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biomontools

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

https://github.com/leppott/biomontools

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (17.1%) to scientific vocabulary

Keywords

benthic bioassessment biomonitoring fish macorinvertebrates metric periphyton r-package rbp
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 14
  • Watchers: 7
  • Forks: 5
  • Open Issues: 33
  • Releases: 4
Topics
benthic bioassessment biomonitoring fish macorinvertebrates metric periphyton r-package rbp
Created over 7 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog 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

  • Name: Erik Leppo
  • Login: leppott
  • Kind: user
  • Company: Tetra Tech

Environment Scientist / Data Scientist

GitHub Events

Total
  • Issues event: 8
  • Watch event: 1
  • Issue comment event: 12
  • Push event: 21
Last Year
  • Issues event: 8
  • Watch event: 1
  • Issue comment event: 12
  • Push event: 21

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 369
  • Total Committers: 2
  • Avg Commits per committer: 184.5
  • Development Distribution Score (DDS): 0.073
Past Year
  • Commits: 28
  • Committers: 2
  • Avg Commits per committer: 14.0
  • Development Distribution Score (DDS): 0.036
Top Committers
Name Email Commits
Erik Leppo E****o@t****m 342
Blocktt 6****t 27
Committer Domains (Top 20 + Academic)
tetratech.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 92
  • Total pull requests: 17
  • Average time to close issues: 4 months
  • Average time to close pull requests: 10 days
  • Total issue authors: 3
  • Total pull request authors: 2
  • Average comments per issue: 2.02
  • Average comments per pull request: 0.59
  • Merged pull requests: 10
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.83
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • leppott (89)
  • Blocktt (2)
  • johnzastrow (1)
Pull Request Authors
  • Blocktt (16)
  • leppott (1)
Top Labels
Issue Labels
metrics (40) enhancement (8) bug (4) on hold (3) Add "test" (3) HIGH PRIORITY (1) test (investigate) (1) wontfix (1) documentation (1) good first issue (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads: unknown
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 10
proxy.golang.org: github.com/leppott/BioMonTools
  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/leppott/biomontools
  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.3.3 depends
  • dplyr * imports
  • maps * imports
  • stats * imports
  • tidyr * imports
  • tidyselect * imports
  • DT * suggests
  • DataExplorer * suggests
  • ggplot2 * suggests
  • knitr * suggests
  • lazyeval * suggests
  • readxl * suggests
  • reshape2 * suggests
  • rmarkdown * suggests
  • shiny * suggests
  • shinyWidgets * suggests
  • shinydashboard * suggests
  • shinydashboardPlus * suggests
  • shinyjs * suggests
  • testthat * suggests
  • writexl * suggests
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
.github/workflows/test-coverage.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite