corncob0.4.1 package

Maximum Likelihood for the Beta-binomial Distribution

Check for nested models

Rename taxa

Identify differentially-abundant and differentially-variable taxa usin...

Function to subset and convert phyloseq data

Corncob package documentation.

Hyperbolic cotangent transformation

Betabinomial density

Negative betabinomial density

Densities of beta binomial distributions, permitting non integer x and...

Identify differentially-abundant and differentially-variable taxa

Function to run a bootstrap iteration

Fisher's z transformation

Generate initialization for optimization

Get index of restricted terms for Wald test

Parameter Gradient Vector

Get highest density interval of beta-binomial

Compute Hessian matrix at the MLE

Inverse Fisher's z transformation

Inverse logit transformation

Logit transformation

Likelihood ratio test

Objective function

Transform OTUs to their taxonomic label

Parametric bootstrap likelihood ratio test

Parametric bootstrap Rao test

Parametric bootstrap Wald test

Pipe operator

Plotting function

differentialTest plot function

Print function

differentialTest print function

Print summary function

Get quantiles of beta binom

Rao-type chi-squared test (model-based or robust)

Compute sandwich estimate of variance-covariance matrix

Compute sandwich standard errors. Legacy function. Use sand_vcov inste...

Compute score at the MLE

Simulate from beta-binomial model

Summary function

Wald-type chi-squared test

Wald-type chi-squared test statistic (model-based or robust)

Wald-type t test (model-based or robust)

Function to throw error if the phyloseq package is called but it is ...