R Observatory: Metrics for PathwaySpace version 1.5.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PathwaySpace

1.5.2Package record

Spatial Projection of Network Signals along Geodesic Paths

0packages depend

4Kdownloads / year

–test coverage

10/13flavors OK

Overview

About

Maintained by Mauro CastroCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 1.5.2

Improved backward compatibility with RGraphSpace.

From inst/NEWS.Rd in the release

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. 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-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). 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

3WARNING10OK

Check messages

WARNINGRd filesr-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

prepare_Rd: ./man/PathwaySpace-class.Rd:11: unexpected TEXT '[RGraphSpace]', expecting '{'
prepare_Rd: ./man/PathwaySpace-class.Rd:34: unexpected TEXT '[RGraphSpace]', expecting '{'
checkRd: (-1) PathwaySpace-class.Rd:11: Lost braces
    11 | \code{PathwaySpace} extends the \linkS4class[RGraphSpace]{GraphSpace} class with
       |                                                          ^
checkRd: (-1) PathwaySpace-class.Rd:34: Lost braces
    34 | \linkS4class[RGraphSpace]{GraphSpace},
       |                          ^

WARNINGwhether package can be installedr-oldrel-macos-arm64, r-oldrel-macos-x86_64, r-oldrel-windows-x86_64

r-oldrel-macos-arm64

Found the following significant warnings:
  Warning: /Volumes/Builds/packages/big-sur-arm64/results/4.5/PathwaySpace.Rcheck/00_pkg_src/PathwaySpace/man/PathwaySpace-class.Rd:11: unexpected TEXT '[RGraphSpace]', expecting '{'
  Warning: /Volumes/Builds/packages/big-sur-arm64/results/4.5/PathwaySpace.Rcheck/00_pkg_src/PathwaySpace/man/PathwaySpace-class.Rd:34: unexpected TEXT '[RGraphSpace]', expecting '{'
See ‘/Volumes/Builds/packages/big-sur-arm64/results/4.5/PathwaySpace.Rcheck/00install.out’ for details.

r-oldrel-macos-x86_64

Found the following significant warnings:
  Warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/PathwaySpace.Rcheck/00_pkg_src/PathwaySpace/man/PathwaySpace-class.Rd:11: unexpected TEXT '[RGraphSpace]', expecting '{'
  Warning: /Volumes/Builds/packages/big-sur-x86_64/results/4.5/PathwaySpace.Rcheck/00_pkg_src/PathwaySpace/man/PathwaySpace-class.Rd:34: unexpected TEXT '[RGraphSpace]', expecting '{'
See ‘/Volumes/Builds/packages/big-sur-x86_64/results/4.5/PathwaySpace.Rcheck/00install.out’ for details.

r-oldrel-windows-x86_64

Found the following significant warnings:
  Warning: D:/temp/2026_10_16_17_16_37_22563/RtmpEXgwpn/R.INSTALL50ef437f34d8/PathwaySpace/man/PathwaySpace-class.Rd:11: unexpected TEXT '[RGraphSpace]', expecting '{'
  Warning: D:/temp/2026_10_16_17_16_37_22563/RtmpEXgwpn/R.INSTALL50ef437f34d8/PathwaySpace/man/PathwaySpace-class.Rd:34: unexpected TEXT '[RGraphSpace]', expecting '{'
See 'd:/Rcompile/CRANpkg/local/4.5/PathwaySpace.Rcheck/00install.out' for details.

CRAN check page ↗

Slowest check: 4.3 min · r-release-macos-x86_64

Status changes

WARNING10 OK, 3 WARNING2026-09-08
ERROR9 OK, 3 WARNING, 1 ERROR2026-09-07
WARNING10 OK, 3 WARNING2026-06-27
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08

Show 1 earlier changeHide 1 earlier change

OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.5.2

READMENoVignettesYes · 1 · dynamicNEWSYes · mentions 1.5.2Citation fileYes · cites a publicationWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 29 (1 internal)includes a package overview page
Examples that run: 96%24 run in a plain check · 1 hold no code
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 14%

Vignettes (1)

PathwaySpace: signals along geodesic paths

How these are measured

Downloads

4K

CRAN downloads in the past year

Rank #6,309 · ~11/day · ~335/mo

Releases R versions

Daily download trend is not available in this view yet.

50030 days

1.3K90 days

4K1 year

Compare downloads with other packages →

Also on166 r2u5 autocran

How downloads are counted

Repository

sysbiolab/pathwayspace ↗Organization: sysbiolab

3Stars

2Forks

0Open issues

0Open PRs

0Releases

264Commits

2Commit identities

bioinformaticsbiological-networksgraphr

264 commits · Last activity 2026-09-30 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 223

Stars over time

2025-01-07 · 22026-08-07 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/sysbiolab/pathwayspace on 2026-10-18.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-09-30

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing PathwaySpace adds 48 packages (29 with compiled code, 49 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, igraph 4.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (7)

Mauro Castro

Maintainer since 0.99.4 (2024)

Sysbiolab Team

Author · added in 1.2.0

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

Releases (12)

Pick two releases to compare their code metrics.

1.5.2Latest
record
2026-10-02 · current release · diff ↗
1.5.1
record
2026-08-24 · diff ↗
1.5.0
record
2026-07-30 · diff ↗
1.4.1
record
2026-06-26 · diff ↗ ·
removed 1 export
signalDecay

added 1 export
annotation_pspace_signal
1.3.0
record
2026-05-23 · diff ↗
1.2.0
record
2026-04-25 · diff ↗ ·
added 1 export
getNearestNode
R
R 4.6.0 released · 2026-04-24
1.1.1
record
2026-02-28 · diff ↗ ·
added 1 export
pspace.pals
1.1.0
record
2025-11-07 · diff ↗ ·
added 1 export
polarDecay
1.0.2
record
2025-07-28 · diff ↗ ·
added 2 exports
signalAggregation, signalDecay
R
R 4.5.0 released · 2025-04-11
1.0.1
record
2025-04-08 · diff ↗
1.0.0
record
2024-11-12 · diff ↗
0.99.4
record
2024-09-03
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-03
Total releases: 12 / 2 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 4.5
Bundled data: 1.2 MB / 6 files
Download size: 3.0 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("PathwaySpace")

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

It points to 10.1016/j.xpro.2025.103681, 10.1016/j.ccell.2024.12.002.

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 1.5.2 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →