| 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... |
| 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... |
| differentialTest | Identify differentially-abundant and differentially-variable... |
| 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 |
| pipe | Pipe operator |
| 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 | 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... |
| soil_phylum_contrasts_sample | Small soil phylum data for contrasts examples, sample data as... |
| 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... |
| soil_phylum_small_sample | Small soil phylum data for examples, sample data as data... |
| 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... |
