# Count Regression for Correlated Observations with the Beta-Binomial

## Documentation for package ‘corncob’ version 0.4.1

- 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
dbetabinom_cts | Densities of beta binomial distributions, permitting non integer x and size
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 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