, PCA) |
| sppscores |
Add or Replace Species Scores in Distance-Based Ordination |
| sppscores<- |
Add or Replace Species Scores in Distance-Based Ordination |
| sppscores<-.capscale |
Add or Replace Species Scores in Distance-Based Ordination |
| sppscores<-.dbrda |
Add or Replace Species Scores in Distance-Based Ordination |
| sppscores<-.metaMDS |
Add or Replace Species Scores in Distance-Based Ordination |
| SSarrhenius |
Self-Starting nls Species-Area Models |
| SSD.cca |
Linear Model Diagnostics for Constrained Ordination |
| SSgitay |
Self-Starting nls Species-Area Models |
| SSgleason |
Self-Starting nls Species-Area Models |
| SSlomolino |
Self-Starting nls Species-Area Models |
| stepacross |
Stepacross as Flexible Shortest Paths or Extended Dissimilarities |
| str.nullmodel |
Null Model and Simulation |
| stressplot |
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling |
| stressplot.capscale |
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations |
| stressplot.cca |
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations |
| stressplot.dbrda |
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations |
| stressplot.default |
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling |
| stressplot.monoMDS |
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling |
| stressplot.prcomp |
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations |
| stressplot.princomp |
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations |
| stressplot.rda |
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations |
| stressplot.wcmdscale |
Display Ordination Distances Against Observed Distances in Eigenvector Ordinations |
| summary.anosim |
Analysis of Similarities |
| summary.bioenv |
Best Subset of Environmental Variables with Maximum (Rank) Correlation with Community Dissimilarities |
| summary.cca |
Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis |
| summary.clamtest |
Multinomial Species Classification Method (CLAM) |
| summary.decorana |
Detrended Correspondence Analysis and Basic Reciprocal Averaging |
| summary.dispweight |
Dispersion-based weighting of species counts |
| summary.eigenvals |
Extract Eigenvalues from an Ordination Object |
| summary.isomap |
Isometric Feature Mapping Ordination |
| summary.meandist |
Multi Response Permutation Procedure and Mean Dissimilarity Matrix |
| summary.ordiellipse |
Display Groups or Factor Levels in Ordination Diagrams |
| summary.ordihull |
Display Groups or Factor Levels in Ordination Diagrams |
| summary.permat |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
| summary.permustats |
Extract, Analyse and Display Permutation Results |
| summary.poolaccum |
Extrapolated Species Richness in a Species Pool |
| summary.prc |
Principal Response Curves for Treatments with Repeated Observations |
| summary.procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
| summary.radfit.frame |
Rank - Abundance or Dominance / Diversity Models |
| summary.simper |
Similarity Percentages |
| summary.specaccum |
Species Accumulation Curves |
| summary.taxondive |
Indices of Taxonomic Diversity and Distinctness |
| summary.varpart |
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices |
| swan |
Beals Smoothing and Degree of Absence |
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