Man pages for breakaway
Species Richness Estimation and Modeling

alpha_estimatealpha_estimate
alpha_estimatesalpha_estimates
apples(Data) Frequency count table of soil microbes in an apples...
bettaModelling total diversity with betta
betta_lincomConfidence intervals and testing for linear combinations of...
betta_picfunction for plotting total diversity
betta_randommodelling total diversity with random effects
breakawaySpecies richness estimation with breakaway
breakaway_nof1species richness estimation without singletons
build_frequency_count_tablesBuild frequency count tables from an OTU table
chao1Chao1 species richness estimator
chao1_bcBias-corrected Chao1 species richness estimator
chao_bungeChao-Bunge species richness estimator
chao_shenThe Chao-Shen estimate of Shannon diversity
check_formatRun some basic checks on a possible frequency count table
convertconvert between different inputs for alpha-diversity...
cutoff_wrapFind a cut-off for estimates relying on contiguous counts
F_testConduct F test of null hypothesis LB = 0 using output from...
get_F_statCalculate F statistic under null hypothesis LB = 0 using...
good_turingThe Good-Turing estimate of species richness
hawaii(Data) Frequency count table of soil microbes in Hawaii.
kempSpecies richness estimation with Kemp-type models
make_design_matrixMake design matrix
make_frequency_count_tableDraw frequency count subtables from an OTU table
objective_bayes_geometricEstimate species richness with an objective Bayes method...
objective_bayes_mixedgeoObjective Bayes species richness estimate with the...
objective_bayes_negbinObjective Bayes species richness estimate with the Negative...
objective_bayes_poissonObjective Bayes species richness estimate with the Poisson...
pasolli_et_al(Data) Data frame of covariate information about...
physeq_wrapWrapper for phyloseq objects
pipePipe operator
plot.alpha_estimatesPlot function for alpha_estimates class
poisson_modelPoissonModel
poisson_model_nof1PoissonModelNof1
proportions_insteadOTU table to relative abundances
rnbinomtableNegative binomially distributed frequency count tables.
rztnbinomtablebeta version: Zero-truncated negative binomially distributed...
sample_inverse_simpsonPlug-in Inverse Simpson diversity
sample_richnessSample richness estimator
sample_shannonPlug-in Shannon diversity
sample_shannon_ePlug-in Shannon's E ("Equitability")
sample_simpsonPlug-in Simpson diversity
sample_size_estimateEstimate the sample size needed to do an unpaired one-way...
sample_size_figurePlot the power obtained with sample size
simulate_bettaSimulate from a fitted betta model
simulate_betta_randomSimulate from a fitted betta_random model
soil_phylo(Data) Data frame of soil data from whitman_et_al.
test_submodelConduct F test of null hypothesis LB = 0 using output from...
toy_metadata(Data) Data frame of covariate information about...
toy_otu_table(Data) A toy OTU table.
toy_taxonomy(Data) The taxonomy of the OTUs in 'toy_otu_table'.
true_giniCalculate the true Gini-Simpson index
true_hillCalculate the true Hill numbers
true_inverse_simpsonCalculate the true Inverse Simpson index
true_shannonCalculate the true Shannon index based on proportions
true_shannon_eCalculate the true Shannon's equitability index
true_simpsonCalculate the true Simpson index
wlrm_transformedThe transformed weighted linear regression estimator for...
wlrm_untransformedThe untransformed weighted linear regression estimator for...
breakaway documentation built on Nov. 22, 2022, 5:08 p.m.