# Generated by roxygen2: do not edit by hand

S3method("$",diffAnalysisClass)
S3method("[",diffAnalysisClass)
S3method("[",tbl_mpse)
S3method("[[",diffAnalysisClass)
S3method(arrange,MPSE)
S3method(arrange,grouped_df_mpse)
S3method(arrange,tbl_mpse)
S3method(as.data.frame,MPSE)
S3method(as.data.frame,alphasample)
S3method(as.data.frame,diffAnalysisClass)
S3method(as.phyloseq,MPSE)
S3method(as.phyloseq,grouped_df_mpse)
S3method(as.phyloseq,tbl_mpse)
S3method(as.treedata,taxonomyTable)
S3method(as.treedata,treedata)
S3method(as_tibble,MPSE)
S3method(as_tibble,grouped_df_mpse)
S3method(as_tibble,phyloseq)
S3method(diff_analysis,data.frame)
S3method(diff_analysis,phyloseq)
S3method(dim,diffAnalysisClass)
S3method(distinct,MPSE)
S3method(distinct,grouped_df_mpse)
S3method(distinct,tbl_mpse)
S3method(extract_binary_offspring,phylo)
S3method(extract_binary_offspring,treedata)
S3method(filter,MPSE)
S3method(filter,alphasample)
S3method(filter,diffAnalysisClass)
S3method(filter,grouped_df_mpse)
S3method(filter,tbl_mpse)
S3method(generalizedFC,default)
S3method(generalizedFC,formula)
S3method(get_clust,data.frame)
S3method(get_clust,dist)
S3method(get_clust,phyloseq)
S3method(get_coord,pcoa)
S3method(get_coord,prcomp)
S3method(get_dist,data.frame)
S3method(get_dist,phyloseq)
S3method(get_pca,data.frame)
S3method(get_pca,phyloseq)
S3method(get_pcoa,data.frame)
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,data.frame)
S3method(ggbartax,phyloseq)
S3method(ggclust,treedata)
S3method(ggdiffclade,data.frame)
S3method(ggdiffclade,diffAnalysisClass)
S3method(ggdifftaxbar,featureMeanMedian)
S3method(ggeffectsize,data.frame)
S3method(ggeffectsize,diffAnalysisClass)
S3method(ggordpoint,default)
S3method(ggordpoint,pcasample)
S3method(ggplot_add,ScaleDiffClade)
S3method(ggrarecurve,data.frame)
S3method(ggrarecurve,phyloseq)
S3method(ggrarecurve,rarecurve)
S3method(group_by,MPSE)
S3method(group_by,tbl_mpse)
S3method(head,alphasample)
S3method(head,diffAnalysisClass)
S3method(left_join,MPSE)
S3method(left_join,tbl_mpse)
S3method(mp_fortify,anosim)
S3method(mp_fortify,anova.cca)
S3method(mp_fortify,envfit)
S3method(mp_fortify,mantel)
S3method(mp_fortify,mantel.partial)
S3method(mp_fortify,mrpp)
S3method(mutate,MPSE)
S3method(mutate,grouped_df_mpse)
S3method(mutate,tbl_mpse)
S3method(nest,grouped_df_mpse)
S3method(nest,tbl_mpse)
S3method(print,MPSE)
S3method(print,grouped_df_mpse)
S3method(print,rarecurve)
S3method(print,tbl_mpse)
S3method(pull,MPSE)
S3method(rename,MPSE)
S3method(rename,grouped_df_mpse)
S3method(rename,tbl_mpse)
S3method(select,MPSE)
S3method(select,alphasample)
S3method(select,diffAnalysisClass)
S3method(select,grouped_df_mpse)
S3method(select,tbl_mpse)
S3method(slice,MPSE)
S3method(tail,diffAnalysisClass)
S3method(ungroup,grouped_df_mpse)
S3method(unnest,tbl_mpse_nest)
export("%<>%")
export("%>%")
export("colData<-")
export("otutree<-")
export("refsequence<-")
export("taxatree<-")
export("taxonomy<-")
export(MPSE)
export(arrange)
export(as.MPSE)
export(as.mpse)
export(as.phyloseq)
export(as.treedata)
export(as_phyloseq)
export(as_tibble)
export(build_tree)
export(convert_to_treedata)
export(diff_analysis)
export(distinct)
export(dr_extract)
export(drop_taxa)
export(extract)
export(extract_binary_offspring)
export(filter)
export(generalizedFC)
export(get_NRI_NTI)
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_rarecurve)
export(get_ratio)
export(get_sampledflist)
export(get_taxadf)
export(get_upset)
export(get_varct)
export(get_vennlist)
export(ggbartax)
export(ggbartaxa)
export(ggbox)
export(ggclust)
