R Observatory: Metrics for seriation version 1.6.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

seriation

1.6.0Package record

Infrastructure for Ordering Objects Using Seriation

13packages dependsuggested by 15

446.1Kdownloads / year

37.1%test coverage

13/13flavors OK

Overview

About

Maintained by Michael HahslerCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.6.0

Changes

Methods from vegan need now to be registered before use.
Raised required R version.
Added howto vignettes.
Spelling, fixed broken links.
Renamed method "SGD" to "SGLS" (stochastic greedy local search) for distances. The old "SGD" name remains available as a deprecated alias and issues a warning.

Bug Fixes

Fixed method warning for seriate.TSP.

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("seriation", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("mhahsler/seriation")

Development version from mhahsler/seriation. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-seriation

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-seriation

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-seriation

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 8.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-08
WARNING12 OK, 1 WARNING2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.6.0

READMEYes · 1,425 wordsVignettesYes · 9 · dynamicNEWSYes · 100% structured · mentions 1.6.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Cites a JSS article

Help pages: 39 (1 internal)includes a package overview page
Examples that run: 81%30 run in a plain check · 7 never run
Exported functions with examples: 97%
Documented parameters: 83%
Return-value docs: 100%
Help pages citing references: 67%

Vignettes (9)

How these are measured

Downloads

446.1K

CRAN downloads in the past year

Rank #586 · ~1.2K/day · ~37.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

34.6K30 days

109.5K90 days

446.1K1 year

Compare downloads with other packages →

Also on4.4K r2u141 autocran19.4K conda_forge217 c2d4u

How downloads are counted

Repository

mhahsler/seriation ↗Account: mhahsler

87Stars

17Forks

2Open issues

0Open PRs

20Releases

380Commits

7Commit identities

seriationcranrcombinatorial-optimizationordination

License file reads as GPL-3.0 · 380 commits · Last activity 2026-10-07 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-17 · 832026-08-04 · 87

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/mhahsler/seriation on 2026-10-11.

Continuous integration (1)

GitHub Actions

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-07 · The repository has a site deploy workflow

pkgdown site last built 2026-10-07

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Installing seriation adds 8 packages (3 with compiled code, 4.1 MB of source tarballs). Heaviest: colorspace 2.0 MB, TSP 704 KB, qap 515 KB.

Depends (1)

R >= 4.3.0

Imports (12)

caclustercolorspace foreach gclusgrDevicesgridMASSqap registrystatsTSP

LinkingTo (0)

none

Suggests (24)

cba corrgram corrplot corrr dbscan DendSer dendextend doParallel DT dplyr GA ggplot2 heatmaply keras Rtsne scales smacof tensorflow testthat umap vegan viridis knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

13direct

24indirect

Depends 3 · Imports 10

Suggested by 15

Show all 28 packagesHide all 28 packages

Depends, Imports or LinkingTo, most downloaded first

corrr arulesViz heatmaply DendSer adepro treeheatr RMaCzek baizer elaborator MEDseq ClusteredMutations GAPR ockc

Suggests, most downloaded first

corrplot dendextend ggraph tidygraph flexclust vcdExtra corrgram dendsort ChemoSpec futurize protti disclapmix cellGeometry PairViz Proximum

How these are counted

Code & Tests

Datasets

People & History

People (9)

Michael Hahsler

Christian Buchta

Author, Copyright holder

Kurt Hornik

Author, Copyright holder

David Barnett

Contributor · added in 1.4.1

Michael Brusco

Contributor, Copyright holder · added in 1.0-11

Michael Friendly

Contributor · added in 1.4.0

Hans-Friedrich Koehn

Contributor, Copyright holder · added in 1.0-11

Fionn Murtagh

Contributor, Copyright holder · added in 1.0-11

Stephanie Stahl

Contributor, Copyright holder · added in 1.0-11

Releases (67)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
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R 4.5.0 released · 2025-04-11
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R 4.4.0 released · 2024-04-24
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R 4.3.0 released · 2023-04-21
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R 4.2.0 released · 2022-04-22
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R 4.1.0 released · 2021-05-18
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R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
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R 3.5.0 released · 2018-04-23
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R 3.4.0 released · 2017-04-21
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R 3.3.0 released · 2016-05-03
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R 3.2.0 released · 2015-04-16
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R 3.1.0 released · 2014-04-10
3.0.3Latest
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2014-02-18 · current release · diff ↗
3.0.2
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2013-09-06 · diff ↗
R
R 3.0.0 released · 2013-04-03

