R Observatory: Metrics for BioMonTools version 1.3.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

BioMonTools

1.3.2

Biomonitoring and Bioassessment Calculations

1packages depend

3.3Kdownloads / year

72.0%test coverage

13/13checks pass

Overview

About

Maintained by Erik W. LeppoFirst published 2025-10-093 releasesCRAN page ↗GitHub ↗

An aid for manipulating data associated with biomonitoring and bioassessment. Calculations include metric calculation, marking of excluded taxa, subsampling, and multimetric index calculation. Targeted communities are benthic macroinvertebrates, fish, periphyton, and coral. As described in the Revised Rapid Bioassessment Protocols (Barbour et al. 1999) https://archive.epa.gov/water/archive/web/html/index-14.html.

Install

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

install.packages("BioMonTools", 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("leppott/BioMonTools")

Development version from leppott/BioMonTools. 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-biomontools

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-BioMonTools

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-BioMonTools

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 5.5 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.39

72.0%

Coverage · measured lines

100%

Documentation · exports

6

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 284 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

3.3K

CRAN downloads in the past year

Rank #13,259 · ~9/day · ~278/mo

Releases R versions

Daily download trend is not available in this view yet.

25530 days

76490 days

3.3K1 year

Compare downloads with other packages →

Also on360 r2u53 autocran

Repository

GitHub ↗ leppott/biomontools

15Stars

6Forks

39Open issues

0Open PRs

5Releases

453Commits

2Contributors

rbpbiomonitoringbioassessmentmetricbenthicmacorinvertebratesfishperiphyton

453 commits · Last activity 2026-08-12 · 0% stars, 30d

Stars over time

2025-06-05 · 132026-07-07 · 15

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/leppott/biomontools on 2026-08-16.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

Show all practices

Governance and community (1)

Issue templates

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

Dependencies

Declared dependencies

23 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (6)

dplyr maps rlangstatstidyselect tidyr

LinkingTo (0)

none

Suggests (19)

DataExplorer DT ggplot2 knitr lazyeval readxl reshape2 rmarkdown testthat shiny shinydashboard shinydashboardPlus shinyjs shinyWidgetsutilswritexl shinyalert stringr stringdist

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

BCGcalc

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Erik W. Leppo

Author, Maintainer

Authors (1)

Erik W. Leppo

Author, Maintainer

Contributors (3)

Ben Block

Contributor

Jen Stamp

Contributor

John van Sickles

Contributor

Package Timeline

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

1.3.2Latest
2026-08-05 · current release · diff ↗
1.3.1
2026-07-23 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.2.4
2026-03-10
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-10-09
Total releases: 3 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 521 KB / 16 files
Download size: 1.5 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("BioMonTools")

Format

Leppo, E. W., Block, B., Stamp, J., & van Sickles, J. (2026). BioMonTools: Biomonitoring and Bioassessment Calculations (Version 1.3.2) [Computer software]. https://doi.org/10.32614/CRAN.package.BioMonTools

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 BioMonTools version 1.3.2 [Data set]. HJJB, LLC. Data release v2026-08-17. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-17, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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