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()andkemp(): 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.