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2.15.3
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2013-02-15 · diff ↗
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2012-09-24 · diff ↗
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R 2.15.0 released · 2012-03-30
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R 2.14.0 released · 2011-10-31
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2011-10-18 · diff ↗
2.13.2
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2011-09-01 · diff ↗ ·
added 2 exports
bertin_cut_line, panel.blocks
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R 2.13.0 released · 2011-04-13
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R 2.12.0 released · 2010-10-15
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R 2.11.0 released · 2010-04-22
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R 2.10.0 released · 2009-10-26
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R 2.9.0 released · 2009-04-17
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R 2.8.0 released · 2008-10-20
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2008-08-21 · diff ↗
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R 2.7.0 released · 2008-04-22
2.7.0
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2008-04-04 · diff ↗
2.6.2
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2008-02-01 · diff ↗ ·
added 8 exports
set_criterion_method, get_criterion_method, list_criterion_methods, show_criterion_methods, set_seriation_method, get_seriation_method, list_seriation_methods, show_seriation_methods
R
R 2.6.0 released · 2007-10-03
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R 2.5.0 released · 2007-04-24
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R 2.4.0 released · 2006-10-03
2.4.0
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2006-08-30 · diff ↗ ·
added 15 exports
bertinplot, criterion, dissplot, get_method, get_order, hmap, panel.bars, panel.circles, panel.squares, panel.lines, permute, ser_permutation, ser_permutation_vector, pimage, seriate
1.6.0
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2026-10-07 · diff ↗ ·
added 1 export
register_vegan
·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-07 00:16 UTC, so it stayed less than the time between readings.
1.5.8
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2023-07-20 · diff ↗
1.5.0
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2023-07-20 · diff ↗ ·
removed 1 export
orderplot

added 8 exports
MDS_stress, get_config, lle, plot_config, register_smacof, seriate_best, seriate_improve, seriate_rep
1.4.2
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2023-03-08 · diff ↗
1.4.1
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1.4.0
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1.3.6
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1.3.5
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2022-03-28 · diff ↗ ·
added 4 exports
register_DendSer, register_optics, register_tsne, register_umap
1.3.4
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2022-03-17 · diff ↗
1.3.3
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2022-03-07 · diff ↗ ·
removed 6 exports
show_criterion_methods, show_seriation_methods, register_DendSer, register_tsne, register_umap, register_optics
1.3.2
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2022-02-10 · diff ↗
1.3.1
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2021-10-16 · diff ↗ ·
added 3 exports
register_tsne, register_umap, register_optics
1.3.0
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2021-06-30 · diff ↗ ·
added 11 exports
ggbertinplot, ggdissplot, panel.rectangles, panel.tiles, ggpimage, gghmap, ggVAT, ggiVAT, reds, blues, greens
1.2-9
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2020-10-01 · diff ↗
1.2-8
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1.2-2
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2017-05-09 · diff ↗ ·
added 6 exports
orderplot, uniscale, LS_insert, LS_swap, LS_reverse, LS_mixed
1.2-1
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2016-08-07 · diff ↗
1.2-0
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2016-02-22 · diff ↗ ·
added 3 exports
register_DendSer, register_GA, gaperm_mixedMutation
1.1-3
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2015-12-19 · diff ↗ ·
added 2 exports
is.robinson, random.robinson
1.1-2
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2015-08-23 · diff ↗ ·
removed 3 exports
seriation_dist, seriation_cor, seriation_align

added 4 exports
get_rank, ser_dist, ser_cor, ser_align
1.1-1
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2015-07-01 · diff ↗ ·
removed 1 export
get_rank

added 1 export
get_permutation_matrix
1.1-0
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2015-06-10 · diff ↗ ·
added 17 exports
get_rank, permutation_matrix2vector, permutation_vector2matrix, path_dist, VAT, iVAT, create_lines_data, create_ordered_data, bluered, greenred, grays, greys, registry_criterion, registry_seriate, seriation_dist, seriation_cor, seriation_align
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0.1-1
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2007-09-01
R
R 2.3.0 released · 2006-04-24

Across CRAN, the median accepted release of the past year spent 19 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2006-08-30
Total releases: 67 / 20 yrs
License: GPL-3 OSI
Copyright: The code in src/bbwrcg.f, src/arsa.f and src/bburcg.f are Copyright (C) 2005 M. Brusco, H.F. Koehn, and S. Stahl. All other code is Copyright (C) Michael Hahsler, Christian Buchta, and Kurt Hornik.
Minimum R: ≥ 4.3.0
Bundled data: 266 KB / 8 files
Download size: 4.3 MB

Appears in task views

Cluster Analysis & Finite Mixture Models

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("seriation")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for seriation version 1.6.0 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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