Species Richness Estimation and Modeling


[Up] [Top]

Documentation for package ‘breakaway’ version 4.7.9

Help Pages

alpha_estimate alpha_estimate
alpha_estimates alpha_estimates
apples (Data) Frequency count table of soil microbes in an apples orchard.
atacama A canonical QIIME2 dataset
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
dv DivNet model fitted to 'soil_phylo' dataset
dv_days_1_2 DivNet model fitted to 'soil_phylo' dataset including observations on day 1
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
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
submodel_test Output from test_submodel() for use in hypothesis testing vignette
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