BioMonTools

1.3.1

Biomonitoring and Bioassessment Calculations

0packages depend

3.1Kdownloads / year

72.1%test coverage

13/13checks pass

Overview

About

Maintained by Erik W. LeppoFirst published 2025-10-092 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: 8.6 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.39

72.1%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 283 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

3.1K

CRAN downloads in the past year

Rank #15,526 · ~8/day · ~257/mo

Releases R versions

Daily download trend is not available in this view yet.

26130 days

72690 days

3.1K1 year

Compare downloads with other packages →

Also on339 r2u84 autocran

Repository

GitHub ↗ leppott/biomontools

15Stars

5Forks

38Open issues

0Open PRs

5Releases

434Commits

2Contributors

rbpbiomonitoringbioassessmentmetricbenthicmacorinvertebratesfishperiphyton

434 commits · Last activity 2026-07-21 · +7.1% 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 2026-07-19.

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

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 19,147 (82%)Rd 3,464 (15%)Vignettes 796 (3%)Other 1 (0%)

Code characteristics

Cyclomatic complexity: 9.5 median / 76 max
Test cases: 46 / 0.39 per code line

Test coverage

Line coverage

72%

Expression

48.8%

Tests / Examples

72.1% / 45% ex

Functions

22 22 exported

Complexity

15.2 avg / 76 max

Call network

22 nodes / 9 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

22 functions

Function	Cyclo	Coverage
MapTaxaObs exp	12	0%
markExcluded exp	10	0%
metric.stats2 exp	3	0%
metvalgrpxl exp	6	0%
qc.checks exp	4	0%
qc_taxa exp	1	0%

Datasets

Bundled datasets · 16

Name	Class	Rows × Cols	Also ships in
TaxaMaster_Ben_BCG_PacNW	data.frame	684 × 20	–
data_Taxa_MA	data.frame	2,675 × 15	–
data_algae_names_official	tbl_df/tbl/data.frame	3,271 × 8	–
data_algae_names_user	tbl_df/tbl/data.frame	3,271 × 1	–
data_benthos_MBSS	data.frame	5,066 × 42	–
data_benthos_PacNW	data.frame	598 × 39	–
data_bio2rarify	data.frame	350 × 3	–
data_coral_bcg_metric_dev	data.frame	2,138 × 25	–
data_coral_bcg_metric_qc	data.frame	100 × 19	–
data_diatom_mmi_dev	data.frame	24,797 × 48	–
data_diatom_mmi_qc	data.frame	497 × 250	–
data_fish_MBSS	data.frame	1,694 × 30	–
data_metval_scmb_ibi	data.frame	20 × 13	–
data_mmi_dev	data.frame	10,574 × 34	–
data_mmi_dev_small	data.frame	1,374 × 36	–
data_taxa_names_issues	tbl_df/tbl/data.frame	215 × 3	–

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

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

1.3.1Latest
2026-07-23 · current release · 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: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 521 KB / 16 files
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →