# Generated by roxygen2: do not edit by hand

S3method(ClusteringEntropy,"NULL")
S3method(ClusteringEntropy,Splits)
S3method(ClusteringEntropy,list)
S3method(ClusteringEntropy,multiPhylo)
S3method(ClusteringEntropy,phylo)
S3method(ClusteringInfo,"NULL")
S3method(ClusteringInfo,Splits)
S3method(ClusteringInfo,list)
S3method(ClusteringInfo,multiPhylo)
S3method(ClusteringInfo,phylo)
S3method(DistanceFromMedian,dist)
S3method(DistanceFromMedian,numeric)
S3method(KCDiameter,list)
S3method(KCDiameter,multiPhylo)
S3method(KCDiameter,numeric)
S3method(KCDiameter,phylo)
S3method(KMeansPP,dist)
S3method(KMeansPP,matrix)
S3method(KMeansPP,numeric)
S3method(MeanMSTEdge,dist)
S3method(MeanMSTEdge,numeric)
S3method(MeanNN,dist)
S3method(MeanNN,numeric)
S3method(NNIDiameter,list)
S3method(NNIDiameter,multiPhylo)
S3method(NNIDiameter,numeric)
S3method(NNIDiameter,phylo)
S3method(NNIMaxStep,list)
S3method(NNIMaxStep,multiPhylo)
S3method(NNIMaxStep,numeric)
S3method(NNIMaxStep,phylo)
S3method(NTip,HPart)
S3method(RenumberTips,HPart)
S3method(SPRDist,list)
S3method(SPRDist,multiPhylo)
S3method(SPRDist,phylo)
S3method(SplitwiseInfo,"NULL")
S3method(SplitwiseInfo,Splits)
S3method(SplitwiseInfo,list)
S3method(SplitwiseInfo,multiPhylo)
S3method(SplitwiseInfo,phylo)
S3method(as.HPart,HPart)
S3method(as.HPart,default)
S3method(as.HPart,list)
S3method(as.HPart,phylo)
S3method(as.phylo,HPart)
S3method(clone,HPart)
S3method(median,multiPhylo)
S3method(plot,HPart)
S3method(print,HPart)
export(.ThreeDPlotServer)
export(.TreeDistance)
export(AHMI)
export(AllSplitPairings)
export(CalculateTreeDistance)
export(ClusteringEntropy)
export(ClusteringInfo)
export(ClusteringInfoDist)
export(ClusteringInfoDistance)
export(CompareAll)
export(ConsensusInfo)
export(DifferentPhylogeneticInfo)
export(DisplayMatching)
export(DistFromMed)
export(DistanceFromMedian)
export(EHMI)
export(Entropy)
export(ExpectedVariation)
export(GeneralizedRF)
export(GetParallel)
export(HH)
export(HMI)
export(HierarchicalMutualInfo)
export(HierarchicalMutualInformation)
export(InfoRobinsonFoulds)
export(InfoRobinsonFouldsSplits)
export(Islands)
export(JaccardRobinsonFoulds)
export(JaccardSplitSimilarity)
export(KCDiameter)
export(KCVector)
export(KMeansPP)
export(KendallColijn)
export(LAPJV)
export(LnTreesConsistentWithTwoSplits)
export(Log2TreesConsistentWithTwoSplits)
export(MASTInfo)
export(MASTSize)
export(MCITree)
export(MSTSegments)
export(MapTrees)
export(MappingQuality)
export(MatchingSplitDistance)
export(MatchingSplitDistanceSplits)
export(MatchingSplitInfo)
export(MatchingSplitInfoDistance)
export(MatchingSplitInfoSplits)
export(MeanCentDist)
export(MeanCentroidDist)
export(MeanCentroidDistance)
export(MeanMSTEdge)
export(MeanNN)
export(MeilaMutualInformation)
export(MeilaVariationOfInformation)
export(MutualClusteringInfo)
export(MutualClusteringInfoSplits)
export(MutualClusteringInformation)
export(NNIDiameter)
export(NNIDist)
export(NNIMaxStep)
export(NormalizeInfo)
export(Ntropy)
export(NyeSimilarity)
export(NyeSplitSimilarity)
export(PathDist)
export(PathVector)
export(PhylogeneticInfoDistance)
export(Plot3)
export(PlotMatching)
export(Project)
export(ProjectionQuality)
export(ReduceTrees)
export(ReportMatching)
export(RobinsonFoulds)
export(RobinsonFouldsInfo)
export(RobinsonFouldsMatching)
export(RobinsonFouldsSplits)
export(SPRDist)
export(SelfHMI)
export(SetParallel)
export(SharedPhylogeneticInfo)
export(SharedPhylogeneticInfoSplits)
export(SpectralClustering)
export(SpectralEigens)
export(SplitDifferentInformation)
export(SplitEntropy)
export(SplitSharedInformation)
export(SplitVector)
export(SplitsCompatible)
export(SplitwiseInfo)
export(StartParallel)
export(StopParallel)
export(StrainCol)
export(SumOfRanges)
export(SumOfVariances)
export(SumOfVars)
export(TransferConsensus)
export(TransferDist)
export(TransferDistSplits)
export(TransferDistance)
export(TreeDistPlot)
export(TreeDistance)
export(TreesConsistentWithTwoSplits)
export(VisualiseMatching)
export(VisualizeMatching)
export(as.HPart)
export(clone)
export(entropy_int)
export(is.HPart)
importFrom(Rdpack,reprompt)
importFrom(TreeTools,
  AllAncestors,
  Consensus,
  DropTip,
  FirstMatchingSplit,
  KeepTip,
  KeepTipPostorder,
  LnRooted.int,
  LnTreesMatchingSplit,
  Log2Rooted.int,
  Log2TreesMatchingSplit,
  Log2Unrooted,
  Log2Unrooted.int,
  MSTEdges,
  MSTLength,
  MatchStrings,
  NRooted,
  NSplits,
  NTip,
  PairwiseDistances,
  PectinateTree,
  Postorder,
  PostorderOrder,
  Preorder,
  RenumberTips,
  RootOnNode,
  RootTree,
  SplitFrequency,
  SplitInformation,
  SplitsInBinaryTree,
  StarTree,
  TipLabels,
  TipsInSplits,
  TreeIsRooted,
  TreesMatchingSplit,
  as.ClusterTable,
  as.Splits,
  edge_to_splits
)
importFrom(ape,
  Nnode.phylo,
  as.phylo,
  drop.tip,
  edgelabels,
  nodelabels,
  plot.phylo
)
importFrom(cli,
  cli_alert_danger,
  cli_alert_info,
  cli_alert_success,
  cli_progress_along,
  cli_progress_bar,
  cli_progress_update
)
importFrom(grDevices,
  colorRamp,
  hcl,
  hcl.colors,
  rgb
)
importFrom(graphics,
  par,
  plot,
  points,
  rect,
  segments
)
importFrom(parallel,
  makeCluster,
  parCapply,
  parLapply,
  stopCluster
)
importFrom(shiny,runApp)
importFrom(shinyjs,useShinyjs)
importFrom(stats,
  as.dist,
  dist,
  kmeans,
  median,
  sd,
  setNames,
  var
)
importFrom(utils,
  combn,
  install.packages
)
useDynLib(TreeDist, .registration = TRUE)
