R Observatory: Metrics for denim version 1.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

denim

1.2.3Package record

Generate and Simulate Deterministic Compartmental Models

0packages depend

4.9Kdownloads / year

39.9%test coverage

13/13flavors OK

Overview

About

Maintained by Anh PhanCRAN page ↗GitHub ↗Website ↗Issues ↗

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. 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-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). 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: 5.3 min · r-devel-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
OK12 OK2026-04-25

Show 3 earlier changesHide 3 earlier changes

NOTE11 OK, 3 NOTE2026-04-22
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.2.3

READMEYes · 125 wordsVignettesYes · 5 · dynamicNEWSYes · 100% structured · mentions 1.2.3Citation fileNoWebsiteYes · pkgdown

Help pages: 10 (1 internal)includes a package overview page
Examples that run: 100%8 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (5)

denim: deterministic model with memory HTML
denim DSL HTML
deSolve to denim HTML
nonparametric distribution HTML
transition to multiple states HTML

How these are measured

Downloads

4.9K

CRAN downloads in the past year

Rank #8,471 · ~14/day · ~411/mo

Releases R versions

Daily download trend is not available in this view yet.

42430 days

1.1K90 days

4.9K1 year

Compare downloads with other packages →

Also on387 r2u6 autocran

How downloads are counted

Repository

thinhong/denim ↗Account: thinhong

3Stars

2Forks

15Open issues

1Open PRs

3Releases

248Commits

5Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 36
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-10-17 · 32026-07-07 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/thinhong/denim on 2026-10-18.

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 (2)

Code of conductContributing guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-12-31 · The repository has a site deploy workflow

Coverage (2)

Coverage reporting (Codecov).covrignore

Show all practicesHide 2 practices

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing denim adds 26 packages (13 with compiled code, 10 MB of source tarballs). Heaviest: colorspace 2.0 MB, Rcpp 1.8 MB, fs 1.4 MB.

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.

How these are counted

Code & Tests

People & History

People (7)

Anh Phan

Author, Maintainer since 1.0.0 (2024)

Marc Choisy

Author

Thinh Ong

Author, Copyright holder

Ingo Berg

Contributor, Copyright holder

Author of the bundled MuParser C++ library

Bjoern Hoehrmann

Contributor, Copyright holder

Author of UTF-8 validation code in the bundled JSON C++ library

Niels Lohman

Contributor, Copyright holder

Author of the bundled JSON C++ library

Florian Loitsch

Contributor, Copyright holder

Author of the binary to decimal floating-point conversion code in the bundled JSON C++ library

Releases (7)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.2.3Latest
record
2026-01-14 · current release · diff ↗
1.2.2
record
2025-08-21 · diff ↗
1.2.1
record
2025-06-02 · diff ↗
1.2.0
record
2025-05-30 · diff ↗ ·
added 1 export
denim_dsl
1.1.0
record
2025-05-16 · diff ↗ ·
removed 3 exports
constant, multinomial, transprob
R
R 4.5.0 released · 2025-04-11
1.0.1
record
2025-03-17 · diff ↗
1.0.0
record
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

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 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 denim version 1.2.3 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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