add1.cca |
Add or Drop Single Terms to a Constrained Ordination Model |
ade2vegancca |
Plot or Extract Results of Constrained Correspondence Analysis
or Redundancy Analysis |
adipart |
Additive Diversity Partitioning and Hierarchical Null Model Testing |
adonis |
Permutational Multivariate Analysis of Variance Using Distance Matrices |
AIC.radfit |
Rank - Abundance or Dominance / Diversity Models |
alias.cca |
Diagnostic Tools for [Constrained] Ordination (CCA,
RDA, DCA, CA, PCA) |
allPerms |
Utility functions for permutation schemes |
anosim |
Analysis of Similarities |
anova.betadisper |
Multivariate homogeneity of groups dispersions (variances) |
anova.cca |
Permutation Test for Constrained Correspondence Analysis,
Redundancy Analysis and Constrained Analysis of Principal Coordinates |
anova.ccabyaxis |
Permutation Test for Constrained Correspondence Analysis,
Redundancy Analysis and Constrained Analysis of Principal Coordinates |
anova.ccabymargin |
Permutation Test for Constrained Correspondence Analysis,
Redundancy Analysis and Constrained Analysis of Principal Coordinates |
anova.ccabyterm |
Permutation Test for Constrained Correspondence Analysis,
Redundancy Analysis and Constrained Analysis of Principal Coordinates |
anova.ccanull |
Permutation Test for Constrained Correspondence Analysis,
Redundancy Analysis and Constrained Analysis of Principal Coordinates |
as.fisher |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
as.mcmc.oecosimu |
Null Models for Biological Communities |
as.mcmc.permat |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
as.mlm |
Refit Constrained Ordination as a Multiple Response Linear Model |
as.mlm.cca |
Refit Constrained Ordination as a Multiple Response Linear Model |
as.mlm.rda |
Refit Constrained Ordination as a Multiple Response Linear Model |
as.preston |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
as.rad |
Rank - Abundance or Dominance / Diversity Models |
as.ts.oecosimu |
Null Models for Biological Communities |
as.ts.permat |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
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 |
permCheck |
Utility functions for permutation schemes |
permControl |
Unrestricted and restricted permutations |
permuplot |
Utility functions for permutation schemes |
permute |
Unrestricted and restricted permutations |
permuted.index2 |
Unrestricted and restricted permutations |
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 |
permutest.default |
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.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.fisherfit |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
plot.humpfit |
No-interaction Model for Hump-backed Species Richness vs. Biomass |
plot.isomap |
Isometric Feature Mapping Ordination |
plot.mantel.correlog |
Mantel Correlogram |
plot.meandist |
Multi Response Permutation Procedure of Within- versus
Among-Group Dissimilarities |
plot.metaMDS |
Nonmetric Multidimensional Scaling with Stable Solution from
Random Starts, Axis Scaling and Species Scores |
plot.nestedtemp |
Nestedness Indices for Communities of Islands or Patches |
plot.orditkplot |
Ordination Plot with Movable Labels |
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.prestonfit |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
plot.procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
plot.profile.fisherfit |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
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 |
points.cca |
Plot or Extract Results of Constrained Correspondence Analysis
or Redundancy Analysis |
points.decorana |
Detrended Correspondence Analysis and Basic Reciprocal Averaging |
points.humpfit |
No-interaction Model for Hump-backed Species Richness vs. Biomass |
points.metaMDS |
Nonmetric Multidimensional Scaling with Stable Solution from
Random Starts, Axis Scaling and Species Scores |
points.ordiplot |
Alternative plot and identify Functions for Ordination |
points.orditkplot |
Ordination Plot with Movable Labels |
points.procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
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.decorana |
Prediction Tools for [Constrained] Ordination (CCA,
RDA, DCA, CA, PCA) |
predict.humpfit |
No-interaction Model for Hump-backed Species Richness vs. Biomass |
predict.rda |
Prediction Tools for [Constrained] Ordination (CCA,
RDA, DCA, CA, PCA) |
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.adipart |
Additive Diversity Partitioning and Hierarchical Null Model Testing |
print.adonis |
Permutational Multivariate Analysis of Variance Using Distance Matrices |
print.allPerms |
Utility functions for permutation schemes |
print.anosim |
Analysis of Similarities |
print.betadisper |
Multivariate homogeneity of groups dispersions (variances) |
print.bioenv |
Best Subset of Environmental Variables with
Maximum (Rank) Correlation with Community Dissimilarities |
print.capscale |
[Partial] Constrained Analysis of Principal Coordinates or
distance-based RDA |
print.cca |
[Partial] [Constrained] Correspondence Analysis and Redundancy
Analysis |
print.CCorA |
Canonical Correlation Analysis |
print.decorana |
Detrended Correspondence Analysis and Basic Reciprocal Averaging |
print.eigenvals |
Extract Eigenvalues from an Ordination Object |
print.envfit |
Fits an Environmental Vector or Factor onto an Ordination |
print.factorfit |
Fits an Environmental Vector or Factor onto an Ordination |
print.fisherfit |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
print.hiersimu |
Additive Diversity Partitioning and Hierarchical Null Model Testing |
print.humpfit |
No-interaction Model for Hump-backed Species Richness vs. Biomass |
print.isomap |
Isometric Feature Mapping Ordination |
print.mantel |
Mantel and Partial Mantel Tests for Dissimilarity Matrices |