export(ggdiffbartaxa)
export(ggdiffbox)
export(ggdiffclade)
export(ggdifftaxbar)
export(ggeffectsize)
export(ggordpoint)
export(ggrarecurve)
export(group_by)
export(import_dada2)
export(import_qiime2)
export(left_join)
export(mp_adonis)
export(mp_aggregate)
export(mp_aggregate_clade)
export(mp_anosim)
export(mp_balance_clade)
export(mp_cal_abundance)
export(mp_cal_alpha)
export(mp_cal_cca)
export(mp_cal_clust)
export(mp_cal_dca)
export(mp_cal_dist)
export(mp_cal_divergence)
export(mp_cal_nmds)
export(mp_cal_pca)
export(mp_cal_pcoa)
export(mp_cal_pd_metric)
export(mp_cal_rarecurve)
export(mp_cal_rda)
export(mp_cal_upset)
export(mp_cal_venn)
export(mp_decostand)
export(mp_diff_analysis)
export(mp_diff_clade)
export(mp_dmn)
export(mp_dmngroup)
export(mp_envfit)
export(mp_extract_abundance)
export(mp_extract_assays)
export(mp_extract_dist)
export(mp_extract_feature)
export(mp_extract_internal_attr)
export(mp_extract_otutree)
export(mp_extract_rarecurve)
export(mp_extract_refseq)
export(mp_extract_sample)
export(mp_extract_taxatree)
export(mp_extract_taxonomy)
export(mp_extract_tree)
export(mp_filter_taxa)
export(mp_fortify)
export(mp_import_biom)
export(mp_import_dada2)
export(mp_import_metaphlan)
export(mp_import_qiime)
export(mp_import_qiime2)
export(mp_mantel)
export(mp_mrpp)
export(mp_plot_abundance)
export(mp_plot_alpha)
export(mp_plot_diff_boxplot)
export(mp_plot_diff_cladogram)
export(mp_plot_diff_manhattan)
export(mp_plot_diff_res)
export(mp_plot_dist)
export(mp_plot_ord)
export(mp_plot_rarecurve)
export(mp_plot_upset)
export(mp_plot_venn)
export(mp_rrarefy)
export(mp_select_as_tip)
export(mp_stat_taxa)
export(multi_compare)
export(mutate)
export(nest)
export(otutree)
export(pull)
export(read_qza)
export(refsequence)
export(remove_missing)
export(rename)
export(scale_fill_diff_cladogram)
export(select)
export(set_diff_boxplot_color)
export(set_scale_theme)
export(slice)
export(split_data)
export(split_str_to_list)
export(tax_table)
export(taxatree)
export(taxonomy)
export(td_filter)
export(td_unnest)
export(theme_taxbar)
export(ungroup)
export(unnest)
exportClasses(MPSE)
exportClasses(alphasample)
exportClasses(diffAnalysisClass)
exportClasses(ordplotClass)
exportClasses(pcasample)
exportMethods("[")
exportMethods("colData<-")
exportMethods("otutree<-")
exportMethods("refsequence<-")
exportMethods("rownames<-")
exportMethods("taxatree<-")
exportMethods("taxonomy<-")
exportMethods(build_tree)
exportMethods(drop_taxa)
exportMethods(get_NRI_NTI)
exportMethods(get_alltaxadf)
exportMethods(get_alphaindex)
exportMethods(get_rarecurve)
exportMethods(get_taxadf)
exportMethods(get_upset)
exportMethods(get_vennlist)
exportMethods(ggbox)
exportMethods(ggdiffbox)
exportMethods(ggdifftaxbar)
exportMethods(mp_adonis)
exportMethods(mp_aggregate)
exportMethods(mp_aggregate_clade)
exportMethods(mp_anosim)
exportMethods(mp_balance_clade)
exportMethods(mp_cal_abundance)
exportMethods(mp_cal_alpha)
exportMethods(mp_cal_cca)
exportMethods(mp_cal_clust)
exportMethods(mp_cal_dca)
exportMethods(mp_cal_dist)
exportMethods(mp_cal_divergence)
exportMethods(mp_cal_nmds)
exportMethods(mp_cal_pca)
exportMethods(mp_cal_pcoa)
exportMethods(mp_cal_pd_metric)
exportMethods(mp_cal_rarecurve)
exportMethods(mp_cal_rda)
exportMethods(mp_cal_upset)
exportMethods(mp_cal_venn)
exportMethods(mp_decostand)
exportMethods(mp_diff_analysis)
exportMethods(mp_diff_clade)
exportMethods(mp_dmn)
exportMethods(mp_dmngroup)
exportMethods(mp_envfit)
exportMethods(mp_extract_assays)
exportMethods(mp_extract_dist)
exportMethods(mp_extract_feature)
