# Count Regression for Correlated Observations with the Beta-Binomial

## Documentation for package ‘corncob’ version 0.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

corncob-package | Corncob package documentation.
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 | 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
HDIbetabinom | Get highest density interval of beta-binomial
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