R Observatory: Metrics for tcpl version 3.3.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tcpl

3.3.1

ToxCast Data Analysis Pipeline

3packages depend

12.7Kdownloads / year

21.1%test coverage

10/13checks pass

Overview

About

Maintained by Madison FeshukFirst published 2016-05-0714 releasesCRAN page ↗GitHub ↗

The ToxCast Data Analysis Pipeline ('tcpl') is an R package that manages, curve-fits, plots, and stores ToxCast data to populate its linked MySQL database, 'invitrodb'. The package was developed for the chemical screening data curated by the US EPA's Toxicity Forecaster (ToxCast) program, but 'tcpl' can be used to support diverse chemical screening efforts.

Install

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

install.packages("tcpl", 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("USEPA/CompTox-ToxCast-tcpl")

Development version from USEPA/CompTox-ToxCast-tcpl. 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-tcpl

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-tcpl

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

Health

CRAN checks

1ERROR2NOTE10OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
ERROR r-release-macos-arm64

Slowest check: 9.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.29

21.1%

Coverage · measured lines

100%

Documentation · exports

22

Dependencies · direct

Check history

ERROR2026-04-27
11 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 244 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 25%
Documented parameters: 98%
Return-value docs: 53%
References docs: 0%

Downloads

12.7K

CRAN downloads in the past year

Rank #4,475 · ~35/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

38530 days

1.7K90 days

12.7K1 year

Compare downloads with other packages →

Also on143 r2u2.1K conda_forge

Repository

GitHub ↗ usepa/comptox-toxcast-tcpl

46Stars

21Forks

29Open issues

1Open PRs

4Releases

1,403Commits

29Contributors

ordcomptoxcctetoxcastresearch

1,403 commits · Last activity 2026-03-02 · +2.2% stars, 30d

Stars over time

2025-08-21 · 382026-08-22 · 46

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/usepa/comptox-toxcast-tcpl on 2026-08-23.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

31 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (22)

data.table DBI RMariaDB numDeriv RColorBrewerutilsstatsmethodsgraphicsgrDevicessqldf dplyr tidyr plotly tcplfit2 ggplot2 gridExtra stringr rlang ctxR viridis gt

LinkingTo (0)

none

Suggests (14)

roxygen2 knitr prettydoc rmarkdown htmlTable testthat reshape2 kableExtra colorspace magrittr vdiffr httptest rmdformats gtable

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

Rcurvep tcplfit2 toxEval

Code & Tests

Datasets

People & History

People (18)

Maintainer (1)

Madison Feshuk

Maintainer · added in 3.0.0

Authors (1)

Dayne L Filer

Author

Contributors (16)

Jason Brown

Contributor · added in 2.0.0

Kelly Carstens

Contributor · added in 3.2.0

Sarah E Davidson-Fritz

Contributor · added in 3.0.0

Kurt Dunham

Contributor · added in 3.1.0

Elizabeth Gilson

Contributor · added in 3.3.0

Richard S Judson

Contributor, Thesis advisor

Lindsay Knupp

Contributor · added in 3.3.0

Ashley Ko

Contributor · added in 3.1.0

Show 8 more contributors

Lori Kolaczkowski

Contributor · added in 3.0.0

Parth Kothiya

Contributor

Matthew T Martin

Contributor, Thesis advisor

Katie Paul Friedman

Contributor · added in 2.0.2

Woodrow R Setzer

Contributor

Carter Thunes

Contributor · added in 3.1.0

Zhihui Zhao

Contributor · added in 3.3.0

Todd Zurlinden

Contributor · added in 2.0.2

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
3.3.1Latest
2025-10-17 · current release · diff ↗
3.3.0
2025-05-05 · diff ↗
R
R 4.5.0 released · 2025-04-11
3.2.1
2025-04-09 · diff ↗
3.2.0
2024-10-09 · diff ↗
R
R 4.4.0 released · 2024-04-24
3.1.0
2023-10-06 · diff ↗
R
R 4.3.0 released · 2023-04-21
3.0.1
2022-11-08 · diff ↗
3.0.0
2022-08-31 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.0
2022-03-03 · diff ↗
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
2.0.2
2019-07-26 · diff ↗

Show 9 earlier events

R
R 3.6.0 released · 2019-04-26
2.0.1
2018-11-16 · diff ↗
2.0.0
2018-11-10 · diff ↗
1.4.3
2018-05-20 · diff ↗
1.2.2
2018-05-10 · diff ↗
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
1.2
2016-05-07
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-05-07
Total releases: 14 / 10 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 131 KB / 10 files
Download size: 2.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("tcpl")

Format

Feshuk, M., Brown, J., Carstens, K., Davidson-Fritz, S. E., Dunham, K., Filer, D. L., Gilson, E., Judson, R. S., Knupp, L., Ko, A., Kolaczkowski, L., Kothiya, P., Martin, M. T., Paul Friedman, K., Setzer, W. R., Thunes, C., Zhao, Z., & Zurlinden, T. (2025). tcpl: ToxCast Data Analysis Pipeline (Version 3.3.1) [Computer software]. https://doi.org/10.32614/CRAN.package.tcpl

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 tcpl version 3.3.1 [Data set]. HJJB, LLC. Data release v2026-08-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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