|
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 |
|
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 |
|
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 |