R Observatory: Metrics for toxSummary version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

toxSummary

1.0.1Package record

Visualize and Summarize Repeat-Dose Toxicology Study Results

0packages depend

2.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Yousuf AliCRAN page ↗GitHub ↗Website ↗Issues ↗

A 'shiny' app that generates plots and summary tables from repeat-dose toxicology study results to facilitate holistic evaluation of the drug safety of active pharmaceutical ingredients (API) prior to initiation of clinical trials.

Install

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

install.packages("toxSummary", 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("phuse-org/toxSummary")

Development version from phuse-org/toxSummary. 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-toxsummary

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-toxSummary

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-toxSummary

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: 2.0 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
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 753 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsiteYes · pkgdown

The repository also keeps web-only articles.

Help pages: 1
Examples that run: 100%1 run in a plain check (under a condition)
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Introduction HTML

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #12,494 · ~7/day · ~220/mo

Releases R versions

Daily download trend is not available in this view yet.

41230 days

90090 days

2.6K1 year

Compare downloads with other packages →

Also on75 r2u5 autocran

How downloads are counted

Repository

phuse-org/toxsummary ↗Organization: phuse-org

10Stars

6Forks

3Open issues

1Open PRs

0Releases

426Commits

5Commit identities

r-shiny-apptoxicologyvisualizationcdisc-send

426 commits · Last activity 2024-04-17 · +11.1% stars, 30d · The default branch showed an older version (1.0.0) than CRAN on 2026-10-21 · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 85
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2024-11-11 · 82026-10-05 · 10

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/phuse-org/toxsummary on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows

Docs source (3)

pkgdown

GitHub Pages site last deployed 2023-09-01 · The repository has a site deploy workflow

Reproducibility and dev environment (2)

data-raw/Dev Container

Lint, format, editor (2)

lintrVS Code

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

Dependencies

Declared dependencies

22 external dependencies (excludes base and recommended)

Installing toxSummary adds 92 packages (50 with compiled code, 85 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 2.10

Imports (19)

cicerone data.table DBI dplyr DT flextable fs ggiraph ggplot2 htmltools magrittr patchwork rlang RSQLite scales shiny shinycssloaders shinydisconnect stringr

LinkingTo (0)

none

Suggests (3)

knitr officer rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Yousuf Ali

Maintainer since 1.0.0 (2024), Author

Kevin Snyder

Author

FDA

Copyright holder

Releases (2)

Pick two releases to compare their code metrics.

1.0.1Latest
record
2026-09-23 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.0
record
2024-02-27
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2024-02-27
Total releases: 2 / 2 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Download size: 3.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("toxSummary")

Format

Ali, Y., FDA, & Snyder, K. (2026). toxSummary: Visualize and Summarize Repeat-Dose Toxicology Study Results (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.toxSummary

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 toxSummary version 1.0.1 [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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