# Infrastructure for Ordering Objects Using Seriation

## Documentation for package ‘seriation’ version 1.5.8

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

B C D G H I L M O P R S T U V W Z misc

## -- B --

bertinplot | Plot a Bertin Matrix
bertin_cut_line | Plot a Bertin Matrix
bluered | Different Useful Color Palettes
blues | Different Useful Color Palettes

## -- C --

c.ser_permutation | Class ser_permutation - A Collection of Permutation Vectors for Seriation
c.ser_permutation_vector | Class ser_permutation_vector - A Single Permutation Vector for Seriation
Chameleon | 2D Data Sets used for the CHAMELEON Clustering Algorithm
chameleon | 2D Data Sets used for the CHAMELEON Clustering Algorithm
chameleon_ds4 | 2D Data Sets used for the CHAMELEON Clustering Algorithm
chameleon_ds5 | 2D Data Sets used for the CHAMELEON Clustering Algorithm
chameleon_ds7 | 2D Data Sets used for the CHAMELEON Clustering Algorithm
chameleon_ds8 | 2D Data Sets used for the CHAMELEON Clustering Algorithm
colors | Different Useful Color Palettes
create_lines_data | Create Simulated Data for Seriation Evaluation
create_ordered_data | Create Simulated Data for Seriation Evaluation
criterion | Criterion for a Loss/Merit Function for Data Given a Permutation
criterion.array | Criterion for a Loss/Merit Function for Data Given a Permutation
criterion.data.frame | Criterion for a Loss/Merit Function for Data Given a Permutation
criterion.dist | Criterion for a Loss/Merit Function for Data Given a Permutation
criterion.matrix | Criterion for a Loss/Merit Function for Data Given a Permutation
criterion.table | Criterion for a Loss/Merit Function for Data Given a Permutation

## -- D --

DendSer | Register Seriation Methods from Package DendSer
dendser | Register Seriation Methods from Package DendSer
dissplot | Dissimilarity Plot

## -- G --

GA | Register a Genetic Algorithm Seriation Method
ga | Register a Genetic Algorithm Seriation Method
gaperm_mixedMutation | Register a Genetic Algorithm Seriation Method
get_config | Fit an Unidimensional Scaling for a Seriation Order
get_criterion_method | Registry for Criterion Methods
get_method | Class ser_permutation_vector - A Single Permutation Vector for Seriation
get_order | Extracting Order Information from a Permutation Object
get_order.dendrogram | Extracting Order Information from a Permutation Object
get_order.hclust | Extracting Order Information from a Permutation Object
get_order.integer | Extracting Order Information from a Permutation Object
get_order.numeric | Extracting Order Information from a Permutation Object
get_order.ser_permutation | Extracting Order Information from a Permutation Object
get_order.ser_permutation_vector | Extracting Order Information from a Permutation Object
get_permutation_matrix | Extracting Order Information from a Permutation Object
get_rank | Extracting Order Information from a Permutation Object
get_seriation_method | Registry for Seriation Methods
ggbertinplot | Plot a Bertin Matrix
ggdissplot | Dissimilarity Plot
gghmap | Plot Heat Map Reordered Using Seriation
ggiVAT | Visual Analysis for Cluster Tendency Assessment (VAT/iVAT)
ggpimage | Permutation Image Plot
ggpimage.dist | Permutation Image Plot
ggpimage.matrix | Permutation Image Plot
ggVAT | Visual Analysis for Cluster Tendency Assessment (VAT/iVAT)
grays | Different Useful Color Palettes
greenred | Different Useful Color Palettes
greens | Different Useful Color Palettes
greys | Different Useful Color Palettes

## -- H --

hmap | Plot Heat Map Reordered Using Seriation

## -- I --

Irish | Irish Referendum Data Set
is.robinson | Create and Recognize Robinson and Pre-Robinson Matrices
iVAT | Visual Analysis for Cluster Tendency Assessment (VAT/iVAT)

## -- L --

length.ser_permutation_vector | Class ser_permutation_vector - A Single Permutation Vector for Seriation
list_criterion_methods | Registry for Criterion Methods
list_seriation_methods | Registry for Seriation Methods
LLE | Locally Linear Embedding (LLE)
lle | Locally Linear Embedding (LLE)
LS | Neighborhood functions for Seriation Method SA
LS_insert | Neighborhood functions for Seriation Method SA
LS_mixed | Neighborhood functions for Seriation Method SA
LS_reverse | Neighborhood functions for Seriation Method SA
LS_swap | Neighborhood functions for Seriation Method SA

## -- M --

MDS_stress | Fit an Unidimensional Scaling for a Seriation Order
Munsingen | Hodson's Munsingen Data Set

## -- O --

OPTICS | Register Seriation Based on OPTICS
optics | Register Seriation Based on OPTICS

## -- P --

palette | Different Useful Color Palettes
panel.bars | Plot a Bertin Matrix
panel.blocks | Plot a Bertin Matrix
panel.circles | Plot a Bertin Matrix
panel.lines | Plot a Bertin Matrix
panel.rectangles | Plot a Bertin Matrix
panel.squares | Plot a Bertin Matrix
panel.tiles | Plot a Bertin Matrix
path_dist | Visual Analysis for Cluster Tendency Assessment (VAT/iVAT)
permutation_matrix2vector | Conversion Between Permutation Vector and Permutation Matrix
permutation_vector2matrix | Conversion Between Permutation Vector and Permutation Matrix
permute | Permute the Order in Various Objects
permute.array | Permute the Order in Various Objects
permute.character | Permute the Order in Various Objects
permute.data.frame | Permute the Order in Various Objects
permute.dendrogram | Permute the Order in Various Objects
permute.dist | Permute the Order in Various Objects
permute.hclust | Permute the Order in Various Objects
permute.list | Permute the Order in Various Objects
permute.matrix | Permute the Order in Various Objects
permute.numeric | Permute the Order in Various Objects
permute.table | Permute the Order in Various Objects
pimage | Permutation Image Plot
pimage.data.frame | Permutation Image Plot
pimage.dist | Permutation Image Plot
pimage.matrix | Permutation Image Plot
pimage.table | Permutation Image Plot
plot.reordered_cluster_dissimilarity_matrix | Dissimilarity Plot
plot_config | Fit an Unidimensional Scaling for a Seriation Order
print.criterion_method | Registry for Criterion Methods
print.reordered_cluster_dissimilarity_matrix | Dissimilarity Plot
print.seriation_method | Registry for Seriation Methods
print.ser_permutation | Class ser_permutation - A Collection of Permutation Vectors for Seriation
print.ser_permutation_vector | Class ser_permutation_vector - A Single Permutation Vector for Seriation
Psych24 | Results of 24 Psychological Test for 8th Grade Students

## -- R --

random.robinson | Create and Recognize Robinson and Pre-Robinson Matrices
reds | Different Useful Color Palettes
registersmacof | Register Seriation Methods from Package smacof
register_DendSer | Register Seriation Methods from Package DendSer
register_GA | Register a Genetic Algorithm Seriation Method
register_optics | Register Seriation Based on OPTICS
register_smacof | Register Seriation Methods from Package smacof
register_tsne | Register Seriation Based on 1D t-SNE
register_umap | Register Seriation Based on 1D UMAP
registry_criterion | Registry for Criterion Methods
registry_for_criterion_methods | Registry for Criterion Methods
registry_for_seriation_methods | Registry for Seriation Methods
registry_seriate | Registry for Seriation Methods
reorder | Reorder Dendrograms using Optimal Leaf Ordering
reorder.hclust | Reorder Dendrograms using Optimal Leaf Ordering
rev.ser_permutation_vector | Class ser_permutation_vector - A Single Permutation Vector for Seriation
Robinson | Create and Recognize Robinson and Pre-Robinson Matrices
robinson | Create and Recognize Robinson and Pre-Robinson Matrices

## -- S --

seriate | Seriate Dissimilarity Matrices, Matrices or Arrays
seriate.array | Seriate Dissimilarity Matrices, Matrices or Arrays
seriate.data.frame | Seriate Dissimilarity Matrices, Matrices or Arrays
seriate.dist | Seriate Dissimilarity Matrices, Matrices or Arrays
seriate.matrix | Seriate Dissimilarity Matrices, Matrices or Arrays
seriate.table | Seriate Dissimilarity Matrices, Matrices or Arrays
seriate_best | Best Seriation
seriate_improve | Best Seriation
seriate_rep | Best Seriation
ser_align | Dissimilarities and Correlations Between Seriation Orders
ser_cor | Dissimilarities and Correlations Between Seriation Orders
ser_dist | Dissimilarities and Correlations Between Seriation Orders
ser_permutation | Class ser_permutation - A Collection of Permutation Vectors for Seriation
ser_permutation_vector | Class ser_permutation_vector - A Single Permutation Vector for Seriation
set_criterion_method | Registry for Criterion Methods
set_seriation_method | Registry for Seriation Methods
smacof | Register Seriation Methods from Package smacof
summary.ser_permutation | Class ser_permutation - A Collection of Permutation Vectors for Seriation
summary.ser_permutation_vector | Class ser_permutation_vector - A Single Permutation Vector for Seriation
SupremeCourt | Voting Patterns in the Second Rehnquist U.S. Supreme Court

## -- T --

Townships | Bertin's Characteristics of Townships
tSNE | Register Seriation Based on 1D t-SNE
tsne | Register Seriation Based on 1D t-SNE

## -- U --

umap | Register Seriation Based on 1D UMAP
uniscale | Fit an Unidimensional Scaling for a Seriation Order

## -- V --

VAT | Visual Analysis for Cluster Tendency Assessment (VAT/iVAT)

## -- W --

Wood | Gene Expression Data for Wood Formation in Poplar Trees

## -- Z --

Zoo | Zoo Data Set

## -- misc --

[.ser_permutation | Class ser_permutation - A Collection of Permutation Vectors for Seriation