NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(as.data.frame,alphasample)
S3method(as.data.frame,diffAnalysisClass)
S3method(diff_analysis,data.frame)
S3method(diff_analysis,phyloseq)
S3method(generalizedFC,default)
S3method(generalizedFC,formula)
S3method(get_clust,default)
S3method(get_clust,dist)
S3method(get_clust,phyloseq)
S3method(get_coord,pcoa)
S3method(get_coord,prcomp)
S3method(get_dist,default)
S3method(get_dist,phyloseq)
S3method(get_pca,default)
S3method(get_pca,phyloseq)
S3method(get_pcoa,default)
S3method(get_pcoa,dist)
S3method(get_pcoa,phyloseq)
S3method(get_pvalue,QuadTypeIndependenceTest)
S3method(get_pvalue,ScalarIndependenceTest)
S3method(get_pvalue,glm)
S3method(get_pvalue,htest)
S3method(get_pvalue,lm)
S3method(get_pvalue,lme)
S3method(get_pvalue,negbin)
S3method(get_varct,pcasample)
S3method(get_varct,pcoa)
S3method(get_varct,prcomp)
S3method(ggbartax,default)
S3method(ggbartax,phyloseq)
S3method(ggclust,clustplotClass)
S3method(ggdiffclade,data.frame)
S3method(ggdiffclade,diffAnalysisClass)
S3method(ggdifftaxbar,featureMeanMedian)
S3method(ggeffectsize,data.frame)
S3method(ggeffectsize,diffAnalysisClass)
S3method(ggordpoint,default)
S3method(ggordpoint,pcasample)
S3method(ggrarecurve,default)
S3method(ggrarecurve,phyloseq)
export(build_tree)
export(convert_to_treedata)
export(diff_analysis)
export(drop_taxa)
export(generalizedFC)
export(get_alltaxadf)
export(get_alphaindex)
export(get_clust)
export(get_coord)
export(get_count)
export(get_dist)
export(get_mean_median)
export(get_pca)
export(get_pcoa)
export(get_pvalue)
export(get_ratio)
export(get_sampledflist)
export(get_taxadf)
export(get_upset)
export(get_varct)
export(get_vennlist)
export(ggbartax)
export(ggbox)
export(ggclust)
export(ggdiffbox)
export(ggdiffclade)
export(ggdifftaxbar)
export(ggeffectsize)
export(ggordpoint)
export(ggrarecurve)
export(import_dada2)
export(import_qiime2)
export(mapply_retrieve_seq)
export(multi_compare)
export(read_qza)
export(retrieve_seq)
export(split_data)
export(split_str_to_list)
export(theme_taxbar)
exportClasses(alphasample)
exportClasses(clustplotClass)
exportClasses(diffAnalysisClass)
exportClasses(ordplotClass)
exportClasses(pcasample)
exportMethods(build_tree)
exportMethods(drop_taxa)
exportMethods(get_alltaxadf)
exportMethods(get_alphaindex)
exportMethods(get_taxadf)
exportMethods(get_upset)
exportMethods(get_vennlist)
exportMethods(ggbox)
exportMethods(ggdiffbox)
exportMethods(ggdifftaxbar)
exportMethods(show)
importClassesFrom(phyloseq,phylo)
importFrom(Biostrings,DNAStringSet)
importFrom(Biostrings,readBStringSet)
importFrom(Biostrings,readDNAStringSet)
importFrom(DECIPHER,AlignSeqs)
importFrom(MASS,lda)
importFrom(Rmisc,CI)
importFrom(Rmisc,summarySE)
importFrom(ape,as.phylo)
importFrom(ape,drop.tip)
importFrom(ape,pcoa)
importFrom(ape,read.tree)
importFrom(biomformat,biom_data)
importFrom(biomformat,read_biom)
importFrom(coin,pvalue)
importFrom(dplyr,bind_rows)
importFrom(dplyr,filter)
importFrom(dplyr,group_by_)
importFrom(dplyr,mutate)
importFrom(dplyr,rename)
importFrom(dplyr,rename_)
importFrom(dplyr,select)
importFrom(ggplot2,Stat)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,arrow)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_boxplot)
importFrom(ggplot2,geom_errorbar)
importFrom(ggplot2,geom_errorbarh)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_rect)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,layer)
importFrom(ggplot2,margin)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_linetype_manual)
importFrom(ggplot2,scale_size_continuous)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_text_repel)
importFrom(ggsignif,geom_signif)
importFrom(ggtree,"%<+%")
importFrom(ggtree,geom_point)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,geom_tiplab2)
importFrom(ggtree,geom_tippoint)
importFrom(ggtree,ggtree)
importFrom(grDevices,chull)
importFrom(grDevices,colorRampPalette)
importFrom(gtools,combinations)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(methods,show)
importFrom(patchwork,plot_layout)
importFrom(phangorn,NJ)
importFrom(phangorn,dist.ml)
importFrom(phangorn,optim.pml)
importFrom(phangorn,phyDat)
importFrom(phangorn,pml)
importFrom(phangorn,pml.control)
importFrom(phyloseq,build_tax_table)
importFrom(phyloseq,distance)
importFrom(phyloseq,import_qiime_sample_data)
importFrom(phyloseq,otu_table)
importFrom(phyloseq,parse_taxonomy_greengenes)
importFrom(phyloseq,parse_taxonomy_qiime)
importFrom(phyloseq,phy_tree)
importFrom(phyloseq,phyloseq)
importFrom(phyloseq,rank_names)
importFrom(phyloseq,sample_data)
importFrom(phyloseq,tax_table)
importFrom(phyloseq,taxa_are_rows)
importFrom(plyr,ddply)
importFrom(plyr,llply)
importFrom(plyr,numcolwise)
importFrom(randomForest,importance)
importFrom(randomForest,randomForest)
importFrom(rentrez,entrez_fetch)
importFrom(reshape,melt)
importFrom(rlang,.data)
importFrom(rlang,as_name)
importFrom(rlang,new_formula)
importFrom(scales,squish)
importFrom(stats,aggregate)
importFrom(stats,anova)
importFrom(stats,as.formula)
importFrom(stats,cov)
importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,p.adjust)
importFrom(stats,pnorm)
importFrom(stats,prcomp)
importFrom(stats,quantile)
importFrom(stats,setNames)
importFrom(stats,terms)
importFrom(stats,update)
importFrom(stats,var)
importFrom(stats,wilcox.test)
importFrom(tibble,as_tibble)
importFrom(tibble,column_to_rownames)
importFrom(tibble,rownames_to_column)
importFrom(tidyr,separate)
importFrom(tidytree,treedata)
importFrom(utils,getFromNamespace)
importFrom(utils,modifyList)
importFrom(utils,read.table)
importFrom(utils,unzip)
importFrom(vegan,decostand)
importFrom(vegan,diversity)
importFrom(vegan,estimateR)
importFrom(vegan,rrarefy)
importFrom(vegan,specnumber)
importFrom(yaml,read_yaml)
importFrom(zoo,na.locf)