Statistical Exploration of Landscapes of Phylogenetic Trees

DengueBEASTMCC | Dengue fever BEAST MCC tree |

DengueSeqs | Dengue fever sequences |

DengueTrees | BEAST analysis of Dengue fever |

findGroves | Identify clusters of similar trees |

findMRCIs | Find MRCIs |

fluTrees | BEAST analysis of seasonal influenza (A/H3N2) |

linearMrca | Linear MRCA function |

makeCollapsedTree | Collapse a tree into a single tip per category |

medTree | Geometric median tree function |

multiDist | Metric function for 'multiPhylo' input |

plotGroves | Scatterplot of groups of trees |

plotGrovesD3 | Scatterplot of groups of trees using 'scatterD3' |

plotTreeDiff | Plot tree differences |

refTreeDist | Metric function for comparing a reference 'phylo' to... |

relatedTreeDist | Tree distance when trees have "related" tips |

simulateIndTree | Simulate randomised "individuals" tree |

tipDiff | Find tip position differences |

tipsMRCAdepths | Tip-tip MRCA depths |

treeConcordance | Tree concordance |

treeDist | Metric function |

treespace | Phylogenetic tree exploration |

treespaceServer | Web-based tree explorer |

treeVec | Tree vector function |

wiwMedTree | Median transmission tree |

wiwTreeDist | Transmission tree distance |

woodmiceTrees | Bootstrap trees from woodmouse dataset |

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