breakaway

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 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:

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!

Documentation

  • The best place to start is the vignettes.
  • Documentation for functions can be found here
  • A pdf of all documentation can be found in the breakaway-manual.pdf
  • We try to answer frequently asked questions on the wiki

Humans

Maintainer: Amy Willis

Authors: Amy Willis, John Bunge, Bryan Martin, Pauline Trinh, Kathryn Barger, David Clausen and Sarah Teichman.

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. We receive a lot of emails from users, so we try to answer questions on the Wiki rather than responding to everyone individually.