API for TreeDist
Calculate and Map Distances Between Phylogenetic Trees
| Global functions | |
|---|---|
| .AHMISEM | Source code |
| .AllTipsSame | Source code |
| .CheckLabelsSame | Source code |
| .DegenerateDistance | Source code |
| .DistanceFromMedian | Source code |
| .DistanceFromMedian.dist | Source code |
| .EuclideanDistance | Source code Source code |
| .GetPFromLabels | Source code |
| .MASTSizeEdges | Man page Source code |
| .MASTSizeSingle | Source code |
| .MaxValue | Source code |
| .MeanCentroidDist | Source code |
| .MeanMSTEdge | Source code |
| .MeanMSTEdge.dist | Source code |
| .MeanNN | Source code |
| .MeanNN.dist | Source code |
| .MeanOfTwo | Source code |
| .MultipleTrees | Source code |
| .NNIDistSingle | Source code |
| .PairMean | Man page Source code |
| .PathDist11 | Source code |
| .PathDist1Many | Source code |
| .PathDistManyMany | Source code |
| .PathDistManySelf | Source code |
| .SPRFunc | Source code |
| .SPRPairDeO | Source code |
| .SharedOnly | Source code |
| .SortingNumber | Source code |
| .SplitDistanceAllPairs | Source code |
| .SplitDistanceManyMany | Source code |
| .SplitDistanceOneMany | Source code |
| .SplitDistanceOneOne | Source code |
| .SumOfRanges | Source code |
| .SumOfVariances | Source code |
| .TreeDistance | Man page Source code |
| .TreeDistanceManyMany | Source code |
| .TreeDistanceOneMany | Source code |
| .TrustSum | Source code |
| .onUnload | Source code |
| AHMI | Man page Source code |
| AllSplitPairings | Man page |
| COMCLUST | Source code |
| CalculateTreeDistance | Man page Source code |
| ClusteringEntropy | Man page Source code |
| ClusteringEntropy.NULL | Source code |
| ClusteringEntropy.Splits | Man page Source code |
| ClusteringEntropy.list | Man page Source code |
| ClusteringEntropy.multiPhylo | Man page |
| ClusteringEntropy.phylo | Man page Source code |
| ClusteringInfo | Man page Source code |
| ClusteringInfo.NULL | Source code |
| ClusteringInfo.Splits | Man page Source code |
| ClusteringInfo.list | Man page Source code |
| ClusteringInfo.multiPhylo | Man page |
| ClusteringInfo.phylo | Man page Source code |
| ClusteringInfoDist | Man page |
| ClusteringInfoDistance | Man page Source code |
| CompareAll | Man page Source code |
| ConsensusInfo | Man page Source code |
| DifferentPhylogeneticInfo | Man page Source code |
| DisplayMatching | Man page |
| DistFromMed | Man page |
| DistanceFromMedian | Man page Source code |
| DistanceFromMedian.dist | Source code |
| DistanceFromMedian.numeric | Source code |
| EHMI | Man page Source code |
| EHMI_xptr | Source code |
| Entropy | Man page Source code |
| ExpectedVariation | Man page Source code |
| GeneralizedRF | Man page Source code |
| GetParallel | Man page Source code |
| HH | Man page |
| HH_xptr | Source code |
| HMI | Man page |
| HMI_xptr | Source code |
| HPart | Man page |
| HierarchicalMutualInfo | Man page Source code |
| HierarchicalMutualInformation | Man page |
| InfoRobinsonFoulds | Man page Source code |
| InfoRobinsonFouldsSplits | Man page Source code |
| Islands | Man page Source code |
| JaccardRobinsonFoulds | Man page Source code |
| JaccardSplitSimilarity | Man page Source code |
| KCDiameter | Man page Source code |
| KCDiameter.list | Source code |
| KCDiameter.multiPhylo | Source code |
| KCDiameter.numeric | Source code |
| KCDiameter.phylo | Source code |
| KCVector | Man page Source code |
| KMeansPP | Man page Source code |
| KMeansPP.dist | Source code |
| KMeansPP.matrix | Source code |
| KMeansPP.numeric | Source code |
| KendallColijn | Man page Source code |
| LAPJV | Man page Source code |
| LnTreesConsistentWithTwoSplits | Man page Source code |
| Log2TreesConsistentWithTwoSplits | Man page Source code Source code |
| MASTInfo | Man page Source code |
| MASTSize | Man page Source code |
| MSTSegments | Man page Source code |
| MapTrees | Man page Source code |
| MappingQuality | Man page Source code |
| MatchingSplitDistance | Man page Source code |
| MatchingSplitDistanceSplits | Man page Source code |
| MatchingSplitInfo | Man page Source code |
| MatchingSplitInfoDistance | Man page Source code |
| MatchingSplitInfoSplits | Man page Source code |
| MeanCentDist | Man page |
