HDIbetabinom            Get highest density interval of beta-binomial
bbdml                   Maximum Likelihood for the Beta-binomial
                        Distribution
checkNested             Check for nested models
clean_taxa_names        Rename taxa
contrastsTest           Identify differentially-abundant and
                        differentially-variable taxa using contrasts
convert_phylo           Function to subset and convert phyloseq data
corncob-package         Corncob package documentation.
coth                    Hyperbolic cotangent transformation
dbetabin                Betabinomial density
dbetabin_neg            Negative betabinomial density
dbetabinom_cts          Densities of beta binomial distributions,
                        permitting non integer x and size
differentialTest        Identify differentially-abundant and
                        differentially-variable taxa
doBoot                  Function to run a bootstrap iteration
fishZ                   Fisher's z transformation
genInits                Generate initialization for optimization
getRestrictionTerms     Get index of restricted terms for Wald test
gr_full                 Parameter Gradient Vector
hessian                 Compute Hessian matrix at the MLE
ibd_phylo_otu           IBD data, OTU count data frame.
ibd_phylo_sample        IBD data, sample data frame.
ibd_phylo_taxa          IBD data, taxonomy data frame.
invfishZ                Inverse Fisher's z transformation
invlogit                Inverse logit transformation
logit                   Logit transformation
lrtest                  Likelihood ratio test
objfun                  Objective function
otu_to_taxonomy         Transform OTUs to their taxonomic label
pbLRT                   Parametric bootstrap likelihood ratio test
pbRao                   Parametric bootstrap Rao test
pbWald                  Parametric bootstrap Wald test
plot.bbdml              Plotting function
plot.differentialTest   differentialTest plot function
print.bbdml             Print function
print.differentialTest
                        differentialTest print function
print.summary.bbdml     Print summary function
qbetabinom              Get quantiles of beta binom
raotest                 Rao-type chi-squared test (model-based or
                        robust)
sandSE                  Compute sandwich standard errors. Legacy
                        function. Use sand_vcov instead.
sand_vcov               Compute sandwich estimate of
                        variance-covariance matrix
score                   Compute score at the MLE
simulate.bbdml          Simulate from beta-binomial model
soil_phylo_otu          Soil data, otu table as data frame.
soil_phylo_sample       Soil data, sample data.
soil_phylo_taxa         Soil data, taxa table as data frame.
soil_phylum_contrasts_otu
                        Small soil phylum data for contrasts examples,
                        otu table as data frame
soil_phylum_contrasts_sample
                        Small soil phylum data for contrasts examples,
                        sample data as data frame
soil_phylum_small_otu   Small soil phylum data for examples, otu table
                        as data frame
soil_phylum_small_otu1
                        Small soil phylum data for examples, sample
                        data as data frame combined with counts for OTU
                        1 and sequencing depth.
soil_phylum_small_sample
                        Small soil phylum data for examples, sample
                        data as data frame
summary.bbdml           Summary function
waldchisq               Wald-type chi-squared test
waldchisq_test          Wald-type chi-squared test statistic
                        (model-based or robust)
waldt                   Wald-type t test (model-based or robust)
warn_phyloseq           Function to throw error if the 'phyloseq'
                        package is called but it is not installed
