R Observatory: Metrics for GeneralizedUmatrix version 1.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GeneralizedUmatrix

1.3.1Package record

Credible Visualization for Two-Dimensional Projections of Data

3packages dependsuggested by 1

6.9Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

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

Projections are common dimensionality reduction methods, which represent high-dimensional data in a two-dimensional space. However, when restricting the output space to two dimensions, which results in a two dimensional scatter plot (projection) of the data, low dimensional similarities do not represent high dimensional distances coercively [Thrun, 2018] <DOI: 10.1007/978-3-658-20540-9>. This could lead to a misleading interpretation of the underlying structures [Thrun, 2018]. By means of the 3D topographic map the generalized Umatrix is able to depict errors of these two-dimensional scatter plots. The package is derived from the book of Thrun, M.C.: "Projection Based Clustering through Self-Organization and Swarm Intelligence" (2018) DOI:10.1007/978-3-658-20540-9 and the main algorithm called simplified self-organizing map for dimensionality reduction methods is published in <DOI: 10.1016/j.mex.2020.101093>.

Install

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

install.packages("GeneralizedUmatrix", 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("Mthrun/GeneralizedUmatrix")

Development version from Mthrun/GeneralizedUmatrix. 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-generalizedumatrix

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-GeneralizedUmatrix

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-GeneralizedUmatrix

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

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘CalcUstarmatrix.Rd’ ‘EsomNeuronsAsList.Rd’ ‘GeneratePmatrix.Rd’
  ‘ListAsEsomNeurons.Rd’ ‘XYcoords2LinesColumns.Rd’ ‘setdiffMatrix.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 4.6 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.1

READMEYes · 520 wordsVignettesYes · 1 · staticNEWSNoCitation fileYes · cites a publicationWebsiteYes

Help pages: 25includes a package overview page
Examples that run: 88%7 run in a plain check · 1 hold no code
Exported functions with examples: 40%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 64%

Vignettes (1)

Uncovering High-Dimensional Structures of Projections from Dimensionality Reduction Methods

How these are measured

Downloads

6.9K

CRAN downloads in the past year

Rank #5,126 · ~19/day · ~578/mo

Releases R versions

Daily download trend is not available in this view yet.

71130 days

1.6K90 days

6.9K1 year

Compare downloads with other packages →

Also on505 r2u4 autocran67 c2d4u

How downloads are counted

Repository

mthrun/generalizedumatrix ↗Account: Mthrun

1Stars

2Forks

0Open issues

0Open PRs

0Releases

40Commits

3Commit identities

License file reads as GPL-3.0 · 40 commits · Last activity 2025-01-26

Responsiveness

How these are sampled

PRs merged (all time): 67%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2022-05-26 · 12026-07-07 · 1

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/mthrun/generalizedumatrix on 2026-10-18.

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing GeneralizedUmatrix adds 20 packages (10 with compiled code, 17 MB of source tarballs). Heaviest: ggplot2 6.0 MB, Rcpp 1.8 MB, isoband 1.5 MB.

Depends (1)

R >= 3.0

Imports (3)

Rcpp RcppParallel ggplot2

LinkingTo (3)

Rcpp RcppArmadillo RcppParallel

Suggests (13)

DataVisualizations rglgridmgcvpng reshape2 fields ABCanalysis plotly deldirmethodsknitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

6indirect

Imports 3

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

ProjectionBasedClustering DatabionicSwarm GeneralizedUmatrixGPU

Suggests, most downloaded first

FCPS

How these are counted

Code & Tests

Datasets

People & History

People (6)

Michael Thrun

Felix Pape

Contributor, Contractor · added in 1.1.8

Tim Schreier

Contributor, Contractor · added in 1.1.8

Quirin Stier

Contributor, Contractor · added in 1.2.4

Luis Winckelman

Contributor, Contractor · added in 1.1.8

Alfred Ultsch

Thesis advisor

Releases (16)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.3.1Latest
record
2025-01-29 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.2.6
record
2023-05-30 · diff ↗ ·
added 2 exports
EsomNeuronsAsList, ListAsEsomNeurons
R
R 4.3.0 released · 2023-04-21
1.2.5
record
2022-11-28 · diff ↗
1.2.4
record
2022-05-25 · diff ↗ ·
added 4 exports
UniqueBestMatchingUnits, LowLand, ReduceToLowLand, Uheights4Data
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.2.2
record
2021-01-12 · diff ↗
1.2.1
record
2020-10-25 · diff ↗ ·
added 1 export
ExtendToroidalUmatrix
1.2.0
record
2020-08-24 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.9
record
2020-03-23 · diff ↗
1.1.8
record
2020-02-17 · diff ↗ ·
added 2 exports
NormalizeUmatrix, TopviewTopographicMap

Show 10 earlier eventsHide 10 earlier events

1.1.6
record
2019-11-20 · diff ↗ ·
added 3 exports
upscaleUmatrix, GeneratePmatrix, CalcUstarmatrix
R
R 3.6.0 released · 2019-04-26
1.1.5
record
2019-02-03 · diff ↗
1.1.4
record
2019-01-27 · diff ↗ ·
removed 1 export
upscaleUmatrix
1.1.2
record
2018-07-03 · diff ↗ ·
added 1 export
upscaleUmatrix
R
R 3.5.0 released · 2018-04-23
1.0.0
record
2018-01-31 · diff ↗ ·
removed 1 export
interactiveGeneralizedUmatrixIsland
0.9.5
record
2017-08-20 · diff ↗ ·
added 1 export
interactiveGeneralizedUmatrixIsland
0.9.4
record
2017-05-18
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-18
Total releases: 16 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0
Bundled data: 13 KB / 3 files
Download size: 724 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("GeneralizedUmatrix")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1016/j.mex.2020.101093.

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 GeneralizedUmatrix version 1.3.1 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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