R Observatory: Metrics for denim version 1.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

denim

1.2.3

Generate and Simulate Deterministic Compartmental Models

0packages depend

4.7Kdownloads / year

39.9%test coverage

13/13checks pass

Overview

About

Maintained by Anh PhanFirst published 2024-06-057 releasesCRAN page ↗GitHub ↗

R package to build and simulate deterministic compartmental models that can be non-Markovian. Length of stay in each compartment can be defined to follow a parametric distribution (d_exponential(), d_gamma(), d_weibull(), d_lognormal()) or a non-parametric distribution (nonparametric()). Other supported types of transition from one compartment to another includes fixed transition (constant()), multinomial (multinomial()), fixed transition probability (transprob()).

Install

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

install.packages("denim", 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("thinhong/denim")

Development version from thinhong/denim. 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-denim

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-denim

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-denim

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

Health

CRAN checks

13OK

Slowest check: 5.4 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.34

39.9%

Coverage · measured lines

100%

Documentation · exports

4

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 125 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

4.7K

CRAN downloads in the past year

Rank #7,570 · ~13/day · ~388/mo

Releases R versions

Daily download trend is not available in this view yet.

22630 days

1.1K90 days

4.7K1 year

Compare downloads with other packages →

Also on424 r2u7 autocran

Repository

GitHub ↗ thinhong/denim

3Stars

2Forks

15Open issues

1Open PRs

3Releases

248Commits

5Contributors

248 commits · Last activity 2026-01-20 · 0% stars, 30d

Stars over time

2024-11-06 · 22026-07-07 · 3

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/thinhong/denim on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Coverage (2)

Codecov.covrignore

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (4)

Rcpp colorspace rlang glue

LinkingTo (2)

Rcpp testthat

Suggests (9)

covr knitr rmarkdown testthat waldo xml2 deSolve tidyverse DiagrammeR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (7)

Maintainer (1)

Anh Phan

Author, Maintainer

Authors (3)

Anh Phan

Author, Maintainer

Marc Choisy

Author

Thinh Ong

Author, Copyright holder

Contributors (4)

Ingo Berg

Contributor, Copyright holder

Bjoern Hoehrmann

Contributor, Copyright holder

Niels Lohman

Contributor, Copyright holder

Florian Loitsch

Contributor, Copyright holder

Copyright holders (5)

Thinh Ong

Author, Copyright holder

Ingo Berg

Contributor, Copyright holder

Bjoern Hoehrmann

Contributor, Copyright holder

Niels Lohman

Contributor, Copyright holder

Florian Loitsch

Contributor, Copyright holder

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.2.3Latest
2026-01-14 · current release · diff ↗
1.2.2
2025-08-21 · diff ↗
1.2.1
2025-06-02 · diff ↗
1.2.0
2025-05-30 · diff ↗
1.1.0
2025-05-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.0.1
2025-03-17 · diff ↗
1.0.0
2024-06-05
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-06-05
Total releases: 7 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Download size: 2.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("denim")

Format

Phan, A., Berg, I., Choisy, M., Hoehrmann, B., Lohman, N., Loitsch, F., & Ong, T. (2026). denim: Generate and Simulate Deterministic Compartmental Models (Version 1.2.3) [Computer software]. https://doi.org/10.32614/CRAN.package.denim

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 denim version 1.2.3 [Data set]. HJJB, LLC. Data release v2026-08-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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