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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("%>%")
export(agglomerate_taxmap)
export(alpha_diversity_measures)
export(alpha_diversity_plot)
export(as_MicrobiomeR_format)
export(as_analyzed_format)
export(as_basic_format)
export(as_custom_format)
export(as_phyloseq_format)
export(as_raw_format)
export(combination_palette)
export(correlation_data)
export(correlation_plot)
export(correlation_plots)
export(cov_filter)
export(create_phyloseq)
export(create_pub_table)
export(create_taxmap)
export(get_color_palette)
export(heat_tree_parameters)
export(heat_tree_plots)
export(is_analyzed_format)
export(is_basic_format)
export(is_phyloseq_format)
export(is_raw_format)
export(metacoder_comp_func_1)
export(order_metacoder_data)
export(ordination_plot)
export(ordination_plots)
export(otu_id_filter)
export(otu_prevalence_filter)
export(otu_proportion_filter)
export(output_dir)
export(parse_taxonomy_silva_128)
export(permanova)
export(pick_new_outgroup)
export(root_by_longest_edge)
export(root_phyloseq_tree)
export(sample_id_filter)
export(save_alpha_diversity_plots)
export(save_correlation_plots)
export(save_heat_tree_plots)
export(save_ordination_plots)
export(save_stacked_barplots)
export(save_top_coefficients_barplot)
export(scico_palette)
export(stacked_barplot)
export(stacked_barplots)
export(taxa_prevalence_filter)
export(taxon_id_filter)
export(top_coefficients_barplot)
export(transformer)
export(transposer)
export(treatment_matrix)
export(validate_MicrobiomeR_format)
export(viridis_magma_palette)
export(viridis_palette)
export(vlookup)
export(which_format)
import(vegan)
importFrom(ape,Ntip)
importFrom(ape,is.rooted)
importFrom(ape,read.tree)
importFrom(ape,root)
importFrom(ape,write.tree)
importFrom(crayon,bgWhite)
importFrom(crayon,blue)
importFrom(crayon,green)
importFrom(crayon,italic)
importFrom(crayon,red)
importFrom(crayon,silver)
importFrom(crayon,yellow)
importFrom(data.table,data.table)
importFrom(diptest,dip.test)
importFrom(dplyr,arrange)
importFrom(dplyr,as_tibble)
importFrom(dplyr,enquo)
importFrom(dplyr,expr)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,mutate)
importFrom(dplyr,one_of)
importFrom(dplyr,quo_name)
importFrom(dplyr,rename)
importFrom(dplyr,right_join)
importFrom(dplyr,select)
importFrom(dplyr,select_if)
importFrom(dplyr,setdiff)
importFrom(dplyr,summarise_if)
importFrom(dplyr,summarize)
importFrom(dplyr,sym)
importFrom(forcats,fct_reorder)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_bar)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_polygon)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,ggtitle)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_log10)
importFrom(ggplot2,scale_y_log10)
importFrom(ggplot2,theme)
importFrom(ggplot2,unit)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(ggpubr,colnames_style)
importFrom(ggpubr,ggtexttable)
importFrom(ggpubr,ggviolin)
importFrom(ggpubr,stat_compare_means)
importFrom(ggpubr,tbody_style)
importFrom(ggpubr,ttheme)
importFrom(ggrepel,geom_label_repel)
importFrom(ggthemes,theme_pander)
importFrom(glue,glue)
importFrom(grDevices,colorRampPalette)
importFrom(graphics,pie)
importFrom(magrittr,"%>%")
importFrom(metacoder,as_phyloseq)
importFrom(metacoder,calc_obs_props)
importFrom(metacoder,calc_prop_samples)
importFrom(metacoder,calc_taxon_abund)
importFrom(metacoder,compare_groups)
importFrom(metacoder,heat_tree)
importFrom(metacoder,parse_phyloseq)
importFrom(microbiome,abundances)
importFrom(microbiome,alpha)
importFrom(microbiome,meta)
importFrom(modes,bimodality_coefficient)
importFrom(phyloseq,distance)
importFrom(phyloseq,import_biom)
importFrom(phyloseq,import_qiime_sample_data)
importFrom(phyloseq,merge_phyloseq)
importFrom(phyloseq,ordinate)
importFrom(phyloseq,phy_tree)
importFrom(phyloseq,plot_ordination)
importFrom(phyloseq,sample_data)
importFrom(purrr,keep)
importFrom(purrr,list_modify)
importFrom(purrr,map)
importFrom(purrr,modify_at)
importFrom(rlang,enquos)
importFrom(rlang,eval_tidy)
importFrom(rlang,is_quosure)
importFrom(scales,percent)
importFrom(scales,pretty_breaks)
importFrom(scico,scico)
importFrom(shades,saturation)
importFrom(shades,scalefac)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,sd)
importFrom(stats,wilcox.test)
importFrom(stringr,str_count)
importFrom(stringr,str_detect)
importFrom(stringr,str_to_lower)
importFrom(taxa,filter_obs)
importFrom(taxa,filter_taxa)
importFrom(taxa,get_dataset)
importFrom(taxa,n_obs)
importFrom(taxa,taxon_ids)
importFrom(taxa,taxon_names)
importFrom(taxa,taxon_ranks)
importFrom(taxa,taxonomy_table)
importFrom(tibble,is.tibble)
importFrom(tidyr,gather)
importFrom(tidyr,gather_)
importFrom(tidyr,separate)
importFrom(tidyr,spread)
importFrom(tidyr,unite)
importFrom(tools,file_ext)
importFrom(tools,file_path_as_absolute)
importFrom(utils,combn)
importFrom(vegan,adonis)
importFrom(vegan,betadisper)
importFrom(vegan,vegdist)
importFrom(viridis,magma)
importFrom(viridis,viridis)