R Observatory: Metrics for VertexWiseR version 1.5.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

VertexWiseR needs freesurferformats, which CRAN will archive unless its check problems are fixed by Oct 20.

VertexWiseR

1.5.5Package record

Simplified Vertex-Wise Analyses of Whole-Brain and Subcortical Surface

0packages depend

4.7Kdownloads / year

–test coverage

12/13flavors OK

Overview

About

Maintained by Charly BillaudCRAN page ↗Website ↗

Provides functions to run statistical analyses on surface-based neuroimaging data, computing measures including cortical thickness and surface area of the whole-brain and of the hippocampi. It can make use of 'FreeSurfer', 'fMRIprep', 'XCP-D', 'HCP' and 'CAT12' preprocessed datasets, 'HippUnfold' hippocampal outputs and 'SubCortexMesh' subcortical outputs for a given sample by restructuring the data values into a single file. The single file can then be used by the package for analyses independently from its base dataset and without need for its access.

Changes in 1.5.5

NEW FEATURES

New decode_surf_data() function now uses internal R data and code to do the decoding, reproducing NiMARE's ROIAssociationDecoder without calling the python module. It was tested on Example 1, yielding identical results for less than half the original duration.
SCMvextract() is now much faster with more preloaded tables/lists and a different way of extracting the scalars
Silent parameter and end messaging added to HIPvextract().

FIXES

Extraction functions now fail prematurely if the filename argument given has a non-existent path, instead of failing after the full matrix is built.

From NEWS.md in the release

Install

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

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

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

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-vertexwiser

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-VertexWiseR

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-VertexWiseR

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

1ERROR12OK

Check messages

ERRORexamplesr-patched-linux-x86_64

Running examples in ‘VertexWiseR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RFT_vertex_analysis
> ### Title: Vertex-wise analysis with random field theory cluster correction
> ### Aliases: RFT_vertex_analysis
> 
> ### ** Examples
> 
> demodata = readRDS(system.file('demo_data/SPRENG_behdata_site1.rds', 
+ package = 'VertexWiseR'))[1:100,]
> CTv = readRDS(file = url(paste0("https://github.com",
+ "/CogBrainHealthLab/VertexWiseR/blob/main/inst/demo_data/",
+ "SPRENG_CTv_site1.rds?raw=TRUE")))[1:100,] 
Warning in readRDS(file = url(paste0("https://github.com", "/CogBrainHealthLab/VertexWiseR/blob/main/inst/demo_data/",  :
  cannot open URL 'https://github.com/CogBrainHealthLab/VertexWiseR/blob/main/inst/demo_data/SPRENG_CTv_site1.rds?raw=TRUE': HTTP status was '503 Service Unavailable'
Error in readRDS(file = url(paste0("https://github.com", "/CogBrainHealthLab/VertexWiseR/blob/main/inst/demo_data/",  : 
  cannot open the connection to 'https://github.com/CogBrainHealthLab/VertexWiseR/blob/main/inst/demo_data/SPRENG_CTv_site1.rds?raw=TRUE'
Execution halted

CRAN check page ↗

Slowest check: 5.4 min · r-release-macos-x86_64

Status changes

ERROR12 OK, 1 ERRORNow
ERROR10 OK, 3 ERROR2026-10-15
OK13 OK2026-10-14
ERROR12 OK, 1 ERROR2026-10-13
OK13 OK2026-10-04
ERROR12 OK, 1 ERROR2026-10-03

Show 15 earlier changesHide 15 earlier changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-08
ERROR12 OK, 1 ERROR2026-07-07
OK13 OK2026-06-27
ERROR11 OK, 2 ERROR2026-06-21
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-30
ERROR12 OK, 1 ERROR2026-05-29
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.5.5

READMEYes · 1,680 wordsVignettesYes · 12 · dynamicNEWSYes · 100% structured · mentions 1.5.5Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 36
Examples that run: 100%25 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 96%
Help pages citing references: 0%

Vignettes (12)

Show 2 moreHide 2 vignettes

Python troubleshooting HTML
Python troubleshooting HTML

How these are measured

Downloads

4.7K

CRAN downloads in the past year

Rank #6,189 · ~13/day · ~388/mo

Releases R versions

Daily download trend is not available in this view yet.

