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https://github.com/leppott/BioMonTools
Tools for biomonitoring and bioassessment; metric calculation for benthic macroinvertebrates, fish, and periphyton.
https://github.com/leppott/BioMonTools
benthic bioassessment biomonitoring fish macorinvertebrates metric periphyton r-package rbp
Last synced: about 2 months ago
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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 (about 6 years ago)
- Default Branch: main
- Last Pushed: 2024-11-07T13:44:54.000Z (about 2 months ago)
- Last Synced: 2024-11-12T23:38:36.109Z (about 2 months ago)
- Topics: benthic, bioassessment, biomonitoring, fish, macorinvertebrates, metric, periphyton, r-package, rbp
- Language: R
- Homepage: https://leppott.github.io/BioMonTools/
- Size: 103 MB
- Stars: 13
- Watchers: 8
- Forks: 5
- Open Issues: 32
-
Metadata Files:
- Readme: README.Rmd
- Changelog: NEWS
- License: LICENSE
Awesome Lists containing this project
- open-sustainable-technology - BioMonTools - Tools for biomonitoring and bioassessment; metric calculation for benthic macroinvertebrates, fish, and periphyton. (Biosphere / Biodiversity Analysis and Metrics)
README
---
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
[](https://GitHub.com/leppott/BioMonTools/graphs/commit-activity)
[](https://www.tidyverse.org/lifecycle/#stable)
[](https://github.com/leppott/BioMonTools/blob/master/LICENSE)
[](https://www.codefactor.io/repository/github/leppott/BioMonTools)
[](https://codecov.io/gh/leppott/BioMonTools)
[](https://github.com/leppott/BioMonTools/actions/workflows/R-CMD-check.yaml)
[](https://GitHub.com/leppott/BioMonTools/issues/)
[](https://GitHub.com/leppott/BioMonTools/releases/)
[](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