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Species richness with high diversity
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README.md

breakaway

Travis-CI Build Status Coverage status CRAN version

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!

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

Development version

You can install breakaway from github with:

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!

CRAN

For now, breakaway is no longer being updated on CRAN. You can access v3.0 on CRAN here or with

install.packages("breakaway")

Humans

Maintainer: Amy Willis

Authors: Amy Willis, Bryan Martin, Kathryn Barger and John Bunge

Upcoming features

  • extended tutorials
  • phyloseq integration
  • better unit testing
  • better graphics
  • automated estimator selection based on data structure
  • new format for modelling functions

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.

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