Count Regression for Correlated Observations with the Beta-Binomial


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Documentation for package ‘corncob’ version 0.2.0

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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