| MeanCentroidDist | Man page |
| MeanCentroidDistance | Man page Source code |
| MeanMSTEdge | Man page Source code |
| MeanMSTEdge.dist | Source code |
| MeanMSTEdge.numeric | Source code |
| MeanNN | Man page Source code |
| MeanNN.dist | Source code |
| MeanNN.numeric | Source code |
| MeilaMutualInformation | Man page Source code |
| MeilaVariationOfInformation | Man page Source code |
| MutualClusteringInfo | Man page Source code |
| MutualClusteringInfoSplits | Man page Source code |
| MutualClusteringInformation | Man page |
| NNIDiameter | Man page Source code |
| NNIDiameter.list | Source code |
| NNIDiameter.numeric | Source code |
| NNIDiameter.phylo | Source code |
| NNIDist | Man page Source code |
| NTip.HPart | Source code |
| NormalizeInfo | Man page Source code |
| Ntropy | Man page Source code |
| NyeSimilarity | Man page Source code |
| NyeSplitSimilarity | Man page Source code |
| PathDist | Man page Source code |
| PathVector | Man page Source code |
| PhylogeneticInfoDistance | Man page |
| Plot3 | Man page Source code |
| PlotMatching | Man page |
| Project | Man page Source code |
| ProjectionQuality | Man page |
| ReduceTrees | Man page Source code |
| RenumberTips.HPart | Source code |
| ReportMatching | Man page Source code |
| Robinson-Foulds | Man page |
| RobinsonFoulds | Man page Source code |
| RobinsonFouldsInfo | Man page |
| RobinsonFouldsMatching | Man page Source code |
| RobinsonFouldsSplits | Man page Source code |
| SPRDist | Man page |
| SPRDist.list | Man page |
| SPRDist.multiPhylo | Man page |
| SPRDist.phylo | Man page |
| SelfHMI | Man page Source code |
| SetParallel | Man page Source code |
| SharedPhylogeneticInfo | Man page Source code |
| SharedPhylogeneticInfoSplits | Man page Source code |
| SpectralClustering | Man page Source code |
| SpectralEigens | Man page Source code |
| SplitDifferentInformation | Man page Source code |
| SplitEntropy | Man page Source code |
| SplitSharedInformation | Man page Source code |
| SplitVector | Man page Source code |
| SplitsCompatible | Man page Source code |
| SplitwiseInfo | Man page Source code |
| SplitwiseInfo.NULL | Source code |
| SplitwiseInfo.Splits | Source code |
| SplitwiseInfo.multiPhylo | Source code |
| SplitwiseInfo.phylo | Source code |
| StartParallel | Man page Source code |
| StopParallel | Man page Source code |
| StrainCol | Man page Source code |
| SumOfRanges | Man page Source code |
| SumOfVariances | Man page Source code |
| SumOfVars | Man page |
| TreeDist | Man page |
| TreeDist-package | Man page |
| TreeDistPlot | Man page Source code |
| TreeDistance | Man page Source code |
| TreeInfo | Man page |
| TreesConsistentWithTwoSplits | Man page Source code |
| VisualiseMatching | Man page |
| VisualizeMatching | Man page |
| as.HPart | Man page Source code |
| as.HPart.HPart | Man page Source code |
| as.HPart.default | Man page Source code |
| as.HPart.list | Man page Source code |
| as.HPart.phylo | Man page Source code |
| as.phylo.HPart | Man page Source code |
| build_hpart_from_list | Source code |
| build_hpart_from_phylo | Source code |
| clone | Man page Source code |
| clone.HPart | Man page Source code |
| clone_hpart | Source code |
| cluster-statistics | Man page |
| confusion | Source code |
| consensus_info | Source code |
| cpp_jaccard_similarity | Source code |
| cpp_mast | Source code |
| cpp_matching_split_distance | Source code |
| cpp_msi_distance | Source code |
| cpp_mutual_clustering | Source code |
| cpp_nni_distance | Source code |
| cpp_robinson_foulds_distance | Source code |
| cpp_robinson_foulds_info | Source code |
| cpp_shared_phylo | Source code |
| entropy_int | Man page Source code |
| hpart_to_edge | Source code |
| is.HPart | Man page Source code |
| keep_and_reduce | Source code |
| keep_and_reroot | Source code |
| lapjv | Source code |
| median.multiPhylo | Man page Source code |
| mismatch_size | Source code |
| pair_diff_euclidean | Source code |
| path_vector | Source code |
| plot.HPart | Man page Source code |
| print.HPart | Man page Source code |
| reduce_trees | Source code |
| relabel_hpart | Source code |
| release_questions | Source code |
| robinson_foulds_all_pairs | Source code |
| vec_diff_euclidean | Source code |
