ubiquity

2.1.0

PKPD, PBPK, and Systems Pharmacology Modeling Tools

1packages depend

3.3Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by John HarroldFirst published 2019-10-1710 releasesCRAN page ↗GitHub ↗

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'.

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.

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).

Health

CRAN checks

13OK

Slowest check: 4.5 min · r-devel-linux-x86_64-fedora-clang

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 236 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 44%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

3.3K

CRAN downloads in the past year

Rank #11,697 · ~9/day · ~279/mo

Releases R versions

Daily download trend is not available in this view yet.

26830 days

91190 days

3.3K1 year

Compare downloads with other packages →

Also on131 r2u25 autocran38 c2d4u

Repository

GitHub ↗ john-harrold/ubiquity

14Stars

4Forks

8Open issues

0Open PRs

1Releases

369Commits

1Contributors

rpkpdmodeling

369 commits · Last activity 2026-01-07 · 0% stars, 30d

Stars over time

2025-07-01 · 142026-07-07 · 14

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/ubiquity on 2026-07-19.

Continuous integration (1)

GitHub Actions

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

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

1direct

0indirect

ruminate

Code & Tests

Code Composition

R 13,533 (65%)Rd 4,281 (20%)Vignettes 2,903 (14%)YAML 251 (1%)

Code characteristics

Cyclomatic complexity: 4.0 median / 87 max
System requirements: 1 external

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

98 83 exported

Complexity

12.1 avg / 87 max

Call network

98 nodes / 166 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

John Harrold

Author, Maintainer

Authors (1)

John Harrold

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
2.1.0Latest
2025-01-07 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
2.0.3
2024-03-08 · diff ↗
2.0.1
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
2021-09-03 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.0.5
2021-04-25 · diff ↗
1.0.4
2021-04-18 · diff ↗
1.0.3
2020-09-13 · diff ↗
1.0.2
2020-07-05 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.1
2020-01-21 · diff ↗

Show 2 earlier events

1.0.0
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
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Analysis of Pharmacokinetic Data

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