R Observatory: Metrics for PKbioanalysis version 0.5.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

PKbioanalysis

0.5.0Package record

Pharmacokinetic Bioanalysis Experiments Design and Exploration

0packages depend

4.2Kdownloads / year

32.7%test coverage

10/13flavors OK

Overview

About

Maintained by Omar ElashkarCRAN page ↗GitHub ↗Website ↗Issues ↗

Automate pharmacokinetic/pharmacodynamic bioanalytical procedures based on best practices and regulatory recommendations. The package impose regulatory constrains and sanity checking for common bioanalytical procedures. Additionally, 'PKbioanalysis' provides a relational infrastructure for plate management and injection sequence.

Changes in 0.5.0

Bioanalytical group adding allowing more systematic injection sequence creation.
Support for plate generation from study_app GUI
plate generation undo support
tree visualization for plate
Support for analytical blanks
Support for study registration
Injection sequence ending now has specific pattern of letter and number, for instance A2 means location A and repeated 2nd time.
Enhanced naming convention for reinjections and replicates.
AI-assisted chromatogram integration and commenting.
PKmerge to generate final PK datasets.
Export PK profiles to NONMEM format along with codebook.

From NEWS.md in the release

Install

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

install.packages("PKbioanalysis", 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("OmarAshkar/PKbioanalysis")

Development version from OmarAshkar/PKbioanalysis. 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-pkbioanalysis

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-PKbioanalysis

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-PKbioanalysis

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

2ERROR1NOTE10OK

Check messages

ERRORpackage dependenciesr-release-macos-x86_64

Package required but not available: ‘RTMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.

ERRORwhether package can be installedr-devel-linux-x86_64-fedora-clang

Installation failed.
See ‘/data/localhost/ripley/R/packages/tests-clang/PKbioanalysis.Rcheck/00install.out’ for details.

NOTEdependencies in R coder-devel-linux-x86_64-fedora-gcc

Namespace in Imports field not imported from:
  ‘htmlwidgets’
All declared Imports should be used.

CRAN check page ↗

Slowest check: 9.0 min · r-oldrel-macos-x86_64

Status changes

ERROR10 OK, 1 NOTE, 2 ERRORNow
ERROR9 OK, 2 NOTE, 1 ERROR2026-04-25
NOTE9 OK, 5 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.5.0

READMEYes · 830 wordsVignettes· In the repository, left out of the releaseNEWSYes · 67% structured · mentions 0.5.0Citation fileNoWebsiteYes · pkgdown

Help pages: 75 (10 internal)includes a package overview page
Examples that run: 60%6 run in a plain check · 4 never run
Exported functions with examples: 16%
Documented parameters: 100%
Return-value docs: 59%
Help pages citing references: 0%

How these are measured

Downloads

4.2K

CRAN downloads in the past year

Rank #15,385 · ~12/day · ~351/mo

Releases R versions

Daily download trend is not available in this view yet.

29830 days

80090 days

4.2K1 year

Compare downloads with other packages →

Also on102 r2u3 autocran

How downloads are counted

Repository

omarashkar/pkbioanalysis ↗Account: OmarAshkar

1Stars

0Forks

20Open issues

0Open PRs

0Releases

136Commits

1Commit identities

License file reads as AGPL-3.0 · 136 commits · Last activity 2026-06-23 · 0% stars, 30d · Default branch at 0.5.1, ahead of CRAN 0.5.0 (checked 2026-10-22)

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 62
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2026-07-09 · 02026-07-10 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/omarashkar/pkbioanalysis on 2026-10-22.

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)

pkgdown

GitHub Pages site last deployed 2026-07-08 · The repository has a site deploy workflow

pkgdown site last built 2026-06-23

Coverage (1)

Coverage reporting

For agents and models (1)

Agent skills

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

GitHub Copilotfirst seen 2026-02-04
Seen in the repository: .github/chatmodes
Pull request: opened by its own account

Review tools

Copilot code review
Commits: at least 5 accepting its review suggestions

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

52 external dependencies (excludes base and recommended)

Installing PKbioanalysis adds 141 packages (69 with compiled code, 140 MB of source tarballs). Heaviest: stringi 11 MB, duckdb 7.9 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.3.0

Imports (52)

dplyr tidyselect stringr ggplot2 ggforce (>= 0.4.1)tidyr glue checkmate shiny DBI duckdb bslib bsicons cli DiagrammeR DT shinyWidgets shinyjs unitsstatsshinyalert htmltools rlanggrDevicesutilsyaml rhandsontablemethodsreticulate RTMB janitor tibble xml2 RaMS data.tree nloptr forcats ggiraph gt plotly pracma reactable gtools ellmer htmlwidgets jsonlitenlmescales shinychat uuid sortable writexl

LinkingTo (0)

none

Suggests (5)

rxode2 knitr patchwork rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Omar Elashkar

Author, Maintainer since 0.1.0 (2024)

Releases (5)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
0.5.0Latest
record
2026-02-17 · current release · diff ↗ ·
removed 1 export
has_default_RT

added 3 exports
export_pk_profiles, has_default_bounds, nca_table
0.4.0
record
2026-01-14 · diff ↗ ·
removed 3 exports
add_samples_c, plate_app, plot_design

added 36 exports
add_samples_db, area_report.PeakRes, calc_var_summary, chrom_app, create_new_study, cv, estim_dil_limit, estim_lloq, export_integration, export_run, filter_chrom, fit_var, formated_print, get_compound_ID, get_sample_ID, get_sample_names, has_default_RT, install_py_dep, integrate, is_integrated, is_smoothed, plate_tree, plot_RT.PeakRes, plot_chrom, plot_peak_areas.PeakRes, plot_var_pattern, precision_per_vial, prefilter_precision_data, quant_app, read_chrom and 6 more
0.3.0
record
2025-05-21 · diff ↗ ·
removed 1 export
add_qcs

added 4 exports
add_DQC, add_QC, fill_scheme, plot_design
R
R 4.5.0 released · 2025-04-11
0.2.0
record
2024-10-02 · diff ↗
0.1.0
record
2024-09-18
R
R 4.4.0 released · 2024-04-24

Package metadata

First published: 2024-09-18
Total releases: 5 / 2 yrs
License: AGPL (>= 3) OSI
Minimum R: ≥ 4.3.0
Download size: 1.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("PKbioanalysis")

Format

Elashkar, O. (2026). PKbioanalysis: Pharmacokinetic Bioanalysis Experiments Design and Exploration (Version 0.5.0) [Computer software]. https://doi.org/10.32614/CRAN.package.PKbioanalysis

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 PKbioanalysis version 0.5.0 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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