R Observatory: Metrics for ruminate version 0.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ruminate

0.3.2Package record

A Pharmacometrics Data Transformation and Analysis Tool

0packages depend

3.2Kdownloads / year

28.6%test coverage

13/13flavors OK

Overview

About

Maintained by John HarroldCRAN page ↗GitHub ↗Website ↗Issues ↗

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

Status changes

OK13 OK2026-09-20
ERROR11 OK, 2 ERROR2026-09-12
OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 3 earlier changesHide 3 earlier changes

ERROR12 OK, 1 ERROR2026-06-08
WARNING12 OK, 1 WARNING2026-06-07
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.3.2

READMEYes · 461 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · does not mention 0.3.2Citation fileNoWebsiteYes · pkgdown

Help pages: 82includes a package overview page
Examples that run: 72%50 run in a plain check (2 of them under a condition) · 19 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 90%
Documented parameters: 97%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

Deployment and Customization HTML
Noncompartmental Analysis HTML

How these are measured

Downloads

3.2K

CRAN downloads in the past year

Rank #11,662 · ~9/day · ~268/mo

Releases R versions

Daily download trend is not available in this view yet.

44430 days

92390 days

3.2K1 year

Compare downloads with other packages →

Also on93 r2u2 autocran52 c2d4u

How downloads are counted

Repository

john-harrold/ruminate ↗Account: john-harrold

6Stars

3Forks

13Open issues

0Open PRs

1Releases

229Commits

1Commit identities

229 commits · Last activity 2026-02-11 · +20% stars, 30d · Default branch at 0.4.0, ahead of CRAN 0.3.2 (checked 2026-10-18)

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 50
Median days to close, 50 most recently updated closed PRs: 20

Stars over time

2025-01-13 · 22026-09-29 · 6

How these are measured

PracticesBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/john-harrold/ruminate 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

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-02-11

pkgdown site last built 2026-02-11

Coverage (1)

Coverage reporting

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

Dependencies

Declared dependencies

34 external dependencies (excludes base and recommended)

Installing ruminate adds 107 packages (57 with compiled code, 99 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

People & History

People (1)

John Harrold

Author, Maintainer since 0.1.1 (2023)

Releases (8)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.3.2Latest
record
2025-11-04 · current release · diff ↗
R
R 4.5.0 released · 2025-04-11
0.3.1
record
2025-01-10 · diff ↗ ·
added 50 exports
CTS_Server, CTS_add_covariate, CTS_add_rule, CTS_append_report, CTS_change_source_model, CTS_del_current_element, CTS_fetch_code, CTS_fetch_current_element, CTS_fetch_ds, CTS_fetch_sc_meta, CTS_fetch_state, CTS_init_state, CTS_mk_preload, CTS_new_element, CTS_plot_element, CTS_preload, CTS_set_current_element, CTS_sim_isgood, CTS_simulate_element, CTS_test_mksession, CTS_update_checksum, MB_Server, MB_append_report, MB_build_code, MB_del_current_element, MB_fetch_appends, MB_fetch_catalog, MB_fetch_code, MB_fetch_component, MB_fetch_current_element and 20 more
0.2.4
record
2024-05-28 · diff ↗
0.2.3
record
2024-05-19 · diff ↗ ·
added 1 export
ruminate_check
R
R 4.4.0 released · 2024-04-24
0.2.2
record
2024-03-14 · diff ↗
0.2.1
record
2023-12-11 · diff ↗ ·
removed 18 exports
MB_Server, MB_append_report, MB_build_code, MB_del_current_element, MB_fetch_catalog, MB_fetch_code, MB_fetch_component, MB_fetch_current_element, MB_fetch_mdl, MB_fetch_state, MB_init_state, MB_new_element, MB_set_current_element, MB_test_catalog, MB_test_mksession, MB_update_checksum, MB_update_model, mk_rx_obj
0.2.0
record
2023-12-02 · diff ↗ ·
added 19 exports
MB_Server, MB_append_report, MB_build_code, MB_del_current_element, MB_fetch_catalog, MB_fetch_code, MB_fetch_component, MB_fetch_current_element, MB_fetch_mdl, MB_fetch_state, MB_init_state, MB_new_element, MB_set_current_element, MB_test_catalog, MB_test_mksession, MB_update_checksum, MB_update_model, NCA_mkactive_ana, mk_rx_obj
0.1.1
record
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

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 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 ruminate version 0.3.2 [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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