R Observatory: Metrics for GLMMcosinor version 0.2.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GLMMcosinor

0.2.2Package record

Fit a Cosinor Model Using a Generalized Mixed Modeling Framework

0packages depend

6.5Kdownloads / year

95.1%test coverage

13/13flavors OK

Overview

About

Maintained by Rex ParsonsCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funders: Prasad Chunduri and Oliver Rawashdeh

Allows users to fit a cosinor model using the 'glmmTMB' framework. This extends on existing cosinor modeling packages, including 'cosinor' and 'circacompare', by including a wide range of available link functions and the capability to fit mixed models. The cosinor model is described by Cornelissen (2014) doi:10.1186/1742-4682-11-16.

Changes in 0.2.2

Refactor polar_plot() and autoplot() to avoid functions that are defined within other functions. Separate out into separate scripts where necessary.
Add example of using likelihood-ratio test to assess differential rhythmicity.
Use the mean of continuous variables as the reference level, and the first level for factors when creating newdata within autoplot().
Fix test-coverage GHA.
Use reformulas::findbars()/nobars() instead of the now-deprecated lme4::findbars()/nobars(), which were moved to the reformulas package and emitted a one-off deprecation warning that made test-cglmm.R order-dependent and flaky on R-devel. This was the cause of the CRAN archival on 2026-08-22.
Fix autoplot() legends being shown in the wrong order (colour before linetype/shape) when both ranef_plot and a grouping variable are plotted together, caused by a ggplot2 4.0 change to default guide ordering.

From NEWS.md in the release

Install

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

install.packages("GLMMcosinor", 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("ropensci/GLMMcosinor")

Development version from ropensci/GLMMcosinor. 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-glmmcosinor

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-GLMMcosinor

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-GLMMcosinor

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: 6.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-04-13

Show 2 earlier changesHide 2 earlier changes

ERROR13 OK, 1 ERROR2026-03-30
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.2.2

READMEYes · 373 wordsVignettesYes · 6 · dynamicNEWSYes · 100% structured · mentions 0.2.2Citation fileNoWebsiteYes · pkgdown

Help pages: 25 (2 internal)includes a package overview page
Examples that run: 81%17 run in a plain check · 4 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 89%
Documented parameters: 100%
Return-value docs: 89%
Help pages citing references: 4%

Vignettes (6)

How these are measured

Downloads

6.5K

CRAN downloads in the past year

Rank #8,909 · ~18/day · ~542/mo

Releases R versions

Daily download trend is not available in this view yet.

61130 days

1.1K90 days

6.5K1 year

Compare downloads with other packages →

Also on103 r2u

How downloads are counted

Repository

ropensci/glmmcosinor ↗Organization: ropensci

4Stars

0Forks

0Open issues

0Open PRs

3Releases

479Commits

2Commit identities

License file reads as GPL-3.0 · 479 commits · Last activity 2026-09-15 · +33.3% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 81%
Median days to close, 50 most recently updated closed issues: 26
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-05-09 · 32026-10-10 · 4

How these are measured

PracticesBeta

12 development-tooling and community-health practices detected across 9 families in the upstream repository

Checks run against github.com/ropensci/glmmcosinor on 2026-10-25.

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 (inherited from ropensci)

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2023-11-06

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 5 practices

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v4 (2026-10-20)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-09-15
Named in .Rbuildignore: .claude
Pull request it wrote: opened by a project member

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

20 external dependencies (excludes base and recommended)

Installing GLMMcosinor adds 64 packages (39 with compiled code, 63 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, glmmTMB 5.2 MB.

Depends (1)

R >= 4.1.0

Imports (9)

assertthat cowplot ggforce ggplot2 glmmTMB reformulas rlang scalesstats

LinkingTo (0)

none

Suggests (12)

cosinor covr DHARMa dplyr DT flextable ftExtra knitr rmarkdown testthat vdiffr withr

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 (8)

Rex Parsons

Author, Maintainer since 0.2.0 (2024)

Author

Author, Funder

Author

Contributor, Funder

Contributor · added in 0.2.1

Joaquin Cavieres

Reviewer

Michael Sachs

Reviewer

Releases (3)

Pick two releases to compare their code metrics.

unarchivedReturned to CRAN
2026-09-15
0.2.2Latest
record
2026-09-15 · current release · diff ↗
archivedRemoved from CRAN
2026-08-22
issues were not corrected in time
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
0.2.1
record
2024-11-01 · diff ↗ ·
added 1 export
bell
R
R 4.4.0 released · 2024-04-24
0.2.0
record
2024-01-11
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-01-11
Total releases: 3 / 2 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Bundled data: 6.1 KB / 2 files
Download size: 2.1 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GLMMcosinor")

Format

Parsons, R., Cavieres, J., Chunduri, P., Doyle, M., Jayasinghe, O., Rawashdeh, O., Sachs, M., & White, N. (2026). GLMMcosinor: Fit a Cosinor Model Using a Generalized Mixed Modeling Framework (Version 0.2.2) [Computer software]. https://doi.org/10.32614/CRAN.package.GLMMcosinor

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 GLMMcosinor version 0.2.2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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