print.mantel.correlog |
Mantel Correlogram |
print.metaMDS |
Nonmetric Multidimensional Scaling with Stable Solution from
Random Starts, Axis Scaling and Species Scores |
print.mrpp |
Multi Response Permutation Procedure of Within- versus
Among-Group Dissimilarities |
print.mso |
Functions for performing and displaying a spatial partitioning
of cca or rda results |
print.multipart |
Multiplicative Diversity Partitioning |
print.nestedchecker |
Nestedness Indices for Communities of Islands or Patches |
print.nesteddisc |
Nestedness Indices for Communities of Islands or Patches |
print.nestedn0 |
Nestedness Indices for Communities of Islands or Patches |
print.nestednodf |
Nestedness Indices for Communities of Islands or Patches |
print.nestedtemp |
Nestedness Indices for Communities of Islands or Patches |
print.oecosimu |
Null Models for Biological Communities |
print.permat |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
print.permCheck |
Utility functions for permutation schemes |
print.permControl |
Unrestricted and restricted permutations |
print.permutest.betadisper |
Permutation test of multivariate homogeneity of groups dispersions
(variances) |
print.permutest.cca |
Permutation Test for Constrained Correspondence Analysis,
Redundancy Analysis and Constrained Analysis of Principal Coordinates |
print.poolaccum |
Extrapolated Species Richness in a Species Pool |
print.prestonfit |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
print.procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
print.protest |
Procrustes Rotation of Two Configurations and PROTEST |
print.radfit |
Rank - Abundance or Dominance / Diversity Models |
print.radfit.frame |
Rank - Abundance or Dominance / Diversity Models |
print.radline |
Rank - Abundance or Dominance / Diversity Models |
print.specaccum |
Species Accumulation Curves |
print.summary.allPerms |
Utility functions for permutation schemes |
print.summary.bioenv |
Best Subset of Environmental Variables with
Maximum (Rank) Correlation with Community Dissimilarities |
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.humpfit |
No-interaction Model for Hump-backed Species Richness vs. Biomass |
print.summary.isomap |
Isometric Feature Mapping Ordination |
print.summary.meandist |
Multi Response Permutation Procedure of Within- versus
Among-Group Dissimilarities |
print.summary.permat |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
print.summary.permCheck |
Utility functions for permutation schemes |
print.summary.prc |
Principal Response Curves for Treatments with Repeated Observations |
print.summary.procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
print.summary.taxondive |
Indices of Taxonomic Diversity and Distinctness |
print.taxondive |
Indices of Taxonomic Diversity and Distinctness |
print.varpart |
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices |
print.varpart234 |
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices |
print.vectorfit |
Fits an Environmental Vector or Factor onto an Ordination |
procrustes |
Procrustes Rotation of Two Configurations and PROTEST |
profile.fisherfit |
Fit Fisher's Logseries and Preston's Lognormal Model to Abundance Data |
profile.humpfit |
No-interaction Model for Hump-backed Species Richness vs. Biomass |
protest |
Procrustes Rotation of Two Configurations and PROTEST |
pyrifos |
Response of Aquatic Invertebrates to Insecticide Treatment |
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.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.ordiplot |
Alternative plot and identify Functions for Ordination |
scores.orditkplot |
Ordination Plot with Movable Labels |
scores.pcnm |
Principal Coordinates of Neighbourhood Matrix |
scores.rda |
Plot or Extract Results of Constrained Correspondence Analysis
or Redundancy Analysis |
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 |
simpleRDA2 |
Partition the Variation of Community Matrix by 2, 3, or 4 Explanatory Matrices |
simulate.capscale |
Simulate Responses with Gaussian Error for Redundancy Analysis |
simulate.cca |
Simulate Responses with Gaussian Error for Redundancy Analysis |
simulate.rda |
Simulate Responses with Gaussian Error for Redundancy Analysis |
sipoo |
Birds in the Archipelago of Sipoo (Sibbo) |
spandepth |
Minimum Spanning Tree |
spantree |
Minimum Spanning Tree |
specaccum |
Species Accumulation Curves |
specnumber |
Ecological Diversity Indices and Rarefaction Species Richness |
specpool |
Extrapolated Species Richness in a Species Pool |
specpool2vect |
Extrapolated Species Richness in a Species Pool |
spenvcor |
Diagnostic Tools for [Constrained] Ordination (CCA,
RDA, DCA, CA, PCA) |
stepacross |
Stepacross as Flexible Shortest Paths or Extended Dissimilarities |
stressplot |
Goodness of Fit and Shepard Plot for Nonmetric Multidimensional Scaling |
summary.allPerms |
Utility functions for permutation schemes |
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.decorana |
Detrended Correspondence Analysis and Basic Reciprocal Averaging |
summary.eigenvals |
Extract Eigenvalues from an Ordination Object |
summary.humpfit |
No-interaction Model for Hump-backed Species Richness vs. Biomass |
summary.isomap |
Isometric Feature Mapping Ordination |
summary.meandist |
Multi Response Permutation Procedure of Within- versus
Among-Group Dissimilarities |
summary.ordiellipse |
Add Graphical Items to Ordination Diagrams |
summary.ordihull |
Add Graphical Items to Ordination Diagrams |
summary.permat |
Matrix Permutation Algorithms for Presence-Absence and Count Data |
summary.permCheck |
Utility functions for permutation schemes |
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.specaccum |
Species Accumulation Curves |
summary.taxondive |
Indices of Taxonomic Diversity and Distinctness |
swan |
Beals Smoothing and Degree of Absence |