R Observatory: Metrics for toxEval version 1.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

toxEval

1.4.2Package record

Exploring Biological Relevance of Environmental Chemistry Observations

0packages depend

3.6Kdownloads / year

63.9%test coverage

13/13flavors OK

Overview

About

Maintained by Laura DeCiccoCRAN page ↗GitHub ↗Issues ↗

Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) doi:10.1021/acs.est.7b01613.

Changes in 1.4.2

Minor documentation updates

From NEWS in the release

Install

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

install.packages("toxEval", 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("DOI-USGS/toxEval")

Development version from DOI-USGS/toxEval. 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-toxeval

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-toxEval

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-toxEval

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: 3.8 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
OK13 OK2026-05-12

Show 2 earlier changesHide 2 earlier changes

WARNING12 OK, 1 WARNING2026-05-11
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.4.2

READMEYes · 602 wordsVignettesYes · 3 · dynamicNEWSYes · 33% structured · mentions 1.4.2Citation fileNo

Help pages: 27 (2 internal)includes a package overview page
Examples that run: 96%23 run in a plain check (2 of them under a condition) · 1 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 92%
Documented parameters: 100%
Return-value docs: 52%
Help pages citing references: 7%

Vignettes (3)

How these are measured

Downloads

3.6K

CRAN downloads in the past year

Rank #10,672 · ~10/day · ~303/mo

Releases R versions

Daily download trend is not available in this view yet.

41330 days

97490 days

3.6K1 year

Compare downloads with other packages →

Also on124 r2u6 autocran

How downloads are counted

Repository

doi-usgs/toxeval ↗Organization: DOI-USGS

22Stars

11Forks

9Open issues

0Open PRs

36Releases

1,716Commits

10Commit identities

rrstatsr-packagewater-qualitytoxicity

1,716 commits · Last activity 2026-01-23 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 99%
Median days to close, 50 most recently updated closed issues: 5
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-02-27 · 212026-07-07 · 22

How these are measured

PracticesBeta

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

Checks run against github.com/doi-usgs/toxeval on 2026-10-21.

Continuous integration (3)

GitHub ActionsR CMD check workflowGitLab CI

The R CMD check workflow runs on Linux and macOS

Governance and community (1)

Code of conduct

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-01-23 · The repository has a site deploy workflow

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 1 practice

Lint, format, editor (1)

lintr

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

Dependencies

Declared dependencies

19 external dependencies (excludes base and recommended)

Installing toxEval adds 87 packages (45 with compiled code, 85 MB of source tarballs). Heaviest: stringi 11 MB, sf 9.3 MB, ggplot2 6.0 MB.

Depends (1)

R >= 4.1.0

Imports (14)

dplyr tidyr DT leaflet ggplot2 (>= 3.0.0)magrittr shiny shinydashboard RColorBrewer readxltoolsshinyAce shinycssloadersutils

LinkingTo (0)

none

Suggests (7)

rmarkdown testthat knitr here tcpl openxlsx covr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (7)

Laura DeCicco

Author, Maintainer since 1.0.3 (2019)

Author

Author

Author

Author

Reviewer

Reviewed for USGS

Dalma Martinovic

Reviewer

Reviewed for USGS

Releases (10)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
1.4.2Latest
record
2026-01-23 · current release · diff ↗
1.4.1
record
2025-09-30 · diff ↗
R
R 4.5.0 released · 2025-04-11
1.4.0
record
2024-11-22 · diff ↗ ·
added 1 export
flags
R
R 4.4.0 released · 2024-04-24
1.3.2
record
2024-02-08 · diff ↗
1.3.1
record
2024-01-30 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.3.0
record
2023-04-14 · diff ↗ ·
added 1 export
plot_tox_endpoints2
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.2.0
record
2020-10-09 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.1.0
record
2019-11-26 · diff ↗ ·
removed 1 export
is.toxEvl

added 3 exports
get_concentration_summary, plot_chemical_boxplots, side_by_side_data
R
R 3.6.0 released · 2019-04-26

Show 3 earlier eventsHide 3 earlier events

1.0.4
record
2019-03-22 · diff ↗
1.0.3
record
2019-03-06
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2019-03-06
Total releases: 10 / 7 yrs
License: CC0
Copyright: This software is in the public domain because it contains materials that originally came from the United States Geological Survey, an agency of the United States Department of Interior. For more information, see the official USGS copyright policy at https://www.usgs.gov/visual-id/credit_usgs.html#copyright
Minimum R: ≥ 4.1.0
Download size: 3.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("toxEval")

Format

DeCicco, L., Ankley, G., Appling, A., Blackwell, B., Corsi, S., Martinovic, D., & Villeneuve, D. (2026). toxEval: Exploring Biological Relevance of Environmental Chemistry Observations (Version 1.4.2) [Computer software]. https://doi.org/10.32614/CRAN.package.toxEval

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 toxEval version 1.4.2 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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