R Observatory: Metrics for vegan version 2.7-6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

vegan

2.7-6Package record

Community Ecology Package

175packages dependsuggested by 65

1.6Mdownloads / year

27.4%test coverage

8/13flavors OK

Overview

About

Maintained by Jari OksanenCRAN page ↗GitHub ↗Website ↗Issues ↗

Ordination methods, diversity analysis and other functions for community and vegetation ecologists.

Changes in 2.7-6

New Features

Implemented _weighted_ spatial median and used them in ordispider(..., spiders = "median"). These will be automatically used in weighted ordinations (correspondence analysis _etc_) where a warning was issued on ignored weights earlier.
text.decorana is now based on ordiplot and knows arguments such as optimize to improve text location and bg to plot text on opaque background. These features were already available in plot.decorana and text used in pipe.

Bug Fixes

ordisurf always plotted contours, although documented behaviour was to skip contours with select=TRUE (default) when effective degrees of freedom are nearly zero. Polynomial models invoked by setting knots 0, 1 or 2 failed in plot.ordisurf. The name of the variable used as the title of the graph was lost with formula interface.

Show all changes in 2.7-6Hide the rest of the changes in 2.7-6

make.cepnames could make duplicated names. Now makes unique names and warns users on the naming decisions. Issue #787.
summary.isomap failed. Bug was introduced in vegan 2.6-6. PR #789.
tabasco failed with dendrogram() input, see issue #792. In addition, tabasco uses more consistent policy. Argument use takes precedence, and explicit site ordering (site.ind) together with use is an error. On the other hand, sp.ind takes precedence over default species ordering of use. Species dendrogram can be added to all use alternatives.
Fix CRAN check NOTE on deprecated features in very old code (clamtest, showvarparts).

From NEWS.md in the release

Install

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

install.packages("vegan", 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("vegandevs/vegan")

Development version from vegandevs/vegan. 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-vegan

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-vegan

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-vegan

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

NOTEdependencies in R coder-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

r-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

Base package in Suggests/Enhances imported in NAMESPACE:
  ‘parallel’

r-devel-windows-x86_64

Base package in Suggests/Enhances imported in NAMESPACE:
  'parallel'

CRAN check page ↗

Slowest check: 8.5 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-09-12
OK13 OK2026-09-05
NOTE9 OK, 4 NOTE2026-07-24
ERROR9 OK, 3 NOTE, 1 ERROR2026-07-23
NOTE11 OK, 2 NOTE2026-07-16

Show 3 earlier changesHide 3 earlier changes

OK13 OK2026-06-08
NOTE12 OK, 1 NOTE2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.7-6

README· In the repository, left out of the releaseVignettesYes · 5 · dynamicNEWSYes · 67% structured · mentions 2.7-6Citation fileNoWebsiteYes · pkgdown

Help pages: 113 (2 internal)includes a package overview page
Examples that run: 99%105 run in a plain check · 1 never run
Exported functions with examples: 95%
Documented parameters: 87%
Return-value docs: 92%
Help pages citing references: 71%

Vignettes (5)

How these are measured

Downloads

1.6M

CRAN downloads in the past year

Rank #302 · ~4.4K/day · ~133.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

129.5K30 days

367K90 days

1.6M1 year

Compare downloads with other packages →

Also on16.5K r2u154 autocran584.4K conda_forge35.8K bioconda934 c2d4u

How downloads are counted

Repository

vegandevs/vegan ↗Organization: vegandevs

549Stars

113Forks

37Open issues

1Open PRs

28Releases

6,405Commits

43Commit identities

ecological-modellingecologyordinationr

License file reads as GPL-2.0 · 6,405 commits · Last activity 2026-10-14 · +1.1% stars, 30d · Default branch at 2.8-0, ahead of CRAN 2.7-6 (checked 2026-10-11) · Discussions: 130 posts

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2025-10-10 · 4982026-10-16 · 549

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/vegandevs/vegan 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

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-10-11 · The repository has a site deploy workflow

pkgdown site last built 2024-05-20, before release 2.7-6 (2026-08-31)

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing vegan adds 1 package (0 with compiled code, 118 KB of source tarballs). Heaviest: permute 118 KB.

Depends (2)

R >= 4.1.0permute

Imports (4)

MASSclusterlatticemgcv

LinkingTo (0)

none

Suggests (3)

parallelknitr markdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

175direct

148indirect

Depends 24 · Imports 151

Suggested by 65

Show the 48 most downloaded dependentsHide the 48 most downloaded dependents

Depends, Imports or LinkingTo, most downloaded first

and 127 more dependents and 65 packages that suggest it on CRAN ↗

How these are counted

Code & Tests

Datasets

People & History

People (37)

Jari Oksanen

Author, Maintainer since 1.0-1 (2001)

Michael Bedward

Author · added in 2.6-2

F. Guillaume Blanchet

Author · added in 1.17-0

Ben Bolker

Author · added in 2.6-2

Daniel Borcard

Author · added in 2.6-2

Gustavo Carvalho

Author · added in 2.6-2

Miquel De Caceres

Author · added in 2.6-2

Sebastien Durand

Author · added in 2.6-2

Heloisa Beatriz Antoniazi Evangelista

Author · added in 2.6-2

Geoffrey Hannigan

Author · added in 2.6-2

Mark O. Hill

Author · added in 2.6-2

Roeland Kindt

Author · added in 1.6-8

Leo Lahti

Author · added in 2.6-2

Pierre Legendre

Author · added in 1.8-1

Cameron Martino

Author · added in 2.7-1

Peter R. Minchin

Author · added in 2.13.2

R.B. O'Hara

Author · added in 2.6-2

Marie-Helene Ouellette

Author · added in 2.6-2

Eduardo Ribeiro Cunha

Author · added in 2.6-2

Gavin L. Simpson

Author · added in 1.11-0

Tyler Smith

Author · added in 2.6-2

Peter Solymos

Author · added in 1.15-0

M. Henry H. Stevens

Author · added in 1.8-7

Adrian Stier

Author · added in 2.6-2

Eduard Szoecs

Author · added in 2.4-0

Cajo J.F. Ter Braak

Author · added in 2.6-2

Helene Wagner

Author · added in 1.13-1

James Weedon

Author · added in 2.6-2

Matt Barbour

Contributor · added in 2.6-2

Henrik Bengtsson

Contributor · added in 2.7-5

Tuomas Borman

Contributor · added in 2.6-10

Michael Chirico

Contributor · added in 2.6-2

Rich FitzJohn

Contributor · added in 2.6-2

Michael Friendly

Contributor · added in 2.4-0

Brendan Furneaux

Contributor · added in 2.6-2

Isaac Heida

Contributor · added in 2.7-5

Show 1 more contributorHide 1 contributor

Dan McGlinn

Contributor · added in 2.4-0

Listed in earlier versions (3)

Show 3 peopleHide 3 people

Bob O'Hara

no longer listed · 1.6-8 to 2.10.0

R. G. O'Hara

no longer listed · 1.17-0 to 1.17-1

R. B. O'Hara

no longer listed · 1.17-2 to 2.5-7

Releases (127)

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
2013-12-12 · current release · diff ↗
3.0.2
record
2013-09-25 · diff ↗
R
R 3.0.0 released · 2013-04-03

Show 146 earlier eventsHide 146 earlier events

3.0.0
record
2013-03-19 · diff ↗
2.15.3
record
2013-02-11 · diff ↗
2.15.2
record
2012-10-08 · diff ↗
2.15.1
record
2012-06-18 · diff ↗
R
R 2.15.0 released · 2012-03-30
2.14.1
record
2011-11-13 · diff ↗ ·
added 4 exports
nestedbetajac, nestedbetasor, rarecurve, simper
R
R 2.14.0 released · 2011-10-31
2.14.0
record
2011-10-20 · diff ↗
2.13.2
record
2011-09-07 · diff ↗ ·
removed 1 export
pattern:.

added 173 exports
CCorA, MOStest, RsquareAdj, SSarrhenius, SSgitay, SSgleason, SSlomolino, adipart, adonis, anosim, beals, betadisper, betadiver, bgdispersal, bioenv, bstick, cIndexKM, calibrate, capscale, cascadeKM, cca, commsimulator, contribdiv, decorana, decostand, designdist, coverscale, dispindmorisita, distconnected, diversity and 143 more
2.13.1
record
2011-06-14 · diff ↗
R
R 2.13.0 released · 2011-04-13
2.13.0
record
2011-03-31 · diff ↗
2.12.2
record
2011-02-16 · diff ↗
R
R 2.12.0 released · 2010-10-15
2.12.0
record
2010-08-20 · diff ↗
R
R 2.11.0 released · 2010-04-22
2.11.0
record
2010-03-08 · diff ↗
R
R 2.10.0 released · 2009-10-26
2.10.0
record
2009-09-07 · diff ↗
2.9.1
record
2009-06-17 · diff ↗
R
R 2.9.0 released · 2009-04-17
2.9.0
record
2009-04-15 · diff ↗
2.8.1
record
2008-12-19 · diff ↗
R
R 2.8.0 released · 2008-10-20
2.8.0
record
2008-09-30 · diff ↗
2.7-6
record
2026-08-31 · diff ↗
2.7-5
record
2026-05-25 · diff ↗
2.7-3
record
2026-03-04 · diff ↗
2.7-2
record
2025-10-08 · diff ↗
2.7.2
record
2008-08-20 · diff ↗
2.7-1
record
2025-06-06 · diff ↗ ·
removed 1 export
humpfit

