R Observatory: Metrics for ubiquity version 2.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ubiquity

2.1.0Package record

PKPD, PBPK, and Systems Pharmacology Modeling Tools

0packages dependsuggested by 1

3.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

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

Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.

Changes in 2.1.0

Notes

Removed the NONMEM and Monolix outputs
Added translation of nlmixr2 output into NONMEM and Monolix outputs
Added simulation option dynamic set to TRUE by default and when set to FALSE it will fix ODEs to 0 and allow for in vitro analysis.
Applying <OE:?> to variance models in cohort definitions.
Fixed issue where initial conditions were not being passed to nlmixr2 output.

From NEWS.md in the release

Install

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

install.packages("ubiquity", 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/ubiquity")

Development version from john-harrold/ubiquity. 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-ubiquity

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-ubiquity

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-ubiquity

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: 4.2 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
WARNING12 OK, 1 WARNING2026-06-07

Show 2 earlier changesHide 2 earlier changes

OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.0

READMEYes · 236 wordsVignettesYes · 6 · dynamicNEWSYes · 100% structured · mentions 2.1.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 98 (29 internal)
Examples that run: 41%13 run in a plain check · 19 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 39%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (6)

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #9,627 · ~10/day · ~297/mo

Releases R versions

Daily download trend is not available in this view yet.

37830 days

1K90 days

3.6K1 year

Compare downloads with other packages →

Also on83 r2u8 autocran101 c2d4u

How downloads are counted

Repository

john-harrold/ubiquity ↗Account: john-harrold

14Stars

4Forks

9Open issues

0Open PRs

1Releases

369Commits

1Commit identities

rpkpdmodeling

369 commits · Last activity 2026-01-07 · Default branch at 2.1.1, ahead of CRAN 2.1.0 (checked 2026-10-21) · Discussions: 4 posts

Responsiveness

How these are sampled

PRs merged (all time): 0%
Median days to close, 50 most recently updated closed issues: 178
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-07-01 · 142026-07-07 · 14

How these are measured

PracticesBeta

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

Checks run against github.com/john-harrold/ubiquity on 2026-10-21.

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 (2)

pkgdown

GitHub Pages site last deployed 2026-01-07

pkgdown site last built 2026-01-07

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Installing ubiquity adds 97 packages (48 with compiled code, 90 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.2.0

Imports (21)

cli deSolve dplyr digest doParallel flextable foreach ggplot2 knitrMASSonbrand optimx PKNCA pso readxl rmarkdown rhandsontable scalesstatsstringr shiny

LinkingTo (0)

none

Suggests (12)

babelmixr2 GA GGally gridGraphics gridExtragridofficer rxode2 webshot ggrepel rstudioapi testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

ruminate

How these are counted

Code & Tests

People & History

People (1)

John Harrold

Author, Maintainer since 1.0.0 (2019)

Releases (10)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.1.0Latest
record
2025-01-07 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
2.0.3
record
2024-03-08 · diff ↗
2.0.1
record
2023-10-29 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
2.0.0
record
2021-09-03 · diff ↗ ·
removed 20 exports
md_to_officer, md_to_oo, system_fetch_report, system_fetch_report_format, system_glp_save, system_report_doc_add_content, system_report_doc_format_section, system_report_doc_set_ph, system_report_estimation, system_report_glp, system_report_init, system_report_nca, system_report_ph_content, system_report_save, system_report_set, system_report_slide_content, system_report_slide_section, system_report_slide_title, system_report_slide_two_col, system_report_view_layout

added 11 exports
system_fetch_rpt_officer_object, system_fetch_rpt_onbrand_object, system_rpt_add_doc_content, system_rpt_add_slide, system_rpt_estimation, system_rpt_nca, system_rpt_read_template, system_rpt_save_report, system_rpt_template_details, system_set_rpt_officer_object, system_set_rpt_onbrand_object
R
R 4.1.0 released · 2021-05-18
1.0.5
record
2021-04-25 · diff ↗ ·
added 2 exports
tic, toc
1.0.4
record
2021-04-18 · diff ↗ ·
removed 3 exports
system_report_fetch, tic, toc

added 7 exports
md_to_oo, system_fetch_nca, system_fetch_nca_columns, system_fetch_report, system_fetch_report_format, system_nca_parameters_meta, system_nca_summary
1.0.3
record
2020-09-13 · diff ↗ ·
added 1 export
apply_sub_file_COV
1.0.2
record
2020-07-05 · diff ↗ ·
added 3 exports
system_fetch_set, system_log_debug_save, system_new_list
R
R 4.0.0 released · 2020-04-24
1.0.1
record
2020-01-21 · diff ↗ ·
added 2 exports
md_to_officer, system_report_doc_format_section

Show 2 earlier eventsHide 2 earlier events

1.0.0
record
2019-10-17
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-10-17
Total releases: 10 / 7 yrs
License: BSD_2_clause + file LICENSE OSI
Minimum R: ≥ 4.2.0
Download size: 3.4 MB

Appears in task views

Analysis of Pharmacokinetic Data

Cite

Cite this package

Run in R for the authors' entry:

citation("ubiquity")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1007/s10928-014-9352-6.

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 ubiquity version 2.1.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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