Biomonitoring and Bioassessment Calculations

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>.

README-BioMonTools

#> Last Update: 2026-08-04 15:14:46.998886

BioMonTools

Functions to aid the data analysis of bioassessment and biomonitoring data. Suite of functions and tools for metric calculation and scoring for multi-metric indices and related data manipulation.

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Installation

CRAN

To install from CRAN use the code below.

install.packages("BioMonTools")

GitHub

To install the most current version on GitHub use the code below. The use of “force = TRUE” ensures the package is installed even if already present. If the package remotes is missing the code below will install it.

if(!require(remotes)){install.packages("remotes")}  #install if needed
install_github("leppott/BioMonTools", force=TRUE)

Vignettes are not installed by default. If you want the additional documentation (recommended) then use this version of the code.

if(!require(remotes)){install.packages("remotes")}  #install if needed
install_github("leppott/BioMonTools", force=TRUE, build_vignettes=TRUE)

If having issues with install (e.g., ‘cannot open URL’) it could be a latency issue with GitHub.

Use the code below before retrying the above install commands.

options(timeout=400)

Life Cycle Status

Stable and mature.

Usage

By those using involved with bioassessment and biomonitoring and the need for data manipulation.

A common set of tools will standardize outputs across entities. No longer need to use the same database or spreadsheet. Only need to format data for use with these tools.

Documentation

Vignette and install guide updates are planned for the future.

Leppo, E.W., J. Stamp, and B. Block. 2025. BioMonTools: Tools for Biomonitoring and Bioassessment. R package version 1.2.4.9004. https://github.com/leppott/BioMonTools