R Observatory: Metrics for codyn version 2.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

CRAN requires the check problems on this package to be fixed before 2026-08-31 or it will be archived.

codyn

2.0.5

Community Dynamics Metrics

0packages depend

13.8Kdownloads / year

95.6%test coverage

0/13checks pass

Overview

About

Maintained by Matthew B. JonesFirst published 2015-10-209 releasesCRAN page ↗GitHub ↗

Univariate and multivariate temporal and spatial diversity indices, rank abundance curves, and community stability measures. The functions implement measures that are either explicitly temporal and include the option to calculate them over multiple replicates, or spatial and include the option to calculate them over multiple time points. Functions fall into five categories: static diversity indices, temporal diversity indices, spatial diversity indices, rank abundance curves, and community stability measures. The diversity indices are temporal and spatial analogs to traditional diversity indices. Specifically, the package includes functions to calculate community richness, evenness and diversity at a given point in space and time. In addition, it contains functions to calculate species turnover, mean rank shifts, and lags in community similarity between two time points. Details of the methods are available in Hallett et al. (2016) doi:10.1111/2041-210X.12569 and Avolio et al. (2019) doi:10.1002/ecs2.2881.

Install

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

install.packages("codyn", 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("NCEAS/codyn")

Development version from NCEAS/codyn. 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-codyn

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-codyn

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-codyn

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

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.57

95.6%

Coverage · measured lines

100%

Documentation · exports

4

Dependencies · direct

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 426 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 75%

Downloads

13.8K

CRAN downloads in the past year

Rank #4,026 · ~38/day · ~1.2K/mo

Releases R versions

Daily download trend is not available in this view yet.

42530 days

2K90 days

13.8K1 year

Compare downloads with other packages →

Also on105 r2u30 autocran

Repository

GitHub ↗ nceas/codyn

37Stars

9Forks

12Open issues

0Open PRs

9Releases

981Commits

16Contributors

981 commits · Last activity 2022-06-14 · -2.6% stars, 30d

Stars over time

2024-11-16 · 342026-08-10 · 37

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/nceas/codyn on 2026-08-23.

Continuous integration (1)

Travis CI

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.2.0

Imports (4)

assertthatstatspermute vegan

LinkingTo (0)

none

Suggests (8)

testthat knitr ggplot2 pillar reshape2 devtools dplyr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (11)

Maintainer (1)

Matthew B. Jones

Author, Maintainer

Authors (11)

Matthew B. Jones

Author, Maintainer

Meghan L. Avolio

Author · added in 2.0.0

Ian T. Carroll

Author · added in 2.0.0

Author

Author

Author

Author

Author

A. Andrew M. MacDonald

Author · added in 1.1.0

Julie Ripplinger

Author

Peter Slaughter

Author

Listed in earlier versions (1)

Andrew A. MacDonald

no longer listed · 1.0.0 to 1.0.1

Package Timeline

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

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
2.0.5Latest
2020-12-01 · current release · diff ↗
2.0.4
2020-05-06 · diff ↗
unarchivedReturned to CRAN
2020-05-06
R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-04-09
check problems were not corrected despite reminders
2.0.3
2019-09-17 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.0.2
2019-04-09 · diff ↗
2.0.1
2019-03-08 · diff ↗
2.0.0
2018-06-12 · diff ↗

Show 7 earlier events

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
1.1.0
2016-04-27 · diff ↗
1.0.1
2016-01-15 · diff ↗
1.0.0
2015-10-20
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-10-20
Total releases: 9 / 11 yrs
License: Apache License (== 2.0)
Minimum R: ≥ 3.2.0
Bundled data: 61 KB / 3 files
Download size: 549 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("codyn")

Format

Jones, M. B., Avolio, M. L., Carroll, I. T., Collins, S. L., Flynn, D. F. B., Gries, C., Hallett, L., Jones, S. K., MacDonald, A. A. M., Ripplinger, J., & Slaughter, P. (2020). codyn: Community Dynamics Metrics (Version 2.0.5) [Computer software]. https://doi.org/10.32614/CRAN.package.codyn

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 codyn version 2.0.5 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, 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 →