R Observatory: Metrics for toxpiR version 1.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

toxpiR

1.3.2Package record

Create ToxPi Prioritization Models

0packages depend

4.8Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Jonathon F FlemingCRAN page ↗GitHub ↗Website ↗Issues ↗Declared funders: Dayne L Filer, Alison A Motsinger-Reif and 1 more

Enables users to build 'ToxPi' prioritization models and provides functionality within the grid framework for plotting ToxPi graphs. 'toxpiR' allows for more customization than the 'ToxPi GUI' (https://toxpi.github.io/) and integration into existing workflows for greater ease-of-use, reproducibility, and transparency. toxpiR package behaves nearly identically to the GUI; the package documentation includes notes about all differences. The vignettes download example files from https://github.com/ToxPi/ToxPi-example-files.

Changes in 1.3.2

Fixed an issue where txp_example_model contained embedded namespace references

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)

install.packages("toxpiR", 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("ToxPi/toxpiR")

Development version from ToxPi/toxpiR. 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-toxpir

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

Health

CRAN checks

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘TxpResultParam-class.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 4.8 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK13 OK2026-05-06
WARNING10 OK, 3 NOTE, 1 WARNING2026-04-23
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.2

README· In the repository, left out of the releaseVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 1.3.2Citation fileNoWebsiteYes · pkgdown

Help pages: 19 (1 internal)includes a package overview page
Examples that run: 92%12 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 83%
Documented parameters: 92%
Return-value docs: 33%
Help pages citing references: 0%

Vignettes (3)

How these are measured

Downloads

4.8K

CRAN downloads in the past year

Rank #6,801 · ~13/day · ~400/mo

Releases R versions

Daily download trend is not available in this view yet.

40530 days

1.3K90 days

4.8K1 year

Compare downloads with other packages →

Also on155 r2u

How downloads are counted

Repository

toxpi/toxpir ↗Organization: ToxPi

11Stars

5Forks

7Open issues

0Open PRs

3Releases

67Commits

7Commit identities

rr-packagedata-sciencemodelingtoxicology

License file reads as GPL-3.0 · 67 commits · Last activity 2026-05-01 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 86%
Median days to close, 50 most recently updated closed issues: 36
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2024-11-11 · 112026-07-07 · 11

How these are measured

PracticesBeta

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

Checks run against github.com/toxpi/toxpir 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

Governance and community (1)

Contributing guide

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-05-06 · The repository has a site deploy workflow

pkgdown site last built 2026-05-06

Coverage (1)

Coverage reporting (Codecov)

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

Dependencies

Declared dependencies

10 external dependencies (excludes base and recommended)

Installing toxpiR adds 29 packages (15 with compiled code, 28 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, isoband 1.5 MB. 2 more not on CRAN are not measured.

Depends (1)

R >= 4.0

Imports (10)

grDevicesmethodsS4VectorsgridrlangstatsBiocGenerics tidyrutilsggplot2

LinkingTo (0)

none

Suggests (5)

rmarkdown knitr testthat covr DBI

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 (7)

Jonathon F Fleming

Author, Maintainer since 1.3.0 (2024) · added in 1.3.0

Author, Funder

Author

Author

Author, Funder

Author

Alison A Motsinger-Reif

Funder · added in 1.0.3

Previously maintained by Dayne L Filer (1.0.2 to 1.2.1).

Releases (6)

Pick two releases to compare their code metrics.

1.3.2Latest
record
2026-05-01 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
1.3.1
record
2025-12-16 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.3.0
record
2024-09-12 · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
1.2.1
record
2022-07-20 · diff ↗ ·
added 1 export
txpExportGui
R
R 4.2.0 released · 2022-04-22
1.0.3
record
2022-02-18 · diff ↗
1.0.2
record
2022-02-07
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-02-07
Total releases: 6 / 4 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.0
Bundled data: 1.1 KB / 2 files
Download size: 9.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("toxpiR")

Format

Fleming, J. F., Filer, D. L., Lloyd, D. T., Marvel, S. W., Motsinger-Reif, A. A., Reif, D. M., & Thunga, P. (2026). toxpiR: Create ToxPi Prioritization Models (Version 1.3.2) [Computer software]. https://doi.org/10.32614/CRAN.package.toxpiR

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 toxpiR version 1.3.2 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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