R Observatory: Metrics for codyn version 2.0.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

codyn

2.0.6Package record

Community Dynamics Metrics

0packages depend

9.3Kdownloads / year

95.6%test coverage

13/13flavors OK

Overview

About

Maintained by Matthew B. JonesCRAN page ↗GitHub ↗Issues ↗

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.

Changes in 2.0.6

BUG FIXES

Fixed roxygen documentation errors by switching to RMarkdown syntax (Issue #135)
Fixed package documentation to use _PACKAGE (Issue #135)
Fixed docs for community_stability (Issue #128)

From NEWS.md in the release

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

Status changes

OK13 OK2026-09-30
NOTE14 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.6

READMEYes · 426 wordsVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 2.0.6Citation fileYes · computed when R runs it

The repository also keeps web-only articles.

Help pages: 24 (1 internal)includes a package overview page
Examples that run: 100%19 run in a plain check
Exported functions with examples: 95%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 58%

Vignettes (3)

How these are measured

Downloads

9.3K

CRAN downloads in the past year

Rank #4,230 · ~26/day · ~776/mo

Releases R versions

Daily download trend is not available in this view yet.

1.1K30 days

2.1K90 days

9.3K1 year

Compare downloads with other packages →

Also on129 r2u17 autocran

How downloads are counted

Repository

nceas/codyn ↗Organization: NCEAS

38Stars

10Forks

11Open issues

0Open PRs

10Releases

1,002Commits

16Commit identities

community-dynamicsecologyr-packagespatial-dynamicstemporal-dynamics

1,002 commits · Last activity 2026-09-29 · +2.7% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 19
Median days to close, 50 most recently updated closed PRs: 2

Stars over time

2024-11-16 · 342026-09-30 · 38

How these are measured

PracticesBeta

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

Checks run against github.com/nceas/codyn on 2026-10-11.

Continuous integration (1)

GitHub Actions

Governance and community (1)

Contributing guide

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-09-29 · The repository has a site deploy workflow

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Research and citation (1)

codemeta.json

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-09-28
Commits: at least 8 crediting it in the message

Models named in its commits

Claude Opus 5.58 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

12 external dependencies (excludes base and recommended)

Installing codyn adds 3 packages (1 with compiled code, 1.5 MB of source tarballs). Heaviest: vegan 1.4 MB, permute 118 KB, assertthat 12 KB.

Depends (1)

R >= 3.2.0

Imports (4)

assertthatstatspermute vegan

LinkingTo (0)

none

Suggests (9)

testthat knitr ggplot2 pillar reshape2 devtools dplyr rmarkdown spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (11)

Matthew B. Jones

Author, Maintainer since 1.0.0 (2015)

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

Releases (10)

Pick two releases to compare their code metrics.

2.0.6Latest
record
2026-09-18 · current release · diff ↗
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
2.0.5
record
2020-12-01 · diff ↗
unarchivedReturned to CRAN
2020-05-06
2.0.4
record
2020-05-06 · diff ↗
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
record
2019-09-17 · diff ↗
R
R 3.6.0 released · 2019-04-26
2.0.2
record
2019-04-09 · diff ↗
2.0.1
record
2019-03-08 · diff ↗

Show 8 earlier eventsHide 8 earlier events

2.0.0
record
2018-06-12 · diff ↗ ·
added 10 exports
RAC_change, RAC_difference, abundance_change, abundance_difference, community_diversity, community_structure, curve_change, curve_difference, multivariate_change, multivariate_difference
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
record
2016-04-27 · diff ↗ ·
removed 2 exports
temporal_torus_translation, temporal_torus_translation_CI

added 2 exports
cyclic_shift, rank_shift
1.0.1
record
2016-01-15 · diff ↗
1.0.0
record
2015-10-20
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2015-10-20
Total releases: 10 / 11 yrs
License: Apache License (== 2.0)
Minimum R: ≥ 3.2.0
Bundled data: 61 KB / 3 files
Download size: 553 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("codyn")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 2.0.6 [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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