Installation | Seriate a dissimilarity matrix | Assess the quality of a seriation order | Seriate a data matrix | Choose a method | Where to go next
Package: seriation 1.6.0
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:
seriation_1.6.0.tar.gz
seriation_1.6.0.zip(r-4.7-x86_64)seriation_1.6.0.zip(r-4.7-arm64)seriation_1.6.0.zip(r-4.6-x86_64)seriation_1.6.0.zip(r-4.6-arm64)seriation_1.6.0.zip(r-4.5-x86_64)
seriation_1.6.0.tgz(r-4.6-x86_64)seriation_1.6.0.tgz(r-4.6-arm64)seriation_1.6.0.tgz(r-4.5-x86_64)seriation_1.6.0.tgz(r-4.5-arm64)
seriation_1.6.0.tar.gz(r-4.7-arm64)seriation_1.6.0.tar.gz(r-4.7-x86_64)seriation_1.6.0.tar.gz(r-4.6-arm64)seriation_1.6.0.tar.gz(r-4.6-x86_64)
seriation_1.6.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
seriation/json (API)
| # Install 'seriation' in R: |
| install.packages('seriation', repos = c('https://mhahsler.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/mhahsler/seriation/issues
Pkgdown/docs site:https://michael.hahsler.net
Datasets:
- 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
- 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
combinatorial-optimizationordinationseriation
Last updated from:03d5bdd102. Checks:14 OK, 1 WARNING. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 193 | ||
| linux-devel-x86_64 | OK | 257 | ||
| source / vignettes | OK | 387 | ||
| linux-release-arm64 | OK | 179 | ||
| linux-release-x86_64 | OK | 256 | ||
| macos-release-arm64 | OK | 156 | ||
| macos-release-x86_64 | OK | 294 | ||
| macos-oldrel-arm64 | OK | 226 | ||
| macos-oldrel-x86_64 | OK | 433 | ||
| windows-devel-arm64 | OK | 287 | ||
| windows-devel-x86_64 | OK | 266 | ||
| windows-release-arm64 | WARNING | 298 | ||
| windows-release-x86_64 | OK | 195 | ||
| windows-oldrel-x86_64 | OK | 236 | ||
| wasm-release | OK | 139 |
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_umapregister_veganregistry_criterionregistry_seriateser_alignser_corser_distser_permutationser_permutation_vectorseriateseriate_bestseriate_improveseriate_repset_criterion_methodset_seriation_methoduniscaleVAT
Dependencies:caclustercodetoolscolorspaceforeachgclusiteratorsMASSqapregistryTSP
Getting started with seriation
Last update: 2026-10-07
Started: 2026-09-27
Seriation Methods implemented in the R package seriation
Methods for dissimilarity data (dist) | Methods for data matrices, tables and data.frames | References
Last update: 2026-10-06
Started: 2026-09-26
Correlation Matrix Visualization with Package Seriation
Introduction | Prepare the data | Visualization options | Using other seriation methods | Other packages | Package corrgram | Package corrr | Package corrplot | References
Last update: 2026-10-06
Started: 2026-09-26
Heatmaps with Package Seriation
Introduction | Prepare the data | Reordering in seriation | Built-in heatmap function | Without dendrograms: pimage | With dendrograms: hmap | With distance matrices instead of dendrograms: hmap | colors with pimage and hmap | ggplot2 | Using seriation with other packages | heatmap in package stats | Package heatmaply
Last update: 2026-10-06
Started: 2026-09-26
An Introduction to the R package seriation
Introduction | Seriation as a combinatorial optimization problem | Seriation methods | The package infrastructure | Examples and applications | Conclusion
Last update: 2026-10-06
Started: 2026-09-27
How to Evaluate Clusters Using Dissimilarity Plots
Introduction | Examples | Ruspini: A simple dataset | Votes: High dimensional data | Conclusion | References
Last update: 2026-10-06
Started: 2026-09-26
Seriation Criteria implemented in the R package seriation
Criteria for dissimilarity data (dist) | Criteria for data matrices, tables and data.frames | References
Last update: 2026-09-26
Started: 2026-09-26
A Comparison of Seriation Methods
