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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# breakaway <img src="docs/breakaway-logo.png" align="right" width="165px"/>
[](https://travis-ci.org/adw96/breakaway)
[](https://codecov.io/github/adw96/breakaway?branch=master)
`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.
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.
[`DivNet`](https://github.com/adw96/DivNet) is a new package by the same 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!
`breakaway` has undergone substantial renovations to make it more modern, easy-to-use, and robust. If functionality that you previously enjoyed in `breakaway` no longer exists, please submit an [issue](https://github.com/adw96/breakaway/issues)!
### 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), [Bryan Martin](https://bryandmartin.github.io/), [Pauline Trinh](https://twitter.com/paulinetrinh), [Kathryn Barger](http://hnrca.tufts.edu/kathryn-barger-ph-d/) and [John Bunge](https://stat.cornell.edu/people/faculty/john-bunge)
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 [wiki](https://github.com/adw96/breakaway/wiki), then shoot us an email. We receive a lot of emails from users, so we try to answer questions on the Wiki rather than responding to everyone individually.