R Observatory: Metrics for neurobase version 1.34.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

neurobase

1.34.0Package record

'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects

6packages depend

10.8Kdownloads / year

13.1%test coverage

8/13flavors OK

Overview

About

Maintained by John MuschelliCRAN page ↗GitHub ↗Issues ↗

Base package for 'Neuroconductor', which includes many helper functions that interact with objects of class 'nifti', implemented by package 'oro.nifti', for reading/writing and also other manipulation functions.

Changes in 1.34.0

Added ... to plots.
Fixed xaxt and yaxt.

From NEWS.md in the release

Install

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

install.packages("neurobase", 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("muschellij2/neurobase")

Development version from muschellij2/neurobase. 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-neurobase

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-neurobase

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-neurobase

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

5NOTE8OK

Check messages

NOTER code for possible problemsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

Found calls to structure() using deprecated special names:
  neurobase/tests/testthat/test-cog.R (.Names: 1)
'.Names' should be changed to 'names'.

CRAN check page ↗

Slowest check: 24.2 min · r-release-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-07-16
OK14 OK2026-04-24
ERROR13 OK, 1 ERROR2026-04-23
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.34.0

READMEYes · 48 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.34.0Citation fileNo

Help pages: 75
Examples that run: 96%55 run in a plain check · 2 never run
Exported functions with examples: 74%
Documented parameters: 100%
Return-value docs: 91%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

10.8K

CRAN downloads in the past year

Rank #4,173 · ~30/day · ~904/mo

Releases R versions

Daily download trend is not available in this view yet.

78630 days

2.1K90 days

10.8K1 year

Compare downloads with other packages →

Also on149 r2u5 autocran170 c2d4u

How downloads are counted

Repository

muschellij2/neurobase ↗Account: muschellij2

7Stars

3Forks

2Open issues

0Open PRs

15Releases

271Commits

1Commit identities

271 commits · Last activity 2025-10-16 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 71
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-08-24 · 62026-07-07 · 7

How these are measured

PracticesBeta

10 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/muschellij2/neurobase on 2026-10-22.

Continuous integration (4)

GitHub ActionsR CMD check workflowTravis CI (config file)AppVeyor

The R CMD check workflow runs on Linux

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-10-16

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing neurobase adds 9 packages (4 with compiled code, 9.3 MB of source tarballs). Heaviest: oro.nifti 5.0 MB, Rcpp 1.8 MB, RNifti 1.5 MB.

Depends (2)

R >= 3.2.0oro.nifti

Imports (8)

methodsabind matrixStats R.utilsgraphicsgrDevicesstatsRNifti

LinkingTo (0)

none

Suggests (9)

testthat ggplot2 knitr rmarkdown dplyr reshape2 httr covr brainR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

6direct

0indirect

Depends 1 · Imports 5

Depends, Imports or LinkingTo, most downloaded first

fslr freesurfer WhiteStripe BSPBSS CICA MRIreduce

How these are counted

Code & Tests

People & History

People (1)

John Muschelli

Author, Maintainer since 1.1.1.1 (2016)

Releases (14)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.34.0Latest
record
2025-10-17 · current release · diff ↗
1.33.0
record
2025-07-23 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.32.4
record
2024-05-09 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.32.3
record
2022-10-23 · diff ↗
unarchivedReturned to CRAN
2022-08-24
1.32.2
record
2022-08-24 · diff ↗
R
R 4.2.0 released · 2022-04-22
archivedRemoved from CRAN
2022-04-18
'coercion to logical' errors were not corrected in time See https://www.stats.ox.ac.uk/pub/bdr/LENGTH1/
R
R 4.1.0 released · 2021-05-18
1.32.1
record
2021-04-07 · diff ↗ ·
added 1 export
read_rpi
1.32.0
record
2021-03-31 · diff ↗ ·
added 7 exports
is_rpi_oriented, orient_rpi, orient_rpi_file, replaceEmptyImageDimensions, replace_empty_dim, reverse_orient_rpi, reverse_orient_rpi_file
R
R 4.0.0 released · 2020-04-24

Show 11 earlier eventsHide 11 earlier events

1.29.0
record
2020-01-14 · diff ↗ ·
added 2 exports
multi_overlay_diff, random_nifti
1.27.11
record
2019-09-10 · diff ↗ ·
added 3 exports
fast_dice, fast_dice_tab, multi_overlay_center
R
R 3.6.0 released · 2019-04-26
1.27.6
record
2018-11-20 · diff ↗
R
R 3.5.0 released · 2018-04-23
1.26.1
record
2018-02-01 · diff ↗ ·
added 17 exports
check_nifti_header, dicer, emptyImageDimensionsMask, empty_dim_mask, ensure_array, flip_img, img_color_df, img_colour_df, img_list_to_ts, img_ts_to_df, img_ts_to_list, img_ts_to_matrix, minmax_img, separate_img, slice_colour_df, subset_dti, write_nifti
R
R 3.4.0 released · 2017-04-21
1.13.2
record
2017-03-03 · diff ↗ ·
added 2 exports
remap_filename, replace_outside_surface
1.9.2
record
2017-01-06 · diff ↗ ·
added 6 exports
mask_vals<-, fast_readnii, images2matrix, img_indices, mask_vals, randomize_mask
1.1.1.1
record
2016-09-27
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-09-27
Total releases: 14 / 10 yrs
License: GPL-2 OSI
Minimum R: ≥ 3.2.0
Download size: 1.4 MB

Appears in task views

Medical Image Analysis

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("neurobase")

Format

Muschelli, J. (2025). neurobase: 'Neuroconductor' Base Package with Helper Functions for 'nifti' Objects (Version 1.34.0) [Computer software]. https://doi.org/10.32614/CRAN.package.neurobase

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 neurobase version 1.34.0 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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