BioMonTools

Tools for biomonitoring and bioassessment; metric calculation for benthic macroinvertebrates, fish, and periphyton.
https://github.com/leppott/biomontools

Category: Biosphere
Sub Category: Biodiversity Analysis and Metrics

Keywords

benthic bioassessment biomonitoring fish macorinvertebrates metric periphyton r-package rbp

Last synced: about 22 hours ago
JSON representation

Repository metadata

Tools for biomonitoring and bioassessment; metric calculation for benthic macroinvertebrates, fish, and periphyton.

• Host: GitHub
• URL: https://github.com/leppott/biomontools
• Owner: leppott
• License: other
• Created: 2018-11-16T14:55:10.000Z (over 7 years ago)
• Default Branch: main
• Last Pushed: 2026-01-12T19:36:13.000Z (2 months ago)
• Last Synced: 2026-01-24T10:34:07.094Z (about 2 months ago)
• Topics: benthic, bioassessment, biomonitoring, fish, macorinvertebrates, metric, periphyton, r-package, rbp
• Language: R
• Homepage: https://leppott.github.io/BioMonTools/
• Size: 107 MB
• Stars: 15
• Watchers: 6
• Forks: 5
• Open Issues: 31
• Releases: 5
• Metadata Files:
  • Readme: README.Rmd
  • Changelog: NEWS
  • License: LICENSE

README.Rmd

          ---
title: "README-BioMonTools"
output: github_document
---



```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```

```{r, echo = FALSE}
cat(paste0("Last Update: ",Sys.time()))
```
# 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.

 
 
# Badges
[![Maintenance](https://img.shields.io/badge/Maintained%3F-yes-green.svg)](https://GitHub.com/leppott/BioMonTools/graphs/commit-activity)
[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![Life Cycle](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
[![GitHub license](https://img.shields.io/github/license/leppott/BioMonTools.svg)](https://github.com/leppott/BioMonTools/blob/master/LICENSE)

[![CodeFactor](https://www.codefactor.io/repository/github/leppott/BioMonTools/badge)](https://www.codefactor.io/repository/github/leppott/BioMonTools)
[![codecov](https://codecov.io/gh/leppott/BioMonTools/branch/master/graph/badge.svg)](https://app.codecov.io/gh/leppott/BioMonTools)
[![R-CMD-check](https://github.com/leppott/BioMonTools/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/leppott/BioMonTools/actions/workflows/R-CMD-check.yaml)

[![CRAN release](https://www.r-pkg.org/badges/version/badger?color=orange)](https://cran.r-project.org/package=badger)
[![CRAN downloads](http://cranlogs.r-pkg.org/badges/grand-total/BioMonTools?color=blue)](https://cran.r-project.org/package=BioMonTools)

[![GitHub issues](https://img.shields.io/github/issues/leppott/BioMonTools.svg)](https://GitHub.com/leppott/BioMonTools/issues/)


# Installation
## CRAN
To install from CRAN use the code below.
```{r, eval=FALSE}
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.

```{r, eval=FALSE}
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.

```{r, eval=FALSE}
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.

```{r, eval=FALSE}
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

# Issues
https://github.com/leppott/BioMonTools/issues

# Planned Updates

Add as issues for tracking purposes.  Will add metrics and indices as needed.

Updates to CRAN as have time.

        

---

Owner metadata

• Name: Erik Leppo
• Login: leppott
• Email:
• Kind: user
• Description: Environment Scientist / Data Scientist
• Website:
• Location:
• Twitter:
• Company: Tetra Tech
• Icon url: https://avatars.githubusercontent.com/u/24276278?v=4
• Repositories: 31
• Last ynced at: 2024-03-15T03:14:11.440Z
• Profile URL: https://github.com/leppott

---

GitHub Events

Total

• Issues event: 9
• Watch event: 1
• Issue comment event: 14
• Push event: 42

Last Year

• Issues event: 9
• Watch event: 1
• Issue comment event: 14
• Push event: 29

---

Committers metadata

Last synced: 3 months ago

Name	Email	Commits
Erik Leppo	E****o@t****m	370
Blocktt	6****t	27

Committer domains:

• tetratech.com: 1

---

Issue and Pull Request metadata

Last synced: 3 months ago

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/leppott/biomontools

---

---

---

Package metadata

• Total packages: 3
• Total downloads:
  • cran: 1,000 last-month
• Total dependent packages: 0 (may contain duplicates)
• Total dependent repositories: 0 (may contain duplicates)
• Total versions: 11
• Total maintainers: 1

---

Dependencies

Score: 11.43054335636426