R Observatory: Metrics for PathwaySpace version 1.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PathwaySpace

1.5.0

Spatial Projection of Network Signals along Geodesic Paths

0packages depend

3.3Kdownloads / year

–test coverage

10/13checks pass

Overview

About

Maintained by Mauro CastroFirst published 2024-09-0310 releasesCRAN page ↗GitHub ↗

For a given graph containing vertices, edges, and a signal associated with the vertices, the 'PathwaySpace' package performs a convolution operation, which involves a weighted combination of neighboring vertices and their associated signals. The package uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' has various applications, such as visualizing network data in a graphical format that highlights the relationships and signal strengths between vertices. By combining graph theory, signal processing, and visualization, 'PathwaySpace' provides a way of representing graph data on a continuous projection space. Based on methods introduced in Tercan et al. (2025) doi:10.1016/j.xpro.2025.103681 and Ellrott et al. (2025) doi:10.1016/j.ccell.2024.12.002.

Install

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

install.packages("PathwaySpace", 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("sysbiolab/PathwaySpace")

Development version from sysbiolab/PathwaySpace. 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-pathwayspace

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-PathwaySpace

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-PathwaySpace

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

3WARNING10OK

Failing flavors

WARNING r-oldrel-macos-arm64
WARNING r-oldrel-macos-x86_64
WARNING r-oldrel-windows-x86_64

Slowest check: 4.5 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.02

not tracked

Coverage

100%

Documentation · exports

14

Dependencies · direct

Check history

WARNING2026-06-27
10 OK · 0 NOTE · 3 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 14%

Downloads

3.3K

CRAN downloads in the past year

Rank #6,659 · ~9/day · ~277/mo

Releases R versions

Daily download trend is not available in this view yet.

30430 days

1.3K90 days

3.3K1 year

Compare downloads with other packages →

Also on227 r2u

Repository

GitHub ↗ sysbiolab/pathwayspace

3Stars

2Forks

0Open issues

0Open PRs

0Releases

261Commits

2Contributors

bioinformaticsbiological-networksgraphr

261 commits · Last activity 2026-07-28 · +50% stars, 30d

Stars over time

2025-01-07 · 22026-08-07 · 3

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/sysbiolab/pathwayspace on 2026-08-16.

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (3)

R >= 4.5methodsRGraphSpace

Imports (12)

grDevicesrlangstatsscales RANN igraph ggplot2gridggnewscale ggrepel colorspace lifecycle

LinkingTo (0)

none

Suggests (5)

knitr rmarkdown testthat RedeR patchwork

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (7)

Maintainer (1)

Mauro Castro

Maintainer

Authors (1)

Sysbiolab Team

Author · added in 1.2.0

Contributors (5)

Victor Apolonio

Contributor

Jonathan Back

Contributor · added in 1.2.0

Vinicius Chagas

Contributor

Lana Querne

Contributor · added in 1.2.0

Bahar Tercan

Contributor · added in 1.2.0

Listed in earlier versions (1)

Sysbiolab and Collaborators

no longer listed · 1.1.0 to 1.1.1

Package Timeline

10 releases. Pick two to compare their code metrics. R releases are shown for context.

1.5.0Latest
2026-07-30 · current release · diff ↗
1.4.1
2026-06-26 · diff ↗
1.3.0
2026-05-23 · diff ↗
1.2.0
2026-04-25 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.1.1
2026-02-28 · diff ↗
1.1.0
2025-11-07 · diff ↗
1.0.2
2025-07-28 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.1
2025-04-08 · diff ↗
1.0.0
2024-11-12 · diff ↗
0.99.4
2024-09-03
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-03
Total releases: 10 / 2 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 4.5
Bundled data: 1.2 MB / 6 files
Download size: 3.1 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PathwaySpace")

Format

Castro, M., Sysbiolab Team, Apolonio, V., Back, J., Chagas, V., Querne, L., & Tercan, B. (2026). PathwaySpace: Spatial Projection of Network Signals along Geodesic Paths (Version 1.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.PathwaySpace

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 PathwaySpace version 1.5.0 [Data set]. HJJB, LLC. Data release v2026-08-16. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-16, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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