# Generated by roxygen2: do not edit by hand

S3method(as.data.frame,bifrost_search_tuning_grid)
S3method(as.data.frame,bifrost_search_tuning_selection)
S3method(as.data.frame,bifrost_shift_recovery_evaluation)
S3method(as.data.frame,bifrost_simulation_study)
S3method(as.data.frame,rate_distribution_fit)
S3method(as.data.frame,regime_correlation_pca)
S3method(as.data.frame,regime_integration_relationships)
S3method(as.data.frame,regime_module_diagnostics)
S3method(as.data.frame,shift_magnitude_comparison)
S3method(as.data.frame,shift_magnitude_comparison_set)
S3method(as.data.frame,shift_magnitude_count_set)
S3method(as.data.frame,shift_magnitude_counts)
S3method(as.data.frame,shift_node_marks)
S3method(as.data.frame,waiting_time_distribution_fit)
S3method(icTrajectory,bifrost_search)
S3method(icTrajectory,default)
S3method(icTrajectory,list)
S3method(plot,icTrajectory)
S3method(plot,rateMap)
S3method(plot,rate_distribution_fit)
S3method(plot,regime_correlation_pca)
S3method(plot,regime_integration_relationships)
S3method(plot,regime_module_diagnostics)
S3method(plot,shift_magnitude_comparison)
S3method(plot,shift_magnitude_comparison_set)
S3method(plot,shift_magnitude_count_set)
S3method(plot,shift_magnitude_counts)
S3method(plot,shift_node_marks)
S3method(print,bifrost_search)
S3method(print,bifrost_search_tuning_grid)
S3method(print,bifrost_search_tuning_selection)
S3method(print,bifrost_shift_recovery_evaluation)
S3method(print,bifrost_simulation_study)
S3method(print,bifrost_simulation_template)
S3method(print,rateMap)
export(bifrost_example_file)
export(bootstrap_rate_distribution)
export(compare_shift_magnitudes)
export(createSimulationTemplate)
export(evaluateShiftRecovery)
export(fisher_z_transform)
export(fit_rate_distribution)
export(fit_regime_covariance_runs)
export(fit_regime_covariances)
export(fit_waiting_time_distribution)
export(generateViridisColorScale)
export(icTrajectory)
export(lineage_rates)
export(rateMap)
export(rateMapControl)
export(rateMapRateFlags)
export(rateMapView)
export(regime_correlation_pca)
export(regime_integration_pgls)
export(regime_integration_relationships)
export(regime_module_diagnostics)
export(runFalsePositiveSimulationStudy)
export(runSearchTuningGrid)
export(runShiftRecoverySimulationStudy)
export(searchOptimalConfiguration)
export(selectTunedSearchParameters)
export(shift_magnitude_counts)
export(shift_magnitude_groups)
export(shift_node_marks)
export(shift_transitions)
export(shift_waiting_times)
export(simulateNullDataset)
export(simulateShiftedDataset)
export(summarize_regime_covariance_runs)
export(summarize_regime_covariances)
importFrom(ape,
  Nnode,
  Ntip,
  as.phylo,
  compute.brlen,
  getMRCA,
  is.rooted,
  nodelabels,
  root
)
importFrom(future,
  multicore,
  multisession,
  plan,
  sequential
)
importFrom(future.apply,future_lapply)
importFrom(grDevices,
  rainbow,
  rgb
)
importFrom(graphics,
  axis,
  layout,
  legend,
  lines,
  mtext,
  par,
  plot,
  points,
  segments,
  text,
  title
)
importFrom(mvMORPH,
  GIC,
  aicw,
  mvgls
)
importFrom(phytools,
  getDescendants,
  getParent,
  getStates,
  paintSubTree,
  plotSimmap
)
importFrom(plotrix,getYmult)
importFrom(stats,
  BIC,
  as.formula,
  setNames
)
importFrom(viridis,viridis)
