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
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
ibd_phylo               IBD data.
import_phyloseq         Import phyloseq classes for data
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
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
sandSE                  Compute sandwich standard error
score                   Compute score
simulate.bbdml          Simulate from beta-binomial model
soil_phylo              Soil data.
soil_phylum_small       Small soil phylum data for examples
summary.bbdml           Summary function
waldchisq               Wald-type chi-squared test
waldchisq_test          Wald-type chi-squared test statistic
waldt                   Wald-type t test