exportMethods(mp_extract_internal_attr)
exportMethods(mp_extract_rarecurve)
exportMethods(mp_extract_sample)
exportMethods(mp_extract_taxonomy)
exportMethods(mp_extract_tree)
exportMethods(mp_filter_taxa)
exportMethods(mp_mantel)
exportMethods(mp_mrpp)
exportMethods(mp_rrarefy)
exportMethods(mp_stat_taxa)
exportMethods(otutree)
exportMethods(refsequence)
exportMethods(show)
exportMethods(tax_table)
exportMethods(taxatree)
exportMethods(taxonomy)
importClassesFrom(Biostrings,XStringSet)
importClassesFrom(SummarizedExperiment,SummarizedExperiment)
importClassesFrom(tidytree,treedata)
importFrom(MASS,lda)
importFrom(SummarizedExperiment,"colData<-")
importFrom(ape,as.phylo)
importFrom(ape,pcoa)
importFrom(ape,read.tree)
importFrom(cli,cli_inform)
importFrom(cli,make_ansi_style)
importFrom(coin,pvalue)
importFrom(data.table,setDT)
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,group_by_drop_default)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,pull)
importFrom(dplyr,rename)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,ungroup)
importFrom(foreach,"%dopar%")
importFrom(ggplot2,Stat)
importFrom(ggplot2,aes)
importFrom(ggplot2,aes_)
importFrom(ggplot2,aes_string)
importFrom(ggplot2,arrow)
importFrom(ggplot2,coord_cartesian)
importFrom(ggplot2,coord_flip)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
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_col)
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_tile)
importFrom(ggplot2,geom_violin)
importFrom(ggplot2,geom_vline)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_add)
importFrom(ggplot2,ggproto)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,guide_axis)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,labs)
importFrom(ggplot2,layer)
importFrom(ggplot2,margin)
importFrom(ggplot2,position_dodge)
importFrom(ggplot2,remove_missing)
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_x_discrete)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_bw)
importFrom(ggplot2,unit)
importFrom(ggplot2,waiver)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggrepel,geom_text_repel)
importFrom(ggsignif,geom_signif)
importFrom(ggstar,geom_star)
importFrom(ggstar,scale_starshape_manual)
importFrom(ggtree,geom_point)
importFrom(ggtree,geom_tiplab)
importFrom(ggtree,geom_tippoint)
importFrom(ggtree,ggtree)
importFrom(ggtree,td_filter)
importFrom(ggtree,td_mutate)
importFrom(ggtree,td_unnest)
importFrom(ggtreeExtra,geom_fruit)
importFrom(grDevices,chull)
importFrom(grDevices,colorRampPalette)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(magrittr,extract)
importFrom(methods,new)
importFrom(methods,show)
importFrom(patchwork,plot_layout)
importFrom(pillar,tbl_format_setup)
importFrom(plyr,ddply)
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,as_name)
importFrom(rlang,expr)
importFrom(rlang,new_formula)
importFrom(rlang,quos)
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,qt)
importFrom(stats,quantile)
importFrom(stats,sd)
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,nest)
importFrom(tidyr,pivot_longer)
importFrom(tidyr,separate)
importFrom(tidyr,unnest)
importFrom(tidyselect,eval_select)
importFrom(tidytree,as.treedata)
importFrom(tidytree,treedata)
importFrom(treeio,drop.tip)
importFrom(utils,getFromNamespace)
importFrom(utils,globalVariables)
importFrom(utils,head)
importFrom(utils,modifyList)
importFrom(utils,packageDescription)
importFrom(utils,tail)
importFrom(utils,unzip)
importFrom(vegan,decostand)
importFrom(vegan,diversity)
importFrom(vegan,estimateR)
importFrom(vegan,specnumber)
importFrom(zoo,na.locf)