added 6 exports
betadistances, designdist2, dist2xy, MDSaddpoints, optspace, permulattice
2.7.1
record
2008-06-11 · diff ↗
R
R 2.7.0 released · 2008-04-22
2.7.0
record
2008-04-20 · diff ↗
2.6-10
record
2025-01-29 · diff ↗
2.6-8
record
2024-08-28 · diff ↗ ·
added 3 exports
ca, pca, pco
2.6-6.1
record
2024-05-21 · diff ↗
2.6-6
record
2024-05-14 · diff ↗
2.6-4
record
2022-10-11 · diff ↗ ·
added 2 exports
decobackstand, toCoda
2.6-2
record
2022-04-17 · diff ↗ ·
added 1 export
simpson.unb
2.6.0
record
2007-10-03 · diff ↗
2.5-7
record
2020-11-28 · diff ↗
2.5-6
record
2019-09-01 · diff ↗
2.5-5
record
2019-05-12 · diff ↗ ·
removed 1 export
sigma.cca
2.5-4
record
2019-02-04 · diff ↗
2.5-3
record
2018-10-25 · diff ↗
2.5-2
record
2018-05-17 · diff ↗ ·
added 1 export
sigma.cca
2.5-1
record
2018-04-14 · diff ↗ ·
removed 1 export
oldCapscale

added 5 exports
chaodist, cutreeord, sppscores<-, sppscores, avgdist
R
R 2.6.0 released · 2007-10-03
2.5.1
record
2007-05-09 · diff ↗
R
R 2.5.0 released · 2007-04-24
2.5.0
record
2007-01-11 · diff ↗
2.4-6
record
2018-01-24 · diff ↗
2.4-5
record
2017-12-01 · diff ↗
2.4-4
record
2017-08-24 · diff ↗
2.4-3
record
2017-04-07 · diff ↗ ·
added 1 export
ordiYbar
2.4-2
record
2017-01-17 · diff ↗
2.4-1
record
2016-09-07 · diff ↗
2.4-0
record
2016-06-15 · diff ↗ ·
removed 1 export
metaMDSrotate

added 5 exports
dbrda, smbind, ordibar, oldCapscale, adonis2
R
R 2.4.0 released · 2006-10-03
2.4.0
record
2006-09-29 · diff ↗
2.3-5
record
2016-04-09 · diff ↗
2.3-4
record
2016-02-26 · diff ↗
2.3-3
record
2016-01-12 · diff ↗
2.3-2
record
2015-11-19 · diff ↗
2.3-1
record
2015-09-25 · diff ↗
2.3-0
record
2015-05-26 · diff ↗ ·
added 4 exports
ordiArrowMul, ordiArrowTextXY, rareslope, specslope
2.2-1
record
2015-01-12 · diff ↗
2.2-0
record
2014-11-17 · diff ↗ ·
removed 10 exports
ordiplot3d, ordirgl, orglpoints, orglsegments, orglspider, orgltext, permuted.index2, getNumObs, rgl.isomap, rgl.renyiaccum

