Man pages for corncob
Count Regression for Correlated Observations with the 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... |
| 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... |
| 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 |
| 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 |
| 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 |
