R Observatory: Metrics for fMRIscrub version 0.15.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

fMRIscrub

0.15.0Package record

Scrubbing and Other Data Cleaning Routines for fMRI

1packages depend

5.1Kdownloads / year

69.1%test coverage

13/13flavors OK

Overview

About

Maintained by Amanda MejiaCRAN page ↗GitHub ↗Issues ↗

Data-driven fMRI denoising with projection scrubbing (Pham et al (2022) doi:10.1016/j.neuroimage.2023.119972). Also includes routines for DVARS (Derivatives VARianceS) (Afyouni and Nichols (2018) doi:10.1016/j.neuroimage.2017.12.098), motion scrubbing (Power et al (2012) doi:10.1016/j.neuroimage.2011.10.018), aCompCor (anatomical Components Correction) (Muschelli et al (2014) doi:10.1016/j.neuroimage.2014.03.028), detrending, and nuisance regression. Projection scrubbing is also applicable to other outlier detection tasks involving high-dimensional data.

Changes in 0.15.0

Robust outlier detection methods have been moved to the rrobot R package.
TR_for_resp_filt argument to modified FD added

From NEWS.md in the release

Install

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

install.packages("fMRIscrub", 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("mandymejia/fMRIscrub")

Development version from mandymejia/fMRIscrub. 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-fmriscrub

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-fMRIscrub

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-fMRIscrub

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: 3.6 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.15.0

READMEYes · 306 wordsVignettes· In the repository, left out of the releaseNEWSYes · 100% structured · mentions 0.15.0Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 30 (11 internal)includes a package overview page
Examples that run: 100%1 run in a plain check
Exported functions with examples: 10%
Documented parameters: 89%
Return-value docs: 100%
Help pages citing references: 0% with a bibliography file

How these are measured

Downloads

5.1K

CRAN downloads in the past year

Rank #6,572 · ~14/day · ~429/mo

Releases R versions

Daily download trend is not available in this view yet.

53130 days

1.3K90 days

5.1K1 year

Compare downloads with other packages →

Also on105 r2u6 autocran

How downloads are counted

Repository

mandymejia/fmriscrub ↗Account: mandymejiaFork of muschellij2/clever

6Stars

7Forks

0Open PRs

2Releases

522Commits

20Commit identities

522 commits · Last activity 2025-03-28 · 0% stars, 30d · The default branch showed an older version (0.13.0) than CRAN on 2026-10-21

Responsiveness

How these are sampled

PRs merged (all time): 72%
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

2025-07-22 · 52026-07-07 · 6

How these are measured

PracticesBeta

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

Checks run against github.com/mandymejia/fmriscrub on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Docs source (1)

README.Rmd

Coverage (1)

Coverage reporting (Codecov)

Reproducibility and dev environment (1)

data-raw/

Show all practicesHide 2 practices

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing fMRIscrub adds 7 packages (4 with compiled code, 2.9 MB of source tarballs). Heaviest: robustbase 2.2 MB, e1071 311 KB, matrixStats 207 KB.

Depends (1)

R >= 3.5.0

Imports (7)

MASSe1071 fMRItools pesel robustbasestatsutils

LinkingTo (0)

none

Suggests (13)

corpcor cowplot ciftiTools gifti gsignal knitr rmarkdown RNifti ggplot2 fastICA oro.nifti testthat (>= 3.0.0)covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

templateICAr

How these are counted

Code & Tests

Datasets

People & History

People (5)

Amanda Mejia

Author, Maintainer since 0.8.2 (2021)

Author

Author

Contributor

Contributor · added in 0.13.0

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.15.0Latest
record
2026-03-19 · current release · diff ↗ ·
removed 3 exports
SHASH_out, SHASH_to_normal, robdist

added 3 exports
IDvols, IDvols_xifti, flags2spikes
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.14.5
record
2023-10-25 · diff ↗
0.14.4
record
2023-10-23 · diff ↗
0.13.0
record
2023-06-07 · diff ↗ ·
added 4 exports
SHASH_out, SHASH_to_normal, flags_to_nuis_spikes, robdist
R
R 4.3.0 released · 2023-04-21
0.12.1
record
2023-01-25 · diff ↗ ·
removed 13 exports
CompCor, CompCor_HCP, bandstop_filter, carpetplot, carpetplot_stack, dct_bases, dct_convert, detrend, erode_vol, fsl_bptf, nuisance_regression, pct_sig, unmask_vol
unarchivedReturned to CRAN
2022-07-08
0.11.2
record
2022-07-08 · diff ↗ ·
removed 2 exports
fusedPCA, rob_scale

added 5 exports
bandstop_filter, carpetplot, carpetplot_stack, detrend, rob_stabilize
archivedRemoved from CRAN
2022-05-02
check problems were not corrected in time
R
R 4.2.0 released · 2022-04-22
unarchivedReturned to CRAN
2021-09-20
0.8.6
record
2021-09-20 · diff ↗ ·
added 1 export
dct_convert
archivedRemoved from CRAN
2021-09-03
check problems were not corrected in time

Show 2 earlier eventsHide 2 earlier events

0.8.2
record
2021-08-20
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-08-20
Total releases: 8 / 5 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 1.2 MB / 2 files
Download size: 1.3 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("fMRIscrub")

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 fMRIscrub version 0.15.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, 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 →