added 9 exports
bioenvdist, commsim, dispweight, gdispweight, make.commsim, nullmodel, ordiareatest, permustats, panel.ordiarrows
R
R 2.3.0 released · 2006-04-24
R
R 2.2.0 released · 2005-10-06
2.2.0
record
2005-09-26 · diff ↗
2.1.1
record
2005-04-22 · diff ↗
2.1.0
record
2005-04-18 · diff ↗
2.0-10
record
2013-12-12 · diff ↗
2.0-9
record
2013-09-25 · diff ↗
2.0-8
record
2013-07-10 · diff ↗
2.0-7
record
2013-03-19 · diff ↗ ·
added 1 export
tabasco
2.0-6
record
2013-02-11 · diff ↗
2.0-5
record
2012-10-08 · diff ↗
2.0-4
record
2012-06-19 · diff ↗
2.0-3
record
2012-03-03 · diff ↗ ·
added 4 exports
nestedbetajac, nestedbetasor, rarecurve, simper
2.0-2
record
2011-11-15 · diff ↗ ·
removed 4 exports
nestedbetajac, nestedbetasor, rarecurve, simper
2.0-1
record
2011-10-20 · diff ↗ ·
added 2 exports
clamtest, raupcrick
R
R 2.1.0 released · 2005-04-18
2.0.1
record
2004-10-13 · diff ↗
2.0-0
record
2011-09-08 · diff ↗
R
R 2.0.0 released · 2004-10-04
2.0.0
record
2004-06-10 · diff ↗
1.17-12
record
2011-08-17 · diff ↗ ·
added 1 export
pattern:.
1.17-11
record
2011-06-15 · diff ↗
1.17-10
record
2011-04-27 · diff ↗
1.17-9
record
2011-03-31 · diff ↗
1.17-8
record
2011-03-02 · diff ↗
1.17-7
record
2011-02-16 · diff ↗
1.17-6
record
2011-01-10 · diff ↗
1.17-5
record
2010-12-18 · diff ↗
1.17-4
record
2010-08-20 · diff ↗
1.17-3
record
2010-06-16 · diff ↗
1.17-2
record
2010-03-08 · diff ↗
1.17-1
record
2010-02-18 · diff ↗
1.17-0
record
2010-01-11 · diff ↗
1.15-4
record
2009-09-07 · diff ↗
1.15-3
record
2009-06-17 · diff ↗
1.15-2
record
2009-04-15 · diff ↗
1.15-1
record
2008-12-19 · diff ↗
1.15-0
record
2008-09-30 · diff ↗
1.13-2
record
2008-08-20 · diff ↗
1.13-1
record
2008-06-11 · diff ↗
1.13-0
record
2008-05-21 · diff ↗
1.11-4
record
2008-04-24 · diff ↗
1.11-3
record
2008-04-10 · diff ↗
1.11-2
record
2008-03-21 · diff ↗
1.11-0
record
2008-02-21 · diff ↗
1.8-8
record
2007-10-03 · diff ↗
1.8-7
record
2007-08-25 · diff ↗
1.8-6
record
2007-05-10 · diff ↗
1.8-5
record
2007-01-11 · diff ↗
1.8-4
record
2007-01-08 · diff ↗
1.8-3
record
2006-09-29 · diff ↗
1.8-2
record
2006-06-14 · diff ↗
1.8-1
record
2006-06-12 · diff ↗
1.6-10
record
2005-09-26 · diff ↗
1.6-9
record
2005-04-22 · diff ↗
1.6-8
record
2005-04-18 · diff ↗
1.6-7
record
2005-01-25 · diff ↗
1.6-6
record
2005-01-09 · diff ↗
1.6-5
record
2004-10-13 · diff ↗
1.6-4
record
2004-06-11 · diff ↗
R
R 1.9.0 released · 2004-04-12
1.6-3
record
2004-03-22 · diff ↗
1.6-2
record
2004-01-22 · diff ↗
1.6-1
record
2003-12-12 · diff ↗
1.6-0
record
2003-10-20 · diff ↗
R
R 1.8.0 released · 2003-10-08
1.4-4
record
2003-05-19 · diff ↗
1.4-3
record
2003-04-22 · diff ↗
R
R 1.7.0 released · 2003-04-16
1.4-2
record
2003-02-07 · diff ↗
1.4-1
record
2002-10-04 · diff ↗
R
R 1.6.0 released · 2002-10-01
1.4-0
record
2002-05-03 · diff ↗
R
R 1.5.0 released · 2002-04-29
1.2-1
record
2001-12-18 · diff ↗
1.2-0
record
2001-11-19 · diff ↗
1.0-1
record
2001-09-06

Package metadata

First published: 2001-09-06
Total releases: 127 / 25 yrs
License: GPL-2 OSI
Minimum R: ≥ 4.1.0
Bundled data: 46 KB / 15 files
Download size: 1.4 MB

Appears in task views

Analysis of Ecological and Environmental Data Phylogenetics Psychometric Models and Methods Analysis of Spatial Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("vegan")

Format

Oksanen, J., Barbour, M., Bedward, M., Bengtsson, H., Blanchet, F. G., Bolker, B., Borcard, D., Borman, T., Carvalho, G., Chirico, M., De Caceres, M., Durand, S., Evangelista, H. B. A., FitzJohn, R., Friendly, M., Furneaux, B., Hannigan, G., Heida, I., Hill, M. O., Kindt, R., Lahti, L., Legendre, P., Martino, C., McGlinn, D., Minchin, P. R., O'Hara, R. B., Ouellette, M., Ribeiro Cunha, E., Simpson, G. L., Smith, T., Solymos, P., Stevens, M. H. H., Stier, A., Szoecs, E., Ter Braak, C. J. F., Wagner, H., & Weedon, J. (2026). vegan: Community Ecology Package (Version 2.7-6) [Computer software]. https://doi.org/10.32614/CRAN.package.vegan

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 vegan version 2.7-6 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, 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 →