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 3 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: mit
• Created: 2018-11-16T14:55:10.000Z (over 6 years ago)
• Default Branch: main
• Last Pushed: 2025-04-04T16:01:38.000Z (23 days ago)
• Last Synced: 2025-04-20T09:04:38.078Z (7 days ago)
• Topics: benthic, bioassessment, biomonitoring, fish, macorinvertebrates, metric, periphyton, r-package, rbp
• Language: R
• Homepage: https://leppott.github.io/BioMonTools/
• Size: 106 MB
• Stars: 13
• Watchers: 7
• Forks: 5
• Open Issues: 32
• Releases: 4
• 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 mult-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)
[![](https://img.shields.io/badge/lifecycle-stable-green.svg)](https://www.tidyverse.org/lifecycle/#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://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)

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

[![GitHub release](https://img.shields.io/github/release/leppott/BioMonTools.svg)](https://GitHub.com/leppott/BioMonTools/releases/)
[![Github all releases](https://img.shields.io/github/downloads/leppott/BioMonTools/total.svg)](https://GitHub.com/leppott/BioMonTools/releases/)


# Installation
To install the current version use the code below to install from GitHub.  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)
```

# Status
In development. 

# 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.

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

# Planned Updates

* None at this time.

# Future Possible Updates

* Periphyton metrics.
* Coral and Fish metrics (Puerto Rico and US Virgin Islands)
* TaxaList Check
* Map taxon observations

        

---

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: 4
• Issue comment event: 4
• Push event: 18

Last Year

• Issues event: 4
• Issue comment event: 4
• Push event: 18

---

Committers metadata

Last synced: 6 days ago

Name	Email	Commits
Erik Leppo	E****o@t****m	339
Blocktt	6****t	26

Committer domains:

• tetratech.com: 1

---

Issue and Pull Request metadata

Last synced: 1 day ago

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

---

---

---

Dependencies

Score: 4.499809670330265