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