Introduction | Distance seriation | Comparison between methods | Visualize the results | Matrix seriation
Last update: 2026-09-26
Started: 2026-09-26
How to use Tree-Penalized Path Length Criterion with Package seriation
Introduction | Numeric Example
Last update: 2026-09-26
Started: 2026-09-26
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Plot a Bertin Matrix | bertinplot 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 Algorithm | Chameleon chameleon chameleon_ds4 chameleon_ds5 chameleon_ds7 chameleon_ds8 |
| Create Simulated Data for Seriation Evaluation | create_lines_data create_ordered_data |
| Criterion for a Loss/Merit Function for Data Given a Permutation | criterion criterion.array criterion.data.frame criterion.dist criterion.matrix criterion.table |
| Dissimilarity Plot | dissplot ggdissplot plot.reordered_cluster_dissimilarity_matrix print.reordered_cluster_dissimilarity_matrix |
| Extracting Order Information from a Permutation Object | get_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 Seriation | gghmap hmap |
| Irish Referendum Data Set | Irish |
| Create and Recognize Robinson and Pre-Robinson Matrices | is.robinson random.robinson Robinson robinson |
| Locally Linear Embedding (LLE) | LLE lle |
| Neighborhood functions for Seriation Method SA | LS LS_insert LS_mixed LS_reverse LS_swap |
| Hodson's Munsingen Data Set | Munsingen |
| Different Useful Color Palettes | bluered blues colors grays greenred greens greys palette reds |
| Conversion Between Permutation Vector and Permutation Matrix | permutation_matrix2vector permutation_vector2matrix |
| Permute the Order in Various Objects | permute permute.array permute.character permute.data.frame permute.dendrogram permute.dist permute.hclust permute.list permute.matrix permute.numeric permute.table |
| Permutation Image Plot | ggpimage ggpimage.dist ggpimage.matrix pimage pimage.data.frame pimage.dist pimage.matrix pimage.table |
| Results of 24 Psychological Test for 8th Grade Students | Psych24 |
| Register Seriation Methods from Package DendSer | DendSer dendser register_DendSer |
| Register a Genetic Algorithm Seriation Method | GA ga gaperm_mixedMutation register_GA |
| Register Seriation Based on OPTICS | OPTICS optics register_optics |
| Register Seriation Methods from Package smacof | registersmacof register_smacof smacof |
| Register Seriation Based on 1D t-SNE | register_tsne tSNE tsne |
| Register Seriation Based on 1D UMAP | register_umap umap |
| Register Seriation Methods from Package vegan | isomap metaMDS monoMDS register_vegan |
| Registry for Criterion Methods | get_criterion_method list_criterion_methods print.criterion_method registry_criterion registry_for_criterion_methods set_criterion_method |
| Registry for Seriation Methods | get_seriation_method list_seriation_methods print.seriation_method registry_for_seriation_methods registry_seriate set_seriation_method |
| Reorder Dendrograms using Optimal Leaf Ordering | reorder reorder.hclust |
| Dissimilarities and Correlations Between Seriation Orders | ser_align ser_cor ser_dist |
| Class ser_permutation - A Collection of Permutation Vectors for Seriation | c.ser_permutation print.ser_permutation ser_permutation summary.ser_permutation [.ser_permutation |
| Class ser_permutation_vector - A Single Permutation Vector for Seriation | c.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 Arrays | seriate seriate.array seriate.data.frame seriate.dist seriate.matrix seriate.table |
| Best Seriation | seriate_best seriate_improve seriate_rep |
| Voting Patterns in the Second Rehnquist U.S. Supreme Court | SupremeCourt |
| Bertin's Characteristics of Townships | Townships |
| Fit an Unidimensional Scaling for a Seriation Order | get_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 Trees | Wood |
| Zoo Data Set | Zoo |