├── .Rbuildignore ├── .github ├── .gitignore └── workflows │ ├── R-CMD-check.yaml │ ├── pkgdown.yaml │ └── test-coverage.yaml ├── .gitignore ├── CRAN-SUBMISSION ├── DESCRIPTION ├── Dockerfile ├── NAMESPACE ├── R ├── HDIbetabinom.R ├── bbdml.R ├── checkNested.R ├── clean_taxa_names.R ├── contrastsTest.R ├── convert_phylo.R ├── convert_sumexp.R ├── corncob.R ├── dbetabin.R ├── dbetabinom_ee.R ├── differentialTest.R ├── doBoot.R ├── genInits.R ├── getRestrictionTerms.R ├── gr_full.R ├── hessian.R ├── ibd_phylo_otu.R ├── ibd_phylo_sample.R ├── ibd_phylo_taxa.R ├── links.R ├── lrtest.R ├── objfun.R ├── otu_to_taxonomy.R ├── pbLRT.R ├── pbRao.R ├── pbWald.R ├── plot_bbdml.R ├── plot_differentialTest.R ├── print_bbdml.R ├── print_differentialTest.R ├── print_summary_bbdml.R ├── qbetabinom.R ├── rao.R ├── sandSE.R ├── score.R ├── separation.R ├── simulate.R ├── soil_phylo_otu.R ├── soil_phylo_sample.R ├── soil_phylo_taxa.R ├── soil_phylum_contrasts_otu.R ├── soil_phylum_contrasts_sample.R ├── soil_phylum_small_otu.R ├── soil_phylum_small_otu1.R ├── soil_phylum_small_sample.R ├── summary_bbdml.R ├── utils-pipe.R ├── wald.R └── warn_phyloseq.R ├── README.md ├── _pkgdown.yml ├── corncob.Rproj ├── cran-comments.md ├── data ├── ibd_phylo_otu.rda ├── ibd_phylo_sample.rda ├── ibd_phylo_taxa.rda ├── soil_phylo_otu.rda ├── soil_phylo_sample.rda ├── soil_phylo_taxa.rda ├── soil_phylum_contrasts_otu.rda ├── soil_phylum_contrasts_sample.rda ├── soil_phylum_small_otu.rda ├── soil_phylum_small_otu1.rda └── soil_phylum_small_sample.rda ├── man ├── HDIbetabinom.Rd ├── bbdml.Rd ├── checkNested.Rd ├── clean_taxa_names.Rd ├── clean_taxa_names_se.Rd ├── contrastsTest.Rd ├── convert_phylo.Rd ├── convert_sumexp.Rd ├── corncob-package.Rd ├── coth.Rd ├── dbetabin.Rd ├── dbetabin_neg.Rd ├── dbetabinom_cts.Rd ├── differentialTest.Rd ├── doBoot.Rd ├── figures │ └── logo.png ├── fishZ.Rd ├── genInits.Rd ├── getRestrictionTerms.Rd ├── gr_full.Rd ├── hessian.Rd ├── ibd_phylo_otu.Rd ├── ibd_phylo_sample.Rd ├── ibd_phylo_taxa.Rd ├── invfishZ.Rd ├── invlogit.Rd ├── logit.Rd ├── lrtest.Rd ├── objfun.Rd ├── otu_to_taxonomy.Rd ├── otu_to_taxonomy_se.Rd ├── pbLRT.Rd ├── pbRao.Rd ├── pbWald.Rd ├── pipe.Rd ├── plot.bbdml.Rd ├── plot.differentialTest.Rd ├── print.bbdml.Rd ├── print.differentialTest.Rd ├── print.summary.bbdml.Rd ├── qbetabinom.Rd ├── raotest.Rd ├── sandSE.Rd ├── sand_vcov.Rd ├── score.Rd ├── simulate.bbdml.Rd ├── soil_phylo_otu.Rd ├── soil_phylo_sample.Rd ├── soil_phylo_taxa.Rd ├── soil_phylum_contrasts_otu.Rd ├── soil_phylum_contrasts_sample.Rd ├── soil_phylum_small_otu.Rd ├── soil_phylum_small_otu1.Rd ├── soil_phylum_small_sample.Rd ├── summary.bbdml.Rd ├── waldchisq.Rd ├── waldchisq_test.Rd ├── waldt.Rd ├── warn_phyloseq.Rd └── warn_sumexp.Rd ├── pkgdown └── favicon │ ├── apple-touch-icon-120x120.png │ ├── apple-touch-icon-152x152.png │ ├── apple-touch-icon-180x180.png │ ├── apple-touch-icon-60x60.png │ ├── apple-touch-icon-76x76.png │ ├── 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