R Observatory: Metrics for nat version 1.8.26

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nat

1.8.26

NeuroAnatomy Toolbox for Analysis of 3D Image Data

5packages depend

11.8Kdownloads / year

77.3%test coverage

13/13checks pass

Overview

About

Maintained by Gregory JefferisFirst published 2014-02-0427 releasesCRAN page ↗GitHub ↗

NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).

Install

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

install.packages("nat", 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("natverse/nat")

Development version from natverse/nat. 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-nat

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-nat

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-nat

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

Health

CRAN checks

13OK

Slowest check: 4.8 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 2.05

77.3%

Coverage · measured lines

100%

Documentation · exports

9

Dependencies · direct

Check history

OK2026-08-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-07-16
11 OK · 2 NOTE · 0 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

READMEYes · 331 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 74%
Documented parameters: 95%
Return-value docs: 67%
References docs: 6%

Downloads

11.8K

CRAN downloads in the past year

Rank #6,173 · ~32/day · ~980/mo

Releases R versions

Daily download trend is not available in this view yet.

43030 days

1.3K90 days

11.8K1 year

Compare downloads with other packages →

Also on165 r2u19 autocran

Repository

GitHub ↗ natverse/nat

78Stars

27Forks

48Open issues

9Open PRs

26Releases

2,880Commits

12Contributors

rneuroanatomy-toolboxcranneuronneuroscience3dvisualisationimage-analysis

2,880 commits · Last activity 2026-07-30 · +1.3% stars, 30d

Stars over time

2025-08-05 · 692026-08-06 · 78

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/natverse/nat on 2026-08-09.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (2)

R >= 2.15.1rgl

Imports (8)

nabor igraphmethodsfilehash digest nat.utils plyr yaml

LinkingTo (0)

none

Suggests (10)

Rvcg testthat httr XML knitr rmarkdown markdownMASSalphashape3d webshot2

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

5direct

0indirect

nat.nblast nat.templatebrains BoneDensityMapping RIA cmtkr

Code & Tests

People & History

People (3)

Maintainer (1)

Gregory Jefferis

Author, Maintainer · added in 1.8.7

Authors (2)

Gregory Jefferis

Author, Maintainer · added in 1.8.7

James Manton

Author · added in 1.4.10

Contributors (1)

Dominik Krzeminski

Contributor · added in 1.8.19

Listed in earlier versions (2)

Greg Jefferis with contributions from Ashley Manton

no longer listed · 2.15.3 to 1.4.6

Greg Jefferis

no longer listed · 1.4.10 to 1.8.4

Package Timeline

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

1.8.26Latest
2026-08-04 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.8.25
2025-08-18 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.8.24
2024-02-05 · diff ↗
1.8.23
2023-08-25 · diff ↗
1.8.22
2023-06-07 · diff ↗
unarchivedReturned to CRAN
2023-06-07
archivedRemoved from CRAN
2023-06-05
requires archived package 'nat.utils'
R
R 4.3.0 released · 2023-04-21
1.8.21
2023-01-29 · diff ↗
R
R 4.2.0 released · 2022-04-22
1.8.19
2022-04-06 · diff ↗
1.8.18
2021-09-06 · diff ↗
1.8.17
2021-09-03 · diff ↗

Show 28 earlier events

R
R 4.1.0 released · 2021-05-18
1.8.16
2020-09-22 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.8.14
2020-02-07 · diff ↗
1.8.13
2019-08-22 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.8.11
2017-11-12 · diff ↗
1.8.9
2017-05-08 · diff ↗
R
R 3.4.0 released · 2017-04-21
1.8.7
2016-11-10 · diff ↗
1.8.4
2016-07-18 · diff ↗
R
R 3.3.0 released · 2016-05-03
1.8.1
2015-12-30 · diff ↗
1.7.0
2015-07-01 · diff ↗
1.6.6
2015-05-28 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.6.4
2015-02-10 · diff ↗
1.5.12
2014-08-21 · diff ↗
1.4.10
2014-04-30 · diff ↗
R
R 3.1.0 released · 2014-04-10
1.4.6
2014-03-30 · diff ↗
1.4.5
2014-03-28 · diff ↗
1.0.1
2014-02-07 · diff ↗
1.0
2014-02-04 · diff ↗
R
R 3.0.0 released · 2013-04-03
2.15.3
2013-02-06
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2014-02-04
Total releases: 27 / 12 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.15.1
Bundled data: 690 KB / 3 files
Download size: 2.2 MB for 1.8.25
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("nat")

Format

Jefferis, G., Krzeminski, D., & Manton, J. (2026). nat: NeuroAnatomy Toolbox for Analysis of 3D Image Data (Version 1.8.26) [Computer software]. https://doi.org/10.32614/CRAN.package.nat

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 nat version 1.8.26 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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