Species Richness Estimation and Modeling

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Documentation for package ‘breakaway’ version 4.8.4

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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
F_test	Conduct F test of null hypothesis LB = 0 using output from betta() or betta_random()
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