breakaway: Species Richness Estimation and Modeling
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 species richness, as well as the most commonly used estimates. Methods uniquely available in this package include objective Bayes estimators described in Barger and Bunge (2010) <doi:10.1214/10-BA527>, frequency-ratio-based estimators described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, and as described in Willis, Whitman, and Bunge (2016) <doi:10.1111/rssc.12206>, a linear modeling approach for detecting changes in diversity.
| Version: | 4.7.9 |
| Depends: | R (≥ 3.5.0) |
| Imports: | ggplot2, graphics, lme4, magrittr, MASS, phyloseq, stats, tibble, utils |
| Suggests: | corncob, covr, devtools, dplyr, DT, knitr, openxlsx, plyr, RCurl, reshape2, R.rsp, remotes, rmarkdown, testthat, tidyverse |
| Published: | 2022-03-09 |
| Author: | Amy Willis  [aut,
cre],
Bryan D Martin
[aut],
Pauline Trinh [aut],
Sarah Teichman [aut],
David Clausen [aut],
Kathryn Barger [aut],
John Bunge [aut] |
| Maintainer: | Amy Willis <adwillis at uw.edu> |
| BugReports: | https://github.com/adw96/breakaway/issues |
| License: | GPL-2 |
| URL: | https://adw96.github.io/breakaway/ |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | breakaway results |
Documentation:
| Reference manual: | breakaway.pdf |
| Vignettes: |
getting-started intro-hypothesis-testing intro-diversity-estimation |
Downloads:
| Package source: | breakaway_4.7.9.tar.gz |
| Windows binaries: | r-devel: breakaway_4.7.9.zip, r-release: breakaway_4.7.9.zip, r-oldrel: breakaway_4.7.9.zip |
| macOS binaries: | r-release (arm64): breakaway_4.7.9.tgz, r-oldrel (arm64): breakaway_4.7.9.tgz, r-release (x86_64): breakaway_4.7.9.tgz, r-oldrel (x86_64): breakaway_4.7.9.tgz |
| Old sources: | breakaway archive |
Linking:
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