R Observatory: Metrics for permute version 0.9-10

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

permute

0.9-10Package record

Functions for Generating Restricted Permutations of Data

25packages dependsuggested by 7

1.2Mdownloads / year

90.5%test coverage

13/13flavors OK

Overview

About

Maintained by Gavin L. SimpsonCRAN page ↗GitHub ↗Issues ↗

A set of restricted permutation designs for freely exchangeable, line transects (time series), and spatial grid designs plus permutation of blocks (groups of samples) is provided. 'permute' also allows split-plot designs, in which the whole-plots or split-plots or both can be freely-exchangeable or one of the restricted designs. The 'permute' package is modelled after the permutation schemes of 'Canoco 3.1' (and later) by Cajo ter Braak.

Changes in 0.9-10

User visible changes

*permute* now depends on R versions >= 3.6.0

Bug fixes

numPerms() tries harder to avoid floating point issues when computing the number of permutations for the current design. #41

From NEWS.md in the release

Install

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

install.packages("permute", 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("gavinsimpson/permute")

Development version from gavinsimpson/permute. 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-permute

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-permute

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-permute

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: 2.4 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-15
ERROR13 OK, 1 ERROR2026-04-11
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9-10

READMEYes · 168 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.9-10Citation fileNo

Help pages: 12
Examples that run: 100%11 run in a plain check
Exported functions with examples: 100%
Documented parameters: 92%
Return-value docs: 100%
Help pages citing references: 42%

Vignettes (1)

Restricted permutations; using the permute package HTML

How these are measured

Downloads

1.2M

CRAN downloads in the past year

Rank #351 · ~3.3K/day · ~99.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

90K30 days

271.8K90 days

1.2M1 year

Compare downloads with other packages →

Also on16K r2u233 autocran580.5K conda_forge795 bioconda850 c2d4u

How downloads are counted

Repository

gavinsimpson/permute ↗Account: gavinsimpson

24Stars

4Forks

2Open issues

0Open PRs

8Releases

580Commits

4Commit identities

permutationrrestricted-permutationsr-packages

License file reads as GPL-2.0 · 580 commits · Last activity 2026-10-18 · Default branch at 0.9-10-7, ahead of CRAN 0.9-10 (checked 2026-10-11) · Discussions: 6 posts

Responsiveness

How these are sampled

PRs merged (all time): 80%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-07-09 · 242026-07-07 · 24

How these are measured

PracticesBeta

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

Checks run against github.com/gavinsimpson/permute on 2026-10-11.

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 (2)

Funding links: GitHub Sponsors, Buy Me a Coffee

The repository owner accepts GitHub Sponsors

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-09-05 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting

Show all practicesHide 3 practices

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing permute adds no packages beyond those that come with R.

Depends (1)

R >= 3.6.0

Imports (1)

stats

LinkingTo (0)

none

Suggests (7)

vegan testthatparallelknitr rmarkdown bookdown sessioninfo

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

25direct

322indirect

Depends 4 · Imports 21

Suggested by 7

Show all 32 packagesHide all 32 packages

Depends, Imports or LinkingTo, most downloaded first

vegan bipartite indicspecies iCAMP codyn permuco NST brainGraph LOCOM2 douconca SYNCSA text2map MiRKAT npcure readyomics LDM mixAR monoClust rankdist ProcMod TestNet randomizationInference pRF Storm RHC

Suggests, most downloaded first

BiodiversityR ecostats ggvegan MiscMetabar ggordiplots LorMe pctax

How these are counted

Code & Tests

Datasets

People & History

People (4)

Gavin L. Simpson

Douglas M. Bates

Contributor · added in 3.0.3

Jari Oksanen

Contributor · added in 3.0.3

R Core Team

Copyright holder · added in 3.0.3

Releases (17)

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
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
3.0.3Latest
record
2013-11-30 · current release · diff ↗ ·
removed 18 exports
`allPerms`, `Blocks`, `numPerms`, `check`, `permCheck`, `permControl`, `permute`, `shuffle`, `Within`, `shuffleFree`, `shuffleSeries`, `shuffleGrid`, `shuffleStrata`, `getBlocks`, `getWithin`, `getStrata`, `shuffleSet`, `permuplot`

added 50 exports
allPerms, Blocks, check, getBlocks, getWithin, getStrata, getType, getMirror, getConstant, getPlots, getRow, getCol, getDim, getNperm, getMaxperm, getMinperm, getComplete, getMake, getObserved, getAllperms, how, numPerms, permCheck, permControl, permute, Plots, setBlocks<-, setWithin<-, setStrata<-, setType<- and 20 more
R
R 3.0.0 released · 2013-04-03
R
R 2.15.0 released · 2012-03-30

Show 18 earlier eventsHide 18 earlier events

2.14.2
record
2012-02-09 · diff ↗
2.14.1
record
2011-11-01 · diff ↗
R
R 2.14.0 released · 2011-10-31
2.13.2
record
2011-09-09 · diff ↗
0.9-10
record
2026-02-06 · diff ↗
0.9-8
record
2025-06-25 · diff ↗
0.9-7
record
2022-01-27 · diff ↗
0.9-5
record
2019-03-12 · diff ↗
0.9-4
record
2016-09-09 · diff ↗ ·
added 3 exports
as.allPerms, getControl, getHow
0.9-0
record
2016-01-24 · diff ↗ ·
removed 2 exports
permCheck, permControl
0.8-4
record
2015-05-19 · diff ↗
0.8-3
record
2014-01-29 · diff ↗
0.8-0
record
2013-12-01 · diff ↗
0.7-0
record
2012-04-05 · diff ↗
0.6-3
record
2011-11-02 · diff ↗
0.6-2
record
2011-09-28 · diff ↗
0.6-1
record
2011-09-08
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-09-08
Total releases: 17 / 15 yrs
License: GPL-2 OSI
Copyright: see file COPYRIGHTS
Minimum R: ≥ 3.6.0
Bundled data: 0.2 KB / 1 file
Download size: 118 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("permute")

Format

Simpson, G. L., R Core Team, Bates, D. M., & Oksanen, J. (2026). permute: Functions for Generating Restricted Permutations of Data (Version 0.9-10) [Computer software]. https://doi.org/10.32614/CRAN.package.permute

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 permute version 0.9-10 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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