R Observatory: Metrics for ruminate version 0.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ruminate

0.3.2

A Pharmacometrics Data Transformation and Analysis Tool

0packages depend

2.9Kdownloads / year

28.6%test coverage

13/13checks pass

Overview

About

Maintained by John HarroldFirst published 2023-08-298 releasesCRAN page ↗GitHub ↗

Exploration of pharmacometrics data involves both general tools (transformation and plotting) and specific techniques (non-compartmental analysis). This kind of exploration is generally accomplished by utilizing different packages. The purpose of 'ruminate' is to create a 'shiny' interface to make these tools more broadly available while creating reproducible results.

Install

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

install.packages("ruminate", 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("john-harrold/ruminate")

Development version from john-harrold/ruminate. 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-ruminate

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-ruminate

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-ruminate

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

Health

CRAN checks

13OK

Slowest check: 8.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

28.6%

Coverage · measured lines

100%

Documentation · exports

20

Dependencies · direct

Check history

OK2026-08-04
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
WARNING2026-06-07
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE

Show 1 earlier snapshots

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 461 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 90%
Documented parameters: 97%
Return-value docs: 100%
References docs: 0%

Downloads

2.9K

CRAN downloads in the past year

Rank #12,985 · ~8/day · ~240/mo

Releases R versions

Daily download trend is not available in this view yet.

22430 days

78490 days

2.9K1 year

Compare downloads with other packages →

Also on125 r2u15 autocran32 c2d4u

Repository

GitHub ↗ john-harrold/ruminate

5Stars

3Forks

13Open issues

0Open PRs

1Releases

229Commits

1Contributors

229 commits · Last activity 2026-02-11 · 0% stars, 30d

Stars over time

2025-01-13 · 22026-07-07 · 5

Repository practices

Upstream repositoryBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/john-harrold/ruminate on 2026-08-09.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

34 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.2.0

Imports (20)

digest dplyr DT flextable formods ggplot2 onbrand PKNCA plotly rhandsontable rlang shiny shinyAce shinyWidgetsstatsstringr tidyrutilsyaml zip

LinkingTo (0)

none

Suggests (16)

babelmixr2 cli clipr gridExtra knitr nlmixr2lib(>= 0.3.0)nonmem2rx nlmixr2 prompter rmarkdown readxl rxode2 shinybusy shinydashboard testthat ubiquity

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

John Harrold

Author, Maintainer

Authors (1)

John Harrold

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.3.2Latest
2025-11-04 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.3.1
2025-01-10 · diff ↗
0.2.4
2024-05-28 · diff ↗
0.2.3
2024-05-19 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.2.2
2024-03-14 · diff ↗
0.2.1
2023-12-11 · diff ↗
0.2.0
2023-12-02 · diff ↗
0.1.1
2023-08-29
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-08-29
Total releases: 8 / 3 yrs
License: BSD_2_clause + file LICENSE OSI
Minimum R: ≥ 4.2.0
Download size: 743 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Analysis of Pharmacokinetic Data

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ruminate")

Format

Harrold, J. (2025). ruminate: A Pharmacometrics Data Transformation and Analysis Tool (Version 0.3.2) [Computer software]. https://doi.org/10.32614/CRAN.package.ruminate

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 ruminate version 0.3.2 [Data set]. HJJB, LLC. Data release v2026-08-15. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-15, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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