All functions

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

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

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

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