59030 days

1.3K90 days

4.7K1 year

Compare downloads with other packages →

Also on203 r2u8 autocran

How downloads are counted

Repository

cogbrainhealthlab/vertexwiser ↗Account: CogBrainHealthLab

12Stars

2Forks

2Open issues

0Open PRs

0Releases

1,387Commits

3Commit identities

License file reads as GPL-3.0 · 1,387 commits · Last activity 2026-10-16 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 18
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-23 · 92026-09-16 · 12

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/cogbrainhealthlab/vertexwiser on 2026-10-11.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-09-25

pkgdown site last built 2026-09-24, before release 1.5.5 (2026-10-16)

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing VertexWiseR adds 82 packages (40 with compiled code, 75 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.0.0

Imports (20)

doParallel doSNOW foreach freesurferformats fs giftigrDevicesgridigraphmethodsparallelplotly png rappdirs RColorBrewer reticulatestatsstringrtoolsutils

LinkingTo (0)

none

Suggests (1)

R.rsp

Enhances (0)

none

Dependencies facing archival

CRAN will archive these unless their check problems are fixed by the date shown. This package needs each one to install.

freesurferformatsfix by Oct 20

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Charly Billaud

Author, Maintainer since 1.0.0 (2024)

Junhong Yu

Author

Releases (20)

Pick two releases to compare their code metrics.

1.5.5Latest
record
2026-10-16 · current release · diff ↗
1.5.4
record
2026-09-16 · diff ↗
1.5.3
record
2026-09-03 · diff ↗
1.5.2
record
2026-06-25 · diff ↗ ·
added 2 exports
fs5_to_fslr, fslr_to_fs5
R
R 4.6.0 released · 2026-04-24
1.5.1
record
2026-04-08 · diff ↗ ·
removed 1 export
ASEGvextract

added 1 export
SCMvextract
1.5.0
record
2026-03-12 · diff ↗ ·
added 1 export
ASEGvextract
1.4.5
record
2025-12-15 · diff ↗
1.4.4
record
2025-12-04 · diff ↗
1.4.3
record
2025-10-21 · diff ↗
1.4.2
record
2025-10-01 · diff ↗
1.4.1
record
2025-08-19 · diff ↗
1.4.0
record
2025-07-30 · diff ↗ ·
added 3 exports
DTSERIESvextract, getting_started, plot_overlay_surf
1.3.2
record
2025-06-11 · diff ↗
1.3.1
record
2025-04-14 · diff ↗
R
R 4.5.0 released · 2025-04-11

Show 7 earlier eventsHide 7 earlier events

1.3.0
record
2025-03-18 · diff ↗
1.2.1
record
2025-03-10 · diff ↗
1.2.0
record
2024-12-12 · diff ↗ ·
added 1 export
CAT12vextract
1.1.0
record
2024-10-10 · diff ↗ ·
added 1 export
plot_surf3d
1.0.1
record
2024-09-06 · diff ↗ ·
removed 4 exports
TFCE.threshold, TFCE.vertex_analysis, TFCE.vertex_analysis.mixed, vertex_analysis

added 6 exports
FSLRvextract, RFT_vertex_analysis, TFCE_threshold, TFCE_vertex_analysis, TFCE_vertex_analysis_mixed, fs_stats
1.0.0
record
2024-06-13
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-13
Total releases: 20 / 2 yrs
License: GPL-3 OSI
Minimum R: ≥ 4.0.0
Bundled data: 885 KB / 8 files
Download size: 2.4 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("VertexWiseR")

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

It points to 10.1162/imag_a_00372.

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 VertexWiseR version 1.5.5 [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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