Package: seriation 1.5.6.1

seriation: Infrastructure for Ordering Objects Using Seriation

Infrastructure for ordering objects with an implementation of several seriation/sequencing/ordination techniques to reorder matrices, dissimilarity matrices, and dendrograms. Also provides (optimally) reordered heatmaps, color images and clustering visualizations like dissimilarity plots, and visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.

Authors:Michael Hahsler [aut, cre, cph], Christian Buchta [aut, cph], Kurt Hornik [aut, cph], David Barnett [ctb], Michael Brusco [ctb, cph], Michael Friendly [ctb], Hans-Friedrich Koehn [ctb, cph], Fionn Murtagh [ctb, cph], Stephanie Stahl [ctb, cph]

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seriation.pdf |seriation.html✨
seriation/json (API)
NEWS

# Install 'seriation' in R:
install.packages('seriation', repos = c('https://mhahsler.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/mhahsler/seriation/issues

Datasets:
  • Irish - Irish Referendum Data Set
  • Munsingen - Hodson's Munsingen Data Set
  • Psych24 - Results of 24 Psychological Test for 8th Grade Students
  • SupremeCourt - Voting Patterns in the Second Rehnquist U.S. Supreme Court
  • Townships - Bertin's Characteristics of Townships
  • Wood - Gene Expression Data for Wood Formation in Poplar Trees
  • Zoo - Zoo Data Set
  • 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

On CRAN:

combinatorial-optimizationordinationseriation

14.02 score 75 stars 79 packages 580 scripts 31k downloads 14 mentions 73 exports 17 dependencies

Last updated 26 days agofrom:5231a4f9f9. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 24 2024
R-4.5-win-x86_64OKOct 24 2024
R-4.5-linux-x86_64OKOct 24 2024
R-4.4-win-x86_64OKOct 24 2024
R-4.4-mac-x86_64OKOct 24 2024
R-4.4-mac-aarch64OKOct 24 2024
R-4.3-win-x86_64OKOct 24 2024
R-4.3-mac-x86_64OKOct 24 2024
R-4.3-mac-aarch64OKOct 24 2024

Exports:bertin_cut_linebertinplotblueredbluescreate_lines_datacreate_ordered_datacriteriondissplotgaperm_mixedMutationget_configget_criterion_methodget_methodget_orderget_permutation_matrixget_rankget_seriation_methodggbertinplotggdissplotgghmapggiVATggpimageggVATgraysgreenredgreensgreyshmapis.robinsoniVATlist_criterion_methodslist_seriation_methodslleLS_insertLS_mixedLS_reverseLS_swapMDS_stresspanel.barspanel.blockspanel.circlespanel.linespanel.rectanglespanel.squarespanel.tilespath_distpermutation_matrix2vectorpermutation_vector2matrixpermutepimageplot_configrandom.robinsonredsregister_DendSerregister_GAregister_opticsregister_smacofregister_tsneregister_umapregistry_criterionregistry_seriateser_alignser_corser_distser_permutationser_permutation_vectorseriateseriate_bestseriate_improveseriate_repset_criterion_methodset_seriation_methoduniscaleVAT

Dependencies:caclustercodetoolscolorspaceforeachgclusiteratorslatticeMASSMatrixmgcvnlmepermuteqapregistryTSPvegan

An Introduction to the R package seriation

Rendered fromseriation.Rnwusingutils::Sweaveon Oct 24 2024.

Last update: 2023-07-20
Started: 2015-10-11

Readme and manuals

Help Manual

Help pageTopics
Plot a Bertin Matrixbertinplot bertin_cut_line ggbertinplot panel.bars panel.blocks panel.circles panel.lines panel.rectangles panel.squares panel.tiles
2D Data Sets used for the CHAMELEON Clustering AlgorithmChameleon chameleon chameleon_ds4 chameleon_ds5 chameleon_ds7 chameleon_ds8
Create Simulated Data for Seriation Evaluationcreate_lines_data create_ordered_data
Criterion for a Loss/Merit Function for Data Given a Permutationcriterion criterion.array criterion.data.frame criterion.dist criterion.matrix criterion.table
Dissimilarity Plotdissplot ggdissplot plot.reordered_cluster_dissimilarity_matrix print.reordered_cluster_dissimilarity_matrix
Extracting Order Information from a Permutation Objectget_order get_order.dendrogram get_order.hclust get_order.integer get_order.numeric get_order.ser_permutation get_order.ser_permutation_vector get_permutation_matrix get_rank
Plot Heat Map Reordered Using Seriationgghmap hmap
Irish Referendum Data SetIrish
Create and Recognize Robinson and Pre-Robinson Matricesis.robinson random.robinson Robinson robinson
Locally Linear Embedding (LLE)LLE lle
Neighborhood functions for Seriation Method SALS LS_insert LS_mixed LS_reverse LS_swap
Hodson's Munsingen Data SetMunsingen
Different Useful Color Palettesbluered blues colors grays greenred greens greys palette reds
Conversion Between Permutation Vector and Permutation Matrixpermutation_matrix2vector permutation_vector2matrix
Permute the Order in Various Objectspermute permute.array permute.character permute.data.frame permute.dendrogram permute.dist permute.hclust permute.list permute.matrix permute.numeric permute.table
Permutation Image Plotggpimage ggpimage.dist ggpimage.matrix pimage pimage.data.frame pimage.dist pimage.matrix pimage.table
Results of 24 Psychological Test for 8th Grade StudentsPsych24
Register Seriation Methods from Package DendSerDendSer dendser register_DendSer
Register a Genetic Algorithm Seriation MethodGA ga gaperm_mixedMutation register_GA
Register Seriation Based on OPTICSOPTICS optics register_optics
Register Seriation Methods from Package smacofregistersmacof register_smacof smacof
Register Seriation Based on 1D t-SNEregister_tsne tSNE tsne
Register Seriation Based on 1D UMAPregister_umap umap
Registry for Criterion Methodsget_criterion_method list_criterion_methods print.criterion_method registry_criterion registry_for_criterion_methods set_criterion_method
Registry for Seriation Methodsget_seriation_method list_seriation_methods print.seriation_method registry_for_seriation_methods registry_seriate set_seriation_method
Reorder Dendrograms using Optimal Leaf Orderingreorder reorder.hclust
Dissimilarities and Correlations Between Seriation Ordersser_align ser_cor ser_dist
Class ser_permutation - A Collection of Permutation Vectors for Seriationc.ser_permutation print.ser_permutation ser_permutation summary.ser_permutation [.ser_permutation
Class ser_permutation_vector - A Single Permutation Vector for Seriationc.ser_permutation_vector get_method length.ser_permutation_vector print.ser_permutation_vector rev.ser_permutation_vector ser_permutation_vector summary.ser_permutation_vector
Seriate Dissimilarity Matrices, Matrices or Arraysseriate seriate.array seriate.data.frame seriate.dist seriate.matrix seriate.table
Best Seriationseriate_best seriate_improve seriate_rep
Voting Patterns in the Second Rehnquist U.S. Supreme CourtSupremeCourt
Bertin's Characteristics of TownshipsTownships
Fit an Unidimensional Scaling for a Seriation Orderget_config MDS_stress plot_config uniscale
Visual Analysis for Cluster Tendency Assessment (VAT/iVAT)ggiVAT ggVAT iVAT path_dist VAT
Gene Expression Data for Wood Formation in Poplar TreesWood
Zoo Data SetZoo