Package index • corncob

All functions

HDIbetabinom(): Get highest density interval of 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 taxa using contrasts

convert_phylo(): Function to subset and convert phyloseq data

corncob-package corncob: Corncob package documentation.

coth(): Hyperbolic cotangent transformation

dbetabin(): Betabinomial density

dbetabin_neg(): Negative betabinomial density

dbetabinom_cts(): Densities of beta binomial distributions, permitting non integer x and size

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

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