R Observatory: Metrics for nat version 1.8.26

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

nat

1.8.26Package record

NeuroAnatomy Toolbox for Analysis of 3D Image Data

3packages dependsuggested by 2

7.5Kdownloads / year

77.3%test coverage

13/13flavors OK

Overview

About

Maintained by Gregory JefferisCRAN page ↗GitHub ↗Website ↗Issues ↗

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).

Changes in 1.8.26

replace deprecated structure() special names (.Names/.Dim/.Dimnames) flagged by CRAN

From NEWS in the release

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. 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-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). 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: 4.4 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-12
NOTE11 OK, 2 NOTE2026-07-16
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.8.26

READMEYes · 331 wordsVignettesYes · 2 · dynamicNEWSYes · 33% structured · mentions 1.8.26Citation fileYesWebsiteYes · pkgdown

Help pages: 144includes a package overview page
Examples that run: 67%55 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran) · 22 never run
Exported functions with examples: 50%
Documented parameters: 95%
Return-value docs: 67%
Help pages citing references: 6%

Vignettes (2)

Installation Details HTML
Introduction to neurons and neuronlists HTML

How these are measured

Downloads

7.5K

CRAN downloads in the past year

Rank #4,472 · ~21/day · ~628/mo

Releases R versions

Daily download trend is not available in this view yet.

69330 days

1.9K90 days

7.5K1 year

Compare downloads with other packages →

Also on294 r2u2 autocran

How downloads are counted

Repository

natverse/nat ↗Organization: natverse

79Stars

28Forks

48Open issues

9Open PRs

26Releases

2,891Commits

12Commit identities

rneuroanatomy-toolboxcranneuronneuroscience3dvisualisationimage-analysis

2,891 commits · Last activity 2026-09-29 · 0% stars, 30d · Default branch at 1.11.1, ahead of CRAN 1.8.26 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 83%
Median days to close, 50 most recently updated closed issues: 9
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-10-11 · 732026-09-13 · 79

How these are measured

PracticesBeta

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

Checks run against github.com/natverse/nat on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (1)

Code of conduct

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-09-29

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-07-30
Named in .Rbuildignore: .claude
Pull request it wrote: opened by a project member
Commits: at least 2 crediting it in the message

Models named in its commits

Claude Opus 4.82 commits · Sep 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Installing nat adds 42 packages (26 with compiled code, 47 MB of source tarballs). Heaviest: BH 14 MB, bslib 5.6 MB, igraph 4.8 MB.

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

3direct

0indirect

Depends 2 · Imports 1

Suggested by 2

Depends, Imports or LinkingTo, most downloaded first

BoneDensityMapping nat.nblast nat.templatebrains

Suggests, most downloaded first

RIA cmtkr

How these are counted

Code & Tests

Datasets

People & History

People (3)

Gregory Jefferis

Author, Maintainer · added in 1.8.7

James Manton

Author · added in 1.4.10

Dominik Krzeminski

Contributor · added in 1.8.19

Maintainer since 1.0 (2014)

Listed in earlier versions (2)

Greg Jefferis

no longer listed · 2.15.3 to 1.8.4

Ashley Manton

no longer listed · 2.15.3 to 1.4.6

Releases (27)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
R
R 3.0.0 released · 2013-04-03

Show 28 earlier eventsHide 28 earlier events

2.15.3Latest
record
2013-02-06 · current release · diff ↗ ·
added 49 exports
xyzmatrix<-, affmat2cmtkparams, amiratype, as.cmtkreg, as.dotprops, as.neuron, as.neuronlist, as.neuronlistfh, as.ngraph, as.seglist, branchpoints, cmtk.bindir, cmtk.dof2mat, cmtk.mat2dof, cmtklandmarks, cmtkparams2affmat, cmtkreg, cmtkreglist, dotprops, endpoints, is.amiramesh, is.cmtkreg, is.dotprops, is.neuron, is.neuronlist, mirror, neuron, neuronlist, nlapply, read.amiralandmarks and 19 more
1.8.26
record
2026-08-04 · diff ↗
1.8.25
record
2025-08-18 · diff ↗
1.8.24
record
2024-02-05 · diff ↗
1.8.23
record
2023-08-25 · diff ↗
1.8.22
record
2023-06-07 · diff ↗
1.8.21
record
2023-01-29 · diff ↗
1.8.19
record
2022-04-06 · diff ↗
1.8.18
record
2021-09-06 · diff ↗
1.8.17
record
2021-09-03 · diff ↗
1.8.16
record
2020-09-22 · diff ↗
1.8.14
record
2020-02-07 · diff ↗
1.8.13
record
2019-08-22 · diff ↗ ·
added 1 export
nview3d
1.8.11
record
2017-11-12 · diff ↗
1.8.9
record
2017-05-08 · diff ↗ ·
removed 1 export
as.mesh3d

added 2 exports
as.hxsurf, nvertices
1.8.7
record
2016-11-10 · diff ↗ ·
added 4 exports
cmtk.system2, invert_reglist, smooth_neuron, write.vtk
1.8.4
record
2016-07-18 · diff ↗ ·
added 5 exports
mask, prune_edges, read.ngraph.swc, reglist, simplify_reglist
1.8.1
record
2015-12-30 · diff ↗ ·
added 4 exports
prune_strahler, prune_vertices, segmentgraph, strahler_order
1.7.0
record
2015-07-01 · diff ↗ ·
added 3 exports
data.frame<-, write.nrrd.header, write.nrrd.header.for.file
1.6.6
record
2015-05-28 · diff ↗
1.6.4
record
2015-02-10 · diff ↗ ·
removed 5 exports
cmtklandmarks, read.amiralandmarks, read.cmtklandmarks, write.amiralandmarks, write.cmtklandmarks

added 15 exports
cmtk.extract_affine, find.soma, intersect, is.fijitraces, is.swc, nlscan, normalise_swc, read.landmarks, read.morphml, read.neuron.fiji, read.neuron.neuroml, setdiff, union, write.landmarks, xformimage
1.5.12
record
2014-08-21 · diff ↗ ·
added 10 exports
as.mesh3d, cmtk.statistics, cmtk.version, is.vaa3draw, npop3d, pointsinside, potential_synapses, read.vaa3draw, resample, seglengths
1.4.10
record
2014-04-30 · diff ↗ ·
added 9 exports
as.im3d, coord2ind, ind2coord, materials, ngraph, nmapply, prune, spine, sub2ind
1.4.6
record
2014-03-30 · diff ↗
1.4.5
record
2014-03-28 · diff ↗ ·
added 39 exports
boundingbox<-, boundingbox, clampmax, cmtk.call, cmtk.reformatx, cmtk.targetvolume, fileformats, find.neuron, flip, getformatreader, getformatwriter, ijkpos, im3d, imexpand.grid, imscalebar, imslice, is.nrrd, ndigest, neuronlistfh, nopen3d, nrrd.voxdims, origin, projection, read.im3d, read.nrrd, read.nrrd.header, registerformat, remotesync, threshold, unmask and 9 more
1.0.1
record
2014-02-07 · diff ↗
1.0
record
2014-02-04
R
R 2.15.0 released · 2012-03-30

Package metadata

First published: 2013-02-06
Total releases: 27 / 13 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.15.1
Bundled data: 690 KB / 3 files
Download size: 2.2 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("nat")

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

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 v2026-10-21. 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.

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