Count Regression for Correlated Observations with the Beta-Binomial

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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