Package index • breakaway

All functions
`F_test()`	Conduct F test of null hypothesis LB = 0 using output from betta() or betta_random()
`alpha_estimate()`	alpha_estimate
`alpha_estimates()`	alpha_estimates
`apples`	(Data) Frequency count table of soil microbes in an apples orchard.
`betta()`	Modelling total diversity with betta
`betta_lincom()`	Confidence intervals and testing for linear combinations of fixed effects estimated via betta() or betta_random()
`betta_pic()`	function for plotting total diversity
`betta_random()`	modelling total diversity with random effects
`breakaway()`	Species richness estimation with breakaway
`breakaway_nof1()`	species richness estimation without singletons
`build_frequency_count_tables()`	Build frequency count tables from an OTU table
`chao1()`	Chao1 species richness estimator
`chao1_bc()`	Bias-corrected Chao1 species richness estimator
`chao_bunge()`	Chao-Bunge species richness estimator
`chao_shen()`	The Chao-Shen estimate of Shannon diversity
`check_format()`	Run some basic checks on a possible frequency count table
`convert()`	convert between different inputs for alpha-diversity estimates
`cutoff_wrap()`	Find a cut-off for estimates relying on contiguous counts
`get_F_stat()`	Calculate F statistic under null hypothesis LB = 0 using output from betta() or betta_random()
`good_turing()`	The Good-Turing estimate of species richness
`hawaii`	(Data) Frequency count table of soil microbes in Hawaii.
`kemp()`	Species richness estimation with Kemp-type models
`make_design_matrix()`	Make design matrix
`make_frequency_count_table()`	Draw frequency count subtables from an OTU table
`objective_bayes_geometric()`	Estimate species richness with an objective Bayes method using a geometric model
`objective_bayes_mixedgeo()`	Objective Bayes species richness estimate with the mixed-geometric model
`objective_bayes_negbin()`	Objective Bayes species richness estimate with the Negative Binomial model
`objective_bayes_poisson()`	Objective Bayes species richness estimate with the Poisson model
`pasolli_et_al`	(Data) Data frame of covariate information about pasolli_et_al.
`physeq_wrap()`	Wrapper for phyloseq objects
`plot(<alpha_estimates>)`	Plot function for alpha_estimates class
`poisson_model()`	PoissonModel
`poisson_model_nof1()`	PoissonModelNof1
`proportions_instead()`	OTU table to relative abundances
`rnbinomtable()`	Negative binomially distributed frequency count tables.
`rztnbinomtable()`	beta version: Zero-truncated negative binomially distributed frequency count tables.
`sample_inverse_simpson()`	Plug-in Inverse Simpson diversity
`sample_richness()`	Sample richness estimator
`sample_shannon()`	Plug-in Shannon diversity
`sample_shannon_e()`	Plug-in Shannon's E ("Equitability")
`sample_simpson()`	Plug-in Simpson diversity
`sample_size_estimate()`	Estimate the sample size needed to do an unpaired one-way test using betta
`sample_size_figure()`	Plot the power obtained with sample size
`simulate_betta()`	Simulate from a fitted betta model
`simulate_betta_random()`	Simulate from a fitted betta_random model
`soil_phylo`	(Data) Data frame of soil data from whitman_et_al.
`test_submodel()`	Conduct F test of null hypothesis LB = 0 using output from betta() or betta_random()
`toy_metadata`	(Data) Data frame of covariate information about toy_otu_table.
`toy_otu_table`	(Data) A toy OTU table.
`toy_taxonomy`	(Data) The taxonomy of the OTUs in `toy_otu_table`.
`true_gini()`	Calculate the true Gini-Simpson index
`true_hill()`	Calculate the true Hill numbers
`true_inverse_simpson()`	Calculate the true Inverse Simpson index
`true_shannon()`	Calculate the true Shannon index based on proportions
`true_shannon_e()`	Calculate the true Shannon's equitability index
`true_simpson()`	Calculate the true Simpson index
`wlrm_transformed()`	The transformed weighted linear regression estimator for species richness estimation
`wlrm_untransformed()`	The untransformed weighted linear regression estimator for species richness estimation

Reference

All functions