Science Score: 36.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓.zenodo.json file
Found .zenodo.json file -
○DOI references
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✓Committers with academic emails
8 of 14 committers (57.1%) from academic institutions -
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary
Last synced: 10 months ago
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JSON representation
Repository
Species richness with high diversity
Basic Info
- Host: GitHub
- Owner: adw96
- Language: R
- Default Branch: main
- Size: 11.5 MB
Statistics
- Stars: 68
- Watchers: 10
- Forks: 18
- Open Issues: 8
- Releases: 0
Created about 10 years ago
· Last pushed about 1 year ago
Metadata Files
Readme
README.Rmd
---
output: github_document
---
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# breakaway 
[](https://github.com/adw96/breakaway/actions)
[](https://codecov.io/github/adw96/breakaway?branch=main)
Understanding the drivers of microbial diversity is an important frontier of microbial ecology, and investigating the diversity of samples from microbial ecosystems is a common step in any microbiome analysis.
`breakaway` is the premier package for statistical analysis of microbial diversity. `breakaway` implements the latest and greatest estimates of richness, as well as the most commonly used estimates.
[`DivNet`](https://github.com/adw96/DivNet) is a package by the `breakaway` authors for estimating Shannon diversity, and other diversity indices. `breakaway` focuses on richness while `DivNet` focuses on Shannon, Simpson, and other alpha diversities as well as some beta diversity indices. Check it out!
### Citing breakaway
The `R` package `breakaway` implements a number of different richness estimates. Please cite the following if you use them:
- `breakaway()` and `kemp()`: Willis, A. & Bunge, J. (2015). Estimating diversity via frequency ratios. Biometrics.
- `betta()`: Willis, A., Bunge, J., & Whitman, T. (2017). Improved detection of changes in species richness in high diversity microbial communities. JRSS-C.
- `breakaway_nof1()`: Willis, A. (2016+). Species richness estimation with high diversity but spurious singletons. arXiv.
- `objective_bayes_*()`: Barger, K. & Bunge, J. (2010). Objective Bayesian estimation for the number of species. Bayesian Analysis.
## Installation
You can install `breakaway` from github by running:
```R
install.packages("devtools")
devtools::install_github("adw96/breakaway")
```
`breakaway` is actively maintained and continually expanding and developing its scope! Is there a method you would like to have implemented in breakaway? Submit a pull request or contact the [maintainer](http://statisticaldiversitylab.com/team/amy-willis)!
### Documentation
- The best place to start is the [vignettes](https://adw96.github.io/breakaway/articles/).
- Documentation for functions can be found [here](https://adw96.github.io/breakaway/reference/index.html)
- A pdf of all documentation can be found in the [breakaway-manual.pdf](https://github.com/adw96/breakaway/tree/master/breakaway-manual.pdf)
- We try to answer frequently asked questions on the [wiki](https://github.com/adw96/breakaway/wiki)
## Humans
Maintainer: [Amy Willis](http://statisticaldiversitylab.com)
Authors: [Amy Willis](http://statisticaldiversitylab.com), John Bunge, [Bryan Martin](https://bryandmartin.github.io/), [Pauline Trinh](https://twitter.com/paulinetrinh), Kathryn Barger, [David Clausen](https://www.biostat.washington.edu/people/david-clausen) and [Sarah Teichman](https://svteichman.github.io/).
Do you have a request for us? Let us know! We want folks to use `breakaway` and are committed to making it as easy to use as possible.
Do you have a question? Check out the above documentation list, then shoot us an email or open a [Discussion](https://github.com/adw96/breakaway/discussions). We receive a lot of emails from users, so we try to answer questions on the Wiki rather than responding to everyone individually.
Owner
- Name: AmyW
- Login: adw96
- Kind: user
- Location: Seattle, WA
- Company: University of Washington
- Website: statisticaldiversitylab.com
- Twitter: AmyDWillis
- Repositories: 3
- Profile: https://github.com/adw96
statistician, biodiversity enthusiast, assistant professor
GitHub Events
Total
- Issues event: 10
- Issue comment event: 18
- Push event: 1
- Pull request review event: 2
- Pull request event: 2
Last Year
- Issues event: 10
- Issue comment event: 18
- Push event: 1
- Pull request review event: 2
- Pull request event: 2
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Amy Willis | a****7@g****m | 139 |
| adw96 | a****6@c****u | 62 |
| Sarah Teichman | t****s@u****u | 54 |
| Bryan Martin | b****6@u****u | 35 |
| ailurophilia | d****4@u****u | 15 |
| Sarah Teichman | s****8@a****u | 13 |
| Pauline Trinh | p****h@P****e | 10 |
| Pauline Trinh | p****h@P****l | 3 |
| kathrynbarger | k****r@g****m | 3 |
| Maria Valdez Cabrera | l****a@M****l | 2 |
| Kathryn Barger | k****2@a****u | 1 |
| Nate Olson | n****n@n****v | 1 |
| kathrynbarger | k****3@g****m | 1 |
| paulinetrinh | p****8@u****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 60
- Total pull requests: 55
- Average time to close issues: 4 months
- Average time to close pull requests: 13 days
- Total issue authors: 40
- Total pull request authors: 5
- Average comments per issue: 2.9
- Average comments per pull request: 0.76
- Merged pull requests: 34
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 6
- Pull requests: 2
- Average time to close issues: 2 months
- Average time to close pull requests: 3 months
- Issue authors: 4
- Pull request authors: 1
- Average comments per issue: 2.83
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- adw96 (10)
- svteichman (5)
- AlexaBennett (2)
- jehaab (2)
- msmcfarlin (2)
- naurasd (2)
- gabrielet (2)
- dleopold (2)
- ivanllampy (2)
- adriaaula (1)
- ailurophilia (1)
- cjburgess (1)
- nicholascdove (1)
- icar-y (1)
- kunstner (1)
Pull Request Authors
- ailurophilia (23)
- svteichman (22)
- paulinetrinh (6)
- MariaAVC (3)
- AliceSommer (1)
Top Labels
Issue Labels
enhancement (7)
not-an-issue (3)
help wanted (2)
question (2)
bug (2)
urgent (1)
not-amys-fault (1)
not urgent (1)
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- cran 1,294 last-month
- Total dependent packages: 0
- Total dependent repositories: 3
- Total versions: 7
- Total maintainers: 1
cran.r-project.org: breakaway
Species Richness Estimation and Modeling
- Homepage: https://adw96.github.io/breakaway/
- Documentation: http://cran.r-project.org/web/packages/breakaway/breakaway.pdf
- License: GPL-2
-
Latest release: 4.8.4
published over 3 years ago
Rankings
Forks count: 4.1%
Stargazers count: 5.4%
Average: 15.5%
Dependent repos count: 16.4%
Downloads: 22.9%
Dependent packages count: 28.6%
Maintainers (1)
Last synced:
11 months ago
Dependencies
DESCRIPTION
cran
- R >= 3.5.0 depends
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.github/workflows/R-CMD-check.yaml
actions
- actions/cache v3 composite
- actions/checkout v3 composite
- actions/upload-artifact main composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
.github/workflows/test-coverage.yaml
actions
- actions/cache v3 composite
- actions/checkout v3 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite