Species Richness Estimation and Modeling
alpha_estimate
alpha_estimates
Modelling total diversity with betta
Confidence intervals and testing for linear combinations of fixed effe...
function for plotting total diversity
modelling total diversity with random effects
Species richness estimation with breakaway
species richness estimation without singletons
Build frequency count tables from an OTU table
Chao-Bunge species richness estimator
The Chao-Shen estimate of Shannon diversity
Chao1 species richness estimator
Bias-corrected Chao1 species richness estimator
Run some basic checks on a possible frequency count table
convert between different inputs for alpha-diversity estimates
Find a cut-off for estimates relying on contiguous counts
Conduct F test of null hypothesis LB = 0 using output from betta() or ...
Calculate F statistic under null hypothesis LB = 0 using output from b...
The Good-Turing estimate of species richness
Species richness estimation with Kemp-type models
Make design matrix
Draw frequency count subtables from an OTU table
Estimate species richness with an objective Bayes method using a geome...
Objective Bayes species richness estimate with the mixed-geometric mod...
Objective Bayes species richness estimate with the Negative Binomial m...
Objective Bayes species richness estimate with the Poisson model
Wrapper for phyloseq objects
Pipe operator
Plot function for alpha_estimates class
PoissonModel
PoissonModelNof1
OTU table to relative abundances
Negative binomially distributed frequency count tables.
beta version: Zero-truncated negative binomially distributed frequency...
Plug-in Inverse Simpson diversity
Sample richness estimator
Plug-in Shannon diversity
Plug-in Shannon's E ("Equitability")
Plug-in Simpson diversity
Estimate the sample size needed to do an unpaired one-way test using b...
Plot the power obtained with sample size
Simulate from a fitted betta model
Simulate from a fitted betta_random model
Conduct F test of null hypothesis LB = 0 using output from betta() or ...
Calculate the true Gini-Simpson index
Calculate the true Hill numbers
Calculate the true Inverse Simpson index
Calculate the true Shannon index based on proportions
Calculate the true Shannon's equitability index
Calculate the true Simpson index
The transformed weighted linear regression estimator for species richn...
The untransformed weighted linear regression estimator for species ric...
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, described in Willis and Bunge (2015) <doi:10.1111/biom.12332>, Willis et al. (2017) <doi:10.1111/rssc.12206>, and Willis (2016) <arXiv:1604.02598>, as well as the most commonly used estimates, including the objective Bayes approach described in Barger and Bunge (2010) <doi:10.1214/10-BA527>.