# Generated by roxygen2: do not edit by hand

export(abundances)
export(add_besthit)
export(add_refseq)
export(aggregate_rare)
export(aggregate_taxa)
export(alpha)
export(associate)
export(baseline)
export(bimodality)
export(boxplot_abundance)
export(boxplot_alpha)
export(collapse_replicates)
export(combine_otu_tax)
export(core)
export(core_abundance)
export(core_members)
export(coverage)
export(default_colors)
export(divergence)
export(diversity)
export(dominance)
export(dominant)
export(evenness)
export(gktau)
export(group_age)
export(group_bmi)
export(heat)
export(hotplot)
export(inequality)
export(intermediate_stability)
export(is_compositional)
export(log_modulo_skewness)
export(low_abundance)
export(map_levels)
export(merge_taxa2)
export(meta)
export(multimodality)
export(neat)
export(neatsort)
export(otu_tibble)
export(overlap)
export(plot_atlas)
export(plot_composition)
export(plot_core)
export(plot_density)
export(plot_frequencies)
export(plot_landscape)
export(plot_regression)
export(plot_taxa_prevalence)
export(plot_tipping)
export(potential_analysis)
export(prevalence)
export(psmelt2)
export(quiet)
export(rare)
export(rare_abundance)
export(rare_members)
export(rarity)
export(read_biom2phyloseq)
export(read_csv2phyloseq)
export(read_mothur2phyloseq)
export(read_phyloseq)
export(readcount)
export(remove_samples)
export(remove_taxa)
export(richness)
export(sample_tibble)
export(spreadplot)
export(summarize_phyloseq)
export(tax_tibble)
export(taxa)
export(time_normalize)
export(time_sort)
export(timesplit)
export(top)
export(top_taxa)
export(transform)
importFrom(Biostrings,DNAStringSet)
importFrom(Rtsne,Rtsne)
importFrom(dplyr,
  "%>%",
  arrange,
  do,
  filter,
  group_by,
  mutate,
  n,
  rename,
  select,
  summarise
)
importFrom(ggplot2,
  aes,
  aes_string,
  coord_cartesian,
  coord_flip,
  element_blank,
  element_rect,
  element_text,
  facet_grid,
  facet_wrap,
  geom_bar,
  geom_boxplot,
  geom_density,
  geom_histogram,
  geom_hline,
  geom_jitter,
  geom_line,
  geom_linerange,
  geom_path,
  geom_point,
  geom_polygon,
  geom_smooth,
  geom_text,
  geom_tile,
  geom_violin,
  geom_vline,
  ggplot,
  ggtitle,
  guide_legend,
  guides,
  labs,
  position_jitter,
  scale_alpha_continuous,
  scale_color_manual,
  scale_colour_gradient2,
  scale_fill_gradient,
  scale_fill_gradientn,
  scale_size,
  scale_size_manual,
  scale_x_continuous,
  scale_x_discrete,
  scale_x_log10,
  scale_y_continuous,
  scale_y_discrete,
  scale_y_log10,
  stat_density2d,
  theme,
  theme_bw,
  theme_set,
  xlab,
  ylab
)
importFrom(methods,
  as,
  is
)
importFrom(phyloseq,
  "otu_table<-",
  "sample_data<-",
  "tax_table<-",
  "taxa_are_rows<-",
  "taxa_names<-",
  distance,
  estimate_richness,
  get_taxa,
  get_variable,
  import_biom,
  merge_phyloseq,
  merge_taxa,
  nsamples,
  ntaxa,
  ordinate,
  otu_table,
  parse_taxonomy_default,
  phyloseq,
  prune_samples,
  prune_taxa,
  psmelt,
  rank_names,
  sample_data,
  sample_names,
  sample_sums,
  tax_glom,
  tax_table,
  taxa_are_rows,
  taxa_names,
  taxa_sums
)
importFrom(reshape2,melt)
importFrom(scales,percent)
importFrom(stats,
  aggregate,
  as.dist,
  coef,
  cor,
  cor.test,
  density,
  dist,
  dnorm,
  frequency,
  hclust,
  kernel,
  lm,
  loess,
  loess.control,
  median,
  na.fail,
  na.omit,
  p.adjust,
  pnorm,
  predict,
  princomp,
  quantile,
  rnorm,
  sd,
  time
)
importFrom(tibble,data_frame)
importFrom(tidyr,separate)
importFrom(utils,
  capture.output,
  flush.console,
  head,
  read.csv,
  read.table,
  tail,
  write.csv
)
importFrom(vegan,
  decostand,
  fisher.alpha,
  metaMDS,
  scores,
  vegdist,
  wascores
)
