Title: Species Richness Estimation and Modeling
Description: Species richness estimation is an important problem in biodiversity analysis. This package provides methods for total species richness estimation (observed plus unobserved) and a method for modelling total diversity with covariates. breakaway() estimates total (observed plus unobserved) species richness. Microbial diversity datasets are characterized by a large number of rare species and a small number of highly abundant species. The class of models implemented by breakaway() is flexible enough to model both these features. breakaway_nof1() implements a similar procedure however does not require a singleton count. betta() provides a method for modelling total diversity with covariates in a way that accounts for its estimated nature and thus accounts for unobserved taxa.

Description: Species richness estimation is an important problem in biodiversity analysis. This package provides methods for total species richness estimation (observed plus unobserved) and a method for modelling total diversity with covariates. breakaway() estimates total (observed plus unobserved) species richness. Microbial diversity datasets are characterized by a large number of rare species and a small number of highly abundant species. The class of models implemented by breakaway() is flexible enough to model both these features. breakaway_nof1() implements a similar procedure however does not require a singleton count. betta() provides a method for modelling total diversity with covariates in a way that accounts for its estimated nature and thus accounts for unobserved taxa, and betta_random() permits random effects modelling.

person("Amy", "Willis", email = "adwillis@uw.edu", role = c("aut", "cre"),
person("Bryan D", "Martin", role = "aut",
person("Pauline", "Trinh", role = "aut"),
person("Sarah", "Teichman", role = "aut"),
person("David", "Clausen", role = "aut"),
person("Kathryn", "Barger", role =  "aut"),
Description: 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.
Imports: ggplot2, graphics, lme4, magrittr, MASS, phyloseq, stats,
Suggests: corncob, covr, devtools, dplyr, DT, knitr, openxlsx, plyr,
RCurl, reshape2, R.rsp, remotes, rmarkdown, testthat, tidyverse
Packaged: 2022-02-10 20:08:28 UTC; davidclausen
Author: Amy Willis [aut, cre] (<https://orcid.org/0000-0002-2802-4317>),