# Generated by roxygen2: do not edit by hand

S3method(plot,labeled.phenotype.trees)
export(above_minimum_genes)
export(add.below.LOD)
export(add.sig.descs)
export(adjust.db)
export(alt.multi.enrich)
export(ashr.diff.abund)
export(augment_with_enrichments)
export(calc.alpha.power)
export(calc.ess)
export(calculate_phenotypes)
export(change.presence.tax.level)
export(change.tree.tax.level)
export(check.process.metadata)
export(check_data_found)
export(clean.pheno)
export(correl.clr)
export(data_to_phenotypes)
export(do.clust.plot)
export(do.fisher)
export(enrich_downloaded_KEGG)
export(gene.annot)
export(get.appspam.results)
export(get.pheno.plotting.scales)
export(get.top.N)
export(get.vsearch.results)
export(getClinDT)
export(get_all_associated_genes)
export(get_enrichment_tbls)
export(get_signif_associated_genes)
export(gg.cont.tree)
export(harmonize.abd.meta)
export(import.pz.db)
export(install_data)
export(interactive.plot)
export(kable.recolor)
export(keep.tips)
export(kegg.enrich.single)
export(knitPrintListObjects)
export(knitPrintListPlots)
export(lm.fx.pv)
export(logistic)
export(logit)
export(logit_auc_pheno)
export(make.pos.sig)
export(make.results.matrix)
export(make.signs)
export(make.sigs)
export(matrix.POMS)
export(matrix.plm)
export(multi.enrich)
export(multi.kegg.enrich)
export(non.interactive.plot)
export(nonequiv.pos.sig)
export(nonparallel.results.generator)
export(output.enr.table)
export(pheno_nonzero_var)
export(phylogenize)
export(phylogenize_core)
export(phylolm.fx.pv)
export(plot.pheno.distributions)
export(plot.phenotype.trees)
export(prepare.vsearch.input)
export(prev.addw)
export(process.16s)
export(pv1)
export(pz.error)
export(pz.message)
export(pz.options)
export(pz.warning)
export(quant_norm)
export(quantile_normalize)
export(read.abd.metadata)
export(remove.allzero.abundances)
export(render_core_report)
export(result.wrapper.plm)
export(results.report)
export(retain.observed.taxa)
export(run.vsearch)
export(sanity.check.abundance)
export(sanity.check.metadata)
export(set_data_internal)
export(single.cluster.plot)
export(sum.nonunique.vsearch)
export(tax.annot)
export(tbl.result.qvs)
export(threshold.pos.sigs)
import(Matrix)
importFrom(ggtree,"%<+%")
importFrom(settings,clone_and_merge)
