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 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!
breakaway implements a number of different richness estimates. Please cite the following if you use them:
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.
You can install
breakaway from github with:
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!
breakaway is no longer being updated on CRAN. You can access v3.0 on CRAN here or with
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.