# Generated by roxygen2: do not edit by hand

export(abundanceFit)
export(ani_distance)
export(caseControlFit)
export(comp_ani_diff_and_posthoc_test)
export(compute_eb_priors)
export(define_priors)
export(estimate_beta_diversity)
export(estimate_sample_richness)
export(extract_fixef_priors)
export(extract_strainspy)
export(filter_by_presence)
export(getCoefficients)
export(getContigNames)
export(getConvergence)
export(getDesign)
export(getFamily)
export(getFitCall)
export(getGenomes)
export(getPValues)
export(getPriorsDf)
export(getResiduals)
export(getRowData)
export(getSamples)
export(getStdErrors)
export(getVcov)
export(getZICoefficients)
export(getZIPValues)
export(getZIStdErrors)
export(getZIVcov)
export(glmObFit)
export(glmQBFit)
export(glmZiBFit)
export(hadjust)
export(isScaleContinuous)
export(merge_metaphlan_files)
export(merge_sourmash_files)
export(merge_sylph_files)
export(modify_metadata)
export(plot_ani_dist)
export(plot_histogram)
export(plot_manhattan)
export(plot_mds)
export(plot_pca_biplot)
export(plot_prior_bootstrap)
export(plot_volcano)
export(prep_for_prediction)
export(read_metaphlan)
export(read_sourmash)
export(read_sylph)
export(read_taxonomy)
export(strainspy)
export(top_hits)
exportClasses(strainspy_fit)
exportClasses(strainspy_priors)
exportMethods(extract_fixef_priors)
exportMethods(getCoefficients)
exportMethods(getContigNames)
exportMethods(getConvergence)
exportMethods(getDesign)
exportMethods(getFamily)
exportMethods(getFitCall)
exportMethods(getGenomes)
exportMethods(getPValues)
exportMethods(getPriorsDf)
exportMethods(getResiduals)
exportMethods(getRowData)
exportMethods(getSamples)
exportMethods(getStdErrors)
exportMethods(getVcov)
exportMethods(getZICoefficients)
exportMethods(getZIPValues)
exportMethods(getZIStdErrors)
exportMethods(getZIVcov)
exportMethods(isScaleContinuous)
exportMethods(plot_prior_bootstrap)
exportMethods(show)
exportMethods(summary)
import(SummarizedExperiment)
import(ggplot2)
importClassesFrom(S4Vectors,DataFrame)
importClassesFrom(S4Vectors,List)
importFrom(BiocParallel,
  SerialParam,
  SnowParam,
  bplapply
)
importFrom(Matrix,sparseMatrix)
importFrom(R.utils,gunzip)
importFrom(S4Vectors,
  DataFrame,
  List,
  complete.cases,
  na.omit
)
importFrom(SummarizedExperiment,
  SummarizedExperiment,
  assay,
  assays,
  rowData
)
importFrom(ape,as.phylo)
importFrom(data.table,
  ":=",
  .BY,
  .EACHI,
  .GRP,
  .I,
  .N,
  .NGRP,
  .SD,
  data.table,
  fread,
  merge.data.table,
  set,
  tstrsplit
)
importFrom(dplyr,
  across,
  all_of,
  arrange,
  filter,
  group_by,
  left_join,
  mutate,
  n,
  pull,
  rename,
  summarise,
  where
)
importFrom(ggforce,geom_sina)
importFrom(ggplot2,
  aes,
  element_blank,
  element_text,
  geom_hline,
  geom_point,
  geom_violin,
  ggplot,
  labs,
  scale_color_manual,
  scale_fill_brewer,
  theme,
  theme_minimal
)
importFrom(ggrepel,geom_text_repel)
importFrom(ggthemes,theme_clean)
importFrom(ggtree,
  "%<+%",
  geom_tippoint,
  ggtree,
  theme_tree2
)
importFrom(glmmTMB,glmmTMB)
importFrom(grDevices,rainbow)
importFrom(graphics,abline)
importFrom(harmonicmeanp,p.hmp)
importFrom(lmerTest,lmer)
importFrom(magrittr,"%>%")
importFrom(methods,
  as,
  is,
  new,
  slotNames
)
importFrom(patchwork,plot_layout)
importFrom(purrr,
  map,
  map_dfr
)
importFrom(rlang,sym)
importFrom(stats,
  as.formula,
  binomial,
  dist,
  logLik,
  median,
  model.matrix,
  p.adjust,
  prcomp,
  quantile,
  rbinom,
  residuals,
  sd,
  setNames,
  terms
)
importFrom(stringr,str_detect)
importFrom(tibble,
  add_column,
  as_tibble
)
importFrom(tidyr,pivot_longer)
importFrom(tools,file_path_sans_ext)
importFrom(utils,
  capture.output,
  head
)
importFrom(viridis,viridis)
importMethodsFrom(S4Vectors,show)
