Comparison of Phylogenetic Trees Using Quartet and Split
Measures
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Documentation for package ‘Quartet’ version 1.2.6
Help Pages
| AllPairsQuartetAgreement | Direct entry points to "tqDist" functions |
| AllPairsQuartetDistance | Direct entry points to "tqDist" functions |
| AllPairsTripletDistance | Direct entry points to "tqDist" functions |
| AllQuartets | List all quartets |
| AllQuartets.numeric | List all quartets |
| AllQuartets.phylo | List all quartets |
| BipartitionPoints | Plot tree differences on ternary plots |
| BipartitionStatus | Matching partitions |
| CompareBipartitions | Compare status of splits |
| CompareQuartets | Compare quartet states by explicit enumeration |
| CompareQuartetsMulti | Compare one tree's quartets against others' |
| CompareSplits | Compare status of splits |
| Distances | Direct entry points to "tqDist" functions |
| DoNotConflict | Tree similarity measures |
| ExplicitlyAgree | Tree similarity measures |
| ManyToManyQuartetAgreement | Status of quartets |
| MarczewskiSteinhaus | Tree similarity measures |
| OneToManyQuartetAgreement | Direct entry points to "tqDist" functions |
| PairsQuartetDistance | Direct entry points to "tqDist" functions |
| PairsTripletDistance | Direct entry points to "tqDist" functions |
| PlotQuartet | Plot quartet on tree topologies |
| QuartetAgreement | Direct entry points to "tqDist" functions |
| QuartetDistance | Direct entry points to "tqDist" functions |
| QuartetDivergence | Tree similarity measures |
| QuartetPoints | Plot tree differences on ternary plots |
| QuartetState | Quartet State(s) |
| QuartetStates | Quartet State(s) |
| QuartetStates.list | Quartet State(s) |
| QuartetStates.multiPhylo | Quartet State(s) |
| QuartetStates.Splits | Quartet State(s) |
| QuartetStatus | Status of quartets |
| RawSymmetricDifference | Tree similarity measures |
| ResolvedQuartets | Count resolved quartets |
| ResolvedTriplets | Count resolved quartets |
| RobinsonFoulds | Tree similarity measures |
| SemiStrictJointAssertions | Tree similarity measures |
| SharedBipartitionStatus | Matching partitions |
| SharedQuartetStatus | Status of quartets |
| SharedSplitStatus | Matching partitions |
| SimilarityMetrics | Tree similarity measures |
| SimilarityToReference | Tree similarity measures |
| SingleTreeQuartetAgreement | Status of quartets |
| SplitPoints | Plot tree differences on ternary plots |
| SplitStatus | Matching partitions |
| sq_trees | Eighteen example trees |
| SteelPenny | Tree similarity measures |
| StrictJointAssertions | Tree similarity measures |
| SymmetricDifference | Tree similarity measures |
| SymmetricDifferenceLineEnds | Plot contours of equal symmetric difference on a ternary plot |
| SymmetricDifferenceLines | Plot contours of equal symmetric difference on a ternary plot |
| TQAE | Wrapper for tqDist |
| TQDist | Wrapper for tqDist |
| TripletDistance | Direct entry points to "tqDist" functions |
| TwoListQuartetAgreement | Status of quartets |
| VisualizeQuartets | Visualize quartet difference on trees, by split |